COG database update: focus on microbial diversity, model organisms, and widespread pathogens

Galperin, Michael Y.; Wolf, Yuri I.; Makarova, Kira S.; Alvarez, Roberto Vera; Landsman, David; Koonin, Eugene V.

doi:10.1093/nar/gkaa1018

Cited by 588 publications

(539 citation statements)

References 66 publications

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“…The conserved ribosomal protein (RP) set, extracted from the current release of the COG database (28), consisted of 54 core RPs: 33 from the 50S subunit (L1-L7/L12, L9-L11, L13-L25, and L27-L36) and 21 (S1-S21) from the 30S subunit (1–5). Several additional proteins, such as S22 (RpsV, Sra) and S31e (Thx), which are associated with ribosomes in some bacteria (37, 38), are not covered in the COG database and have not been included in the analyzed set.…”

Section: Resultsmentioning

confidence: 99%

“…Here, we report the patterns of presence and absence of RP genes in the current release of the Clusters of Orthologous Genes (COGs) database (28). The COG database is a particularly convenient tool for the analysis of gene gain and loss because it includes a limited number of high-quality complete microbial genomes and features COG-specific patterns of presence and absence of evolutionarily conserved genes in the respective organisms (29–31).…”

Section: Introductionmentioning

confidence: 99%

“…The current version of the COG database (28) features a selection of COGs grouped by metabolic pathways and functional complexes, including the RPs of the 50S and 30S ribosome subunits as well as a group of archaea-specific RPs. Examination of the phyletic patterns of the COGs for all three groups allowed us to (i) compile the list of about 500 RP genes missing in some bacterial and/or archaeal genomes (some actually lost and some missing because of sequencing problems); (ii) identify more than 50 RP genes that have been overlooked in the course of genome annotation, and (iii) establish the patterns of RP gene loss during bacterial and archaeal evolution, and iv) correlate the experimentally-derived and computationally-generated sets of the likely non-essential RP genes.…”

Section: Introductionmentioning

confidence: 99%

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Non-essential ribosomal proteins in bacteria and archaea identified using COGs

Galperin

Wolf

Garushyants

et al. 2021

Preprint

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Ribosomal proteins (RPs) are highly conserved across the bacterial and archaeal domains. Although many RPs are essential for survival, genome analysis demonstrates the absence of some RP genes in many bacterial and archaeal genomes. Furthermore, global transposon mutagenesis and/or targeted deletion showed that elimination of some RP genes had only a moderate effect on the bacterial growth rate. Here, we systematically analyze the evolutionary conservation of RPs in prokaryotes by compiling the list of the ribosomal genes that are missing from the one or more genomes in the recently updated version of the Clusters of Orthologous Genes (COG) database. Some of these absences occurred because the respective genes carried frameshifts, presumably, resulting from sequencing errors, while others were overlooked and not translated during genome annotation. Apart from these annotation errors, we identified multiple genuine losses of RP genes in a variety of bacteria and archaea. Some of these losses are clade-specific, whereas others occur in symbionts and parasites with dramatically reduced genomes. The lists of computationally and experimentally defined non-essential ribosomal genes show a substantial overlap, revealing a common trend in prokaryote ribosome evolution that could be linked to the architecture and assembly of the ribosomes. Thus, RPs that are located at the surface of the ribosome and/or are incorporated at a late stage of ribosome assembly are more likely to be non-essential and to be lost during microbial evolution, particularly, in the course of genome compaction.IMPORTANCEIn many prokaryote genomes, one or more ribosomal protein (RP) genes are missing. Analysis of 1,309 prokaryote genomes included in the COG database shows that only about half of the RPs are universally conserved in bacteria and archaea. In contrast, up to 21 other RPs are missing in some genomes, primarily, tiny (<1 Mb) genomes of host-associated bacteria and archaea. Ten universal and nine archaea-specific ribosomal proteins show clear patterns of lineage-specific gene loss. Most of the RPs that are frequently lost from bacterial genomes are located on the ribosome periphery and are non-essential in Escherichia coli and Bacillus subtilis. These results reveal general trends and common constraints in the architecture and evolution of ribosomes in prokaryotes.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Non-essential ribosomal proteins in bacteria and archaea identified using COGs

