Home Repository Download Help About Statistics Taxonomy Blastx
Links
PULDB
CAZy
dbCAN2
dbCAN-seq
run_dbcan
CAZypedia
PlantCAZyme
Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0316

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

5366976-5388576

Substrate

agar,porphyran

Loci

ZOBELLIA_4655-ZOBELLIA_4669

Species

Zobellia galactanivorans/63186

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

bgaF ZOBELLIA_4655 CAZ98790.1 0 - 2538 (-) FP476056.1:5366976-5369514 3.2.1.23
rhaT2 ZOBELLIA_4656 CAZ98791.1 2653 - 3670 (-) FP476056.1:5369629-5370646 -
mroA6 ZOBELLIA_4657 CAZ98792.1 3730 - 4774 (-) FP476056.1:5370706-5371750 5.1.3.3
- ZOBELLIA_4658 CAZ98793.1 4811 - 5906 (-) FP476056.1:5371787-5372882 4.2.1.6
aldA ZOBELLIA_4659 CAZ98794.1 5906 - 7361 (-) FP476056.1:5372882-5374337 1.2.1.22
- ZOBELLIA_4660 CAZ98795.1 7374 - 8763 (-) FP476056.1:5374350-5375739 3.1.6.-
kduD1 ZOBELLIA_4661 CAZ98796.1 8808 - 9579 (-) FP476056.1:5375784-5376555 1.1.1.125
- ZOBELLIA_4662 CAZ98797.1 9603 - 10620 (-) FP476056.1:5376579-5377596 1.1.1.-
- ZOBELLIA_4663 CAZ98798.1 10633 - 11860 (-) FP476056.1:5377609-5378836 -
- ZOBELLIA_4664 CAZ98799.1 11911 - 12643 (-) FP476056.1:5378887-5379619 -
- ZOBELLIA_4665 CAZ98800.1 12887 - 13679 (-) FP476056.1:5379863-5380655 -
- ZOBELLIA_4666 CAZ98801.1 13774 - 15418 (-) FP476056.1:5380750-5382394 -
- ZOBELLIA_4667 CAZ98802.1 15421 - 15667 (-) FP476056.1:5382397-5382643 -
- ZOBELLIA_4668 CAZ98803.1 16649 - 18398 (-) FP476056.1:5383625-5385374 -
- ZOBELLIA_4669 CAZ98804.1 18418 - 21601 (-) FP476056.1:5385394-5388577 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

bgaF 1 - 2538 (-) CAZyme: GH2 Yes
rhaT2 2654 - 3670 (-) other Yes
mroA6 3731 - 4774 (-) other Yes
- 4812 - 5906 (-) other Yes
aldA 5907 - 7361 (-) other Yes
- 7375 - 8763 (-) other Yes
kduD1 8809 - 9579 (-) other Yes
- 9604 - 10620 (-) other Yes
- 10634 - 11860 (-) CAZyme: GH117 Yes
- 11912 - 12643 (-) TF: DBD-Pfam|HTH_AraC,DBD-SUPERFAMILY|0036286,DBD-SUPERFAMILY|0035607 Yes
- 12888 - 13679 (-) TF: DBD-SUPERFAMILY|0040266 Yes
- 13775 - 15418 (-) TF: DBD-Pfam|GerE Yes
- 15422 - 15667 (-) other Yes
- 16650 - 18398 (-) other Yes
- 18419 - 21601 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes

PUL ID

PUL0316

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.