TL;DR
- By modelling the kinetochore from scratch, researchers get a step closer to creating artificial chromosomes.
- Researchers offer a new understanding of how gene activity directs plant growth, and how quickly plants respond to their environment — with shifting light conditions triggering molecular changes in as little as five minutes. The findings provide insights into how to increase yield and safeguard world food production as climate change shrinks the planet’s arable land.
- New research shows that in order to survive life threatening injuries, cancer cells use a technique in which they eat parts of the membrane surrounding them.
- A connective tissue protein known to support the framework of organs also encourages immune responses that fight bacterial infections, while restraining responses that can be deadly in the condition called sepsis.
- An international study has elucidated the structure of a protein that is required for the assembly and stability of photosynthetic membranes.
- Hereditary information is passed from parent to offspring in the genetic code, DNA, and epigenetically through chemically induced modifications around the DNA. New research has uncovered a mechanism which adjusts these modifications, altering the way information beyond the genetic code is passed down the generations.
- When regions of the human genome where the DNA can fold into unusual three-dimensional structures called G-quadruplexes (G4s) are located in regulatory sequences or other functional, but non-protein coding, regions of the genome, they are maintained by selection, are more common, and their unusual structures are more stable. Together, these lines of evidence suggest that G4 elements should be added to the list of functional elements of the genome.
- A new technique called sci-Space, combined with data from other technologies, could lead to four-dimensional atlases of gene expression across diverse cells during embryonic development of mammals. Such atlases would map how the gene transcripts in individual cells reflect the passage of time, cell lineages, cell migration, and location on the developing embryo. They would also help illuminate the spatial regulation of gene expression.
- Zeolites are extremely porous materials: Ten grams can have an internal surface area the size of a soccer field. Their cavities make them useful in catalyzing chemical reactions and thus saving energy. An international research team has now made new findings regarding the role of water molecules in these processes. One important application is the conversion of biomass into biofuel.
- Researchers have succeeded in developing a method to label mRNA molecules, and thereby follow, in real time, their path through cells, using a microscope — without affecting their properties or subsequent activity. The breakthrough could be of great importance in facilitating the development of new RNA-based medicines.
- 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
Assembly principles and stoichiometry of a complete human kinetochore module
by Kai Walstein, Arsen Petrovic, Dongqing Pan, Birte Hagemeier, Dorothee Vogt, Ingrid R. Vetter, Andrea Musacchio in Science Advances
It’s a cellular process going on since one billion years, yet we are not able to replicate it, nor to fully understand it. Mitosis, the mechanism of cell division that is so important for life, involves more that 100 proteins at its core. Now, the group of Prof. Dr. Andrea Musacchio from the Max Planck Institute of Molecular Physiology in Dortmund has been able to fully reconstitute the engine of the mitosis machinery, called kinetochore. Being able to model a functioning kinetochore is the first step towards the making of artificial chromosomes, that may one day be used to restore missing functions in cells.
As a human cell begins division, its 23 chromosomes duplicate into identical copies that remain joined at a region called the centromere. Here lies the kinetochore, a complicated assembly of proteins that binds to thread-like structures, the microtubules. As mitosis progresses, the kinetochore gives green light to the microtubules to tear the DNA copies apart, towards the new forming cells. “The kinetochore is a beautiful, flawless machine: You almost never lose a chromosome in a normal cell!,” says Musacchio. “We already know the proteins that constitute it, yet important questions about how the kinetochore works are still open: How does it rebuild itself during chromosome replication? How does it bind to the microtubules? And how does it control them?”
Musacchio’s quest for answers started more than 20 years ago and has been guided by a simple motto: “Before we understand how things go wrong, we better understand why and how things work.” He therefore embarked in the mission of rebuilding the kinetochore in vitro. In 2016 he could synthesize a partial kinetochore made of 21 proteins. In the new publication, Musacchio, graduate student Kai Walstein, and their colleagues at MPI Dortmund have been able to fully reconstruct the system: All subunits, from the ones that bind the centromere to the ones that bind the microtubules, are now present in the right numbers and stoichiometry. Scientists proved that the new system functions properly, by successfully substituting parts of the original kinetochore in the cell with artificial ones.
“This is a real milestone in the reconstruction of an object that exists, unaltered, in all eukaryotic cells since more than one billion years!,” says Musacchio. This breakthrough paves the way towards the making of synthetic chromosomes carrying functions that can be replicated in organisms. “The potential for biotech applications could be huge,” he says.
MPI scientists had to overcome a major hurdle to rebuild the kinetochore, namely to fully reconstruct the highly flexible Centromeric Protein C (CENP-C). This is an essential protein that bridges the centromeric region to the outer proteins of the kinetochore. Researchers rebuilt CENP-C by “gluing” together the two ends of it.
A highly organised laboratory, similar to a factory, is fundamental for the reconstitution of complex protein assemblies. For each protein of the kinetochore, MPI scientists built a production pipeline to isolate the genes, express them in insects’ cells, and collect them. “When we put them together in vitro, these proteins click-in to form the kinetochore, just like LEGO pieces following the instructions,” he says. Other than the famous toys though, each kinetochore protein has a different interface and interaction with closer proteins.
