rainbow experiment video

• Activities for Kids

6 Incredibly Easy Rainbow Science Experiments

If you can’t find one, make one of your own, right in your kitchen, porch, or stoop

No rainbow in the sky today? No problem. Just pick one (or all) of these easy kid-friendly science experiments with your rainbow-making know-how. From reflection (mirror) to refraction (water glass) to learning about density, we’ve found six science experiments to make or learn from the rainbow. If you want more ideas, check out our sidewalk science ideas or dry ice science experiments .

1. The Mirror Method

Lesson: Demonstrate the principles of reflection and refraction with this easy experiment . Light bending, aka refraction, takes place as light waves pass through the water. When you shine your flashlight (or position your glass so the sun comes in) you are bending the light waves, each one of the waves at slightly different angles resulting in the different colors of the rainbow. This is the same basic principle that occurs when water and sunlight create a rainbow in the sky. Reflection is the light bouncing off of the mirrored surface.

You will need:

A small mirror (like a compact mirror)

A glass of water (big enough to hold the mirror)

A flashlight (or sunlight) 

A piece of white paper or a white wall

1. Put the mirror in the glass of water.

2. Turn off the lights and draw the curtains. Make sure the room is totally dark.

3. Shine the flashlight on the mirror and check out the cool mini-rainbows that appear above the mirror. Put your hand behind the glass for extra fun. 

2. The Garden Hose Technique

Lesson: Refraction, as above. This time, instead of using a mirror to reflect the light, you are going to basically mimic the natural formation of a rainbow by causing the water to hit the light in a fine mist.

A spray bottle or a hose

1. Put the hose on mist or grab your mister and spray it into an area of your yard/house/garden that has natural sunlight hitting it.

2. Let the kids ooh and ahh over your rainbow-making skills, then let each of them take a turn.

3. Water Density Rainbow

Lesson: By adding more or less sugar to each water solution you are creating different density levels. When you add coloring to the glasses you will be able to see which solution is the heaviest. Add the colors in rainbow order to impress the kids. Visit Little Bins for Little Hands for the experiment that shows you how to make a rainbow. 

Food coloring

Five glasses or plastic cups (clear)

4. The Glass o’ Water Approach

Lesson: The most simple form of light bending, this lesson in the light waves is similar to #1 above.

A glass of water

A piece of paper

1. Put the glass of water in the sunlight.

2. Put the paper next to it.

3. Let the sunlight stream through the water and create a rainbow on the paper.

5. Advanced Glass o’ Water Approach:

A spray bottle

1. Put the glass of water on a table or windowsill where there is sunlight.

2. Put the piece of paper on the floor where the sunlight hits, in the line of the glass.

3. Spray the window with warm water where the sun is coming through, and so it lines up with the paper. 

4. Move the glass and paper around until you see a neat little rainbow on the paper.

6. The Bubble Method

It doesn't get any easier than making a rainbow by blowing bubbles. You can use regular dish soap and a bit of water and shake ingredients inside a bottle, or just blow bubbles and observe. Want to up the fun factor? Make your own bubble mixture out of ordinary kitchen ingredients.

Need some fresh ideas?

Subscribe to our weekly newsletter for expert parenting tips and simple solutions that make life instantly better.

By subscribing you agree to Tinybeans Terms and Privacy Policy

Related reads

Why Are Gen Z Kids Covering Their Noses in Family Photos?

Screen Time for Babies Linked to Sensory Differences in Toddlerhood, Study Shows

Kids Shouldn’t Have to Finish Dinner to Get Dessert, Dietitian Explains

The Questions Parents Should Be Asking Their Pediatrician—but Aren’t

6 Better Phrases to Say Instead of ‘Be Careful’ When Kids Are Taking Risks

• your daily dose

• and connection

• Your daily dose

Cool Science Experiments Headquarters

Making Science Fun, Easy to Teach and Exciting to Learn!

Science Experiments

Rainbow in a Jar Science Experiment

Want to make your own rainbow? In this simple science experiment, kids can build their own rainbow in a jar while exploring density, mass, and volume.

Watch our demonstration video, gather your supplies, and print out our detailed instructions to get started. An easy to understand explanation of how it works is included below.

JUMP TO SECTION: Instructions | Video Tutorial | How it Works

Supplies Needed

• Tall Glass Jar
• Food Coloring: Red, Blue and Green
• 1/4 cup Honey
• 1/4 cup Blue Dish Soap
• 1/4 cup Water
• 1/4 cup Olive Oil
• 1/4 cup Rubbing Alcohol
• Jars for mixing and pouring
• Teaspoons for mixing

Rainbow in a Jar Science Lab Kit – Only $5

Use our easy Rainbow in a Jar Science Lab Kit to grab your students’ attention without the stress of planning!

It’s everything you need to  make science easy for teachers and fun for students  — using inexpensive materials you probably already have in your storage closet!

Rainbow in a Jar Science ExperimentInstructions

Step 1 – Add one drop of red food coloring and one drop of blue food coloring to 1/4 cup of honey and stir until combined. This creates a purple color liquid. Pour the purple liquid carefully into the tall jar.

Step 2 – Next add about 1/4 cup of blue dish soap to the tall jar.

Step 3 – Add a few drops of green food coloring to 1/4 cup of water and mix until combined. Then, carefully pour the green liquid into the tall jar. Tip: When pouring in the green liquid, tilt the jar so the liquid runs down the side of the jar slowly.

Step 4 – Wait a few moments and then slowly pour 1/4 cup of olive oil into the jar. Again, be very careful when pouring in the liquid. Make sure to tilt the jar and pour very slowly so the colors don’t mix.

Step 5 – Add a few drops of red food coloring to 1/4 cup of rubbing alcohol and mix until combined. Then, carefully pour the red liquid into the tall jar. Tip: I can’t stress enough how important it is to tilt the jar and pour slow. Otherwise, the colors will mix together and you won’t get a distinct rainbow.

Do you know why you were able to make the liquids form the rainbow in a jar? Find out the answer in the how does this experiment work section below.

Video Tutorial

How Does the Science Experiment Work

Density is the reason that this experiment works! Density is a measure of how much mass (or “stuff”) there is in a given volume. Density is a ratio of mass to volume and can be found by dividing an object’s mass by its volume (D=m/v).

Based on this equation, if the mass of something increases but the volume stays constant, then the density increases. Also, if mass decreases but the volume stays constant, then the density decreases. Density is all about how tightly packed the matter making up the material is in a given volume. Lighter liquids (like olive oil and rubbing alcohol) are less dense than heavier liquids (like honey and dish soap) because they have less matter in a given volume. Because olive oil and rubbing alcohol are less dense, they will float on top of liquids like water, dish soap, and honey. Liquids with a lower density will always float on top of liquids with a higher density.

All liquids have their own unique density. Water has a density of 1 g/mL (g/cm3). Objects will float in water if their density is less than 1 g/mL. Objects will sink in water if their density is greater than 1 g/mL.

I hope you enjoyed the experiment. Here are some printable instructions:

Instructions

• Add one drop of red food coloring and one drop of blue food coloring to 1/4 cup of honey and stir until combined. This is create a purple color liquid. Pour the purple liquid carefully into the tall jar.
• Next add about 1/4 cup of blue dish soap to the tall jar.
• Then add a few drops of green food coloring to 1/4 cup of water and mix until combined. Then carefully pour the green liquid into the tall jar. Tip: When pouring in the green liquid, tilt the jar so the liquid runs down the side of the jar slowly.
• Wait a few moments and then slowly pour 1/4 cup of olive oil into the jar. Tip: Again, be very careful when pouring in the liquid. Make sure to tilt the jar and pour very slowly so the colors don’t mix.
• Add a few drops of red food coloring to 1/4 cup of rubbing alcohol and mix until combined. Then carefully pour the red liquid into the tall jar. Tip: I can’t stress enough how important it is to tilt the jar and pour slow. Otherwise the colors will mix together and you won’t get a distinct rainbow.

Reader Interactions

October 15, 2017 at 3:22 pm

It was cool. Was it density

October 30, 2017 at 11:33 am

Hi it was Cooooolllllll….. It was because of the density

June 12, 2018 at 10:22 am

my kids enjoyed this presentation. They are doing it for a stem project

March 25, 2019 at 3:41 pm

How long did this project take to make and how long did it last until the colors started to mix? Also, what would be the guiding question of an experiment like this?

March 2, 2023 at 11:46 am

1.This experiment took around 20 minutes to put together. 2. It lasts for as long as you need if nobody touches it. 3. A leading question to this experiment could be ” Will all of the ingredients mix while i am pouring?”

I hope this helped:)

January 23, 2020 at 12:41 pm

its amazing my students loved it!

March 2, 2023 at 11:40 am

I did this exact project for the science fair this year and I won 2nd place. I made a full board about destiny and I made a question saying ” If I do not tip the jar or if i pour too fast, will the colors mix? The answer is yes! The colors did mix whenever I didn’t tip the jar and the rubbing alcohol sank down and mixed with the green and then since the extra liquid was in the green it mixed with the blue dish soap and began to be a big bubbly mess! 🙂

June 12, 2023 at 10:15 am

Can you put a top on the jar, shake the jar, mixing the liquids, will the liquids separate after sitting for hours or days?

Leave a Reply Cancel reply

Your email address will not be published. Required fields are marked *

Save my name, email, and website in this browser for the next time I comment.

• Privacy Policy
• Disclosure Policy

Copyright © 2024 · Cool Science Experiments HQ

Save Your Favorite Ideas

Grow a Rainbow Experiment

Want to grow your own rainbow? Try this simple science experiment! You only need paper towel, water and washable markers. Kids will love to see their rainbow “grow” in this easy activity!

RELATED: Surprise Rainbow Activities 

You will love seeing the rainbow come together in this simple science experiment! You can even do different patterns and colors too.

Grow a Rainbow Experiment for Kids

Here is what you will need for this activity:  

• Paper Towel
• Washable Markers
• 2 Small Glasses

Watch the Full Video Tutorial Here

What is the science behind this experiment.

This science experiment is a great example of chromatography. Chromatography is a way of separating out a mixture of chemicals. If you ever got a paper with ink wet you would have seen the ink move across the page in streaks.

Capillary action makes the marker dye move up the paper towel.  The water moves upward through the paper towel, lifting the washable dye molecules with it. Because the washable markers are water based, they disperse in water.

Set up a few different scenarios and hypotheses. For example, if you were to try this experiment without any dye, you would still see the water rising upwards towards the center of the paper towel.

If you were try this experiment with permanent markers it would not work. This is because the markers are not water based (they are alcohol based) so the dye in the marker does not travel with the water. You can also show that permanent markers will disperse with rubbing alcohol but not with water.

• You need absorbent paper towel or napkin – we used the brand Bounty
• You must use washable markers – make sure to check it’s washable as not all Crayola brands are washable
• Do not place the end of the paper towel too deep into the water or the dye will dissolve into the water instead of traveling up the paper towel
• The shorter the paper towel – the better it works as there is less for the marker dye to have to travel across
• Add lots of marker to the ends.  You need lots of dye for it to travel upwards.

Growing Rainbow Experiment Instructions

1. Fold over a piece of paper towel (so you have 2 pieces on top of each other). Trim the length to be 7.5 inches (any longer and the rainbow may not connect fully).

