GN/ Synthetic biology and 3D printing produces programmable living materials
Genetics biweekly vol.56, 25th April — 10th May
TL;DR
- Scientists are leveraging cells to create advanced materials with self-repairing capabilities and responsiveness to their surroundings, known as engineered living materials. These materials are crafted by embedding cells into a matrix, forming desired shapes, and even utilizing genetically modified plant cells in 3D printed bioink. Potential applications of these programmable materials include biomanufacturing and eco-friendly construction methods.
- The development of diverse plant structures with multiple cell types is governed by intricate gene networks, evolving from the colonization of Earth’s surface by plants.
- A protein complex called Mediator’s movement along DNA genes may influence cell division, holding significance for disease treatment research.
- Significant advancements have been made in cultivating nephron progenitor cells, crucial for understanding kidney development and disease modeling.
- Understanding the complex enzyme interactions around toll-like receptor 7 enhances our knowledge of the immune system’s defense against viruses.
- CRISPR technology is explored for its potential in editing RNA, expanding its applications beyond DNA editing.
- Cells possess an information processing system enabling rapid adaptations to changing environments, challenging conventional understanding of cellular function.
- Research reveals variations in leukocyte telomere length among African populations, associated with malaria prevalence and partially influenced by genetics.
- Researchers report on the molecular assembly of one of the most common anti-phage systems that is estimated to be used by at least 8.5%, and up to 18%, of all bacteria species on Earth.
- Scientists have made a breakthrough for evolutionary biology of the Solanaceae family, which includes peppers, potatoes and petunias.
- And more!
Overview
Genetic technology is defined as the term that includes a range of activities concerned with the understanding of gene expression, advantages of natural genetic variation, modifying genes and transferring genes to new hosts. Genes are found in all living organisms and are transferred from one generation to the next. Gene technology encompasses several techniques including marker-assisted breeding, RNAi, and genetic modification. Only some gene technologies produce genetically modified organisms.
Modern genetic technologies like genome editing would not be possible without all the previous generations of genetic technologies that have enabled scientists to discover what genes are, what they do, and how DNA can be modified to add, remove, or replace genes. You can find major genetic technologies development milestones via the link.
Gene Technology Market
According to Global Genetic Engineering Market Research Report: The genetic engineering market is projected to grow from USD 1.36 Billion in 2023 to USD 7.73 Billion by 2032, exhibiting a compound annual growth rate (CAGR) of 24.20% during the forecast period (2023–2032).
Growing demand for synthetic genes and increased use of CRISPR genome editing technology across various biotechnology industries are the key market drivers enhancing the market growth. In addition, it’s projected that increased government financing, a rise in the output of genetically modified crops, and an increase in genomics studies will all contribute to the expansion.
Latest Research
Advancing Engineered Plant Living Materials through Tobacco BY-2 Cell Growth and Transfection within Tailored Granular Hydrogel Scaffolds
by Yujie Wang, Zhengao Di, Minglang Qin, Shenming Qu, Wenbo Zhong, Lingfeng Yuan, Jing Zhang, Julian M. Hibberd, Ziyi Yu in ACS Central Science
Scientists are harnessing cells to make new types of materials that can grow, repair themselves and even respond to their environment. These solid “engineered living materials” are made by embedding cells in an inanimate matrix that’s formed in a desired shape. Now, researchers report that they have 3D printed a bioink containing plant cells that were then genetically modified, producing programmable materials. Applications could someday include biomanufacturing and sustainable construction.
Recently, researchers have been developing engineered living materials, primarily relying on bacterial and fungal cells as the live component. But the unique features of plant cells have stirred enthusiasm for their use in engineered plant living materials (EPLMs). However, the plant cell-based materials created to date have had fairly simple structures and limited functionality. Ziyi Yu, Zhengao Di and colleagues wanted to change that by making intricately shaped EPLMs containing genetically engineered plant cells with customizable behaviors and capabilities.
The researchers mixed tobacco plant cells with gelatin and hydrogel microparticles that contained Agrobacterium tumefaciens, a bacterium commonly used to transfer DNA segments into plant genomes. This bioink mixture was then 3D printed on a flat plate or inside a container filled with another gel to form shapes such as grids, snowflakes, leaves and spirals. Next, the hydrogel in the printed materials was cured with blue light, hardening the structures. During the ensuing 48 hours, the bacteria in the EPLMs transferred DNA to the growing tobacco cells. The materials were then washed with antibiotics to kill the bacteria. In the following weeks, as the plant cells grew and replicated in the EPLMs, they began producing proteins dictated by the transferred DNA.
