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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0127

PubMed

30936857, Front Microbiol. 2019 Mar 18;10:504. doi: 10.3389/fmicb.2019.00504. eCollection 2019.

Characterization method

growth assay,sequence homology analysis

Genomic accession number

LR136958.1

Nucelotide position range

3936797-3956397

Substrate

alginate,ulvan

Loci

ALT761_03413-ALT761_03424

Species

Alteromonas sp. 76-1/2358187

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- ALT761_03413 VEL98395.1 0 - 732 (+) LR136958.1:3936797-3937529 -
- ALT761_03414 VEL98396.1 973 - 2437 (+) LR136958.1:3937770-3939234 -
- ALT761_03415 VEL98397.1 2542 - 3484 (-) LR136958.1:3939339-3940281 -
- ALT761_03416 VEL98398.1 3724 - 6757 (-) LR136958.1:3940521-3943554 -
- ALT761_03417 VEL98399.1 6808 - 9526 (-) LR136958.1:3943605-3946323 -
- ALT761_03418 VEL98400.1 9970 - 10972 (-) LR136958.1:3946767-3947769 -
- ALT761_03419 VEL98401.1 11020 - 12316 (-) LR136958.1:3947817-3949113 -
- ALT761_03420 VEL98402.1 12391 - 14713 (-) LR136958.1:3949188-3951510 -
- ALT761_03421 VEL98403.1 15127 - 15874 (-) LR136958.1:3951924-3952671 -
- ALT761_03422 VEL98404.1 16645 - 17524 (+) LR136958.1:3953442-3954321 -
- ALT761_03423 VEL98405.1 17944 - 18289 (+) LR136958.1:3954741-3955086 -
- ALT761_03424 VEL98406.1 18293 - 19601 (+) LR136958.1:3955090-3956398 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 732 (+) TF: DBD-Pfam|GntR,DBD-SUPERFAMILY|0039384 No
- 974 - 2437 (+) CAZyme: PL7|PL7_5|CBM32 Yes
- 2543 - 3484 (-) other Yes
- 3725 - 6757 (-) TC: gnl|TC-DB|Q9A608|1.B.14.12.1 Yes
- 6809 - 9526 (-) CAZyme: PL6_3|PL6 Yes
- 9971 - 10972 (-) CAZyme: PL7|PL7_5 Yes
- 11021 - 12316 (-) TC: gnl|TC-DB|Q07YH1|2.A.1.14.25 Yes
- 12392 - 14713 (-) CAZyme: PL6|PL6_1 Yes
- 15128 - 15874 (-) other Yes
- 16646 - 17524 (+) other Yes
- 17945 - 18289 (+) other Yes
- 18294 - 19601 (+) TC: gnl|TC-DB|Q07YH1|2.A.1.14.25 Yes

PUL ID

PUL0127

PubMed

30936857, Front Microbiol. 2019 Mar 18;10:504. doi: 10.3389/fmicb.2019.00504. eCollection 2019.

Title

Adaptations of Alteromonas sp. 76-1 to Polysaccharide Degradation: A CAZyme Plasmid for Ulvan Degradation and Two Alginolytic Systems.

Author

Koch H, Freese HM, Hahnke RL, Simon M, Wietz M

Abstract

Studying the physiology and genomics of cultured hydrolytic bacteria is a valuable approach to decipher the biogeochemical cycling of marine polysaccharides, major nutrients derived from phytoplankton and macroalgae. We herein describe the profound potential of Alteromonas sp. 76-1, isolated from alginate-enriched seawater at the Patagonian continental shelf, to degrade the algal polysaccharides alginate and ulvan. Phylogenetic analyses indicated that strain 76-1 might represent a novel species, distinguished from its closest relative (Alteromonas naphthalenivorans) by adaptations to their contrasting habitats (productive open ocean vs. coastal sediments). Ecological distinction of 76-1 was particularly manifested in the abundance of carbohydrate-active enzymes (CAZymes), consistent with its isolation from alginate-enriched seawater and elevated abundance of a related OTU in the original microcosm. Strain 76-1 encodes multiple alginate lyases from families PL6, PL7, PL17, and PL18 largely contained in two polysaccharide utilization loci (PUL), which may facilitate the utilization of different alginate structures in nature. Notably, ulvan degradation relates to a 126 Kb plasmid dedicated to polysaccharide utilization, encoding several PL24 and PL25 ulvan lyases and monomer-processing genes. This extensive and versatile CAZyme repertoire allowed substantial growth on polysaccharides, showing comparable doubling times with alginate (2 h) and ulvan (3 h) in relation to glucose (3 h). The finding of homologous ulvanolytic systems in distantly related Alteromonas spp. suggests CAZyme plasmids as effective vehicles for PUL transfer that mediate niche gain. Overall, the demonstrated CAZyme repertoire substantiates the role of Alteromonas in marine polysaccharide degradation and how PUL exchange influences the ecophysiology of this ubiquitous marine taxon.