TIP : The shorter your piece of paper towel, the better it will connect. Also make sure you are using an absorbent paper towel. We used Bounty.

2. Draw rectangles of the rainbow colors on each end.

You want to make sure to fill these colors in well so there is enough dye to travel across the paper towel.

TIP: Add lots of marker to the ends, you want a good amount of dye to travel up the paper towel.

3. Place 2 cups with water filled 3/4 full. You only want the bottom of the paper towel in so leave some space from the top of the cup.

Then place the paper towel into the cups, with one end in each cup.

TIP: Do not place the ends too deep in the water or the dye may dissolve into the water instead of moving up the paper towel.

4. The washable marker dye with slowly make it’s way up with the water to meet the other side in the center of the paper towel.

5. Leave the paper towel for 10-15 minutes and it will eventually connect the colors together.

We love how simple this science experiment is! Expand on the learning by testing with permanent markers or just water to see what happens in those scenarios.

More Rainbow Activities

Your kids will also love to try these surprise rainbow activities !

See this fun rainbow slime. Kids will love building a rainbow out of slime!

Make some rainbow playdough! This playdough recipe is super soft and lasts for months!

For another fun rainbow activity, this rainbow rice is our favorite sensory bin!

Related Ideas:

Cloud Dough

The BEST Playdough Recipe

50+ Christmas Crafts for Kids

Salt Dough Recipe

Share a comment.

We LOVE hearing from you! Submit your question or comment here.

Your email address will not be published. Required fields are marked *

Cancel Reply

8 comments on “grow a rainbow experiment”.

Me and my neighbors did the rainbow paper towel one and had lots of fun!

Hi can you pre color the paper towel? And do the experiment another day? We want to do it for a party and have it pre colored so all the kids have to do is dip it in water. 

Yes that should still work!

I love it. Thanks. I’m doing this as a virtual library lesson for a 25 minute class. If anyone is pressed for time like me it actually works faster with an unfolded cheap paper towel <5 minutes.

BEST experiment crafts I have seen in a long while. I hunt down ideas for my grandchildren when they come to visit and these are all on point and they will love them Thanks. I will use all of them (except the rice) . GREAT ideas.

Thanks so much Lee!

What is the purpose of folding the paper towel in half (step 1)?

We found that the colors moved across the paper better when there are 2 layers.

Sign up for my FREE newsletter and get new ideas to your inbox!

• Skip to primary navigation
• Skip to main content
• Skip to primary sidebar

• FREE Experiments
• Kitchen Science
• Climate Change
• Egg Experiments
• Fairy Tale Science
• Edible Science
• Human Health
• Inspirational Women
• Forces and Motion
• Science Fair Projects
• STEM Challenges
• Science Sparks Books
• Contact Science Sparks
• Science Resources for Home and School

How to Make a Rainbow

November 4, 2015 By Emma Vanstone 2 Comments

Did you know the light around us ( white light ) is actually made up of all the colours of the rainbow?

What are the colours of the rainbow?

Red, orange, yellow, green, blue, indigo and violet

Why do rainbows form?

Rainbows are seen in the sky opposite the sun and are caused by the refraction ( bending of light ) and dispersion ( splitting up ) of sunlight in drops of rain or mist. Sunlight hitting the rain or mist is dispersed into its constituent colours. This is because the light is reflected at varying angles, creating a rainbow as the different colours refract and bend by different amounts. Each colour of the rainbow has a different wavelength.

What is Refraction?

Refraction occurs when light bends as it passes through a transparent material, such as glass, prisms, or raindrops.

How to make a rainbow on a sunny day

Make a rainbow with a hosepipe.

If you have a spray bottle or hosepipe that can make a fine mist of water, you can make a rainbow on a sunny day.

Stand with your back to the sun and spray the hosepipe into the air. You might have to move it around to find the best angle for a rainbow.

Why can you see a rainbow through water?

Tiny drops of water act like a prism, splitting light into individual colours depending on their wavelength. Violet light is bent ( refracted ) the most and red the least.

The bending of light is called refraction , and the splitting of light into a rainbow of colours is called dispersion .

If you have a sunny day, you can also use a prism to make a rainbow.

Make a rainbow with a mirror

Try placing a mirror inside a glass and angling the glass so sunlight hits the mirror. You should be able to reflect a rainbow onto the wall.

Make a rainbow without the sun

Place a mirror inside a glass and shine a torch onto it until you can see a rainbow reflected onto the wall. You might have to adjust the angle of the glass to make it work.

If you can make a room very dark, you might also be able to see a rainbow by shining a torch through a prism.

Find Rainbows in Bubbles

When white light shines through the bubble film, it is reflected and dispersed, which splits the white light into its different wavelengths allowing you to see all the colours of the rainbow in the bubbles .

Rainbow Crafts for kids

Make rainbow paper like The Science Kiddo

We love this rainbow scavenger hunt from Hands On as We Grow .

Or how about a giant collage like The Imagination Tree?

Suitable for Key Stage 2 Science

If you enjoyed these activities don’t forget we have 100s more science experiments for you to try!

Last Updated on July 4, 2024 by Emma Vanstone

Safety Notice

Science Sparks ( Wild Sparks Enterprises Ltd ) are not liable for the actions of activity of any person who uses the information in this resource or in any of the suggested further resources. Science Sparks assume no liability with regard to injuries or damage to property that may occur as a result of using the information and carrying out the practical activities contained in this resource or in any of the suggested further resources.

These activities are designed to be carried out by children working with a parent, guardian or other appropriate adult. The adult involved is fully responsible for ensuring that the activities are carried out safely.

Reader Interactions

November 05, 2015 at 4:50 am

Great. I once did that experiment, where i put mirror in the glass. Love that.

Leave a Reply Cancel reply

Your email address will not be published. Required fields are marked *

Get Your ALL ACCESS Shop Pass here →

Rainbow Science Experiments

Everything is brighter with rainbows even a rainy day because that’s the perfect time to hope to see one! Whether you are looking for a pot of gold at the end or love the way the colors combine, exploring rainbows through science and STEM activities is a great way to get started! Find a fun selection of simple to set up rainbow science experiments to try out all year long. Any time of the year is perfect for exploring rainbows!

Explore Rainbows

Over the past year, we have explored rainbow and rainbow-themed science experiments. The difference? We have studied how real rainbows form and how light science plays a role in creating rainbows.

However, young kids also just love fun, rainbow-themed science activities that also showcase simple science concepts such as reactions , polymers , liquid density and  crystal growing .

Below, we have included both kinds of rainbow science experiments. But before you get into all the fun, read on to learn some rainbow science.

How Rainbows Are Formed

A rainbow is formed when light passes through water droplets in the atmosphere. The water droplets break white sunlight into the seven visible spectrum colors. You can only see a rainbow when the sun is behind you and the rain in front of you.

There are 7 colors in the rainbow: violet, indigo, blue, green, yellow, orange, and red.

Make sure to look out for a rainbow next time it rains! Now, let’s try a rainbow science experiment or two!

Free Printable Rainbow Activities Guide and STEM Cards

Download this free mini Rainbow pack to get started today!

Want to turn a rainbow science experiment into a rainbow science project? Check out our easy science fair project ideas!

1.  Make A Rainbow

Grab some prisms, old CDs and more, and explore how visible light can split into the colors of the rainbow.

2. Rainbow Crystals

Grow crystals using a classic crystal growing recipe with borax and pipe cleaners. This rainbow science activity really grows awesome crystals that are both sturdy and beautiful to look at. Create a science craft with a pipe cleaner rainbow design!

3. Erupting Rainbow Science Experiment

A classic reaction for simple chemistry and a mix of colors to create an erupting rainbow!

4. Walking Water Rainbow

This walking water experiment is incredibly easy and fun to set up for kids. Watch the water travel as it makes a rainbow of color, and learn about capillary action too!

5. Build LEGO Rainbows

Explore symmetry and design with a rainbow LEGO building challenge.

6. Rainbow Density Experiment

Super easy kitchen science using sugar, water, and food coloring. Explore the density of liquids to create a rainbow.

7. Make Rainbow Slime

Learn how to make the easiest slime ever and create a rainbow of colors!

8. Rainbow Fizzing Pots

A leprechaun’s dream with a cool chemical reaction in mini black cauldrons!

10. Rainbow Oobleck

Oobleck is an awesome science activity for exploring non-Newtonian fluids. Do you know what a non-Newtonian fluid is or how it works? Learn more through this hands-on activity that uses basic kitchen ingredients.

11. Rainbow Solubility

Make this fun rainbow craft with a few simple materials and explore solubility in the process.

12. Make a Spectroscope

A spectroscope or a spectrograph is a scientific instrument used to study the properties of light. It breaks light down into different wavelengths, called a spectrum. It works similar to how a prism splits white light into a rainbow .

More Fun Science Topics To Explore

• Baking Soda & Vinegar Experiments
• Simple Machine Projects
• Chemical Reaction Experiments
• Density Experiments
• Water Experiments
• Capillary Action

Helpful Science Resources To Get You Started

Here are a few resources that will help you introduce science more effectively to your kiddos or students and feel confident yourself when presenting materials. You’ll find helpful free printables throughout.

• Best Science Practices (as it relates to the scientific method)
• Science Vocabulary
• 8 Science Books for Kids
• All About Scientists
• Free Science Worksheets
• Science Supplies List
• Science Tools for Kids

Printable Science Projects For Kids

If you’re looking to grab all of our printable science projects in one convenient place plus exclusive worksheets and bonuses like a STEAM Project pack, our Science Project Pack is what you need! Over 300+ Pages!

• 90+ classic science activities  with journal pages, supply lists, set up and process, and science information.  NEW! Activity-specific observation pages!
• Best science practices posters  and our original science method process folders for extra alternatives!
• Be a Collector activities pack  introduces kids to the world of making collections through the eyes of a scientist. What will they collect first?
• Know the Words Science vocabulary pack  includes flashcards, crosswords, and word searches that illuminate keywords in the experiments!
• My science journal writing prompts  explore what it means to be a scientist!!
• Bonus STEAM Project Pack:  Art meets science with doable projects!
• Bonus Quick Grab Packs for Biology, Earth Science, Chemistry, and Physics

• Pingback: Make Rainbow Slime Recipe for Amazingly Colorful Homemade Slime
• Pingback: St Patricks Day Chemistry Experiments (that are actually easy to set up!)

I love using your projects with my grandson. I am now faced with distance learning for my students. I am a STEM teacher at an elementary school. A lot of your project lend themselves easily to distance learning. What is your position on using some of your projects in my Google Classroom? Please advise. Thank you.

Comments are closed.

Subscribe to receive a free 5-Day STEM Challenge Guide

~ projects to try now ~.

Walking Water Rainbow Science Experiment

Let’s make a walking water rainbow! There’s no better way for little scientists to learn about capillary action and color mixing than by making water walk (yes – walk!) in this colorful rainbow science experiment. This science experiment is a favorite of ours because it’s so easy to set up and the results are almost immediate.

Check out the simple step-by-step below and then gra b 30 more jaw-dropping (but easy prep!) science experiments kids will love from our shop!