In this proof-of-concept study, the transferred DNA enabled the tobacco plant cells to produce green fluorescent proteins or betalains — red or yellow plant pigments that are valued as natural colorants and dietary supplements. By printing a leaf-shaped EPLM with two different bioinks — one that created red pigment along the veins and the other a yellow pigment in the rest of the leaf — the researchers showed that their technique could produce complex, spatially controlled and multifunctional structures. Such EPLMs, which combine the traits of living organisms with the stability and durability of non-living substances, could find use as cellular factories to churn out plant metabolites or pharmaceutical proteins, or even in sustainable construction applications, according to the researchers.
Genomes of multicellular algal sisters to land plants illuminate signaling network evolution
by Xuehuan Feng, Jinfang Zheng, Iker Irisarri, Huihui Yu, et al in Nature Genetics
Land plants cover the surface of our planet and often tower over us. They form complex bodies with multiple organs that consist of a broad range of cell types. Developing this morphological complexity is underpinned by intricate networks of genes, whose coordinated action shapes plant bodies through various molecular mechanisms. All of these magnificent forms burst forth from a one-off evolutionary event: when plants conquered Earth’s surface, known as plant terrestrialization.
Among those algae most closely related to land plants, diverse body types are found — ranging from single-celled algae to more complex cell filaments. From this group of relatives, an international group of researchers led by the Universities of Göttingen and Nebraska-Lincoln has now generated the first genome data of such complex specimens, on four filamentous “star algae” of the genus Zygnema.
The researchers worked with four algal strains in total, two from a culture collection in the USA and two that have been kept safe in the Algal Culture Collection at Göttingen University (SAG). The research involved more than 50 scientists from nine countries who combined a range of cutting-edge sequencing techniques to elucidate the entire DNA sequence of these algae. The advanced methods enabled them to generate complete genomes for these organisms at the level of whole chromosomes — something that had never been done before on this group of algae. Comparing the genes on the genomes with those of other plants and algae led to the discovery of specific overabundances of signalling genes and environmental response factors.
Dr Iker Irisarri, Leibniz Institute for the Analysis of Biodiversity Change, explains: “Many of these genes underpin molecular functions that were important for the emergence of the first multicellular terrestrial plants. It is fascinating that the genetic building blocks, whose origins predate land plants by millions of years, duplicated and diversified in the ancestors of plants and algae and, in doing so, enabled the evolution of more specialized molecular machinery.”
Professor Jan de Vries, University of Göttingen, says: “Not only do we present a valuable, high-quality resource for the entire plant scientific community, who can now explore these genome data, our analyses uncovered intricate connections between environmental responses. This sheds light on one of land plants’ most important features: their ability to adjust their growth and development so that it aligns with the environment in which they dwell — a process known as developmental plasticity.”
Growth-regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes
by Wael R Abdel-Fattah, Mattias Carlsson, Guo-Zhen Hu, Ajeet Singh, Alexander Vergara, Rameen Aslam, Hans Ronne, Stefan Björklund in Nucleic Acids Research
Researchers at Umeå University, Sweden, have discovered that how a special protein complex called the Mediator moves along genes in DNA may have an impact on how cells divide. The discovery may be important for future research into the treatment of certain diseases.
“We have gained in-depth knowledge of how cell division is controlled, which is important for understanding the causes of various diseases that are due to errors in cell division, such as various tumour diseases,” says Stefan Björklund, professor at the Department of Medical Biochemistry and Biophysics at Umeå University and lead author of the study.
In each cell there is a machinery called the ribosome. It uses DNA as a template to produce proteins, which are necessary for virtually all processes in the cell. First, however, the cells must make a copy of the instructions in the form of mRNA through a process called transcription.
The research team at Umeå University has discovered how the Mediator, a protein complex in the cell nucleus, can bind to DNA and interact with another protein complex, Lsm1–7, to regulate the production of proteins that make up the ribosomes. The study shows that when cells grow too densely, cell division slows down. When this happens, the mediator moves to the end of the genes where it interacts with Lsm1–7. This has the dual effect of both slowing down the reading of the genes and interfering with the maturation of mRNA. This, in turn, leads to a reduced production of ribosomal proteins and thus a slower cell division.
