scholarly journals Gene loss during the transition to multicellularity

2021 ◽  
Author(s):  
Berenice Jiménez-Marín ◽  
Jessica B. Rakijas ◽  
Antariksh Tyagi ◽  
Aakash Pandey ◽  
Erik R. Hanschen ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Gene Loss ◽  
Protein Complexes ◽  
Gene Gain ◽  
Genetic Changes ◽  
Gradual Loss ◽  
Volvocine Algae ◽  
Major Transition ◽  
Network States ◽  
High Degree

SummaryMulticellular evolution is a major transition associated with momentous diversification of multiple lineages and increased developmental complexity. The volvocine algae comprise a valuable system for the study of this transition, as they span from unicellular to undifferentiated and differentiated multicellular morphologies despite their genomes being highly similar, suggesting multicellular evolution requires few genetic changes to undergo dramatic shifts in developmental complexity. Here, the evolutionary dynamics of five volvocine genomes were examined, where a gradual loss of genes was observed in parallel to the co-option of a few key genes. Protein complexes in the five species exhibited a high degree of novel interactions, suggesting that gene loss promotes evolutionary novelty. This finding was supported by gene network modeling, where gene loss outpaces gene gain in generating novel stable network states. These results suggest developmental complexity may be driven by gene loss rather than gene gain.

scholarly journals Ecological Opportunity, Evolution, and the Emergence of Flea-Borne Plague

2016 ◽  
Vol 84 (7) ◽  
pp. 1932-1940 ◽  
Author(s):  
B. Joseph Hinnebusch ◽  
Iman Chouikha ◽  
Yi-Cheng Sun
Keyword(s):  
Yersinia Pseudotuberculosis ◽  
Gene Loss ◽  
Gene Gain ◽  
Loss Of Function ◽  
Ecological Opportunity ◽  
Genetic Changes ◽  
Content Type ◽  
Adaptive Diversification ◽  
Evolutionary Theories ◽  
Rapid Emergence

The plague bacillusYersinia pestisis unique among the pathogenicEnterobacteriaceaein utilizing an arthropod-borne transmission route. Transmission by fleabite is a recent evolutionary adaptation that followed the divergence ofY. pestisfrom the closely related food- and waterborne enteric pathogenYersinia pseudotuberculosis. A combination of population genetics, comparative genomics, and investigations ofYersinia-flea interactions have disclosed the important steps in the evolution and emergence ofY. pestisas a flea-borne pathogen. Only a few genetic changes, representing both gene gain by lateral transfer and gene loss by loss-of-function mutation (pseudogenization), were fundamental to this process. The emergence ofY. pestisfits evolutionary theories that emphasize ecological opportunity in adaptive diversification and rapid emergence of new species.

scholarly journals Molecular genetic changes in kidney tissue in patients with COVID-19

2021 ◽  
Vol 8 (3) ◽  
pp. 45-51
Author(s):  
G. A. Demyashkin ◽  
A. M. Mingazov ◽  
E. A. Kaprina ◽  
V. I. Shchekin ◽  
P. V. Shegay
Keyword(s):  
Protein Complexes ◽  
Molecular Genetic ◽  
Genetic Material ◽  
Kidney Tissue ◽  
Control Group ◽  
Genetic Profile ◽  
Genetic Changes ◽  
Genes Encoding ◽  
Favorable Conditions ◽  
High Degree

Purpose of the study. Assessment of the molecular genetic profile of cytological processes in the kidney tissue of patients with COVID‑19.Material and methods. Kidney fragments from patients with confirmed COVID‑19 (n = 96) were studied by real-time polymerase chain reaction to determine the expression of SARS-CoV‑2 viral RNA and genes encoding protein complexes: ACE‑2 and Furin. Results. In patients affected by COVID‑19, the presence of coronavirus genetic material in kidney tissue was recorded, as well as increased expression of ACE‑2 (7.49 ± 0.27, p < 0.01) and Furin 2.0 times (8.59 ± 0.65, p < 0.01,) compared with the control group (3.9 ± 0.48, p < 0.01 and 4.2 ± 0.8, p < 0.01, respectively), which creates favorable conditions for the invasion of SARS-CoV‑2.Conclusion. According to the results of RT-PCR for SARS-CoV‑2, assessment of the expression of ACE‑2 and Furin, it is possible with a high degree of probability to assert about the viral load and the vulnerability of the kidneys, since these proteins are informative markers of viral damage. Elderly people with increased vulnerability to SARS-CoV‑2.

