Category: Biotechnology News

“The plant we use, Arabidopsis, has large cells and peroxisomes so large that we can see inside them with a light microscope,” said Bonnie Bartel, the Ralph and Dorothy Looney Professor of Biosciences. “The peroxisome gets even larger during the seed to seedling stage, when the plant is relying on fatty acids for energy, before shrinking back down to its normal size once the plant can photosynthesize.”

Protein PEX11 Helps Control Peroxisome Size

Bartel’s team focuses on these enlarged peroxisomes, particularly a protein called PEX11. Scientists have long known that PEX11 plays a role in helping peroxisomes divide. In new research published in Nature Communications, the team found that this protein also helps control how peroxisomes expand and shrink during early plant development.

“Peroxisomes are implicated in some human diseases and used in bioengineering,” said Nathan Tharp, first author of the paper and a Rice graduate student. “They can, however, be rather tricky to study.”

Using CRISPR To Study a Complex Protein

A common strategy for understanding a protein is to disable the gene responsible for making it and observe the effects. In this case, the situation was more complicated. PEX11 is produced by five different genes. Disrupting just one of them had little effect, but removing all five caused the plant to die. This made it difficult to pinpoint the protein’s function.

To get around this problem, Tharp used advanced CRISPR techniques to selectively disable different combinations of the five genes.

“I was able to use recent advances in CRISPR to go in and break specific combinations of the five genes,” said Tharp, who recently defended his thesis. “It was only then that we were able to see that PEX11 is clearly involved in controlling the growth of the peroxisome during the seed to seedling stage.”

Giant Peroxisomes Reveal Growth Control Mechanism

Tharp engineered two types of mutant plants, each missing a particular set of PEX11 genes. In both cases, peroxisomes expanded during the seed to seedling stage as expected. However, instead of shrinking back to their usual size, some continued growing far beyond normal limits. In extreme cases, the peroxisomes stretched from one end of the cell to the other.

These mutant cells also lacked vesicles, small membrane-bound compartments that typically form inside the peroxisome during fatty acid processing. Under normal conditions, these vesicles develop as the peroxisome grows and appear to remove portions of its outer membrane.

“The vesicles taking pieces of membrane as they form may help control the peroxisome’s growth,” Tharp said. “In our PEX11 mutants, these vesicles either don’t form or are abnormally small and rare, and so we see these massive peroxisomes, way larger than normal.”

Findings Extend Beyond Plants to Other Species

Although the research focused on plants, Tharp wanted to know whether the same mechanism might exist in other organisms. To test this idea, he introduced the yeast version of the protein, called Pex11, into the mutant plant cells.

“We put yeast Pex11 into our mutant plant cells to see if it could return the peroxisomes back to normal,” Tharp said. “And it did.”

This result suggests that Pex11 serves a similar function in yeast as it does in plants, despite the vast evolutionary distance between them. Because of this, the protein may also play a comparable role in other types of cells, including human cells.

“Finding that this protein fills the same role in yeast and plant cells suggests that it may be a highly conserved protein,” Bartel said. “Our findings in plants, in this relatively easy-to-study model, may thus be applicable to human cells and cells used for bioengineering.”

Octopuses, squids, cuttlefish, and their cephalopod relatives are masters of camouflage, able to instantly shift their skin color to blend into their surroundings. This extraordinary transformation is driven by a natural pigment called xanthommatin, which plays a key role in their color-changing skin.

For years, researchers and even defense organizations have been captivated by xanthommatin’s light-responsive qualities. Yet replicating and studying this pigment in the lab has been extremely challenging — until now.

In a new breakthrough from UC San Diego’s Scripps Institution of Oceanography, scientists successfully created a method to produce large quantities of xanthommatin. This marks a major step forward in decoding how animals achieve their remarkable camouflage.

Bacteria Turned Into Natural Pigment Factories

Using a biologically inspired approach, the research team was able to generate the pigment inside bacteria, achieving production levels up to 1,000 times greater than previous methods. This innovation could pave the way for sustainable new uses in materials and cosmetics, including applications in photoelectronics, thermal coatings, dyes, and UV-protective products.

