{"database":"ENA","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Fastqsanger.gz":["ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/088/SRR13176088/SRR13176088.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/089/SRR13176089/SRR13176089.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/086/SRR13176086/SRR13176086.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/087/SRR13176087/SRR13176087.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/085/SRR13176085/SRR13176085.fastq.gz","ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/084/SRR13176084/SRR13176084.fastq.gz"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":null,"additional":{"omics_type":["Genomics"],"center_name":["Microbiología Molecular, Bioquímica y Genómica Microbianas, Instituto de Investigaciones Biológicas Clemente Estable"],"full_dataset_link":["https://www.ebi.ac.uk/ena/browser/view/PRJNA681857"],"scientific_name":["Herbaspirillum seropedicae"],"long_description":["Herbaspirillum seropedicae are β-proteobacteria that establish as endophytes in various plants. They are able to consume diverse carbon sources, including hexoses and pentoses like D-xylose. D-xylose catabolism 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. Furthermore, it is found in some potential raw materials such as lignocellulosic biomass. In this work we present a study of D-xylose catabolism pathways in H. seropedicae strain Z69, using RNA-seq analysis and the subsequent study 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 is due to expression of an L-arabinose dehydrogenase encoded by G5B88_05250 gene, and was thus able to use D-xylose as 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: Weimberg pathway that produces α-ketoglutarate and a novel pathway recently described that produces pyruvate and glycolate. This novel pathway seems to be essential since a mutant in the last step of this pathway, Z69∆G5B88_06410, was unable to grow on D‑xylose. Overall design: mRNA profiles of 3 samples: Herbaspirillum seropedicae Z69 grown until mid-log phase in LGI medium supplemented with xylose 30g/l or glycerol 10g/l and a knock-out mutant strain in xylB gene (G5B88_22805) grown until mid-log phase in LGI medium supplemented with xylose 30g/l. The experiment was done in duplicate (biological replicates). Z69 grown on glycerol was used as control condition."],"repository":["ENA"],"name_synonyms":["Herbispirillum seropedicense, D-Xylose, Herbaspirillum seropedicense., D Xylose"],"description_synonyms":["Herbispirillum seropedicense, D-Xylose, Herbaspirillum seropedicense., D Xylose"],"additional_accession":[]},"is_claimable":false,"name":"D-xylose catabolic pathways expressed in Herbaspirillum seropedicae","description":"D-xylose catabolic pathways expressed in Herbaspirillum seropedicae","dates":{"last_updated":"2025-09-24","first_public":"2021-03-02"},"accession":"PRJNA681857","cross_references":{"GEO":["GSE162430"],"taxon":["964"]}}