PUL ID

PUL0134

PubMed

30341080, Appl Environ Microbiol. 2018 Dec 13;85(1). pii: AEM.02114-18. doi: 10.1128/AEM.02114-18. Print 2019 Jan 1.

Characterization method

sequence homology analysis

Genomic accession number

CP016359.1

Nucelotide position range

2419679-2461893

Substrate

pectin

Loci

GRFL_2154-GRFL_2182

Species

Gramella flava/1486245

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- GRFL_2154 APU68878.1 0 - 117 (-) CP016359.1:2419679-2419796 -
- GRFL_2155 APU68879.1 224 - 3371 (+) CP016359.1:2419903-2423050 -
- GRFL_2156 APU68880.1 3383 - 5180 (+) CP016359.1:2423062-2424859 -
- GRFL_2157 APU68881.1 5208 - 6765 (+) CP016359.1:2424887-2426444 -
- GRFL_2158 APU68882.1 6983 - 12446 (+) CP016359.1:2426662-2432125 -
- GRFL_2159 APU68883.1 12442 - 14293 (+) CP016359.1:2432121-2433972 -
- GRFL_2160 APU68884.1 14421 - 15219 (+) CP016359.1:2434100-2434898 1.1.1.57
- GRFL_2161 APU68885.1 15230 - 16235 (+) CP016359.1:2434909-2435914 3.1.3.11
- GRFL_2162 APU68886.1 16335 - 17169 (+) CP016359.1:2436014-2436848 5.3.1.17
- GRFL_2163 APU68887.1 17170 - 17938 (+) CP016359.1:2436849-2437617 1.1.1.125
- GRFL_2164 APU68888.1 17958 - 19362 (+) CP016359.1:2437637-2439041 5.3.1.12
- GRFL_2165 APU68889.1 19361 - 20381 (+) CP016359.1:2439040-2440060 2.7.1.45
- GRFL_2166 APU68890.1 20391 - 21066 (+) CP016359.1:2440070-2440745 4.1.3.16, 4.1.2.14
- GRFL_2167 APU68891.1 21103 - 22042 (+) CP016359.1:2440782-2441721 -
- GRFL_2168 APU68892.1 22046 - 22514 (+) CP016359.1:2441725-2442193 -
- GRFL_2169 APU68893.1 22510 - 23800 (+) CP016359.1:2442189-2443479 -
- GRFL_2170 APU68894.1 23816 - 25280 (+) CP016359.1:2443495-2444959 1.1.1.58
- GRFL_2171 APU68895.1 25292 - 26906 (+) CP016359.1:2444971-2446585 4.2.1.7
- GRFL_2172 APU68896.1 26914 - 28093 (+) CP016359.1:2446593-2447772 -
- GRFL_2173 APU68897.1 28094 - 29147 (-) CP016359.1:2447773-2448826 -
- GRFL_2174 APU68898.1 29476 - 30880 (+) CP016359.1:2449155-2450559 3.2.1.15
- GRFL_2175 APU68899.1 30904 - 31912 (+) CP016359.1:2450583-2451591 -
- GRFL_2176 APU68900.1 31913 - 33161 (+) CP016359.1:2451592-2452840 -
- GRFL_2177 APU68901.1 33173 - 34805 (+) CP016359.1:2452852-2454484 3.2.1.37
- GRFL_2178 APU68902.1 34807 - 37606 (+) CP016359.1:2454486-2457285 3.2.1.15
- GRFL_2179 APU68903.1 37606 - 38407 (+) CP016359.1:2457285-2458086 -
- GRFL_2180 APU68904.1 38409 - 40326 (+) CP016359.1:2458088-2460005 -
- GRFL_2181 APU68905.1 40318 - 41119 (+) CP016359.1:2459997-2460798 -
- GRFL_2182 APU68906.1 41132 - 42215 (+) CP016359.1:2460811-2461894 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 117 (-) CDS No
- 225 - 3371 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 3384 - 5180 (+) TC: gnl|TC-DB|C6Y217|8.A.46.1.3 Yes
- 5209 - 6765 (+) other Yes
- 6984 - 12446 (+) CAZyme: CE8 Yes
- 12443 - 14293 (+) CAZyme: PL9_1 Yes
- 14422 - 15219 (+) other Yes
- 15231 - 16235 (+) other Yes
- 16336 - 17169 (+) other Yes
- 17171 - 17938 (+) other Yes
- 17959 - 19362 (+) other Yes
- 19362 - 20381 (+) STP: STP|PfkB Yes
- 20392 - 21066 (+) other Yes
- 21104 - 22042 (+) TC: gnl|TC-DB|P43020|2.A.56.1.5 Yes
- 22047 - 22514 (+) TC: gnl|TC-DB|Q8ZKR9|2.A.56.1.5 Yes
- 22511 - 23800 (+) TC: gnl|TC-DB|Q8ZKS0|2.A.56.1.5 Yes
- 23817 - 25280 (+) other Yes
- 25293 - 26906 (+) other Yes
- 26915 - 28093 (+) other Yes
- 28095 - 29147 (-) TF: DBD-Pfam|LacI,DBD-SUPERFAMILY|0036955 Yes
- 29477 - 30880 (+) CAZyme: GH28 Yes
- 30905 - 31912 (+) other Yes
- 31914 - 33161 (+) CAZyme: GH105 Yes
- 33174 - 34805 (+) CAZyme: GH43_10 Yes
- 34808 - 37606 (+) CAZyme: GH28|PL9_1 Yes
- 37607 - 38407 (+) CAZyme: CE12 Yes
- 38410 - 40326 (+) CAZyme: CE8|CE10 Yes
- 40319 - 41119 (+) CAZyme: CE12 Yes
- 41133 - 42215 (+) CAZyme: PL10_1 Yes

