Molecular evolution of genes encoding ribonucleases in ruminant species

1995 ◽  
Vol 41 (6) ◽  
Author(s):  
E. Confalone ◽  
J.J. Beintema ◽  
M.P. Sasso ◽  
A. Carsana ◽  
M. Palmieri ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Ruminant Species ◽  
Genes Encoding

Molecular evolution of duplicate copies of genes encoding cytosolic glutamine synthetase in Pisum sativum

1995 ◽  
Vol 29 (6) ◽  
pp. 1111-1125 ◽  
Author(s):  
Elsbeth L. Walker ◽  
N. F. Weeden ◽  
Crispin B. Taylor ◽  
Pamela Green ◽  
Gloria M. Coruzzi
Keyword(s):  
Molecular Evolution ◽  
Pisum Sativum ◽  
Glutamine Synthetase ◽  
Genes Encoding ◽  
Cytosolic Glutamine Synthetase

scholarly journals Molecular evolution of integrins: Genes encoding integrin   subunits from a coral and a sponge

1997 ◽  
Vol 94 (17) ◽  
pp. 9182-9187 ◽  
Author(s):  
D. L. Brower ◽  
S. M. Brower ◽  
D. C. Hayward ◽  
E. E. Ball
Keyword(s):  
Molecular Evolution ◽  
Genes Encoding

scholarly journals Ongoing Assessment of the Molecular Evolution of Peste Des Petits Ruminants Virus Continues to Question Viral Origins

Viruses ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2144
Author(s):  
Mana Mahapatra ◽  
Richa Pachauri ◽  
Saravanan Subramaniam ◽  
Ashley C. Banyard ◽  
Shanmugam ChandraSekar ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
United Arab Emirates ◽  
Viral Evolution ◽  
Virus Detection ◽  
Host Susceptibility ◽  
Peste Des Petits Ruminants ◽  
Ruminant Species ◽  
High Concern ◽  
Viral Emergence ◽  
Evolutionary Emergence

Understanding the evolution of viral pathogens is critical to being able to define how viruses emerge within different landscapes. Host susceptibility, which is spread between different species and is a contributing factor to the subsequent epidemiology of a disease, is defined by virus detection and subsequent characterization. Peste des petits ruminants virus is a plague of small ruminant species that is a considerable burden to the development of sustainable agriculture across Africa and much of Asia. The virus has also had a significant impact on populations of endangered species in recent years, highlighting its significance as a pathogen of high concern across different regions of the globe. Here, we have re-evaluated the molecular evolution of this virus using novel genetic data to try and further resolve the molecular epidemiology of this disease. Viral isolates are genetically characterized into four lineages (I−IV), and the historic origin of these lineages is of considerable interest to the molecular evolution of the virus. Our re-evaluation of viral emergence using novel genome sequences has demonstrated that lineages I, II and IV likely originated in West Africa, in Senegal (I) and Nigeria (II and IV). Lineage III sequences predicted emergence in either East Africa (Ethiopia) or in the Arabian Peninsula (Oman and/or the United Arab Emirates), with a paucity of data precluding a more refined interpretation. Continual refinements of evolutionary emergence, following the generation of new data, is key to both understanding viral evolution from a historic perspective and informing on the ongoing genetic emergence of this virus.

scholarly journals Dynamic sensitivity and nonlinear interactions influence the system-level evolutionary patterns of phototransduction proteins

2015 ◽  
Vol 282 (1820) ◽  
pp. 20152215 ◽  
Author(s):  
Brandon M. Invergo ◽  
Ludovica Montanucci ◽  
Jaume Bertranpetit
Keyword(s):  
Molecular Evolution ◽  
System Dynamics ◽  
Molecular System ◽  
System Level ◽  
Evolutionary Constraint ◽  
Nonlinear Interactions ◽  
Evolutionary Patterns ◽  
Genes Encoding ◽  
System Output ◽  
High Level

Determining the influence of complex, molecular-system dynamics on the evolution of proteins is hindered by the significant challenge of quantifying the control exerted by the proteins on system output. We have employed a combination of systems biology and molecular evolution analyses in a first attempt to unravel this relationship. We employed a comprehensive mathematical model of mammalian phototransduction to predict the degree of influence that each protein in the system exerts on the high-level dynamic behaviour. We found that the genes encoding the most dynamically sensitive proteins exhibit relatively relaxed evolutionary constraint. We also investigated the evolutionary and epistatic influences of the many nonlinear interactions between proteins in the system and found several pairs to have coevolved, including those whose interactions are purely dynamical with respect to system output. This evidence points to a key role played by nonlinear system dynamics in influencing patterns of molecular evolution.

