scholarly journals Phylogenomics Provides New Insights into Gains and Losses of Selenoproteins among Archaeplastida

2019 ◽  
Vol 20 (12) ◽  
pp. 3020 ◽  
Author(s):  
Hongping Liang ◽  
Tong Wei ◽  
Yan Xu ◽  
Linzhou Li ◽  
Sunil Kumar Sahu ◽  
...  
Keyword(s):  
Horizontal Gene Transfer ◽  
Evolutionary Dynamics ◽  
Viral Infections ◽  
Land Plants ◽  
Acidic Environment ◽  
Transcriptome Data ◽  
Photosynthetic Eukaryotes ◽  
Redox Active ◽  
Genomic Search ◽  
Gains And Losses

Selenoproteins that contain selenocysteine (Sec) are found in all kingdoms of life. Although they constitute a small proportion of the proteome, selenoproteins play essential roles in many organisms. In photosynthetic eukaryotes, selenoproteins have been found in algae but are missing in land plants (embryophytes). In this study, we explored the evolutionary dynamics of Sec incorporation by conveying a genomic search for the Sec machinery and selenoproteins across Archaeplastida. We identified a complete Sec machinery and variable sizes of selenoproteomes in the main algal lineages. However, the entire Sec machinery was missing in the Bangiophyceae-Florideophyceae clade (BV) of Rhodoplantae (red algae) and only partial machinery was found in three species of Archaeplastida, indicating parallel loss of Sec incorporation in different groups of algae. Further analysis of genome and transcriptome data suggests that all major lineages of streptophyte algae display a complete Sec machinery, although the number of selenoproteins is low in this group, especially in subaerial taxa. We conclude that selenoproteins tend to be lost in Archaeplastida upon adaptation to a subaerial or acidic environment. The high number of redox-active selenoproteins found in some bloom-forming marine microalgae may be related to defense against viral infections. Some of the selenoproteins in these organisms may have been gained by horizontal gene transfer from bacteria.

scholarly journals Phylogenomics provides new insights into gains and losses of selenoproteins among Archaeplastida

2019 ◽  
Author(s):  
Hongping Liang ◽  
Tong Wei ◽  
Yan Xu ◽  
Linzhou Li ◽  
Sunil Kumar Sahu ◽  
...  
Keyword(s):  
Horizontal Gene Transfer ◽  
Evolutionary Dynamics ◽  
Viral Infections ◽  
Land Plants ◽  
Acidic Environment ◽  
Transcriptome Data ◽  
Photosynthetic Eukaryotes ◽  
Redox Active ◽  
Genomic Search ◽  
Gains And Losses

AbstractSelenoproteins that contain selenocysteine (Sec) are found in all kingdoms of life. Although they constitute a small proportion of the proteome, selenoproteins play essential roles in many organisms. In photosynthetic eukaryotes, selenoproteins have been found in algae but are missing in land plants (embryophytes). In this study, we explored the evolutionary dynamics of Sec incorporation by conveying a genomic search for the Sec machinery and selenoproteins across Archaeplastida. We identified a complete Sec machinery and variable sizes of selenoproteomes in the main algal lineages. However, the entire Sec machinery was missing in the BV clade (Bangiophyceae-Florideophyceae) of Rhodoplantae (red algae) and only partial machinery was found in three species of Archaeplastida, indicating parallel loss of Sec incorporation in different groups of algae. Further analysis of genome and transcriptome data suggests that all major lineages of streptophyte algae display a complete Sec machinery, although the number of selenoproteins is low in this group, especially in subaerial taxa. We conclude that selenoproteins tend to be lost in Archaeplastida upon adaptation to a subaerial or acidic environment. The high number of redox-active selenoproteins found in some bloom-forming marine microalgae may be related to defense against viral infections. Some of the selenoproteins in these organisms may have been gained by horizontal gene transfer from bacteria.

scholarly journals Horizontal Gene Transfer Clarifies Taxonomic Confusion and Promotes the Genetic Diversity and Pathogenicity of Plesiomonas shigelloides

mSystems ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Zhiqiu Yin ◽  
Si Zhang ◽  
Yi Wei ◽  
Meng Wang ◽  
Shuangshuang Ma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Evolutionary Dynamics ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Content Type ◽  
Pan Genome ◽  
Long Time ◽  
Taxonomic Confusion

The taxonomic position of P. shigelloides has been the subject of debate for a long time, and until now, the evolutionary dynamics and pathogenesis of P. shigelloides were unclear. In this study, pan-genome analysis indicated extensive genetic diversity and the presence of large and variable gene repertoires. Our results revealed that horizontal gene transfer was the focal driving force for the genetic diversity of the P. shigelloides pan-genome and might have contributed to the emergence of novel properties. Vibrionaceae and Aeromonadaceae were found to be the predominant donor taxa for horizontal genes, which might have caused the taxonomic confusion historically. Comparative genomic analysis revealed the potential of P. shigelloides to cause intestinal and invasive diseases. Our results could advance the understanding of the evolution and pathogenesis of P. shigelloides, particularly in elucidating the role of horizontal gene transfer and investigating virulence-related elements.