PUL ID

PUL0134

PubMed

30341080, Appl Environ Microbiol. 2018 Dec 13;85(1). pii: AEM.02114-18. doi: 10.1128/AEM.02114-18. Print 2019 Jan 1.

Title

Biochemical Reconstruction of a Metabolic Pathway from a Marine Bacterium Reveals Its Mechanism of Pectin Depolymerization.

Author

Hobbs JK, Hettle AG, Vickers C, Boraston AB

Abstract

Pectin is a complex uronic acid-containing polysaccharide typically found in plant cell walls, though forms of pectin are also found in marine diatoms and seagrasses. Genetic loci that target pectin have recently been identified in two phyla of marine bacteria. These loci appear to encode a pectin saccharification pathway that is distinct from the canonical pathway typically associated with phytopathogenic terrestrial bacteria. However, very few components of the marine pectin metabolism pathway have been experimentally validated. Here, we biochemically reconstructed the pectin saccharification pathway from a marine Pseudoalteromonas sp. in vitro and show that it results in the production of galacturonate and the key metabolic intermediate 5-keto-4-deoxyuronate (DKI). We demonstrate the sequential de-esterification and depolymerization of pectin into oligosaccharides and the synergistic action of glycoside hydrolases (GHs) to fully degrade these oligosaccharides into monosaccharides. Furthermore, we show that this pathway relies on enzymes belonging to GH family 105 to carry out the equivalent chemistry afforded by an exolytic polysaccharide lyase (PL) and KdgF in the canonical pectin pathway. Finally, we synthesize our findings into a model of marine pectin degradation and compare it with the canonical pathway. Our results underline the shifting view of pectin as a solely terrestrial polysaccharide and highlight the importance of marine pectin as a carbon source for suitably adapted marine heterotrophs. This alternate pathway has the potential to be exploited in the growing field of biofuel production from plant waste.IMPORTANCE Marine polysaccharides, found in the cell walls of seaweeds and other marine macrophytes, represent a vast sink of photosynthetically fixed carbon. As such, their breakdown by marine microbes contributes significantly to global carbon cycling. Pectin is an abundant polysaccharide found in the cell walls of terrestrial plants, but it has recently been reported that some marine bacteria possess the genetic capacity to degrade it. In this study, we biochemically characterized seven key enzymes from a marine bacterium that, together, fully degrade the backbone of pectin into its constituent monosaccharides. Our findings highlight the importance of pectin as a marine carbon source available to bacteria that possess this pathway. The characterized enzymes also have the potential to be utilized in the production of biofuels from plant waste.