A possible direction of future research may be to study whether it is possible to control the position of the mediator, in order to inhibit rapid cell division, for example in tumours.
“We are still early in the research in the field, so more studies are needed before we can say that this is a viable path, but it is an exciting opportunity,” says Stefan Björklund.
The study has been conducted in yeast cells that serve as a good model when it comes to understanding basic mechanisms that work in a similar way in more complex systems such as animal and plant cells.
Long-term expandable mouse and human-induced nephron progenitor cells enable kidney organoid maturation and modeling of plasticity and disease
by Biao Huang, Zipeng Zeng, Sunghyun Kim, Connor C. Fausto, et al in Cell Stem Cell
In a new study, USC scientists report significant progress in cultivating nephron progenitor cells (NPCs), the cells destined to form the kidney’s filtration system, the nephrons. NPCs hold immense promise for understanding kidney development, modeling diseases, and discovering new treatments.
“By enhancing our capability to grow NPCs from human stem cells, we create a new avenue for understanding and combating congenital kidney diseases and cancer,” said corresponding and lead author Zhongwei Li, an assistant professor of medicine, and stem cell biology and regenerative medicine at the Keck School of Medicine of USC.
In the study, Li Lab postdocs Biao Huang and Zipeng Zeng and their collaborators improved the chemical cocktail for generating and growing NPCs in the laboratory. This improved cocktail enables the sustained growth of both mouse and human NPCs in a simple 2-dimensional format. This marks a major improvement over the previous 3-dimensional system, which was not only more cumbersome, but also limited the ability to perform genome editing on the cells.
The cocktail also enables the expansion of induced NPCs (iNPCs) from human pluripotent stem cells. These iNPCs closely resemble native human NPCs. With this approach, iNPCs can be generated from any individual starting with a simple blood or skin biopsy. This approach will facilitate the creation of patient-specific kidney disease models and enhance efforts to identify nephron targeted drugs. Moreover, the cocktail is powerful enough to reprogram a differentiated type of kidney cell known as a podocyte into an NPC-like state.
Demonstrating the practical applications of their breakthrough, the scientists performed genome editing on the NPCs to screen for genes related to kidney development and disease. This screening identified previously implicated genes, as well as novel candidates.
In a further demonstration, the scientists introduced the genetic mutations responsible for polycystic kidney disease (PKD) into the NPCs. These NPCs developed into mini-kidney structures, known as organoids, exhibiting cysts — the hallmark symptom of PKD. The team then used the organoids to screen for drug-like compounds that inhibited cyst formation.
“This breakthrough has potential for advancing kidney research in many critical ways — from accelerating drug discovery to unraveling the genetic underpinnings of kidney development, disease, and cancer,” said Li. “Importantly, it also provides supplies of NPCs as critical building blocks to build synthetic kidneys for kidney replacement therapy.”
Lysosomal endonuclease RNase T2 and PLD exonucleases cooperatively generate RNA ligands for TLR7 activation
by Marleen Bérouti, Katja Lammens, Matthias Heiss, Larissa Hansbauer, Stefan Bauernfried, Jan Stöckl, Francesca Pinci, Ignazio Piseddu, Wilhelm Greulich, Meiyue Wang, Christophe Jung, Thomas Fröhlich, Thomas Carell, Karl-Peter Hopfner, Veit Hornung in Immunity
LMU researchers have deciphered the complex interplay of various enzymes around the innate immune receptor toll-like receptor 7 (TLR7), which plays an important role in defending our bodies against viruses.
Toll-like receptor 7 (TLR7), located in the dendritic cells of our immune system, plays a crucial role in our natural defense against viruses. TLR7 recognizes single-stranded viral and other foreign RNA and activates the release of inflammatory mediators. Dysfunctions of this receptor also play a key role in autoimmune diseases, making it all the more important to understand, and ideally modulate, the exact activation mechanism of TLR7.
Researchers led by Professor Veit Hornung and Marleen Bérouti from the Gene Center Munich and the Department of Biochemistry at LMU have now managed to gain deeper insights into the complex activation mechanism. It was known from earlier studies that complex RNA molecules have to be cut up first so that the receptor is able to recognize them. Using a wide range of technologies from cell biology to cryogenic electron microscopy, the LMU researchers have revealed how single-stranded foreign RNA is processed to be detected by TLR7.
