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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0738

PubMed

38569650, FEMS Microbiol Ecol. 2024 Apr 10;100(5):fiae045. doi: 10.1093/femsec/fiae045.

Characterization method

mass spectrometry,SDS-PAGE,growth assay

Genomic accession number

NZ_VISB01000001.1

Nucelotide position range

3238797-3314997

Substrate

arabinogalactan

Loci

JM81_RS13670-JM81_RS13905

Species

Maribacter sp. MAR_2009_72/1250050

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- JM81_RS13665 WP_144804243.1 0 - 4 (+) NZ_VISB01000001.1:3238797-3238801 -
- JM81_RS13670 WP_144804245.1 0 - 687 (+) NZ_VISB01000001.1:3238797-3239484 -
pth JM81_RS13675 WP_144804247.1 687 - 1317 (-) NZ_VISB01000001.1:3239484-3240114 3.1.1.29
- JM81_RS13680 WP_144804249.1 1401 - 2034 (-) NZ_VISB01000001.1:3240198-3240831 -
- JM81_RS13685 WP_144804251.1 2109 - 3051 (-) NZ_VISB01000001.1:3240906-3241848 2.7.6.1
- JM81_RS13695 WP_261375058.1 3566 - 4664 (-) NZ_VISB01000001.1:3242363-3243461 3.2.1.-
- JM81_RS13700 WP_144804253.1 4675 - 6094 (-) NZ_VISB01000001.1:3243472-3244891 3.2.1.51
- JM81_RS13705 WP_144804255.1 6544 - 7903 (+) NZ_VISB01000001.1:3245341-3246700 -
- JM81_RS13710 WP_144804257.1 7915 - 8992 (+) NZ_VISB01000001.1:3246712-3247789 -
- JM81_RS13715 WP_144804259.1 8997 - 9603 (+) NZ_VISB01000001.1:3247794-3248400 -
- JM81_RS13720 WP_144804261.1 9681 - 10719 (+) NZ_VISB01000001.1:3248478-3249516 -
- JM81_RS13725 WP_144804263.1 10798 - 12457 (-) NZ_VISB01000001.1:3249595-3251254 -
- JM81_RS13730 WP_144804265.1 12498 - 15573 (-) NZ_VISB01000001.1:3251295-3254370 -
- JM81_RS13735 WP_144804267.1 15955 - 16849 (-) NZ_VISB01000001.1:3254752-3255646 -
dinB JM81_RS13740 WP_144804269.1 17090 - 18305 (+) NZ_VISB01000001.1:3255887-3257102 2.7.7.7
- JM81_RS13745 WP_144805648.1 18550 - 21592 (+) NZ_VISB01000001.1:3257347-3260389 2.7.7.7
- JM81_RS13750 WP_261375059.1 21798 - 22659 (-) NZ_VISB01000001.1:3260595-3261456 -
hxlB JM81_RS13755 WP_144804271.1 22867 - 23452 (+) NZ_VISB01000001.1:3261664-3262249 5.3.1.27
hxlA JM81_RS13760 WP_144804273.1 23501 - 24131 (+) NZ_VISB01000001.1:3262298-3262928 4.1.2.43
- JM81_RS13765 WP_144804275.1 24327 - 24540 (+) NZ_VISB01000001.1:3263124-3263337 -
- JM81_RS18460 WP_027065147.1 24607 - 24745 (-) NZ_VISB01000001.1:3263404-3263542 -
- JM81_RS13770 WP_144804277.1 24867 - 26499 (-) NZ_VISB01000001.1:3263664-3265296 3.1.1.-
- JM81_RS13775 WP_144804279.1 26680 - 28102 (-) NZ_VISB01000001.1:3265477-3266899 -
- JM81_RS13780 WP_144804281.1 28116 - 29268 (-) NZ_VISB01000001.1:3266913-3268065 1.-.-.-
- JM81_RS13785 WP_144804283.1 29277 - 30648 (-) NZ_VISB01000001.1:3268074-3269445 2.7.1.-
- JM81_RS13790 WP_144804285.1 30651 - 31932 (-) NZ_VISB01000001.1:3269448-3270729 -
- JM81_RS13795 WP_144804287.1 32001 - 34098 (-) NZ_VISB01000001.1:3270798-3272895 -
- JM81_RS13800 WP_186435578.1 34297 - 35344 (+) NZ_VISB01000001.1:3273094-3274141 -
- JM81_RS13805 WP_144804291.1 35517 - 36750 (+) NZ_VISB01000001.1:3274314-3275547 -
- JM81_RS13810 WP_144804293.1 36763 - 39619 (+) NZ_VISB01000001.1:3275560-3278416 -
- JM81_RS13815 WP_144804295.1 39621 - 41133 (+) NZ_VISB01000001.1:3278418-3279930 -
- JM81_RS13820 WP_144804297.1 41137 - 43579 (-) NZ_VISB01000001.1:3279934-3282376 -
- JM81_RS13825 WP_144804299.1 43586 - 45731 (-) NZ_VISB01000001.1:3282383-3284528 -
