PMC:4301621 / 10823-15084 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":"Identification of essential genes and reactions in iCY1106\nWhen cultured on minimal growth medium (MG) containing glucose, KH2PO4, MgSO4 and NaNO3 [23], 86 M. alpina genes (7.78% of the total) were identified as essential for growth using the FBA method (Additional file 3). In contrast, on yeast extract (YE) medium (based on MG but including all 20 regular amino acids) only 49 genes were identified as essential. On MG medium, over half of the essential genes were involved in amino acid (36.05%) and nucleotide metabolism (23.26%; Figure 2). However on YE medium, most of the essential genes were associated with nucleotide metabolism (38.78%).\nFigure 2 Essential genes identified by MG and YE medium in model i CY1106.\nThe 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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