title: Molecular Insight into Evolution of Symbiosis between Breast-Fed Infants and a Member of the Human Gut Microbiome Bifidobacterium longum.
abstract: Breast-fed infants generally have a bifidobacteria-rich microbiota with recent studies indicating that human milk oligosaccharides (HMOs) selectively promote bifidobacterial growth. Bifidobacterium bifidum possesses a glycoside hydrolase family 20 lacto-N-biosidase for liberating lacto-N-biose I from lacto-N-tetraose, an abundant HMO unique to human milk, while Bifidobacterium longum subsp. longum has a non-classified enzyme (LnbX). Here, we determined the crystal structure of the catalytic domain of LnbX and provide evidence for creation of a novel glycoside hydrolase family, GH136. The structure, in combination with inhibition and mutation studies, provides insight into the molecular mechanism and broader substrate specificity of this enzyme. Moreover, through genetic studies, we show that lnbX is indispensable for B. longum growth on lacto-N-tetraose and is a key genetic factor for persistence in the gut of breast-fed infants. Overall, this study reveals possible evolutionary routes for the emergence of symbiosis between humans and bifidobacterial species in the infant gut.
authors.affiliation: Department of Biotechnology, The University of Tokyo, Tokyo 113-8657, Japan; Graduate School of Biostudies, Kyoto University, Kyoto 606-8052, Japan.
authors.forename: Chihaya
authors.initials: C
authors.lastname: Yamada
authors.affiliation: Graduate School of Biostudies, Kyoto University, Kyoto 606-8052, Japan.
authors.forename: Aina
authors.initials: A
authors.lastname: Gotoh
authors.affiliation: Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Ishikawa 921-8836, Japan.
authors.forename: Mikiyasu
authors.initials: M
authors.lastname: Sakanaka
authors.affiliation: School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia.
authors.forename: Mitchell
authors.initials: M
authors.lastname: Hattie
authors.affiliation: School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA 6009, Australia.
authors.forename: Keith A
authors.initials: KA
authors.lastname: Stubbs
authors.affiliation: Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Ishikawa 921-8836, Japan.
authors.forename: Ayako
authors.initials: A
authors.lastname: Katayama-Ikegami
authors.affiliation: School of Human Cultures, The University of Shiga Prefecture, Hikone, Shiga 522-8533, Japan.
authors.forename: Junko
authors.initials: J
authors.lastname: Hirose
authors.affiliation: Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Ishikawa 921-8836, Japan.
authors.forename: Shin
authors.initials: S
authors.lastname: Kurihara
authors.affiliation: Department of Biotechnology, The University of Tokyo, Tokyo 113-8657, Japan.
authors.forename: Takatoshi
authors.initials: T
authors.lastname: Arakawa
authors.affiliation: Food Research Institute, National Agriculture and Food Research Organization, Ibaraki 305-8642, Japan.
authors.forename: Motomitsu
authors.initials: M
authors.lastname: Kitaoka
authors.affiliation: Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan.
authors.forename: Shujiro
authors.initials: S
authors.lastname: Okuda
authors.affiliation: Graduate School of Biostudies, Kyoto University, Kyoto 606-8052, Japan; Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Ishikawa 921-8836, Japan. Electronic address: takane@lif.kyoto-u.ac.jp.
authors.forename: Takane
authors.initials: T
authors.lastname: Katayama
authors.affiliation: Department of Biotechnology, The University of Tokyo, Tokyo 113-8657, Japan. Electronic address: asfushi@mail.ecc.u-tokyo.ac.jp.
authors.forename: Shinya
authors.initials: S
authors.lastname: Fushinobu
mesh_terms: D000069978:Bifidobacterium longum / Q000187:drug effects / Q000201:enzymology / Q000254:growth & development*; D001665:Binding Sites; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D019143:Evolution, Molecular; D005243:Feces / Q000382:microbiology; D000069196:Gastrointestinal Microbiome; D065089:Glycoside Hydrolase Inhibitors / Q000138:chemical synthesis / Q000737:chemistry / Q000378:metabolism; D006026:Glycoside Hydrolases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D006801:Humans; D007223:Infant; D007700:Kinetics; D008895:Milk, Human / Q000378:metabolism*; D062105:Molecular Docking Simulation; D016297:Mutagenesis, Site-Directed; D009844:Oligosaccharides / Q000494:pharmacology; D012336:RNA, Ribosomal, 16S / Q000235:genetics / Q000378:metabolism; D013379:Substrate Specificity; D013559:Symbiosis
chemical_list: D065089:Glycoside Hydrolase Inhibitors; D009844:Oligosaccharides; D012336:RNA, Ribosomal, 16S; D006026:Glycoside Hydrolases
keywords: X-ray crystallography; bifidobacteria; glycoside hydrolase; human microbe co-evolution; human microbe symbiosis; human milk oligosaccharides; infant gut microbiota; inhibitors; lacto-N-biosidase; lacto-N-tetraose