Genetics biweekly vol.23, 23d February — 9th March
TL;DR
- More than 20 years after the first release of the human genome, scientists have for the first time deciphered the highly complex genome of the potato. Their impressive technical feat will accelerate efforts to breed superior varieties.
- A researcher has made a discovery that alters our understanding of how the body’s DNA repair process works and may lead to new chemotherapy treatments for cancer and other disorders. Researchers discovered that base excision repair has a built-in mechanism to increase its effectiveness — it just needs to be captured at a very precise point in the cell life cycle.
- In laboratory experiments involving a class of mutations in people with a rare collection of immune system disorders, researchers say they have uncovered new details about how immune system cells respond to disease-causing bacteria, fungi and viruses such as SARS-CoV-2.
- Recent molecular findings offer new details on how Nipah and Hendra viruses attack cells, and the immune responses that try to counter this onslaught. The results point toward multi-pronged tactics to prevent and treat these deadly illnesses.
- Researchers found a bull ant venom component that exploits a pain pathway in mammals, which they believe evolved to stop echidnas attacking the ant’s nests.
- Cell division ensures growth or renewal and is thus vital for all organisms. However, the process differs somewhat in animals, bacteria, fungi, plants, and algae. Until now, little was known about how cell division occurs in algae. Researchers have used confocal laser scanning microscopy (CLSM) to capture the very first high-resolution three-dimensional images of cell division in live cells of the microalga Volvox carteri, and have identified new cellular structures involved in the process.
- Researchers have used a novel method to replicate mussel-adhesive proteins, creating a stronger glue than the material they set out to mimic.
- A high-fat diet is not enough to cause short-term fatty liver disease. However, if this diet is combined with the intake of beverages sweetened with liquid fructose, the accumulation of fats in the liver accelerates and hypertriglyceridemia — a cardiovascular risk factor — can appear, according to researchers.
- A team of student researchers has discovered human microRNA genes not shared with any other primate species and which may have played an important role in the unique evolution of the human species. The students found at least three families of microRNA genes on chromosome 21.
- Genomes are made up of thousands of individual pieces — genes — which are expressed at different levels. Researchers have shed light on how the placement of a gene affects its expression, as well as that of its neighbors.
- 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
Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar
by Hequan Sun, Wen-Biao Jiao, Kristin Krause, José A. Campoy, Manish Goel, Kat Folz-Donahue, Christian Kukat, Bruno Huettel, Korbinian Schneeberger in Nature Genetics
More than 20 years after the first releasse of the human genome, scientists at the Ludwig-Maximilians-Universität München and the Max Planck Institute for Plant Breeding Research in Cologne, have for the first time decoded the highly complex genome of the potato. This technically demanding study lays the biotechnological foundation to accelerate the breeding of more robust varieties — a goal in plant breeding for many years and an important step for global food security.
When shopping for potatoes on a market today, buyers may well be going home with a variety that was already available more than 100 years ago. Traditional potato varieties are popular. And yet this example also highlights a lack of diversity among the predominant potato varieties. However, that could soon change: researchers in the group of geneticist Korbinian Schneeberger were able to generate the first full assembly of a potato genome. This paves the way for breeding new, robust varieties:
“The potato is becoming more and more integral to diets worldwide including even Asian countries like China where rice is the traditional staple food. Building on this work, we can now implement genome-assisted breeding of new potato varieties that will be more productive and also resistant to climate change — this could have a huge impact on delivering food security in the decades to come.”
Especially the low diversity makes potato plants susceptible to diseases. This can have stark consequences, most dramatically during the Irish famine of the 1840s, where for several years nearly the entire potato crop rotted in the ground, and millions of people in Europe suffered from starvation simply because the single variety that was grown was not resistant to newly emerging tuber blight. During the Green Revolution of the 1950s and 1960s, scientists and plant breeders succeeded in achieving large increases in the yields of many of our major crop staples like rice or wheat. However, the potato has seen no comparable boost, and efforts to breed new varieties with higher yields have remained largely unsuccessful to the current day.
The reason for this is simple but has proven difficult to tackle — instead of inheriting one copy of every chromosome from both the father and from the mother (as in humans) potatoes inherit two copies of each chromosome from each parent, making them a species with four copies of each chromosome (tetraploid). Four copies of each chromosome also mean four copies of each gene, and this makes it highly challenging and time-consuming to generate new varieties that harbour a desired combination of individual properties; what’s more, multiple copies of each chromosome also make the reconstruction of the potato genome a far greater technical challenge than was the case for the human genome.
The researchers have overcome this longstanding hurdle using a simple yet elegant trick. Instead of trying to differentiate the four, often very similar, chromosome copies from each other, Korbinian Schneeberger together with his colleague Hequan Sun and other co-workers circumvented this problem by sequencing the DNA of large numbers of individual pollen cells. In contrast to all other cells, each pollen cell contains only two random copies of each chromosome; this facilitated the reconstruction of the sequence of the entire genome.
An overview of the complete DNA sequence of cultivated potato has the potential of greatly facilitating breeding and has been an ambition of scientists and plant breeders alike for many years already. With this information in hand, scientists can now more easily identify gene variants responsible for desirable or undesirable.