“We’ve developed a new technique that has sped up our capabilities to make a material, in this case xanthommatin, in a bacterium for the first time,” said Bradley Moore, senior author of the study and a marine chemist with appointments at Scripps Oceanography and the UC San Diego Skaggs School of Pharmacy and Pharmaceutical Sciences. “This natural pigment is what gives an octopus or a squid its ability to camouflage — a fantastic superpower — and our achievement to advance production of this material is just the tip of the iceberg.”

Published today (Nov. 3) in Nature Biotechnology, the study received support from the National Institutes of Health, the Office of Naval Research, the Swiss National Science Foundation, and the Novo Nordisk Foundation.

According to the researchers, this achievement not only deepens our understanding of the biological and chemical foundations of animal coloration, but also highlights a powerful new biotechnology. The same technique could be used to create other valuable compounds, helping industries transition away from petroleum-based products toward more sustainable, nature-inspired materials.

A Promising Pigment

Beyond cephalopods, xanthommatin is also found in insects within the arthropod group, contributing to the brilliant orange and yellow hues of monarch butterfly wings and the bright reds seen in dragonfly bodies and fly eyes.

Despite xanthommatin’s fantastic color properties, it is poorly understood due to a persistent supply challenge. Harvesting the pigment from animals isn’t scalable or efficient, and traditional lab methods are labor intensive, reliant on chemical synthesis that is low yielding.

Researchers in the Moore Lab at Scripps Oceanography sought to change that, working with colleagues across UC San Diego and at the Novo Nordisk Foundation Center for Biosustainability in Denmark to design a solution, a sort of growth feedback loop they call “growth coupled biosynthesis.”

The way in which they bioengineered the octopus pigment, a chemical, in a bacterium represents a novel departure from typical biotechnological approaches. Their approach intimately connected the production of the pigment with the survival of the bacterium that made it.

“We needed a whole new approach to address this problem,” said Leah Bushin, lead author of the study, now a faculty member at Stanford University and formerly a postdoctoral researcher in the Moore Lab at Scripps Oceanography, where her work was conducted. “Essentially, we came up with a way to trick the bacteria into making more of the material that we needed.”

Typically, when researchers try to get a microbe to produce a foreign compound, it creates a major metabolic burden. Without significant genetic manipulation, the microbe resists diverting its essential resources to produce something unfamiliar.

By linking the cell’s survival to the production of their target compound, the team was able to trick the microbe into creating xanthommatin. To do this, they started with a genetically engineered “sick” cell, one that could only survive if it produced both the desired pigment, along with a second chemical called formic acid. For every molecule of pigment generated, the cell also produced one molecule of formic acid. The formic acid, in turn, provides fuel for the cell’s growth, creating a self-sustaining loop that drives pigment production.

“We made it such that activity through this pathway, of making the compound of interest, is absolutely essential for life. If the organism doesn’t make xanthommatin, it won’t grow,” said Bushin.

To push the bacteria to make even more pigment, the researchers turned to robotics and automation. They used robotic systems to guide the microbes through two rounds of high-throughput adaptive laboratory evolution, a process designed to help the cells gradually improve their performance. This advanced method was developed by the lab of study co-author Adam Feist, a professor in the Shu Chien-Gene Lay Department of Bioengineering at the UC San Diego Jacobs School of Engineering and a senior scientist at the Novo Nordisk Foundation Center for Biosustainability.

The researchers also used specialized bioinformatics software from the Feist Lab to pinpoint genetic changes that increased the microbes’ productivity. These key mutations allowed the engineered bacteria to produce the pigment efficiently using only a single nutrient source.

“This project gives a glimpse into a future where biology enables the sustainable production of valuable compounds and materials through advanced automation, data integration and computationally driven design,” said Feist. “Here, we show how we can accelerate innovation in biomanufacturing by bringing together engineers, biologists and chemists using some of the most advanced strain-engineering techniques to develop and optimize a novel product in a relatively short time.”