Nucleotide sequence and molecular evolution of two tomato genes encoding the small subunit of ribulose-1,5-bisphosphate carboxylase

Gene ◽  
1986 ◽  
Vol 48 (1) ◽  
pp. 23-32 ◽  
Author(s):  
Thomas D. McKnight ◽  
Danny C. Alexander ◽  
Marla S. Babcock ◽  
Robert B. Simpson
Keyword(s):  
Molecular Evolution ◽  
Nucleotide Sequence ◽  
Small Subunit ◽  
Bisphosphate Carboxylase ◽  
Genes Encoding

scholarly journals Origins and Molecular Evolution of the NusG Paralog RfaH

mBio ◽  
2020 ◽  
Vol 11 (5) ◽  
Author(s):  
Bing Wang ◽  
Vadim M. Gumerov ◽  
Ekaterina P. Andrianova ◽  
Igor B. Zhulin ◽  
Irina Artsimovitch
Keyword(s):  
Transcription Factors ◽  
Molecular Evolution ◽  
Rna Polymerase ◽  
Housekeeping Genes ◽  
Content Type ◽  
Bacterial Phyla ◽  
Evolutionary Origins ◽  
Genes Encoding ◽  
Domains Of Life ◽  
Polymerase Binding

ABSTRACT The only universally conserved family of transcription factors comprises housekeeping regulators and their specialized paralogs, represented by well-studied NusG and RfaH. Despite their ubiquity, little information is available on the evolutionary origins, functions, and gene targets of the NusG family members. We built a hidden Markov model profile of RfaH and identified its homologs in sequenced genomes. While NusG is widespread among bacterial phyla and coresides with genes encoding RNA polymerase and ribosome in all except extremely reduced genomes, RfaH is mostly limited to Proteobacteria and lacks common gene neighbors. RfaH activates only a few xenogeneic operons that are otherwise silenced by NusG and Rho. Phylogenetic reconstructions reveal extensive duplications and horizontal transfer of rfaH genes, including those borne by plasmids, and the molecular evolution pathway of RfaH, from “early” exclusion of the Rho terminator and tightened RNA polymerase binding to “late” interactions with the ops DNA element and autoinhibition, which together define the RfaH regulon. Remarkably, NusG is not only ubiquitous in Bacteria but also common in plants, where it likely modulates the transcription of plastid genes. IMPORTANCE In all domains of life, NusG-like proteins make contacts similar to those of RNA polymerase and promote pause-free transcription yet may play different roles, defined by their divergent interactions with nucleic acids and accessory proteins, in the same cell. This duality is illustrated by Escherichia coli NusG and RfaH, which silence and activate xenogenes, respectively. We combined sequence analysis and recent functional and structural insights to envision the evolutionary transformation of NusG, a core regulator that we show is present in all cells using bacterial RNA polymerase, into a virulence factor, RfaH. Our results suggest a stepwise conversion of a NusG duplicate copy into a sequence-specific regulator which excludes NusG from its targets but does not compromise the regulation of housekeeping genes. We find that gene duplication and lateral transfer give rise to a surprising diversity within the only ubiquitous family of transcription factors.

scholarly journals Phylogenetic analysis of selected representatives of the genus Erica based on the genes encoding the DNA-dependent RNA polymerase I

2017 ◽  
Vol 46 (1) ◽  
pp. 1-18 ◽  
Author(s):  
Angelika Maria Gomolińska ◽  
Monika Szczecińska ◽  
Jakub Sawicki ◽  
Katarzyna Krawczyk ◽  
Piotr Szkudlarz
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Evolution ◽  
Rna Polymerase I ◽  
Mutation Rates ◽  
Phylogenetic Marker ◽  
Phylogenetic Informativeness ◽  
Rate Of Molecular Evolution ◽  
Genes Encoding ◽  
Multiple Levels ◽  
Polymerase I