Interlocking activities of DNA polymerase β in the base excision repair pathway
by Adarsh Kumar, Andrew J. Reed, Walter J. Zahurancik, Sasha M. Daskalova, Sidney M. Hecht, Zucai Suo in Proceedings of the National Academy of Sciences
A Florida State University College of Medicine researcher has made a discovery that alters our understanding of how the body’s DNA repair process works and may lead to new chemotherapy treatments for cancer and other disorders.
The fact that DNA can be repaired after it has been damaged is one of the great mysteries of medical science, but pathways involved in the repair process vary during different stages of the cell life cycle. In one of the repair pathways known as base excision repair (BER), the damaged material is removed, and a combination of proteins and enzymes work together to create DNA to fill in and then seal the gaps.
Led by Eminent Professor Zucai Suo, FSU researchers discovered that BER has a built-in mechanism to increase its effectiveness — it just needs to be captured at a very precise point in the cell life cycle. In BER, an enzyme called polymerase beta (PolyB) fulfills two functions: It creates DNA, and it initiates a reaction to clean up the leftover “chemical junk.” Through five years of study, Suo’s team learned that by capturing PolyB when it is naturally cross-linked with DNA, the enzyme will create new genetic material at a speed 17 times faster than when the two are not cross-linked. This suggests that the two functions of PolyB are interlocked, not independent, during BER.
The research improves the understanding of cellular genomic stability, drug efficacy and resistance associated with chemotherapy.
“Cancer cells replicate at high speed, and their DNA endures a lot of damage,” Suo said. “When a doctor uses certain drugs to attack cancer cells’ DNA, the cancer cells must cope with additional DNA damage. If the cancer cells cannot rapidly fix DNA damage, they will die. Otherwise, the cancer cells survive, and drug resistance appears.
This research examined naturally cross-linked PolyB and DNA, unlike previous research that mimicked the process. Prior to this study, researchers had identified the enzymes involved in BER but didn’t fully understand how they work together.
“When we have nicks in DNA, bad things can happen, like the double strand breaking in DNA,” said Thomas Spratt, a professor of biochemistry and molecular biology at Penn State University College of Medicine who was not a part of the research team. “What Zucai found provides us with something we didn’t understand before, and he used many different methods to reach his findings.”
In addition to revealing PolyB’s functional dynamics, the team proposed a modified BER pathway and is testing the pathway in human cells.
“We have been able to dig deeper into a fundamental pathway for which the pioneer Tomas Lindahl shared the Nobel Prize in Chemistry in 2015,” Suo said.
Mechanistic impact of oligomer poisoning by dominant-negative CARD11 variants
by Jacquelyn R. Bedsaul, Neha Shah, Shelby M. Hutcherson, Joel L. Pomerantz in iScience
In laboratory experiments involving a class of mutations in people with a rare collection of immune system disorders, Johns Hopkins Medicine researchers say they have uncovered new details about how immune system cells respond to disease-causing bacteria, fungi and viruses such as SARS-CoV-2.
The findings, the scientists report, reveal a critical step in the molecular circuitry inside what are known as B and T cells that mobilizes the immune system to fight off foreign invaders. Though the researchers studied rare disease mutations, they believe the findings point to subtle genetic variations among all human populations that may help explain the wide variability in individual responses to infections.
Researchers focused on the cell biology and genetics of three inherited conditions classified as primary immunodeficiency syndromes, which are caused by mutations in the CARD11 gene in B and T immune cells. People with the syndromes are unable to mount immune defenses to pathogens, and are prone to life-threatening fungal infections, pneumonia, upper respiratory infections, and food and environmental allergies.
The culprit, an altered version of the CARD11 gene, fails to activate a signaling pathway that in turn spurs the immune system to recognize pathogens and launch defenses against them. The pathway is the same one activated by most vaccines.
Normally, the CARD11 gene encodes instructions for a cluster of proteins called an oligomer. When one or both copies of a gene is mutated, producing an abnormal form of the oligomer, the faulty copy overrides the potential to launch protective responses. Unlike some other gene mutations, in which one normal, functional copy of a gene can provide some protection, some CARD11 mutations severely impact the oligomer regardless of whether one or both gene copies are mutated.
“Proteins in an oligomer sometimes need every protein subunit in the cluster to be fully functional for it to do its job,” says Joel Pomerantz, Ph.D., associate professor of biological chemistry at the Johns Hopkins University School of Medicine. “In certain CARD11-related syndromes, one bad copy of the gene can disrupt the whole cluster.”
To pinpoint how this happens, Pomerantz and Jacquelyn Bedsaul, the study report’s first author and a graduate student at Johns Hopkins, focused on identifying which step in the signaling cascade requires all of the CARD11 protein subunits in the cluster to be functional.
Using laboratory-grown T cells with both functioning and mutated CARD11 genes, they tracked protein levels and the cells’ ability to become activated and signal other immune cells. They learned that CARD11 mutations primarily affect how the protein cluster opens itself to bind with other proteins in a series of chain reactions that awaken T cells to foreign pathogens. Specifically, they found that the mutated version of CARD11 prevents the protein cluster from opening at all. If it’s closed, the CARD11 cluster can’t signal to other proteins to start an immune response.
