Genetics biweekly vol.55, 11th April — 26th April
TL;DR
- DNA gyrase’s role in DNA entanglement resolution is unveiled, offering insights into biological mechanisms with potential clinical applications in bacterial infection and cancer treatment.
- RNA-targeting tool, Cas13d-NCS, facilitates efficient neutralization of RNA viruses within the cytoplasm, enhancing precision medicine and viral defense strategies.
- Genetic predisposition for higher muscle strength correlates with longer lifespan and reduced risk of common diseases, revealed by a large-scale international study.
- Proteasomes, traditionally viewed as cellular garbage disposals, show broader functions in nerve cells, hinting at novel roles beyond protein degradation.
- Genomic exploration sheds light on the evolution of multicellularity in macroalgae, revealing viral origins of genes crucial for cell adhesion and differentiation.
- Certain genetic variants may increase susceptibility to persistent HPV infections, potentially elevating the risk of cervical cancer.
- Regulatory mechanisms involving growth factor proteins influence branching patterns in organs like the lungs, as shown in mouse lung development studies.
- Understanding organelle genesis and structure is crucial for deciphering cell function and associated pathologies.
- Researchers uncover repair mechanisms during genetic transcription, advancing knowledge in DNA maintenance.
- Detailed protein structure of TAS2R14, a bitter taste receptor, is decoded, offering insights into bitter taste perception and potential drug development targeting taste receptors.
- And more!
Overview
Genetic technology is defined as the term that includes a range of activities concerned with the understanding of gene expression, advantages of natural genetic variation, modifying genes and transferring genes to new hosts. Genes are found in all living organisms and are transferred from one generation to the next. Gene technology encompasses several techniques including marker-assisted breeding, RNAi, and genetic modification. Only some gene technologies produce genetically modified organisms.
Modern genetic technologies like genome editing would not be possible without all the previous generations of genetic technologies that have enabled scientists to discover what genes are, what they do, and how DNA can be modified to add, remove, or replace genes. You can find major genetic technologies development milestones via the link.
Gene Technology Market
According to Global Genetic Engineering Market Research Report: The genetic engineering market is projected to grow from USD 1.36 Billion in 2023 to USD 7.73 Billion by 2032, exhibiting a compound annual growth rate (CAGR) of 24.20% during the forecast period (2023–2032). Growing demand for synthetic genes and increased use of CRISPR genome editing technology across various biotechnology industries are the key market drivers enhancing the market growth. In addition, it’s projected that increased government financing, a rise in the output of genetically modified crops, and an increase in genomics studies will all contribute to the expansion.
Latest Research
Structural basis of DNA crossover capture by Escherichia coli DNA gyrase
by Marlène Vayssières, Nils Marechal, Long Yun, Brian Lopez Duran, Naveen Kumar Murugasamy, Jonathan M. Fogg, Lynn Zechiedrich, Marc Nadal, Valérie Lamour in Science
Picture in your mind a traditional “landline” telephone with a coiled cord connecting the handset to the phone. The coiled telephone cord and the DNA double helix that stores the genetic material in every cell in the body have one thing in common; they both supercoil, or coil about themselves, and tangle in ways that can be difficult to undo. In the case of DNA, if this overwinding is not dealt with, essential processes such as copying DNA and cell division grind to a halt. Fortunately, cells have an ingenious solution to carefully regulate DNA supercoiling.
In this study, researchers at Baylor College of Medicine, Université de Strasbourg, Université Paris Cité and collaborating institutions reveal how DNA gyrase resolves DNA entanglements. The findings not only provide novel insights into this fundamental biological mechanism but also have potential practical applications. Gyrases are biomedical targets for the treatment of bacterial infections and the similar human versions of the enzymes are targets for many anti-cancer drugs. Better understanding of how gyrases work at the molecular level can potentially improve clinical treatments.
Some DNA supercoiling is essential to make DNA accessible to allow the cell to read and make copies of the genetic information, but either too little or too much supercoiling is detrimental. For example, the act of copying and reading DNA overwinds it ahead of the enzymes that read and copy the genetic code, interrupting the process. I
“We typically picture DNA as the straight double helix structure, but inside cells, DNA exists in supercoiled loops. Understanding the molecular interactions between the supercoils and the enzymes that participate in DNA functions has been technically challenging, so we typically use linear DNA molecules instead of coiled DNA to study the interactions,” said study author Dr. Lynn Zechiedrich, Kyle and Josephine Morrow Chair in Molecular Virology and Microbiology and professor of theVerna and Marrs McLean Department of Biochemistry and Molecular Pharmacology at Baylor College of Medicine. “One goal of our laboratory has been to study these interactions using a DNA structure that more closely mimics the actual supercoiled and looped DNA form present in living cells.”
