fig1

Figure 1. Glycoside hydrolases involved in the degradation of AGP side chains. A: Gene clusters in Bifidobacterium pseudocatenulatum MCC10289 and B. longum JCM7052 involved in the degradation of AGP. The glycoside hydrolases (GHs) in the Carbohydrate-Active EnZymes (CAZy) Database are shown inside the black arrowheads. The shaded arrows indicate the transcriptional regulator and the light gray arrows indicate the ABC transporter. The percentage in the light gray bars indicates sequence identity between GHs from B. pseudocatenulatum and B. longum; B: The domain structure of MCC10289_0425 and MCC10289_0426 in B. pseudocatenulatum MCC10289. The domain structures were predicted using SignalP5.0 (http://www.cbs.dtu.dk/services/SignalP/) and InterPro (https://www.ebi.ac.uk/interpro/) servers. The structure comprises the SP, GH39 catalytic domain, and three galactose-binding domain-like regions; C: The phylogenetic relationships of bifidobacterial GH36 α-galactosidases and β-L-arabinopyranosidases. The phylogenetic tree of B. pseudocatenulatum MCC10289_0426 with homologous proteins from bifidobacteria was constructed by the neighbor-joining method using the aligned sequences; for the construction, the program Clustal W was implemented in the MEGA11 software. B. pseudocatenulatum_MCC10289_0426 is indicated by a dashed-line box. The protein names or locus tags are shown alongside Bifidobacterium strains as follows: B. adolescentis Aga (GenBank ID: AAD30994.2), B. bifidum MelA (ABD96085.1), B. breve Aga (AAK96217.2), B. breve Aga2 (ABB76662.1), B. longum GalA1 (ACD98928.1), B. longum AgA (AAN25312.1), B. longum AglL (AAG02023.1), B. breve RafA (ABE96531.1), B. breve MelE (ABE96518.1), B. longum BLLJ_1872 (BAJ67536.1), B. longum BLLJ_1885 (BAJ67549.1), B. longum BlAga3 (BBV22622.1), B. longum BlAga1 (BBV24464.1), and B. longum BlAga2 (BBV24450.1), B. longum MCC00300_11120 (WP_077381863.1), B. reuteri EMO92_RS04025 (WP_150335335.1), B. catenulatum BBCT_0489 (BAR01457.1 ), B. adolescentis BADO_0439 (AII75864.1), B. lemurum BL8807_01475 (QOL34630.1), B. dentium BBDE_0465 (BAQ26459.1), B. adolescentis BAD_1528 (BBD14080.1), B. pseudocatenulatum BBPC_1670 (BAR04348.1), B. catenulatum BBCT_1564 (BAR02532.1), B. kashiwanohense AH68_09535 (AIZ15229.1), B. dentium BDP_2102 (ADB10663.1), and B. scardovii BBSC_0165 (BAQ30245.1). Asterisk indicates characterized enzymes.