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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0329

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

398120-434831

Substrate

xylan

Loci

GRFL_0317-GRFL_0341

Species

Gramella flava/1486245

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- GRFL_0317 APU67041.1 0 - 1551 (-) CP016359.1:398120-399671 -
- GRFL_0318 APU67042.1 1561 - 3307 (-) CP016359.1:399681-401427 3.2.1.37
- GRFL_0319 APU67043.1 3318 - 4431 (-) CP016359.1:401438-402551 5.1.3.3
- GRFL_0320 APU67044.1 4758 - 6705 (-) CP016359.1:402878-404825 -
- GRFL_0321 APU67045.1 6701 - 7877 (-) CP016359.1:404821-405997 -
- GRFL_0322 APU67046.1 8108 - 11234 (+) CP016359.1:406228-409354 -
- GRFL_0323 APU67047.1 11243 - 13169 (+) CP016359.1:409363-411289 -
- GRFL_0324 APU67048.1 13308 - 15111 (+) CP016359.1:411428-413231 2.1.3.-
- GRFL_0325 APU67049.1 15110 - 15260 (+) CP016359.1:413230-413380 -
- GRFL_0326 APU67050.1 15240 - 15453 (-) CP016359.1:413360-413573 -
- GRFL_0327 APU67051.1 15451 - 15619 (+) CP016359.1:413571-413739 -
- GRFL_0328 APU67052.1 15621 - 17265 (-) CP016359.1:413741-415385 -
- GRFL_0329 APU67053.1 17426 - 17558 (-) CP016359.1:415546-415678 -
- GRFL_0330 APU67054.1 17743 - 18823 (+) CP016359.1:415863-416943 -
- GRFL_0331 APU67055.1 18962 - 20366 (-) CP016359.1:417082-418486 5.3.1.12
- GRFL_0332 APU67056.1 20375 - 22583 (-) CP016359.1:418495-420703 3.2.1.21
- GRFL_0333 APU67057.1 22706 - 24938 (+) CP016359.1:420826-423058 3.2.1.139
- GRFL_0334 APU67058.1 24943 - 25687 (+) CP016359.1:423063-423807 1.1.1.100
- GRFL_0335 APU67059.1 25697 - 26858 (+) CP016359.1:423817-424978 4.2.1.8
- GRFL_0336 APU67060.1 26870 - 28019 (+) CP016359.1:424990-426139 3.2.1.8
- GRFL_0337 APU67061.1 27999 - 30843 (+) CP016359.1:426119-428963 -
- GRFL_0338 APU67062.1 30859 - 32179 (-) CP016359.1:428979-430299 -
- GRFL_0339 APU67063.1 32270 - 33587 (-) CP016359.1:430390-431707 5.3.1.5
- GRFL_0340 APU67064.1 33595 - 35086 (-) CP016359.1:431715-433206 2.7.1.17
- GRFL_0341 APU67065.1 35092 - 36712 (-) CP016359.1:433212-434832 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1551 (-) CAZyme: GH43_10|GH43|CBM22 Yes
- 1562 - 3307 (-) CAZyme: GH43|GH43_12 Yes
- 3319 - 4431 (-) other Yes
- 4759 - 6705 (-) other Yes
- 6702 - 7877 (-) CAZyme: GH43|GH43_1 Yes
- 8109 - 11234 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 11244 - 13169 (+) other Yes
- 13309 - 15111 (+) other Yes
- 15111 - 15260 (+) other Yes
- 15241 - 15453 (-) other Yes
- 15452 - 15619 (+) other Yes
- 15622 - 17265 (-) other Yes
- 17427 - 17558 (-) other Yes
- 17744 - 18823 (+) TF: DBD-Pfam|LacI,DBD-SUPERFAMILY|0036955 Yes
- 18963 - 20366 (-) other Yes
- 20376 - 22583 (-) CAZyme: GH3 Yes
- 22707 - 24938 (+) CAZyme: GH67 Yes
- 24944 - 25687 (+) other Yes
- 25698 - 26858 (+) other Yes
- 26871 - 28019 (+) CAZyme: GH10 Yes
- 28000 - 30843 (+) CAZyme: GH115 Yes
- 30860 - 32179 (-) CAZyme: CE15 Yes
- 32271 - 33587 (-) other Yes
- 33596 - 35086 (-) other Yes
- 35093 - 36712 (-) TC: gnl|TC-DB|Q8AAV7|2.A.21.3.19 Yes

PUL ID

PUL0329

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.