After years of work, the Zechiedrich lab has created small loops of supercoiled DNA. In essence, they took the familiar straight linear DNA double helix and twisted it in either direction once, twice, three times or more and connected the ends together to form a loop. Their previous study looking at the 3-D structures of the resulting supercoiled minicircles revealed that these loops form a variety of shapes that they hypothesized enzymes such as gyrase would recognize.
In the current study, their hypothesis was proven correct. The team of researchers combined their expertise to study the interactions of DNA gyrase with DNA minicircles using recent technology advances in electron cryomicroscopy, an imaging technique that produces high-resolution 3-D views of large molecules, and other technologies.
“My lab has long been interested in understanding how molecular nanomachines operate in the cell. We have been studying DNA gyrases, very large enzymes that regulate DNA supercoiling,” said co-corresponding author Dr. Valérie Lamour, associate professor at the Institut de Génétique et de Biologie Moléculaire et Cellulaire, Université de Strasbourg. “Among other functions, supercoiling is the cell’s way of confining about 2 meters (6.6 feet) of linear DNA into the microscopic nucleus of the cell.”
As the DNA supercoils inside the nucleus, it twists and folds in different forms. Imagine twisting that telephone cord mentioned at the beginning, several times on itself. It will overwind and form a loop by crossing over DNA chains, tightening the structure.
“We found, just as we had hypothesized, that gyrase is attracted to the supercoiled minicircle and places itself in the inside of this supercoiled loop,” said co-author, Dr. Jonathan Fogg, senior staff scientist of molecular virology and microbiology, and biochemistry and molecular pharmacology in the Zechiedrich lab.
“This is the first step of the mechanism that prompts the enzyme for resolving DNA entanglements,” Lamour said.
“DNA gyrase, now surrounded by a tightly supercoiled loop, will cut one DNA helix in the loop, pass the other DNA helix through the cut in the other, and reseal the break, which relaxes the overwinding and eases the tangles, regulating DNA supercoiling to control DNA activity,” Zechiedrich said. “Imagine watching the rodeo. Like roping cattle with a lasso, supercoiled looped DNA captures gyrase in the first step. Gyrase then cuts one double-helix of the DNA lasso and passes the other helix through the break to get free.”
Co-corresponding author, Dr. Marc Nadal, professor at the École Normale in Paris confirmed the observation of the path of the DNA wrapped in the loop around gyrase using magnetic tweezers, a biophysical technique that allows to measure the deformation and fluctuations in the length of a single molecule of DNA. Observing a single molecule provides information that is often obscured when looking at thousands of molecules in traditional so-called “ensemble” experiments in a test tube.
Interestingly, the “DNA strand inversion model” for gyrase activity was proposed in 1979 by Drs. Patrick O. Brown and the late Nicholas R. Cozzarelli, well before researchers had access to supercoiled minicircles or the 3-D molecular structure of the enzyme. “It’s especially meaningful to me that 45 years later, we finally provide experimental evidence supporting their hypothesis because Nick was my postdoctoral mentor,” Zechiedrich said.
“This work opens a myriad of perspectives to study the mechanism of this conserved class of enzymes, which are of great clinical value,” Lamour said.
“This work supports new ideas on how DNA activities are regulated. We propose that DNA is not a passive biomolecule acted upon by enzymes, but an active one that uses supercoiling, looping and 3-D shapes to direct accessibility of enzymes such as gyrase to specific DNA sequences in a variety of situations, which will likely impact cellular responses to antibiotics or other treatments,” Fogg said.
Engineered, nucleocytoplasmic shuttling Cas13d enables highly efficient cytosolic RNA targeting
by Christoph Gruber, Lea Krautner, Valter Bergant, Vincent Grass, Zhe Ma, Lara Rheinemann, Ariane Krus, Friederike Reinhardt, Lyupka Mazneykova, Marianne Rocha-Hasler, Dong-Jiunn Jeffery Truong, Gil Gregor Westmeyer, Andreas Pichlmair, Gregor Ebert, Florian Giesert, Wolfgang Wurst in Cell Discovery
The rise of RNA viruses like SARS-CoV-2 highlights the need for new ways to fight them. RNA-targeting tools like CRISPR/Cas13 are powerful but inefficient in the cytoplasm of cells, where many RNA viruses replicate. Scientists from Helmholtz Munich and the Technical University of Munich (TUM) have devised a solution: Cas13d-NCS. This new molecular tool allows CRISPR RNA molecules that are located within the nucleus of a cell to move to the cytoplasm, making it highly effective at neutralizing RNA viruses. This advancement opens doors for precision medicine and proactive viral defense strategies. The findings were published in Cell Discovery.
