GN/ Decoding a key part of the cell, atom by atom
Genetics biweekly vol.30, 1st June — 15th June
TL;DR
- A team led by André Hoelz has made two big leaps forward in our understanding of the nuclear pore complex, a vital cellular gateway.
- A new synthesis method offers hope for creation of advance mRNA vaccines to fight viruses and even cancers.
- Researchers show which signaling pathways make plants more resistant to flooding. The molecule ethylene is a warning signal for plants that they are under water and switches on the emergency supply for survival without oxygen. A team shows that plants can survive longer without oxygen when pretreated with ethylene.
- Researchers now reveal that nature’s storage solution first evolved in ancient microbes living on Earth between one and two billion years ago.
- A pioneering study has shed new light on how subcellular organelles divide and multiply.
- Researchers are hoping to catch stomach cancer before it develops in at-risk patients. Researchers identified a genetic variation that could help identify when patients with Helicobacter pylori are more likely to develop stomach cancer.
- The tip of rotavirus B spike protein is not only totally different from the corresponding structure in rotavirus A and C, but also no other protein before had been reported to have this structure.
- A new study examines mathematical models designed to draw inferences about how evolution operates at the level of populations of organisms. The study concludes that such models must be constructed with the greatest care, avoiding unwarranted initial assumptions, weighing the quality of existing knowledge and remaining open to alternate explanations.
- Using advanced microscopy techniques, researchers have visualized in unprecedented detail the machinery that the cells’ powerhouses, the mitochondria, use to form their proteins. The results raise hopes of more specific antibiotics and new cancer drugs in the future.
- Occasionally, single-letter misspellings in the genetic code, known as point mutations, occur. Point mutations that alter the resulting protein sequences are called nonsynonymous mutations, while those that do not alter protein sequences are called silent or synonymous mutations. Between one-quarter and one-third of point mutations in protein-coding DNA sequences are synonymous. Those mutations have generally been assumed to be neutral, or nearly so. A new study involving the genetic manipulation of yeast cells shows that most synonymous mutations are strongly harmful.
- And more!
Overview
Genetic technology is defined as the term which 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
- The valuation of the genetic engineering market is projected to escalate to USD 6.90 MN by the end of 2027.
- Global Genetic Engineering Market is projected to grow at 12.48% CAGR during the assessment period (2017–2027).
- North America holds the largest share in the global genetic engineering market, followed by Europe and the Asia Pacific, respectively.
- Another research provider, MarketsandMarkets, forecasts the genome editing, genome engineering market to grow from USD 3.19 billion in 2017 to USD 6.28 billion by 2022, at a compounded annual growth rate (CAGR) of 14.5% during the forecast period. The key factors propelling market growth are rising government funding and growth in the number of genomics projects, high prevalence of infectious diseases (like COVID-19) and cancer, technological advancements, increasing production of genetically modified (GM) crops, and growing application areas of genomics.
Latest News & Research
Architecture of the linker-scaffold in the nuclear pore
by Stefan Petrovic, Dipanjan Samanta, Thibaud Perriches, Christopher J. Bley, Karsten Thierbach, Bonnie Brown, Si Nie, George W. Mobbs, Taylor A. Stevens, Xiaoyu Liu, Giovani Pinton Tomaleri, Lucas Schaus, André Hoelz in Science
Whatever you are doing, whether it is driving a car, going for a jog, or even at your laziest, eating chips and watching TV on the couch, there is an entire suite of molecular machinery inside each of your cells hard at work. That machinery, far too small to see with the naked eye or even with many microscopes, creates energy for the cell, manufactures its proteins, makes copies of its DNA, and much more.
Among those pieces of machinery, and one of the most complex, is something known as the nuclear pore complex (NPC). The NPC, which is made of more than 1,000 individual proteins, is an incredibly discriminating gatekeeper for the cell’s nucleus, the membrane-bound region inside a cell that holds that cell’s genetic material. Anything going in or out of the nucleus has to pass through the NPC on its way.
The NPC’s role as a gatekeeper of the nucleus means it is vital for the operations of the cell. Within the nucleus, DNA, the cell’s permanent genetic code, is copied into RNA. That RNA is then carried out of the nucleus so it can be used to manufacture the proteins the cell needs. The NPC ensures the nucleus gets the materials it needs for synthesizing RNA, while also protecting the DNA from the harsh environment outside the nucleus and enabling the RNA to leave the nucleus after it has been made.
“It’s a little like an airplane hangar where you can repair 747s, and the door opens to let the 747 come in, but there’s a person standing there who can keep a single marble from getting out while the doors are open,” says Caltech’s André Hoelz, professor of chemistry and biochemistry and a Faculty Scholar of the Howard Hughes Medical Institute. For more than two decades, Hoelz has been studying and deciphering the structure of the NPC in relation to its function. Over the years, he has steadily chipped away at its secrets, unraveling them piece by piece by piece by piece.
The implications of this research are potentially huge. Not only is the NPC central to the operations of the cell, it is also involved in many diseases. Mutations in the NPC are responsible for some incurable cancers, for neurodegenerative and autoimmune diseases such as amyotrophic lateral sclerosis (ALS) and acute necrotizing encephalopathy, and for heart conditions including atrial fibrillation and early sudden cardiac death. Additionally, many viruses, including the one responsible for COVID-19, target and shutdown the NPC during the course of their lifecycles.