- JM81_RS13830 WP_144804301.1 45752 - 47234 (-) NZ_VISB01000001.1:3284549-3286031 3.2.1.-
rhaM JM81_RS13835 WP_144804303.1 47271 - 47586 (-) NZ_VISB01000001.1:3286068-3286383 5.1.3.32
- JM81_RS13840 WP_144804305.1 47590 - 48946 (-) NZ_VISB01000001.1:3286387-3287743 -
- JM81_RS13845 WP_261375061.1 48949 - 50251 (-) NZ_VISB01000001.1:3287746-3289048 3.2.1.-
- JM81_RS13850 WP_144804309.1 50324 - 51602 (-) NZ_VISB01000001.1:3289121-3290399 -
- JM81_RS13855 WP_144804311.1 51614 - 52874 (-) NZ_VISB01000001.1:3290411-3291671 -
- JM81_RS13860 WP_222430306.1 52968 - 54546 (-) NZ_VISB01000001.1:3291765-3293343 -
- JM81_RS13865 WP_144804315.1 54578 - 57563 (-) NZ_VISB01000001.1:3293375-3296360 -
- JM81_RS13870 WP_144804317.1 57806 - 59750 (-) NZ_VISB01000001.1:3296603-3298547 -
- JM81_RS13875 WP_144804319.1 59782 - 62914 (-) NZ_VISB01000001.1:3298579-3301711 -
- JM81_RS18530 WP_222430307.1 63170 - 63722 (-) NZ_VISB01000001.1:3301967-3302519 -
- JM81_RS13880 WP_222430308.1 63718 - 65593 (-) NZ_VISB01000001.1:3302515-3304390 -
- JM81_RS13885 WP_261375062.1 65700 - 68529 (+) NZ_VISB01000001.1:3304497-3307326 -
- JM81_RS13890 WP_144804321.1 68539 - 69664 (+) NZ_VISB01000001.1:3307336-3308461 -
- JM81_RS13895 WP_144804323.1 69688 - 71470 (+) NZ_VISB01000001.1:3308485-3310267 -
- JM81_RS13900 WP_144804325.1 71543 - 75179 (+) NZ_VISB01000001.1:3310340-3313976 -
- JM81_RS13905 WP_144804327.1 75220 - 76201 (-) NZ_VISB01000001.1:3314017-3314998 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 4 (+) CDS No
- 1 - 687 (+) CDS No
- 688 - 1317 (-) CDS No
- 1402 - 2034 (-) CDS No
- 2110 - 3051 (-) STP: STP|Pribosyltran No
- 3567 - 4664 (-) CAZyme: GH33 Yes
- 4676 - 6094 (-) CAZyme: GH29 Yes
- 6545 - 7903 (+) other Yes
- 7916 - 8992 (+) other Yes
- 8998 - 9603 (+) other Yes
- 9682 - 10719 (+) TF: DBD-Pfam|LacI,DBD-SUPERFAMILY|0036955 Yes
- 10799 - 12457 (-) TC: gnl|TC-DB|G0IYY9|8.A.46.1.6 Yes
- 12499 - 15573 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 15956 - 16849 (-) other Yes
- 17091 - 18305 (+) other Yes
- 18551 - 21592 (+) other Yes
- 21799 - 22659 (-) TF: DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0035607 Yes
hxlB 22868 - 23452 (+) STP: STP|SIS Yes
- 23502 - 24131 (+) other Yes
- 24328 - 24540 (+) other Yes
- 24608 - 24745 (-) other Yes
- 24868 - 26499 (-) other Yes
- 26681 - 28102 (-) TC: gnl|TC-DB|Q082R8|2.A.39.5.1 Yes
- 28117 - 29268 (-) other Yes
- 29278 - 30648 (-) other Yes
- 30652 - 31932 (-) other Yes
- 32002 - 34098 (-) other Yes
- 34298 - 35344 (+) TF: DBD-Pfam|GntR,DBD-SUPERFAMILY|0037767 Yes
- 35518 - 36750 (+) CAZyme: CE12 Yes
- 36764 - 39619 (+) CAZyme: GH2 Yes
- 39622 - 41133 (+) CAZyme: CE12|CE12 Yes
- 41138 - 43579 (-) CAZyme: GH115 Yes
- 43587 - 45731 (-) other Yes
- 45753 - 47234 (-) CAZyme: GH28 Yes
- 47272 - 47586 (-) other Yes
- 47591 - 48946 (-) other Yes
- 48950 - 50251 (-) CAZyme: GH105 Yes
- 50325 - 51602 (-) other Yes
- 51615 - 52874 (-) other Yes
- 52969 - 54546 (-) TC: gnl|TC-DB|G0IYY9|8.A.46.1.6 Yes
- 54579 - 57563 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 57807 - 59750 (-) other Yes
- 59783 - 62914 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 63171 - 63722 (-) other Yes
- 63719 - 65593 (-) CAZyme: GH31_9 Yes
- 65701 - 68529 (+) CAZyme: GH106 Yes
- 68540 - 69664 (+) CAZyme: GH105 Yes
- 69689 - 71470 (+) CAZyme: GH43_18 Yes
- 71544 - 75179 (+) CAZyme: CBM67|GH78 Yes
- 75221 - 76201 (-) CAZyme: GH179 Yes

