title: Strand-specific RNA-seq analysis of the Lactobacillus delbrueckii subsp. bulgaricus transcriptome.
abstract: Lactobacillus delbrueckii subsp. bulgaricus 2038 (Lb. bulgaricus 2038) is an industrial bacterium that is used as a starter for dairy products. We proposed several hypotheses concerning its industrial features previously. Here, we utilized RNA-seq to explore the transcriptome of Lb. bulgaricus 2038 from four different growth phases under whey conditions. The most abundantly expressed genes in the four stages were mainly involved in translation (for the logarithmic stage), glycolysis (for control/lag stages), lactic acid production (all the four stages), and 10-formyl tetrahydrofolate production (for the stationary stage). The high expression of genes like d-lactate dehydrogenase was thought as a result of energy production, and consistent expression of EPS synthesis genes, the restriction-modification (RM) system and the CRISPR/Cas system were validated for explaining the advantage of this strain in yoghurt production. Several postulations, like NADPH production through GapN bypass, converting aspartate into carbon-skeleton intermediates, and formate production through degrading GTP, were proved not working under these culture conditions. The high expression of helicase genes and co-expressed amino acids/oligopeptides transporting proteins indicated that the helicase might mediate the strain obtaining nitrogen source from the environment. The transport system of Lb. bulgaricus 2038 was found to be regulated by antisense RNA, hinting the potential application of non-coding RNA in regulating lactic acid bacteria (LAB) gene expression. Our study has primarily uncovered Lb. bulgaricus 2038 transcriptome, which could gain a better understanding of the regulation system in Lb. bulgaricus and promote its industrial application.
authors.affiliation: Laboratory of Medical Foods, Shanghai Institute of Planned Parenthood Research, 2140 Xie-Tu Road, Shanghai 200032, China. zai-si_ji@kta.biglobe.ne.jp.
authors.forename: Huajun
authors.initials: H
authors.lastname: Zheng
authors.affiliation: Laboratory of Medical Foods, Shanghai Institute of Planned Parenthood Research, 2140 Xie-Tu Road, Shanghai 200032, China. zai-si_ji@kta.biglobe.ne.jp.
authors.forename: Enuo
authors.initials: E
authors.lastname: Liu
authors.affiliation: Laboratory of Medical Foods, Shanghai Institute of Planned Parenthood Research, 2140 Xie-Tu Road, Shanghai 200032, China. zai-si_ji@kta.biglobe.ne.jp.
authors.forename: Tao
authors.initials: T
authors.lastname: Shi
authors.affiliation: Laboratory of Medical Foods, Shanghai Institute of Planned Parenthood Research, 2140 Xie-Tu Road, Shanghai 200032, China. zai-si_ji@kta.biglobe.ne.jp.
authors.forename: Luyi
authors.initials: L
authors.lastname: Ye
authors.affiliation: Division of Research and Development, Meiji Co., Ltd, 540 Naruda, Odawara, Kanagawa 250-0862, Japan.
authors.forename: Tomonobu
authors.initials: T
authors.lastname: Konno
authors.affiliation: Graduate School of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa City, Kanagawa 252-0880, Japan.
authors.forename: Munehiro
authors.initials: M
authors.lastname: Oda
authors.affiliation: Laboratory of Medical Foods, Shanghai Institute of Planned Parenthood Research, 2140 Xie-Tu Road, Shanghai 200032, China. zai-si_ji@kta.biglobe.ne.jp and Division of Research and Development, Meiji Co., Ltd, 540 Naruda, Odawara, Kanagawa 250-0862, Japan.
authors.forename: Zai-Si
authors.initials: ZS
authors.lastname: Ji
mesh_terms: D000596:Amino Acids / Q000096:biosynthesis; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D053898:Biosynthetic Pathways; D050260:Carbohydrate Metabolism; D004265:DNA Helicases / Q000235:genetics / Q000378:metabolism; D004734:Energy Metabolism; D005285:Fermentation; D005798:Genes, Bacterial; D048668:Lactobacillus delbrueckii / Q000235:genetics* / Q000378:metabolism; D009876:Operon; D011544:Pseudogenes; D012329:RNA, Bacterial / Q000235:genetics / Q000378:metabolism; D022661:RNA, Untranslated; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D020506:Untranslated Regions
chemical_list: D000596:Amino Acids; D001426:Bacterial Proteins; D012329:RNA, Bacterial; D022661:RNA, Untranslated; D020506:Untranslated Regions; D004265:DNA Helicases