title: Putative Alginate Assimilation Process of the Marine Bacterium Saccharophagus degradans 2-40 Based on Quantitative Proteomic Analysis.
abstract: Quantitative proteomic analysis was conducted to assess the assimilation processes of Saccharophagus degradans cultured with glucose, pectin, and alginate as carbon sources. A liquid chromatography-tandem mass spectrometry approach was used, employing our unique, long monolithic silica capillary column. In an attempt to select candidate proteins that correlated to alginate assimilation, the production of 23 alginate-specific proteins was identified by statistical analyses of the quantitative proteomic data. Based on the analysis, we propose that S. degradans has an alginate-specific gene cluster for efficient alginate utilization. The alginate-specific proteins of S. degradans were comprised of alginate lyases, enzymes related to carbohydrate metabolism, membrane transporters, and transcription factors. Among them, the short-chain dehydrogenase/reductase Sde_3281 annotated in the alginate-specific cluster showed 4-deoxy-L-erythro-5-hexoseulose uronic acid reductase (DehR) activity. Furthermore, we found two different genes (Sde_3280 and Sde_0939) encoding 2-keto-3-deoxy-D-gluconic acid (KDG) kinases (KdgK) that metabolize the KDG derived from alginate and pectin in S. degradans. S. degradans used Sde_3280 to phosphorylate the KDG derived from alginate and Sde_0939 to phosphorylate the KDG derived from pectin. The distinct selection of KdgKs provides an important clue toward the elucidation of how S. degradans recognizes and processes polysaccharides.
authors.affiliation: Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto, 606-8502, Japan. takagi.toshiyuki.42a@st.kyoto-u.ac.jp.|JST, CREST, Kawaguchi, Saitama, 332-0012, Japan. takagi.toshiyuki.42a@st.kyoto-u.ac.jp.|Japan Society for the Promotion of Science, Sakyo, Kyoto, 606-8502, Japan. takagi.toshiyuki.42a@st.kyoto-u.ac.jp.
authors.forename: Toshiyuki
authors.initials: T
authors.lastname: Takagi
authors.affiliation: Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto, 606-8502, Japan. morisaka@kais.kyoto-u.ac.jp.|JST, CREST, Kawaguchi, Saitama, 332-0012, Japan. morisaka@kais.kyoto-u.ac.jp.
authors.forename: Hironobu
authors.initials: H
authors.lastname: Morisaka
authors.affiliation: Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto, 606-8502, Japan. aburaya.shunsuke.37r@st.kyoto-u.ac.jp.|JST, CREST, Kawaguchi, Saitama, 332-0012, Japan. aburaya.shunsuke.37r@st.kyoto-u.ac.jp.
authors.forename: Shunsuke
authors.initials: S
authors.lastname: Aburaya
authors.affiliation: Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto, 606-8502, Japan. tatsukami.youhei.88a@st.kyoto-u.ac.jp.|JST, CREST, Kawaguchi, Saitama, 332-0012, Japan. tatsukami.youhei.88a@st.kyoto-u.ac.jp.|Japan Society for the Promotion of Science, Sakyo, Kyoto, 606-8502, Japan. tatsukami.youhei.88a@st.kyoto-u.ac.jp.
authors.forename: Yohei
authors.initials: Y
authors.lastname: Tatsukami
authors.affiliation: Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto, 606-8502, Japan. k_kuro@kais.kyoto-u.ac.jp.|JST, CREST, Kawaguchi, Saitama, 332-0012, Japan. k_kuro@kais.kyoto-u.ac.jp.
authors.forename: Kouichi
authors.initials: K
authors.lastname: Kuroda
authors.affiliation: Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto, 606-8502, Japan. miueda@kais.kyoto-u.ac.jp.|JST, CREST, Kawaguchi, Saitama, 332-0012, Japan. miueda@kais.kyoto-u.ac.jp.
authors.forename: Mitsuyoshi
authors.initials: M
authors.lastname: Ueda
mesh_terms: D000464:Alginates / Q000378:metabolism*; D059001:Aquatic Organisms / Q000378:metabolism*; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism*; D020563:Gammaproteobacteria / Q000378:metabolism*; D020723:Glucuronic Acid / Q000378:metabolism; D006603:Hexuronic Acids / Q000378:metabolism; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology
chemical_list: D000464:Alginates; D001426:Bacterial Proteins; D006603:Hexuronic Acids; D020543:Proteome; D020723:Glucuronic Acid
keywords: 4-Deoxy-L-erythro-5-hexoseulose uronic acid reductase; Alginate; Marine bacterium; Quantitative proteomic analysis; Saccharophagus degradans