Now Hoelz and his research team describe two important breakthroughs: the determination of the structure of the outer face of the NPC and the elucidation of the mechanism by which special proteins act like a molecular glue to hold the NPC together. Hoelz and his research team describe how they mapped the structure of the side of the NPC that faces outward from the nucleus and into the cells’ cytoplasm. To do this, they had to solve the equivalent of a very tiny 3-D jigsaw puzzle, using imaging techniques such as electron microscopy and X-ray crystallography on each puzzle piece.
Stefan Petrovic, a graduate student in biochemistry and molecular biophysics and one of the co-first authors of the papers, says the process began with Escherichia coli bacteria (a strain of bacteria commonly used in labs) that were genetically engineered to produce the proteins that make up the human NPC.
“If you walk into the lab, you can see this giant wall of flasks in which cultures are growing,” Petrovic says. “We express each individual protein in E. coli cells, break those cells open, and chemically purify each protein component.”
Once that purification — which can require as much as 1,500 liters of bacterial culture to get enough material for a single experiment — was complete, the research team began to painstakingly test how the pieces of the NPC fit together.
George Mobbs, a senior postdoctoral scholar research associate in chemistry and another co- first author of the paper, says the assembly happened in a “stepwise” fashion; rather than pouring all the proteins together into a test tube at the same time, the researchers tested pairs of proteins to see which ones would fit together, like two puzzle pieces. If a pair was found that fit together, the researchers would then test the two now-combined proteins against a third protein until they found one that fit with that pair, and then the resulting three-piece structure was tested against other proteins, and so on. Working their way through the proteins in this way eventually produced the final result of their paper: a 16-protein wedge that is repeated eight times, like slices of a pizza, to form the face of the NPC.
“We reported the first complete structure of the entire cytoplasmic face of the human NPC, along with rigorous validation, instead of reporting a series of incremental advances of fragments or portions based on partial, incomplete, or low-resolution observation,” says Si Nie, postdoctoral scholar research associate in chemistry and also a co-first author of the paper. “We decided to patiently wait until we had acquired all necessary data, reporting a humungous amount of new information.”
Their work complemented research conducted by Martin Beck of the Max Planck Institute of Biophysics in Frankfurt, Germany, whose team used cryo-electron tomography to generate a map that provided the contours of a puzzle into which the researchers had to place the pieces. To accelerate the completion of the puzzle of the human NPC structure, Hoelz and Beck exchanged data more than two years ago and then independently built structures of the entire NPC. “The substantially improved Beck map showed much more clearly where each piece of the NPC — for which we determined the atomic structures — had to be placed, akin to a wooden frame that defines the edge of a puzzle,” Hoelz says.
The experimentally determined structures of the NPC pieces from the Hoelz group served to validate the modeling by the Beck group. “We placed the structures into the map independently, using different approaches, but the final results completely agreed. It was very satisfying to see that,” Petrovic says.
“We built a framework on which a lot of experiments can now be done,” says Christopher Bley, a senior postdoctoral scholar research associate in chemistry and also co-first author. “We have this composite structure now, and it enables and informs future experiments on NPC function, or even diseases. There are a lot of mutations in the NPC that are associated with terrible diseases, and knowing where they are in the structure and how they come together can help design the next set of experiments to try and answer the questions of what these mutations are doing.”
The research team describes how it determined the entire structure of what is known as the NPC’s linker-scaffold — the collection of proteins that help hold the NPC together while also providing it with the flexibility it needs to open and close and to adjust itself to fit the molecules that pass through. Hoelz likens the NPC to something built out of Lego bricks that fit together without locking together and are instead lashed together by rubber bands that keep them mostly in place while still allowing them to move around a bit.
“I call these unstructured glue pieces the ‘dark matter of the pore,’” Hoelz says. “This elegant arrangement of spaghetti noodles holds everything together.”
The process for characterizing the structure of the linker-scaffold was much the same as the process used to characterize the other parts of the NPC. The team manufactured and purified large amounts of the many types linker and scaffold proteins, used a variety of biochemical experiments and imaging techniques to examine individual interactions, and tested them piece by piece to see how they fit together in the intact NPC.
To check their work, they introduced mutations into the genes that code for each of those linker proteins in a living cell. Since they knew how those mutations would change the chemical properties and shape of a specific linker protein, making it defective, they could predict what would happen to the structure of the cell’s NPCs when those defective proteins were introduced. If the cell’s NPCs were functionally and structurally defective in the way they expected, they knew they had the correct arrangement of the linker proteins.
“A cell is much more complicated than the simple system we create in a test tube, so it is necessary to verify that results obtained from in vitro experiments hold up in vivo,” Petrovic says.
The assembly of the NPC’s outer face also helped solve a longtime mystery about the nuclear envelope, the double membrane system that surrounds the nucleus. Like the membrane of the cell within which the nucleus resides, the nuclear membrane is not perfectly smooth. Rather, it is studded with molecules called integral membrane proteins (IMPs) that serve in a variety of roles, including acting as receptors and helping to catalyze biochemical reactions.
Although IMPs can be found on both the inner and outer sides of the nuclear envelope, it had been unclear how they actually traveled from one side to the other. Indeed, because IMPs are stuck inside of the membrane, they cannot just glide through the central transport channel of the NPC as do free-floating molecules.
Once Hoelz’s team understood the structure of the NPC’s linker-scaffold, they realized that it allows for the formation of little “gutters” around its outside edge that allow the IMPs to slip past the NPC from one side of the nuclear envelope to the other while always staying embedded in the membrane itself.
