• Journal of Life Science
• /
• v.28 no.3
• /
• pp.369-375
• /
• 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
• /
• v.32 no.3
• /
• pp.249-255
• /
• 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.

• Restorative Dentistry and Endodontics
• /
• v.17 no.1
• /
• pp.83-94
• /
• 1992

This study was executed to measure the biosynthesis of arachidonic acid metabolic products in chronic periapical lesions, to compare the products among periapical granuloma, periapical cyst and chronic periapical abscess, and to understand the pathogensis of chronic periapical lesions. Tissues from 33 chronic periapical lesions of human teeth were enucleated during endodontic surgery. large part of each tissue was contained in liquid nitrogen immediately and the other was examined histologically. In histologically diagnosed 8 cases of periapical granuloma, 9 cases of periapical cyst and 8 cases of chronic periapical abscess. the tissues were homogenatecl and incubated with $_{14}C$-arachidonic acid. Lipid solvent extracts were separated by thin layer chromatography to be analyzed by autoradiography and TLC analyzer. 1. $TXB_2$, 6-keto-$PGF_1{\alpha}$ and $PGE_2$, $LTB_4$, HETEs, and unidentified product which are metabolic products of arachidonic acid were measured in the tissues of chronic peripaical lesions. 2. In all of periapical granuloma, cyst and abscess, the conversion rate of HETEs among all products was the highest(P<0.05), and the percentage of HETEs in total converted products was also the highest(P<0.05). 3. The concentration of each arachidonic acid product was higher in chronic periapical absecss than in periapical granuloma and cyst(P<0.05). The concentration of $TXB_2$ and HETEs in periapical cyst were hight than in periapical granuloma. 4. The relative amounts of total products from lipoxygenase pathway to those from cyclo-oxygenase pathway were about 7 fold in chronic periapical lesions. There was no difference among periapical granuloma, cyst and abscess(P<0.05). The total amount of products from each pathway were higher in chronic periapical abscess than in periapical cyst and granuloma.

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

• Restorative Dentistry and Endodontics
• /
• v.27 no.5
• /
• pp.543-551
• /
• 2002

Nitric oxide (NO) is a small molecule (mol. wt. 30 Da) and oxidative free radical. It is uncharged and can therefore diffuse freely within and between cells across membrane. Such characteristics make it a biologically important messenger in physiologic processes such as neurotransmission and the control of vascular tone. NO is also highly toxic and is known to acts as a mediator of cytotoxicity during host defense. NO is synthesized by nitric oxide synthase (NOS) through L-arginine/nitric oxide pathway which is a dioxygenation process. NO synthesis involves several participants, three co-substrates, five electrons, five co-factors and two prosthetic groups. Under normal condition, low levels of NO are synthesized by type I and III NOS for a short period of time and mediates many physiologic processes. Under condition of oxidant stress, high levels of NO are synthesized by type II NOS and inhibits a variety of metabolic processes and can also cause direct damage to DNA. Such interaction result in cytostasis, energy depletion and ultimately cell death. NO has the potential to interact with a variety of intercellular targets producing diverse array of metabolic effects. It is known that NO is involved in hemodynamic regulation, neurogenic inflammation, re-innervation, management of dentin hypersensitivity on teeth. Under basal condition of pulpal blood flow, NO provides constant vasodilator tone acting against sympathetic vasoconstriction. Substance P, a well known vasodilator, was reported to be mediated partly by NO, while calcitonin-gene related peptide has provided no evidence of its relation with NO. This review describes the roles of NO in dental pulp in addition to the known general roles of it.