PMC:4301621 / 11548-15085 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/4301621","sourcedb":"PMC","sourceid":"4301621","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4301621","text":"The identified genes were compared with the database of essential genes (DEG), and 40 genes were found to share high homology with genes identified by DEG (identity ≥ 40%, E-value ≤ 1.0E-30; Table 2). One gene, UTP-glucose-1-phosphate uridylyltransferase (MA-090-485), is involved in the synthesis of the cell wall component 1,3-beta-D-glucan (Table 2). MA-090-485 is highly homologous with the Saccharomyces cerevisiae enzyme (sequence identity = 62.58%, e-value = 0) identified in the DEG search. Similarly, nucleoside diphosphate kinase (MA-120-261), which is involved in the synthesis of CTP and GTP, also shared high homology with one of the essential genes identified by DEG (identity = 66.89%, e-value = 2.0E-68). Besides, in MG, there were 46 genes that did not match with DEG (Additional file 3). Of these, when nitrate was used as nitrogen source, nitrate reductase (MA-291-2) and nitrite reductase (MA-291-3), which together convert nitrate into NH3 for cell growth, were essential under this condition. Another two essential genes, delta 5 desaturase (MA-326-160) and delta 12 desaturase (MA-334-414) are vital for the synthesis of ARA in M. alpina. In addition, most of these essential genes were distributed in the Amino Acid Metabolism category (28.3%). This was understandable since essential gene identified by DEG were in a rich medium in which genes involving amino acid synthesis may not be essential.\nTable 2 Essential genes identified on different mediums which are high homology with DEG\nGene Enzyme Essentiality Subsystem\nMG YE\nMA-133-4 Ribose-5-phosphate isomerase E E Carbohydrate metabolism\nMA-090-485 UTP-glucose-1-phosphate uridylyltransferase E E\nMA-101-200 Mannose-6-phosphate isomerase E E\nMA-120-141 Phosphoacetylglucosamine mutase E E\nMA-184-380 Acetyl-CoA carboxylase E E\nMA-072-196 Argininosuccinate lyase E NE Amino acid metabolism\nMA-213-50 Adenylosuccinate synthase E E\nMA-213-539 Adenylosuccinate lyase E E\nMA-326-6 Aspartate carbamoyltransferase E E\nMA-334-434 Phosphoribosylanthranilate isomerase E NE\nMA-120-148 2-Acetolactate methylmutase E NE\nMA-090-434 Dihydroxy-acid dehydratase E NE\nMA-139-331 Homoaconitate hydratase E NE\nMA-323-77 Saccharopine dehydrogenase E NE\nMA-326-106 Ornithine carbamoyltransferase E NE\nMA-101-393 Imidazole-4-carboxamide isomerase E NE\nMA-184-558 Imidazoleglycerol-phosphate dehydratase E NE\nMA-090-452 Glutamine amidotransferase:cyclase E NE\nMA-320-159 3-dehydroquinate synthase E NE\nMA-139-157 Chorismate synthase E NE\nMA-073-62 3-deoxy-7-phosphoheptulonate synthase E NE\nMA-213-547 Tryptophan synthase E NE\nMA-297-40 Chorismate mutase E NE\nMA-120-157 Thioredoxin reductase E E\nMA-173-30 Purine-nucleoside phosphorylase E E Nucleotide metabolism\nMA-213-65 IMP dehydrogenase E E\nMA-120-261 Nucleoside diphosphate kinase E E\nMA-139-347 Guanylate kinase E E\nMA-120-138 Ribonucleoside-diphosphate reductase E E\nMA-055-211 Ribonucleoside-diphosphate reductase E E\nMA-323-58 Ribonucleoside-diphosphate reductase E E\nMA-334-356 Thymidylate synthase E E\nMA-153-455 3(2),5-bisphosphate nucleotidase E NE\nMA-111-23 phosphoadenylyl-sulfate reductase E NE Energy metabolism\nMA-182-360 6,7-dimethyl-8-ribityllumazine synthase E E Cofactors and vitamins\nMA-184-368 Riboflavin synthase E E\nMA-210-311 Aspartate dehydrogenase E E\nMA-055-340 Fatty-acyl-CoA synthase E E Lipid metabolism\nMA-162-131 Palmitoyl-protein thioesterase E E\nMA-334-239 Very-long-chain enoyl-CoA reductase E E\nE: essential gene; NE: non-essential gene. MG: minimal medium; YE: yeast extract 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