scholarly journals Periprotein lipidomes of Saccharomyces cerevisiae provide a flexible environment for conformational changes of membrane proteins

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Joury S van 't Klooster ◽  
Tan-Yun Cheng ◽  
Hendrik R Sikkema ◽  
Aike Jeucken ◽  
Branch Moody ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Membrane Proteins ◽  
Small Molecules ◽  
Conformational Changes ◽  
Direct Detection ◽  
Protein Complexes ◽  
Lateral Diffusion ◽  
Low Ph ◽  
Lipid Particles ◽  
High Degree

Yeast tolerates a low pH and high solvent concentrations. The permeability of the plasma membrane (PM) for small molecules is low and lateral diffusion of proteins is slow. These findings suggest a high degree of lipid order, which raises the question of how membrane proteins function in such an environment. The yeast PM is segregated into the Micro-Compartment-of-Can1 (MCC) and Pma1 (MCP), which have different lipid compositions. We extracted proteins from these microdomains via stoichiometric capture of lipids and proteins in styrene-maleic-acid-lipid-particles (SMALPs). We purified SMALP-lipid-protein complexes by chromatography and quantitatively analyzed periprotein lipids located within the diameter defined by one SMALP. Phospholipid and sterol concentrations are similar for MCC and MCP, but sphingolipids are enriched in MCP. Ergosterol is depleted from this periprotein lipidome, whereas phosphatidylserine is enriched relative to the bulk of the plasma membrane. Direct detection of PM lipids in the 'periprotein space' supports the conclusion that proteins function in the presence of a locally disordered lipid state.

scholarly journals Allelic variation contributes to bacterial host specificity

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Min Yue ◽  
Xiangan Han ◽  
Leon De Masi ◽  
Chunhong Zhu ◽  
Xun Ma ◽  
...  
Keyword(s):  
Allelic Variation ◽  
Multinomial Logistic Regression ◽  
Gene Gain ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
Serovar Typhimurium ◽  
Functional Analyses ◽  
High Degree

Abstract Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population and functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. Together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts.

scholarly journals Interplay of Various Evolutionary Modes in Genome Diversification and Adaptive Evolution of the Family Sulfolobaceae

2021 ◽  
Vol 12 ◽  
Author(s):  
Rachana Banerjee ◽  
Narendrakumar M. Chaudhari ◽  
Abhishake Lahiri ◽  
Anupam Gautam ◽  
Debaleena Bhowmik ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Sulfur Metabolism ◽  
Purifying Selection ◽  
Gene Gain ◽  
Sulfolobus Islandicus ◽  
Gene Acquisition ◽  
Genomic Adaptation ◽  
Differential Gene ◽  
Gain Loss ◽  
Geographical Locations

Sulfolobaceae family, comprising diverse thermoacidophilic and aerobic sulfur-metabolizing Archaea from various geographical locations, offers an ideal opportunity to infer the evolutionary dynamics across the members of this family. Comparative pan-genomics coupled with evolutionary analyses has revealed asymmetric genome evolution within the Sulfolobaceae family. The trend of genome streamlining followed by periods of differential gene gains resulted in an overall genome expansion in some species of this family, whereas there was reduction in others. Among the core genes, both Sulfolobus islandicus and Saccharolobus solfataricus showed a considerable fraction of positively selected genes and also higher frequencies of gene acquisition. In contrast, Sulfolobus acidocaldarius genomes experienced substantial amount of gene loss and strong purifying selection as manifested by relatively lower genome size and higher genome conservation. Central carbohydrate metabolism and sulfur metabolism coevolved with the genome diversification pattern of this archaeal family. The autotrophic CO2 fixation with three significant positively selected enzymes from S. islandicus and S. solfataricus was found to be more imperative than heterotrophic CO2 fixation for Sulfolobaceae. Overall, our analysis provides an insight into the interplay of various genomic adaptation strategies including gene gain–loss, mutation, and selection influencing genome diversification of Sulfolobaceae at various taxonomic levels and geographical locations.

