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PlantCAZyme
Cite: NAR/gkaa742 2020

Because CGCFinder predicted no CGC for this PUL, the gene cluster depicted below contains dbCAN2 and CGC signature predictions for all genes in the PUL, instead of a predicted CGC.


PUL General Information

Literature Information

PUL ID

PUL0319

PubMed

28983288, Front Microbiol. 2017 Sep 21;8:1808. doi: 10.3389/fmicb.2017.01808. eCollection 2017.

Characterization method

microarray

Genomic accession number

FP476056.1

Nucelotide position range

3465709-3473860

Substrate

carrageenan

Loci

ZOBELLIA_2985-ZOBELLIA_2988

Species

Zobellia galactanivorans/63186

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- ZOBELLIA_2985 CAZ97131.1 0 - 2061 (-) FP476056.1:3465709-3467770 -
- ZOBELLIA_2986 CAZ97132.1 2313 - 3843 (-) FP476056.1:3468022-3469552 3.2.1.-
- ZOBELLIA_2987 CAZ97133.1 3839 - 5069 (-) FP476056.1:3469548-3470778 -
- ZOBELLIA_2988 CAZ97134.1 5065 - 8152 (-) FP476056.1:3470774-3473861 -

Cluster number

0

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 2061 (-) STP: STP|TPR_1 No
- 2314 - 3843 (-) CAZyme: GH5_42|GH5 No
- 3840 - 5069 (-) CDS No
- 5066 - 8152 (-) CDS No

PUL ID

PUL0319

PubMed

28983288, Front Microbiol. 2017 Sep 21;8:1808. doi: 10.3389/fmicb.2017.01808. eCollection 2017.

Title

Gene Expression Analysis of Zobellia galactanivorans during the Degradation of Algal Polysaccharides Reveals both Substrate-Specific and Shared Transcriptome-Wide Responses.

Author

Thomas F, Bordron P, Eveillard D, Michel G

Abstract

Flavobacteriia are recognized as key players in the marine carbon cycle, due to their ability to efficiently degrade algal polysaccharides both in the open ocean and in coastal regions. The chemical complexity of algal polysaccharides, their differences between algal groups and variations through time and space, imply that marine flavobacteria have evolved dedicated degradation mechanisms and regulation of their metabolism during interactions with algae. In the present study, we report the first transcriptome-wide gene expression analysis for an alga-associated flavobacterium during polysaccharide degradation. Zobellia galactanivorans Dsij(T), originally isolated from a red alga, was grown in minimal medium with either glucose (used as a reference monosaccharide) or one selected algal polysaccharide from brown (alginate, laminarin) or red algae (agar, porphyran, iota- or kappa-carrageenan) as sole carbon source. Expression profiles were determined using whole-genome microarrays. Integration of genomic knowledge with the automatic building of a co-expression network allowed the experimental validation of operon-like transcription units. Differential expression analysis revealed large transcriptomic shifts depending on the carbon source. Unexpectedly, transcriptomes shared common signatures when growing on chemically divergent polysaccharides from the same algal phylum. Together with the induction of numerous transcription factors, this hints at complex regulation events that fine-tune the cell behavior during interactions with algal biomass in the marine environment. The results further highlight genes and loci that may participate in polysaccharide utilization, notably encoding Carbohydrate Active enZymes (CAZymes) and glycan binding proteins together with a number of proteins of unknown function. This constitutes a set of candidate genes potentially representing new substrate specificities. By providing an unprecedented view of global transcriptomic responses during polysaccharide utilization in an alga-associated model flavobacterium, this study expands the current knowledge on the functional role of flavobacteria in the marine carbon cycle and on their interactions with algae.