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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0739

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

3898483-3974612

Substrate

arabinogalactan

Loci

JM81_RS16360-JM81_RS16640

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_RS16360 WP_089259778.1 0 - 222 (-) NZ_VISB01000001.1:3898483-3898705 -
kduI JM81_RS16365 WP_144804988.1 577 - 1414 (+) NZ_VISB01000001.1:3899060-3899897 5.3.1.17
- JM81_RS16370 WP_186435596.1 1416 - 2202 (+) NZ_VISB01000001.1:3899899-3900685 1.1.1.69
uxaC JM81_RS16375 WP_144804992.1 2201 - 3620 (+) NZ_VISB01000001.1:3900684-3902103 5.3.1.12
- JM81_RS16380 WP_089259602.1 3643 - 4684 (+) NZ_VISB01000001.1:3902126-3903167 2.7.1.-
- JM81_RS16385 WP_144804994.1 4755 - 5427 (+) NZ_VISB01000001.1:3903238-3903910 4.1.2.14, 4.1.3.16
- JM81_RS16390 WP_218822479.1 5428 - 6409 (+) NZ_VISB01000001.1:3903911-3904892 -
- JM81_RS16395 WP_261375112.1 6413 - 6872 (+) NZ_VISB01000001.1:3904896-3905355 -
- JM81_RS16400 WP_089259780.1 6871 - 8167 (+) NZ_VISB01000001.1:3905354-3906650 -
- JM81_RS16405 WP_144804996.1 8191 - 9628 (+) NZ_VISB01000001.1:3906674-3908111 -
- JM81_RS16410 WP_144804998.1 9644 - 11261 (+) NZ_VISB01000001.1:3908127-3909744 -
- JM81_RS16415 WP_144805000.1 11276 - 12299 (-) NZ_VISB01000001.1:3909759-3910782 -
- JM81_RS16420 WP_186435597.1 12606 - 14043 (-) NZ_VISB01000001.1:3911089-3912526 4.2.2.-
- JM81_RS16425 WP_144805002.1 14055 - 15501 (-) NZ_VISB01000001.1:3912538-3913984 -
- JM81_RS16430 WP_144805004.1 15542 - 17030 (-) NZ_VISB01000001.1:3914025-3915513 -
- JM81_RS16435 WP_144805006.1 17067 - 18525 (-) NZ_VISB01000001.1:3915550-3917008 -
- JM81_RS16440 WP_222430312.1 18537 - 19839 (-) NZ_VISB01000001.1:3917020-3918322 -
- JM81_RS16445 WP_144805008.1 19876 - 21505 (-) NZ_VISB01000001.1:3918359-3919988 -
- JM81_RS16450 WP_144805011.1 21540 - 22962 (-) NZ_VISB01000001.1:3920023-3921445 3.2.1.-
- JM81_RS16455 WP_144805012.1 24758 - 27878 (+) NZ_VISB01000001.1:3923241-3926361 -
- JM81_RS16460 WP_144805014.1 27888 - 29544 (+) NZ_VISB01000001.1:3926371-3928027 -
- JM81_RS16465 WP_144805016.1 29691 - 30681 (+) NZ_VISB01000001.1:3928174-3929164 -
- JM81_RS16470 WP_144805018.1 30688 - 31918 (+) NZ_VISB01000001.1:3929171-3930401 3.2.1.-
- JM81_RS16475 WP_144805020.1 31939 - 33184 (+) NZ_VISB01000001.1:3930422-3931667 3.2.1.-
- JM81_RS16480 WP_144805022.1 33371 - 34415 (+) NZ_VISB01000001.1:3931854-3932898 -
pelA JM81_RS16485 WP_261375114.1 34470 - 36462 (+) NZ_VISB01000001.1:3932953-3934945 4.2.2.2