Crystal structure of the pseudoenzyme PDX1.2 in complex with its cognate enzyme PDX1.3: a total eclipse

2019 ◽  
Vol 75 (4) ◽  
pp. 400-415 ◽  
Author(s):  
Graham C. Robinson ◽  
Markus Kaufmann ◽  
Céline Roux ◽  
Jacobo Martinez-Font ◽  
Michael Hothorn ◽  
...  
Keyword(s):  
Active Sites ◽  
Protein Complexes ◽  
Structural Similarity ◽  
Cellular Protein ◽  
Vitamin B ◽  
Protein Activity ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Individual ◽  
High Degree

Pseudoenzymes have burst into the limelight recently as they provide another dimension to regulation of cellular protein activity. In the eudicot plant lineage, the pseudoenzyme PDX1.2 and its cognate enzyme PDX1.3 interact to regulate vitamin B6 biosynthesis. This partnership is important for plant fitness during environmental stress, in particular heat stress. PDX1.2 increases the catalytic activity of PDX1.3, with an overall increase in vitamin B6 biosynthesis. However, the mechanism by which this is achieved is not known. In this study, the Arabidopsis thaliana PDX1.2–PDX1.3 complex was crystallized in the absence and presence of ligands, and attempts were made to solve the X-ray structures. Three PDX1.2–PDX1.3 complex structures are presented: the PDX1.2–PDX1.3 complex as isolated, PDX1.2–PDX1.3-intermediate (in the presence of substrates) and a catalytically inactive complex, PDX1.2–PDX1.3-K97A. Data were also collected from a crystal of a selenomethionine-substituted complex, PDX1.2–PDX1.3-SeMet. In all cases the protein complexes assemble as dodecamers, similar to the recently reported individual PDX1.3 homomer. Intriguingly, the crystals of the protein complex are statistically disordered owing to the high degree of structural similarity of the individual PDX1 proteins, such that the resulting configuration is a composite of both proteins. Despite the differential methionine content, selenomethionine substitution of the PDX1.2–PDX1.3 complex did not resolve the problem. Furthermore, a comparison of the catalytically competent complex with a noncatalytic complex did not facilitate the resolution of the individual proteins. Interestingly, another catalytic lysine in PDX1.3 (Lys165) that pivots between the two active sites in PDX1 (P1 and P2), and the corresponding glutamine (Gln169) in PDX1.2, point towards P1, which is distinctive to the initial priming for catalytic action. This state was previously only observed upon trapping PDX1.3 in a catalytically operational state, as Lys165 points towards P2 in the resting state. Overall, the study shows that the integration of PDX1.2 into a heteromeric dodecamer assembly with PDX1.3 does not cause a major structural deviation from the overall architecture of the homomeric complex. Nonetheless, the structure of the PDX1.2–PDX1.3 complex highlights enhanced flexibility in key catalytic regions for the initial steps of vitamin B6 biosynthesis. This report highlights what may be an intrinsic limitation of X-ray crystallography in the structural investigation of pseudoenzymes.

scholarly journals Rational Savings Account Models for Backward-Looking Interest Rate Benchmarks

Risks ◽  
2020 ◽  
Vol 8 (1) ◽  
pp. 23 ◽  
Author(s):  
Andrea Macrina ◽  
David Skovmand
Keyword(s):  
Interest Rate ◽  
Cash Flows ◽  
Rate System ◽  
Rational Form ◽  
Adjusted Risk ◽  
New Class ◽  
Discount Factors ◽  
Major Transition ◽  
Risk Free Rate ◽  
High Degree