Abstract The rpo genes are characterized by rapidly-evolving sequences. They encode subunits of plastid-encoded (PEP) polymerase (rpoA, rpoB, rpoC1 and rpoC2). This polymerase is one of the most important enzymes in the chloroplasts. The primary aim of the research was to study the rate of molecular evolution in the rpo genes and to estimate these genes as phylogenetic markers based on the example of the genus Erica (Ericaceae). The tested rpo genes demonstrated similarities on multiple levels, for example: phylogenetic informativeness, variation level, intragenic mutation rates and the effect of intragenic mutations on the properties of encoded peptides. This study did not confirm that the analyzed rpo genes are reliable markers and may be helpful in understanding phylogenetic relationships between species that belong to the same genus. The rpoC2 gene was found to be a most useful phylogenetic marker in the Erica genus, while rpoC1 was found to be the least promising gene.

scholarly journals Molecular evolution of genes encoding allergen proteins in the peanuts genus Arachis: Structural and functional implications

PLoS ONE ◽  
2019 ◽  
Vol 14 (11) ◽  
pp. e0222440
Author(s):  
Khidir W. Hilu ◽  
Sheena A. Friend ◽  
Viruthika Vallanadu ◽  
Anne M. Brown ◽  
Louis R. Hollingsworth ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Functional Implications ◽  
Genes Encoding

Molecular evolution of the genes encoding receptor tyrosine kinase with immunoglobulinlike domains

1995 ◽  
Vol 41 (4) ◽  
pp. 421-429 ◽  
Author(s):  
Dominique Rousset ◽  
Fran�ois Agn�s ◽  
Philippe Lachaume ◽  
Catherine Andr� ◽  
Francis Galibert
Keyword(s):  
Molecular Evolution ◽  
Tyrosine Kinase ◽  
Receptor Tyrosine Kinase ◽  
Genes Encoding

scholarly journals Molecular evolution of DNMT1 in vertebrates: duplications in marsupials followed by positive selection

2018 ◽  
Author(s):  
David Alvarez-Ponce ◽  
María Torres-Sánchez ◽  
Felix Feyertag ◽  
Asmita Kulkarni ◽  
Taylen Nappi
Keyword(s):  
Dna Methylation ◽  
Molecular Evolution ◽  
Positive Selection ◽  
Phylogenetic Analyses ◽  
Purifying Selection ◽  
Single Copy ◽  
Tammar Wallaby ◽  
Dna Methyltransferases ◽  
Tasmanian Devil ◽  
Genes Encoding

AbstractDNA methylation is mediated by a conserved family of DNA methyltransferases (Dnmts). The human genome encodes five Dnmts: Dnmt1, Dnmt2, Dnmt3a, Dnmt3b and Dnmt3L. Despite their high degree of conservation among different species, genes encoding Dnmts have been duplicated and/or lost in multiple lineages throughout evolution, indicating that the DNA methylation machinery has some potential to undergo evolutionary change. However, little is known about the extent to which this machinery, or the methylome, varies among vertebrates. Here, we study the molecular evolution of Dnmt1, the enzyme responsible for maintenance of DNA methylation patterns after replication, in 79 vertebrate species. Our analyses show that all studied species exhibit a single copy of DNMT1, with the exception of tilapia and marsupials (tammar wallaby, koala, Tasmanian devil and opossum), each of which exhibits two apparently functional DNMT1 copies. Our phylogenetic analyses indicate that DNMT1 duplicated before the divergence of marsupials (i.e., at least ~75 million years ago), thus giving rise to two DNMT1 copies in marsupials (copy 1 and copy 2). In the opossum lineage, copy 2 was lost, and copy 1 recently duplicated again, generating three DNMT1 copies: two putatively functional genes (copy 1a and 1b) and one pseudogene (copy 1ψ). Both marsupial copies (DNMT1 copies 1 and 2) are under purifying selection, and copy 2 exhibits elevated rates of evolution and signatures of positive selection, suggesting a scenario of neofunctionalization. This gene duplication might have resulted in modifications in marsupial methylomes and their dynamics.

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