The researchers also conducted experiments to learn if the opening phase is the only step affected by the mutated CARD11 gene. To determine this, they used genetically engineered T cells that have CARD11 proteins perpetually in the open state. The researchers found that even when CARD11 proteins are open, a mutation in CARD11 blocks the signaling pathway.
“The mutation also appears to disrupt the ability of the protein subunits to interact with other signalizing partners and function normally,” says Pomerantz.
The conditions arising from CARD11 mutations in their most severe forms are rare in humans. Pomerantz hopes that, eventually, scientists can develop gene editing techniques to correct CARD11 mutations in immune cells in these patients. For people with genetic variants less severe than those studied for this report, Pomerantz says the findings offer insight into the wide variation among immune system responses, and could someday explain why some people are at higher risk of bad outcomes when exposed to disease-causing pathogens.
“When we understand the fundamental mechanisms of how our immune cells operate, we’ll gain a better understanding of how genetic variation in immune-related genes in the human population can lead to different immunologic outcomes,” says Pomerantz.
The evolution of de novo human‐specific microRNA genes on chromosome 21
by Hunter R. Johnson, Jessica A. Blandino, Beatriz C. Mercado, José A. Galván, William J. Higgins, Nathan H. Lents in American Journal of Biological Anthropology
A team of student researchers from John Jay College of Criminal Justice has discovered human microRNA genes not shared with any other primate species and which may have played an important role in the unique evolution of the human species. The students, under the direction of John Jay Professors Dr. Hunter R. Johnson and Dr. Nathan H. Lents, found at least three families of microRNA genes on chromosome 21.
The team utilized genome alignment tools to compare the most recent drafts of human and chimpanzee genomes, meticulously scanning for novel genetic elements unique to humans. Beginning with the smallest human chromosome, chromosome 21, the researchers were surprised to find a large region of human-unique DNA, called 21p11, that harbors several orphan microRNA genes.
Although the team found that the long arm of human chromosome 21 aligns well with that of other extant ape species, the short arm aligned poorly, suggesting that this region of the human genome has recently and substantially diverged from that of other primates.
According to their analysis of prehistoric human genomes, these changes predate the divergence of Neanderthals and modern humans. The genes also show little to no sequence-based variation within the modern human population. The team therefore theorized that the microRNA (miRNA) genes found in that region [miR3648 and miR6724] likely evolved in the time since the chimpanzee and human lineages split, sometime in the last seven million years, and are specific to humans.
Using computational tools, the team discovered with a high degree of likelihood that the predicted gene targets of the relevant miRNAs are related to embryonic development. Both miR3648 and miR6724 have been detected in tissues throughout the human body, including the brain, and may conceivably play a role in the evolution of humankind’s most unique organ. The findings point to the intriguing idea that these microRNA genes contributed to the distinct evolution of our species and the uniqueness of humankind.
“Understanding the genetic basis for human uniqueness is an important undertaking because, despite sharing nearly 99% of our DNA sequences with the chimpanzee, we’re remarkably different organisms,” said student researcher José Galván. “Small post-transcriptional regulatory elements like miRNAs and siRNAs [small interfering RNA] are under-appreciated and often misunderstood in the effort to understand our genetic differences.”
Thanks to their small size and structural simplicity, miRNA genes have fewer barriers to de novo creation than other gene types. MicroRNA genes can be extremely prolific in their regulation of other genes, meaning that modest changes to DNA sequence can result in wide-ranging impacts to the human genome. The creation of miR3648 and miR6724 serve as excellent examples of this process. This study revealed a new possible mechanism for the creation of new miRNA genes through duplications of rRNA genes, which calls for further research on how general this phenomenon may be.
Architecture and antigenicity of the Nipah virus attachment glycoprotein
by Zhaoqian Wang, Moushimi Amaya, Amin Addetia, Ha V. Dang, Gabriella Reggiano, Lianying Yan, Andrew C. Hickey, Frank DiMaio, Christopher C. Broder and David Veesler in Science
Recent molecular findings offer new details on how Nipah and Hendra viruses attack cells, and the immune responses that try to counter this onslaught. The results point toward multi-pronged tactics to prevent and treat these deadly illnesses.
Both Nipah virus and Hendra virus are carried by bats native to certain parts of the world. These henipaviruses jump species and can infect many other mammals, including humans. The viruses cause brain inflammation and respiratory symptoms. People acquiring either of these diseases stand a 50% to 100% chance of succumbing.
There is a vaccine approved for use in horses and a modified version entered a human clinical trial. Horses can spread Hendra, possibly contracted from eating bat-contaminated fruit, to their caretakers through saliva and nasal secretions. An experimental, but not yet approved, cross-reactive antibody expected to work against both Nipah and Hendra viruses has been given to fifteen people who had a high-risk exposure. This was done under emergency compassionate use guidelines. This antibody is in a clinical trial in Australia, where it has just completed the Phase 1 stage of testing. There are no approved vaccines or therapies for use in humans against these henipaviruses, other than supportive care in the limited hope that the patient can overcome the virus.
