Transcriptomic characterization of recombinant Clostridium beijerinckii NCIMB 8052 expressing methylglyoxal synthase and glyoxal reductase from Clostridium pasteurianum ATCC 6013

• Published in: Applied and environmental microbiology 2024-10, Vol.90 (10), p.e0101224
• Main Authors: Kumar, Santosh, Agyeman-Duah, Eric, Awaga-Cromwell, Marian M, Ujor, Victor C
• Format: Article
• Language: English
• Subjects: Abundance; Amino acids; Asparagine; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Bioconversion; Biological effects; Biosynthesis; Biotechnology; Butanol; Butanols - metabolism; Capsular polysaccharides; Cellular manufacture; Cellular stress response; Chemicals; Clostridium - enzymology; Clostridium - genetics; Clostridium - metabolism; Clostridium beijerinckii; Clostridium beijerinckii - enzymology; Clostridium beijerinckii - genetics; Clostridium beijerinckii - metabolism; Cysteine; Decarbonization; Food conversion; Food processing; Food processing industry wastes; Food waste; Gene expression; Genes; Glycine; Iron; Iron-sulfur proteins; Lactose; Lactose - metabolism; Lysine; Metabolic Engineering; Metabolic networks; Metabolism; Methionine; Methylglyoxal synthase; Microorganisms; Polysaccharides; Pyrimidines; Pyruvaldehyde; Reductases; Saccharides; Signal transduction; Transcriptome; Transcriptomics; Tryptophan; Vitamin B12; Vitamins; Waste management; Waste streams; Whey; Whey - metabolism
• ISSN: 0099-2240; 1098-5336; 1098-5336
• DOI: 10.1128/aem.01012-24

Bioconversion of abundant lactose-replete whey permeate to value-added chemicals holds promise for valorization of this expanding food processing waste. Efficient conversion of whey permeate-borne lactose requires adroit microbial engineering to direct carbon to the desired chemical. An engineered strain of NCIMB 8052 ( _mgsA+mgR) that produces 87% more butanol on lactose than the control strain was assessed for global transcriptomic changes. The results revealed broadly contrasting gene expression patterns in _mgsA+mgR relative to the control strain. These were characterized by widespread decreases in the abundance of mRNAs of Fe-S proteins in _mgsA+mgR, coupled with increased differential expression of lactose uptake and catabolic genes, iron uptake genes, two-component signal transduction and motility genes, and genes involved in the biosynthesis of vitamins B and B , aromatic amino acids (particularly tryptophan), arginine, and pyrimidines. Conversely, the mRNA patterns suggest that the L-aspartate-dependent biosynthesis of NAD as well as biosynthesis of lysine and asparagine and metabolism of glycine and threonine were likely down-regulated. Furthermore, genes involved in cysteine and methionine biosynthesis and metabolism, including cysteine desulfurase-a central player in Fe-S cluster biosynthesis-equally showed reductions in mRNA abundance. Genes involved in biosynthesis of capsular polysaccharides and stress response also showed reduced mRNA abundance in _mgsA+mgR. The results suggest that remodeling of cellular and metabolic networks in _mgsA+mgR to counter anticipated effects of methylglyoxal production from heterologous expression of methylglyoxal synthase led to enhanced growth and butanol production in _mgsA+mgR. Biological production of commodity chemicals from abundant waste streams such as whey permeate represents an opportunity for decarbonizing chemical production. Whey permeate remains a vastly underutilized feedstock for bioproduction purposes. Thus, enhanced understanding of the cellular and metabolic repertoires of lactose-mediated production of chemicals such as butanol promises to identify new targets that can be fine tuned in recombinant and native microbial strains to engender stronger coupling of whey permeate-borne lactose to value-added chemicals. Our results highlight new genetic targets for future engineering of for improved butanol production on lactose and ultimately in whey permeate.