As the world prepares for future and ongoing global health threats from RNA viruses such as the SARS-CoV-2 pandemic, breakthrough advances in antiviral development are becoming a critical weapon in the fight against these infectious diseases. At the heart of this innovation is the exploration of CRISPR/Cas13 systems, which are known for their programmable capabilities to manipulate RNAs and have become indispensable tools for various RNA targeting applications. However, a significant obstacle has hampered the effectiveness of Cas13d: its restriction to the nucleus of mammalian cells. This drastically limited its utility in cytosolic applications, such as programmable antiviral therapies.
A scientific team working with Prof. Wolfgang Wurst, Dr. Christoph Gruber and Dr. Florian Giesert (Institute of Developmental Genetics at Helmholtz Munich and Chair of Developmental Genetics at TUM), which intensively collaborated with the teams of Dr. Gregor Ebert (Institute of Virology at Helmholtz Munich and at TUM) and of Prof. Andreas Pichlmair (Institute of Virology at TUM), successfully overcame this challenge associated with the cytosolic inactivity of Cas13d. Through careful screening and optimization, the researchers developed a transformative solution: Cas13d-NCS, a novel system capable of transferring nuclear crRNAs into the cytosol. crRNAs, or CRISPR RNAs, are short RNA molecules that guide the CRISPR-Cas complex to specific target sequences for precise modifications. In the cytosol, the protein/crRNA complex targets complementary RNAs and degrades them with unprecedented precision. With remarkable efficiency, Cas13d-NCS outperforms its predecessors in degrading mRNA targets and neutralizing self-replicating RNA, including replicating sequences of Venezuelan equine encephalitis (VEE) RNA virus and several variants of SARS-CoV-2, unlocking the full potential of Cas13d as a programmable antiviral-tool.
This important achievement represents a significant step towards combating pandemics and strengthening defenses against future outbreaks. The impact of the study goes beyond traditional antiviral strategies and CRISPR systems and ushers in a new era of precision medicine by enabling the strategic manipulation of subcellular localization of CRISPR-based interventions.
“This breakthrough in antiviral development with Cas13d-NCS marks a pivotal moment in our ongoing battle against RNA viruses,” says Prof. Wolfgang Wurst, coordinator of the study. “This achievement showcases the power of collaborative innovation and human ingenuity in our quest for a healthier and more resilient world.”
Genome-Wide Polygenic Score for Muscle Strength Predicts Risk for Common Diseases and Lifespan: A Prospective Cohort Study
by Päivi Herranen, Kaisa Koivunen, Teemu Palviainen, Urho M Kujala, Samuli Ripatti, Jaakko Kaprio, Elina Sillanpää, FinnGen in The Journals of Gerontology, Series A: Biological Sciences and Medical Sciences
A study conducted at the Faculty of Sport and Health Sciences at the University of Jyväskylä showed that a genetic predisposition for higher muscle strength predicts a longer lifespan and a lower risk for developing common diseases. This is the most comprehensive international study to date on hereditary muscle strength and its relationship to morbidity. The genome and health data of more than 340,000 Finns was used in the research.
Muscle strength, especially hand grip strength, can indicate an individual’s physiological resources to protect against age-related diseases and disabilities, as well as their ability to cope with them. Age-related loss of muscle strength is individual and influenced not only by lifestyle but also by genetics.
The study revealed that individuals with a genetic predisposition for higher muscle strength have a slightly lower risk for common noncommunicable diseases and premature mortality. However, it did not predict better survival after acute adverse health events compared to the time before illness onset.
“It seems that a genetic predisposition for higher muscle strength reflects more on an individual’s intrinsic ability to resist and protect oneself against pathological changes that occur during aging than the ability to recover or completely bounce back after severe adversity,” says doctoral researcher Päivi Herranen from the Faculty of Sport and Health Sciences.
Muscle strength is a multifactorial trait influenced by lifestyle and environmental factors but also by numerous genetic variants, each with a very small effect on muscle strength. In this study, the genetic predisposition for muscle strength was defined by constructing a polygenic score for muscle strength, which summarizes the effects of hundreds of thousands of genetic variants into a single score. The polygenic score makes it possible to compare participants with an exceptionally high or low genetic predisposition for muscle strength, and to investigate associations with inherited muscle strength and other phenotypes, in this case, common diseases.
“In this study, we were able to utilize both genetic information and health outcomes from over 340,000 Finnish men and women,” Herranen explains. “To our knowledge, this is the first study to investigate the association between a genetic predisposition for muscle strength and various diseases on this scale.”
Information about the genetic predisposition for muscle strength could be used alongside traditional risk assessment in identifying individuals who are at particularly high risk of common diseases and health adversities. However, further research on the topic is still needed.
