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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0328

PubMed

28261179, Front Microbiol. 2017 Feb 14;8:220. doi: 10.3389/fmicb.2017.00220. eCollection 2017.

Characterization method

microarray,gas chromatography and mass spectrometry

Genomic accession number

CP016359.1

Nucelotide position range

364304-380160

Substrate

xylan

Loci

GRFL_0296-GRFL_0304

Species

Gramella flava/1486245

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- GRFL_0296 APU67020.1 0 - 2169 (-) CP016359.1:364304-366473 -
- GRFL_0297 APU67021.1 2187 - 4629 (-) CP016359.1:366491-368933 -
- GRFL_0298 APU67022.1 4637 - 5780 (-) CP016359.1:368941-370084 5.1.3.3
- GRFL_0299 APU67023.1 5808 - 6909 (-) CP016359.1:370112-371213 3.2.1.55
- GRFL_0300 APU67024.1 6917 - 8738 (-) CP016359.1:371221-373042 3.2.1.23
- GRFL_0301 APU67025.1 8780 - 9956 (-) CP016359.1:373084-374260 -
- GRFL_0302 APU67026.1 10102 - 10795 (-) CP016359.1:374406-375099 -
- GRFL_0303 APU67027.1 10814 - 12710 (-) CP016359.1:375118-377014 -
- GRFL_0304 APU67028.1 12716 - 15857 (-) CP016359.1:377020-380161 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 19 (-) CDS No
- 1 - 2169 (-) CAZyme: GH127|CBM13 Yes
- 2188 - 4629 (-) other Yes
- 4638 - 5780 (-) other Yes
- 5809 - 6909 (-) CAZyme: GH43|GH43_26 Yes
- 6918 - 8738 (-) CAZyme: GH2 Yes
- 8781 - 9956 (-) CAZyme: GH5|GH5_13 Yes
- 10103 - 10795 (-) other Yes
- 10815 - 12710 (-) other Yes
- 12717 - 15857 (-) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes

PUL ID

PUL0328

PubMed

28261179, Front Microbiol. 2017 Feb 14;8:220. doi: 10.3389/fmicb.2017.00220. eCollection 2017.

Title

Characterization of Potential Polysaccharide Utilization Systems in the Marine Bacteroidetes Gramella Flava JLT2011 Using a Multi-Omics Approach.

Author

Tang K, Lin Y, Han Y, Jiao N

Abstract

Members of phylum Bacteroidetes are distributed across diverse marine niches and Flavobacteria is often the predominant bacterial class decomposing algae-derived polysaccharides. Here, we report the complete genome of Gramella flava JLT2011 (Flavobacteria) isolated from surface water of the southeastern Pacific. A remarkable genomic feature is that the number of glycoside hydrolase (GH) genes in the genome of G. flava JLT2011 is more than 2-fold higher than that of other Gramella species. The functional profiles of the GHs suggest extensive variation in Gramella species. Growth experiments revealed that G. flava JLT2011 has the ability to utilize a wide range of polysaccharides for growth such as xylan and homogalacturonan in pectin. Nearly half of all GH genes were located on the multi-gene polysaccharide utilization loci (PUL) or PUL-like systems in G. flava JLT2011. This species was also found to harbor the two xylan PULs and a pectin PUL, respectively. Gene expression data indicated that more GHs and sugar-specific outer-membrane susC-susD systems were found in the presence of xylan than in the presence of pectin, suggesting a different strategy for heteropolymeric xylan and homoglacturonan utilization. Multi-omics data (transcriptomics, proteomics, and metabolomics) indicated that xylan PULs and pectin PUL are respectively involved in the catabolism of their corresponding polysaccharides. This work presents a comparison of polysaccharide decomposition within a genus and expands current knowledge on the diversity and function of PULs in marine Bacteroidetes, thereby deepening our understanding of their ecological role in polysaccharide remineralization in the marine system.