Traditional approaches yield around five milligrams of pigment per liter “if you’re lucky,” said Bushin, while the new method yields between one to three grams per liter.

Getting from the planning stages to the actual experimentation in the lab took several years of dedicated work, but once the plan was put into motion, the results were almost immediate.

“It was one of my best days in the lab,” Bushin recalled of the first successful experiment. “I’d set up the experiment and left it overnight. When I came in the next morning and realized it worked and it was producing a lot of pigment, I was thrilled. Moments like that are why I do science.”

Next Steps

Moore anticipates that this new biotech methodology, which is fully nature-inspired and non-invasive, will transform the way in which biochemicals are produced.

“We’ve really disrupted the way that people think about how you engineer a cell,” he said. “Our innovative technological approach sparked a huge leap in production capability. This new method solves a supply challenge and could now make this biomaterial much more broadly available.”

While some applications for this material are far-out, the authors noted active interest from the U.S. Department of Defense and cosmetics companies. According to the researchers, collaborators are interested in exploring the material’s natural camouflage capabilities, while skincare companies are interested in using it in natural sunscreens. Other industries see potential uses ranging from color-changing household paints to environmental sensors.

“As we look to the future, humans will want to rethink how we make materials to support our synthetic lifestyle of 8 billion people on Earth,” said Moore. “Thanks to federal funding, we’ve unlocked a promising new pathway for designing nature-inspired materials that are better for people and the planet.”

Additional study authors are Tobias Alter, María Alván-Vargas, Daniel Volke, Òscar Puiggené and Pablo Nikel from the Novo Nordisk Foundation Center for Biosustainability; Elina Olson from UC San Diego’s Shu Chien-Gene Lay Department of Bioengineering; Lara Dürr and Mariah Avila from Scripps Institution of Oceanography at UC San Diego; and Taehwan Kim and Leila Deravi from Northeastern University.

After division, scientists thought, the DNA would slowly rebuild its complex, folded structure, which is key to regulating which genes are active in a given cell.

Now, new research from MIT reveals that this long-accepted model isn’t quite right. Using a powerful, high-resolution genome mapping method, the team found that small 3D loops — connections between regulatory DNA elements and genes — remain intact even during cell division, a stage known as mitosis.

“This study really helps to clarify how we should think about mitosis. In the past, mitosis was thought of as a blank slate, with no transcription and no structure related to gene activity. And we now know that that’s not quite the case,” says Anders Sejr Hansen, an associate professor of biological engineering at MIT. “What we see is that there’s always structure. It never goes away.”

DNA Loops That Help Cells “Remember”

The researchers also discovered that these DNA loops actually strengthen as chromosomes condense in preparation for division. This tightening brings distant regulatory elements closer together, encouraging them to stick. According to the team, this could allow cells to “remember” which genetic interactions existed before division and reestablish them afterward.

“The findings help to bridge the structure of the genome to its function in managing how genes are turned on and off, which has been an outstanding challenge in the field for decades,” says Viraat Goel PhD ’25, the lead author of the study.

Hansen and Edward Banigan, a research scientist at MIT’s Institute for Medical Engineering and Science, are senior authors of the study, published in Nature Structural and Molecular Biology. Co-authors include MIT professors Leonid Mirny and Gerd Blobel of the University of Pennsylvania’s Perelman School of Medicine.

Mapping the Hidden Architecture of DNA

Over the last two decades, scientists have uncovered that DNA in the cell nucleus organizes itself into 3D loops. Many of these loops allow genes to interact with distant regulatory regions — sometimes millions of base pairs apart — while others form during mitosis to pack chromosomes tightly.

Most of this mapping has relied on a tool called Hi-C, a technique co-developed by MIT researchers and Job Dekker at the University of Massachusetts Chan Medical School. Hi-C works by cutting DNA into small fragments and linking together those that are near each other in the cell nucleus before sequencing them to identify which regions interact.

While effective, Hi-C lacks the resolution needed to detect fine-scale interactions between genes and regulatory sequences known as enhancers. Enhancers are short DNA segments that activate genes by binding to promoters, the regions where transcription begins.

