PUL ID

PUL0330

PubMed

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

Characterization method

fosmid library screen, enzyme activity assay, thin layer chromatography

Genomic accession number

CP016359.1

Nucelotide position range

2419903-2461893

Substrate

pectin

Loci

GRFL_2155-GRFL_2182

Species

Gramella flava/1486245

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- GRFL_2155 APU68879.1 0 - 3147 (+) CP016359.1:2419903-2423050 -
- GRFL_2156 APU68880.1 3159 - 4956 (+) CP016359.1:2423062-2424859 -
- GRFL_2157 APU68881.1 4984 - 6541 (+) CP016359.1:2424887-2426444 -
- GRFL_2158 APU68882.1 6759 - 12222 (+) CP016359.1:2426662-2432125 -
- GRFL_2159 APU68883.1 12218 - 14069 (+) CP016359.1:2432121-2433972 -
- GRFL_2160 APU68884.1 14197 - 14995 (+) CP016359.1:2434100-2434898 1.1.1.57
- GRFL_2161 APU68885.1 15006 - 16011 (+) CP016359.1:2434909-2435914 3.1.3.11
- GRFL_2162 APU68886.1 16111 - 16945 (+) CP016359.1:2436014-2436848 5.3.1.17
- GRFL_2163 APU68887.1 16946 - 17714 (+) CP016359.1:2436849-2437617 1.1.1.125
- GRFL_2164 APU68888.1 17734 - 19138 (+) CP016359.1:2437637-2439041 5.3.1.12
- GRFL_2165 APU68889.1 19137 - 20157 (+) CP016359.1:2439040-2440060 2.7.1.45
- GRFL_2166 APU68890.1 20167 - 20842 (+) CP016359.1:2440070-2440745 4.1.3.16, 4.1.2.14
- GRFL_2167 APU68891.1 20879 - 21818 (+) CP016359.1:2440782-2441721 -
- GRFL_2168 APU68892.1 21822 - 22290 (+) CP016359.1:2441725-2442193 -
- GRFL_2169 APU68893.1 22286 - 23576 (+) CP016359.1:2442189-2443479 -
- GRFL_2170 APU68894.1 23592 - 25056 (+) CP016359.1:2443495-2444959 1.1.1.58
- GRFL_2171 APU68895.1 25068 - 26682 (+) CP016359.1:2444971-2446585 4.2.1.7
- GRFL_2172 APU68896.1 26690 - 27869 (+) CP016359.1:2446593-2447772 -
- GRFL_2173 APU68897.1 27870 - 28923 (-) CP016359.1:2447773-2448826 -
- GRFL_2174 APU68898.1 29252 - 30656 (+) CP016359.1:2449155-2450559 3.2.1.15
- GRFL_2175 APU68899.1 30680 - 31688 (+) CP016359.1:2450583-2451591 -
- GRFL_2176 APU68900.1 31689 - 32937 (+) CP016359.1:2451592-2452840 -
- GRFL_2177 APU68901.1 32949 - 34581 (+) CP016359.1:2452852-2454484 3.2.1.37
- GRFL_2178 APU68902.1 34583 - 37382 (+) CP016359.1:2454486-2457285 3.2.1.15
- GRFL_2179 APU68903.1 37382 - 38183 (+) CP016359.1:2457285-2458086 -
- GRFL_2180 APU68904.1 38185 - 40102 (+) CP016359.1:2458088-2460005 -
- GRFL_2181 APU68905.1 40094 - 40895 (+) CP016359.1:2459997-2460798 -
- GRFL_2182 APU68906.1 40908 - 41991 (+) CP016359.1:2460811-2461894 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 3147 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 3160 - 4956 (+) TC: gnl|TC-DB|C6Y217|8.A.46.1.3 Yes
- 4985 - 6541 (+) other Yes
- 6760 - 12222 (+) CAZyme: CE8 Yes
- 12219 - 14069 (+) CAZyme: PL9_1 Yes
- 14198 - 14995 (+) other Yes
- 15007 - 16011 (+) other Yes
- 16112 - 16945 (+) other Yes
- 16947 - 17714 (+) other Yes
- 17735 - 19138 (+) other Yes
- 19138 - 20157 (+) STP: STP|PfkB Yes
- 20168 - 20842 (+) other Yes
- 20880 - 21818 (+) TC: gnl|TC-DB|P43020|2.A.56.1.5 Yes
- 21823 - 22290 (+) TC: gnl|TC-DB|Q8ZKR9|2.A.56.1.5 Yes
- 22287 - 23576 (+) TC: gnl|TC-DB|Q8ZKS0|2.A.56.1.5 Yes
- 23593 - 25056 (+) other Yes
- 25069 - 26682 (+) other Yes
- 26691 - 27869 (+) other Yes
- 27871 - 28923 (-) TF: DBD-Pfam|LacI,DBD-SUPERFAMILY|0036955 Yes
- 29253 - 30656 (+) CAZyme: GH28 Yes
- 30681 - 31688 (+) other Yes
- 31690 - 32937 (+) CAZyme: GH105 Yes
- 32950 - 34581 (+) CAZyme: GH43_10 Yes
- 34584 - 37382 (+) CAZyme: GH28|PL9_1 Yes
- 37383 - 38183 (+) CAZyme: CE12 Yes
- 38186 - 40102 (+) CAZyme: CE8|CE10 Yes
- 40095 - 40895 (+) CAZyme: CE12 Yes
- 40909 - 41991 (+) CAZyme: PL10_1 Yes

PUL ID

PUL0330

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.