“It explains a lot of things that have been enigmatic in the field. I am very happy to see that the central transport channel indeed has the ability to dilate and form lateral gates for these IMPs, as we had originally proposed more than a decade ago,” Hoelz says.
Taken together, the findings of the two papers represent a leap forward in scientists’ understanding of how the human NPC is built and how it works. The team’s discoveries open the door for much more research. “Having determined its structure, we can now focus on working out the molecular bases for the NPC’s functions, such as how mRNA gets exported and the underlying causes for the many NPC-associated diseases with the goal of developing novel therapies,” Hoelz says.
Complete Chemical Synthesis of Minimal Messenger RNA by Efficient Chemical Capping Reaction
by Naoko Abe, Akihiro Imaeda, Masahito Inagaki, Zhenmin Li, Daisuke Kawaguchi, Kaoru Onda, Yuko Nakashima, Satoshi Uchida, Fumitaka Hashiya, Yasuaki Kimura, Hiroshi Abe in ACS Chemical Biology
Researchers at Nagoya University in Japan have developed a new chemical-only process that may represent an important breakthrough in creating customized mRNA vaccines for a variety of diseases and allow for the inexpensive preparation of mRNA in large quantities.
During the COVID-19 pandemic, mRNA vaccines were successfully used to boost immunity. These vaccines teach cells how to make a protein that triggers the body’s immune response, allowing its natural defenses to recognize the invading virus. However, current vaccines that use biological processes do not allow for the precise molecular design of mRNA, which limits their use in creating new vaccines as variants emerge.
A research group led by Professor Hiroshi Abe and Associate Professor Naoko Abe of the Graduate School of Science at Nagoya University has developed the first completely chemical synthesis method for mRNA. In their study, the group synthesized a part of the mRNA called the cap. The cap is important because it promotes the translation of mRNA into proteins and protects mRNA from degradation. To prepare synthetic mRNA, such as that used in vaccines, the two currently used biological methods rely on enzymes to incorporate the cap structure into the mRNA. However, the researchers found that their technique could synthesize a variety of chemically modified mRNA strands with a cap structure.
According to Professor Hiroshi Abe: “our research suggests that it is possible to make mRNAs with precisely introduced chemical modifications with complete control over the process. The molecular design reported in our study exhibits five times higher translational activity than that of enzyme-produced natural-type mRNA. This means that mRNA can be synthesized in large quantities at low cost using chemical synthesis.”
Chemically modified mRNA could be used to create customized vaccines against a variety of infectious diseases including viruses and cancers. Professor Abe explains, “By introducing these chemical modifications, the mRNA becomes stable. This could allow for the creation of long-lasting and effective mRNA vaccines. In addition, it could allow mRNA to be administered directly instead of using lipid nanoparticles, which are used for delivery in current vaccines.”
“One of the exciting implications of this research is that this could be used in the next generation of vaccines,” the researchers said. “We hope that the capping method reported here will be of great use in the development of RNA therapeutics.”
Ethylene augments root hypoxia tolerance via growth cessation and reactive oxygen species amelioration
by Zeguang Liu, Sjon Hartman, Hans van Veen, et al in Plant Physiology
Extreme weather phenomena are on the rise worldwide, including frequent droughts and fires. Floods are also a clear consequence of climate change. For agriculture, a flooded field means major losses: about 15 percent of global crop losses are due to flooding. As part of a collaboration between Freiburg, Utrecht in the Netherlands, and other institutes, Junior Professor Dr. Sjon Hartman from the Cluster of Excellence CIBSS — Centre for Integrative Biological Signalling Studies at the University of Freiburg, has now discovered that a signaling molecule can make plants more resistant to flooding. The gaseous plant hormone ethylene causes the plant to switch on a kind of molecular emergency power system that helps it survive the lack of oxygen during flooding. The team had previously demonstrated that ethylene sends a signal to the plant that it is underwater. Pretreating the experimental plants with the hormone improved their chances of survival. The results should help to combat waterlogging and flooding in agriculture and, for example, to develop resistant plant varieties.
Plant species differ greatly in their ability to survive periods of flooding or waterlogging. “In the case of potatoes, the roots die after two days due to a lack of oxygen. Rice plants are much more resistant, able to survive their entire lives in waterlogged paddy fields,” Hartman explains. The Arabidopsis thaliana, a model organism for plant research, can be used to study the genes and proteins that make up this adaptation. “Plants notice that they are surrounded by water because the gas ethylene, which all plant cells produce, can no longer escape into the air,” Hartman continues. The researchers showed this in previous studies at Utrecht University. Receptors throughout the plant subsequently respond to increased concentrations of the hormone.
The team simulated flooding by placing Arabidopsis seedlings in a bell jar without light or oxygen. When the seedlings were previously exposed to ethylene gas, the root tip cells survived longer. The treated plants stopped root growth and switched energy production in the cells to oxygen-free metabolic processes. In addition, the ethylene caused the cells to be better protected against harmful oxygen radicals that accumulate in oxygen-deprived plants. This was revealed by analyses of gene activity and protein composition of the cells.
“Taken together, these rearrangements that ethylene triggers improve plant survival during and after flooding,” Hartman summarizes. “As we better understand these signaling pathways, we can learn to make crops more resilient to flooding to combat climate change.”
Synonymous mutations in representative yeast genes are mostly strongly nonneutral
by Xukang Shen, Siliang Song, Chuan Li & Jianzhi Zhang in Nature
In the early 1960s, University of Michigan alumnus Marshall Nirenberg and a few other scientists deciphered the genetic code of life, determining the rules by which information in DNA molecules is translated into proteins, the working parts of living cells.