A Breakthrough Tool: Region-Capture Micro-C

In 2023, Hansen and colleagues developed a next-generation technique that can map genome structures with up to 1,000 times greater precision. The method, called Region-Capture Micro-C (RC-MC), uses a different enzyme to cut DNA into evenly sized fragments and focuses on a smaller portion of the genome. This allows researchers to create highly detailed 3D maps of targeted DNA regions.

Using RC-MC, the team identified a new structural feature they named “microcompartments.” These are tiny, densely connected loops that form when nearby enhancers and promoters attach to one another.

Earlier work had shown that microcompartments formed by a different mechanism than larger 3D genome structures, but the team didn’t yet understand how. To explore this, they decided to examine what happens to these structures as cells go through mitosis. During this phase, chromosomes compact dramatically to ensure they can be duplicated and evenly distributed between daughter cells. As this occurs, large genome domains known as A/B compartments and topologically associating domains (TADs) typically disappear.

Unexpected Stability During Cell Division

The researchers expected microcompartments to vanish as well. To test this, they monitored cells throughout the entire division cycle to see how these loops behaved before and after mitosis.

“During mitosis, it has been thought that almost all gene transcription is shut off. And before our paper, it was also thought that all 3D structure related to gene regulation was lost and replaced by compaction. It’s a complete reset every cell cycle,” Hansen says.

To their surprise, the loops didn’t disappear. In fact, they became even more pronounced as cells divided.

“We went into this study thinking, well, the one thing we know for sure is that there’s no regulatory structure in mitosis, and then we accidentally found structure in mitosis,” Hansen says.

Using their technique, the researchers also confirmed that larger structures such as A/B compartments and TADs do disappear during mitosis, as had been seen before.

“This study leverages the unprecedented genomic resolution of the RC-MC assay to reveal new and surprising aspects of mitotic chromatin organization, which we have overlooked in the past using traditional 3C-based assays. The authors reveal that, contrary to the well-described dramatic loss of TADs and compartmentalization during mitosis, fine-scale “microcompartments” — nested interactions between active regulatory elements — are maintained or even transiently strengthened,” says Effie Apostolou, an associate professor of molecular biology in medicine at Weill Cornell Medicine, who was not involved in the study.

Explaining a Mysterious Burst of Gene Activity

The discovery may also explain a long-observed burst in gene transcription that occurs near the end of mitosis. Since the 1960s, scientists believed transcription stopped entirely during cell division. However, studies in 2016 and 2017 revealed a brief spike of gene activity before it shuts down again.

In their new study, the MIT team found that during mitosis, microcompartments are more likely to be found near the genes that spike during cell division. They also discovered that these loops appear to form as a result of the genome compaction that occurs during mitosis. This compaction brings enhancers and promoters closer together, allowing them to stick together to form microcompartments.

Once formed, the loops that constitute microcompartments may activate gene transcription somewhat by accident, which is then shut off by the cell. When the cell finishes dividing, entering a state known as G1, many of these small loops become weaker or disappear.

“It almost seems like this transcriptional spiking in mitosis is an undesirable accident that arises from generating a uniquely favorable environment for microcompartments to form during mitosis,” Hansen says. “Then, the cell quickly prunes and filters many of those loops out when it enters G1.”

Because chromosome compaction can also be influenced by a cell’s size and shape, the researchers are now exploring how variations in those features affect the structure of the genome and in turn, gene regulation.

“We are thinking about some natural biological settings where cells change shape and size, and whether we can perhaps explain some 3D genome changes that previously lack an explanation,” Hansen says. “Another key question is how does the cell then pick what are the microcompartments to keep and what are the microcompartments to remove when you enter G1, to ensure fidelity of gene expression?”

The research was funded in part by the National Institutes of Health, a National Science Foundation CAREER Award, the Gene Regulation Observatory of the Broad Institute, a Pew-Steward Scholar Award for Cancer Research, the Mathers Foundation, the MIT Westaway Fund, the Bridge Project of the Koch Institute and Dana-Farber/Harvard Cancer Center, and the Koch Institute Support (core) Grant from the National Cancer Institute.