The group will now step up to the next level of complexity: investigating how the kinetochore functions and interacts in the presence of microtubules and supplied energy (in the form of ATP).
Nurse cell–derived small RNAs define paternal epigenetic inheritance in Arabidopsis
by Jincheng Long, James Walker, Wenjing She, Billy Aldridge, Hongbo Gao, Samuel Deans, Martin Vickers, Xiaoqi Feng in Science
Hereditary information is passed from parent to offspring in the genetic code, DNA, and epigenetically through chemically induced modifications around the DNA.
New research from the John Innes Centre has uncovered a mechanism which adjusts these modifications, altering the way information beyond the genetic code is passed down the generations.
DNA methylation, one example of these epigenetic modifications, happens when a methyl group or chemical cap is added to the DNA, switching a gene, or genes, on or off.
As germline (eggs and sperm) cells develop some of the methyl markers are reset, affecting the information passed onto the next generation.
How this process works during plant reproduction has been unclear.
The exciting research reveals the molecular mechanism of DNA methylation reprogramming in the male germline of plants.
Inside the plant’s male reproductive parts (the anthers), cells that will divide to produce the sperm (meiocytes) are surrounded by cells that nourish them. These nurse cells are called tapetal cells.
The John Innes Centre team discovered that tapetal cells produce an abundance of small RNA molecules and observed that this is caused by a protein called CLSY3, found specifically within tapetal cells in the anther. These small RNAs were shown to move from the tapetal cells into the meiocytes. Here they add new methyl marks to transposons (unstable genetic elements) with the same DNA code.
“This discovery changes the way we think about epigenetic inheritance across generations in plants. Small RNAs produced by germline nurse cells can determine the DNA methylome in the sperm. The key role played by these small RNAs in determining the inherited DNA methylome indicates convergent functional evolution between plant and animal reproduction,” says corresponding author Dr Xiaoqi Feng, group leader at the John Innes Centre.
This reprogramming stops the transposons from jumping around in the germ cells, and this protects the integrity of the genome between generations.
In the meiocytes, these small RNAs also target genes with similar DNA sequences as the source transposons, helping to control gene expression and facilitate meiosis, a type of cell division that leads to the production of sperm.
The findings have wide application across plant and animal kingdoms and provide a vital new clue for the world-wide community of researchers studying epigenetics. Previous work has shown that cereal crops, like maize and rice, have similar tapetal small RNAs, however, it was unclear why these small RNAs are important for fertility and yield. The mechanistic insight generated by this study points to new directions of investigations and may help develop biotechnology to target DNA methylation in commercial crops.
Joint first author Dr Jincheng Long said: “Our study could open a new avenue of crop biotechnology. For example, through the manipulation of small RNA directed DNA methylation of the cells that directly contribute to seed formation and the breeding process.”
The study is also important in fundamental biological terms, joint first author Dr James Walker explains, “Our work demonstrates that paternal epigenetic inheritance is determined by tapetal cells, which drive reprogramming at a scale unprecedented in plants.
“The molecular mechanism our work revealed pushes our understanding of de novo DNA methylation to the next level, showing how new methyl marks are established at specific sites in specific cells.”
Restructuring of the plasma membrane upon damage by LC3-associated macropinocytosis
by Stine Lauritzen Sønder, Swantje Christin Häger, Anne Sofie Busk Heitmann, Lisa B. Frankel, Catarina Dias, Adam Cohen Simonsen, Jesper Nylandsted in Science Advances
To survive life threatening injuries, cancer cells use a technique in which they eat parts of the membrane surrounding them. This is shown for the first time in research from a team of Danish researchers.
It is the membrane of cancer cells that is at the focus of the new research now showing a completely new way in which cancer cells can repair the damage that can otherwise kill them.
In both normal cells and cancer cells, the cell membrane acts as the skin of the cells. And damage to the membrane can be life threatening. The interior of cells is fluid, and if a hole is made in the membrane, the cell simply floats out and dies — a bit like a hole in a water balloon.
Therefore, damage to the cell membrane must be repaired quickly, and now research from a team of Danish researchers shows that cancer cells use a technique called macropinocytosis. The technique, which is already a known tool for cells in other contexts, consists in the cancer cells pulling the intact cell membrane in over the damaged area and sealing the hole in a matter of minutes. Next, the damaged part of the cell membrane is separated into small spheres and transported to the cells’ ‘stomach’ — the so-called lysosomes, where they are broken down.
In the laboratory, the researchers damaged the membrane of the cancer cells using a laser that shoots small holes in the membrane and triggers macropinocytosis. Here they can see that if the process is inhibited with substances blocking the formation of the small membrane spheres, the cancer cell can no longer repair the damage and dies.
“Our research provides very basic knowledge about how cancer cells survive. In our experiments, we have also shown that cancer cells die if the process is inhibited, and this points towards macropinocytosis as a target for future treatment. It is a long-term perspective, but it is interesting,” says group leader Jesper Nylandsted from the Danish Cancer Society’s Research Center and the University of Copenhagen, who has headed the new research and who for many years has investigated how cancer cells repair their membranes.
One of the most dangerous properties of cancer is when the disease spreads in the body. If tumors occur in new parts of the body, the disease becomes more difficult to treat and typically requires more extensive forms of treatment. It is also when cancer cells spread through the body’s tissues that they are particularly prone to damage to their membrane.