Getting Ready

To prep, I gathered our supplies:

• 6 wide-mouth glasses or jars
• Paper towels (use the kind where you can select a size)
• Food dye or liquid water colors (red, yellow, and blue)

I grabbed the six small glasses first .  We’ve had success using wide-mouth drinking cups and canning jars, too.  Even though they all worked, just remember that bigger glasses will need more food coloring.

I ripped off six sheets of paper towel and folded each sheet in thirds, lengthwise.

We were using pretty small glasses, so I cut a few inches off the folded paper towel so it would fit in the glasses.

It’s a good idea to test your paper towel strip to make sure they fit properly in your glasses.  They should be able to go from the bottom of one jar to the next without sticking up in the air too much. The paper towel on the left shows the just-right height.  It’s important to set up this rainbow science experiment for success!

Making a Rainbow

This colorful rainbow science experiment is so simple and quick, it’s perfect for even the youngest little scientists.  My 3 year old, Q, couldn’t wait to get started.

First, I had him line up the glasses and fill the first one with a good squirt of red watercolor , the third with yellow, and the fifth glass with blue.  We left the other glasses empty.

Next, I helped Q add water to the glasses with color until the colored water almost reached the top.

We moved the glasses into a circle and added the paper towels .  Starting with the red, we added one end of the paper towel and then put the other end in the empty glass next to it.

We continued around until the last paper towel was placed into the red glass.

We saw the color wick up the paper towel right away.  This rainbow science experiment doesn’t take long to get going!

After another several minutes, the colored water had almost travelled the whole length of each paper towel.

Five minutes later, the water had traveled all the way up and then down the paper towel and was dripping into the empty glass.

The yellow and red water dripped into the empty cup to make orange!  It made for a good lesson on color mixing.

After another five minutes, we could see the water level had dropped in the red, yellow, and blue glasses and rose in the once empty glasses as the water continued to travel from the more full glasses to the less full glasses.

We grabbed a snack and watched our beautiful rainbow science experiment during the next 20 minutes. The water continued to walk from the primary colored glasses to fill the secondary-colored glasses until all the jars were filled equally.

Not Working?

If you aren’t seeing much movement within a few minutes, it may be that you need to add more water to your colored water glasses.  It really needs to be almost at the top for the water to walk quickly.  So try topping off those glasses and seeing if that gets things moving.

If you see the water moving up the paper towel but it seems like it’s taking forever , it may be the type of paper towel you are using.  You want a paper towel that will really hold a lot of water.  We have used Bounty Select-a-Size and Target’s Up and Up Brand Select-a-Size with success.

It really is worth the extra effort of trying different cups and paper towels to get this activity to work.  And once you have had success, don’t throw out those beautifully-colored paper towels or the colored water!  We gently squeezed out our paper towels and let them dry in a heap on a baking sheet.  We ended up with gorgeous tie-dyed looking paper towels to use for crafts and we used the leftover water as watercolors for painting with later.

The Science Behind It

This rainbow science experiment is as magic as the science behind it.  The colored water travels up the paper towel by a process called capillary action . Capillary action is the ability of a liquid to flow upward, against gravity, in narrow spaces.  This is the same thing that helps water climb from a plant’s roots to the leaves in the tree tops.

Paper towels, and all paper products, are made from fibers found in plants called cellulose .  In this demonstration, the water flowed upwards through the tiny gaps between the cellulose fibers.  The gaps in the towel acted like capillary tubes, pulling the water upwards.

The water is able to defy gravity as it travels upward due to the attractive forces between the water and the cellulose fibers.

The water molecules tend to cling to the cellulose fibers in the paper towel.  This is called adhesion .

The water molecules are also attracted to each other and stick close together, a process called cohesion .  So, as the water slowly moves up the tiny gaps in the paper towel fibers, the cohesive forces help to draw more water upwards.

At some point, the adhesive forces between the water and cellulose and the cohesive forces between the water molecules will be overcome by the gravitational forces on the weight of the water in the paper towel.  

When that happens, the water will not travel up the paper towel anymore. That is why it helps to shorten the length that colored water has to travel by making sure your paper towel isn’t too tall and making sure you fill your colored liquid to the top of the glass.

Rainbow Science Activity Extensions

Turn this demonstration into a true experiment by varying the water level (volume) you start with and seeing how long it takes the water to reach the empty glass.

Or start with the same volume of colored water and change the brand, type (single vs double ply, quilted vs not) or length of paper towel to see how long it takes for the water to “walk” to the empty glass.

You could even use the same volume of water, same length and brand of paper towel but vary the height of the filled glass , by raising them up on books, to see how that affects the speed of the water as it “walks” to the empty glass.

Have you had enough fun with the paper towels?  Try using other paper products to see how the type of paper effects the results.  Try toilet paper, printer paper, newspaper or a page from a glossy magazine.  What do you predict will happen?

Grab a Record Sheet

Help kids keep track of their results by grabbing our free record sheet! Then grab 30 more jaw-dropping (but easy prep!) science experiments kids will love from our shop!

Similar Posts

Valentine Box STEAM Challenge

Number Bingo

Mammal Sort

Leprechaun Toothpaste

Flower Symmetry Activities

Expanded Form Roll and Write

11 comments.

• Pingback: Ice Color Mixing - The Stem Laboratory
• Pingback: Color Matching Fish - Teach Me Mommy
• Pingback: EXPLODING PAINT ROCKETS STEAM ACTIVITY
• Pingback: FREE Rainbow Train Preschool Counting Game - Stay At Home Educator
• Pingback: Coloring Sheets - Playdough To Plato
• Pingback: Matching Colors and Numbers 1-6 | Liz's Early Learning Spot
• Pingback: Color Hunt Around the Room - Mrs. Jones' Creation Station
• Pingback: Colors Sorting Mats Game
• Pingback: Ultimate Boredom Buster: 101 Things To Do When Kids Are Bored
• Pingback: 15 Color Activities | Happy Days in First Grade
• Pingback: 5 Easy Science Experiments for Kids [With Video] – Baba Blast!

Leave a Reply Cancel reply

Your email address will not be published. Required fields are marked *

Fizzy Rainbow Science Experiment

This fizzy rainbow science experiment just takes a few simple ingredients that you probably already have at home! This experiment is perfect for kids of all ages and is sure to bring some colorful fun to your day.

This baking soda experiment is sure to be a hit. Your kids will love watching all the different colors erupt in the baking soda!

Be sure to check out these Rainbow Science Experiments too!

Rainbow Walking Water Grow a Rainbow Skittle Rainbow Science Experiment

Fizzy Rainbow Science Experiment Instructions

To get started, you’ll need the following supplies :

• Shallow container or tray
• Baking soda
• Food coloring (red, blue, green, and yellow)

1. Fill each cup or glass half full with vinegar.

2. Put a few squirts of the food coloring in the cups and mix with a spoon.

3. Fill up the tray with a layer of baking powder. Use a spoon to flatten out any chunks of baking soda.

4. Using a dropper, squirt out the colored baking soda mixture onto the tray. You’ll want to move quickly as the reaction will start happening immediately and you don’t want to miss any of the fun.

5. Watch as the vinegar and baking soda mixture react, causing a fizzy eruption. As the reaction slows down, you’ll see the colors start to blend together, creating a beautiful fizzy rainbow effect.

6. If you want to extend the fun, you can add more baking soda and food coloring to keep the reaction going.

Tips for this baking soda and vinegar experiment:

• This will stain, so put this on a tray or some kind of protective layer over your table.
• If you are not seeing a lot of bubbles, squeeze the mixture out of the droppers faster.

Fizzy Rainbow Science Experiment Video

How does this simple science activity work.

Not only is this experiment a blast to watch, but it also teaches us about chemical reactions and how different substances can interact with each other. The baking soda and the acid in the vinegar react when they interact with each other by trapping the carbon dioxide to form bubbles. The mix creates a liquid and a gas which become a foam.

Plus, it’s an opportunity to practice our observation and prediction skills as we try to predict what will happen next.

So gather your supplies and get ready to create your own fizzy rainbow. Happy experimenting!

Printable Rainbow Math & Literacy Pack

These  rainbow theme math and literacy centers  are perfect for preschool, pre-k and kindergarten. Your students will have a blast with these fun  rainbow activities  for your math and literacy stations, centers, or homeschool units!

More Science Fun

Grow a Rainbow with this fun science experiment! This is quick to setup and you just need markers, a paper towel and two cups of water!

Your kids will love this fun skittles rainbow activity ! This also comes with free recording sheets to add to your lesson plans!

Your kids will love watching the flowers change color with this color changing flowers science experiment !

Looking more fun science experiments? Here are 30 fun science experiments your kids will love!

Science at Home for Kids

Easy and fun science experiments using household items! Follow us on Instagram @scienceathomekids for more cool science!

Rainbow Rain

This rainbow experiment is so cool, and I hope it will blow your minds as much as it did mine. Watching the bursts of color fall through the water is so mesmerizing, and I would watch it all day if I could. I hope you enjoy this experiment!

What you need:

• Food coloring

• Pour the oil into a bowl and add your favorite colors of food coloring.

• Using the spoon, stir together all the droplets of food coloring. Make sure to do the next step quickly so the droplets do not start combining to form one big, black blob of food coloring.

• Fill the jar with water.

• Pour the oil and food coloring into the jar. Wait a couple seconds, and then watch your rainbow rain fall throughout the jar!

What caused this rainbow rain?

Water and oil cannot mix because water is polar while oil is not. Food coloring is water based, which means it is made with water. When you pour the food coloring into the oil, it cannot mix with the oil. When you pour the food coloring and oil into the water, the food coloring separates from the oil and mixes with the water.

Really enjoyed this article, can you make it so I get an alert email when you write a new article?

Wonderful post, very informative! I wonder why I haven’t noticed this website before. You should continue your writing. I’m sure, you’ve a great readers’ base already!

Good post! I always love trying out your posts with my children. We always have a blast!

Leave a Reply Cancel reply

Your email address will not be published. Required fields are marked *

Save my name, email, and website in this browser for the next time I comment.

• arts & crafts
• _famous artists
• _process art
• _paint recipes
• _keepsake crafts
• _book activities
• _sensory bins
• _sensory play recipes
• _science experiments
• _free printables
• _colouring pages
• _valentines day
• _st patrick's day
• _mother's day
• _father's day
• _thanksgiving

Rainbow baking soda science experiment for kids

• rainbow walking water science experiment ,
• rainbow skittles science experiment ,
• colour changing flower science experiment .

Rainbow Baking Soda Science Experiment

Supplies needed for your rainbow baking soda science experiment.

• 2-ounce paper cups (or any small containers you can find)
• Baking soda
• Food colouring

Directions to make yourrainbow baking soda science experiment

Step 1: gather your supplies.

STEP 2: Prepare paper cups

STEP 3: Add food colouring

STEP 4: Add vinegar

• — Share It —

No comments

Hello & Welcome!

Follow By Email

Join the fun subscribe to our newsletter to have fun ideas delivered to your inbox subscribe.

Super Fun Rainbow Science Activities Just For Kids

March 8, 2018 by Editor Leave a Comment

Rainbows are one of my favorite parts of Spring. It usually means that the sun is shining and I’m always happy with that. Even though it usually means it is raining as well, but I’ll take the sunshine when I can get it! Incorporating rainbows in science activities is not only fun but super easy. These Rainbow Science activities are perfect for the classroom or at home. Most of them don’t require much prep but all of them will have kids smiling in science giddiness!

