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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0654

PubMed

33912144, Front Microbiol. 2021 Apr 12;12:628055. doi: 10.3389/fmicb.2021.628055. eCollection 2021.

Characterization method

sequence homology analysis

Genomic accession number

NZ_CAJQES010000007.1

Nucelotide position range

56564-116108

Substrate

alginate

Loci

KCP55_RS03985-KCP55_RS04175

Species

Maribacter dokdonensis 62-1/320912

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- KCP55_RS03990 WP_210706750.1 250 - 3007 (+) NZ_CAJQES010000007.1:56814-59571 -
- KCP55_RS03995 WP_210706751.1 3270 - 6309 (+) NZ_CAJQES010000007.1:59834-62873 -
- KCP55_RS04000 WP_210706752.1 6319 - 7867 (+) NZ_CAJQES010000007.1:62883-64431 -
- KCP55_RS04005 WP_210706753.1 7878 - 9678 (+) NZ_CAJQES010000007.1:64442-66242 -
- KCP55_RS04010 WP_210706754.1 9722 - 11081 (+) NZ_CAJQES010000007.1:66286-67645 -
- KCP55_RS04015 WP_244745075.1 11077 - 12514 (+) NZ_CAJQES010000007.1:67641-69078 -
- KCP55_RS04020 WP_210706755.1 12503 - 13298 (+) NZ_CAJQES010000007.1:69067-69862 -
bglX KCP55_RS04025 WP_210706756.1 13320 - 15591 (+) NZ_CAJQES010000007.1:69884-72155 3.2.1.21
- KCP55_RS04030 WP_210706757.1 15630 - 17268 (+) NZ_CAJQES010000007.1:72194-73832 -
- KCP55_RS04035 WP_210706758.1 17264 - 17699 (-) NZ_CAJQES010000007.1:73828-74263 -
- KCP55_RS04040 WP_210706759.1 17923 - 18397 (+) NZ_CAJQES010000007.1:74487-74961 -
- KCP55_RS04045 WP_058105204.1 18508 - 19018 (+) NZ_CAJQES010000007.1:75072-75582 -
cas2 KCP55_RS04050 WP_210706790.1 19679 - 20027 (-) NZ_CAJQES010000007.1:76243-76591 -
cas1 KCP55_RS04055 WP_210706760.1 20065 - 20959 (-) NZ_CAJQES010000007.1:76629-77523 -
- KCP55_RS04060 WP_210706761.1 20963 - 25502 (-) NZ_CAJQES010000007.1:77527-82066 -
- KCP55_RS04065 WP_074669965.1 25762 - 26479 (-) NZ_CAJQES010000007.1:82326-83043 -
- KCP55_RS04070 WP_210706762.1 26498 - 27470 (-) NZ_CAJQES010000007.1:83062-84034 -
- KCP55_RS04075 WP_210706763.1 27676 - 29995 (+) NZ_CAJQES010000007.1:84240-86559 -
- KCP55_RS04080 WP_210706764.1 30006 - 32232 (+) NZ_CAJQES010000007.1:86570-88796 -
- KCP55_RS04085 WP_210706765.1 32480 - 34814 (+) NZ_CAJQES010000007.1:89044-91378 -
- KCP55_RS04090 WP_244745080.1 34885 - 37054 (+) NZ_CAJQES010000007.1:91449-93618 -
- KCP55_RS04095 WP_058105197.1 37069 - 37444 (+) NZ_CAJQES010000007.1:93633-94008 -
- KCP55_RS04100 WP_074669971.1 37611 - 38862 (+) NZ_CAJQES010000007.1:94175-95426 -
- KCP55_RS04105 WP_210706767.1 38966 - 40067 (-) NZ_CAJQES010000007.1:95530-96631 -
- KCP55_RS04110 WP_099191247.1 40662 - 43698 (+) NZ_CAJQES010000007.1:97226-100262 -
- KCP55_RS04115 WP_210706768.1 43724 - 45254 (+) NZ_CAJQES010000007.1:100288-101818 -
- KCP55_RS04120 WP_058105191.1 45459 - 46161 (+) NZ_CAJQES010000007.1:102023-102725 -
- KCP55_RS04125 WP_058105190.1 46279 - 47569 (+) NZ_CAJQES010000007.1:102843-104133 -
- KCP55_RS04130 WP_058105189.1 47592 - 48354 (+) NZ_CAJQES010000007.1:104156-104918 -
- KCP55_RS04135 WP_210706769.1 48406 - 49423 (-) NZ_CAJQES010000007.1:104970-105987 -
- KCP55_RS04140 WP_058105187.1 49573 - 50620 (+) NZ_CAJQES010000007.1:106137-107184 -
- KCP55_RS04145 WP_210706770.1 50656 - 51877 (+) NZ_CAJQES010000007.1:107220-108441 2.7.1.11
- KCP55_RS04150 WP_071340327.1 51884 - 52553 (+) NZ_CAJQES010000007.1:108448-109117 4.1.2.14, 4.1.3.16
- KCP55_RS04155 WP_210706771.1 52830 - 54495 (+) NZ_CAJQES010000007.1:109394-111059 -
- KCP55_RS04160 WP_099191241.1 54498 - 55164 (+) NZ_CAJQES010000007.1:111062-111728 -
- KCP55_RS04165 WP_058105182.1 55362 - 56085 (+) NZ_CAJQES010000007.1:111926-112649 -
- KCP55_RS04170 WP_210706772.1 56090 - 56981 (-) NZ_CAJQES010000007.1:112654-113545 -
- KCP55_RS04175 WP_210706773.1 56983 - 59545 (-) NZ_CAJQES010000007.1:113547-116109 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 251 - 3007 (+) TF: DBD-Pfam|GerE No
- 3271 - 6309 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 6320 - 7867 (+) other Yes
- 7879 - 9678 (+) other Yes
- 9723 - 11081 (+) CAZyme: GH144|GH144 Yes
- 11078 - 12514 (+) CAZyme: GH144|GH144 Yes
- 12504 - 13298 (+) other Yes
bglX 13321 - 15591 (+) CAZyme: GH3| GH3 Yes
- 15631 - 17268 (+) other Yes
- 17265 - 17699 (-) STP: STP|BLUF Yes
- 17924 - 18397 (+) other Yes
- 18509 - 19018 (+) other Yes
cas2 19680 - 20027 (-) other Yes
cas1 20066 - 20959 (-) other Yes
- 20964 - 25502 (-) other Yes
- 25763 - 26479 (-) other Yes
- 26499 - 27470 (-) other Yes
- 27677 - 29995 (+) CAZyme: PL6_1|PL6| PL6_1 Yes
- 30007 - 32232 (+) CAZyme: PL12| PL12 Yes
- 32481 - 34814 (+) CAZyme: PL6_1|PL6| PL6_1 Yes
- 34886 - 37054 (+) CAZyme: PL17| PL17_2|PL17_2 Yes
- 37070 - 37444 (+) STP: STP|AraC_binding Yes
- 37612 - 38862 (+) other Yes
- 38967 - 40067 (-) other Yes
- 40663 - 43698 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 43725 - 45254 (+) TC: gnl|TC-DB|C6Y217|8.A.46.1.3 Yes
- 45460 - 46161 (+) TF: DBD-Pfam|GntR,DBD-SUPERFAMILY|0039384 Yes
- 46280 - 47569 (+) TC: gnl|TC-DB|Q07YH1|2.A.1.14.25 Yes
- 47593 - 48354 (+) CDS No
- 48407 - 49423 (-) TF: DBD-Pfam|LacI,DBD-SUPERFAMILY|0036955 No
- 49574 - 50620 (+) STP: STP|PfkB No
- 50657 - 51877 (+) CDS No
- 51885 - 52553 (+) CDS No
- 52831 - 54495 (+) STP: STP|TPR_2 No
- 54499 - 55164 (+) STP: STP|Response_reg No
- 55363 - 56085 (+) CDS No
- 56091 - 56981 (-) CDS No
- 56984 - 59545 (-) CDS No

