Transcriptome differences between Cupriavidus necator NH9 grown with 3-chlorobenzoate and that grown with benzoate

• Published in: Bioscience, biotechnology, and biochemistry biotechnology, and biochemistry, 2021-05, Vol.85 (6), p.1546-1561
• Main Authors: Moriuchi, Ryota, Dohra, Hideo, Kanesaki, Yu, Ogawa, Naoto
• Format: Article
• Language: English
• ISSN: 1347-6947; 1347-6947
• DOI: 10.1093/bbb/zbab044

ABSTRACT RNA-seq analysis of Cupriavidus necator NH9, a 3-chlorobenzoate degradative bacterium, cultured with 3-chlorobenzaote and benzoate, revealed strong induction of genes encoding enzymes in degradation pathways of the respective compound, including the genes to convert 3-chlorobenzaote and benzoate to chlorocatechol and catechol, respectively, and the genes of chlorocatechol ortho-cleavage pathway for conversion to central metabolites. The genes encoding transporters, components of the stress response, flagellar proteins, and chemotaxis proteins showed altered expression patterns between 3-chlorobenzoate and benzoate. Gene Ontology enrichment analysis revealed that chemotaxis-related terms were significantly upregulated by benzoate compared with 3-chlorobenzoate. Consistent with this, in semisolid agar plate assays, NH9 cells showed stronger chemotaxis to benzoate than to 3-chlorobenzoate. These results, combined with the absence of genes related to uptake/chemotaxis for 3-chlorobenzoate located closely to the degradation genes of 3-chlorobenzoate, suggested that NH9 has not fully adapted to the utilization of chlorinated benzoate, unlike benzoate, in nature. Graphical Abstract Graphical Abstract RNA-seq analysis showed that 3-chlorobenzoate and benzoate induced the expression of genes for aromatic degradation, transport, and/or chemotaxis strongly in Cupriavidus necator NH9.