scholarly journals Compositional diversity and evolutionary pattern of coronavirus accessory proteins

2020 ◽  
Author(s):  
Jingzhe Shang ◽  
Na Han ◽  
Ziyi Chen ◽  
Yousong Peng ◽  
Liang Li ◽  
...  
Keyword(s):  
Genome Annotation ◽  
Regulatory Sequence ◽  
Accessory Proteins ◽  
Evolutionary Analysis ◽  
Evolutionary Patterns ◽  
Reading Frame ◽  
Evolutionary Pattern ◽  
Host Interaction ◽  
Sequence Recognition ◽  
Compositional Diversity

Abstract Accessory proteins play important roles in the interaction between coronaviruses and their hosts. Accordingly, a comprehensive study of the compositional diversity and evolutionary patterns of accessory proteins is critical to understanding the host adaptation and epidemic variation of coronaviruses. Here, we developed a standardized genome annotation tool for coronavirus (CoroAnnoter) by combining open reading frame prediction, transcription regulatory sequence recognition and homologous alignment. Using CoroAnnoter, we annotated 39 representative coronavirus strains to form a compositional profile for all of the accessary proteins. Large variations were observed in the number of accessory proteins of 1–10 for different coronaviruses, with SARS-CoV-2 and SARS-CoV having the most (9 and 10, respectively). The variation between SARS-CoV and SARS-CoV-2 accessory proteins could be traced back to related coronaviruses in other hosts. The genomic distribution of accessory proteins had significant intra-genus conservation and inter-genus diversity and could be grouped into 1, 4, 2 and 1 types for alpha-, beta-, gamma-, and delta-coronaviruses, respectively. Evolutionary analysis suggested that accessory proteins are more conservative locating before the N-terminal of proteins E and M (E-M), while they are more diverse after these proteins. Furthermore, comparison of virus-host interaction networks of SARS-CoV-2 and SARS-CoV accessory proteins showed that they share multiple antiviral signaling pathways, those involved in the apoptotic process, viral life cycle and response to oxidative stress. In summary, our study provides a tool for coronavirus genome annotation and builds a comprehensive profile for coronavirus accessory proteins covering their composition, classification, evolutionary pattern and host interaction.

scholarly journals Concerted and Independent Evolution of Control Regions 1 and 2 of Water Monitor Lizards (Varanus salvator macromaculatus) and Different Phylogenetic Informative Markers

Animals ◽  
2022 ◽  
Vol 12 (2) ◽  
pp. 148
Author(s):  
Watcharaporn Thapana ◽  
Nattakan Ariyaraphong ◽  
Parinya Wongtienchai ◽  
Nararat Laopichienpong ◽  
Worapong Singchat ◽  
...  
Keyword(s):  
Evolutionary Process ◽  
Mitochondrial Genomes ◽  
Sequence Analyses ◽  
Evolutionary Patterns ◽  
Evolutionary Pattern ◽  
Independent Evolution ◽  
Substitution Saturation ◽  
Varanus Salvator ◽  
Monitor Lizards ◽  
Control Regions

Duplicate control regions (CRs) have been observed in the mitochondrial genomes (mitogenomes) of most varanids. Duplicate CRs have evolved in either concerted or independent evolution in vertebrates, but whether an evolutionary pattern exists in varanids remains unknown. Therefore, we conducted this study to analyze the evolutionary patterns and phylogenetic utilities of duplicate CRs in 72 individuals of Varanus salvator macromaculatus and other varanids. Sequence analyses and phylogenetic relationships revealed that divergence between orthologous copies from different individuals was lower than in paralogous copies from the same individual, suggesting an independent evolution of the two CRs. Distinct trees and recombination testing derived from CR1 and CR2 suggested that recombination events occurred between CRs during the evolutionary process. A comparison of substitution saturation showed the potential of CR2 as a phylogenetic marker. By contrast, duplicate CRs of the four examined varanids had similar sequences within species, suggesting typical characteristics of concerted evolution. The results provide a better understanding of the molecular evolutionary processes related to the mitogenomes of the varanid lineage.

scholarly journals Molecular Phylogenetics and Evolutionary Analysis of a Highly Recombinant Begomovirus, Cotton Leaf Curl Multan Virus and Associated Satellites

2021 ◽  
Author(s):  
Tahir Farooq ◽  
Muhammad Umar ◽  
Xiaoman She ◽  
Yafei Tang ◽  
Zifu He
Keyword(s):  
Molecular Phylogenetics ◽  
Management Strategies ◽  
Purifying Selection ◽  
Genomic Diversity ◽  
Cotton Leaf ◽  
Evolutionary Analysis ◽  
Cotton Production ◽  
Evolutionary Patterns ◽  
Satellite Sequences ◽  
Leaf Curl