In the course of evolution, the immune system has specialized in recognizing pathogens from their genetic material. For example, the innate immune receptor TLR7 is stimulated by viral RNA. We can picture viral RNAs as long threads of molecules, which are much too large to be recognized as ligands for TLR7. This is where nucleases come in — molecular cutting tools that chop the ‘RNA thread’ into small pieces. Endonucleases cut the RNA molecules through the middle like scissors, while exonucleases cleave the thread from one end to the other. This process generates various RNA snippets, which can now bind to two different pockets of the TLR7 receptor. Only once both binding pockets of the receptor are occupied by these RNA pieces a signaling cascade set in motion, which activates the cell and triggers a state of alarm.
The researchers discovered that RNA recognition by TLR7 requires the activity of the endonuclease RNase T2 operating in conjunction with the exonucleases PLD3 and PLD4 (phospholipase D3 and D4).
“Although it was known that these enzymes can degrade RNAs,” says Hornung, “we have now demonstrated that they interact and thereby activate TLR7.”
The researchers also found that the PLD exonucleases have a dual role within immune cells. In the case of TLR7, they have a pro-inflammatory effect, whereas in the case of another TLR receptor, TLR9, they have an anti-inflammatory effect.
“This dual role of PLD exonucleases points to a finely coordinated balance for controlling appropriate immune responses,” explains Bérouti. “The simultaneous promotion and inhibition of inflammation by these enzymes could serve as an important protective mechanism for preventing dysfunctions arising in the system.”
What role other enzymes could have on this signaling pathway and whether the molecules involved are suitable as target structures for therapies are subjects for further investigations.
Repair of CRISPR-guided RNA breaks enables site-specific RNA excision in human cells
by Anna Nemudraia, Artem Nemudryi, Blake Wiedenheft in Science
A team at Montana State University published research that shows how RNA, the close chemical cousin to DNA, can be edited using CRISPRs. The work reveals a new process in human cells that has potential for treating a wide variety of genetic diseases. Postdoctoral researchers Artem Nemudryi and Anna Nemudraia conducted the research alongside Blake Wiedenheft, professor in the Department of Microbiology and Cell Biology in MSU’s College of Agriculture.
CRISPR, which stands for Clustered Regularly Interspaced Short Palindromic Repeats, is a type of immune system that bacteria use to recognize and fight off viruses. Wiedenheft, one of the nation’s leading CRISPR researchers, said that the system has been used for years to cut and edit DNA, but that applying similar technology to RNA is unprecedented. DNA editing uses a CRISPR-associated protein called Cas9, while editing RNA requires the use of a different CRISPR system, called type-III.
“In our previous work, we used type-III CRISPRs to edit viral RNA in a test tube,” said Nemudryi. “But we wondered, can we program manipulation of RNA in a living human cell?”
To explore that question, the team programmed type-III CRISPR proteins to cut RNA containing a mutation that causes cystic fibrosis, restoring cell function.
“We were confident that we could use these CRISPR systems to cut RNA in a programmable manner, but we were all surprised when we sequenced the RNA and realized that the cell had stitched the RNA back together in a way that removed the mutation,” said Wiedenheft.
Nemudryi noted that RNA is transient within the cell; it is constantly being destroyed and replaced.
“The general belief is that there’s not much point in repairing RNA,” he said. “We speculated that RNA would be repaired in living human cells, and it turned out to be true.”
Wiedenheft has mentored the two postdoctoral researchers since their arrival at MSU nearly six years ago, and said that the impact of their scientific contributions will lead to significant and continued advancements.
“The work done by Artem and Anna suggests that RNA repair might be a fundamental aspect of biology and that harnessing this activity may lead to new lifesaving cures,” said Wiedenheft. “Artem and Anna are two of the most brilliant scientists I have ever encountered, and I’m confident that their work is going to have a lasting impact on humanity.”
RNA editing has important applications in the search for treatments of genetic diseases, Nemudryi said. RNA is a temporary copy of a cell’s DNA, which serves as a template. Manipulating the template by editing DNA could cause unwanted and potentially irreversible collateral changes, but because RNA is a temporary copy, he said, edits made are essentially reversible and carry far less risk.
“People used Cas9 to break DNA and study how cells repair these breaks. Then, based on these patterns, they improved Cas9 editors,” said Nemudraia. “Here, we hope the same will happen with RNA editing. We created a tool that allows us to study how the cells repair their RNA, and we hope to use this knowledge to make RNA editors more efficient.”