They identified three-letter units in DNA sequences, known as codons, that specify each of the 20 amino acids that make up proteins, work for which Nirenberg later shared a Nobel Prize with two others. Occasionally, single-letter misspellings in the genetic code, known as point mutations, occur. Point mutations that alter the resulting protein sequences are called nonsynonymous mutations, while those that do not alter protein sequences are called silent or synonymous mutations.
Between one-quarter and one-third of point mutations in protein-coding DNA sequences are synonymous. Ever since the genetic code was cracked, those mutations have generally been assumed to be neutral, or nearly so. But in a study that involved the genetic manipulation of yeast cells in the laboratory, University of Michigan biologists show that most synonymous mutations are strongly harmful.
The strong nonneutrality of most synonymous mutations — if found to be true for other genes and in other organisms — would have major implications for the study of human disease mechanisms, population and conservation biology, and evolutionary biology, according to the study authors.
“Since the genetic code was solved in the 1960s, synonymous mutations have been generally thought to be benign. We now show that this belief is false,” said study senior author Jianzhi “George” Zhang, the Marshall W. Nirenberg Collegiate Professor in the U-M Department of Ecology and Evolutionary Biology.
“Because many biological conclusions rely on the presumption that synonymous mutations are neutral, its invalidation has broad implications. For example, synonymous mutations are generally ignored in the study of disease-causing mutations, but they might be an underappreciated and common mechanism.”
In the past decade, anecdotal evidence has suggested that some synonymous mutations are nonneutral. Zhang and his colleagues wanted to know if such cases are the exception or the rule. They chose to address this question in budding yeast (Saccharomyces cerevisiae) because the organism’s short generation time (about 80 minutes) and small size allowed them to measure the effects of a large number of synonymous mutations relatively quickly, precisely and conveniently. They used CRISPR/Cas9 genome editing to construct more than 8,000 mutant yeast strains, each carrying a synonymous, nonsynonymous or nonsense mutation in one of 21 genes the researchers targeted.
Then they quantified the “fitness” of each mutant strain by measuring how quickly it reproduced relative to the nonmutant strain. Darwinian fitness, simply put, refers to the number of offspring an individual has. In this case, measuring the reproductive rates of the yeast strains showed whether the mutations were beneficial, harmful or neutral. To their surprise, the researchers found that 75.9% of synonymous mutations were significantly deleterious, while 1.3% were significantly beneficial.
“The previous anecdotes of nonneutral synonymous mutations turned out to be the tip of the iceberg,” said study lead author Xukang Shen, a graduate student research assistant in Zhang’s lab.
“We also studied the mechanisms through which synonymous mutations affect fitness and found that at least one reason is that both synonymous and nonsynonymous mutations alter the gene-expression level, and the extent of this expression effect predicts the fitness effect.”
Zhang said the researchers knew beforehand, based on the anecdotal reports, that some synonymous mutations would likely turn out to be nonneutral.
“But we were shocked by the large number of such mutations,” he said. “Our results imply that synonymous mutations are nearly as important as nonsynonymous mutations in causing disease and call for strengthened effort in predicting and identifying pathogenic synonymous mutations.”
The U-M-led team said that while there is no particular reason why their results would be restricted to yeast, confirmations in diverse organisms are required to verify the generality of their findings.
A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution
by Xavier Grau-Bové, Cristina Navarrete, Cristina Chiva, et al in Nature Ecology & Evolution
In almost every human cell, two metres-long DNA has to fit within a nucleus that is just 8 millionths of a metre wide. Like wool around a spool, the extreme space challenge requires DNA to wrap around structural proteins called histones. This coiled genetic architecture, known as chromatin, protects DNA from damage and has a key role in gene regulation.
Histones are present in both eukaryotes, living organisms that have specialised cellular machinery such as nuclei and microtubules, and archaea, another branch of the tree of life consisting of single-celled microbes that are prokaryotic, meaning they lack a nucleus.
In eukaryotic cells, histones are modified by enzymes, continuously shapeshifting the genomic landscape to regulate gene expression and other genomic processes. Despite this fundamental role, the exact origin of chromatin has been shrouded in mystery. Researchers at the Centre for Genomic Regulation (CRG) now reveal that nature’s storage solution first evolved in ancient microbes living on Earth between one and two billion years ago.
To go back in time, the researchers used information written in the genomes of modern organisms, organizing life forms according to the evolution of genes and proteins linked to chromatin. They studied thirty different species obtained from water samples in Canada and France. The microbes were identified thanks to modern gene-sequencing technologies that allow the identification of species by filtering DNA. They were subsequently grown in the lab for proteomic and genome sequencing.
The researchers found that prokaryotes lack the machinery necessary to modify histones, suggesting archaeal chromatin at the time could have played a basic structural role but did not regulate the genome. In contrast, researchers found ample evidence of proteins that read, write and erase histone modifications in early diverging eukaryotic lineages such as the malawimonad Gefionella okellyi, the ancyromonad Fabomonas tropica, or the discoban Naegleria gruberi, microbes that had not been sampled until now.
“Our results underscore that the structural and regulatory roles of chromatin are as old as eukaryotes themselves. These functions are essential for eukaryotic life — since chromatin first appeared, it’s never been lost again in any life form,” says Dr. Xavier Grau-Bové, a post-doctoral researcher at the CRG and first author of the study. “We are now a bit closer to understanding its origin, thanks to the power of comparative analyses to uncover evolutionary events that occurred billions of years ago.”