- JM81_RS16490 WP_144805024.1 36518 - 37319 (+) NZ_VISB01000001.1:3935001-3935802 -
- JM81_RS16495 WP_144805026.1 37344 - 38085 (+) NZ_VISB01000001.1:3935827-3936568 -
- JM81_RS16500 WP_261375115.1 38131 - 39181 (+) NZ_VISB01000001.1:3936614-3937664 3.-.-.-
- JM81_RS16505 WP_144805028.1 39187 - 39880 (-) NZ_VISB01000001.1:3937670-3938363 3.6.1.-
- JM81_RS16510 WP_144805030.1 40086 - 42264 (+) NZ_VISB01000001.1:3938569-3940747 -
- JM81_RS16515 WP_144805032.1 42268 - 43816 (+) NZ_VISB01000001.1:3940751-3942299 -
- JM81_RS16520 WP_144805034.1 43926 - 45600 (+) NZ_VISB01000001.1:3942409-3944083 2.7.1.16
- JM81_RS16525 WP_144805036.1 45604 - 46306 (+) NZ_VISB01000001.1:3944087-3944789 5.1.3.4
araA JM81_RS16530 WP_144805038.1 46330 - 47830 (+) NZ_VISB01000001.1:3944813-3946313 5.3.1.4
- JM81_RS16535 WP_261375117.1 47924 - 49031 (+) NZ_VISB01000001.1:3946407-3947514 5.1.3.-
- JM81_RS16540 WP_144805042.1 49039 - 50659 (+) NZ_VISB01000001.1:3947522-3949142 -
- JM81_RS16545 WP_089259634.1 50813 - 51632 (+) NZ_VISB01000001.1:3949296-3950115 -
- JM81_RS16550 WP_144805044.1 51685 - 52222 (-) NZ_VISB01000001.1:3950168-3950705 -
- JM81_RS16555 WP_144805046.1 52490 - 52679 (+) NZ_VISB01000001.1:3950973-3951162 -
- JM81_RS16560 WP_261375118.1 52742 - 53576 (-) NZ_VISB01000001.1:3951225-3952059 -
- JM81_RS16565 WP_144805048.1 53726 - 55775 (-) NZ_VISB01000001.1:3952209-3954258 2.7.13.3
uxaC JM81_RS16570 WP_144805050.1 56020 - 57418 (-) NZ_VISB01000001.1:3954503-3955901 5.3.1.12
- JM81_RS16575 WP_144805052.1 57481 - 58411 (-) NZ_VISB01000001.1:3955964-3956894 -
- JM81_RS16580 WP_144805054.1 58420 - 59437 (-) NZ_VISB01000001.1:3956903-3957920 -
- JM81_RS16585 WP_261375119.1 59692 - 62764 (+) NZ_VISB01000001.1:3958175-3961247 -
- JM81_RS16590 WP_144805056.1 62776 - 64450 (+) NZ_VISB01000001.1:3961259-3962933 -
- JM81_RS16595 WP_144805058.1 64624 - 65842 (+) NZ_VISB01000001.1:3963107-3964325 -
- JM81_RS16600 WP_144805060.1 65854 - 67231 (+) NZ_VISB01000001.1:3964337-3965714 -
- JM81_RS16605 WP_144805062.1 67367 - 68759 (+) NZ_VISB01000001.1:3965850-3967242 -
- JM81_RS16610 WP_089259646.1 68759 - 69578 (+) NZ_VISB01000001.1:3967242-3968061 -
uxuA JM81_RS16615 WP_144805064.1 69663 - 70860 (+) NZ_VISB01000001.1:3968146-3969343 4.2.1.8
- JM81_RS16620 WP_144805066.1 70869 - 71895 (+) NZ_VISB01000001.1:3969352-3970378 -
- JM81_RS16625 WP_089259649.1 71894 - 72368 (+) NZ_VISB01000001.1:3970377-3970851 -
- JM81_RS16630 WP_186435598.1 72368 - 73679 (+) NZ_VISB01000001.1:3970851-3972162 -