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PUL ID

PUL0738

PubMed

38569650, FEMS Microbiol Ecol. 2024 Apr 10;100(5):fiae045. doi: 10.1093/femsec/fiae045.

Title

Proteomic insight into arabinogalactan utilization by particle-associated Maribacter sp. MAR_2009_72.

Author

Kalenborn S, Zuhlke D, Riedel K, Amann RI, Harder J

Abstract

Arabinose and galactose are major, rapidly metabolized components of marine particulate and dissolved organic matter. In this study, we observed for the first time large microbiomes for the degradation of arabinogalactan and report a detailed investigation of arabinogalactan utilization by the flavobacterium Maribacter sp. MAR_2009_72. Cellular extracts hydrolysed arabinogalactan in vitro. Comparative proteomic analyses of cells grown on arabinogalactan, arabinose, galactose, and glucose revealed the expression of specific proteins in the presence of arabinogalactan, mainly glycoside hydrolases (GH). Extracellular glycan hydrolysis involved five alpha-l-arabinofuranosidases affiliating with glycoside hydrolase families 43 and 51, four unsaturated rhamnogalacturonylhydrolases (GH105) and a protein with a glycoside hydrolase family-like domain. We detected expression of three induced TonB-dependent SusC/D transporter systems, one SusC, and nine glycoside hydrolases with a predicted periplasmatic location. These are affiliated with the families GH3, GH10, GH29, GH31, GH67, GH78, and GH115. The genes are located outside of and within canonical polysaccharide utilization loci classified as specific for arabinogalactan, for galactose-containing glycans, and for arabinose-containing glycans. The breadth of enzymatic functions expressed in Maribacter sp. MAR_2009_72 as response to arabinogalactan from the terrestrial plant larch suggests that Flavobacteriia are main catalysts of the rapid turnover of arabinogalactans in the marine environment.