Tracking atmospheric methane to its specific sources and quantifying their importance remains a challenge, however. Scientists are pretty good at tracing the sources of the main greenhouse gas, carbon dioxide, to focus on mitigating these emissions. But to trace methane’s origins, scientists often have to measure the isotopic composition of methane’s component atoms, carbon and hydrogen, to use as a fingerprint of various environmental sources.

A new paper by researchers at the University of California, Berkeley, reveals how the activity of one of the main microbial enzymes involved in producing methane affects this isotope composition. The finding could change how scientists calculate the contributions of different environmental sources to Earth’s total methane budget.

“When we integrate all the sources and sinks of carbon dioxide into the atmosphere, we kind of get the number that we’re expecting from direct measurement in the atmosphere. But for methane, large uncertainties in fluxes exist — within tens of percents for some of the fluxes — that challenge our ability to precisely quantify the relative importance and changes in time of the sources,” said UC Berkeley postdoctoral fellow Jonathan Gropp, who is first author of the paper. “To quantify the actual sources of methane, you need to really understand the isotopic processes that are used to constrain these fluxes.”

Gropp teamed up with a molecular biologist and a geochemist at UC Berkeley to, for the first time, employ CRISPR to manipulate the activity of this key enzyme to reveal how these methanogens interact with their food supply to produce methane.

“It is well understood that methane levels are rising, but there is a lot of disagreement on the underlying cause,” said co-author Dipti Nayak, UC Berkeley assistant professor of molecular and cell biology. “This study is the first time the disciplines of molecular biology and isotope biogeochemistry have been fused to provide better constraints on how the biology of methanogens controls the isotopic composition of methane.”

Many elements have heavier or lighter versions, called isotopes, that are found in small proportions in nature. Humans are about 99% carbon-12 and 1% carbon-13, which is slightly heavier because it has an extra neutron in its nucleus. The hydrogen in water is 99.985% hydrogen-1 and 0.015% deuterium or hydrogen-2, which is twice as heavy because it has a neutron in its nucleus.

The natural abundances of isotopes are reflected in all biologically produced molecules and variations can be used to study and fingerprint various biological metabolisms.

“Over the last 70 years, people have shown that methane produced by different organisms and other processes can have distinctive isotopic fingerprints,” said geochemist and co-author Daniel Stolper, UC Berkeley associate professor of earth and planetary science. “Natural gas from oil deposits often looks one way. Methane made by the methanogens within cow guts looks another way. Methane made in deep sea sediments by microorganisms has a different fingerprint. Methanogens can consume or ‘eat’, if you will, a variety of compounds including methanol, acetate or hydrogen; make methane; and generate energy from the process. Scientists have commonly assumed that the isotopic fingerprint depends on what the organisms are eating, which often varies from environment to environment, creating our ability to link isotopes to methane origins.”

“I think what’s unique about the paper is, we learned that the isotopic composition of microbial methane isn’t just based on what methanogens eat,” Nayak said. “What you ‘eat’ matters, of course, but the amount of these substrates and the environmental conditions matter too, and perhaps more importantly, how microbes react to those changes.”

“Microbes respond to the environment by manipulating their gene expression, and then the isotopic compositions change as well,” Gropp said. “This should cause us to think more carefully when we analyze data from the environment.”

The paper will appear Aug. 14 in the journal Science.

Vinegar- and alcohol-eating microbes

Methanogens — microorganisms that are archaea, which are on an entirely separate branch of the tree of life from bacteria — are essential to ridding the world of dead and decaying matter. They ingest simple molecules — molecular hydrogen, acetate or methanol, for example — excreted by other organisms and produce methane gas as waste. This natural methane can be observed in the pale Will-o’-the-wisps seen around swamps and marshes at night, but it’s also released invisibly in cow burps, bubbles up from rice paddies and natural wetlands and leaks out of landfills. While most of the methane in the natural gas we burn formed in association with hydrocarbon generation, some deposits were originally produced by methanogens eating buried organic matter.