In the new publication, the team shows that a mutation causing cystic fibrosis can be successfully removed from the RNA. But this is only one of thousands of known mutations that cause disease. The question of how many of them could be addressed with this new RNA editing technology will guide future work for Nemudryi and Nemudraia as they finish their postdoctoral training at MSU and prepare for faculty positions at the University of Florida this fall. Both credited Wiedenheft as a life-changing mentor.
“Blake taught us not to be afraid of testing any ideas,” said Nemudraia. “As a scientist, you should be brave and not be afraid to fail. RNA editing and repair is the terra incognita. It’s scary but also exciting. You feel you’re working on the edge of science, pushing the limits to where nobody has been before.”
Modeling non-genetic information dynamics in cells using reservoir computing
by Dipesh Niraula, Issam El Naqa, Jack Adam Tuszynski, Robert A. Gatenby in iScience
Cells constantly navigate a dynamic environment, facing ever-changing conditions and challenges. But how do cells swiftly adapt to these environmental fluctuations? A new Moffitt Cancer Center study, is answering that question by challenging our understanding of how cells function. A team of researchers suggests that cells possess a previously unknown information processing system that allows them to make rapid decisions independent of their genes.
For decades, scientists have viewed DNA as the sole source of cellular information. This DNA blueprint instructs cells on how to build proteins and carry out essential functions. However, new research at Moffitt led by Dipesh Niraula, Ph.D., and Robert Gatenby, M.D., discovered a nongenomic information system that operates alongside DNA, enabling cells to gather information from the environment and respond quickly to changes.
The study focused on the role of ion gradients across the cell membrane. These gradients, maintained by specialized pumps, require large energy expenditure to generate varying transmembrane electrical potentials. The researchers proposed that the gradients represent an enormous reservoir of information that allows cells to monitor their environment continuously. When information is received at some point on the cell membrane, it interacts with specialized gates in ion-specific channels, which then open, allowing those ions to flow along the pre-existing gradients to form a communication channel. The ion fluxes trigger a cascade of events adjacent to the membrane, allowing the cell to analyze and rapidly respond to the information. When the ion fluxes are large or prolonged, they can cause self-assembly of the microtubules and microfilaments for the cytoskeleton.
Typically, the cytoskeleton network provides mechanical support for the cell and is responsible for cell shape and movement. However, the Moffitt researchers noted that proteins from the cytoskeleton are also excellent ion conductors. This allows the cytoskeleton to act as a highly dynamic intracellular wiring network to transmit ion-based information from the membrane to the intracellular organelles, including mitochondria, endoplasmic reticulum and the nucleus. The researchers suggested that this system, which allows for rapid and local responses to specific signals, can also generate coordinated regional or global responses to larger environmental changes.
“Our research reveals the capability of cells to harness transmembrane ion gradients as a means of communication, allowing them to sense and respond to changes in their surroundings rapidly,” said Niraula, an applied research scientist in the Department of Machine Learning. “This intricate network enables cells to make swift and informed decisions, critical for their survival and function.”
The researchers believe that this nongenomic information system is critical for forming and maintaining normal multicellular tissue and suggests the well described ion fluxes in neurons represent a specialized example of this broad information network. Disruption of these dynamics may also be a critical component of cancer development. They demonstrated their model was consistent with multiple experimental observations and highlighted several testable predictions arising from their model, hopefully paving the way for future experiments to validate their theory and shed light on the intricacies of cellular decision-making.
“This study challenges the implicit assumption in biology that the genome is the sole source of information, and that the nucleus acts as a kind of central processor. We present an entirely new network of information that allows rapid adaptation and sophisticated communication necessary for cell survival and probably deeply involved in the intercellular signaling that permits functioning multicellular organisms,” said Gatenby, co-director of the Center of Excellence for Evolutionary Therapy at Moffitt.
Association between telomere length and Plasmodium falciparum malaria endemicity in sub-Saharan Africans
by Michael A. McQuillan, Simon Verhulst, Matthew E.B. Hansen, William Beggs, Dawit Wolde Meskel, Gurja Belay, Thomas Nyambo, Sununguko Wata Mpoloka, Gaonyadiwe George Mokone, Charles Fokunang, Alfred K. Njamnshi, Stephen J. Chanock, Abraham Aviv, Sarah A. Tishkoff in The American Journal of Human Genetics
The length of telomeres in white blood cells, known as leukocytes, varies significantly among sub-Saharan African populations, researchers report. Moreover, leukocyte telomere length (LTL) is negatively associated with malaria endemicity and only partly explained by genetic factors.