- JM81_RS16635 WP_144805068.1 73721 - 75956 (+) NZ_VISB01000001.1:3972204-3974439 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 222 (-) CDS No
- 578 - 1414 (+) CDS No
- 1417 - 2202 (+) CDS No
- 2202 - 3620 (+) CDS No
- 3644 - 4684 (+) STP: STP|PfkB No
- 4756 - 5427 (+) CDS No
- 5429 - 6409 (+) TC: gnl|TC-DB|P43020|2.A.56.1.5 Yes
- 6414 - 6872 (+) TC: gnl|TC-DB|Q8ZKR9|2.A.56.1.5 Yes
- 6872 - 8167 (+) TC: gnl|TC-DB|Q8ZKS0|2.A.56.1.5 Yes
- 8192 - 9628 (+) other Yes
- 9645 - 11261 (+) other Yes
- 11277 - 12299 (-) TF: DBD-Pfam|LacI,DBD-SUPERFAMILY|0036955 Yes
- 12607 - 14043 (-) CAZyme: PL1_2 Yes
- 14056 - 15501 (-) other Yes
- 15543 - 17030 (-) CAZyme: GH140 Yes
- 17068 - 18525 (-) other Yes
- 18538 - 19839 (-) other Yes
- 19877 - 21505 (-) CAZyme: GH43_10|CBM91 Yes
- 21541 - 22962 (-) CAZyme: GH28 Yes
- 24759 - 27878 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 27889 - 29544 (+) TC: gnl|TC-DB|G0IYY9|8.A.46.1.6 Yes
- 29692 - 30681 (+) other Yes
- 30689 - 31918 (+) CAZyme: GH105 Yes
- 31940 - 33184 (+) CAZyme: GH105 Yes
- 33372 - 34415 (+) CAZyme: GH179 Yes
pelA 34471 - 36462 (+) CAZyme: PL10_1|CE8 Yes
- 36519 - 37319 (+) STP: STP|AraC_binding,STP|AraC_binding Yes
- 37345 - 38085 (+) CAZyme: CE12 Yes
- 38132 - 39181 (+) other Yes
- 39188 - 39880 (-) STP: STP|NUDIX Yes
- 40087 - 42264 (+) CAZyme: GH43_19|GH43_34 Yes
- 42269 - 43816 (+) CAZyme: GH51_1 Yes
- 43927 - 45600 (+) other Yes
- 45605 - 46306 (+) other Yes
- 46331 - 47830 (+) other Yes
- 47925 - 49031 (+) other Yes
- 49040 - 50659 (+) TC: gnl|TC-DB|Q8AAV7|2.A.21.3.19 Yes
- 50814 - 51632 (+) other Yes
- 51686 - 52222 (-) other Yes
- 52491 - 52679 (+) other Yes
- 52743 - 53576 (-) TC: gnl|TC-DB|Q7V7U0|2.A.7.28.11 Yes
- 53727 - 55775 (-) STP: STP|TPR_1,STP|HisKA,STP|HATPase_c Yes
- 56021 - 57418 (-) other Yes
- 57482 - 58411 (-) other Yes
- 58421 - 59437 (-) TF: DBD-Pfam|LacI,DBD-SUPERFAMILY|0036955 Yes
- 59693 - 62764 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 62777 - 64450 (+) TC: gnl|TC-DB|G0IYY9|8.A.46.1.6 Yes
- 64625 - 65842 (+) other Yes
- 65855 - 67231 (+) CAZyme: GH177 Yes
- 67368 - 68759 (+) other Yes
- 68760 - 69578 (+) other Yes
- 69664 - 70860 (+) other Yes
- 70870 - 71895 (+) TC: gnl|TC-DB|P43020|2.A.56.1.5 Yes
- 71895 - 72368 (+) TC: gnl|TC-DB|Q8ZKR9|2.A.56.1.5 Yes
- 72369 - 73679 (+) TC: gnl|TC-DB|Q8ZKS0|2.A.56.1.5 Yes
- 73722 - 75956 (+) CDS No

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PUL ID

PUL0739

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.