New attempts to design life-saving preventatives and treatments became even more urgent after a new strain of Hendra was discovered a few months ago. Outbreaks of Nipah virus have appeared nearly every year over the past two decades in Bangladesh. The disease also has been seen in India and the Philippines. Henipavirus antibodies have been detected in people and Pteropus bats in Africa. It’s estimated that 2 billion people live in the parts of the world where henipavirus spillovers from bats, or intermediary animal vectors, could be a threat.
The senior author of the latest henipavirus paper in Science is David Veesler, associate professor of biochemistry at the University of Washington School of Medicine and a Howard Hughes Medical Investigator. He studies bat immunity to many dangerous viruses, and conducts molecular structure and function studies of the infectivity machinery in coronaviruses, other related viruses, and henipaviruses. His lab also researches antibody and virus interactions that hold clues for designing antivirals and vaccines for these two families of viruses. The lead author is Zhaoqian Wang, a UW graduate student in biochemistry. Christopher Broder’s lab collaborated on the research at the Uniformed Services University and the Henry M. Jackson Foundation for the Advancement of Military Medicine.
The researchers explained that Nipah and Hendra viruses enter into cells through attachment and fusion glycoproteins, which work in a coordinated fashion. These glycoproteins are the key targets for the antibody defense system. Through cryoelectron microscopy, the scientists were able to determine the structure of a critical component of the Nipah viruses’ infection mechanism in an interaction with a fragment of a broadly neutralizing antibody. They also observed that a mixture or “cocktail” of antibodies work better together to disarm Nipah viruses. Similar synergistic effects were seen in a set of antibodies against Hendra viruses. This combining of forces also helped keep escape mutants from emerging to sidestep the antibody response.
Examining the antibody response in laboratory animals inoculated with a critical section of the Nipah virus infection machinery provided vital information. The analysis indicated which area of the virus receptor binding protein was dominant in eliciting an immune response.
Before this study, the researchers said, nothing was available on the structure of a critical portion of henipaviruses responsible for eliciting antibody response, called the HNV G protein. This lack of information was an obstacle to understanding immunity and to improving the design of vaccine candidates. Now that the researchers have uncovered the 3D organization and some of the conformational dynamics of the HNV G protein, science may be closer to creating a template for building new and improved vaccines.
In a simplified description of the more complex findings, an important part of the attachment structure has a neck and four heads. Only one of the four heads turns its receptor binding site in the direction of the potential host cell; the other three turn away toward the virus’ membrane. This gives the viral structure the freedom to re-orient the head domain to engage with the host receptor.
The scientists noted that the architecture then “adopts a unique two heads up and two heads down conformation that is different from any other paramyxovirus attachment glycoprotein.” The paramyxovirus is a large family of single-strand RNA viruses. They cause several distinct types of diseases, most of which are transmitted on respiratory droplets. They include measles, mumps, distemper, parainfluenza, and the henipavirus diseases that have more recently crossed from animals to humans.
In investigating the nature of antibody responses to the Nipah virus and Hendra virus attachment protein G, the scientists examined two animals that were immunized with that glycoprotein. A potent, diverse neutralizing antibody response ensued. The head domain was found to be the main, if not exclusive target, of the immunization-induced antibody neutralization, even though the full tetramer was used. This indicated that the antibody response narrowed in on the receptor-binding area.
These findings, the researchers noted, “provide a blueprint for engineering next-generation vaccine candidates with improved stability and immunogenicity.” The s would focus on the vulnerability of the head domain. They anticipate a design approach like that employed for newer computer-engineered SARS-CoV-2 and respiratory syncytial virus candidates. A mosaic of head antigens would be presented to the body in an ordered array on a multivalent display. Using only the head domain rather than the full G protein could also make manufacturing large supplies of vaccine simpler.
A peptide toxin in ant venom mimics vertebrate EGF-like hormones to cause long-lasting hypersensitivity in mammals
by David A. Eagles, Natalie J. Saez, Bankala Krishnarjuna, Julia J. Bradford, Yanni K.-Y. Chin, Hana Starobova, Alexander Mueller, Melissa E. Reichelt, Eivind A. B. Undheim, Raymond S. Norton, Walter G. Thomas, Irina Vetter, Glenn F. King, Samuel D. Robinson in Proceedings of the National Academy of Sciences
Australian bull ants have evolved a venom molecule perfectly tuned to target one of their predators — the echidna — that also could have implications for people with long-term pain, University of Queensland researchers say.
Dr Sam Robinson and David Eagles from UQ’s Institute for Molecular Bioscience found a bull ant venom component that exploits a pain pathway in mammals, which they believe evolved to stop echidnas attacking the ant’s nests.
“Venoms are complex cocktails and while bull ant venom contains molecules similar to those found in honey bee stings which cause immediate pain, we also found an intriguing new molecule that was different,” Dr Robinson said.
Whilst searching databases for similar amino-acid sequences, Dr Robinson found that the molecule matched the sequence of mammalian hormones related to Epidermal Growth Factor (EGF), and of these, was most closely related to that of the echidna.
“We tested the venom molecule on mammalian EGF receptors and it was very potent — this convinced us that the venom molecule was there to defend against mammals,” he said. “We went on to show that while it didn’t cause direct pain, the molecule did cause long-lasting hypersensitivity.