Abstract Cotton leaf curl Multan virus (CLCuMuV) and its associated satellites are a major part of the cotton leaf curl disease (CLCuD) caused by the begomovirus species complex. Despite the implementation of potential disease management strategies, the incessant resurgence of resistance-breaking variants of CLCuMuV imposes a continuous threat to cotton production. Here, we present a focused effort to map the geographical prevalence, genomic diversity and molecular evolutionary endpoints that enhance disease complexity by facilitating the successful adaptation of CLCuMuV populations to the diversified ecosystems. Our results demonstrate that CLCuMuV populations are predominantly distributed in China while the majority of alphasatellites and betasatellites exist in Pakistan. We demonstrate that together with frequent recombination, an uneven genetic variation mainly drives CLCuMuV and its satellite’s virulence and evolvability. However, the pattern and distribution of recombination breakpoints greatly vary among viral and satellite sequences. The CLCuMuV, Cotton leaf curl Multan alphasatellite (CLCuMuA) and Cotton leaf curl Multan betasatellite (CLCuMuB) populations arising from distinct regions exhibit high mutation rates. Though evolutionary linked, these populations are independently evolving under strong purifying selection. These findings will facilitate to comprehensively understand the standing genetic variability and evolutionary patterns existing among CLCuMuV populations across major cotton-producing regions of the world.

scholarly journals Genetic characterization of a novel picornavirus in Algerian bats: co-evolution analysis of bat-related picornaviruses

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Safia Zeghbib ◽  
Róbert Herczeg ◽  
Gábor Kemenesi ◽  
Brigitta Zana ◽  
Kornélia Kurucz ◽  
...  
Keyword(s):  
Geographical Location ◽  
Data Sets ◽  
Evolutionary Analysis ◽  
Evolutionary Patterns ◽  
Host Genus ◽  
Evolution Analysis ◽  
Zoonotic Viruses ◽  
History Of ◽  
First Time

Abstract Bats are reservoirs of numerous zoonotic viruses. The Picornaviridae family comprises important pathogens which may infect both humans and animals. In this study, a bat-related picornavirus was detected from Algerian Minioptreus schreibersii bats for the first time in the country. Molecular analyses revealed the new virus originates to the Mischivirus genus. In the operational use of the acquired sequence and all available data regarding bat picornaviruses, we performed a co-evolutionary analysis of mischiviruses and their hosts, to authentically reveal evolutionary patterns within this genus. Based on this analysis, we enlarged the dataset, and examined the co-evolutionary history of all bat-related picornaviruses including their hosts, to effectively compile all possible species jumping events during their evolution. Furthermore, we explored the phylogeny association with geographical location, host-genus and host-species in both data sets.

scholarly journals Origins and Evolutionary Patterns of the 1.688 Satellite DNA Family in Drosophila Phylogeny

2020 ◽  
Vol 10 (11) ◽  
pp. 4129-4146
Author(s):  
Leonardo G. de Lima ◽  
Stacey L. Hanlon ◽  
Jennifer L. Gerton
Keyword(s):  
Repetitive Sequences ◽  
Specific Pattern ◽  
Evolutionary Patterns ◽  
Satellite Dnas ◽  
Evolutionary Pattern ◽  
Functional Roles ◽  
Drosophila Phylogeny ◽  
Species Specific ◽  
Future Work ◽  
Eukaryotic Genomes

Satellite DNAs (satDNAs) are a ubiquitous feature of eukaryotic genomes and are usually the major components of constitutive heterochromatin. The 1.688 satDNA, also known as the 359 bp satellite, is one of the most abundant repetitive sequences in Drosophila melanogaster and has been linked to several different biological functions. We investigated the presence and evolution of the 1.688 satDNA in 16 Drosophila genomes. We find that the 1.688 satDNA family is much more ancient than previously appreciated, being shared among part of the melanogaster group that diverged from a common ancestor ∼27 Mya. We found that the 1.688 satDNA family has two major subfamilies spread throughout Drosophila phylogeny (∼360 bp and ∼190 bp). Phylogenetic analysis of ∼10,000 repeats extracted from 14 of the species revealed that the 1.688 satDNA family is present within heterochromatin and euchromatin. A high number of euchromatic repeats are gene proximal, suggesting the potential for local gene regulation. Notably, heterochromatic copies display concerted evolution and a species-specific pattern, whereas euchromatic repeats display a more typical evolutionary pattern, suggesting that chromatin domains may influence the evolution of these sequences. Overall, our data indicate the 1.688 satDNA as the most perduring satDNA family described in Drosophila phylogeny to date. Our study provides a strong foundation for future work on the functional roles of 1.688 satDNA across many Drosophila species.