“Based on these results, we cannot say how lifestyle factors, such as physical activity, modify an individual’s intrinsic ability to resist diseases and whether their impact on health differs among individuals due to genetics,” Herranen notes.
The study utilized the internationally unique FinnGen dataset, compiled through the collaboration of Finnish biobanks. The dataset consisted of 342,443 Finns who had given their consent and provided a biobank sample. The participants were aged 40 to 108 years, and 53% of them were women. The diagnoses selected for the study were based on the leading causes of death and the most significant noncommunicable diseases in Finland. Selected diagnoses included the most common cardiometabolic and pulmonary diseases, musculoskeletal and connective tissue diseases, falls and fractures, mental health and cognitive disorders, cancers, as well as overall mortality and mortality from cardiovascular diseases.
The nociceptive activity of peripheral sensory neurons is modulated by the neuronal membrane proteasome
by Eric Villalón Landeros, Samuel C. Kho, Taylor R. Church, Anna Brennan, Fulya Türker, Michael Delannoy, Michael J. Caterina, Seth S. Margolis in Cell Reports
The typical job of the proteasome, the garbage disposal of the cell, is to grind down proteins into smaller bits and recycle some of those bits and parts. That’s still the case, for the most part, but, Johns Hopkins Medicine researchers, studying nerve cells grown in the lab and mice, say that the proteasome’s role may go well beyond that.
Its additional role, say the researchers, may shift from trash sorter to signal messenger in dorsal root ganglion neurons — cells that convey sensory signals from nerve cells close to the skin to the central nervous system. Results of their experiments show that proteasomes may help those specialized neurons sense the surrounding environment, send signals to each other and potentially differentiate between sensing pain and itch, a finding that could help scientists better understand these sensory processes and new targets for treating pain and other sensory problems.
“Neurons live next to each other for a long time, and they need ways to communicate with each other about what they’re doing and who they are,” says Seth S. Margolis, Ph.D., associate professor of biological chemistry at the Johns Hopkins University School of Medicine. “Proteasomes in the membrane of neurons may help the cells fine tune this messaging process.”
“Proteasomes are more complicated than they appear,” says Margolis. He and his colleagues first found proteasomes in the plasma membranes of central nervous system neurons in mice in 2017, which they dubbed neuronal membrane proteasomes, and have continued studying how these special proteasomes promote messaging, or crosstalk, among neurons.
At the time, Margolis’ focus was on the central nervous system, encompassing the brain and spinal cord. But later, he collaborated with neurobiologist Eric Villalón Landeros, Ph.D., postdoctoral fellow in Margolis’ laboratory at Johns Hopkins, whose work focuses on the peripheral nervous system, the network of neurons running through the rest of the body, closer to the skin, capturing sensory information from the environment. Margolis and Villalón Landeros wondered whether proteasomes could be found in peripheral neurons, and if so, what they might do.
Using mouse antibodies that glom on to proteasomes, and other methods, the investigators found the proteasomes on the surface of neurons in the spinal cord, dorsal root ganglia, sciatic nerve and peripheral nerves innervating skin. The researchers were also able to find proteasomes in the same type of peripheral neurons grown in laboratory culture dishes. To understand the proteasome’s function in peripheral sensory neurons, the researchers gave mice biotin-epoxomicin, a cell membrane-impermeable proteasome inhibitor that blocks the function of neuronal membrane proteasomes. Then, they performed classic sensory tests. The researchers found that the mice that got injections of the proteasome-blocking drug biotin-epoxomicin on one side of the body were between 25% to 50% slower than the other side to respond to sensory tests.
“This suggests that membrane proteasomes are important for sensation, and they must be facilitating this at the signaling level,” says Margolis.
The researchers used single cell sequencing technology to determine that membrane proteasomes were expressed in a subpopulation of neurons involved in itch sensation and known to be sensitive to histamine, an immune system compound that launches an animal’s (including human’s) response to allergens.
In laboratory culture dishes, the researchers stimulated both itch-related and non-itch related neurons and blocked their membrane proteasomes with biotin-epoxomicin. This resulted in changes to activity in all of the cells. “Blocking proteasomes seems to have an activity-modulatory effect across all the cells, despite being expressed in a subpopulation, suggesting that proteasomes facilitate a kind of cross talk between these cells,” says Margolis. Proteasome blockers, including one called Velcade, are currently used to treat certain types of cancer.
Villalón Landeros and Margolis plan to continue working together to determine how neuronal membrane proteasomes function in sensory neurons and in sensing pain versus itch. “We want to see if we can manipulate neuronal membrane proteasomes to have a different outcome on pain and itch sensation,” says Villalón Landeros.