“Many small carnivorous marsupials, like bandicoots, eat individual ants, but only the echidna is known to attack bull ant nests and target their young — we think that making the echidna sensitive to pain, in tandem with the immediate ‘bee-sting’ pain, may dissuade it from returning to the nests.
“You can see clearly in the ant’s DNA that it is producing a molecule that mimics a hormone of its natural enemy and is using it as a weapon against it — it brings to mind the ancient proverb ‘to know your enemy, you must become your enemy.’”
The team believes the links between EGF signalling and chronic pain are building momentum and is confident this study could inspire new ways to treat long-term pain. EGF-inhibitor drugs are readily available on the market and used in anti-cancer therapy to slow tumour growth, with evidence suggesting patients that take them experience less long-term pain.
“We hope that by highlighting the role of this signalling pathway in pain, we can encourage different strategies for pain treatment, especially long-term pain for which treatment is currently limited,” Dr Robinson said.
Molecular and cellular dynamics of early embryonic cell divisions in Volvox carteri
by Eva Laura von der Heyde, Armin Hallmann in The Plant Cell
Cell division ensures growth or renewal and is thus vital for all organisms. However, the process differs somewhat in animals, bacteria, fungi, plants, and algae. Until now, little was known about how cell division occurs in algae. Researchers at Bielefeld University have used confocal laser scanning microscopy (CLSM) to capture the very first high-resolution three-dimensional images of cell division in live cells of the microalga Volvox carteri, and have identified new cellular structures involved in the process. Professor Dr Armin Hallmann from the Faculty of Biology is leading the study.
The cell is the smallest organisational unit of life. It contains the necessary building blocks of life in a compact form and is the place where vital biochemical reactions take place. With the help of enzymes, substance and energy transformations take place, which are processes also known as metabolism. The cell interior is separated and thus protected from the environment by the cell membrane. Genetic material, the cell’s information store, is often located in the cell nucleus as DNA. When a cell divides by mitosis, it first divides its nucleus into two identical daughter nuclei with the same genetic material. Then the rest of the cell divides and two identical daughter cells are produced. The complex, genetically determined process of mitosis in particular must take place very precisely: the entire genetic material, divided into chromosomes, must be segregated accurately into the two daughter cell nuclei.
‘Cell division is one of the most fundamental processes in living organisms. It has basically been preserved over countless millions of years of evolution and can be found in all organisms,’ says Professor Dr Armin Hallmann, head of the Cellular and Developmental Biology of Plants research group at Bielefeld University. Yet the mechanisms of cell division in animals, fungi, plants, and algae each have characteristic features. The multicellular green alga Volvox carteri is a particularly interesting case in point. ‘It exhibits both animal and plant features in mitosis,’ says Hallmann. The researchers have now been able to clarify this phenomenon in their study. ‘Until now, researchers knew very little about the exact process of mitosis in this green alga.’
With their analyses, the scientists have been able to identify five characteristics that are crucial for mitosis in the microalga Volvox carteri. The first two features concern the envelope of the microalgal nucleus.
‘The nuclear envelope does not disintegrate at the beginning of mitosis, as is often the case, but remains in place until shortly before nuclear division is completed,’ says Armin Hallmann. ‘Instead, it becomes porous and permeable, so that cellular components are exchanged between the inside of the cell nucleus and the cytosol — a fluid that surrounds the cell nucleus. Hence, for a certain period of time, the cell nucleus loses its typical property as a confined reaction space, although the nuclear envelope is still present.’
The third feature is related to the centrosomes of the cell. These are cell structures that play a central role in the organisation of the mitotic spindle here. The mitotic spindle arranges the chromosomes in such a way that they can be segregated accurately into the two newly forming cell nuclei. ‘We have been able to show that the centrosomes play a crucial role in the mitosis of Volvox carteri even though they are located outside the nuclear envelope. They form the basic structure for organising the precise division of the genetic material with the help of the nuclear division spindle within the nuclear envelope. Until now, we only knew about an organisation of the spindle by centrosomes from cell division in animals,’ says Hallmann.
A fourth feature is the formation of a specific filamentous structure, the phycoplast, at the end of mitosis. After the cell nucleus has divided, the rest of the cell must also divide so that the newly formed cells can finally separate from each other. The dynamic phycoplast is the basis for the formation of a cleavage furrow which ultimately divides the cell, whereas plants form a different structure which ultimately leads to the formation of a separating, solid cell wall. ‘The special thing about algae is that the phycoplast is formed directly by recycling the nuclear division spindle, which is then no longer required,’ explains the scientist. Finally, the researchers were able to detect an enormous dynamic of the entire inner architecture of the cell as well as of the nuclear envelope during cell division.
The researchers were able to record the cell division processes by producing fluorescent proteins (proteins that glow when exposed to light) and tracking them in the cell using confocal laser scanning microscopy (CLSM). For the first time, scientists have succeeded in imaging the mitosis of microalgae in three dimensions in live cells and characterising it in detail, using Volvox carteri as an example.