scholarly journals Characterization of the Androgen-Regulated Prostate-Specific T Cell Receptor γ-Chain Alternate Reading Frame Protein (TARP) Promoter

Endocrinology ◽  
2003 ◽  
Vol 144 (8) ◽  
pp. 3433-3440 ◽  
Author(s):  
Wing-Shing Cheng ◽  
Valeria Giandomenico ◽  
Ira Pastan ◽  
Magnus Essand
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
T Cell ◽  
Cancer Cells ◽  
T Cell Receptor ◽  
Cell Receptor ◽  
Regulatory Sequence ◽  
Prostate Cancer Cells ◽  
Reading Frame ◽  
Alternate Reading Frame Protein

Abstract TARP (T cell receptor γ-chain alternate reading frame protein) is uniquely expressed in males in prostate epithelial cells and prostate cancer cells. Here we demonstrate that TARP expression is regulated by testosterone at the transcriptional level through specific binding of androgen receptor to an androgen response element in the proximal TARP promoter. We further demonstrate that the promoter specifically initiates reporter gene expression in TARP-positive prostate cancer cell lines. To develop a regulatory sequence for prostate-specific gene expression, we constructed a chimeric sequence consisting of the TARP promoter and the prostate-specific antigen (PSA) enhancer. We found that in the prostatic adenocarcinoma cell line LNCaP, the transcriptional activity of the regulatory sequence consisting of a TARP promoter and PSA enhancer is 20 times higher than the activity of a regulatory sequence consisting of the PSA promoter and PSA enhancer. Thus, our studies define a regulatory sequence that may be used to restrict expression of therapeutic genes to prostate cancer cells and may therefore play a role in prostate cancer gene therapy.

scholarly journals The Open Reading Frame 3a Protein of Severe Acute Respiratory Syndrome-Associated Coronavirus Promotes Membrane Rearrangement and Cell Death

2009 ◽  
Vol 84 (2) ◽  
pp. 1097-1109 ◽  
Author(s):  
Eric C. Freundt ◽  
Li Yu ◽  
Cynthia S. Goldsmith ◽  
Sarah Welsh ◽  
Aaron Cheng ◽  
...  
Keyword(s):  
Cell Death ◽  
Severe Acute Respiratory Syndrome ◽  
Vero Cells ◽  
Small Gtpase ◽  
Open Reading Frames ◽  
Accessory Proteins ◽  
Reading Frame ◽  
Golgi Fragmentation

ABSTRACT The genome of the severe acute respiratory syndrome-associated coronavirus (SARS-CoV) contains eight open reading frames (ORFs) that encode novel proteins. These accessory proteins are dispensable for in vitro and in vivo replication and thus may be important for other aspects of virus-host interactions. We investigated the functions of the largest of the accessory proteins, the ORF 3a protein, using a 3a-deficient strain of SARS-CoV. Cell death of Vero cells after infection with SARS-CoV was reduced upon deletion of ORF 3a. Electron microscopy of infected cells revealed a role for ORF 3a in SARS-CoV induced vesicle formation, a prominent feature of cells from SARS patients. In addition, we report that ORF 3a is both necessary and sufficient for SARS-CoV-induced Golgi fragmentation and that the 3a protein accumulates and localizes to vesicles containing markers for late endosomes. Finally, overexpression of ADP-ribosylation factor 1 (Arf1), a small GTPase essential for the maintenance of the Golgi apparatus, restored Golgi morphology during infection. These results establish an important role for ORF 3a in SARS-CoV-induced cell death, Golgi fragmentation, and the accumulation of intracellular vesicles.

scholarly journals Regulation of Expression of Avirulence Gene avrRxv and Identification of a Family of Host Interaction Factors by Sequence Analysis of avrBsT

1999 ◽  
Vol 12 (1) ◽  
pp. 35-44 ◽  
Author(s):  
L. D. Ciesiolka ◽  
T. Hwin ◽  
J. D. Gearlds ◽  
G. V. Minsavage ◽  
R. Saenz ◽  
...  
Keyword(s):  
Xanthomonas Campestris ◽  
Inducible Promoter ◽  
Avirulence Gene ◽  
In Planta ◽  
Regulation Of Expression ◽  
Reading Frame ◽  
Pathogen Virulence ◽  
Host Interaction ◽  
Interaction Factor ◽  
Interaction Factors