Macroalgal deep genomics illuminate multiple paths to aquatic, photosynthetic multicellularity
by David R. Nelson, Alexandra Mystikou, Ashish Jaiswal, Cecilia Rad-Menendez, Michael J. Preston, Frederik De Boever, Diana C. El Assal, Sarah Daakour, Michael W. Lomas, Jean-Claude Twizere, David H. Green, William C. Ratcliff, Kourosh Salehi-Ashtiani in Molecular Plant
A deep dive into macroalgae genetics has uncovered the genetic underpinnings that enabled macroalgae, or “seaweed,” to evolve multicellularity. Three lineages of macroalgae developed multicellularity independently and during very different time periods by acquiring genes that enable cell adhesion, extracellular matrix formation, and cell differentiation, researchers report. Surprisingly, many of these multicellular-enabling genes had viral origins. The study, which increased the total number of sequenced macroalgal genomes from 14 to 124, is the first to investigate macroalgal evolution through the lens of genomics.
“This is a big genomic resource that will open the door for many more studies,” says co-first author and algal biologist Alexandra Mystikou of New York University Abu Dhabi and the Technology Innovation Institute, United Arab Emirates. “Macroalgae play an important role in global climate regulation and ecosystems, and they have numerous commercial and ecoengineering applications, but until now, there wasn’t a lot of information about their genomes.”
Macroalgae live in both fresh and seawater and are complex multicellular organisms with distinct organs and tissues, in contrast to microalgae, which are microscopic and unicellular. There are three main groups of macroalgae — red (Rhodophyta), green (Chlorophyta), and brown (Ochrophyta) — that independently evolved multicellularity at very different times and in very different environmental conditions. Rhodophytes and Chlorophytes both evolved multicellularity over a billion years ago, while Ochrophytes only became multicellular in the past 200,000 years.
To investigate the evolution of macroalgal multicellularity, the researchers sequenced 110 new macroalgal genomes from 105 different species originating from fresh and saltwater habitats in diverse geographies and climates.
The researchers identified several metabolic pathways that distinguish macroalgae from microalgae, some of which may be responsible for the success of invasive macroalgal species. Many of these metabolic genes appear to have been donated by algae-infecting viruses, and genes with a viral origin were especially prevalent in the more recently evolved brown algae.
They found that macroalgae acquired many new genes that are not present in microalgae on their road to multicellularity. For all three lineages, key acquisitions included genes involved in cell adhesion (which enables cells to stick together), cell differentiation (which allows different cells to develop specialized functions), cell communication, and inter-cellular transport.
“Many brown algal genes associated with multicellular functions had signature motifs that were only otherwise present in the viruses that infect them,” says co-first author and bioinformatician David Nelson of New York University Abu Dhabi. “It’s kind of a wild theory that’s only been hinted at in the past, but from our data it looks like these horizontally transferred genes were critical factors for evolving multicellularity in the brown algae.”
The team also identified other features that were distinct between the macroalgal lineages. They observed much more diversity between different species of Rhodophyte, which evolved multicellularity first and have thus had longer to diverge. They also found that Chlorophytes share many genomic features with land plants, suggesting that these genes may have already been present in the last common ancestor of Chlorophytes and plants.
“By no means have we exhaustively explored all that there is in these genomes,” says senior author and systems biologist Kourosh Salehi-Ashtiani of New York University Abu Dhabi. “There is a ton of information that we have not touched in the present paper that can be mined by whoever who is interested.”
The researchers are already digging into the dataset to investigate environmental and habitat adaptations amongst macroalgae. In future, they hope to sequence and analyze even more macroalgal genomes.
“We want to explore some of these features in more detail, meaning more genomes if we can get our hands on them,” says Salehi-Ashtiani.
Genome, HLA and polygenic risk score analyses for prevalent and persistent cervical human papillomavirus (HPV) infections
by Sally N. Adebamowo, Adebowale Adeyemo, et al in European Journal of Human Genetics
Human papillomavirus (HPV) is the second most common cancer-causing virus, accounting for 690,000 cervical and other cancers each year worldwide. While the immune system usually clears HPV infections, those that persist can lead to cancer, and a new finding suggests that certain women may have a genetic susceptibility for persistent or frequent HPV infections. These genetic variants, identified in a study led by University of Maryland School of Medicine researchers, could raise a woman’s risk of getting cervical cancer from a high-risk HPV infection.
The research team conducted a genome-wide association study of high-risk HPV infections in a cohort of over 10,000 women, whose data were collected as part of the African Collaborative Center for Microbiome and Genomics Research (ACCME) cohort study. A total of 903 of the participants had high-risk HPV infections when the study began, with 224 participants having HPV infections that resolved, and 679 having persistent HPV infections. More than 9,800 HPV-negative women from the ACCME study served as controls.
