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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0128

PubMed

30635377, Appl Environ Microbiol. 2019 Mar 6;85(6):e02582-18. doi: 10.1128/AEM.02582-18. Print 2019 Mar 15.

Characterization method

RT-PCR,enzyme activity assay

Genomic accession number

AP010888.1

Nucelotide position range

2209677-2271591

Substrate

hemicellulose

Loci

BLLJ_1836-BLLJ_1859

Species

Bifidobacterium longum subsp. longum JCM 1217/565042

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BLLJ_1836 BAJ67500.1 0 - 1830 (-) AP010888.1:2209677-2211507 -
- BLLJ_1837 BAJ67501.1 2043 - 3915 (-) AP010888.1:2211720-2213592 -
- BLLJ_1838 BAJ67502.1 4101 - 4500 (-) AP010888.1:2213778-2214177 -
- BLLJ_1839 BAJ67503.1 4984 - 5578 (+) AP010888.1:2214661-2215255 -
- BLLJ_1840 BAJ67504.1 6033 - 9870 (-) AP010888.1:2215710-2219547 -
- BLLJ_1841 BAJ67505.1 10081 - 14623 (-) AP010888.1:2219758-2224300 -
- BLLJ_1842 BAJ67506.1 14926 - 16453 (-) AP010888.1:2224603-2226130 -
- BLLJ_1843 BAJ67507.1 16762 - 18286 (-) AP010888.1:2226439-2227963 -
- BLLJ_1844 BAJ67508.1 18473 - 22181 (-) AP010888.1:2228150-2231858 -
- BLLJ_1845 BAJ67509.1 22245 - 22947 (-) AP010888.1:2231922-2232624 -
- BLLJ_1846 BAJ67510.1 23090 - 23660 (+) AP010888.1:2232767-2233337 -
- BLLJ_1847 BAJ67511.1 23882 - 25364 (+) AP010888.1:2233559-2235041 -
- BLLJ_1848 BAJ67512.1 25486 - 31441 (-) AP010888.1:2235163-2241118 -
- BLLJ_1849 BAJ67513.1 32028 - 33132 (+) AP010888.1:2241705-2242809 -
- BLLJ_1850 BAJ67514.1 33236 - 38231 (-) AP010888.1:2242913-2247908 -
- BLLJ_1851 BAJ67515.1 38357 - 44360 (-) AP010888.1:2248034-2254037 -
- BLLJ_1852 BAJ67516.1 45248 - 48989 (-) AP010888.1:2254925-2258666 -
- BLLJ_1853 BAJ67517.1 49232 - 52526 (-) AP010888.1:2258909-2262203 -
- BLLJ_1854 BAJ67518.1 52872 - 56070 (-) AP010888.1:2262549-2265747 -
- BLLJ_1855 BAJ67519.1 56407 - 57013 (-) AP010888.1:2266084-2266690 -
- BLLJ_1856 BAJ67520.1 57218 - 58061 (-) AP010888.1:2266895-2267738 -
- BLLJ_1857 BAJ67521.1 58060 - 58915 (-) AP010888.1:2267737-2268592 -
- BLLJ_1858 BAJ67522.1 59297 - 60314 (+) AP010888.1:2268974-2269991 -
- BLLJ_1859 BAJ67523.1 60568 - 61915 (-) AP010888.1:2270245-2271592 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1830 (-) TC: gnl|TC-DB|E8MFM3|3.A.1.135.6 Yes
- 2044 - 3915 (-) TC: gnl|TC-DB|E8MFM4|3.A.1.135.6 Yes
- 4102 - 4500 (-) TF: DBD-Pfam|MarR,DBD-SUPERFAMILY|0040586 Yes
- 4985 - 5578 (+) other Yes
- 6034 - 9870 (-) CAZyme: GH43|GH43_24 Yes
- 10082 - 14623 (-) CAZyme: GH30_5|GH30|CBM13 Yes
- 14927 - 16453 (-) TF: DBD-SUPERFAMILY|0045030 Yes
- 16763 - 18286 (-) TC: gnl|TC-DB|F2HQ24|2.A.3.1.20 Yes
- 18474 - 22181 (-) other Yes
- 22246 - 22947 (-) TC: gnl|TC-DB|A8TDW7|3.A.1.122.7 Yes
- 23091 - 23660 (+) TF: DBD-Pfam|HTH_11 Yes
- 23883 - 25364 (+) TC: gnl|TC-DB|P15993|2.A.3.1.3 Yes
- 25487 - 31441 (-) CAZyme: GH146 Yes
- 32029 - 33132 (+) other Yes
- 33237 - 38231 (-) CAZyme: GH43|GH43_34|GH43_22 Yes
- 38358 - 44360 (-) CAZyme: GH43|GH43_22|GH43_26 Yes
- 45249 - 48989 (-) CAZyme: GH43_27|GH43 Yes
- 49233 - 52526 (-) CAZyme: GH43_22 Yes
- 52873 - 56070 (-) CAZyme: GH43_22 Yes
- 56408 - 57013 (-) TC: gnl|TC-DB|E4R229|9.B.28.1.3 Yes
- 57219 - 58061 (-) TC: gnl|TC-DB|Q8NMV5|3.A.1.1.45 Yes
- 58061 - 58915 (-) TC: gnl|TC-DB|Q8NMV4|3.A.1.1.45 Yes
- 59298 - 60314 (+) TF: DBD-Pfam|LacI,DBD-SUPERFAMILY|0036955 Yes
- 60569 - 61915 (-) TC: gnl|TC-DB|Q8NMV3|3.A.1.1.45 Yes