Researchers at the Danish Cancer Society have previously shown how cancer cells can use another technique to repair the membrane, namely by tying off the damaged part, rather like when a lizard throws its tail.
However, the experiments in the laboratory could indicate that especially the aggressive cancer cells use macropinocytosis. This may be due to the fact that the cancer cell has the opportunity to reuse the damaged membrane when it is degraded in the lysosomes. This type of recycling will be useful for cancer cells because they divide frequently, requiring large amounts of energy and material for the new cells.
And although the researchers have now published the new results, their work is not over. This is explained by another member of the research team, postdoc Stine Lauritzen Sønder:
“We continue to work and investigate how cancer cells protect their membranes. In connection with macropinocytosis in particular, it is also interesting to see what happens after the membrane is closed. We believe that the first patching is a bit rough and that a more thorough repair of the membrane is needed afterwards. It can be another weak point in the cancer cells, and is something we want to examine closer,” she says.
Role of the ionic environment in enhancing the activity of reacting molecules in zeolite pores
by Niklas Pfriem, Peter H. Hintermeier, Sebastian Eckstein, Sungmin Kim, Qiang Liu, Hui Shi, Lara Milakovic, Yuanshuai Liu, Gary L. Haller, Eszter Baráth, Yue Liu, Johannes A. Lercher in Science
Zeolites are extremely porous materials: ten grams can have an internal surface area the size of a soccer field. Their cavities make them useful in catalyzing chemical reactions and thus saving energy. An international research team has now made new findings regarding the role of water molecules in these processes. One important application is the conversion of biomass into biofuel.
Fuel made from biomass is considered to be climate-neutral, although energy is still needed to produce it: the desired chemical reactions require high levels of temperature and pressure.
“If we are to do without fossil energy sources in the future and make efficient large-scale use of biomass, we will also have to find ways to reduce the energy required for processing the biomass,” says Johannes Lercher, professor for Chemical Technology at the Technical University of Munich (TUM) and Director of the Institute for Integrated Catalysis at the Pacific Northwest National Laboratory in Richland, Washington (USA).
Working together with an international research team, Lercher has taken a closer look at the role of water molecules in reactions inside the zeolite’s pores, which are less than one nanometer in size.
One characteristic of an acid is that it easily donates protons. Thus, when added to water, hydrochloric acid splits into negatively charged chloride anions, like those found in table salt crystals, and positively charged protons which attach themselves to the water molecules. This results in a positively charged hydronium ion, which looks to further pass on this proton, for example to an organic molecule.
When the organic molecule is “forced” to accept a proton, it tries to stabilize itself. Thus, an alcohol can give rise to a molecule with a double bond — a typical reaction step on the path from biomass to biofuel. The zeolite walls stabilize transitional states occurring during conversion and, thus, help to minimize the amount of energy required by the reaction to occur.
Zeolites contain oxygen atoms in their crystal structure which already carry a proton. Like molecular acids they form hydronium ions through the interactions with water.
However, while hydronium ions disperse in water, they remain closely associated with the zeolite. Chemical pre-treatment can vary the number of these active centers and, thus, establish a certain density of hydronium ions in the pores of the zeolite.
By systematically varying the size of the cavities, the density of the active sites and the amount of water, the research team was able to elucidate the pore sizes and concentrations of water which best catalyzed selected example reactions.
“In general, it’s possible to increase the reaction rate by making the pores smaller and raising the charge density,” Johannes Lercher explains. “However, this increase has its limits: When things get too crowded and the charges are too close to one another, the reaction rate drops again. This makes it possible to find the optimum conditions for every reaction.”
“Zeolites are generally suitable as nanoreactors for all chemical reactions whose reaction partners fit into the pores and in which an acid is used as a catalyst,” emphasizes Lercher. “We are at the very beginning of a development with the potential to increase the reactivity of molecules even at low temperatures and, thus, to save considerable amounts of energy in the production of fuels or chemicals.”
Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome
by Wilfried M. Guiblet, Michael DeGiorgio, Xiaoheng Cheng, Francesca Chiaromonte, Kristin A. Eckert, Yi-Fei Huang, Kateryna D. Makova in Genome Research
Some regions of the human genome where the DNA can fold into unusual three-dimensional structures called G-quadruplexes (G4s) show signs that they are preserved by natural selection. When G4s are located in the regulatory sequences that control how genes are expressed or in other functional, but non-protein coding, regions of the genome, they are maintained by selection, are more common, and their unusual structures are more stable, according to a new study. Conversely, the structures are less common, less stable, and evolve neutrally outside of these regions, including within the protein-coding regions of genes themselves.
Together, these lines of evidence suggest that G4 elements should be added to the list of functional elements of the genome along with genes, regulatory sequences, and non-protein coding RNAs, among others.
“There have been only a handful of studies that provided experimental evidence for individual G4 elements playing functional roles,” said Wilfried Guiblet, first author of the paper, a graduate student at Penn State at the time of research, and now a postdoctoral scholar at the National Cancer Institute. “Our study is the first to look at G4s across the genome to see if they show the characteristics of functional elements as a general rule.”