scholarly journals Experimental Evolution of Bacillus subtilis Reveals the Evolutionary Dynamics of Horizontal Gene Transfer and Suggests Adaptive and Neutral Effects

Genetics ◽  
2020 ◽  
Vol 216 (2) ◽  
pp. 543-558
Author(s):  
Shai Slomka ◽  
Itamar Françoise ◽  
Gil Hornung ◽  
Omer Asraf ◽  
Tammy Biniashvili ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Growth Yield ◽  
Genomic Variation ◽  
Bacterial Populations ◽  
Flagellar Proteins ◽  
Foreign Dna

Tracing evolutionary processes that lead to fixation of genomic variation in wild bacterial populations is a prime challenge in molecular evolution. In particular, the relative contribution of horizontal gene transfer (HGT) vs.de novo mutations during adaptation to a new environment is poorly understood. To gain a better understanding of the dynamics of HGT and its effect on adaptation, we subjected several populations of competent Bacillus subtilis to a serial dilution evolution on a high-salt-containing medium, either with or without foreign DNA from diverse pre-adapted or naturally salt tolerant species. Following 504 generations of evolution, all populations improved growth yield on the medium. Sequencing of evolved populations revealed extensive acquisition of foreign DNA from close Bacillus donors but not from more remote donors. HGT occurred in bursts, whereby a single bacterial cell appears to have acquired dozens of fragments at once. In the largest burst, close to 2% of the genome has been replaced by HGT. Acquired segments tend to be clustered in integration hotspots. Other than HGT, genomes also acquired spontaneous mutations. Many of these mutations occurred within, and seem to alter, the sequence of flagellar proteins. Finally, we show that, while some HGT fragments could be neutral, others are adaptive and accelerate evolution.

scholarly journals Yellow Fever Virus Exhibits Slower Evolutionary Dynamics than Dengue Virus

2009 ◽  
Vol 84 (2) ◽  
pp. 765-772 ◽  
Author(s):  
Amadou A. Sall ◽  
Ousmane Faye ◽  
Mawlouth Diallo ◽  
Cadhla Firth ◽  
Andrew Kitchen ◽  
...  
Keyword(s):  
Dengue Virus ◽  
Yellow Fever ◽  
Central African Republic ◽  
Evolutionary Dynamics ◽  
Nucleotide Substitution ◽  
Viral Infections ◽  
Yellow Fever Virus ◽  
Fever Virus ◽  
Limited Information ◽  
Reduced Rate

ABSTRACT Although yellow fever has historically been one of the most important viral infections of humans, relatively little is known about the evolutionary processes that shape its genetic diversity. Similarly, there is limited information on the molecular epidemiology of yellow fever virus (YFV) in Africa even though it most likely first emerged on this continent. Through an analysis of complete E gene sequences, including a newly acquired viral collection from Central and West Africa (Senegal, Cameroon, Central African Republic, Côte d'Ivoire, Mali, and Mauritania), we show that YFV exhibits markedly lower rates of evolutionary change than dengue virus, despite numerous biological similarities between these two viruses. From this observation, along with a lack of clock-like evolutionary behavior in YFV, we suggest that vertical transmission, itself characterized by lower replication rates, may play an important role in the evolution of YFV in its enzootic setting. Despite a reduced rate of nucleotide substitution, phylogenetic patterns and estimates of times to common ancestry in YFV still accord well with the dual histories of colonialism and the slave trade, with areas of sylvatic transmission (such as Kedougou, Senegal) acting as enzootic/epidemic foci.

scholarly journals The Ecology of Bacterial Genes and the Survival of the New

2012 ◽  
Vol 2012 ◽  
pp. 1-14 ◽  
Author(s):  
M. Pilar Francino
Keyword(s):  
Evolutionary Dynamics ◽  
Environmental Changes ◽  
Gene Families ◽  
Relative Importance ◽  
Gene Duplications ◽  
Bacterial Genomes ◽  
Selective Pressures ◽  
Different Types ◽  
Bacterial Genes ◽  
Gains And Losses

Much of the observed variation among closely related bacterial genomes is attributable to gains and losses of genes that are acquired horizontally as well as to gene duplications and larger amplifications. The genomic flexibility that results from these mechanisms certainly contributes to the ability of bacteria to survive and adapt in varying environmental challenges. However, the duplicability and transferability of individual genes imply that natural selection should operate, not only at the organismal level, but also at the level of the gene. Genes can be considered semiautonomous entities that possess specific functional niches and evolutionary dynamics. The evolution of bacterial genes should respond both to selective pressures that favor competition, mostly among orthologs or paralogs that may occupy the same functional niches, and cooperation, with the majority of other genes coexisting in a given genome. The relative importance of either type of selection is likely to vary among different types of genes, based on the functional niches they cover and on the tightness of their association with specific organismal lineages. The frequent availability of new functional niches caused by environmental changes and biotic evolution should enable the constant diversification of gene families and the survival of new lineages of genes.