Rainbow Science Activities

Finally a rainbow discovery bottle that the colors don’t run together! I’ve been trying and experimenting for a while now and finally figured it out! It’s not quite liquid and not solid either. It’s a perfect combination of awesomeness! Want to make one of your own? The full tutorial is here .

We’ve all done baking soda and vinegar experiments, right? This  Baking Soda & Vinegar Reaction  though is the most colorful I have seen and I can just imagine how excited kids will be to see the rainbow foam explosions!

Oil and water make science experiments super easy and fun. This  Rainbow Jar  is extra fun, not only because of the colors, but it is mesmerizing how the colors stack up on top of each other!

These candies are fun to eat but even more fun to play with. This  Skittle Rainbow  is beyond the best candy experiment I have seen. I could watch this for hours!

Chromatography is a fun way to incorporate science and art together. These  Rainbow Filters  are fun to create but then also fun to create with!

Did you know that dish soap can do magical things? This  Magic Rainbow Milk  is purely magical. The colors move seemingly on their own, but are they moving on their own?

When science and sensory connect, it is always a great activity. This  Scented Rainbow Science  is perfect for sensory seekers! Plus, adding the scent is probably the easiest part!

This  Exploding Rainbow  is exciting to create and even more exciting to watch. Kids will enjoy these hands-on mini ‘explosion’. Even if we know it is only a simple reaction, kids will love to pretend their rainbows are exploding!

There is something incredibly fun about swirling your hand around in a big bowl of soap foam! This  Rainbow Foam Bubbles  activity is not only a fun sensory activity but also helps teach about color mixing as well.

Rainbows are pretty but  Giant Crystal Rainbows  are even more beautiful. Kids will enjoy watching the crystals grow on their rainbow! It may take a day but the magic of the crystallizing process will not be lost!

This  Fizzy Rainbow Slush  takes baking soda and vinegar to a whole new level. Plus if it is hot outside, you can place this slush in the fridge for a while and the kids can play in cold slush!

This  Rainbow Sugar Water Density  shows that adding sugar to colored water can help the colors separate instead of mixing together, which is excellent for younger children. This is also a fantastic way to introduce or teach about density for older children!

Pumpkin Seeds are not only for fall. These  Pumpkin Seed Discovery Bottles  are rainbow all the way and is a go-to activity for any time of the year!

Do your kids love playing with ice? And melting ice with hot water? This  Rainbow Ice Tower  is filled with colorful items frozen into a tower and the excitement is getting them out! I can see kids being occupied for quite a while with this one!

Science these days is not complete without slime and this  Rainbow Slime  is a MUST. It is absolutely beautiful how the colors connect but don’t mold together. This recipe is anything but icky!

Just like with the skittles experiment above, this  M&M Rainbows  is mesmerizing! It is incredible how candy can taste AND look so beautiful!

I love how this  Erupting Rainbow  comes out of little test tubes. Kids will feel like real scientists even though this experiment is incredibly simple!

This twisted rainbow is sparkly in all the right ways. Kids will enjoy creating this  Salt Crystal Rainbow  and displaying it all Spring long!

Sometimes science is simple and other times it is purely magical. The art that this  Rainbow Paper  experiment can make is fantastic! This would be beautiful to put on the front of cards or notes!

This  Walking Rainbow  experiment has me screaming HOW in my head. I want to explore this experiment because it just looks unreal. Science is so fascinating and this is one of those worldly mysteries that would be fun to solve!

This  Ice & Salt Rainbow  actually creates craters. As pretty as it is, it can do crazy things when combined together. This would be a fun science activity to add to a small world play with dinosaurs or superheroes!

This  Rainbow Colored Ants  activity is purely fascinating. This would be a fun lesson to teach for either a bug unit or even Spring. Super interesting!

Rainbows are beautiful in the sky and can create magic in the real world. These Rainbow Science activities are a close second to being magical in the real world. Whether you are teaching a spring unit, teaching about the weather or just wanting some fun colorful activities – these science activities are sure to please!

• Recent Posts

• Valentine’s Day Letter Formation Mats - February 4, 2024
• January Preschool Themes You’re Going to Love! - January 1, 2024
• December Preschool Themes You’re Going to Love! - December 1, 2023

Leave a Reply Cancel reply

Your email address will not be published. Required fields are marked *

Notify me of follow-up comments by email.

Notify me of new posts by email.

This site uses Akismet to reduce spam. Learn how your comment data is processed .

How to Make a Rainbow Experiment for Kids

If you are as infatuated with rainbows as we are right now, you will love this super simple science discovery for kids. Now, you and your kids can make a rainbow with items you most likely have in your kitchen drunk drawer. How cool is that?

* This post may contain affiliate links for your convenience. Click here for my full disclosure.

We are full of rainbow love lately. From our simple flip a rainbow experiment to our rainbow parfaits, we pretty much have been taken over by rainbows in our house.

How to Make a Rainbow | Simple Science Experiment

CD Flashlight Black or white paper

Optional: Dish Water

How to Make a Rainbow with Kids

There are a few ways you can make rainbows with kids and the discovery of what items work best is half the fun. We have tried a few methods here.

Making Rainbows with a CD and White Paper

With just a flashlight, white paper and a cd you can make a rainbow but it can be challenging. We found we needed the lights turned down but that makes it a little harder to take the pictures needed to show you this cool discovery activity.

Experiment with various methods of getting the light to reflect from the CD onto the paper. Do you see it? There is a small rainbow appearing.

Let’s try it with black paper, now….

Making a Rainbow with a CD and Black Paper

The process for this one is pretty much the exact same as before, however this time you are reflecting onto black paper to see if you can make a brighter rainbow! Looks brighter to me.

Now, can we make a REAL Rainbow… You know the kind you see after rain? For that, I asked my children what we needed and they decided to add water to the discovery to see if they could make an even brighter and bigger rainbow.

Making a Rainbow with Water and a CD

Starting with a shallow dish, add a CD to the dish at a slant (we used silly putty to get ours to sit still). You can experiment with mirrors, metal, and CDs to see which ones create the best rainbows.

Use water to fill the dish with water until the CD is covered at least half way. Again, this is something you can mess with to see if it makes a difference in the intensity of the rainbow you create.

More Adventures in Learning

FREE DOWNLOAD

Discover how to get siblings to get along even when all they do is annoy each other with the Sibling “Get Along” Poster Pack!

5 thoughts on “How to Make a Rainbow Experiment for Kids”

Pingback: Rainbow Number Bonds

Pingback: Rainbow Patterns Activity Free Printable - Life Over Cs

Pingback: A New Rainbow Fingerplay and Rainbow Books - This Library Love

Pingback: 6 Albums with Spring Songs for Preschool | Laptime Songs

Pingback: Rainbow Colour Mixing Lab ⋆ Sugar, Spice and Glitter

Leave a Comment Cancel Reply

Your email address will not be published. Required fields are marked *

Save my name, email, and website in this browser for the next time I comment.

CONNECT WITH ME

We’re fighting to restore access to 500,000+ books in court this week. Join us!

Internet Archive Audio

• This Just In
• Grateful Dead
• Old Time Radio
• 78 RPMs and Cylinder Recordings
• Audio Books & Poetry
• Computers, Technology and Science
• Music, Arts & Culture
• News & Public Affairs
• Spirituality & Religion
• Radio News Archive

• Flickr Commons
• Occupy Wall Street Flickr
• NASA Images
• Solar System Collection
• Ames Research Center

• All Software
• Old School Emulation
• MS-DOS Games
• Historical Software
• Classic PC Games
• Software Library
• Kodi Archive and Support File
• Vintage Software
• CD-ROM Software
• CD-ROM Software Library
• Software Sites
• Tucows Software Library
• Shareware CD-ROMs
• Software Capsules Compilation
• CD-ROM Images
• ZX Spectrum
• DOOM Level CD

• Smithsonian Libraries
• FEDLINK (US)
• Lincoln Collection
• American Libraries
• Canadian Libraries
• Universal Library
• Project Gutenberg
• Children's Library
• Biodiversity Heritage Library
• Books by Language
• Additional Collections

• Prelinger Archives
• Democracy Now!
• Occupy Wall Street
• TV NSA Clip Library
• Animation & Cartoons
• Arts & Music
• Computers & Technology
• Cultural & Academic Films
• Ephemeral Films
• Sports Videos
• Videogame Videos
• Youth Media

Search the history of over 866 billion web pages on the Internet.

Mobile Apps

• Wayback Machine (iOS)
• Wayback Machine (Android)

Browser Extensions

Archive-it subscription.

• Explore the Collections
• Build Collections

Save Page Now

Capture a web page as it appears now for use as a trusted citation in the future.

Please enter a valid web address

• Donate Donate icon An illustration of a heart shape

Video Album

Audio with external links item preview.

Share or Embed This Item

Flag this item for.

• Graphic Violence
• Explicit Sexual Content
• Hate Speech
• Misinformation/Disinformation
• Marketing/Phishing/Advertising
• Misleading/Inaccurate/Missing Metadata

plus-circle Add Review comment Reviews

Download options, in collections.

Uploaded by dpanice on July 19, 2024

SIMILAR ITEMS (based on metadata)

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

• View all journals
• Explore content
• About the journal
• Publish with us
• Sign up for alerts
• Published: 21 August 2024

Lysosomes drive the piecemeal removal of mitochondrial inner membrane

• Akriti Prashar 1   nAff6 ,
• Claudio Bussi   ORCID: orcid.org/0000-0002-9396-9042 2   na1   nAff7 ,
• Antony Fearns   ORCID: orcid.org/0000-0001-9937-8545 2   na1 ,
• Mariana I. Capurro   ORCID: orcid.org/0000-0002-4560-7186 1 ,
• Xiaodong Gao 1 ,
• Hiromi Sesaki 3 ,
• Maximiliano G. Gutierrez   ORCID: orcid.org/0000-0003-3199-0337 2 &
• Nicola L. Jones   ORCID: orcid.org/0000-0001-5495-0739 1 , 4 , 5  

Nature ( 2024 ) Cite this article

6492 Accesses

1 Citations

176 Altmetric

Metrics details

• Membrane trafficking
• Mitochondria

Mitochondrial membranes define distinct structural and functional compartments. Cristae of the inner mitochondrial membrane (IMM) function as independent bioenergetic units that undergo rapid and transient remodelling, but the significance of this compartmentalized organization is unknown 1 . Using super-resolution microscopy, here we show that cytosolic IMM vesicles, devoid of outer mitochondrial membrane or mitochondrial matrix, are formed during resting state. These vesicles derived from the IMM (VDIMs) are formed by IMM herniation through pores formed by voltage-dependent anion channel 1 in the outer mitochondrial membrane. Live-cell imaging showed that lysosomes in proximity to mitochondria engulfed the herniating IMM and, aided by the endosomal sorting complex required for transport machinery, led to the formation of VDIMs in a microautophagy-like process, sparing the remainder of the organelle. VDIM formation was enhanced in mitochondria undergoing oxidative stress, suggesting their potential role in maintenance of mitochondrial function. Furthermore, the formation of VDIMs required calcium release by the reactive oxygen species-activated, lysosomal calcium channel, transient receptor potential mucolipin 1, showing an interorganelle communication pathway for maintenance of mitochondrial homeostasis. Thus, IMM compartmentalization could allow for the selective removal of damaged IMM sections via VDIMs, which should protect mitochondria from localized injury. Our findings show a new pathway of intramitochondrial quality control.