As much as 1% of the genome can fold into G4s, rather than the typical double helix (in comparison, protein-coding genes occupy approximately 1.5% of the genome). G4s are one of several non-canonical shapes into which DNA can fold, collectively known as “non-B DNA.” The G4 structure forms in DNA sequences rich in the nucleotide guanine, the “G” in the ACGT alphabet of the genome. G4s have been implicated in several key cellular processes and have been suggested to play a role in several human diseases, including neurological disorders and cancer.
To better understand the function of G4s at a genome-wide scale, the research team looked at their distribution across the genome, their thermostability, and whether or not they showed signs of being under the influence of natural selection, all in relation to other functional elements of the genome. They confirmed that, as a rule, G4s are more common in regions of the genome known to have important cellular functions and that the G4s in these regions are more stable than elsewhere in the genome.
“The three-dimensional structure of G4s can form transiently and how stable their structure is depends on their underlying DNA sequence and other factors,” said Guilbet. “We found that, usually, G4s located within functional regions of the genome tend to be more stable. In other words, it’s more likely that the DNA is folded into a G4 at any given time and thus, more likely that the G4 is there for a functional reason.”
Functional regions of the genome are generally maintained by a type of natural selection called purifying selection. Mutations in these regions could disrupt their function and be harmful to the organism. The mutations therefore are usually eliminated by purifying selection, which keeps the DNA sequence relatively unchanged over time. In nonfunctional regions of the genome, a mutation may have no impact and can persist in the genome without any consequences. These regions of the genome are said to evolve neutrally. Where G4s fall in this spectrum depends on their location in the genome.
“We can look at the patterns of change in a DNA sequence among human individuals and between humans and our close primate relatives as a test of natural selection and then use selection as an indicator of function,” said Yi-Fei Huang, assistant professor of biology at Penn State and a leader of the research team. “Our tests show that G4s located within functional regions of the genome appear to be under purifying selections, which is further evidence that G4s should be considered as functional elements. The only exception from this pattern were protein-coding regions of genes, where G4s are relatively uncommon, rather unstable, and do not evolve under purifying selection. G4s in protein-coding regions of genes might be nonfunctional and costly to maintain.”
The research team has recently shown that G4s, along with other types of non-B DNA, have increased mutation rates. The fact that G4s located outside of protein-coding regions are maintained by purifying selection, despite their high mutagenic potential, adds further weight to the evidence for classifying G4s as functional elements.
“We think that we are seeing evidence for a paradigm shift for how scientists define function in the genome,” said Kateryna Makova, Verne M. Willaman Chair of Life Sciences at Penn State and a leader of the research team. “First, geneticists focused almost exclusively on protein-coding genes, then we became aware of many functional non-coding elements, and now we have G4s and possibly other non-B DNA elements. Three-dimensional structure may be just as important for defining function as the underlying DNA sequence.”
“Defining the full complement of functional genome elements is crucial for interpreting the potential disease consequences not only of inherited genetic variants but also of mutations arising within tissues over the lifetime of individuals,” said Kristin Eckert, professor of pathology at the Penn State College of Medicine, co-author of the paper, and a member of the research team.
Embryo-scale, single-cell spatial transcriptomics
by Sanjay R. Srivatsan, Mary C. Regier, Eliza Barkan, Jennifer M. Franks, Jonathan S. Packer, Parker Grosjean, Madeleine Duran, Sarah Saxton, Jon J Ladd, Malte Spielmann, Carlos Lois, Paul D. Lampe, Jay Shendure, Kelly R. Stevens, Cole Trapnell in Science
A new technique called sci-Space, combined with data from other technologies, could lead to four-dimensional atlases of gene expression across diverse cells during embryonic development of mammals.
Such atlases would map how the gene transcripts in individual cells reflect the passage of time, cell lineages, cell migration, and location on the developing embryo. They would also help illuminate the spatial regulation of gene expression.
Mammalian embryonic development is a remarkable phenomenon: a fertilized egg divides repeatedly and turns, in a matter of weeks or months, into a complex organism capable of a myriad of physiological processes and composed of a variety of cells, tissues, organs, anatomical structures.
A better understanding of how mammals form before birth — particularly the prenatal spatial patterns of gene expression at a single-cell level during embryonic development — could advance biomedical and veterinary research on a variety of conditions. These range from inherited disorders to congenital malformations and developmental delays. Understanding how organs originate might also assist future regenerative medicine efforts.
An international team led by scientists at UW Medicine, Howard Hughes Medical Institute and the Brotman Baty Institute for Precision Medicine in Seattle demonstrated the proof-of-concept of their sci-Space technique in mouse embryos. The researchers observed the orchestration of genes in 120,000 cell nuclei. All the body’s somatic cells contain the same DNA code. The researchers captured information on which genes were turned on or off in these nuclei as mouse embryos took shape. The scientists also investigated how cells’ locations in an embryo affected which genes were activated during development.
This technique builds on previous work in which these scientists and other groups developed ways of conducting whole-organism profiling of gene expression and DNA-code accessibility, in thousands of single cells, during embryonic development. They did so to track the emergence and trajectory of various cell types.