Galperin

Wolf

Garushyants

et al. 2021

Preprint

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“…Gm18 is absent in Gram-positive Bacteria with a few exceptions such as the thermophilic Geobacillus sp (reviewed in [ 31 ]). This modification is accomplished by the dimeric S-adenosyl-L-methionine (SAM)-dependent methyltransferase (MTase) TrmH belonging to the SPOUT superfamily [ 32 ] (COG0566–Cluster of Orthologous Genes, see [ 33 ]). Two types of TrmH enzymes exist with different tRNA recognition specificities: one methylating all tRNA types, like TrmH of Thermus thermophilus , and the other one methylating only a specific subset of tRNAs like TrmH of Escherichia coli and Aquifex aeolicus [ 34 , 35 , 36 ], reviewed in [ 37 ].…”

Section: The Enzymatic Toolbox For Nucleotide Modifications At Posmentioning

confidence: 99%

Post-Transcriptional Modifications of Conserved Nucleotides in the T-Loop of tRNA: A Tale of Functional Convergent Evolution

Roovers¹,

Droogmans

Grosjean

2021

Genes

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The high conservation of nucleotides of the T-loop, including their chemical identity, are hallmarks of tRNAs from organisms belonging to the three Domains of Life. These structural characteristics allow the T-loop to adopt a peculiar intraloop conformation able to interact specifically with other conserved residues of the D-loop, which ultimately folds the mature tRNA in a unique functional canonical L-shaped architecture. Paradoxically, despite the high conservation of modified nucleotides in the T-loop, enzymes catalyzing their formation depend mostly on the considered organism, attesting for an independent but convergent evolution of the post-transcriptional modification processes. The driving force behind this is the preservation of a native conformation of the tRNA elbow that underlies the various interactions of tRNA molecules with different cellular components.

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“…In the section on protein sequence and structure databases, users of protein family and domain databases are particularly well-served. COG ( 21 ) returns to report well over 200 new protein families and a similar number of families updated to reflect recent experimental characterisation. The current COG includes almost 5000 COGs and annotates genomes of over 1200 microbes.…”

Section: New and Updated Databasesmentioning

confidence: 99%

The 2021 Nucleic Acids Research database issue and the online molecular biology database collection

Rigden

Fernández

2020

Nucleic Acids Research

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The 2021 Nucleic Acids Research database Issue contains 189 papers spanning a wide range of biological fields and investigation. It includes 89 papers reporting on new databases and 90 covering recent changes to resources previously published in the Issue. A further ten are updates on databases most recently published elsewhere. Seven new databases focus on COVID-19 and SARS-CoV-2 and many others offer resources for studying the virus. Major returning nucleic acid databases include NONCODE, Rfam and RNAcentral. Protein family and domain databases include COG, Pfam, SMART and Panther. Protein structures are covered by RCSB PDB and dispersed proteins by PED and MobiDB. In metabolism and signalling, STRING, KEGG and WikiPathways are featured, along with returning KLIFS and new DKK and KinaseMD, all focused on kinases. IMG/M and IMG/VR update in the microbial and viral genome resources section, while human and model organism genomics resources include Flybase, Ensembl and UCSC Genome Browser. Cancer studies are covered by updates from canSAR and PINA, as well as newcomers CNCdatabase and Oncovar for cancer drivers. Plant comparative genomics is catered for by updates from Gramene and GreenPhylDB. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been substantially updated, revisiting nearly 1000 entries, adding 90 new resources and eliminating 86 obsolete databases, bringing the current total to 1641 databases. It is available at https://www.oxfordjournals.org/nar/database/c/.

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COG database update: focus on microbial diversity, model organisms, and widespread pathogens

Cited by 588 publications

References 66 publications

Non-essential ribosomal proteins in bacteria and archaea identified using COGs

Non-essential ribosomal proteins in bacteria and archaea identified using COGs

Post-Transcriptional Modifications of Conserved Nucleotides in the T-Loop of tRNA: A Tale of Functional Convergent Evolution

The 2021 Nucleic Acids Research database issue and the online molecular biology database collection

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