“We highlight the contributions of genetic and environmental factors influencing LTL, and we have uncovered a potential role of malaria in shortening LTL across sub-Saharan Africa,” says Sarah Tishkoff of the University of Pennsylvania, a co-senior author on the study. “This association between malaria and LTL appears larger than any other known exposure or behavior that has been investigated in large-scale studies.”
Telomeres are regions of repetitive DNA sequences that protect the ends of chromosomes from becoming frayed or tangled. LTL shows vast person-to-person variation, with individuals of African ancestry generally having longer LTL than non-Africans. It shortens with age and is a predictor of a range of aging-related diseases and mortality. LTL is a highly heritable human trait, and LTL variation at birth largely determines LTL variation throughout the life course.
“However, the majority of large-scale studies examining LTL variation among humans have focused primarily on populations of European ancestry,” Tishkoff says. “This under-representation of diverse populations hampers our ability to understand the genetic and environmental drivers of LTL variation and their effects on telomere-related disease risk.”
In particular, little is known about the genetic, environmental, and evolutionary forces that have shaped the vast LTL variation across sub-Saharan African populations. This variation in LTL is largely explained by genetic factors, but environmental factors could also play a role. Exposure to Plasmodium falciparum malaria is one environmental factor of particular interest in impacting LTL, due to recent studies demonstrating a link between malaria infection and LTL.
While these studies suggest a link between malaria infection and telomere shortening, they rely on single, acute infection events where participants received rapid medical treatment. It remains unknown whether repeated malaria exposures throughout life in populations living in endemic regions has a lasting effect on LTL. It is also unclear whether having longer leukocyte telomeres at birth in malaria endemic regions or regions with a high pathogen burden could be selectively advantageous.
To fill these knowledge gaps, Tishkoff and co-senior study author Abraham Aviv of Rutgers University examined LTL from diverse environmental contexts across Africa, including those where malaria is highly endemic. The authors extracted DNA from blood cells and genotyped individuals and measured LTL in 1,818 ethnically diverse adults from Tanzania, Botswana, Ethiopia, and Cameroon.
The results revealed significant variation in LTL among populations. The San hunter-gatherers from Botswana have the longest leukocyte telomeres, and the Fulani pastoralists from Cameroon have the shortest telomeres. Genetic factors explain roughly half of LTL variation among individuals.
Moreover, LTL is shorter in adults indigenous to regions of high malaria endemicity than in those indigenous to regions of low malaria endemicity. The potential impact of malaria endemicity on LTL reported in this study appears larger than previously identified environmental factors that impact LTL. One potential mechanism by which malaria may shorten LTL may involve malaria-induced bouts of massive destruction of erythrocytes (i.e., red blood cells) and the process of making new cells to restore this loss.
“Circulating erythrocytes outnumber circulating leukocytes by approximately a thousand to one and comprise 84% of all somatic cells in the body,” Tishkoff explains. “The telomere length reserves of the hematopoietic system are, thus, principally spent on building and maintaining the massive pool of about 25 trillion erythrocytes in the average human adult.”
The authors say a longitudinal study in children and adults indigenous to regions of high and low malaria endemicity would provide more insightful information.
“We propose that the effect of malaria on hematopoietic cell telomere shortening with age primarily unfolds during childhood, yet our LTL data are derived from adults,” Tishkoff says. “Clearly, the next step in testing the relationship between malaria and LTL is to characterize LTL dynamics in children born and raised in regions of high malaria endemicity versus those born and raised in regions of low or no malaria endemicity.”
Molecular basis of Gabija anti-phage supramolecular assemblies
by Xiao-Yuan Yang, Zhangfei Shen, Jiale Xie, Jacelyn Greenwald, Ila Marathe, Qingpeng Lin, Wen Jun Xie, Vicki H. Wysocki, Tian-Min Fu in Nature Structural & Molecular Biology
One of the many secrets to bacteria’s success is their ability to defend themselves from viruses, called phages, that infect bacteria and use their cellular machinery to make copies of themselves.
Technological advances have enabled recent identification of the proteins involved in these systems, but scientists are still digging deeper into what those proteins do.
In a new study, a team from The Ohio State University has reported on the molecular assembly of one of the most common anti-phage systems — from the family of proteins called Gabija — that is estimated to be used by at least 8.5%, and up to 18%, of all bacteria species on Earth. Researchers found that one protein appears to have the power to fend off a phage, but when it binds to a partner protein, the resulting complex is highly adept at snipping the genome of an invading phage to render it unable to replicate.
