scholarly journals Global In-Silico Scenario of tRNA Genes and Their Organization in Virus Genomes

Viruses ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 180 ◽  
Author(s):  
Sergio Morgado ◽  
Ana Vicente
Keyword(s):  
In Silico ◽  
Large Scale ◽  
Trna Gene ◽  
Gene Clusters ◽  
Trna Genes ◽  
Genome Survey ◽  
In Silico Study ◽  
Domains Of Life ◽  
Dsdna Viruses ◽  
Virus Genomes

Viruses are known to be highly dependent on the host translation machinery for their protein synthesis. However, tRNA genes are occasionally identified in such organisms, and in addition, few of them harbor tRNA gene clusters comprising dozens of genes. Recently, tRNA gene clusters have been shown to occur among the three domains of life. In such a scenario, the viruses could play a role in the dispersion of such structures among these organisms. Thus, in order to reveal the prevalence of tRNA genes as well as tRNA gene clusters in viruses, we performed an unbiased large-scale genome survey. Interestingly, tRNA genes were predicted in ssDNA (single-stranded DNA) and ssRNA (single-stranded RNA) viruses as well in many other dsDNA viruses of families from Caudovirales order. In the latter group, tRNA gene clusters composed of 15 to 37 tRNA genes were characterized, mainly in bacteriophages, enlarging the occurrence of such structures within viruses. These bacteriophages were from hosts that encompass five phyla and 34 genera. This in-silico study presents the current global scenario of tRNA genes and their organization in virus genomes, contributing and opening questions to be explored in further studies concerning the role of the translation apparatus in these organisms.

scholarly journals In silico study of wall-associated kinase family reveals large-scale genomic expansion potentially connected with functional diversification in Populus

2014 ◽  
Vol 10 (5) ◽  
pp. 1135-1147 ◽  
Author(s):  
Kévin Tocquard ◽  
Clément Lafon-Placette ◽  
Daniel Auguin ◽  
Beatriz Muries ◽  
Gisèle Bronner ◽  
...  
Keyword(s):  
In Silico ◽  
Large Scale ◽  
Functional Diversification ◽  
Kinase Family ◽  
In Silico Study ◽  
Genomic Expansion

scholarly journals Exploring tRNA gene cluster in archaea

2018 ◽  
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Gene Cluster ◽  
Trna Gene ◽  
Gene Clusters ◽  
Gene Organization ◽  
Trna Genes ◽  
Genomic Analyses ◽  
Living Organisms

AbstractShared traits between prokaryotes and eukaryotes are helpful in the understanding of the tree of life evolution. In bacteria and eukaryotes, it has been shown a particular organization of tRNA genes as clusters, but this trait has not been explored in archaea domain. Here, based on analyses of complete and draft archaeal genomes, we demonstrated the prevalence of tRNA gene clusters in archaea. tRNA gene cluster was identified at least in three Archaea class, Halobacteria, Methanobacteria and Methanomicrobia from Euryarchaeota supergroup. Genomic analyses also revealed evidence of tRNA gene cluster associated with mobile genetic elements and horizontal gene transfer inter/intra-domain. The presence of tRNA gene clusters in the three domain of life suggests a role of this type of tRNA gene organization in the biology of the living organisms.

scholarly journals The birth of a bacterial tRNA gene by large-scale, tandem duplication events

2020 ◽  
Author(s):  
Gökçe B. Ayan ◽  
Hye Jin Park ◽  
Jenna Gallie
Keyword(s):  
Large Scale ◽  
Trna Gene ◽  
Single Copy ◽  
Growth Defect ◽  
Trna Genes ◽  
Evolutionary Mechanisms ◽  
Gene Set ◽  
Gene Copies ◽  
Laboratory Populations ◽  
Duplication Events

ABSTRACTOrganisms differ in the types and numbers of tRNA genes that they carry. While the evolutionary mechanisms behind tRNA gene set evolution have been investigated theoretically and computationally, direct observations of tRNA gene set evolution remain rare. Here, we report the evolution of a tRNA gene set in laboratory populations of the bacterium Pseudomonas fluorescens SBW25. The growth defect caused by deleting the single-copy tRNA gene, serCGA, is rapidly compensated by large-scale (45-290 kb) duplications in the chromosome. Each duplication encompasses a second, compensatory tRNA gene (serTGA) and is associated with a rise in tRNA-Ser(UGA) in the mature tRNA pool. We postulate that tRNA-Ser(CGA) elimination increases the translational demand for tRNA-Ser(UGA), a pressure relieved by increasing serTGA copy number. This work demonstrates that tRNA gene sets can evolve through duplication of existing tRNA genes, a phenomenon that may contribute to the presence of multiple, identical tRNA gene copies within genomes.

scholarly journals The birth of a bacterial tRNA gene by large-scale, tandem duplication events

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Gökçe B Ayan ◽  
Hye Jin Park ◽  
Jenna Gallie
Keyword(s):  
Large Scale ◽  
Trna Gene ◽  
Single Copy ◽  
Growth Defect ◽  
Trna Genes ◽  
Evolutionary Mechanisms ◽  
Gene Set ◽  
Gene Copies ◽  
Laboratory Populations ◽  
Duplication Events

