title: Lactobacillus oligofermentans glucose, ribose and xylose transcriptomes show higher similarity between glucose and xylose catabolism-induced responses in the early exponential growth phase.
abstract: Lactobacillus oligofermentans has been mostly isolated from cold-stored packaged meat products in connection with their spoilage, but its precise role in meat spoilage is unknown. It belongs to the L. vaccinostercus group of obligate heterofermentative lactobacilli that generally ferment pentoses (e.g. xylose and ribose) more efficiently than hexoses (e.g. glucose). However, more efficient hexose utilization can be induced. The regulation mechanisms of the carbohydrate catabolism in such bacteria have been scarcely studied. To address this question, we provided the complete genome sequence of L. oligofermentans LMG 22743(T) and generated time course transcriptomes during its growth on glucose, ribose and xylose.
  
  
  
  The genome was manually annotated and its main functional features were examined. L. oligofermentans was confirmed to be able to efficiently utilize several hexoses and maltose, which is, presumably, induced by its repeated cultivation with glucose in vitro. Unexpectedly, in the beginning of the exponential growth phase, glucose- and xylose-induced transcriptome responses were more similar, whereas toward the end of the growth phase xylose and ribose transcriptomes became more alike. The promoter regions of genes simultaneously upregulated both on glucose and xylose in comparison with ribose (particularly, hexose and xylose utilization genes) were found to be enriched in the CcpA- binding site. Transcriptionally, no glucose-induced carbon catabolite repression was detected. The catabolism of glucose, which requires initial oxidation, led to significant overexpression of the NAD(P)H re-oxidation genes, the upstream regions of which were found to contain a motif, which was highly similar to a Rex repressor binding site.
  
  
  
  This paper presents the second complete genome and the first study of carbohydrate catabolism-dependent transcriptome response for a member of the L. vaccinostercus group. The transcriptomic changes detected in L. oligofermentans for growth with different carbohydrates differ significantly from those of facultative heterofermentative lactobacilli. The mechanism of CcpA regulation, putatively contributing to the observed similarities between glucose- and xylose-induced transcriptome responses and the absence of stringent carbon catabolite control, requires further studies. Finally, the cell redox balance maintenance, in terms of the NAD(P)+/NAD(P)H ratio, was predicted to be regulated by the Rex transcriptional regulator, supporting the previously made inference of Rex-regulons for members of the Lactobacillaceae family.
authors.affiliation: Institute of Biotechnology, University of Helsinki, Helsinki, Finland. margarita.andreevskaya@helsinki.fi.
authors.forename: Margarita
authors.identifier: 0000-0003-4052-3861
authors.initials: M
authors.lastname: Andreevskaya
authors.affiliation: Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland.
authors.forename: Per
authors.initials: P
authors.lastname: Johansson
authors.affiliation: Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland.
authors.forename: Elina
authors.initials: E
authors.lastname: Jääskeläinen
authors.affiliation: Institute of Biotechnology, University of Helsinki, Helsinki, Finland.|Present Address: The National Bureau of Investigation, Vantaa, Finland.
authors.forename: Tanja
authors.initials: T
authors.lastname: Rämö
authors.affiliation: Institute of Biotechnology, University of Helsinki, Helsinki, Finland.|Present Address: Finnish Red Cross Blood Service, Helsinki, Finland.
authors.forename: Jarmo
authors.initials: J
authors.lastname: Ritari
authors.affiliation: Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
authors.forename: Lars
authors.initials: L
authors.lastname: Paulin
authors.affiliation: Department of Food Hygiene and Environmental Health, University of Helsinki, Helsinki, Finland.
authors.forename: Johanna
authors.initials: J
authors.lastname: Björkroth
authors.affiliation: Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
authors.forename: Petri
authors.initials: P
authors.lastname: Auvinen
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D005947:Glucose / Q000378:metabolism; D007778:Lactobacillus / Q000235:genetics / Q000254:growth & development*; D058977:Molecular Sequence Annotation; D009005:Monosaccharides / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D012266:Ribose / Q000378:metabolism; D017422:Sequence Analysis, DNA / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome; D014994:Xylose / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D009005:Monosaccharides; D012266:Ribose; D014994:Xylose; D005947:Glucose
keywords: Carbohydrate catabolism; Carbon catabolite control; CcpA; Lactobacillus oligofermentans; NAD(P)H re-oxidation; Obligate heterofermentative metabolism; RNA-seq based transcriptomes; Redox-sensing transcriptional repressor Rex