• Journal of Life Science
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• v.28 no.3
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• pp.369-375
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• 2018

Mycoplasma genitalium has 367 conserved genes and the smallest genome among mono-culturable prokaryotes. Conservative metabolic pathways were examined among M. genitalium and 14 prokaryotes, one hyperthermophilic exosymbiotic archaeon Nanoarchaeum equitans and 13 intracellular eubacteria of plants or insects, with fewer conserved genes than M. genitalium. They have 11 to 71 metabolic pathways, however complete metabolic pathways ranged from 1 to 24. Totally, metabolic pathway hole is very high due to the lack of 45.8% of the enzymes required for the whole metabolic pathways and it could be suggested that the shared metabolic pathway with the host's enzyme would work or the essential substances are host dependent. The number of genes necessary for mass transfer through the cell membrane is also very low, and it may be considered that the simple diffusion or the protein of the host will function in the cell membrane of these prokaryotes. Although the tRNA charging pathway was distributed in all 15 prokaryotes, each has 5-20 tRNA charging genes. This study would give clues to the understanding of the metabolic pathways of intracellular parasitic bacteria of plant and endosymbiotic bacteria of insects, and could provide basic data for prevention of crop damage, development of insect pests and human medicines.

• 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.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 the Institute of Convergence Signal Processing
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• v.6 no.1
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• pp.27-32
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• 2005

As a large quantity of Genome sequencing has happened to be done a very much a surprising speed in short period, an automatic genome annotation process has become prerequisite. The most difficult process among with this kind of genome annotation works is to finding out the protein-coding genes within a genome. The main 2 subjects of gene prediction are Eukaryotes and Prokaryotes ; their genes have different structures, therefore, their gene prediction methods will also obviously varies. Until now, it is found that among of the 231 genome sequenced species, 200 have been found to be prokaryotes, therefore, for study of biotechnology studies, through comparative genomics, prokaryotes, rather than eukaryotes could may be more appropriate than eukaryotes. Even more, prokaryotes does not have the gene structure called an intron, so it makes the gene prediction easier. Former prokaryotes gene predictions have been shown to be 80%～ to 90% of accuracy. A recent study is aiming at 100% of gene prediction accuracy. In this paper, especially in the case of the E. coli K-12 and S. typhi genomes, gene prediction accuracy which showed 98.5% and 98.7% was more efficient than previous GLIMMER.

• 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.

• Journal of Life Science
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• v.29 no.1
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• pp.123-128
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• 2019

The use of 16S rDNA is commonplace in the determination of prokaryotic species. However, it has limitations, and there are few studies at the genus level. We investigated conserved genes and metabolic pathways at the genus level in 28 strains of 13 genera of prokaryotes using the COG database (conserved genes) and MetaCyc database (metabolic pathways). Conserved genes compared to total genes (core genome) at the genus level ranged from 27.62%(Nostoc genus) to 71.76%(Spiribacter genus), with an average of 46.72%. The lower ratio of core genome meant the higher ratio of peculiar genes of a prokaryote, namely specific biological activities or the habitat may be varied. The ratio of common metabolic pathways at the genus level was higher than the ratio of core genomes, from 58.79% (Clostridium genus) to 96.31%(Mycoplasma genus), with an average of 75.86%. When compared among other genera, members of the same genus were positioned in the closest nodes to each other. Interestingly, Bacillus and Clostridium genera were positioned in closer nodes than those of the other genera. Archaebacterial genera were grouped together in the ortholog and metabolic pathway nodes in a phylogenetic tree. The genera Granulicella, Nostoc, and Bradyrhizobium of the Acidobacteria, Cyanobacteria, and Proteobacteria phyla, respectively, were grouped in an ortholog content tree. The results of this study can be used for (i) the identification of common genes and metabolic pathways at each phylogenetic level and (ii) the improvement of strains through horizontal gene transfer or site-directed mutagenesis.

• Journal of Life Science
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• v.13 no.6
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• pp.856-864
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• 2003

The 16S rRNA gene is the most common gene in the phylogenetic analysis of procaryotes. However very high conservative of 16S rRNA has limitation in the discrimination of highly related organisms, hence other molecule was applied in this study and the result was compared with that of 16S rRNA. Three COGs (Clusters of Orthologous of protein) were only detected in 42 procaryotes ; transcription elongation facto. (COG0195), bacterial DNA primase (COG0358) and uridylate kinase (COG0528). Uridylate kinase gene was selected because of the similarity and one single copy number in each genome. Bacteria, belong to same genus, and Archaebacteria were same position with high bootstrap value in phylogenetic tree like the tree of 16S rRNA. However, alpha and epsilon Proteobcteria showed different position and Spirochaetales of Eubarteria was grouped together with Archaebacteria unlike the result of 16S rRNA. Uridylate kinase may compensate the problem of very high conservative of 16S rRNA gene and it would help to access more accurate discrimination and phylogenetic analysis of bacteria.

• 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.25 no.9
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• pp.1007-1013
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• 2015

A COG (Cluster of Orthologous Groups of proteins) algorithm was applied to detect conserved genes in 711 prokaryotes. Only COG0080 (ribosomal protein L11) was common among all the 711 prokaryotes analyzed and 58 COGs were common in more than 700 prokaryotes. Nine COGs among 58, including COG0197 (endonuclease III) and COG0088 (ribosomal protein L4), were conserved in a form of one gene per one organism. COG0008 represented 1356 genes in 709 of the prokaryotes and this was the highest number of genes among 58 COGs. Twenty-two COGs were conserved in more than 708 prokaryotes. Of these, two were transcription related, four were tRNA synthetases, eight were large ribosomal subunits, seven were small ribosomal subunits, and one was translation elongation factor. Among 58 conserved COGs in more than 700 prokaryotes, 50 (86.2%) were translation related, and four (6.9%) were transcription related, pointing to the importance of protein-synthesis in prokaryotes. Among these 58 COGs, the most conserved COG was COG0060 (isoleucyl tRNA synthetase), and the least conserved was COG0143 (methionyl tRNA synthetase). Archaea and eubacteria were discriminated in the genomic analysis by the average distance and variation in distance of common COGs. The identification of these conserved genes could be useful in basic and applied research, such as antibiotic development and cancer therapeutics.

• Journal of Life Science
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• v.32 no.6
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• pp.463-467
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• 2022

As a result of applying the COG (Cluster of Orthologous Groups of Protein) algorithm to 1,309 species to confirm the conserved genes of prokaryotes, ribosomal protein S11 (COG0100) was identified. The numbers of conservative genes were 2, 5, 5, and 6 in 1,308, 1,307, 1,306, and 1,305 species, respectively. Twenty-nine genes were conserved in over 1,302 species, and they encoded 23 ribosomal proteins, 3 tRNA synthetases, 2 translation factors, and 1 RNA polymerase subunit. Most of them were related to protein production, suggesting the importance of protein expression in prokaryotes. The highest conservative COG was COG0048 (ribosomal protein S12) among the 29 COGs. The 29 conserved genes usually have one protein for each prokaryote. COG0090 (ribosomal protein L2) had not only the lowest conservation value but also the largest standard deviation of phylogenetic distance value. As COG0090 is not only a member of the ribosome, but also a regulator of replication and transcription, it could be inferred that prokaryotes have large variations in COG0090 to survive in various environments. This study could provide data necessary for basic science, tumor control, and development of antibacterial agents.