Using the sequence data, the researchers reconstructed the repertoire of genes held by the Last Eukaryotic Common Ancestor, the cell that gave rise to all eukaryotes. This living organism had dozens of histone-modifying genes and lived between one and two billion years ago on Earth, which is itself estimated to be 4.5 billion years old. The authors of the study hypothesise that chromatin evolved in this microbe as a result of selective pressures in the primordial environment of Earth.
Dr. Arnau Sebe-Pedrós, researcher at the CRG and senior author of the study, points out that “viruses and transposable elements are genome parasites that regularly attack DNA of single-celled organisms. This could have led to an evolutionary arms-race to protect the genome, resulting in the development of chromatin as a defensive mechanism in the cell that gave rise to all known eukaryotic life on Earth. Later on, these mechanisms were co-opted into elaborate gene regulation, as we observe in modern eukaryotes, particularly multicellular organisms.”
According to the authors of the study, future research could look at the evolution of histone-modifying enzymes in Asgardian archaea, microbes named after a mythological region inhabited by Norse gods that are often described as an evolutionary stepping stone between archaea and eukaryotes. The researchers found evidence that some species of Asgardian microbes, such as Lokiarchaeota, have histones with eukaryotic-like features, and could be the result of convergent evolution.
PEX11β and FIS1 cooperate in peroxisome division independent of Mitochondrial Fission Factor
by Tina A. Schrader, Ruth E. Carmichael, Markus Islinger, Joseph L. Costello, Christian Hacker, Nina A. Bonekamp, Jochen H. Weishaupt, Peter M. Andersen, Michael Schrader in Journal of Cell Science
A pioneering study has shed new light on how subcellular organelles divide and multiply.
The study, led by Professor Michael Schrader from the University of Exeter, has explored on peroxisome dynamics and revealed alternative pathways for their division.
Organelles are the functional units of a cell. They perform specialised functions, and defects in their enzymes performing those functions can result in metabolic disorders. However, organelles are also highly dynamic, allowing them to multiply by increasing in size and then dividing to adapt their number and functions to changing cellular needs.
Recently, scientists have identified a new group of disorders, characterised by defects in the membrane dynamics and division of organelles rather than by loss of metabolic functions. Patients with defects in organelle division present with developmental and neurological abnormalities. Those disorders are caused by mutations in genes encoding for the organelle division machinery, such as Mitochondrial fission factor (MFF) — a key component of the division machinery of two organelles, mitochondria and peroxisomes.
MFF functions as an adaptor protein to recruit a mechanochemical enzyme, Dynamin-related protein 1 (DRP1), to mitochondria and peroxisomes. This enzyme can constrict and divide membranes and is essential for membrane fission and organelle multiplication. Loss of MFF function results in highly elongated peroxisomes (and mitochondria) in patient cells. It was therefore assumed that MFF is the key factor in peroxisome division.
An international, multi-disciplinary team of scientists, led by Professor Schrader, has now revealed an alternative pathway for their division. Peroxisomes fulfil important protective functions in the cell and are vital for health; they contribute to cellular lipid metabolism and redox balance, which links them to the control of energy regulation, cellular ageing and age-related disorders.
“In this study, we show that the peroxisomal membrane protein PEX11β can divide the highly elongated, fission-incompetent peroxisomes in MFF-deficient cells, when the PEX11β levels are increased,” said Professor Schrader.
“However, PEX11β does not have the ability of divide peroxisomes on its own. “It requires FIS1 (Fission factor 1), another membrane adaptor for DRP1, whose exact role was previously unclear.”
Tina Schrader, first author of the paper and senior research technician in the team, said: “Interestingly, we observed that increased levels of MFF can also divide peroxisomes in PEX11β-deficient cells and restore a normal peroxisome morphology.” Patients suffering from a loss of PEX11β function display a short statue, progressive hearing loss and neurological abnormalities.
“We show that alternative pathways for peroxisome division exist; one using MFF and DRP1, and another using PEX11β, FIS1 and DRP1,” said Dr Ruth Carmichael, joint first author of the paper.
Professor Michael Schrader pointed out that: “Our observations suggest that modulation of MFF or PEX11β protein levels may represent a therapeutic option to overcome the defects in peroxisome dynamics.
“Pharmacological agents that up-regulate MFF or PEX11β may therefore be of therapeutic value to restore peroxisome dynamics in certain disease conditions.
“This might also be relevant to age-related conditions like dementia, deafness and blindness, as peroxisomal dynamics are known to have important protective functions within sensory cells.”
Toll-like Receptor 9 Pathway Mediates Schlafen+-MDSC Polarization During Helicobacter-induced Gastric Metaplasias
by Lin Ding, Jayati Chakrabarti, Sulaiman Sheriff, Qian Li, Hahn Nguyen Thi Hong, Ricky A. Sontz, Zoe E. Mendoza, Amanda Schreibeis, Michael A. Helmrath, Yana Zavros, Juanita L. Merchant in Gastroenterology
Researchers at the University of Arizona Health Sciences are hoping to catch stomach cancer before it develops in at-risk patients. In a paper published in Gastroenterology, researchers identified a genetic variation that could help identify when patients with Helicobacter pylori are more likely to develop stomach cancer.
The National Cancer Institute cites infection with H. pylori as the primary identified cause of certain types of stomach cancer. H. pylori is a bacterium that grows in the mucosa, or membrane layer that lines the stomach.