Organisms differ in the types and numbers of tRNA genes that they carry. While the evolutionary mechanisms behind tRNA gene set evolution have been investigated theoretically and computationally, direct observations of tRNA gene set evolution remain rare. Here, we report the evolution of a tRNA gene set in laboratory populations of the bacterium Pseudomonas fluorescens SBW25. The growth defect caused by deleting the single-copy tRNA gene, serCGA, is rapidly compensated by large-scale (45–290 kb) duplications in the chromosome. Each duplication encompasses a second, compensatory tRNA gene (serTGA) and is associated with a rise in tRNA-Ser(UGA) in the mature tRNA pool. We postulate that tRNA-Ser(CGA) elimination increases the translational demand for tRNA-Ser(UGA), a pressure relieved by increasing serTGA copy number. This work demonstrates that tRNA gene sets can evolve through duplication of existing tRNA genes, a phenomenon that may contribute to the presence of multiple, identical tRNA gene copies within genomes.

scholarly journals In Silico Studies on Compounds Derived from Calceolaria: Phenylethanoid Glycosides as Potential Multitarget Inhibitors for the Development of Pesticides

Biomolecules ◽  
2018 ◽  
Vol 8 (4) ◽  
pp. 121 ◽  
Author(s):  
Marco Loza-Mejía ◽  
Juan Salazar ◽  
Juan Sánchez-Tejeda
Keyword(s):  
In Silico ◽  
Large Scale ◽  
Insect Pests ◽  
Insect Growth Regulator ◽  
Mechanisms Of Action ◽  
Ecdysone Receptor ◽  
Phenylethanoid Glycosides ◽  
In Silico Studies ◽  
In Silico Study ◽  
Potential Applications

An increasing occurrence of resistance in insect pests and high mammal toxicity exhibited by common pesticides increase the need for new alternative molecules. Among these alternatives, bioinsecticides are considered to be environmentally friendly and safer than synthetic insecticides. Particularly, plant extracts have shown great potential in laboratory conditions. However, the lack of studies that confirm their mechanisms of action diminishes their potential applications on a large scale. Previously, we have reported the insect growth regulator and insecticidal activities of secondary metabolites isolated from plants of the Calceolaria genus. Herein, we report an in silico study of compounds isolated from Calceolaria against acetylcholinesterase, prophenoloxidase, and ecdysone receptor. The molecular docking results are consistent with the previously reported experimental results, which were obtained during the bioevaluation of Calceolaria extracts. Among the compounds, phenylethanoid glycosides, such as verbascoside, exhibited good theoretical affinity to all the analyzed targets. In light of these results, we developed an index to evaluate potential multitarget insecticides based on docking scores.

Complete genome of mangrove-derived anti-MRSA streptomycete, Streptomyces pluripotens MUSC 135T

2018 ◽  
Vol 1 (1) ◽  
Author(s):  
Hooi-Leng Ser ◽  
Kok-Gan Chan ◽  
Wen-Si Tan ◽  
Wai-Fong Yin ◽  
Bey-Hing Goh ◽  
...  
Keyword(s):  
Complete Genome ◽  
Methicillin Resistant Staphylococcus Aureus ◽  
Gene Clusters ◽  
Salmonella Typhi ◽  
Bacteriocin Production ◽  
Trna Genes ◽  
Genus Streptomyces ◽  
Mining Tool ◽  
Bioactive Potential ◽  
Effective Drugs

Microorganisms serve as attractive resources, owing to their ability to synthesize structurally-diverse substanceswith various bioactivities. Within the Bacteria domain, members of the genus Streptomyces have demonstrated remarkableability to produce clinically useful, secondary metabolites such as anticancer, antioxidants, antivirals and antibacterials.Streptomyces pluripotens MUSC 135T was isolated as novel strain from mangrove forest in Malaysia. This strain exhibitedbroad spectrum bacteriocin against several pathogens including methicillin-resistant Staphylococcus aureus (MRSA) strainATCC BAA-44, Salmonella typhi ATCC 19430T and Aeromonas hydrophila ATCC 7966T. Thus, the strain was selected forwhole genome sequencing as an attempt to explore its bioactive potential. Here we report the first complete genome of S.pluripotens MUSC 135T genome which comprise of 7.35 Mbp with G+C content of 69.9 %. A total of 6,404 open readingframes (ORFs) were predicted, along with 18 rRNA and 69 tRNA genes. Using bacteriocin mining tool, BAGEL detectedeights gene clusters associated with bacteriocin production including lanthipeptides and linear azol(in)e-containing peptides(LAPs). Members of Streptomyces have contributed greatly towards improving lives, particularly against deadly infectionsand chronic diseases. The availability of S. pluripotens MUSC 135T genome sequence has opened new window for drugdiscovery, particularly for effective drugs against harmful pathogens such as MRSA and certainly deserves further detailedstudy.

In Silico Study of Structural and Geometrical Requirements of Natural Sesquiterpene Lactones with Trypanocidal Activity

2013 ◽  
Vol 13 (10) ◽  
pp. 1407-1414 ◽  
Author(s):  
L. Fabian ◽  
V. Sulsen ◽  
F. Frank ◽  
S. Cazorla ◽  
E. Malchiodi ◽  
...  
Keyword(s):  
In Silico ◽  
Sesquiterpene Lactones ◽  
Trypanocidal Activity ◽  
In Silico Study
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