“We think the two proteins need to form the complex to play a role in phage prevention, but we also believe one protein alone does have some anti-phage function,” said Zhangfei Shen, co-lead author of the study and a postdoctoral scholar in biological chemistry and pharmacology at Ohio State’s College of Medicine. “The full role of the second protein needs to be further studied.”
The findings add to scientific understanding of microorganisms’ evolutionary strategies and could one day be translated into biomedical applications, researchers say. Shen and co-lead author Xiaoyuan Yang, a PhD student, work in the lab of senior author Tianmin Fu, assistant professor of biological chemistry and pharmacology at Ohio State.
The two proteins that make up this defense system are called Gabija A and Gabija B, or GajA and GajB for short. Researchers used cryo-electron microscopy to determine the biochemical structures of GajA and GajB individually and of what is called a supramolecular complex, GajAB, created when the two bind to form a cluster consisting of four molecules from each protein.
In experiments using Bacillus cereus bacteria as a model, researchers observed the activity of the complex in the presence of phages to gain insight into how the defense system works. Though GajA alone showed signs of activity that could disable a phage’s DNA, the complex it formed with GajB was much more effective at ensuring phages would not be able take over the bacterial cell.
“That’s the mysterious part,” Yang said. “GajA alone is sufficient to cleave the phage nucleus, but it also does form the complex with GajB when we incubate them together. Our hypothesis is that GajA recognizes the phage’s genomic sequence, but GajB enhances that recognition and helps to cut the phage DNA.”
The large size and elongated configuration of the complex made it difficult to get the full picture of GajB’s functional contributions when bound to GajA, Shen said, leaving the team to make some assumptions about protein roles that have yet to be confirmed.
“We only know GajB helps enhance GajA activity, but we don’t yet know how it works because we only see about 50% of it on the complex,” Shen said.
One of their hypotheses is that GajB may influence the concentration level of an energy source, the nucleotide ATP (adenosine triphosphate), in the cellular environment — specifically, by driving ATP down upon detection of the phage’s presence. That would have the dual effect of expanding GajA’s phage DNA-disabling activity and stealing energy that a phage would need to start replicating, Yang said.
Tomato root specialized metabolites evolved through gene duplication and regulatory divergence within a biosynthetic gene cluster
by Rachel E. Kerwin, Jaynee E. Hart, Paul D. Fiesel, Yann-Ru Lou, Pengxiang Fan, A. Daniel Jones, Robert L. Last in Science Advances
In a new paper, Michigan State University researchers have unraveled a surprising genetic mystery centered on sugars found in what gardeners know as “tomato tar.”
Anyone who has pruned tomato plants barehanded has likely found their fingers darkened with a sticky, gold-black substance that won’t quite wash off. This tomato tar is sticky for good reason. It’s made of sugars — acylsugars, to be precise — and acts as a sort of natural flypaper for would-be pests.
“Plants have evolved to make so many amazing poisons and other biologically active compounds,” said Michigan State researcher Robert Last, leader of the new study.
The Last lab specializes in acylsugars and the tiny, hair-like structures where they’re produced and stored, known as trichomes. Once thought to be exclusively found in trichomes, other researchers recently reported finding acylsugars in tomato roots as well. This was a surprise for the plant science community.
In their study, the team at MSU wanted to learn how these root acylsugars functioned and just where they came from. They found that not only do tomato plants synthesize chemically unique acylsugars in their roots and trichomes, but these acylsugars are produced through two parallel metabolic pathways. This is the equivalent of assembly lines in an auto factory making two different models of the same car, but never interacting. These discoveries are helping scientists to better understand the resilience and evolutionary story of Solanaceae, or nightshades, a sprawling family of plants that includes tomatoes, eggplants, potatoes, peppers, tobacco and petunias. They could also help inform researchers looking to develop molecules made by plants into compounds to help humanity.
“From pharmaceuticals, to pesticides, to sunscreens, many small molecules that humans have adapted for different uses come from the arms race between plants, microbes and insects,” Last said.
Beyond key chemicals essential for growth, plants also produce a treasure trove of compounds that play a crucial role in environmental interactions. These can attract useful pollinators and are the first line of defense against harmful organisms.