‘The question we posed ourselves was: how exactly does cell division work in green algae? Which structures are involved in mitosis and what role do they play in the process?’ says first author Dr Eva Laura von der Heyde. She previously conducted research in Hallmann’s research group as a doctoral student and is now a postdoc. In order to be able to localise important proteins involved in cell division in the cell, their genes are linked to the gene of a fluorescent protein using molecular biology techniques. The proteins involved in cell division thus become fluorescent, which makes them distinguishable from all other proteins in the cell. ‘We used a special laser to excite different fluorescent proteins to glow. Using a confocal laser scanning microscope, we were able to detect the yellow-green glow of the microstructures formed by the proteins in live cells,’ says Eva Laura von der Heyde.
The researchers also recorded on video how the proteins move during cell division, how they form microstructures, and how these structures are rebuilt. In a time-lapse video, which condenses 30 minutes of mitosis to nine seconds and shows it simultaneously in ten optical section planes, it becomes clear how the centrosomes organise the formation of the nuclear division spindle and how the nuclear division spindle finally transforms into the phycoplast after the chromosomes have separated.
In the long term, Armin Hallmann and Eva Laura von der Heyde hope to be able to build on these new findings to learn more about the evolution of cell division. How did the different variants of cell division that are found today in animals, fungi, plants, and algae come about?
‘In evolution, the first land plants developed from primordial green algae. This is why the green alga Volvox carteri also possesses properties that it has in common with land plants growing today. However, it is striking that Volvox carteri also possesses properties that can be found in animals living today. Other of their characteristics are again only found in green algae. These special characteristics also make this model organism so important for our understanding of the evolution of cell division,’ says Hallmann.
ChREBP‐driven DNL and PNPLA3 Expression Induced by Liquid Fructose are Essential in the Production of Fatty Liver and Hypertriglyceridemia in a High‐Fat Diet‐Fed Rat Model
by Ana Magdalena Velázquez, Roger Bentanachs, Aleix Sala‐Vila, Iolanda Lázaro, Jose Rodríguez‐Morató, Rosa M. Sánchez, Marta Alegret, Núria Roglans, Juan Carlos Laguna in Molecular Nutrition & Food Research
A high-fat diet is not enough to cause short-term fatty liver disease. However, if this diet is combined with the intake of beverages sweetened with liquid fructose, the accumulation of fats in the liver accelerates and hypertriglyceridemia — a cardiovascular risk factor — can appear.
This is explained in a study on a mouse experimental model led by Professor Juan Carlos Laguna, from the Faculty of Pharmacy and Food Sciences, the Institute of Biomedicine of the University of Barcelona (IBUB) and the Physiopathology of Obesity and Nutrition Networking Biomedical Research Centre (CIBEROBN). The study counts on the collaboration of the researchers Aleix Sala-Vila and Iolanda Lázaro, from the Hospital del Mar Medical Research Institute (IMIM), and José Rodríguez-Morató, from IMIM-Hospital del Mar and MELIS-Pompeu Fabra University, among other experts.
Fructose is one of the most common sweeteners in the food industry. This simple sugar (monosaccharide) is industrially obtained from corn syrup, a product derived from this gramineae. With a great sweetener power and low production costs, fructose is used by the food industry to sweeten beverages, sauces and processed foods, despite the scientific evidence that associates it with metabolic diseases which are risk factors of cardiovascular pathologies.
According to the new study, the effect caused by fructose in the increase in the synthesis of fatty acids in the liver is more decisive than the external introduction of fats through the diet. “In high-fat diets which are supplemented with liquid fructose, this monosaccharide is able to induce an increase in the de novo lipogenesis — that is, the formation of fats through sugar — and an inhibition of the lipid oxidation in the liver,” says Professor Juan Carlos Laguna, from the Department of Pharmacology, Toxicology and Therapeutical Chemistry.
“In particular, fructose intake affects directly the expression and activity of the nuclear factor ChREBP. Once activated, this factor causes an increase in the expression of enzymes that control the hepatic synthesis of fatty acids,” he continues. “Parallelly, fructose intake reduces the activity of the nuclear receptor PPARalfa, which is the main responsible for the controlling of the expression of genes that code the enzymes involved in the fatty acid oxidation (mitochondrial and peroxisome) in the liver.”
As stated in the preclinical study, the combination of the saturated fat from dietary origin and the induction of the endogen synthesis of fatty acids is what causes the emergence of the fatty liver. “Moreover, we are describing for the first time that fructose — unlike high-fat diets — increases the expression of the PNPLA3 protein, associated with the appearance of hypertriglyceridemia, a risk factor for cardiovascular diseases,” notes Núria Roglans, co-author of the study and member of the mentioned Department.
Several epidemiologic studies related the consumption of drinks that are sweetened with fructose to the non-alcoholic fatty liver disease (NAFLD), a pathology for which there is no specific pharmacological therapy. In these patients, de novo lipogenesis contributes up to a 30% of the lipids accumulated in the liver, while in healthy people, this synthesis brings only the 5% of hepatic lipids.
The animal model characterized by the team will be of potential interest to study future drugs to treat the non-alcoholic fatty liver disease (NAFLD). “People with this pathology have a higher endogenous synthesis of lipids in the liver than healthy people. Therefore, the effects described in this study might appear in humans as well,” note the experts.