How cells are organized spatially — what physical positions they take as an embryo forms — is critical to normal development. Misplacements, disruptions, or cells not showing at the right time in the right spot can cause serious problems or even prenatal death.
However, gaining knowledge on spatial patterns of gene expression has been technically difficult. It has been unwieldy to assay gene transcripts of individual cells over wide swaths of the embryo. This limited the scientific understanding of how spatial organization influences gene expression and, consequently, why which cell types form where, or how neighboring groups of cells influence each other’s future roles.
The scientists on the present study had earlier developed a method to label cell nuclei, a technique they called sci-Plex. They then went on to index single-cell RNA sequencing, with a method called sci-RNA-sequencing.
Now, with sci-Space, by analyzing spatial coordinates and cell gene transcripts the scientists identified thousands of genes whose expression was anatomically patterned. For example, certain genetic profiles emerged in neurons in the brain and spinal cord and others in cardiac muscle cells in the heart.
The scientists also used spatial and gene profile information to annotate subtypes of cells. For example, while both blood vessel cells and heart muscle might both express the gene for a particular growth factor, only the heart muscle cells produced certain growth factor receptors.
The researchers also observed that cell types varied greatly in the extent of their spatial patterning of gene expression. For example, connective tissue progenitor cells showed a relatively large proportion of spatially restricted gene expression. This observation suggests that subtypes of these cells behave in a position-dependent manner throughout the body.
To measure the power of spatial position on a cell type’s gene transcript profile, the researchers also calculated the physical distance between cells and the angular distance of their gene expression profiles.
“For many cell types, as the physical distance between cells increased, so did the angular distance between their transcriptomes,” the researchers noted in their paper. However, they added that this trend varied considerably. It was most pronounced in certain brain and spinal cord cells.
The genetic transcript profiles of some other cell types were highly influenced by their position in the developing embryo. Among these are certain cartilage cells, which become part of the scaffolding for bones of the head and face.
The researchers also studied gene expression dynamics that took place as part of brain cell differentiation and migration during mouse embryonic development. The researchers examined how various brain cell trajectories were anatomically distributed.
“Cells from each trajectory overwhelmingly occupied distinct brain regions,” the researchers noted. They also observed gradients of developmental maturity in different regions of the brain. These gradients revealed both known and new patterns of migration.
In the future, the researchers hope sci-Space will be further applied to serial sections that span the entire mouse embryo and that cover many points of time.
Evolution of networks of protein domain organization
by M. Fayez Aziz, Gustavo Caetano-Anollés in Scientific Reports
Proteins have been quietly taking over our lives since the COVID-19 pandemic began. We’ve been living at the whim of the virus’s so-called “spike” protein, which has mutated dozens of times to create increasingly deadly variants. But the truth is, we have always been ruled by proteins. At the cellular level, they’re responsible for pretty much everything.
Proteins are so fundamental that DNA — the genetic material that makes each of us unique — is essentially just a long sequence of protein blueprints. That’s true for animals, plants, fungi, bacteria, archaea, and even viruses. And just as those groups of organisms evolve and change over time, so too do proteins and their component parts.
A new study from University of Illinois researchers maps the evolutionary history and interrelationships of protein domains, the subunits of protein molecules, over 3.8 billion years.
“Knowing how and why domains combine in proteins during evolution could help scientists understand and engineer the activity of proteins for medicine and bioengineering applications. For example, these insights could guide disease management, such as making better vaccines from the spike protein of COVID-19 viruses,” says Gustavo Caetano-Anollés, professor in the Department of Crop Sciences, affiliate of the Carl R. Woese Institute for Genomic Biology at Illinois, and senior author on the paper.
Caetano-Anollés has studied the evolution of COVID mutations since the early stages of the pandemic, but that timeline represents a vanishingly tiny fraction of what he and doctoral student Fayez Aziz took on in their current study.
The researchers compiled sequences and structures of millions of protein sequences encoded in hundreds of genomes across all taxonomic groups, including higher organisms and microbes. They focused not on whole proteins, but instead on structural domains.
“Most proteins are made of more than one domain. These are compact structural units, or modules, that harbor specialized functions,” Caetano-Anollés says. “More importantly, they are the units of evolution.”
After sorting proteins into domains to build evolutionary trees, they set to work building a network to understand how domains have developed and been shared across proteins throughout billions of years of evolution.
“We built a time series of networks that describe how domains have accumulated and how proteins have rearranged their domains through evolution. This is the first time such a network of ‘domain organization’ has been studied as an evolutionary chronology,” Fayez Aziz says. “Our survey revealed there is a vast evolving network describing how domains combine with each other in proteins.”
Each link of the network represents a moment when a particular domain was recruited into a protein, typically to perform a new function.
“This fact alone strongly suggests domain recruitment is a powerful force in nature,” Fayez Aziz says. The chronology also revealed which domains contributed important protein functions. For example, the researchers were able to trace the origins of domains responsible for environmental sensing as well as secondary metabolites, or toxins used in bacterial and plant defenses.
The analysis showed domains started to combine early in protein evolution, but there were also periods of explosive network growth. For example, the researchers describe a “big bang” of domain combinations 1.5 billion years ago, coinciding with the rise of multicellular organisms and eukaryotes, organisms with membrane-bound nuclei that include humans.
