Herbaspirillum seropedicae expresses non-phosphorylative pathways for d-xylose catabolism

• Published in: Applied microbiology and biotechnology 2021-10, Vol.105 (19), p.7339-7352
• Main Authors: Malán, Ana Karen, Tuleski, Thalita, Catalán, Ana Inés, de Souza, Emanuel Maltempi, Batista, Silvia
• Format: Article
• Language: English
• Subjects: Applied Genetics and Molecular Biotechnology; Arabinose; Biomedical and Life Sciences; Biotechnology; Carbon; Carbon sources; Catabolism; Dehydrogenase; Dehydrogenases; Endophytes; Genes; Herbaspirillum seropedicae; Hexoses; Ketoglutaric acid; Lag phase; Life Sciences; Metabolism; Microbial Genetics and Genomics; Microbiological research; Microbiology; Microorganisms; Monosaccharides; Mutants; NAD; Pentose; Phenotypes; Physiological aspects; Poly-3-hydroxybutyrate; Polyhydroxybutyric acid; Proteobacteria; Pyruvic acid; Substrates; Sugars; XylB gene; Xylose
• ISSN: 0175-7598; 1432-0614
• DOI: 10.1007/s00253-021-11507-4

Herbaspirillum seropedicae is a β-proteobacterium that establishes as an endophyte in various plants. These bacteria can consume diverse carbon sources, including hexoses and pentoses like d -xylose. d -xylose catabolic pathways have been described in some microorganisms, but databases of genes involved in these routes are limited. This is of special interest in biotechnology, considering that d -xylose is the second most abundant sugar in nature and some microorganisms, including H. seropedicae , are able to accumulate poly-3-hydroxybutyrate when consuming this pentose as a carbon source. In this work, we present a study of d -xylose catabolic pathways in H. seropedicae strain Z69 using RNA-seq analysis and subsequent analysis of phenotypes determined in targeted mutants in corresponding identified genes. G5B88_22805 gene, designated xylB , encodes a NAD + -dependent d -xylose dehydrogenase. Mutant Z69∆ xylB was still able to grow on d -xylose, although at a reduced rate. This appears to be due to the expression of an l -arabinose dehydrogenase, encoded by the araB gene (G5B88_05250), that can use d -xylose as a substrate. According to our results, H. seropedicae Z69 uses non-phosphorylative pathways to catabolize d -xylose. The lower portion of metabolism involves co-expression of two routes: the Weimberg pathway that produces α-ketoglutarate and a novel pathway recently described that synthesizes pyruvate and glycolate. This novel pathway appears to contribute to d -xylose metabolism, since a mutant in the last step, Z69∆ mhpD , was able to grow on this pentose only after an extended lag phase (40–50 h). Key points • xylB gene (G5B88_22805) encodes a NAD + -dependent D-xylose dehydrogenase . • araB gene (G5B88_05250) encodes a L-arabinose dehydrogenase able to recognize D-xylose . • A novel route involving mhpD gene is preferred for D-xylose catabolism . Graphical abstract