“Unfortunately, — they continue — the fatty liver is the starting point for more serious pathologies, such as steatohepatitis and cirrhosis. It is a practically asymptomatic pathology, although in some cases, some mild unspecific digestive disorders can appear. Apart from following a healthy diet and physical activity, there is no efficient treatment against this pathology for now.”
The effects described in the study are only observable if fructose is taken in its liquid form. “Regarding sweetened beverages, fructose is quickly absorbed and it reaches the liver massively, producing the described metabolic alterations. To find a comparison, we could talk about the appearance of a fructose overdose when this is taken in sweetened drinks,” notes the team.
“However, when we eat fruit, the amount of taken fructose is a lot lower compared to a sweetened drink. Also, the process of chewing it and the presence of other elements in the fruit, such as fiber, slows down the absorption of fructose and its arrival to the liver,” conclude the authors.
Transcriptional neighborhoods regulate transcript isoform lengths and expression levels
by Aaron N. Brooks, Amanda L. Hughes, Sandra Clauder-Münster, Leslie A. Mitchell, Jef D. Boeke, Lars M. Steinmetz in Science
Genomes are made up of thousands of individual pieces — genes — which are expressed at different levels. Researchers have shed light on how the placement of a gene affects its expression, as well as that of its neighbors.
The celebrated physicist Richard Feynman is credited with the quote, “What I cannot create, I do not understand.” As well as informing Feynman’s approach to theoretical physics, it’s a good way of describing the motivations of synthetic biologists, with their interest in building genomes from scratch. By designing and building synthetic genomes, they hope to better understand the code of life. Synthetic biology has been organised around the concept of using DNA sequences as ‘parts’ with reproducible functions. Now, through successful collaborations and the use of cutting-edge tools, EMBL’s Steinmetz Group has gained an important insight into the variation of gene expression that results from the position or context of these DNA parts within the genome.
Explaining the underlying question motivating the work, Amanda Hughes — co-lead author and postdoc in the Steinmetz Group — said, “In synthetic biology, you tend to break things down into modular, ‘plug-and-play’ parts. These are promotor parts, coding regions, and terminator parts. We wanted to test whether these pieces really are ‘plug-and-play,’ functioning the same way in any context, or whether their position affects their function. We wanted to better understand how the linear organisation of genes affects their functions and identify general design principles that could be applied to building genomes.”
This work was possible because of two key technologies: synthetic yeast strains from the Sc2.0 consortium and long-read direct RNA sequencing. The strains obtained from the Sc2.0 consortium included a design feature called ‘SCRaMbLE’ that provides the ability to rearrange genes into different locations at a previously unachievable scale. The expertise and tools available in the Genomics Core facility at EMBL, including Oxford Nanopore’s GridION, allowed the team to perform long-read direct RNA sequencing, permitting identification of both the start and end of RNA molecules and their assignment to particular rearrangements. The combination of these cutting-edge technologies was critical to measure full-length RNA molecules from genes across many contexts.
The paper showed that context — and in particular transcriptional context — alters the RNA output of a gene. Using long-read direct RNA sequencing, they were able to observe changes in the start, end, and amount of full-length RNA molecules expressed from DNA sequences that had been randomly rearranged in synthetic yeast genomes. Relocating a gene affected the length and abundance of its RNA output; however, these changes were not always explained by the new adjacent DNA sequence. It appeared to be transcription occurring around it, rather than the sequence itself, that altered a gene’s RNA output.
Gleaning general principles from such a large, stochastic dataset was not a trivial task, as the lead author Aaron Brooks explained: “To reach our conclusions, we had to observe genes in many alternative genetic contexts, which were present in the SCRaMbLE strains. Putting the pieces back together, however, was a big effort. We had to generate a massive sequencing dataset, which, in turn, required us to develop new software tools. We had to rely on sophisticated machine learning algorithms to help us understand the complex patterns we were observing.” Modelling a gene’s RNA output based on its new upstream and downstream contexts revealed that features related to surrounding transcriptional patterns predicted RNA boundaries and abundance. For example, if a gene was relocated next to a highly expressed neighbour, its expression also tended to increase.
In addition to illuminating the relationship between RNA abundance and neighbouring gene expression, the researchers also noted a compelling relationship between the end positions of RNAs of convergent genes (genes oriented with ends towards one another). Specifically, they found that the length of an RNA was affected by the proximity and abundance of neighbouring transcripts. Jef Boeke, co-author and Director of the Sc2.0 consortium remarked on these insights: “Deep transcriptional profiling combined with the genomic variations produced using [the] SCRaMbLE system have given us new insights into the flexibility of the yeast genome and pointed out that the rules of where transcripts end can be surprisingly context dependent.”
Ultimately, applying these findings, the researchers were able tune the length of RNA molecules by controlling transcription of a neighbouring gene. The team demonstrated that the lessons learned from studying the transcriptomes of SCRaMbLEd genomes can be applied to engineer genomes with desired functions. The study also proposes a new synthetic biology design concept that the researchers term ‘transcriptional embedding’ that could be used to reversibly tag an RNA, altering its stability, translation into protein, or even localisation. All of this could be accomplished, they believe, by controlling the expression of a convergent, neighbouring gene rather than the gene itself.
