Transcriptomic and metabolomic responses to carbon and nitrogen sources in Methylomicrobium album BG8

Abstract

Methanotrophs use methane as their sole carbon and energy source and represent an attractive platform for converting single-carbon feedstocks into value-added compounds. Optimizing these species for biotechnological applications involves choosing an optimal growth substrate based on an understanding of cellular responses to different nutrients. Although many studies of methanotrophs have examined growth rate, yield, and central carbon flux in cultures grown with different carbon and nitrogen sources, few studies have examined more global cellular responses to different media. Here, we evaluated global transcriptomic and metabolomic profiles of Methylomicrobium album BG8 when grown with methane or methanol as the carbon source and nitrate or ammonium as the nitrogen source. We identified five key physiological changes during growth on methanol: M. album BG8 cultures upregulated transcripts for the Entner-Doudoroff and pentose phosphate pathways for sugar catabolism, produced more ribosomes, remodeled its phospholipid membrane, activated various stress response systems, and upregulated glutathione-dependent formaldehyde detoxification. When using ammonium, M. album BG8 upregulated haoAB hydroxylamine dehydrogenase and the overall central metabolic activity; whereas when using nitrate, cultures upregulated genes for nitrate assimilation and conversion. Overall, we identified several nutrient source-specific responses that could provide a valuable basis for future research on the biotechnological optimization of these species.

RNA Biomarker Trends across Type I and Type II Aerobic Methanotrophs in Response to Methane Oxidation Rates and Transcriptome Response to Short-Term Methane and Oxygen Limitation in Methylomicrobium album BG8

“…Additionally, both limitation conditions had downregulation of the carbon storage regulator, csrA , and significant upregulation of sigma factor rpoE , an expression pattern indicative of stress response ( 71 ). DGE was observed for other genes indicative of stress response as seen for stressed M. album BG8 grown with methanol ( 67 ) ( Fig. 6 ).…”

“…Upregulation of cytochrome oxidase genes in response to O 2 limitation was observed, and such upregulation has been previously observed in Methylomicrobium buryatense 5GB1C ( 20 ); however, a stronger response was observed for CH 4 limitation. Different carbon sources have been found to affect transcriptional responses of both alpha- and gammaproteobacterial methanotrophs ( 55 , 67 ).…”

“…These could be potential strategies for maintaining activity and growth upon substrate limitation. Research on M. buryatense 5GB1 and M. album BG8 grown on methanol suggests that electrons obtained from methanol dehydrogenase are directly transferred to cytochromes and the electron transport chain, bypassing the electron requirements from NADH oxidoreductase complex for ATP production ( 67 ). Some studies have shown that type I methanotrophs potentially perform fermentation-based methanotrophy, in which methane-derived formaldehyde can be used for formation of formate, acetate, succinate, lactate, and hydroxybutyrate under low-oxygen conditions ( 69 ).…”