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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0135

PubMed

30341080, Appl Environ Microbiol. 2018 Dec 13;85(1):e02114-18. doi: 10.1128/AEM.02114-18. Print 2019 Jan 1.

Characterization method

enzyme activity assay,substrate binding assay

Genomic accession number

MH687413

Nucelotide position range

1-27138

Substrate

pectin

Loci

None

Species

Pseudoalteromonas sp./53249

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- - AYK02495.1 0 - 771 (-) MH687413.1:1-772 -
- - AYK02488.1 1335 - 4365 (+) MH687413.1:1336-4366 -
- - AYK02489.1 4367 - 4493 (+) MH687413.1:4368-4494 -
- - AYK02496.1 4583 - 6053 (+) MH687413.1:4584-6054 -
- - AYK02490.1 6067 - 6697 (+) MH687413.1:6068-6698 -
- - AYK02491.1 6761 - 8207 (+) MH687413.1:6762-8208 -
- - AYK02497.1 8264 - 10817 (+) MH687413.1:8265-10818 -
- - AYK02505.1 10846 - 12040 (+) MH687413.1:10847-12041 -
- - AYK02498.1 12049 - 13735 (+) MH687413.1:12050-13736 -
- - AYK02506.1 13737 - 14688 (+) MH687413.1:13738-14689 -
- - AYK02492.1 14859 - 15876 (-) MH687413.1:14860-15877 -
- - AYK02493.1 16139 - 17441 (-) MH687413.1:16140-17442 -
- - AYK02494.1 17440 - 17932 (-) MH687413.1:17441-17933 -
- - AYK02507.1 17938 - 18937 (-) MH687413.1:17939-18938 -
- - AYK02499.1 18966 - 19809 (-) MH687413.1:18967-19810 -
- - AYK02500.1 19830 - 20595 (-) MH687413.1:19831-20596 -
- - AYK02501.1 20726 - 22229 (+) MH687413.1:20727-22230 -
- - AYK02502.1 22230 - 23718 (+) MH687413.1:22231-23719 -
- - AYK02503.1 23718 - 24669 (+) MH687413.1:23719-24670 -
- - AYK02504.1 24761 - 25718 (+) MH687413.1:24762-25719 -
- - AYK02508.1 25734 - 27138 (+) MH687413.1:25735-27139 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 771 (-) CAZyme: CE12|CE4 Yes
- 1336 - 4365 (+) TC: gnl|TC-DB|Q9A608|1.B.14.12.1 Yes
- 4368 - 4493 (+) other Yes
- 4584 - 6053 (+) CAZyme: GH28 Yes
- 6068 - 6697 (+) other Yes
- 6762 - 8207 (+) other Yes
- 8265 - 10817 (+) CAZyme: GH105 Yes
- 10847 - 12040 (+) CAZyme: GH105 Yes
- 12050 - 13735 (+) CAZyme: GH43|GH43_10 Yes
- 13738 - 14688 (+) other Yes
- 14860 - 15876 (-) TF: DBD-Pfam|LacI,DBD-SUPERFAMILY|0036955 Yes
- 16140 - 17441 (-) TC: gnl|TC-DB|Q8ZKS0|2.A.56.1.5 Yes
- 17441 - 17932 (-) TC: gnl|TC-DB|Q8ZKR9|2.A.56.1.5 Yes
- 17939 - 18937 (-) TC: gnl|TC-DB|P43020|2.A.56.1.5 Yes
- 18967 - 19809 (-) other Yes
- 19831 - 20595 (-) other Yes
- 20727 - 22229 (+) other Yes
- 22231 - 23718 (+) other Yes
- 23719 - 24669 (+) STP: STP|PfkB Yes
- 24762 - 25718 (+) CAZyme: CE8 Yes
- 25735 - 27138 (+) CAZyme: PL1_2 Yes

PUL ID

PUL0135

PubMed

30341080, Appl Environ Microbiol. 2018 Dec 13;85(1):e02114-18. 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.