PUL ID

PUL0128

PubMed

30635377, Appl Environ Microbiol. 2019 Mar 6;85(6):e02582-18. doi: 10.1128/AEM.02582-18. Print 2019 Mar 15.

Title

Two Novel alpha-l-Arabinofuranosidases from Bifidobacterium longum subsp. longum Belonging to Glycoside Hydrolase Family 43 Cooperatively Degrade Arabinan.

Author

Komeno M, Hayamizu H, Fujita K, Ashida H

Abstract

Arabinose-containing poly- or oligosaccharides are suitable carbohydrate sources for Bifidobacterium longum subsp. longum However, their degradation pathways are poorly understood. In this study, we cloned and characterized the previously uncharacterized glycoside hydrolase family 43 (GH43) enzymes B. longum subsp. longum ArafC (BlArafC; encoded by BLLJ_1852) and B. longum subsp. longum ArafB (BlArafB; encoded by BLLJ_1853) from B. longum subsp. longum JCM 1217. Both enzymes exhibited alpha-l-arabinofuranosidase activity toward p-nitrophenyl-alpha-l-arabinofuranoside but no activity toward p-nitrophenyl-beta-d-xylopyranoside. The specificities of the two enzymes for l-arabinofuranosyl linkages were different. BlArafC catalyzed the hydrolysis of alpha1,2- and alpha1,3-l-arabinofuranosyl linkages found on the side chains of both arabinan and arabinoxylan. It released l-arabinose 100 times faster from arabinan than from arabinoxylan but did not act on arabinogalactan. On the other hand, BlArafB catalyzed the hydrolysis of the alpha1,5-l-arabinofuranosyl linkage found on the arabinan backbone. It released l-arabinose from arabinan but not from arabinoxylan or arabinogalactan. Coincubation of BlArafC and BlArafB revealed that these two enzymes are able to degrade arabinan in a synergistic manner. Both enzyme activities were suppressed with EDTA treatment, suggesting that they require divalent metal ions. The GH43 domains of BlArafC and BlArafB are classified into GH43 subfamilies 27 and 22, respectively, but show very low similarity (less than 15% identity) with other biochemically characterized members in the corresponding subfamilies. The B. longum subsp. longum strain lacking the GH43 gene cluster that includes BLLJ_1850 to BLLJ_1853 did not grow in arabinan medium, suggesting that BlArafC and BlArafB are important for assimilation of arabinan.IMPORTANCE We identified two novel alpha-l-arabinofuranosidases, BlArafC and BlArafB, from B. longum subsp. longum JCM 1217, both of which are predicted to be extracellular membrane-bound enzymes. The former specifically acts on alpha1,2/3-l-arabinofuranosyl linkages, while the latter acts on the alpha1,5-l-arabinofuranosyl linkage. These enzymes cooperatively degrade arabinan and are required for the efficient growth of bifidobacteria in arabinan-containing medium. The genes encoding these enzymes are located side by side in a gene cluster involved in metabolic pathways for plant-derived polysaccharides, which may confer adaptability in adult intestines.