The isotopic fingerprint of methane produced by methanogens growing on different “food” sources has been well established in laboratory studies, but scientists have found that in the complexity of the real world, methanogens don’t always produce methane with the same isotopic fingerprint as seen in the lab. For example, when grown in the lab, species of methanogens that eat acetate (essentially vinegar), methanol (the simplest alcohol), or molecular hydrogen (H₂) produce methane, CH₄, with a ratio of hydrogen and carbon isotopes different from the ratios observed in the environment.

Gropp had earlier created a computer model of the metabolic network in methanogens to understand better how the isotope composition of methane is determined. When he got a fellowship to come to UC Berkeley, Stolper and Nayak proposed that he experimentally test his model. Stolper’s laboratory specializes in measuring isotope compositions to explore Earth’s history. Nayak studies methanogens and, as a postdoctoral fellow, found a way to use CRISPR gene editing in methanogens. Her group recently altered the expression of the key enzyme in methanogens that produces the methane — methyl-coenzyme M reductase (MCR) — so that its activity can be dialed down. Enzymes are proteins that catalyze chemical reactions.

Experimenting with these CRISPR-edited microbes — in a common methanogen called Methanosarcina acetivorans growing on acetate and methanol — the researchers looked at how the isotopic composition of methane changed when the enzyme activity was reduced, mimicking what is thought to happen when the microbes are starved for their preferred food.

They found that when MCR is at low concentrations, cells respond by altering the activity of many other enzymes in the cell, causing their inputs and outputs to accumulate and the rate of methane generation to slow so much that enzymes begin running both backwards and forwards. In reverse, these other enzymes remove a hydrogen from carbon atoms; running forward, they add a hydrogen. Together with MCR, they ultimately produce methane (CH₄). Each forward and reverse cycle requires one of these enzymes to pull a hydrogen off of the carbon and add a new one ultimately sourced from water. As a result, the isotopic composition of methane’s four hydrogen molecules gradually comes to reflect that of the water, and not just their food source, which starts with three hydrogens.

This is different from typical assumptions for growth on acetate and methanol that assume no exchange between hydrogen derived from water and that from the food source.

“This isotope exchange we found changes the fingerprint of methane generated by acetate and methanol consuming methanogens vs. that typically assumed. Given this, it might be that we have underestimated the contribution of the acetate-consuming microbes, and they might be even more dominant than we have thought,” Gropp said. “We’re proposing that we at least should consider the cellular response of methanogens to their environment when studying isotopic composition of methane.”

Beyond this study, the CRISPR technique for tuning production of enzymes in methanogens could be used to manipulate and study isotope effects in other enzyme networks broadly, which could help researchers answer questions about geobiology and the Earth’s environment today and in the past.

“This opens up a pathway where modern molecular biology is married with isotope-geochemistry to answer environmental problems,” Stolper said. “There are an enormous number of isotopic systems associated with biology and biochemistry that are studied in the environment; I hope we can start looking at them in the way molecular biologists now are looking at these problems in people and other organisms — by controlling gene expression and looking at how the stable isotopes respond.”

For Nayak, the experiments are also a big step in discovering how to alter methanogens to derail production of methane and redirect their energy to producing useful products instead of an environmentally destructive gas.

“By reducing the amount of this enzyme that makes methane and by putting in alternate pathways that the cell can use, we can essentially give them another release valve, if you will, to put those electrons, which they were otherwise putting in carbon to make methane, into something else that would be more useful,” she said.

Other co-authors of the paper are Markus Bill of Lawrence Berkeley National Laboratory and former UC Berkeley postdoc Rebekah Stein, and Max Lloyd, who is a professor at Penn State University. Gropp was supported by a fellowship from the European Molecular Biology Organization. Nayak and Stolper were funded, in part, by Alfred B. Sloan Research Fellowships. Nayak also is an investigator with the Chan-Zuckerberg Biohub.