“This study is proposing that if you are carrying this particular allele, you are more likely to have an aggressive type of response to the bacteria that can result in complications,” said the study’s senior author, Juanita L. Merchant, MD, PhD, Regents Professor of Medicine and chief of the Division of Gastroenterology at the UArizona College of Medicine — Tucson.
In the United States, H. pylori is more prevalent in Hispanics, African Americans and the elderly. Dr. Merchant cited data suggesting that 1–3% of people with H. pylori will develop gastric cancer and that the cure rate is around 30%, which is low compared with some other types of cancer. Current diagnosis of stomach or gastric cancer requires the patient to undergo an upper endoscopy, where a doctor looks for signs of cancer and takes a tissue sample for analysis.
For years, Dr. Merchant and colleagues have been investigating new ways to diagnose stomach cancer in its earliest possible stages. In 2020, they published research on a promising biomarker that appears in some patients before stomach cancer develops. The new study focused on the molecular pathways that control the activation of immune cells in response to H. pylori infection, specifically the action of toll-like receptor 9 (TLR9). Located within immune cells, TLR9 signals the immune system when to fight an infection. However, H. pylori infection can constantly trigger TLR9 activation over long periods of time, leading to the chronic inflammation. The long-term presence of inflammation caused by H. pylori infection is believed to be one of the triggers for cancer developing in the stomach.
“This addresses the question of what role the immune microenvironment has in gastric cancer,” said Dr. Merchant, who is a research member of the UArizona Cancer Center. “We have shown that these immune cells do play an important role.”
Researchers found that the chronic activation of TLR9 in the stomach triggers a series of events that includes increased production of interferon α, a signaling protein that can change the genetic signature of specialized immune cells known as myeloid-derived suppressor cells, or MDSCs. Prior research has linked MDSCs with H. pylori infection.
Dr. Merchant and her team focused on each step of the pathway and identified a specific genetic change — allele rs5743836 TLR9 minor C — that was linked to higher levels of TLR9 and interferon α and a greater incidence of gastric tumors. The allele is a single nucleotide polymorphism, or SNP, which is a genetic change in the DNA between genes.
“Because TLR9 and the SNP can be tested by DNA, they could be used as biomarkers to help us identify which patient populations are going to be more susceptible to the cellular changes that might lead to cancer based on their genetic background,” Dr. Merchant explained. “Those are the patients who could benefit from increased endoscopic surveillance.”
Eventually, the findings may also lead to new therapeutic options for patients.
“We have previously found a real-time biomarker in a blood test, and now we have something we can see in DNA,” Dr. Merchant said. “Our next step is to look at therapy options.”
Novel fold of rotavirus glycan-binding domain predicted by AlphaFold2 and determined by X-ray crystallography
by Liya Hu, Wilhelm Salmen, Banumathi Sankaran, Yi Lasanajak, David F. Smith, Sue E. Crawford, Mary K. Estes, B. V. Venkataram Prasad in Communications Biology
Of the three groups of rotavirus that cause gastroenteritis in people, called groups A, B and C, groups A and C affect mostly children and are the best characterized. On the other hand, of group B, which causes severe diarrhea predominantly in adults, little is known about the tip of the virus’s spike protein, called VP8* domain, which mediates the infection of cells in the gut.
“Determining the structure of VP8* in group B rotavirus is important because it will help us understand how the virus infects gastrointestinal cells and design strategies to prevent and treat this infection that causes severe diarrheal outbreaks,” said corresponding author Dr B. V. Venkataram Prasad, professor of biochemistry and molecular biology at Baylor College of Medicine.
The team’s first step was to determine the 3D structure of VP8* B using X-Ray crystallography, a laborious and time-consuming process. However, this traditional approach was unsuccessful in this case. The researchers then turned to a recently developed artificial intelligence-based computational program called AlphaFold2.
“AlphaFold2 predicts the 3D structure of proteins according to their genetic sequence,” said first author and co-corresponding author Dr. Liya Hu, assistant professor of biochemistry and molecular biology at Baylor. “We knew that the protein sequence of VP8* of rotavirus group B was about 10% similar to the sequences of VP8* of rotavirus A and C, so we expected differences in the 3D structure as well. But we were surprised when AlphaFold2 predicted a 3D structure for the VP8* B that was not just totally different from that of the VP8* domain in rotavirus A and C, but also that no other protein before had been reported to have this structure.”
With this information in hand, the researchers went back to the lab bench and experimentally confirmed that the structure of VP8* B predicted by ALphaFold2 indeed coincided with the actual structure of the protein using X-ray crystallography.
Previous research has shown that rotavirus A and C infect cells by using the VP8* domain to bind to specific sugar components on histo-blood group antigens, including the A, B, AB and O blood groups, present in many cells in the body. It has been proposed that the ability of different rotavirus to bind to different sugars on the histo-group antigens might explain why some of these viruses specifically infect young children while others affect other populations. Unlike the VP8* A and VP8* C, the sugar specificity of VP8* B had not been characterized until now.
“We screened VP8* B against an array of sugars and found that it recognizes N-acetyllactosamine, a sugar common in many cells in the body, that is not recognized by VP8* of rotavirus A and C,” Hu said. “Such a 3D structure that also is capable of binding to sugar has not been described before.”
“I am excited about identifying a novel 3D protein structure. I am also anticipating all the discoveries that will come from this as we investigate how the new structure interacts with cells to infect them and how this process compares to the one from rotavirus A and C,” said co-author Dr. Wilhelm Salmen, a postdoctoral fellow in the Prasad lab.