“We found certain genetic variants were associated with having high-risk HPV infections, while other variants and human leukocyte antigen (HLA) genes were associated with persistent infections, which increase the risk of developing cervical cancer,” said study leader Sally N. Adebamowo, MBBS, MSc, ScD, Associate Professor of Epidemiology & Public Health at UMSOM. “This is a critical finding that suggests genetic underpinnings for cervical cancer risk. It is the first sufficiently powered genome-wide association study of cervical high-risk HPV infections. Our polygenic risk score models should be evaluated in other populations.”
Specifically, she and her colleagues found that the top variant associated with prevalent high-risk HPV infection was rs116471799, on the fourth chromosome near the LDB2 gene, which encodes for proteins. They found persistent HPV was associated with variants clustered around the TPTE2, a protein encoding gene associated with gallbladder cancer. The genes SMAD2 and CDH12 were also associated with persistent high risk HPV infections, and significant polygenic risk scores. Together the findings enabled the research team to develop polygenic risk scores to determine the likelihood that a certain genetic profile would increase the risk of having prevalent or persistent HPV infections.
“Our findings can be used for risk stratification of persistent high-risk HPV infections for precision or personalized cervical cancer prevention. We hope to conduct long-term studies on the integration of PRS and genomic risk factors into the continuum of cervical cancer prevention,” said study corresponding author Clement A. Adebamowo, BM, ChB, ScD, Professor of Epidemiology & Public Health at UMSOM.
A recent report from the American Cancer Society found that cervical cancer among women ages 30 to 44 rose almost 2 percent a year from 2012 to 2019. This is after a big decline in cervical cancer rates over the past half-century due to early detection from Pap smears and HPV screening tests. In addition, rates of cervical cancer, have steadily declined among younger women who were among the first to benefit from HPV vaccines, which were approved for use in 2006.
In the U.S., more than half of women diagnosed with cervical cancer have never been screened or were not screened in the last five years, according to the Centers for Disease Control and Prevention. In Nigeria, only a small percentage of women have access to the HPV vaccine, so those included in the study were largely unvaccinated.
“The results provide insight into the role of antigen processing and presentation, and HLA-DRB1 alleles in immune surveillance and persistence of high-risk HPV infections,” said Mark T. Gladwin, MD, who is the John Z. and Akiko K. Bowers Distinguished Professor and Dean, UMSOM, and Vice President for Medical Affairs, University of Maryland, Baltimore. “Confirmatory studies are crucial to validate these important findings in other populations, with the goal of reducing the burden of high-risk HPV related diseases on global health.”
ERK-mediated curvature feedback regulates branching morphogenesis in lung epithelial tissue
by Tsuyoshi Hirashima, Michiyuki Matsuda in Current Biology
Branching patterns are prevalent in our natural environment and the human body, such as in the lungs and kidneys. For example, specific genes that express growth factor proteins are known to influence the development of the lungs’ complex branches. Still, until now the mechanics behind this phenomenon have remained a mystery.
Kyoto University researchers have unveiled a regulatory system linking signal, force, and shape in mouse lung structure development. The team recognized that the signal protein ERK plays an active role in causing growing lung tissue to curve.
“ERK signals the cell tissue to stretch outward to smoothen its curve,” says Tsuyoshi Hirashima, formerly of KyotoU’s Graduate School of Biostudies and now at the National University of Singapore’s Mechanobiology Institute.
As if choreographed, a mix of chemical signals triggers the cellular mechanics of the lungs of a mouse embryo, resulting in the development of intricate branching patterns.
Mechanobiology has gained increasing attention in recent years, focusing on cell- and tissue-generated forces, intracellular signaling, and their combined interactions with geometric factors that influence morphogenesis.
“ERK’s surprisingly precise signaling response to lung tissue curvature was enlightening. It suggests an elegantly more nuanced developmental orchestration than previously thought,” reflects Hirashima.
Utilizing advanced microscopic imaging techniques, Hirashima’s team observed how ERK behaves in developing lungs in real time by combining a fluorescent biosensor — for quantifying the ERK activity in living cells — with two-photon microscopy, which captures tissue cell and molecular activities in 3D. Results showed that ERK mediates curvature sensing and force generation in epithelial cells, causing a negative feedback loop and a repetitive branching pattern.
“We are particularly interested in exploring how disruptions in this signal-force-shape system might contribute to physiological abnormalities or diseases,” says Hirashima.
These ideas may apply to the developmental processes of other organs and the formation of mouse lungs, a realization that calls for further exploration of fundamental principles.
“Ultimately, our findings offer a deeper understanding of the novel principles of biological regulatory systems, with promising applications in regenerative medicine and organoid research,” concludes Hirashima.