scholarly journals The Relevance of Plant-Derived Se Compounds to Human Health in the SARS-CoV-2 (COVID-19) Pandemic Era

Antioxidants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1031
Author(s):  
Leonardo Warzea Lima ◽  
Serenella Nardi ◽  
Veronica Santoro ◽  
Michela Schiavon
Keyword(s):  
Human Health ◽  
Global Economy ◽  
Viral Infections ◽  
Catalytic Center ◽  
Physiological Processes ◽  
Redox Active ◽  
Active Metal ◽  
Insertion Mechanism ◽  
Novel Coronavirus ◽  
Redox Active Metal

Dietary selenium (Se)-compounds accumulated in plants are essential for human metabolism and normal physiological processes. Inorganic and organic Se species can be readily absorbed by the human body, but are metabolized differently and thus exhibit distinct mechanisms of action. They can act as antioxidants or serve as a source of Se for the synthesis of selenoproteins. Selenocysteine, in particular, is incorporated at the catalytic center of these proteins through a specific insertion mechanism and, due to its electronic features, enhances their catalytic activity against biological oxidants. Selenite and other Se-organic compounds may also act as direct antioxidants in cells due to their strong nucleophilic properties. In addition, Se-amino acids are more easily subjected to oxidation than the corresponding thiols/thioethers and can bind redox-active metal ions. Adequate Se intake aids in preventing several metabolic disorders and affords protection against viral infections. At present, an epidemic caused by a novel coronavirus (SARS-CoV-2) threatens human health across several countries and impacts the global economy. Therefore, Se-supplementation could be a complementary treatment to vaccines and pharmacological drugs to reduce the viral load, mutation frequency, and enhance the immune system of populations with low Se intake in the diet.

scholarly journals From morphogenesis to pathogenesis: A cellulose loosening protein is one of the most widely distributed tools in nature

2019 ◽  
Author(s):  
William R. Chase ◽  
Olga Zhaxybayeva ◽  
Jorge Rocha ◽  
Daniel J. Cosgrove ◽  
Lori R. Shapiro
Keyword(s):  
Cell Wall ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Cell Walls ◽  
Growth And Development ◽  
Land Plants ◽  
Cellulose Microfibrils ◽  
Plant Cell Walls ◽  
Phylogenetic Distribution ◽  
Bacteria And Fungi

AbstractPlants must rearrange the network of complex carbohydrates in their cell walls during normal growth and development. To accomplish this, all plants depend on proteins called expansins that non-enzymatically loosen hydrogen bonds between cellulose microfibrils. Because of their key role in cell wall extension during growth, expansin genes are ubiquitous, diverse, and abundant throughout all land plants. Surprisingly, expansin genes have more recently been found in some bacteria and microbial eukaryotes, where their biological functions are largely unknown. Here, we reconstruct the phylogeny of microbial expansin genes. We find these genes in all eukaryotic microorganisms that have structural cellulose in their cell walls, suggesting expansins evolved in ancient marine microorganisms long before the evolution of land plants. We also find expansins in an unexpectedly high phylogenetic diversity of bacteria and fungi that do not have cellulosic cell walls. These bacteria and fungi with expansin genes inhabit varied ecological contexts mirroring the diversity of terrestrial and aquatic niches where plant and/or algal cellulosic cell walls are present. The microbial expansin phylogeny shows evidence of multiple horizontal gene transfer events within and between bacterial and eukaryotic microbial lineages, which may in part underlie their unusually broad phylogenetic distribution. Taken together, we find expansins to be unexpectedly widespread in both bacterial and eukaryotic genetic backgrounds, and that the contribution of these genes to bacterial and fungal ecological interactions with plants and algae has likely been underappreciated.ImportanceCellulose is the most abundant biopolymer on earth. In plant cell walls, where most global cellulose biomass is found, cellulose microfibrils occur intertwined with hemicelluloses and pectins. The rigidity of this polysaccharide matrix provides plant cell walls with structural support, but this rigidity also restricts cellular growth and development. Irreversible, non-enzymatic loosening of structural carbohydrates by expansin proteins is key to successful cell wall growth in plants and green algae. Here, we find that expansin genes are distributed far more broadly throughout diverse bacterial and fungal lineages lacking cellulosic cell walls than previously known. Multiple horizontal gene transfer events are in part responsible for their unusually wide phylogenetic distribution. Together, these results suggest that in addition to being the key evolutionary innovation by which eukaryotes remodel structural cellulose in their cell walls, expansins likely have remarkably broad and under-recognized utility for microbial species that interact with plant and algal structural cellulose in diverse ecological contexts.

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