“Our lab has been collaborating with Dr. Prasad’s lab for many years to understand the significance of sugar-binding viruses in gastrointestinal infections,” said co-author Dr. Mary Estes, Cullen Foundation Endowed Chair and Distinguished Service Professor of Virology and Microbiology at Baylor. Estes also is a member of Baylor’s Dan L Duncan Comprehensive Cancer Center. “We can’t cultivate the group B virus yet, but our lab will now try to grow these adult viruses in our human organoid systems, a miniature model of the human gut that can help us probe the mechanism of virus entry and growth. This may lead to new therapeutics that are still needed to treat diarrheal disease.”
“This new approach to determine a protein’s 3D structure represents a significant step forward for the field of structural biology,” Hu said.
“I am excited about our findings of a new 3D protein structure from an evolutionary point of view. It exemplifies how viruses can evolve by incorporating structurally distinct modules with similar functionality, but how this structure came about in this group B rotavirus is quite intriguing,” said Prasad, who holds the Alvin Romansky Chair in Biochemistry and is a member of the Dan L Duncan Comprehensive Cancer Center.
Mechanism of mitoribosomal small unit biogenesis and preinitiation
by Yuzuru Itoh, Anas Khawaja, Ivan Laptev, Miriam Cipullo, Ilian Atanassov, Petr Sergiev, Joanna Rorbach and Alexey Amunts in Nature
Using advanced microscopy techniques, researchers at Karolinska Institutet and Stockholm University in Sweden have visualized in unprecedented detail the machinery that the cells’ powerhouses, the mitochondria, use to form their proteins. The results raise hopes of more specific antibiotics and new cancer drugs in the future.
The mitochondria are the cells’ powerhouses that convert energy locked in our food into a functional “energy currency” for the cells. They also have their own protein synthesis factories called ribosomes, which have a different appearance to those found in the cellular cytoplasm. However, little has been known about how the mitochondrial ribosomes are produced — until now.
“We were hoping to obtain a single snapshot of the mitoribosomal large subunit assembly, but our data revealed much more unexpected surprises,” says the study’s joint first author Anas Khawaya, postdoc at the Department of Medical Biochemistry and Biophysics, Karolinska Institutet. “These observations present opportunities to discover the full extent of crosstalk between mitoribosomal assembly and other aspects of mitochondrial function.”
Using a technique called cryogenic electron microscopy, the researchers were able to depict important key players of the complex machinery that manufactures ribosomes. One finding was that a component called ribosome-binding factor A (RBFA) orchestrates the process. The ribosome is made up of two halves, not unlike a hamburger bun. The researchers’ analyses show that a protein called mS37 signals that these two parts can be joined and are ready to start protein synthesis.
The results are an example of basic cell biology research, but the new knowledge can also give rise to medical advances, such as more targeted antibiotics. Mitochondria are similar to bacteria and the antibiotics that currently attack a bacterium’s ability to form proteins also affect our mitochondria.
“Whilst the mechanisms of bacterial and cytosolic translation have been studied for decades, we are only now starting to uncover how mitochondria produce proteins,” says Joanna Rorbach, principal researcher and group leader at the Department of Medical Biochemistry and Biophysics, Karolinska Institutet. “Understanding the differences between how bacteria and mitochondria produce their ribosomes could allow us to design better and more targeted antibiotics.”
The study has been led by Joanna Rorbach together with Alexey Amunts and his research group at the Department of Biochemistry and Biophysics at Stockholm University. Cancer is another future target. Unlike healthy cells, cancer cells grow quickly and divide often, a process that requires the formation of a large number of new proteins.
“One possible approach is to actively inhibit the cancer cells’ mitochondrial ribosomes,” Joanna Rorbach says.
Recommendations for improving statistical inference in population genomics
by Parul Johri, Charles F. Aquadro, Mark Beaumont, Brian Charlesworth, Laurent Excoffier, Adam Eyre-Walker, Peter D. Keightley, Michael Lynch, Gil McVean, Bret A. Payseur, Susanne P. Pfeifer, Wolfgang Stephan, Jeffrey D. Jensen in PLOS Biology
The second century Alexandrian astronomer and mathematician Claudius Ptolemy had a grand ambition. Hoping to make sense of the motion of stars and the paths of planets, he published a magisterial treatise on the subject, known as the Almagest. Ptolemy created a complex mathematical model of the universe that seemed to recapitulate the movements of the celestial objects he observed.
Unfortunately, a fatal flaw lay at the heart of his cosmic scheme. Following the prejudices of his day, Ptolemy worked from the premise that the Earth was the center of the universe. The Ptolemaic universe, composed of complex “epicycles” to account for planet and star movements, has long since been consigned to the history books, though its conclusions remained the scientific dogma for over 1200 years.
The field of evolutionary biology is no less subject to misguided theoretical approaches, sometimes producing impressive models that nevertheless fail to convey the true workings of nature as it shapes the dizzying assortment of living forms on Earth.
A new study examines mathematical models designed to draw inferences about how evolution operates at the level of populations of organisms. The study concludes that such models must be constructed with the greatest care, avoiding unwarranted initial assumptions, weighing the quality of existing knowledge and remaining open to alternate explanations.
Failure to apply strict procedures in null model construction can lead to theories that seem to square with certain aspects of available data derived from DNA sequencing, yet fail to correctly elucidate underlying evolutionary processes, which are often highly complex and multifaceted. Such theoretical frameworks may offer compelling but ultimately flawed pictures of how evolution actually acts on populations over time, be these populations of bacteria, shoals of fish, or human societies and their various migrations during prehistory.