“What’s so remarkable about these specialized metabolites is that they’re typically synthesized in highly precise cells and tissues,” said Rachel Kerwin, a postdoctoral researcher at MSU and first author of the latest paper.
“Take for instance acylsugars. You won’t find them produced in the leaves or stems of a tomato plant. These physically sticky defense metabolites are made right in the tip of the trichomes.”
When it was reported that acylsugars could be found in tomato roots as well, Kerwin took it as a call for old-fashioned genetic detective work.
“The presence of these acylsugars in roots was fascinating and led to so many questions. How did this happen, how are they being made and are they different from the trichome acylsugars we’ve been studying?”
To begin tackling the evolutionary enigma, lab members collaborated with specialists at MSU’s Mass Spectrometry and Metabolomics Core, as well as staff at the Max T. Rogers Nuclear Magnetic Resonance facility. In comparing metabolites from tomato seedlings’ roots and shoots, a variety of differences appeared. The basic chemical make-up of the aboveground and belowground acylsugars were noticeably different, so much so that they could be defined as different classes of acylsugars entirely.
Last, a University Distinguished Professor in MSU’s College of Natural Science’s Department of Biochemistry and Molecular Biology and Department of Plant Biology, offers a useful analogy to explain how a geneticist approaches biology.
“Imagine trying to figure out how a car works by breaking one component at a time,” he said. “If you flatten a car’s tires and notice the engine still runs, you’ve discovered a critical fact even if you don’t know what the tires exactly do.”
Switch out car parts for genes, and you get a clearer picture of the work accomplished by the Last lab to further crack the code on root acylsugars.
Looking at public genetic sequence data, Kerwin noticed that many of the genes expressed in tomato trichome acylsugar production had close relatives in roots. After identifying an enzyme believed to be the first step in root acylsugar biosynthesis, the researchers began “breaking the car.”
When they knocked out the root acylsugar candidate gene, root acylsugar production vanished, leaving trichome acylsugar production untouched. Meanwhile, when the well-studied trichome acylsugar gene was knocked out, root acylsugar production carried on as usual. These findings offered striking proof of a suspected metabolic mirroring.
“Alongside the aboveground acylsugar pathway we’ve been studying for years, here we find this second parallel universe that exists underground,” Last said. “This confirmed we have two pathways co-existing in the same plant,” Kerwin added.
To drive home this breakthrough, Jaynee Hart, a postdoctoral researcher and second author on the latest paper, looked closer at the functions of trichome and root enzymes. Just as trichome enzymes and the acylsugars they produce are a well-studied chemical match, she found a promising link between root enzymes and the root acylsugars as well.
“Studying isolated enzymes is a powerful tool for ascertaining their activity and drawing conclusions about their functional role inside the plant cell,” Hart explained.
These findings were further proof of the parallel metabolic pathways that exist in a single tomato plant.
“Plants and cars are so different, yet similar in that when you open the proverbial hood you become aware of the multitude of parts and connections that make them function. This work gives us new knowledge about one of those parts in tomato plants and prompts further research into its evolution and function and whether we can make use of it in other ways,” said Pankaj Jaiswal, a program director at the U.S. National Science Foundation, which funded the work.
“The more we learn about living things — from tomatoes and other crops, to animals and microbes — the broader the opportunities to employ that learning to benefit society,” he added.
The paper also reports a fascinating and unexpected twist concerned with biosynthetic gene clusters, or BGCs. BGCs are collections of genes that are physically grouped on the chromosome and contribute to a particular metabolic pathway. Previously, the Last lab identified a BGC containing genes linked to trichome acylsugars in tomato plants. Kerwin, Hart, and their collaborators have now discovered the root-expressed acylsugar enzyme resides in the same cluster.
“Usually in BGCs, the genes are co-expressed in the same tissues and under similar conditions,” said Kerwin. “But here, we have two separate yet interlinked groups of genes. Some expressed in trichomes, and some expressed in roots.”
This revelation led Kerwin to dive into the evolutionary trajectory of Solanaceae species, with hopes to identify when and how these two unique acylsugar pathways developed. Specifically, the researchers drew attention to a moment some 19 million years ago when the enzyme responsible for trichome acylsugars was duplicated. This enzyme would one day be responsible for the newly discovered root-expressed acylsugar pathway. The exact mechanism that “switched on” this enzyme in roots remains unknown, paving the way for the Last lab to continue to unpack the evolutionary and metabolic secrets of the nightshade family.
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