Time-series reconstruction of the molecular architecture of human centriole assembly
by Marine H. Laporte, Davide Gambarotto, Éloïse Bertiaux, Lorène Bournonville, Vincent Louvel, José M. Nunes, Susanne Borgers, Virginie Hamel, Paul Guichard in Cell
Cells contain various specialised structures — such as the nucleus, mitochondria or peroxisomes — known as “organelles’’. Tracing their genesis and determining their structure is fundamental to understanding cell function and the pathologies linked to their dysfunction. Scientists at the University of Geneva (UNIGE) have combined high resolution microscopy and kinematic reconstruction techniques to visualise, in motion, the genesis of the human centriole. This organelle, essential to the organisation of the cell skeleton, is associated — in case of dysfunction — with certain cancers, brain disorders or retinal diseases. This work elucidates the complexities of centriole assembly. It also opens up many new avenues for the study of other cell organelles.
Organelle genesis proceeds according to a precise sequence of successive protein recruitment events. Visualising this assembly in real time provides a better understanding of the role of these proteins in organelle structure or function. However, obtaining a video sequence with sufficient resolution to distinguish such complex microscopic components faces a number of technical limitations.
This is particularly true of the centriole. This organelle, measuring less than 500 nanometers (half a thousandth of a millimeter), is constituted of around 100 different proteins organised into six substructural domains. Until a few years ago, it was impossible to visualise the structure of the centriole in detail. The laboratory of Paul Guichard and Virginie Hamel, co-directors of research in the Department of Molecular and Cellular Biology at the UNIGE Faculty of Science, has changed this situation by using the technique of expansion microscopy. This cutting-edge technique enables cells and their constituents to be progressively inflated without being deformed, so that they can then be observed — using conventional microscopes — with very high resolution.
Obtaining images of the centriole with such high resolution enables the exact location of proteins at a given time but gives no information on the order of appearance of substructural domains or of individual proteins. Marine Laporte, a former research and teaching fellow in the UNIGE group and first author of the study, used expansion microscopy to analyse the location of 24 proteins in the six domains in over a thousand centrioles at different stages of growth.
‘’This very tedious work was followed by a pseudo-temporal kinematic reconstruction. In other words, we were able to put these thousands of images taken at random during centriole biogenesis back into chronological order, to reconstruct the various stages in the formation of centriole substructures, using a computer analysis we developed,’’ explains Virginie Hamel, co-leader of the study.
This unique approach, which combines the very high resolution of expansion microscopy and kinematic reconstruction, has enabled us to model the first 4D assembly of the human centriole. ‘’Our work will not only deepen our understanding of centriole formation, but also open up incredible prospects in cellular and molecular biology, since this method can be applied to other macromolecules and cellular structures to study their assembly in space and time,’’ concludes Paul Guichard.
Transcription-coupled repair of DNA–protein cross-links depends on CSA and CSB
by Christopher J. Carnie, Aleida C. Acampora, Aldo S. Bader, Chimeg Erdenebat, Shubo Zhao, Elnatan Bitensky, Diana van den Heuvel, Avital Parnas, Vipul Gupta, Giuseppina D’Alessandro, Matylda Sczaniecka-Clift, Pedro Weickert, Fatih Aygenli, Maximilian J. Götz, Jacqueline Cordes, Isabel Esain-Garcia, Larry Melidis, Annelotte P. Wondergem, Simon Lam, Maria S. Robles, Shankar Balasubramanian, Sheera Adar, Martijn S. Luijsterburg, Stephen P. Jackson, Julian Stingele in Nature Cell Biology
Cockayne syndrome is a severe autosomal recessive disorder caused by defective DNA repair mechanisms. People with the disease have much reduced life expectancy and suffer from facial deformities; growth failure; neurological, cognitive, and sensory impairments; bone, joint, and muscle deformities; kidney problems; and premature aging. Like xeroderma pigmentosum (XP), Cockayne syndrome (CS) is a disease where elements of nucleotide excision repair (NER) do not work properly. The purpose of this repair mechanism is to remove DNA damage caused by ultraviolet (UV) light, chemicals, and various other environmental factors.
Researchers from the group of biochemist Professor Julian Stingele from LMU’s Gene Center Munich have now uncovered important details about the role of the CSB/ERCC6 and CSA/ERCC8 genes involved in Cockayne syndrome. These genes encode two enzymes associated with DNA repair.
“Our data point to a new, previously unknown function of these two genes and their gene products in the repair of covalent DNA-protein interactions in the course of transcription,” reports Stingele, referring to the cytotoxic, biologically undesirable crosslinking of proteins to DNA.
In collaboration with researchers from the University of Cambridge, the scientists demonstrated that DNA-protein crosslinks present a physical obstacle to further transcription. Arresting transcription brings CS proteins to the blockade sites.