In the new study, Jeffrey Jensen, a researcher in the Biodesign Center for Mechanisms of Evolution at Arizona State University and professor in the School of Life Sciences with the Center for Evolution & Medicine, leads a group of international luminaries in the field in providing guidance for future research. Together, they describe a range of criteria that can be used to better ensure the accuracy of models that produce statistical inferences in population genomics — a scientific discipline concerned with large-scale comparisons of DNA sequences within and across populations and species.
“One of our key messages is the importance of considering the contributions of evolutionary processes certain to be in constant operation (such as purifying selection and genetic drift), before simply relying on hypothesized or rare evolutionary processes as the primary drivers of observed population variation (such as positive selection),” Jensen emphasized.
Population genomics arose as early efforts in the field attempted to reconcile Charles Darwin’s notion of evolution by means of natural selection with the first inklings of the mechanisms of inheritance, uncovered by the Augustinian monk, Gregor Mendel. The synthesis culminated in the 1920s and early 30s, largely thanks to the mathematical work of Fisher, Haldane and Wright, who were the first to explore how natural selection together with other evolutionary forces would modify the genetic composition of Mendelian populations over time.
Today, studies in population genomics involve the large-scale application of various genomic technologies to explore the genetic composition of biological populations, and how various factors, including natural selection and genetic drift, produce changes in genetic composition over time.
To accomplish this, population geneticists develop mathematical models quantifying the contributions of these evolutionary processes in shaping gene frequencies, use this theory to design statistical inference approaches for estimating the forces producing observed patterns of genetic variation in actual populations, and test their conclusions against accumulated data.
The study of genomic variation focuses on DNA sequence differences among individuals and populations. Some of these variants are critically important for biological function, including mutations responsible for genetic disease, while others have no detectable biological effects.
Such variation in the human genome can take several forms. One common source of variation is known as single nucleotide polymorphisms, or SNPs, where a single DNA letter in the genome is altered. But larger-scale variation in the genome, involving the simultaneous alteration of hundreds or even thousands of base pairs is also possible. Again, some such alterations may play a role in disease risk and survival while many others have no effect.
Natural selection may occur when different variants segregating in a population have a fitness differential relative to one another. By designing and studying mathematical models governing the corresponding gene frequency change and applying those models to empirical data, population geneticists seek to understand the contributing evolutionary processes in a rigorous, quantitative way. Thus, population genetics is often regarded as the theoretical cornerstone of modern Darwinian evolution.
Although the importance of natural selection to the evolutionary process is undeniable, the role of positive selection in increasing the frequency of beneficial variants — the potential driver of adaptation — is certain to be comparatively rare relative even to other forms of natural selection. For example, purifying selection — the removal of deleterious variants from the population — is a constantly acting and far more pervasive form of selection.
In addition, there are multiple non-selective evolutionary processes of great importance. For example, genetic drift describes the many stochastic fluctuations inherent to evolution. In large populations, natural selection may act more efficently in purging deleterious variation and potentially fixing beneficial variation, whereas as populations become smaller genetic drift will be increasingly dominant.
The distinction can be seen in dramatic form when comparing prokaryotic organisms like bacteria with organisms composed of eukaryotic cells, including humans. In the former case, the vast population sizes tend to result in more efficient selection. In contrast, a weaker selection pressure operating in eukaryotes is more permissive of genomic changes, provided that they are not strongly deleterious.
According to the Neutral Theory of Molecular Evolution — a now guiding principle of evolutionary theory proposed by the population geneticist Motoo Kimura over 50 years ago — most evolutionary changes at the molecular level in real populations are governed not by natural selection, but by genetic drift. The study emphasizes that this critical point is too often missed by evolutionary biologists. As co-author Michael Lynch, director of ASU’s Biodesign Center for Mechanisms in Evolution cogently observes, “natural selection is just one of several evolutionary mechanisms, and the failure to realize this is probably the most significant impediment to a fruitful integration of evolutionary theory with molecular, cellular, and developmental biology.”
The new consensus study further stresses that a failure to consider these alternative evolutionary mechanisms which are certain to be operating, including genetic drift, and incorporate these into models of population genomics, is likely to lead researchers astray. The common overreliance on purely adaptive models to explain genomic variation has led to a raft of interpretations of dubious value, the authors assert.
The study presents a detailed flow chart that can help guide the development of more accurate models used to draw evolutionary inferences, based on genomic data. Biological parameters that vary among species include not only evolutionary variables like population size, mutation rates, recombination rates, and population structure and history, but the way the genome itself is structured and life history traits, including mating behavior. All of these factors play a vital role in dictating observed molecular variation and evolution.
“While these many considerations may sound daunting for some researchers, it is important to note that many excellent research groups at ASU and around the world are actively improving our understanding of these underlying evolutionary parameters, providing constantly improving inference, for example, of mutation and recombination rates,” added co-author Susanne Pfeifer, an Assistant Professor in the Center for Evolution & Medicine and the Biodesign Center for Mechanisms of Evolution.
Where once, theoretical models in population genomics proliferated alongside relatively scant genomic data, today an avalanche of data, enabled by rapid, low-cost DNA sequencing of organisms across the tree of life, has dramatically changed the field. The careful and judicious use of this gold mine of genomic data will help advance the most rigorous models to unlock evolution’s many remaining mysteries.
MISC
Subscribe to Paradigm!
Medium. Twitter. Telegram. Telegram Chat. Reddit. LinkedIn.
Main Sources
Research articles