This is a preview of subscription content, access via your institution

Access options

Access Nature and 54 other Nature Portfolio journals

Get Nature+, our best-value online-access subscription

24,99 € / 30 days

cancel any time

Subscribe to this journal

Receive 51 print issues and online access

185,98 € per year

only 3,65 € per issue

Buy this article

• Purchase on SpringerLink
• Instant access to full article PDF

Prices may be subject to local taxes which are calculated during checkout

Similar content being viewed by others

Hypoxia-reprogramed megamitochondrion contacts and engulfs lysosome to mediate mitochondrial self-digestion

ORP1L mediated PI(4)P signaling at ER-lysosome-mitochondrion three-way contact contributes to mitochondrial division

MIROs and DRP1 drive mitochondrial-derived vesicle biogenesis and promote quality control

Data availability.

All data supporting the conclusions of this study are available in the main text or Extended Data Figs. 1 – 10 . Full versions of blots and gels are provided in Supplementary Figs. 1 and 2 .  Source data are provided with this paper.

Kondadi, A. K., Anand, R. & Reichert, A. S. Cristae membrane dynamics – a paradigm change. Trends Cell Biol. 30 , 923–936 (2020).

Article   CAS   PubMed   Google Scholar  

Soubannier, V. et al. A vesicular transport pathway shuttles cargo from mitochondria to lysosomes. Curr. Biol. 22 , 135–141 (2012).

Li, X. et al. Mitochondria shed their outer membrane in response to infection-induced stress. Science 375 , eabi4343 (2022).

Jiao, H. et al. Mitocytosis, a migrasome-mediated mitochondrial quality-control process. Cell 184 , 2896–2910 (2021).

Ma, X. Mitochondria-lysosome-related organelles mediate mitochondrial clearance during cellular dedifferentiation. Cell Rep . 42 , 113291 (2023).

Hughes, A. L., Hughes, C. E., Henderson, K. A., Yazvenko, N. & Gottschling, D. E. Selective sorting and destruction of mitochondrial membrane proteins in aged yeast. eLife 5 , e13943 (2016).

Article   PubMed   PubMed Central   Google Scholar  

Wolf, D. M. et al. Individual cristae within the same mitochondrion display different membrane potentials and are functionally independent. EMBO J. 38 , e101056 (2019).

Article   CAS   PubMed   PubMed Central   Google Scholar  

Kondadi, A. K. et al. Cristae undergo continuous cycles of membrane remodelling in a MICOS‐dependent manner. EMBO Rep. 21 , e49776 (2020).

Cogliati, S., Enriquez, J. A. & Scorrano, L. Mitochondrial cristae: where beauty meets functionality. Trends Biochem. Sci. 41 , 261–273 (2016).

Correia-Melo, C., Ichim, G., G Tait, S. W. & Passos, F. Depletion of mitochondria in mammalian cells through enforced mitophagy. Nat. Protoc. 12 , 183–194 (2016).

Article   PubMed   Google Scholar  

Stephan, T. et al. MICOS assembly controls mitochondrial inner membrane remodeling and crista junction redistribution to mediate cristae formation. EMBO J. 39 , e104105 (2020).

Sugiura, A., McLelland, G., Fon, E. A. & McBride, H. M. A new pathway for mitochondrial quality control: mitochondrial‐derived vesicles. EMBO J. 33 , 2142–2156 (2014).

König, T. et al. MIROs and DRP1 drive mitochondrial-derived vesicle biogenesis and promote quality control. Nat. Cell Biol. 23 , 1271–1286 (2021).

Article   ADS   PubMed   Google Scholar  

Matheoud, D. et al. Parkinson’s disease-related proteins PINK1 and Parkin repress mitochondrial antigen presentation. Cell 166 , 314–327 (2016).

Schuler, M. H. et al. Mitochondrial-derived compartments facilitate cellular adaptation to amino acid stress. Mol. Cell 81 , 3786–3802 (2021).

Lyamzaev, K. G. et al. MitoCLox: a novel mitochondria-targeted fluorescent probe for tracing lipid peroxidation. Oxid. Med. Cell. Longev. 2019 , 9710208 (2019).

Lyamzaev, K. G. et al. Novel fluorescent mitochondria-targeted probe MitoCLox reports lipid peroxidation in response to oxidative stress i n vivo . Oxid. Med. Cell. Longev. 2020 , 3631272 (2020).

McArthur, K. et al. BAK/BAX macropores facilitate mitochondrial herniation and mtDNA efflux during apoptosis. Science 359 , eaao6047 (2018).

Xian, H. et al. Oxidized DNA fragments exit mitochondria via mPTP- and VDAC-dependent channels to activate NLRP3 inflammasome and interferon signaling. Immunity 55 , 1370–1385 (2022).

Kim, J. et al. VDAC oligomers form mitochondrial pores to release mtDNA fragments and promote lupus-like disease. Science 366 , 1531–1536 (2019).

Article   ADS   CAS   PubMed   PubMed Central   Google Scholar  

Zecchini, V. et al. Fumarate induces vesicular release of mtDNA to drive innate immunity. Nature 615 , 499–506 (2023).

Newman, L. E. et al. Mitochondrial DNA replication stress triggers a pro-inflammatory endosomal pathway of nucleoid disposal. Nat. Cell Biol. 26 , 194–206 (2024).

D’Aco, K. E. et al. Mitochondrial tRNA(Phe) mutation as a cause of end-stage renal disease in childhood. Pediatr. Nephrol. 28 , 515–519 (2013).

Piper, R. C. & Katzmann, D. J. Biogenesis and function of multivesicular bodies. Annu. Rev. Cell Dev. Biol. 23 , 519–547 (2007).

Shelke, G. V., Williamson, C. D., Jarnik, M. & Bonifacino, J. S. Inhibition of endolysosome fusion increases exosome secretion. J. Cell Biol. 222 , e202209084 (2023).

Kleele, T. et al. Distinct fission signatures predict mitochondrial degradation or biogenesis. Nature 593 , 435–439 (2021).

Article   ADS   CAS   PubMed   Google Scholar  

Hoogenboom, B. W., Suda, K., Engel, A. & Fotiadis, D. The supramolecular assemblies of voltage-dependent anion channels in the native membrane. J. Mol. Biol. 370 , 246–255 (2007).

Gonçalves, R. P., Buzhynskyy, N., Prima, V., Sturgis, J. N. & Scheuring, S. Supramolecular assembly of VDAC in native mitochondrial outer membranes. J. Mol. Biol. 369 , 413–418 (2007).

Keinan, N., Tyomkin, D. & Shoshan-Barmatz, V. Oligomerization of the mitochondrial protein voltage-dependent anion channel is coupled to the induction of apoptosis. Mol. Cell. Biol. 30 , 5698–5709 (2010).

Shteinfer-Kuzmine, A. et al. Targeting the mitochondrial protein VDAC1 as a potential therapeutic strategy in ALS. Int. J. Mol. Sci. 23 , 9946 (2022).

Peng, W., Wong, Y. C. & Krainc, D. Mitochondria-lysosome contacts regulate mitochondrial Ca2 + dynamics via lysosomal TRPML1. Proc. Natl Acad. Sci. USA 117 , 19266–19275 (2020).

Zhang, X. et al. MCOLN1 is a ROS sensor in lysosomes that regulates autophagy. Nat. Commun. 7 , 12109 (2016).

Rossi, A., Pizzo, P. & Filadi, R. Calcium, mitochondria and cell metabolism: a functional triangle in bioenergetics. Biochim. Biophys. Acta Mol. Cell. Res. 1866 , 1068–1078 (2019).

Dayam, R. M., Saric, A., Shilliday, R. E. & Botelho, R. J. The phosphoinositide-gated lysosomal Ca 2+ channel, TRPML1, is required for phagosome maturation. Traffic 16 , 1010–1026 (2015).

Chen, C. C. et al. A small molecule restores function to TRPML1 mutant isoforms responsible for mucolipidosis type IV. Nat. Commun. 5 , 4681 (2014).

Dikic, I. & Elazar, Z. Mechanism and medical implications of mammalian autophagy. Nat. Rev. Mol. Cell Biol. 19 , 349–364 (2018).

Kaushik, S. & Cuervo, A. M. The coming of age of chaperone-mediated autophagy. Nat. Rev. Mol. Cell Biol. 19 , 365–381 (2018).

Wang, L., Klionsky, D. J. & Shen, H. M. The emerging mechanisms and functions of microautophagy. Nat. Rev. Mol. Cell Biol. 24 , 186–203 (2023).

Müller, O. et al. Autophagic tubes: vacuolar invaginations involved in lateral membrane sorting and inverse vesicle budding. J. Cell Biol. 151 , 519–528 (2000).

Oku, M. et al. Evidence for ESC RT- and clathrin-dependent microautophagy. J. Cell Biol. 216 , 3263–3274 (2017).

Omari, S. et al. Noncanonical autophagy at ER exit sites regulates procollagen turnover. Proc. Natl Acad. Sci. USA 115 , E10099–E10108 (2018).

Lee, C., Lamech, L., Johns, E. & Overholtzer, M. Selective lysosome membrane turnover is induced by nutrient starvation. Dev. Cell 55 , 289–297 (2020).

Bento, C. F. et al. Mammalian autophagy: how does it work? Annu. Rev. Biochem. 85 , 685–713 (2016).

Pickles, S., Vigi, P. & Youle, R. J. Current biology review mitophagy and quality control mechanisms in mitochondrial maintenance. Curr. Biol. 28 , R170–R185 (2018).

Kuchitsu, Y. & Taguchi, T. Lysosomal microautophagy: an emerging dimension in mammalian autophagy. Trends Cell Biol. 34 , 606–616 (2023).

Palikaras, K., Lionaki, E. & Tavernarakis, N. Mechanisms of mitophagy in cellular homeostasis, physiology and pathology. Nat. Cell Biol. 20 , 1013–1022 (2018).

Vietri, M., Radulovic, M. & Stenmark, H. The many functions of ESCRTs. Nat. Rev. Mol. Cell Biol. 21 , 25–42 (2020).

Scheffer, L. L. et al. Mechanism of Ca2 + -triggered ESCRT assembly and regulation of cell membrane repair. Nat. Commun. 5 , 5646 (2014).

Huang, C., Deng, K. & Wu, M. Mitochondrial cristae in health and disease. Int. J. Biol. Macromol. 235 , 123755 (2023).

Tábara, L. C. et al. MTFP1 controls mitochondrial fusion to regulate inner membrane quality control and maintain mtDNA levels. Cell 187 , 3619–3637 (2024).

Elia, N., Sougrat, R., Spurlin, T. A., Hurley, J. H. & Lippincott-Schwartz, J. Dynamics of endosomal sorting complex required for transport (ESCRT) machinery during cytokinesis and its role in abscission. Proc Natl Acad. Sci. USA 108 , 4846–4851 (2011).

