• Journal of Life Science
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• v.31 no.9
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• pp.834-839
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• 2021

Authors previously reported the results of analyses of COGs (Clusters of Orthologous Groups of proteins) in 711 prokaryotes. The data of COGs were significantly updated for 2020 using 1,309 prokaryotic genomes. Here, we report the results of analyses of 3,455,853 proteins comprising 4,877 updated COGs in terms of COGs and prokaryotes. The numbers of COGs in each prokaryote ranged from 97 to 2,281, with an average of 1,430.0 and a standard deviation of 414.2. Mean numbers of COGs at the phylum level were minimal 497.86 for Mollicutes and maximal 1,642.90 for Cyanobacteria. The top 10 species with the highest COG retention numbers were all Proteobacteria, and 9 out of the bottom 10 were those that could not be cultured in vitro. The numbers of proteins belonging to each COG ranged from 2 to 22,048, with over 12,000 proteins up to the top 11. Five of the top 11 were COGs that bind to DNA and were involved in the gene expression, indicating the importance of regulating gene expression in prokaryotes in a changing environment. COG data are expected to be widely utilized as they can be used for the identification of genes included in the genome and the selection of genes for the strain improvement.

• KSBB Journal
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• v.17 no.6
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• pp.560-565
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• 2002

A COG(clusters of orthologous groups of proteins) algorithm was used to detect conserved genes within Proteobacteria and to figure out their relationships. Restricting comparison to the sequences of 42 procaryotes, 33 eubacteria and 16 Proteobacteria, the number of conserved genes was increased. All analyzed procaryotes shared 75 COGs. COG0195, COG0358 and COG0528 were only represented by the 42 procaryotes. Sixtyfour COGs were added as conserved genes in 33 eubacteria. Each Proteobacteria group has a unique repertoire of COGs. Metabolic COGs were more diverse in the beta Proteobacteria group than in the other groups. These results could be used to determine the origins and the evolutionary relationships of Proteobacteria. The possibilities of detecting new biological molecules is high in phylogenetically related organisms, hence the identification of useful proteins by using this algorithm is possible.

• Journal of Life Science
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• v.23 no.4
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• pp.595-601
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• 2013

The clusters of orthologous groups of proteins (COG) algorithm was applied to identify essential proteins in eukaryotes and to measure the degree of conservation. Sixty-three orthologous groups, which were conserved in 66 microbial genomes, enlarged to 104 eukaryotic orthologous groups (KOGs) and 71 KOGs were conserved at the nuclear genome of 7 eucaryotes. Fifty-four of 71 translation-related genes were conserved, highlighting the importance of proteins in modern organisms. Translation initiation factors (KOG0343, KOG3271) and prolyl-tRNA synthetase (KOG4163) showed high conservation based on the distance value analysis. The genes of Caenorhabditis elegans appear to harbor high genetic variation because the genome showed the highest variation at 71 conserved proteins among 7 genomes. The 71 conserved genes will be valuable in basic and applied research, for example, targeting for antibiotic development.

• 한국생물공학회:학술대회논문집
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• 2003.04a
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• pp.715-718
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• 2003

A COG (clusters of orthologous groups of proteins) algorithm, protein similarities among genomes, was used to detect conserved genes and to figure out their relationships within 42 procaryote, 33 Bacteria and 16 Proteobacteria All analyzed procaryotes shared 75 COGs. COG0195, COG0358 and COG0528 were only represented by the 42 procaryotes. Sixty-four COGs were added as conserved genes in 33 eubacteria. Each Proteobacteria group has a unique repertoire of COGs. Metabolic COGs were more diverse in the beta-Proteobacteria group than in the other groups. The possibilities of detecting new biological molecules is high in phylogenetically related organisms, hence the identification of useful proteins by using this algorithm is possible.

