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The COG database: a tool for genome-scale analysis of protein functions and evolution
TLDR
The database of Clusters of Orthologous Groups of proteins (COGs) is an attempt on a phylogenetic classification of the proteins encoded in 21 complete genomes of bacteria, archaea and eukaryotes.
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The COG database: new developments in phylogenetic classification of proteins from complete genomes
TLDR
The new features added to the COG database include information pages with structural and functional details on each COG and literature references, improvements of the COGNITOR program that is used to fit new proteins into the COGs, and classification of genomes and COGs constructed by using principal component analysis.
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Expanded microbial genome coverage and improved protein family annotation in the COG database
TLDR
An update of the Clusters of Orthologous Groups of proteins, the first since 2003, and a comprehensive revision of the COG annotations and expansion of the genome coverage to include representative complete genomes from all bacterial and archaeal lineages down to the genus level are presented.
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Cyclic di-GMP: the First 25 Years of a Universal Bacterial Second Messenger
TLDR
A historic perspective on the development of the field is provided, common trends are emphasized, and new directions in c-di-GMP research are highlighted that will give a deeper understanding of this truly universal bacterial second messenger.
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Novel domains of the prokaryotic two-component signal transduction systems.
TLDR
Experimental data provides the first direct evidence of the participation of these domains in signal transduction pathways, including regulation of virulence genes and extracellular enzyme production in the human pathogens Bordetella pertussis and Borrelia burgdorferi and the plant pathogen Xanthomonas campestris.
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Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome
TLDR
The genome of P. marinus SS120 is one of the two smallest genomes of a photosynthetic organism known to date and lacks many genes that are involved in photosynthesis, DNA repair, solute uptake, intermediary metabolism, motility, phototaxis, and other functions that are conserved among other cyanobacteria.
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Structural Classification of Bacterial Response Regulators: Diversity of Output Domains and Domain Combinations
TLDR
The diversity of domain architectures and the abundance of alternative domain combinations suggest that fusions between the REC domain and various output domains is a widespread evolutionary mechanism that allows bacterial cells to regulate transcription, enzyme activity, and/or protein-protein interactions in response to environmental challenges.
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PilZ domain is part of the bacterial c-di-GMP binding protein
Recent studies identified c-di-GMP as a universal bacterial secondary messenger regulating biofilm formation, motility, production of extracellular polysaccharide and multicellular behavior in…
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A genomic update on clostridial phylogeny: Gram-negative spore formers and other misplaced clostridia.
TLDR
It is reaffirmed that 16S rRNA and ribosomal protein sequences are better indicators of evolutionary proximity than phenotypic traits, even such key ones as the structure of the cell envelope and Gram-staining pattern.
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Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes
TLDR
Phylogenetic profiles of sporulation genes, compiled in this work, confirm the presence of a common sporulation gene core, but also illuminate the diversity of the sporulation processes within various lineages.
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