Bagshaw, R. D., Callahan, J. W. & Mahuran, D. J. The Arf-family protein, Arl8b, is involved in the spatial distribution of lysosomes. Biochem. Biophys. Res. Commun. 344 , 1186–1191 (2006).

Cemma, M., Kim, P. K. & Brumell, J. H. The ubiquitin-binding adaptor proteins p62/SQSTM1 and NDP52 are recruited independently to bacteria-associated microdomains to target Salmonella to the autophagy pathway. Autophagy 7 , 341–345 (2011).

Boutry, M. & Kim, P. K. ORP1L mediated PI(4)P signaling at ER-lysosome-mitochondrion three-way contact contributes to mitochondrial division. Nat. Commun. 12 , 5354 (2021).

Law, K. B. et al. The peroxisomal AAA ATPase complex prevents pexophagy and development of peroxisome biogenesis disorders. Autophagy 13 , 868–884 (2017).

Sargent, G. et al. PEX2 is the E3 ubiquitin ligase required for pexophagy during starvation. J. Cell Biol. 214 , 677–690 (2016).

Wang, Y., Nartiss, Y., Steipe, B., McQuibban, G. A. & Kim, P. K. ROS-induced mitochondrial depolarization initiates PARK2/PARKIN-dependent mitochondrial degradation by autophagy. Autophagy 8 , 1462–1476 (2012).

Roy, M., Itoh, K., Iijima, M. & Sesaki, H. Parkin suppresses Drp1-independent mitochondrial division. Biochem. Biophys. Res. Commun. 475 , 283–288 (2016).

Kageyama, Y. et al. Parkin‐independent mitophagy requires Drp1 and maintains the integrity of mammalian heart and brain. EMBO J. 33 , 2798–2813 (2014).

Fujita, N. et al. Recruitment of the autophagic machinery to endosomes during infection is mediated by ubiquitin. J. Cell Biol. 203 , 115–128 (2013).

Yan, B. R. et al. C5orf51 is a component of the MON1-CCZ1 complex and controls RAB7A localization and stability during mitophagy. Autophagy 18 , 829–840 (2022).

Durkin, M., Qian, X., Popescu, N. & Lowy, D. Isolation of mouse embryo fibroblasts. Bio Protoc. 3 , e908 (2013).

Paul-Gilloteaux, P. et al. eC-CLEM: flexible multidimensional registration software for correlative microscopies. Nat. Methods 14 , 102–103 (2017).

Download references

Acknowledgements

This work was supported by grants from the Canadian Institute of Health Sciences to N.L.J. (CIHR operating grant nos. 142228 and 173335). A.P. was supported by the Restracomp Fellowship (Hospital for Sick Children). H.S. is supported by NIH grant no. R35GM144103. M.G.G. is supported by Cancer Research UK grant no. FC001092, UK Medical Research Council grant no. CC2081 and Wellcome Trust grant no. CC2081. C.B. was supported by European Respiratory Society–Marie Sklodowska-Curie grant no. 713406. We thank S. Slaugenhaupt (Harvard Medical School, USA) for TRPML1-deficient mice. We thank T. Yoshimori (Osaka University, Tokyo) for generously providing the ATG14 −/− and ATG16L1 −/− MEFs. We thank M. R. Terebiznik (University of Toronto at Scarborough, Toronto) for engaging discussions, and K. Lau and P. Paroutis at the imaging facility at the Hospital for Sick Children for assistance with image analysis.

Author information

Akriti Prashar

Present address: NHLBI, NIH, Bethesda, MD, USA

Claudio Bussi

Present address: School of Biological Sciences, Nanyang Technical University, Singapore, Singapore

These authors contributed equally: Claudio Bussi, Antony Fearns

Authors and Affiliations

Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada

Akriti Prashar, Mariana I. Capurro, Xiaodong Gao & Nicola L. Jones

Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, London, UK

Claudio Bussi, Antony Fearns & Maximiliano G. Gutierrez

Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA

Hiromi Sesaki

Division of Gastroenterology, Hepatology and Nutrition, The Hospital for Sick Children, Toronto, Ontario, Canada

Nicola L. Jones

Departments of Paediatrics and Physiology, University of Toronto, Toronto, Ontario, Canada

You can also search for this author in PubMed   Google Scholar

Contributions

A.P. performed and analysed all light microscopy imaging studies and immunoblots. C.B. and A.F. performed and analysed electron microscopy and CLEM studies. X.G. generated the MCU-mCherry-GFP construct and contributed to the generation of Trpml1 −/− MEFs. M.G.G. and N.L.J. contributed to project supervision. A.P., M.I.C., H.S., M.G.G. and N.L.J. designed the study. A.P. wrote the original draft. C.B., A.F., M.I.C., H.S., M.G.G. and N.L.J. contributed to manuscript writing and editing.

Corresponding author

Correspondence to Nicola L. Jones .

Ethics declarations

Competing interests.

The authors declare no competing interests.

Peer review

Peer review information.

Nature thanks the anonymous reviewers for their contribution to the peer review of this work. Peer reviewer reports are available.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data figures and tables

Extended data fig. 1 cytosolic imm-derived vesicles lack matrix and omm..

a , TOM20 and NAO localization. Inner mitochondrial membranes were labeled with NAO (green) in cells expressing mito-BFP (cyan) and mApple-TOM20 (magenta). Higher magnifications of indicated regions are shown in Fig. 1a . b , Localization of TMRE (magenta), NAO (green) in cells expressing mito-BFP (cyan). Higher magnifications of indicated regions are shown. Arrowheads indicate mito-BFP − /NAO + /TMRE + vesicles. Right : Pixel intensity plots for dashed line. Arrow indicates the vesicle. c , NAO (green), mitotrackerCMXRos (mitotracker) (magenta) localization in cell expressing mito-BFP (cyan). Higher magnifications of indicated regions are shown. Arrowheads indicate mito-BFP − /NAO + /mitotracker + vesicle. Right : Pixel intensity plots for dashed line. Arrow indicates the vesicle. d , Percentage of vesicles positive for IMM markers NAO and mitotracker, but negative for mito-BFP from experiments as in ( c ) (n = 365 vesicles, 30 cells, 3 experiments). Data shown are mean ± SEM shown as large circles and individual data points from corresponding experiments are shown in the same color ( e ) Representative images from at least three independent experiments showing mitotracker (magenta) and TOM20 (green) localization. Higher magnifications of indicated regions are shown in Fig. 1c . Scale bars: main panels 10 μm, magnified panels 3 μm.

Source Data

Extended Data Fig. 2 Validating specificity of IMM in VDIMs.

a , Effect of fixation conditions on mitotracker + /TOM20 − vesicles. Cells labeled with mitotracker (100 nM, 15 min, 37 °C) were either fixed for 15 min at room temperature (RT), 4 °C overnight or at 37 °C in pre-warmed 4% paraformaldehyde for 10 min (n = 60 cells, 3 experiments). b , Effect of mitotracker concentration on mitotracker + /TOM20 − vesicles. Cells were stained with indicated concentrations of mitotracker (n = 62 cells for 50 nM, 64 cells for 100 nM, 53 cells for 200 nM, 3 experiments). c - g , Mitotracker + /TOM20 − vesicles are cell-type independent. Spinning disc confocal images of mitotracker + /TOM20 − vesicles in ( c ) AGS (n = 4 experiments), ( d ) NCI-H292 (n = 4 experiments), ( e ) HeLa (n = 2 experiments), ( f ) COS-1 (n = 2 experiments), and ( g ) Mode-K (n = 3 experiments) cells. For all images, numbers at the bottom indicate the number of vesicles (mean ± SEM), and higher magnifications from indicated regions from main panels are shown to the right. Inverse color micrographs for mitotracker channel are shown. Red circles indicate the mitotracker + /TOM20 − vesicles. h , i , Mitotracker does not label membranes non-specifically. Spinning disc confocal images showing localization of mitotracker (magenta) and ER specific Calnexin (green) ( h ), or Golgi specific GM130 (green) ( i ). Right : Pixel intensity plot for dashed lines. j , Schematic illustrating the protocol for depleting mitochondria from HeLa cells stably expressing Mito-dsRed and pEGFP-Parkin. k , Western blot showing the depletion of mitochondrial proteins in cells from ( j ). Right : Protein expression relative to actin. l , Spinning disc confocal images showing lack of mitochondrial labeling by mitotracker (magenta) in HeLa cells expressing mito-dsRed (blue) and pEGFP-Parkin (green), labeled with anti-TOM20 antibodies (cyan) in an experiment as in ( j ). Data shown are mean ± SEM from three independent experiments. Statistical significance was calculated using One-way ANOVA followed by Tukey’s multiple-comparison test in ( a - b ), and two-tailed Student’s unpaired t-test in ( k ). P values calculated are shown. Gel source data for ( k ) are provided in Supplementary Fig. 1 . Scale bars: main panels 10μm, magnified panels 3μm.

Extended Data Fig. 3 VDIMs are derived from the IMM.

a - i , Localization of mitotracker along with markers associated with different mitochondrial compartments. a , b , Representative images showing localization of mitotracker (magenta) and OMM localized ( a ) Omp25 (green) and TOM20 (cyan), or ( b ) VDAC1 (green) and mEmerald-TOM20 (cyan). Higher magnifications of the indicated regions are shown in Fig. 1g . c , Representative images showing localization of mitotracker (magenta) and mitochondrial intermembrane space-localized cytochrome C (green). OMM was labeled with anti-TOM20 antibodies (cyan). Higher magnifications of the indicated regions are shown in Fig. 1h . d , e , Representative images showing localization of mitotracker (magenta), TOM20 (cyan) and mitochondrial matrix-localized ( d ) SOD2 (green) and ( e ) PDH (green). Higher magnifications of the indicated regions are shown in Fig. 1i . f - i , Representative images showing localization of mitotracker (magenta) in cells expressing mEmerald-TOM20(cyan) and mitochondrial IMM-localized ( f ) UCQCRC2, ( g ) Atp5α, ( h ) COXIV and ( i ) Atp5L (green). Higher magnifications of the indicated regions are shown in Fig. 1j . ( j ) Representative images showing MEFs labeled with mitotracker (magenta), anti-TOM20 antibodies (cyan) and high concentration of DAPI (5 μg/ml). Higher magnifications of indicated regions are shown in Fig. 1m . k , Localization of TOM20 (cyan) and mitotracker (magenta) in cells expressing TFAM-mScarlet (green). Higher magnifications of indicated regions are shown in Fig. 1o . l , Localization of TOM20 (cyan) and mitotracker (magenta) in cells expressing POLG2-tGFP (green). Higher magnifications of indicated regions are shown in Fig. 1q . m , Representative western blot showing the efficiency of Mic60 knockdown. Cells were treated with indicated siRNA. n , VDIM formation in cells treated with indicated siRNA. Mitochondria were labeled with mitotracker (magenta) and anti-TOM20 antibodies (green). Representative confocal images from three independent experiments ( a - l ) and four independent experiments ( n ) are shown. Gel source data for ( m ) are provided in Supplementary Fig. 1 . Scale bars: main panels 10 μm, magnified panels 3 μm. Red circles in the inverted mitotracker micrographs indicate the VDIMs.