Interest rate benchmarks are currently undergoing a major transition. The LIBOR benchmark is planned to be discontinued by the end of 2021 and superseded by what ISDA calls an adjusted risk-free rate (RFR). ISDA has recently announced that the LIBOR replacement will most likely be constructed from a compounded running average of RFR overnight rates over a period matching the LIBOR tenor. This new backward-looking benchmark is markedly different when compared with LIBOR. It is measurable only at the end of the term in contrast to the forward-looking LIBOR, which is measurable at the start of the term. The RFR provides a simplification because the cash flows and the discount factors may be derived from the same discounting curve, thus avoiding—on a superficial level—any multi-curve complications. We develop a new class of savings account models and derive a novel interest rate system specifically designed to facilitate a high degree of tractability for the pricing of RFR-based fixed-income instruments. The rational form of the savings account models under the risk-neutral measure enables the pricing in closed form of caplets, swaptions and futures written on the backward-looking interest rate benchmark.

scholarly journals odNEAT: An Algorithm for Decentralised Online Evolution of Robotic Controllers

2015 ◽  
Vol 23 (3) ◽  
pp. 421-449 ◽  
Author(s):  
Fernando Silva ◽  
Paulo Urbano ◽  
Luís Correia ◽  
Anders Lyhne Christensen
Keyword(s):  
Evolutionary Dynamics ◽  
Autonomous Robots ◽  
Integrated Navigation ◽  
Task Execution ◽  
Neural Controllers ◽  
Novel Approach ◽  
Fixed Topology ◽  
High Degree ◽  
The Impact ◽  
Algorithmic Component

Online evolution gives robots the capacity to learn new tasks and to adapt to changing environmental conditions during task execution. Previous approaches to online evolution of neural controllers are typically limited to the optimisation of weights in networks with a prespecified, fixed topology. In this article, we propose a novel approach to online learning in groups of autonomous robots called odNEAT. odNEAT is a distributed and decentralised neuroevolution algorithm that evolves both weights and network topology. We demonstrate odNEAT in three multirobot tasks: aggregation, integrated navigation and obstacle avoidance, and phototaxis. Results show that odNEAT approximates the performance of rtNEAT, an efficient centralised method, and outperforms IM-([Formula: see text]), a decentralised neuroevolution algorithm. Compared with rtNEAT and IM-([Formula: see text]), odNEAT’s evolutionary dynamics lead to the synthesis of less complex neural controllers with superior generalisation capabilities. We show that robots executing odNEAT can display a high degree of fault tolerance as they are able to adapt and learn new behaviours in the presence of faults. We conclude with a series of ablation studies to analyse the impact of each algorithmic component on performance.

scholarly journals Mother–offspring and nest-mate resemblance but no heritability in early-life telomere length in white-throated dippers

2015 ◽  
Vol 282 (1807) ◽  
pp. 20142924 ◽  
Author(s):  
Philipp J. J. Becker ◽  
Sophie Reichert ◽  
Sandrine Zahn ◽  
Johann Hegelbach ◽  
Sylvie Massemin ◽  
...  
Keyword(s):  
Telomere Length ◽  
Early Life ◽  
Evolutionary Dynamics ◽  
Protein Complexes ◽  
Additive Genetic Variance ◽  
Pedigree Data ◽  
Genes And Environment ◽  
Cinclus Cinclus ◽  
Maternal Imprinting

Telomeres are protective DNA–protein complexes located at the ends of eukaryotic chromosomes, whose length has been shown to predict life-history parameters in various species. Although this suggests that telomere length is subject to natural selection, its evolutionary dynamics crucially depends on its heritability. Using pedigree data for a population of white-throated dippers ( Cinclus cinclus ), we test whether and how variation in early-life relative telomere length (RTL, measured as the number of telomeric repeats relative to a control gene using qPCR) is transmitted across generations. We disentangle the relative effects of genes and environment and test for sex-specific patterns of inheritance. There was strong and significant resemblance among offspring sharing the same nest and offspring of the same cohort. Furthermore, although offspring resemble their mother, and there is some indication for an effect of inbreeding, additive genetic variance and heritability are close to zero. We find no evidence for a role of either maternal imprinting or Z-linked inheritance in generating these patterns, suggesting they are due to non-genetic maternal and common environment effects instead. We conclude that in this wild bird population, environmental factors are the main drivers of variation in early-life RTL, which will severely bias estimates of heritability when not modelled explicitly.

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