“The unbiased and high-throughput nature of the gene reshuffling approach used here leads us to discover functions of genomic sequences in different genomic contexts, something that previously was not possible at scale,” said Lars Steinmetz, group leader at EMBL. “This approach emphasises that context matters in regulating transcript ends — surprisingly, even permitting context-dependent predictions of transcript ends when genes are reshuffled to new locations. Ultimately, the work reveals that there is fine-tuned interlinked regulation between neighbouring genetic elements, spanning multiple genes that determines where transcripts start and stop. The ability to predict these interactions can inform key ‘design principles’ for genome construction; i.e. where are genes best located and how should they be positioned relative to each other. These insights advance tools for engineering transcripts without changing the sequence itself but by modulating neighbouring gene expression.” Their work adds to a growing repertoire of design principles that can be leveraged to realise a grand vision in synthetic biology: designing and building a genome from scratch.
Mussel Adhesive-Inspired Proteomimetic Polymer
by Or Berger, Claudia Battistella, Yusu Chen, Julia Oktawiec, Zofia E. Siwicka, Danielle Tullman-Ercek, Muzhou Wang, Nathan C. Gianneschi in Journal of the American Chemical Society
Those who have tried to pry a mussel from anything from wood to rock know how stubborn the underwater mollusks are — and their gluey secret has long captivated scientists. For years, researchers have attempted to replicate the extraordinary adhesive and its properties in the lab, targeting some of the eight proteins that mussels secrete and use to coat an organ called a foot that mussels use to attach to surfaces.
Now, using a novel method to arrange molecules, researchers at Northwestern University have created a material that performs even better than the glue they were trying to mimic. Their findings expand on how these protein-like polymers can be used as a platform to create new materials and therapeutics.
“The polymer could be used as an adhesive in a biomedical context, which means now you could stick it to a specific tissue in the body,” said Northwestern’s Nathan Gianneschi. “And keep other molecules nearby in one place, which would be useful in wound healing or repair.”
Gianneschi led the study and is the Jacob and Rosaline Cohn Professor of Chemistry in the Weinberg College of Arts and Sciences at Northwestern.
Proteins like those secreted by mussel feet exist around nature. Evolution has made a habit of creating these long, linear chains of amino acids that repeat over and over (called tandem repeat proteins, or TRPs). Appearing at times stretchy, strong and sticky, the protein frameworks show up in insect wings and legs, spider silk and mussel feet. Scientists know the exact primary sequences of amino acids that make up many such proteins, yet have trouble replicating the complicated natural process while still maintaining the extraordinary qualities.
The paper’s first author Or Berger, a postdoctoral researcher in Gianneschi’s lab who studies peptides — these very chains of amino acids — came with an idea for how to arrange amino acid building blocks differently to replicate the properties rather than directly copy the structure of mussel proteins. By taking the building block of one of the proteins (the repeat decapeptide, a 10-amino acid sequence that makes up the mussel foot protein), and plugging it into synthetic polymer, Berger thought the properties may be enhanced.
As associate director of the International Institute for Nanotechnology, Gianneschi has built much of his lab around the idea of mimicking proteins in function by using polymer chemistry. Within precision therapeutics, drug therapies like antibodies and other small molecules combat some diseases, where a nanocarrier is used to deliver a drug to a target more effectively. But Gianneschi says replicating proteins could approach biological problems differently, by changing interactions inside and between cells that are involved in the progression of disease, or between cells, tissues and materials.
“Proteins arrange amino acids as chains, but instead we took them and arranged them in parallel, on a dense synthetic polymer backbone,” Gianneschi said. “This was the same thing we have begun to do for controlling specific biological interactions, so the same platform technology we will use for future therapeutics has really become potentially interesting in materials science.”
The result was something that looks like a brush of peptides rather than looping together amino acids in a straight line as a chain. While the novel process may seem like adding an additional step, forming protein-like polymers (PLPs) skips several steps, requiring researchers to form peptides in a readily available synthesizer and insert them into the tightly packed backbone rather than going through tedious steps of protein expression. To test the new material’s efficacy, the researchers applied either the polymer material or the native mussel protein to glass plates. The researchers placed cells on the plates and then, after washing them, assessed how many cells were present, either attached or not, to gauge how well the materials performed. They found the PLP formed a cellular superglue, leaving the most cells attached compared to the native mixture and untreated plate.
“We actually didn’t mean to improve on the mussel’s properties,” Berger said. “We only meant to mimic it, but when we went and tested it in several different assays, we actually got better properties than the native material in these settings.”
The team hopes the model can be widely applicable across other proteins that repeat their sequence to gain function in a new way to replicate proteins. They hypothesize such a platform could perform better than their native counterparts because they are denser and scalable. Gianneschi said this is the first of many papers to discuss polymer-based protein mimics, and he is already thinking about applications for future materials. Resilin, for example, a stretchy protein found in insect legs and wings, could be used to make flexible drones and other robotics.
“When you talk about polymers, some people immediately think of plastic bags and bottles,” said Gianneschi said. “Instead, these are very functional, advanced precision materials, made accessible.”
MISC
Subscribe to Paradigm!
Medium. Twitter. Telegram. Telegram Chat. Reddit. LinkedIn.
Main Sources
Research articles