“Our results indicate that CSB and CSA then initiate the transcription-coupled repair of the toxic DNA-protein crosslinks,” says Stingele. “This previously unrecognized cellular function of CS proteins leads to the marking of the DNA damage — and thence to its enzymatic breakdown.”
The study also revealed that this newly discovered function of CS proteins works independently of classic TC-NER (transcription-coupled nucleotide excision repair) enzymes, which are deployed, among other things, for repairing DNA damage caused by UV light — and the absence of which leads to xeroderma pigmentosum. “The fact that CS proteins have additional functions is noteworthy. This discovery could help to explain the pathological differences between xeroderma pigmentosum and Cockayne syndrome,” says Stingele. CS is a more severe and more multifaceted disorder than XP, with complex and incompletely understood causes. As their next step, Stingele’s research group plans to decode the exact process of CS-protein-mediated repair.
Bitter taste receptor activation by cholesterol and an intracellular tastant
by Yoojoong Kim, Ryan H. Gumpper, Yongfeng Liu, D. Dewran Kocak, Yan Xiong, Can Cao, Zhijie Deng, Brian E. Krumm, Manish K. Jain, Shicheng Zhang, Jian Jin, Bryan L. Roth in Nature
Humans can sense five different tastes: sour, sweet, umami, bitter, and salty, using specialized sensors on our tongues called taste receptors. Other than allowing us to enjoy delicious foods, the sensation of taste allows us to determine the chemical makeup of food and prevents us from consuming toxic substances.
Researchers at the UNC School of Medicine, including Bryan Roth, MD, PhD, the Michael Hooker Distinguished Professor of Pharmacology, and Yoojoong Kim, PhD, a postdoctoral researcher in the Roth Lab, recently set out to address one very basic question: “How exactly do we perceive bitter taste?”
A new study reveals the detailed protein structure of the TAS2R14 bitter taste receptor. In addition to solving the structure of this taste receptor, the researchers were also able to determine where bitter-tasting substances bind to TAS2R14 and how they activate them, allowing us to taste bitter substances.
“Scientists know very little about the structural make up of sweet, bitter, and umami taste receptors,” said Kim. “Using a combination of biochemical and computational methods, we now know the structure of the bitter taste receptor TAS2R14 and the mechanisms that initializes the sensation of bitter taste in our tongues.”
This detailed information is important for discovering and designing drug candidates that can directly regulate taste receptors, with the potential to treat metabolic diseases such as obesity and diabetes.
TAS2R14s are members of the G protein-coupled receptor (GPCR) family of bitter taste receptors. The receptors are attached to a protein known as a G protein. TAS2R14 stands out from the others in its family because it can identify more than 100 distinct substances known as bitter tastants.
Researchers found that when bitter tastants come into contact with TAS2R14 receptors, the chemicals wedge themselves into to a specific spot on the receptor called an allosteric site, this causes the protein to change its shape, activating the attached G protein. This triggers a series of biochemical reactions within the taste receptor cell, leading to activation of the receptor, which can then send signals to tiny nerve fibers — through the cranial nerves in the face — to an area of the brain called the gustatory cortex. It is here where the brain processes and perceives the signals as bitterness. And of course, this complex signaling system occurs almost instantaneously.
While working to define its structure, researchers found another unique feature of TAS2R14 — that cholesterol is giving it a helping hand in its activation.
“Cholesterol was residing in another binding site called the orthosteric pocket in TAS2R14, while the bitter tastant binds to the allosteric site,” said Kim. “Through molecular dynamics simulations, we also found that the cholesterol puts the receptor in a semi-active state, so it can be easily activated by the bitter tastant.”
Bile acids, which are created in the liver, have similar chemical structures with cholesterol. Previous studies have suggested that bile acids can bind and activate TAS2R14, but little is known about how and where they bind in the receptor. Using their newfound structure, researchers found that bile acids might be binding to the same orthosteric pocket as cholesterol. While the exact role of bile acid or cholesterol in TAS2R14 remains unknown, it may play a role in the metabolism of these substances or in relation to metabolic disorders such as obesity or diabetes.
The discovery of this novel allosteric binding site for bitter tasting substances is unique. The allosteric binding region is located between TAS2R14 and its coupled G protein is called G-protein alpha. This region is critical to form a signaling complex, which helps to transfer the signal from the taste receptor to the G-protein to the taste receptor cells.
“In the future, this structure will be key to discovering and designing drug candidates that can directly regulate G proteins through the allosteric sites,” said Kim. “We also have the ability to affect specific G-protein subtypes, like G-protein alpha or G-protein beta, rather than other G-protein pathways that we don’t want to cause any other side effects.”
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