The existence of biological big bangs is not new. Caetano-Anollés’ team previously reported the massive and early origin of metabolism, and they recently found it again when tracking the history of metabolic networks.
The historical record of a big bang describing the evolutionary patchwork of proteins provides new tools to understand protein makeup.
“This could help identify, for example, why structural variations and genomic recombinations occur often in SARS-CoV-2,” Caetano-Anollés says.
He adds that this new way of understanding proteins could help prevent pandemics by dissecting how virus diseases originate. It could also help mitigate disease by improving vaccine design when outbreaks occur.
Matrix lumican endocytosed by immune cells controls receptor ligand trafficking to promote TLR4 and restrict TLR9 in sepsis
by George Maiti, Jihane Frikeche, Carly Yuen-Man Lam, Asim Biswas, Vishal Shinde, Marie Samanovic, Jonathan C. Kagan, Mark J. Mulligan, Shukti Chakravarti in Proceedings of the National Academy of Sciences
A connective tissue protein known to support the framework of organs also encourages immune responses that fight bacterial infections, while restraining responses that can be deadly in the condition called sepsis, a new study finds.
Led by researchers from NYU Grossman School of Medicine, the work revolves around the extracellular matrix (ECM) of connective tissues, once thought of as an inert framework that shapes bodily compartments, but increasingly recognized as a signaling partner with nearby cells in normal function, and a contributor to disease when signals go awry. Among the key players in the ECM are fibroblasts, the cells that make tough structural matrix proteins like collagen.
The new analysis found that lumican, a protein-sugar combination (proteoglycan) secreted by fibroblasts, and known to partner with collagen in connective tissues, also promotes immune system responses in immune cells called macrophages that fight bacterial infections. At the same time, the study found that lumican protects tissues by restraining a different type of immune response that reacts to DNA, whether from an invading virus, or from human cells that spill their DNA as they die (a signal that tissues are under stress).
Such inflammatory responses represent as a transition into healing, but grow too big in sepsis, damaging the body’s own tissues to the point of organ failure. Sepsis affects 48.9 million people worldwide, the authors say, but the role of the ECM in the condition is largely unknown.
“Lumican may have a dual protective role in ECM tissues, promoting defense against bacteria on the one hand, and on the other, limiting immune overreactions to DNA that cause self-attack, or autoimmunity,” says corresponding study author Shukti Chakravarti, PhD, professor in the departments of Ophthalmology and Pathology at NYU Langone Health.
The findings suggest that connective tissue, and extracellular matrix proteins like lumican, operate outside of cells normally, but as disease or damage break down ECM, get sucked into and regulate immune cells homing in on the damage.
Lumican happens to interact with two proteins on surfaces of immune cells that control the activity of proteins called toll-like receptors known to recognize structural patterns common to molecules made by invading microbes, say the study authors. Because they are less specific than other parts of the immune system, toll-like receptors can also cause attacks by immune cells on the body’s own tissues if over-activated.
The current study authors found that lumican promotes the ability of toll-like receptor (TLR)-4 on the surfaces of immune cells to recognize bacterial cell-wall toxins called lipopolysaccharides (LPS). Specifically, the study found that lumican, by attaching to two proteins, CD14 and Caveolin1, likely using regions normally covered by collagen, stabilizes their interactions with TLR4 to increase its ability to react to LPS. This in turn leads to production of TNF alpha, a signaling protein that amplifies immune responses.
Along with describing the effect of lumican on the surfaces of immune cells, the new study finds that lumican is taken up from outside cells into membrane-bound pouches called endosomes, and pulled into cells. Such compartments deliver ingested bacteria to other endosomes that destroy them, or heighten inflammation or protective interferon responses. Once pulled inside, the researchers found, lumican bolstered TLR4 activity by slowing down its passage into lysosomes, pockets where such proteins are broken down and recycled.
While it encouraged TLR4 activity on cell surfaces, lumican, once inside immune cells, had the opposite effect on toll-like receptor 9 (TLR9), which is known react to DNA instead of bacterial LPS. Experiments showed that lumican’s binding of DNA in endosomes keeps it away from, and prevents it from activating, TLR9.
Experiments confirmed that mice engineered to lack the gene for lumican have trouble both fighting off bacterial infections (less cytokine response, slower clearance, greater weight loss), and trouble restraining the immune overreaction to bacteria (sepsis). The study authors also found elevated lumican levels in human sepsis patients’ blood plasma, and that human immune cells (blood monocytes) treated with lumican had elevated TLR4 activity, but suppressed TLR9 responses.
“As an influencer of both processes, lumican-based peptides could be used as a lever, to tweak inflammation related to TNF-alpha, or endosomal interferon responses, to better resolve inflammation and infections,” says George Maiti, PhD, a post-doctoral fellow in Chakravarti’s lab. “Our results argue for a new role for ECM proteins at sites of injury. Taken up by incoming immune cells it shapes immune responses beyond the cell surface by regulating the movement and interaction of endosomal receptors and signaling partners”.
