scholarly journals Comparative analysis of bacterial genomes: identification of divergent regions in mycobacterial strains using an anchor-based approach

2007 ◽  
Vol 35 (11) ◽  
pp. 3654-3667 ◽  
Author(s):  
Anchal Vishnoi ◽  
Rahul Roy ◽  
Alok Bhattacharya
Keyword(s):  
Comparative Analysis ◽  
Bacterial Genomes

scholarly journals Bacterial CRISPR abundance jumps up at around 45°C

2021 ◽  
Author(s):  
Xin-Ran Lan ◽  
Zhi-Ling Liu ◽  
Deng-Ke Niu
Keyword(s):  
Comparative Analysis ◽  
Adaptive Immunity ◽  
Bacterial Genomes ◽  
Viral Lysis ◽  
Abrupt Decrease ◽  
Bacterial Mortality ◽  
Abrupt Transition ◽  
Thermal Distribution ◽  
Relative Contribution ◽  
Temperature Ranges

Although functioning for adaptive immunity, CRISPR-Cas systems are present in only 40% of bacterial genomes. In this study, we observed an abrupt transition of bacterial CRISPR abundance at around 45°C. Phylogenetic comparative analysis showed that the CRISPR abundance correlates with growth temperature only in temperature ranges around 45°C. The existence of a saltation point indicates that temperature unlikely determines the thermal distribution of CRISPR-Cas systems directly. We put forward a novel hypothesis referring to the predator effect on immune function previously observed in birds. At around 45°C, an abrupt decrease of cellular predators rapidly decreases bacterial mortality resulting from cellular predator grazing. Consequently, the relative contribution of viral lysis in bacterial mortality increases rapidly with temperature; mutants allocating more resources to the adaptive immunity would be favored. In temperature ranges where the abundance of cellular predators does not change with temperature, the temperature effect on CRISPR abundance would be negligible.

A strictly monofunctional bacterial hydroxymethylpyrimidine phosphate kinase precludes damaging errors in thiamin biosynthesis

2017 ◽  
Vol 474 (16) ◽  
pp. 2887-2895 ◽  
Author(s):  
Antje M. Thamm ◽  
Gengnan Li ◽  
Marlene Taja-Moreno ◽  
Svetlana Y. Gerdes ◽  
Valérie de Crécy-Lagard ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Kinase Activity ◽  
Protein Family ◽  
Biosynthesis Pathway ◽  
Bacterial Genomes ◽  
Thiamin Biosynthesis ◽  
Biochemical Analyses ◽  
The Cost

The canonical kinase (ThiD) that converts the thiamin biosynthesis intermediate hydroxymethylpyrimidine (HMP) monophosphate into the diphosphate can also very efficiently convert free HMP into the monophosphate in prokaryotes, plants, and fungi. This HMP kinase activity enables salvage of HMP, but it is not substrate-specific and so allows toxic HMP analogs and damage products to infiltrate the thiamin biosynthesis pathway. Comparative analysis of bacterial genomes uncovered a gene, thiD2, that is often fused to the thiamin synthesis gene thiE and could potentially encode a replacement for ThiD. Standalone ThiD2 proteins and ThiD2 fusion domains are small (∼130 residues) and do not belong to any previously known protein family. Genetic and biochemical analyses showed that representative standalone and fused ThiD2 proteins catalyze phosphorylation of HMP monophosphate, but not of HMP or its toxic analogs and damage products such as bacimethrin and 5-(hydroxymethyl)-2-methylpyrimidin-4-ol. As strictly monofunctional HMP monophosphate kinases, ThiD2 proteins eliminate a potentially fatal vulnerability of canonical ThiD, at the cost of the ability to reclaim HMP formed by thiamin turnover.

scholarly journals MicroScope—an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data

2017 ◽  
Vol 20 (4) ◽  
pp. 1071-1084 ◽  
Author(s):  
Claudine Médigue ◽  
Alexandra Calteau ◽  
Stéphane Cruveiller ◽  
Mathieu Gachet ◽  
Guillaume Gautreau ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Genome Annotation ◽  
Daily Basis ◽  
Original Method ◽  
Graph Representation ◽  
Integrated Analysis ◽  
Sequencing Data ◽  
Bacterial Genomes ◽  
Manual Curation ◽  
Expert Annotation

Abstract The overwhelming list of new bacterial genomes becoming available on a daily basis makes accurate genome annotation an essential step that ultimately determines the relevance of thousands of genomes stored in public databanks. The MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Starting from the results of our syntactic, functional and relational annotation pipelines, MicroScope provides an integrated environment for the expert annotation and comparative analysis of prokaryotic genomes. It combines tools and graphical interfaces to analyze genomes and to perform the manual curation of gene function in a comparative genomics and metabolic context. In this article, we describe the free-of-charge MicroScope services for the annotation and analysis of microbial (meta)genomes, transcriptomic and re-sequencing data. Then, the functionalities of the platform are presented in a way providing practical guidance and help to the nonspecialists in bioinformatics. Newly integrated analysis tools (i.e. prediction of virulence and resistance genes in bacterial genomes) and original method recently developed (the pan-genome graph representation) are also described. Integrated environments such as MicroScope clearly contribute, through the user community, to help maintaining accurate resources.

scholarly journals Comparative analysis of prophage-like elements inHelicobactersp. genomes

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2012 ◽  
Author(s):  
Xiangyu Fan ◽  
Yumei Li ◽  
Rong He ◽  
Qiang Li ◽  
Wenxing He
Keyword(s):  
Antibiotic Resistance ◽  
Comparative Analysis ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Bacterial Virulence ◽  
Comparative Genomic ◽  
Bacterial Genomes ◽  
Resistance Proteins ◽  
Cluster A ◽  
First Time

Prophages are regarded as one of the factors underlying bacterial virulence, genomic diversification, and fitness, and are ubiquitous in bacterial genomes. Information onHelicobactersp. prophages remains scarce. In this study, sixteen prophages were identified and analyzed in detail. Eight of them are described for the first time. Based on a comparative genomic analysis, these sixteen prophages can be classified into four different clusters. Phylogenetic relationships of Cluster AHelicobacterprophages were investigated. Furthermore, genomes ofHelicobacterprophages from Clusters B, C, and D were analyzed. Interestingly, some putative antibiotic resistance proteins and virulence factors were associated withHelicobacterprophages.

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