Fig. 3: Genes involved in phosphate signaling, carbohydrate metabolism and PQQ synthesis were significantly overrepresented in the significant hits from high-throughput screens of acidification by G. oxydans.
A one-sided Fisher’s Exact Test was used to test for gene ontology enrichment (p < 0.05, yellow dashed line). Numbers at the base of bars are how many genes from the significant hits are from that gene ontology (GO), out of the total in the genome (in parentheses). Genes selected for further analysis of endpoint pH and bioleaching (Fig. 4) that contribute to an enriched GO are listed above the bars. A, B Enriched GO terms among genes that decreased and increased the end point pH. C, D Enriched GO terms among genes that increased and decreased the initial acidification rate. FBP fructose-bisphosphate, GDP-Man:DolP dolichyl-phosphate beta-d-mannosyltransferase, GGT glutathione hydrolase, G6P glucose 6-phosphate, HTA homoserine O-acetyltransferase, DD-transepeptidase D-Ala-D-Ala carboxypeptidase, HAG hydroxyacylglutathione, Membr membrane, Moco Mo-molybdopterin cofactor, MS monosaccharide, MT mannosyltransferase, M6P mannose-6-phosphate, Pi inorganic phosphate, PLP pyridoxal phosphate, PQQ pyrroloquinoline quinone, PSK phosphorelay sensor kinase, Q queuosine, RNase H DNA–RNA hybrid ribonuclease, SAM S-adenosyl-l-methionine, TPP thiamine pyrophosphate, TOP1 topoisomerase type 1, HK histidine kinase, UDP-G uracil-diphosphate glucose, 6-PGL 6-phosphogluconolactonase.