• Journal of Life Science
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• v.24 no.7
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• pp.791-797
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• 2014

Sixty-two conserved orthologous groups (OGs) of proteins, in 63 prokaryotes and seven eukaryotes were analyzed to identify essential proteins in the mitochondria of eukaryotes, and their counterparts in prokaryotes. Twenty OGs were common in eukaryotic mitochondria, and all were translation related. Encephalitozoon cuniculi, an obligate parasitic eukaryote, shares no common mitochondrial OGs with the other 69 organisms. Seventeen conserved OGs were mitochondria related in the 69 organisms. Mitochondria related- and nonrelated-OGs were divided into prokaryotic genomes (p<0.001, paired t-test) unlike eukaryotic genomes in the distance value analysis. The most commonly conserved mitochondria-related OG was COG0048-KOG1750 (ribosomal small subunit S12), whereas it was COG0100-KOG0407 (ribosomal small subunit S11) in nonrelated OGs. These results could be applied in scientific research to determine phylogenetic relationships and in areas such as drug development.

• Journal of Life Science
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• v.13 no.3
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• pp.298-307
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• 2003

To figure out the conserved genes and newly added genes at each phylogenetic level of Archaea, COG (clusters of orthologous groups of proteins) algorithm was applied. The number of conserved genes within 9 species of Archaea was 340 and that of 8 species of Euryarchaeota was 388. Many of conserved 265 COGs, which are specific to Archaea and absent in Bacteria and S. cerevisiae, were concerned with 'information storage and processing' (94 COG, 35.5%) and 'metabolism' (82 COG, 30.9%). COGs related to these functions were assumed as highly conserved and permit peculiar life form to Archaea. It seemed that there was some difference in 'nucleotide transport and metabolism' and there was little difference in 'information storage and processing' between Euryarchaeota and Crenarchaeota. Marine-origin Euryarchaeota showed different conserved COGs with terrestrial Euryarchaeota. Conserved COGs, related to carbohydrate transport and metabolism and others, were different between marine- and terrestrial-origin Euryarchaeota. Hence it was assumed that their physiology might be different. This study may help to understand the origin and conserved genes at each phylogenetic level of marine-origin Euryarchaeota and may help in the mining of useful genes in marine Archaea as Manco et al. (Arch. Biochem. Biophy. 373, 182 (2000)).

• Journal of Life Science
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• v.27 no.6
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• pp.694-701
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• 2017

Mycoplasma genitalium represents the smallest genome among mono-cultivable prokaryotes. To discover and compare the orthologs (conservative genes) among M. genitalium and 14 prokaryotes that are uncultivable and have less orthologs than M. genitalium, COG (clusters of orthologous groups of protein) analyses were applied. The analyzed prokaryotes were M. genitalium, one hyperthermophilic exosymbiotic archaeon Nanoarchaeum equitans, four intracellular plant pathogenic eubacteria of Candidatus Phytoplasma genus, and nine endosymbiotic eubacteria of phloem- and xylem-feeding insects. Among 367 orthologs of M. genitalium, 284 orthologs were conservative between M. genitalium and at least one other prokaryote. All 15 prokaryotes commonly have 29 orthologs, representing the significance of proteins in life. They belong to 25 translation-related, including 22 ribosomal proteins, 3 subunits of RNA polymerase, and 1 protein-folding-related. Among the 15 prokaryotes, 40 orthologs were only found in all four Candidatus Phytoplasma. The other nine Candidatus, all endosymbionts with insects, showed only a single common COG0539 (ribosomal protein S1), representing the diversity of orthologs among them. These results might provide clues to understand conservative genes in uncultivable prokaryotes, and may be helpful in industrial areas, such as handling prokaryotes producing amino acids and antibiotics, and as precursors of organic synthesis.

