PUL ID

PUL0136

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

ADOP01000016

Nucelotide position range

43718-80113

Substrate

pectin

Loci

PH505_ap00420-PH505_ap00680

Species

Pseudoalteromonas haloplanktis/228

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

kdgK PH505_ap00420 EGI73591.1 0 - 948 (-) ADOP01000016.2:43718-44666 2.7.1.45
uxaA PH505_ap00430 EGI73592.1 948 - 2436 (-) ADOP01000016.2:44666-46154 4.2.1.7
uxaB PH505_ap00440 EGI73593.1 2437 - 3895 (-) ADOP01000016.2:46155-47613 1.1.1.58
kduD PH505_ap00450 EGI73594.1 4081 - 4846 (+) ADOP01000016.2:47799-48564 1.1.1.125
kduI PH505_ap00460 EGI73595.1 4869 - 5712 (+) ADOP01000016.2:48587-49430 5.3.1.17
dctP PH505_ap00470 EGI73596.1 5780 - 6731 (+) ADOP01000016.2:49498-50449 -
dctQ PH505_ap00480 EGI73597.1 6740 - 7229 (+) ADOP01000016.2:50458-50947 -
dctM PH505_ap00490 EGI73598.1 7228 - 8530 (+) ADOP01000016.2:50946-52248 -
lacI PH505_ap00500 EGI73599.1 8720 - 9722 (+) ADOP01000016.2:52438-53440 -
- PH505_ap00510 EGI73600.1 9938 - 10106 (-) ADOP01000016.2:53656-53824 -
pelA PH505_ap00520 EGI73601.2 10427 - 16586 (-) ADOP01000016.2:54145-60304 -
tbdB PH505_ap00530 EGI73602.2 16664 - 19634 (-) ADOP01000016.2:60382-63352 -
pelC PH505_ap00550 EGI73604.2 19824 - 21282 (+) ADOP01000016.2:63542-65000 -
estP PH505_ap00560 EGI73605.1 21323 - 22280 (-) ADOP01000016.2:65041-65998 -
- PH505_ap00570 EGI73606.2 22286 - 22616 (-) ADOP01000016.2:66004-66334 -
xylB PH505_ap00580 EGI73607.1 22576 - 22807 (-) ADOP01000016.2:66294-66525 -
xylA PH505_ap00590 EGI73608.2 23172 - 23529 (-) ADOP01000016.2:66890-67247 -
ghyA PH505_ap00600 EGI73609.1 23532 - 24744 (-) ADOP01000016.2:67250-68462 -
rpoA PH505_ap00610 EGI73610.1 24854 - 27404 (-) ADOP01000016.2:68572-71122 -
uxaC PH505_ap00620 EGI73611.1 27453 - 28902 (-) ADOP01000016.2:71171-72620 5.3.1.12
kdgA PH505_ap00630 EGI73612.1 28994 - 29618 (-) ADOP01000016.2:72712-73336 4.1.2.14
ghyB PH505_ap00640 EGI73613.2 29631 - 31104 (-) ADOP01000016.2:73349-74822 -
- PH505_ap00650 EGI73614.1 31346 - 31481 (-) ADOP01000016.2:75064-75199 -
tbdC PH505_ap00660 EGI73615.2 31489 - 32014 (-) ADOP01000016.2:75207-75732 -
tbdA PH505_ap00670 EGI73616.1 32502 - 35217 (-) ADOP01000016.2:76220-78935 -
rhgT PH505_ap00680 EGI73617.1 35637 - 36396 (+) ADOP01000016.2:79355-80114 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

kdgK 1 - 948 (-) STP: STP|PfkB No
uxaA 949 - 2436 (-) CDS No
uxaB 2438 - 3895 (-) CDS No
kduD 4082 - 4846 (+) CDS No
kduI 4870 - 5712 (+) CDS No
dctP 5781 - 6731 (+) TC: gnl|TC-DB|P43020|2.A.56.1.5 Yes
dctQ 6741 - 7229 (+) TC: gnl|TC-DB|Q8ZKR9|2.A.56.1.5 Yes
dctM 7229 - 8530 (+) TC: gnl|TC-DB|Q8ZKS0|2.A.56.1.5 Yes
lacI 8721 - 9722 (+) TF: DBD-Pfam|LacI,DBD-SUPERFAMILY|0036955 Yes
- 9939 - 10106 (-) other Yes
pelA 10428 - 16586 (-) CAZyme: PL1|PL1_5|CE8 Yes
tbdB 16665 - 19634 (-) other Yes
pelC 19825 - 21282 (+) CAZyme: PL1|PL1_2 Yes
estP 21324 - 22280 (-) other Yes
- 22287 - 22616 (-) other Yes
xylB 22577 - 22807 (-) other Yes
xylA 23173 - 23529 (-) other Yes
ghyA 23533 - 24744 (-) CAZyme: GH105 Yes
rpoA 24855 - 27404 (-) CAZyme: GH105 Yes
uxaC 27454 - 28902 (-) other Yes
kdgA 28995 - 29618 (-) other Yes
ghyB 29632 - 31104 (-) CAZyme: GH28 Yes
- 31347 - 31481 (-) other Yes
tbdC 31490 - 32014 (-) other Yes
tbdA 32503 - 35217 (-) TC: gnl|TC-DB|Q9A608|1.B.14.12.1 Yes
rhgT 35638 - 36396 (+) CDS No

PUL ID

PUL0136

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.