Stealth Fluorescence Labeling for Live Microscopy Imaging of mRNA Delivery
By Tom Baladi, Jesper R. Nilsson, Audrey Gallud, Emanuele Celauro, Cécile Gasse, Fabienne Levi-Acobas, Ivo Sarac, Marcel R. Hollenstein, Anders Dahlén, Elin K. Esbjörner, L. Marcus Wilhelmsson in Journal of the American Chemical Society
Researchers at Chalmers University of Technology, Sweden, have succeeded in developing a method to label mRNA molecules, and thereby follow, in real time, their path through cells, using a microscope — without affecting their properties or subsequent activity. The breakthrough could be of great importance in facilitating the development of new RNA-based medicines.
RNA-based therapeutics offer a range of new opportunities to prevent, treat and potentially cure diseases. But currently, the delivery of RNA therapeutics into the cell is inefficient. For new therapeutics to fulfil their potential, the delivery methods need to be optimised. Now, a new method can provide an important piece of the puzzle of overcoming these challenges and take the development a major step forward.
“Since our method can help solve one of the biggest problems for drug discovery and development, we see that this research can facilitate a paradigm shift from traditional drugs to RNA-based therapeutics,” says Marcus Wilhelmsson, Professor at the Department of Chemistry and Chemical Engineering at Chalmers University of Technology, and one of the main authors of the article.
The research behind the method has been done in collaboration with chemists and biologists at Chalmers and the biopharmaceuticals company AstraZeneca, through their joint research centre, FoRmulaEx as well as a research group at the Pasteur Institute, Paris.
The method involves replacing one of the building blocks of RNA with a fluorescent variant, which, apart from that feature, maintains the natural properties of the original base. The fluorescent units have been developed with the help of a special chemistry, and the researchers have shown that it can then be used to produce messenger RNA (mRNA), without affecting the mRNA’s ability to be translated into a protein at natural speed. This represents a breakthrough which has never before been done successfully. The fluorescence furthermore allows the researchers to follow functional mRNA molecules in real time, seeing how they are taken up into cells with the help of a microscope.
A challenge when working with mRNA is that the molecules are very large and charged, but at the same time fragile. They cannot get into cells directly and must therefore be packaged. The method that has proven most successful to date uses very small droplets known as lipid nanoparticles to encapsulate the mRNA. There is still a great need to develop new and more efficient lipid nanoparticles — something which the Chalmers researchers are also working on. To be able to do that, it is necessary to understand how mRNA is taken up into cells. The ability to monitor, in real time, how the lipid nanoparticles and mRNA are distributed through the cell is therefore an important tool.
“The great benefit of this method is that we can now easily see where in the cell the delivered mRNA goes, and in which cells the protein is formed, without losing RNA’s natural protein-translating ability,” says Elin Esbjörner, Associate Professor at the Department for Biology and Biotechnology and the second lead author of the article.
Researchers in this area can use the method to gain greater knowledge of how the uptake process works, thus accelerating and streamlining the new medicines’ discovery process. The new method provides more accurate and detailed knowledge than current methods for studying RNA under a microscope.
“Until now, it has not been possible to measure the natural rate and efficiency with which RNA acts in the cell. This means that you get the wrong answers to the questions you ask when trying to develop a new drug. For example, if you want an answer to what rate a process takes place at, and your method gives you an answer that is a fifth of the correct, drug discovery becomes difficult,” explains Marcus Wilhelmsson.
PHYTOCHROME-INTERACTING FACTORs trigger environmentally responsive chromatin dynamics in plants
by Björn C. Willige, Mark Zander, Chan Yul Yoo, Amy Phan, Renee M. Garza, Shelly A. Trigg, Yupeng He, Joseph R. Nery, Huaming Chen, Meng Chen, Joseph R. Ecker, Joanne Chory. in Nature Genetics
Scientists — and gardeners — have long known that plants grow taller and flower sooner when they are shaded by close-growing neighbors. Now, for the first time, researchers at the Salk Institute have shown the detailed inner workings of this process.
The study offers a new understanding of how gene activity directs plant growth, and how quickly plants respond to their environment — with shifting light conditions triggering molecular changes in as little as five minutes. The findings provide insights into how to increase yield and safeguard world food production as climate change shrinks the planet’s arable land.
“This paper shows, in high resolution, how plants respond to subtle environmental changes on the cellular level,” says co-corresponding author Joanne Chory, director of Salk’s Plant Molecular and Cellular Biology Laboratory, Howard Hughes Medical Institute investigator, and holder of the Howard H. and Maryam R. Newman Chair in Plant Biology. “Work that reveals how plants can adapt to greater environmental stresses will be critical as the effects of climate change intensify.”
Plants in the shade grow faster and taller in an effort to break through the canopy and reach more light. At the same time, shaded growing conditions cause them to flower and produce seeds earlier than normal, in order to out-compete other plants. These responses might be helpful to wildflowers growing in a meadow, but on farms they can reduce production and result in bitter, low-quality crops — as any gardener whose lettuce has bolted knows.
In the new study, researchers looked at the role of specific transcription factors in activating this growth response. Transcription factors are proteins that turn genes on or off by binding to DNA.
The team worked with mutant seedlings lacking transcription factors called PIFs (PHYTOCHROME-INTERACTING FACTORs). When they grew these plants in an environment that simulated shade, the plants without certain PIFs did not elongate or speed up their growth, but instead continued to grow normally as if they were in full sunlight. Previously, the Chory lab showed that PIF7 plays the most important role in regulating shade-induced growth.