Extended Data Fig. 4 VDIMs are distinct from MDVs and MDCs.

a , VDIMs are larger than MDVs. Size difference between the Tom20 (green) or PDH (cyan) positive mitochondria derived vesicles (MDVs) (indicated by open circles), and mitotracker + /TOM20 − vesicles (arrowheads). Bottom : Higher magnifications of indicated regions. b , Size difference between the Tom20 (green) or PDH (cyan) positive mitochondria derived vesicles (MDVs) (indicated by open circles), and mitotracker + /TOM20 − vesicles (arrowheads) in experiments as in ( a ) (n = 562 vesicles, 30 cells, 3 experiments for PDH + /TOM20 − vesicles; n = 605 vesicles, 30 cells, 3 experiments for PDH − /TOM20 + vesicles; n = 436 vesicles, 30 cells, 3 experiments for mitotracker + /TOM20 − vesicles). c , Representative spinning disc confocal images showing VDIM formation in WT and Drp1 −/− MEFs. Arrowheads indicate VDIMs. d , Number of VDIMs in WT and Drp1 −/− (KO) MEFs in experiments as in ( c ) (n = 80 cells, 4 experiments). e , Representative western blot (n = 4 experiments) showing loss of Miro1 expression in cells treated with non-targeting (NT) siRNA or siRNA against Miro1. f , Representative spinning disc confocal images showing VDIM formation in cells treated with NT or Miro1 siRNA an experiment as in ( e ). Arrowheads indicate VDIMs. g , Number VDIMs in cells treated with non-targeting (NT) or Miro1 siRNA in experiments as in ( f ) (n = 90 cells, 4 experiments). h , Representative western blot (n = 4 experiments) showing loss of sorting nexin 9 (Snx9) expression in cells treated with non-targeting (NT) siRNA or siRNA against Snx9. i , Representative spinning disc confocal images showing VDIM formation in cells in experiments as in ( h ). j , Number of VDIMs in cells treated with non-targeting (NT) or syntaxin 9 (snx9) siRNA in experiments as in ( i ) (n = 90 cells, 4 experiments). Data shown are mean ± SEM from three independent experiments. Statistical significance was calculated using two-tailed Student’s unpaired t-test. Gel source data for ( e , h ) are provided in Supplementary Fig. 1 . Scale bars: main panels 10 μm, magnified panels 3 μm.

Extended Data Fig. 5 VDIM formation for intramitochondrial QC.

a , VDIM formation is inhibited by quenching ROS. Representative spinning disc confocal micrographs showing the effect of NAC on VDIM formation. Red circles in the inverted color mitotracker micrographs indicate VDIMs. b , c , Representative confocal micrographs showing the effect of inducing oxidative stress on VDIM formation. Cells were treated with ( b ) oligomycinA, mitoTempo or oligomycinA+mitoTempo, or ( c ) with rotenone, mitoTempo or rotenone+mitoTempo. Mitochondria were labeled with mitotracker (magenta) and anti-TOM20 antibodies (green). Red circles in the inverted color mitotracker micrographs indicate VDIMs. d , Representative images showing oxidation of MitoCLox in cells treated with H 2 O 2. e , Representative images showing oxidized MitoCLox in VDIMs (n = 3 experiments). Right : Higher magnification of indicated regions. f , Ratio of oxidized/total MitoCLox in indicated regions from ( e ). g , Localization of 8-OHdG (green) with VDIMs (arrowheads). Bottom: Pixel intensity plot for dashed line. Arrow indicates the vesicle. h , Percentage of VDIMs positive for 8-OHdG in experiments as in ( g ). (n = 272 vesicles, 32 cells, 3 experiments). i , Representative spinning disc confocal images showing localization of TOM20 (cyan), mitotracker (magenta) and LAMP1 (green) in 143bρ 0 and 143bρ + cells. Cells were left untreated or treated with vehicle or Rotenone. Higher magnifications of indicated regions are shown to the right. j , Quantification of VDIM formation in 143b cells lacking mitochondrial DNA (ρ0) along with controls (ρ+) (143bρ 0 n = 70 cells for untreated, 63 cells for vehicle, 60 cells for rotenone and 143bρ + n = 66 cells for untreated, 61 cells for vehicle, 60 cells for rotenone, 3 experiments). Data shown are mean ± SEM shown as large circles and individual data points from corresponding experiments shown in the same colors. Statistical significance was calculated using One-way ANOVA followed by Tukey’s multiple-comparison test. P values calculated are indicated. Scale bars: main panels 10 μm, magnified panels 3 μm.

Extended Data Fig. 6 VDIMs are delivered to lysosomes for degradation.

a , Mitotracker (magenta), TOM20 (cyan) and LAMP1 (green) localization. Higher magnifications of indicated regions are shown in Fig. 3a . b , Localization of mitotracker (grey), TOM20 (cyan) and MCU-GFP-mCherry. Higher magnifications of indicated regions are shown in Fig. 3d . c , Left: Fluorescence, and Right: EM image of cell used for CLEM. Higher magnification of indicated region is shown in Fig. 3f . d , Live-cell imaging showing mito-BFP − /mitotracker + (magenta) vesicles being delivered to lysosomes labeled with dextran (green). Arrowheads indicate the VDIM pinching from the mitochondria and sorted to the lysosome. Images were acquired every 5 s. e - l , VDIMs are not partially degraded mitochondria. e , Representative spinning disc confocal micrographs showing the effect of bafilomycin (BafA1) on VDIM formation. Right : Higher magnifications of indicated regions. Red circles in inverted micrograph for mitotracker indicate the VDIMs. f , Representative spinning disc confocal micrographs showing the effect of chloroquine (CQ) on VDIM formation. Right : Higher magnification of indicated regions. Red circles in inverted micrograph for mitotracker indicate the VDIMs. g , Localization of mitotracker (magenta), TOM20 (cyan) in cells expressing Omp25-GFP (green), treated with vehicle (-) or BafA1. Arrowheads indicate the VDIMs. ( h ) Localization of mitotracker (magenta), TOM20 (cyan) and PDH (green) in cells treated with vehicle (-) or BafA1. Arrowheads indicate the VDIMs. i , Localization of mitotracker (magenta), TOM20 (cyan) in cells expressing SOD2-GFP (green), treated with vehicle (-) or BafA1. Arrowheads indicate the VDIMs. j , Percentage of mitotracker + /TOM20 − VDIMs positive for Omp25 in cells treated with BafA1 compared to vehicle treated cells from experiments as in ( g ) (n = 270 vesicles for vehicle, 503 vesicles for BafA1, 30 cells, 3 experiments). k , Percentage of mitotracker + /TOM20 − VDIMs positive for PDH in cells treated with BafA1 compared to vehicle treated cells from experiments as in ( h ) (n = 270 vesicles for vehicle, 503 vesicles for BafA1, 30 cells, 3 experiments). l , Percentage of mitotracker + /TOM20 − VDIMs positive for SOD2 in cells treated with BafA1 compared to vehicle treated cells from experiments as in ( i ) (n = 369 vesicles for vehicle, 500 vesicles for BafA1, 30 cells, 3 experiments). ( j - l ) Mean ± SEM are shown as large circles and individual data points from corresponding experiments are shown in the same colors. Statistical analysis was performed using two-tailed Student’s unpaired t-test. P values are indicated. Scale bars: main panels 10 μm, magnified panels 3 μm.

Extended Data Fig. 7 VDIMs are not multivesicular bodies (MVB).

a , Representative images showing mitotracker (magenta), TOM20 (cyan), LBPA (grey) in cells expressing LAMP1-GFP (green). Bottom : Higher magnification of indicated regions. Arrowheads indicate VDIMs lacking LBPA. Arrow indicates VDIM positive for LBPA. b , Number of VDIMs positive for LAMP1 or LBPA from experiments as in ( a ) (n = 243 vesicles, 30 cells, 3 experiments). c , Representative images showing mitotracker (magenta), TOM20 (cyan), CD63 (grey) in cells expressing LAMP1-GFP (green). Bottom : Higher magnification of indicated regions. Arrowheads indicate VDIMs lacking CD63. Arrow indicates VDIM positive for CD63. d , Number of VDIMs positive for LAMP1 or CD63 from experiments as in ( c ) (n = 167 vesicles, 17 cells, 2 experiments). e , Schematic illustrating lysosome and MVB fusion regulated by Arl8b GTPase. f , Localization of Lamp1 (magenta) and LBPA (green) in cells expressing GFP-Arl8b-WT (blue) or GFP-Arl8b-DN (blue). Right : Pixel intensity plots for dashed line. Arrows indicate LBPA negative lysosomes in cells expressing GFP-Arl8b-DN. g , VDIM formation in cells expressing GFP-Arl8b-WT (green) or GFP-Arl8b-DN (green). Higher magnification of indicated regions are shown where arrowheads indicate the VDIM. h , Number of VDIMs in cells expressing Arl8b-WT or Arl8b-DN in experiments as in (g) (n = 30 cells, 3 experiments). i , Number of LAMP1 positive VDIMs in cells expressing Arl8b-WT or Arl8b-DN in experiments as in ( g ) (n = 30 cells, 3 experiments). Data shown are mean ± SEM. Statistical significance was calculated using two-tailed Student’s unpaired t-test. P values calculated are indicated. Scale bars: main panels 10 μm, magnified panels 3 μm.

Extended Data Fig. 8 VDAC1 and TRPML1 mediate VDIM formation.

a , VDIM formation in cells treated with vehicle or VBIT-12. b , Representative western blot showing the efficiency of VDAC1 knockdown (n = 4 experiments). c , VDIM formation in cells treated with indicated siRNA. d , VDIM formation in cells treated with BAPTA-AM. e , VDIM formation in cells treated with apilimod. f , VDIM formation in cells treated with ML-SA1. g , Mitotracker (magenta), TOM20 (cyan) and PDH (green) localization in cells treated with VBIT-12 or ML-SA1. Arrowheads indicate the VDIMs. h , Percentage of mitotracker + /TOM20 − VDIMs positive for PDH in experiments as in ( g ) (n = 293 vesicles for vehicle, 535 vesicles for ML-SA1, 30 cells, 3 experiments for ML-SA1; n = 342 vesicles for vehicle, 302 vesicles for VBIT-12, 30 cells, 3 experiments). i , Mitotracker (magenta), TOM20 (cyan) in cells expressing Omp25-GFP (green) treated with VBIT-12 or ML-SA1. Arrowheads indicate the VDIMs. j , Percentage of mitotracker + /TOM20 − VDIMs positive for Omp25 in experiments as in ( i ). k , Validation of gene knockout in TRPML1 −/− MEFs. MLIV gene was amplified from WT and TRPML1 −/− MEFs and from DNA extracted from ear-notches of WT, KO and heterozygous (het) mice (n = 1). l , Representative confocal micrographs showing VDIM formation in WT and TRPML1 −/− MEFs. m , VDIM formation in TRPML1 −/− MEFs treated with BafA1. n , Effect of TRPML1 re-expression on VDIM formation in TRPML1 −/− MEFs. TRPML1 −/− cells transiently transfected with GFP or TRPML1-YFP were treated with vehicle or BafA1. Data shown are means from 3 experiments. Representative spinning disc confocal micrographs are shown in ( a , c - f , l - n ). For all fluorescence images, higher magnifications of indicated regions are shown to the right. Red circles on the inverted fluorescence micrographs for the mitotracker channel indicate the VDIMs. Gel source data for ( b ) are provided in Supplementary Fig. 2 . Scale bars: main panels 10 μm, magnified panels 3 μm.