• Journal of Life Science
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• v.33 no.11
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• pp.944-949
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• 2023

The purpose of this study was to identify conserved metabolic pathways and conserved genes in 122 archaeal species. Using the Clusters of Orthologous Groups of Proteins (COG) database of conserved genes, we analyzed whether 122 species had 63 COG metabolic pathways, the 822 COGs that compose them, and a total of 4,877 COGs. Archaeal ribosomal proteins were the most conserved in metabolic pathways. 46 COGs in seven COG pathways among 63 COG pathways and 20 COGs in others were conserved in 122 species. Some genes involved in cell wall and extracellular matrix synthesis, replication, transcription, translation, and protein metabolism were common to all 122 species. When the distance value of the phylogenetic tree was analyzed at the phylum level or class level, the average was the lowest at the class Halobacteria of the phylum Euryarchaeota. Standard deviation was high for the class Nitosospharia of the phylum Thaumarchaeota, the unclassified members of phylum Thaumarchaeota, the class Halobacteria of the phylum Euryarchaeota, the class Thermoprotei of the phylum Crenarchaeota, and other archaea. Furthermore, the phylogenetic tree analysis revealed six commonalities. The results of this study, along with data on conserved genes, could be used for drug development and gene selection for strain improvement.

• Journal of Life Science
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• v.32 no.3
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• pp.249-255
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• 2022

Metabolism is essential for survival and reproduction, and there is a metabolic pathways entry in the clusters of orthologous groups of proteins (COGs) database, updated in 2020. In this study, the metabolic pathways of 1309 prokaryotes were analyzed using COGs. There were 822 COGs associated with 63 metabolic pathways, and the mean for each taxon was between 200.50 (mollicutes) and 527.07 (cyanobacteria) COGs. The metabolic pathway composition ratio (MPCR) was defined as the number of COGs present in one genome in relation to the total number of COGs constituting each metabolic pathway, and the number of pathways with 100% MPCR ranged from 0 to 26 in each prokaryote. Among 1309 species, the 100% MPCR pathways included murein biosynthesis associated with cell wall synthesis (922 species); glycine cleavage (918); and ribosomal 30S subunit synthesis (903). The metabolic pathways with 0% MPCR were those involving photosystem I (1263 species); archaea/vacuolar-type ATP synthase (1028); and Na⁺-translocation NADH dehydrogenase (976). Depending on the prokaryote, three to 49 metabolic pathways could not be performed at all. The sequence of most highly conserved metabolic pathways was ribosome 30S subunit synthesis (96.1% of 1309 species); murein biosynthesis (86.8%); arginine biosynthesis (80.4%); serine biosynthesis (80.3%); and aminoacyl-tRNA synthesis (82.2%). Protein and cell wall synthesis have been shown to be important metabolic pathways in prokaryotes, and the results of this study of COGs related to such pathways can be utilized in, for example, the development of antibiotics and artificial cells.

• Journal of Life Science
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• v.30 no.9
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• pp.813-818
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• 2020

The archaeal clusters of orthologous genes (arCOG) algorithm, which identifies common genes among archaebacterial genomes, was used to identify conservative genes among 168 archaebacterial strains. The numbers of conserved orthologs were 14, 10, 9, and 8 arCOGs in 168, 167, 166, and 165 strains, respectively. Among 41 conserved arCOGs, 13 were related to function J (translation, ribosomal structure, and biogenesis), and 10 were related to function L (replication, recombination, and repair). Among the 14 conserved arCOGs in all 168 strains, 6 arCOGs of tRNA synthetase comprised the highest proportion. Of the remaining 8 arCOGs, 2 are involved in reactions with ribosomes, 2 for tRNA synthesis, 2 for DNA replication, and 2 for transcription. These results showed the importance of protein expression in archaea. For the classes or orders having 3 or more members, genomic analysis was performed by averaging the distance values of the conservative arCOGs. Classes Archaeoglobi and Thermoplasmata of the phylum Euryarchaeota showed the lowest and the highest average of distance value, respectively. This study can provides data necessary for basic scientific research and the development of antibacterial agents and tumor control.