Resistance in tomato line Hawaii 7998 as well as in several nonhost plants to Xanthomonas campestris pv. vesicatoria tomato strain (XcvT) is mediated in part by the avirulence gene avrRxv. Analysis of growth of wild-type and avrRxv deletion strains indicates that avrRxv plays a crucial role in the ability of XcvT 92–14 to induce resistance on Hawaii 7998. We used avrRxv reporter gene fusions and Northern (RNA) blot analysis to test several growth environments for inductive potential. We found that avrRxv is constitutively expressed at high levels and that growth in planta, in tobacco conditioned medium, and in hrp-inductive medium XVM2 did not affect the high levels of expression. In addition, hrp structural and regulatory mutant backgrounds had no effect. We mutated the bipartite plant inducible promoter (PIP)-box sequence and found that avrRxv activity appears to be independent of an intact PIP-box element. We present the sequence of the avrRxv homologue called avrBsT and align the six AvrRxv host interaction factor family members including mammalian pathogen virulence factors YopJ and YopP from Yersinia spp. and AvrA from Salmonella typhimurium, and open reading frame Y4LO with unknown function from the symbiont Rhizobium sp.

scholarly journals Identification and Characterization of a Serious Multidrug ResistantStenotrophomonas maltophiliaStrain in China

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Yan Zhao ◽  
Wenkai Niu ◽  
Yanxia Sun ◽  
Huaijie Hao ◽  
Dong Yu ◽  
...  
Keyword(s):  
Draft Genome ◽  
Antibiotic Resistance Genes ◽  
Gene Cassette ◽  
Comparative Genomic ◽  
Evolutionary Analysis ◽  
Class 1 Integron ◽  
Interaction Database ◽  
Host Interaction ◽  
Class 1 ◽  
Resistance Gene Cassette

AnS. maltophiliastrain named WJ66 was isolated from a patient; WJ66 showed resistance to more antibiotics than the otherS. maltophiliastrains. This bacteraemia is resistant to sulphonamides, or fluoroquinolones, while the representative strain ofS. maltophilia, K279a, is sensitive to both. To explore drug resistance determinants of this strain, the draft genome sequence of WJ66 was determined and compared to otherS. maltophiliasequences. Genome sequencing and genome-wide evolutionary analysis revealed that WJ66 was highly homologous with the strain K279a, but strain WJ66 contained additional antibiotic resistance genes. Further analysis confirmed that strain WJ66 contained an amino acid substitution (Q83L) in fluoroquinolone target GyrA and carried a class 1 integron, with anaadA2gene in the resistance gene cassette. Homology analysis from the pathogen-host interaction database showed that strain WJ66 lacks raxST and raxA, which is consistent with K279a. Comparative genomic analyses revealed that subtle nucleotide differences contribute to various significant phenotypes in close genetic relationship strains.

scholarly journals Sequence Analysis and Structure Prediction of Malaysia SARS-CoV-2 Strain’s Structural and Accessory Proteins

2021 ◽  
Vol 12 (3) ◽  
pp. 3259-3304
Keyword(s):  
Structure Prediction ◽  
Active Sites ◽  
Homo Sapiens ◽  
Functional Characterization ◽  
Protein Structures ◽  
Three Dimensional ◽  
Experimental Models ◽  
Amino Acid Sequences ◽  
Accessory Proteins ◽  
Evolutionary Analysis

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that transmitted from animal to human became a life-threatening pandemic in 2020. Scientists are currently testing several drugs to eradicate the COVID-19 outbreak. However, there is no 100 % effective drug or vaccine against SARS-CoV-2 has been discovered so far. In this study, we explored the structure prediction and functional analysis of 75 Malaysia SARS-CoV-2 strain’s structural and accessory proteins without the presence of experimental models. Physiochemical analysis, secondary structure analysis, structure prediction, functional characterization, active site identification, and evolutionary analysis based on the amino acid sequences retrieved from National Centre for Biotechnology Information (NCBI). Three-dimensional (3-D) protein structures were built using the Swiss model. The quality of protein models was verified by ERRAT, PROCHECK, and Verify 3D tools. Active prediction analysis revealed the high potential active sites of proteins where the anti-viral drug or vaccine may bind and inhibit the viral activities. Molecular phylogenetic analysis of ORF10, ORF8, and ORF6 proteins from five different species was analyzed. The results from this analysis proved that Homo sapiens SARS-CoV-2 had high genetic similarity with the bat coronavirus. These analyses may help in designing structure-based anti-viral drugs or to develop potential vaccines for SARS-CoV-2.

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