The researchers then took a closer look at the role of histones in this process, in particular the histone variant H2A.Z. Histones are proteins that act like spools for strands of DNA. When histones are exchanged or modified, they can work to activate or suppress certain genes.
The scientists found that canopy shade led to the removal of the histone H2A.Z at growth-regulating genes through the DNA binding of PIF7, which in turn activated their expression.
By using very short time intervals for their experiments, the researchers found that PIF7 gets activated, binds its target genes, and initiates the removal of H2A.Z, all within the first 5 minutes of the plant experiencing canopy shade.
“Our study describes another step towards a mechanistic understanding of how plants alter their gene expression in response to a changing environment,” says co-corresponding author Joseph Ecker, a Howard Hughes Medical Institute investigator and professor in Salk’s Genomic Analysis Laboratory.
Previous studies had identified PIFs and H2A.Z as having important roles in the responses of plants exposed to high temperatures; however, the timing of events was not known, notes co-author Björn Willige, a Howard Hughes Medical Institute research specialist in the Chory lab.
“Our study reveals the mechanism in close detail and also shows the rapid nature of the response. We found that when PIF7 is active, it binds to DNA. And our data indicate that this leads to the removal of H2A.Z from the DNA. Subsequently, genes are activated, and then this induces growth, to outcompete the neighboring plants,” Willige says.
The speed of the process was unexpected, says co-author Mark Zander, an assistant professor at the Waksman Institute of Microbiology at Rutgers University. He noted that, in addition to triggering the stress response within five minutes, the histone landscape also recovered quickly when shade was removed.
“When we removed shade, the levels of H2A.Z at PIF7 target genes went back to normal within 30 minutes,” he says. “I was surprised by how dynamic the process is, which is really the foundation for the elegance of our study.”
PIFs play significant roles in the growth, development and pest defense of plants. Therefore, the team hopes that their findings can be translated to other plant responses that are important for farmers, especially in relation to helping plants be more resilient to climate change. The Salk Institute’s Harnessing Plants Initiative seeks to help solve climate change by optimizing plants’ natural ability to capture and store carbon.
Structural basis for VIPP1 oligomerization and maintenance of thylakoid membrane integrity
by Tilak Kumar Gupta, Sven Klumpe, Karin Gries, Steffen Heinz, Wojciech Wietrzynski, Norikazu Ohnishi, Justus Niemeyer, Benjamin Spaniol, Miroslava Schaffer, Anna Rast, Matthias Ostermeier, Mike Strauss, Jürgen M. Plitzko, Wolfgang Baumeister, Till Rudack, Wataru Sakamoto, Jörg Nickelsen, Jan M. Schuller, Michael Schroda, Benjamin D. Engel in Cell
An international study has elucidated the structure of a protein that is required for the assembly and stability of photosynthetic membranes.
Plants, algae and cyanobacteria convert carbon dioxide and water into biomass and oxygen with the aid of photosynthesis. This process forms the basis of most forms of life on Earth. Global warming is exposing photosynthetic organisms to increasing levels of stress. This reduces growth rates, and in the longer term presents a threat to food supplies for human populations. An international project, in which Ludwig-Maximilians-Universitaet (LMU) in Munich biologist Kärin Nickelsen and his research group played a significant role, has now determined the three-dimensional structure of a protein involved in the formation and maintenance of the membranes in which photosynthesis takes place. The insights provided by the study will facilitate biotechnological efforts to boost the ability of plants to cope with environmental stresses.
The initial steps in photosynthesis take place within the ‘thylakoid’ membranes, which harbor pigment-protein complexes that absorb energy from sunlight. It has been known for decades that, in virtually all photosynthetic organisms, a protein called VIPP1 (which stands for ‘vesicle-inducing protein in plastids’) is indispensable for the assembly of thylakoids. “However, how VIPP1 actually performs this essential function has remained enigmatic up to now,” says Steffen Heinz, a postdoc in Nickelsen’s group and joint first author of the new publication.
The team used cryo-electron microscopy to determine the three-dimensional structure of VIPP1 at high resolution. Analysis of this structure, in combination with functional investigation of the protein’s mode of action, demonstrated how small numbers of VIPP1 molecules form short strands, which are interwoven to form a basket-like structure. This then serves as a scaffold for the assembly of the thylakoid membrane, and determines its curvature. Using a related technique known as cryo-electron tomography, the scientists were also able to image VIPP1 membranes in their natural state in algal cells. By introducing site-specific mutations into VIPP1, they showed that the interaction of VIPP1 with thylakoid membranes is vital for the maintenance of their structural integrity under high levels of light stress. This finding demonstrates that the protein not only mediates the assembly of thylakoids, but also plays a role in enabling them to adapt to environmental fluctuations.
The results provide the basis for a better understanding of the mechanisms that underlie the formation and stabilization of thylakoids. They will also open up new opportunities to enhance the ability of green plants to withstand extreme environmental stresses.
MISC
Subscribe to Paradigm!
Medium. Twitter. Telegram. Telegram Chat. Reddit. LinkedIn.
Main Sources
Research articles