Extended Data Fig. 9 VDIMs form independently of macroautophagy.

a , VDIM formation in MEFs lacking Atg5, Atg12, Atg14 and Atg16. Right : Higher magnification of indicated regions. b , VDIM formation in Atg5−/− MEFs. Representative confocal micrographs showing VDIM pinching off and being directly sorted into a lysosome. Right: 3D- reconstruction of indicated region. c , Effect of scavenging ROS on VDIM formation. Cells were treated with vehicle (−) or NAC (+). d , Number of VDIMs in cells in experiments as in ( c ) (n = 63 cells, 3 experiments). e , Effect of oxidative stress on VDIM formation. Cells were treated with vehicle, oligomycinA, mitoTempo or oligomycinA and mitoTempo together. f , Number of VDIMs in cells in experiments as in (e) (n = 75 cells for vehicle, 64 cells for oligomycinA, 73 cells for mitoTempo, 66 for oligomycinA+mitoTempo, 4 experiments). g , Effect of VDAC inhibition on VDIM formation. h , Number of VDIMs in cells treated with VBIT-12 in experiments as in ( g ) (n = 75 cells, 3 experiments). i , Representative images showing VDIM formation in cells treated with indicated siRNA. j , Representative western blot showing the efficiency of VDAC1 knockdown (n = 4 experiments). k , Number of VDIMs in VDAC1 depleted cells in experiments as in ( i ) (n = 136 cell for NT, 127 for VDAC siRNA, 4 experiments). l , Representative images showing the effect of BAPTA-AM on VDIM formation. m , Number of VDIMs in cells treated with BAPTA-AM in experiments as in ( l ) (n = 87 cells for vehicle, 67 cells for BAPTA-AM, 3 experiments). n , Representative images showing VDIM formation in cells treated with ML-SA1. o , Number of VDIMs in cells treated with ML-SA1 in experiments as in ( n ) (n = 66 cells for vehicle, 69 cells for ML-SA1, 3 experiments). p , Effect of VDAC1 inhibition on MCU-GFP-mCherry positive VDIMs. Cells expressing MCU-GFP-mCherry were treated with VBIT-12. q , Number of VDIMs positive for GFP+mCherry (yellow) and mCherry (red), indicating lysosomal quenching of GFP from experiments as in ( p ) (n = 412 vesicles for vehicle, 336 vesicles for VBIT-12, 30 cells, 3 experiments). r , Effect of TRPML1 activation by ML-SA1 on MCU-GFP-mCherry positive VDIMs. s , Number of VDIMs positive for GFP+mCherry (yellow) and mCherry (red), indicating lysosomal quenching of GFP from experiments as in ( r ) (n = 229 vesicles for vehicle, 194 vesicles for ML-SA1, 20 cells, 2 experiments). t - v , Localization of TOM20 (cyan) and mitotracker (magenta) with indicated autophagy markers. Cells were transfected with ( t ) mCherry-LC3 (green), ( u ) p62-mCherry (green), ( v ) mRFP-Ub (green). Higher magnifications of indicated regions are shown in Fig. 5e . Representative spinning disc confocal micrographs are shown in ( a , c , e , g , i , l , n , p , r ) where higher magnification of indicated regions are shown to the right. Red circles in inverted micrograph for mitotracker indicate the VDIMs. Data shown are mean ± SEM shown as large circles and individual data points from corresponding experiments shown in the same colors. Statistical significance was calculated using two-tailed Student’s unpaired t-test in ( d , h , k , m , o ), and One-way ANOVA followed by Tukey’s multiple-comparison test in ( f , q , s ). P values calculated are indicated. Gel source data for ( j ) are provided in Supplementary Fig. 1 . Scale bars: main panels 10 μm, magnified panels 3 μm.

Extended Data Fig. 10 VDIMs form by ESCRT-mediated, microautophagy-like process.

a , Representative images showing TOM20 (cyan), mitotracker (magenta) and LAMP1 (green). Higher magnifications of indicated regions are shown in Fig. 5g . b , Representative images showing localization of TOM20 (cyan), mitotracker (magenta) and TRPML1 (green). Cells were transiently transfected with TRPML1-YFP. Higher magnifications of indicated regions are shown in Fig. 5h . c , Localization of TOM20 (cyan) and mitotracker (magenta) in cells expressing mCherry-Parkin. Higher magnification of indicated region is shown in Fig. 5i . d , Effect of Parkin overexpression on VDIM formation. Cells were transiently transfected with (top) GFP or (bottom) pEGFP-Parkin. Red circles in inverted micrographs for mitotracker indicate VDIMs. e , Representative images showing VDIM formation in Parkin-/- MEFs compared to WT controls. Circles in the inverted mitotracker micrograph indicate the VDIMs. f - h , Representative images showing localization of TOM20 (cyan), mitotracker (magenta) and LAMP1 (green) in cells transiently transfected with ( f ) Tsg101-GFP (grey), ( g ) Chmp2a-GFP (grey) or ( h ) Chmp4b-RFP (grey). Higher magnifications of indicated regions are shown in Fig. 6a–c . i , Live-cell imaging sequence showing recruitment of Tsg101 (green) at sites of VDIM scission. Images were acquired every 5 s. Arrowheads indicate the VDIMs and arrows indicate the Tsg101 puncta. j , Representative images showing mitotracker (magenta), TOM20 (cyan) and ALG-2 (grey). Higher magnifications of the indicated regions are shown in Fig. 6g . k , Representative western blot showing the efficiency of Tsg101 depletion compared to non-targeting (NT) controls. l , Representative images showing VDIM formation in cells treated with Tsg101 siRNA compared to NT controls. Right : Higher magnification of indicated regions. Red circles in inverted micrograph for mitotracker indicate the VDIMs. All data shown are representative from three independent experiments. d , e , Representative spinning disc confocal images are shown. Gel source data for ( k ) are provided in Supplementary Fig. 1 . Scale bars: main panels 10 μm, magnified panels 3 μm.

Supplementary information

Supplementary information.

This file contains Supplementary Figs. 1 and 2 and legends for Supplementary Videos 1–11.

Reporting Summary

Peer review file, supplementary video 1.

Localization of VDIMs within lysosomes. 3D surface reconstruction of maximum-intensity projections showing mitotracker + (magenta)/TOM20 − (cyan) vesicles inside lysosomes labelled with LAMP1 (green).

Supplementary Video 2

3D reconstruction of CLEM. Z -projection of stacks corresponding to CLEM images showing VDIMs followed by 3D surface reconstruction. Cells expressing mito-BFP (blue) and LAMP1-GFP (green) were labelled with mitotracker (magenta). Fluorescence images were acquired, cells processed for electron microscopy and fluorescence and electron microscopy images were correlated.

Supplementary Video 3

VDIMs are delivered to lysosomes. Single z -plane time lapse of MEFs expressing matrix-localized mito-BFP (blue), labelled with mitotracker (magenta) and dextran (lysosomes, green). Lysosomes were labelled with 10 kDa dextran-Alexa Fluor 488 by overnight pulse and a 3–5 h chase. Images were acquired at 5 s intervals and processed automatically into deconvolved AiryScan images. Mitotracker + (magenta) vesicle, lacking BFP, pinches off from mitochondria and is taken up by the lysosome.

Supplementary Video 4

Lysosomal delivery of VDIMs. Additional example showing lysosomal delivery of a VDIM. Single z -plane time lapse of MEF expressing matrix-localized mito-BFP (blue), labelled with mitotracker (magenta) and dextran (lysosomes, green). Lysosomes were labelled with 10 kDa dextran-Alexa Fluor 488 by overnight pulse and a 3–5 h chase. Images were acquired at 5 s intervals and processed automatically into deconvolved AiryScan images. Mitotracker + (magenta) vesicle, lacking BFP, pinches off from mitochondria and is taken up by the lysosome.

Supplementary Video 5

VDIM formation by microautophagy-like mechanism. Z -stack showing the presence of LAMP1-labelled membranes (green) inside the lumen of lysosomes positive for mitotracker (magenta).

Supplementary Video 6

Tsg101 is recruited to VDIMs. 3D surface reconstruction of maximum-intensity projections showing Tsg101 (greyscale) recruitment at VDIMs.

Supplementary Video 7

Chmp2a-GFP is recruited to VDIMs. 3D surface reconstruction of maximum-intensity projections showing Chmp2a (greyscale) recruitment at VDIMs.

Supplementary Video 8

Chmp4b-RFP is recruited to VDIMs. 3D surface reconstruction of maximum-intensity projections showing Chmp4b (greyscale) recruitment at VDIMs.

Supplementary Video 9

ESCRT machinery contributes to VDIM formation. Single z -plane time lapse of a cell expressing Tsg101-GFP (greyscale), labelled with mitotracker (magenta) and dextran (lysosomes, blue). Lysosomes were labelled with Dextran Cascade blue (blue) by overnight pulse and a 3–5 h chase. Images were acquired at 5 s intervals and processed automatically into deconvolved AiryScan images. Mitotracker + (magenta) vesicle pinches off from mitochondria and is taken up by the lysosome. Tsg101 puncta is recruited before the mitotracker + lysosome pinches off.

Supplementary Video 10

ESCRT machinery contributes to VDIM formation. Additional example showing Tsg101 (green) recruitment to sites of VDIM scission. Mitochondria in cells expressing Tsg101-GFP (green) were labelled with mitotracker (magenta), and lysosomes were labeled with Dextran Cascade blue (blue) by overnight pulse and a 3–5 h chase. Images were acquired every 5 s.

Supplementary Video 11

Absence of ESCRT component Tsg101 impairs VDIM scission. 3D surface reconstruction of maximum-intensity projections from cells in which Tsg101 expression was depleted by siRNA. Mitotracker + (magenta)/TOM20 − (cyan) vesicles inside lysosomes labelled with LAMP1 (green).

Source data

Source data fig. 1, source data fig. 2, source data fig. 3, source data fig. 4, source data fig. 5, source data fig. 6, source data extended data fig. 1, source data extended data fig. 2, source data extended data fig. 4, source data extended data fig. 5, source data extended data fig. 6, source data extended data fig. 7, source data extended data fig. 8, source data extended data fig. 9, rights and permissions.

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Cite this article.

Prashar, A., Bussi, C., Fearns, A. et al. Lysosomes drive the piecemeal removal of mitochondrial inner membrane. Nature (2024). https://doi.org/10.1038/s41586-024-07835-w

Download citation

Received : 05 March 2023

Accepted : 16 July 2024

Published : 21 August 2024

DOI : https://doi.org/10.1038/s41586-024-07835-w

Share this article

Anyone you share the following link with will be able to read this content:

Sorry, a shareable link is not currently available for this article.

Provided by the Springer Nature SharedIt content-sharing initiative

This article is cited by

Inner membrane turns inside out to exit mitochondrial organelles.

• David Pla-Martín
• Andreas S. Reichert

Nature (2024)

By submitting a comment you agree to abide by our Terms and Community Guidelines . If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Quick links

• Explore articles by subject
• Guide to authors
• Editorial policies

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.