PUL ID

PUL0654

PubMed

33912144, Front Microbiol. 2021 Apr 12;12:628055. doi: 10.3389/fmicb.2021.628055. eCollection 2021.

Title

CAZymes in Maribacter dokdonensis 62-1 From the Patagonian Shelf: Genomics and Physiology Compared to Related Flavobacteria and a Co-occurring Alteromonas Strain.

Author

Wolter LA, Mitulla M, Kalem J, Daniel R, Simon M, Wietz M

Abstract

Carbohydrate-active enzymes (CAZymes) are an important feature of bacteria in productive marine systems such as continental shelves, where phytoplankton and macroalgae produce diverse polysaccharides. We herein describe Maribacter dokdonensis 62-1, a novel strain of this flavobacterial species, isolated from alginate-supplemented seawater collected at the Patagonian continental shelf. M. dokdonensis 62-1 harbors a diverse array of CAZymes in multiple polysaccharide utilization loci (PUL). Two PUL encoding polysaccharide lyases from families 6, 7, 12, and 17 allow substantial growth with alginate as sole carbon source, with simultaneous utilization of mannuronate and guluronate as demonstrated by HPLC. Furthermore, strain 62-1 harbors a mixed-feature PUL encoding both ulvan- and fucoidan-targeting CAZymes. Core-genome phylogeny and pangenome analysis revealed variable occurrence of these PUL in related Maribacter and Zobellia strains, indicating specialization to certain "polysaccharide niches." Furthermore, lineage- and strain-specific genomic signatures for exopolysaccharide synthesis possibly mediate distinct strategies for surface attachment and host interaction. The wide detection of CAZyme homologs in algae-derived metagenomes suggests global occurrence in algal holobionts, supported by sharing multiple adaptive features with the hydrolytic model flavobacterium Zobellia galactanivorans. Comparison with Alteromonas sp. 76-1 isolated from the same seawater sample revealed that these co-occurring strains target similar polysaccharides but with different genomic repertoires, coincident with differing growth behavior on alginate that might mediate ecological specialization. Altogether, our study contributes to the perception of Maribacter as versatile flavobacterial polysaccharide degrader, with implications for biogeochemical cycles, niche specialization and bacteria-algae interactions in the oceans.