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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0443

PubMed

28069559, J Proteomics. 2017 Mar 6;156:63-74. doi: 10.1016/j.jprot.2017.01.003. Epub 2017 Jan 6.

Characterization method

mass spectrometry,high performance anion exchange chromatography

Genomic accession number

NC_013132.1

Nucelotide position range

6370913-6392100

Substrate

glucomannan,galactomannan,glucose

Loci

Cpin_5109-Cpin_5117

Species

Chitinophaga pinensis/79329

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- CPIN_RS25335 WP_012792709.1 0 - 1230 (-) NC_013132.1:6370913-6372143 -
- CPIN_RS25340 WP_012792710.1 1511 - 4412 (+) NC_013132.1:6372424-6375325 -
- CPIN_RS25345 WP_012792711.1 4427 - 5072 (+) NC_013132.1:6375340-6375985 -
- CPIN_RS25350 WP_083781147.1 5138 - 6365 (+) NC_013132.1:6376051-6377278 -
- CPIN_RS25355 WP_012792713.1 6599 - 9908 (+) NC_013132.1:6377512-6380821 -
- CPIN_RS25360 WP_012792714.1 9919 - 11362 (+) NC_013132.1:6380832-6382275 -
- CPIN_RS25365 WP_012792715.1 11436 - 13977 (+) NC_013132.1:6382349-6384890 -
- CPIN_RS37445 WP_012792716.1 14310 - 17490 (+) NC_013132.1:6385223-6388403 -
- CPIN_RS37015 WP_012792717.1 17789 - 21188 (+) NC_013132.1:6388702-6392101 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 1230 (-) CAZyme: GH16 Yes
- 1512 - 4412 (+) TF: DBD-Pfam|GerE Yes
- 4428 - 5072 (+) STP: STP|Sigma70_r2,STP|Sigma70_r4_2 Yes
- 5139 - 6365 (+) STP: STP|FecR Yes
- 6600 - 9908 (+) TC: gnl|TC-DB|Q45780|1.B.14.6.1 Yes
- 9920 - 11362 (+) TC: gnl|TC-DB|E4RVP8|8.A.46.1.5 Yes
- 11437 - 13977 (+) other Yes
- 14311 - 17490 (+) STP: STP|Y_Y_Y Yes
- 17790 - 21188 (+) CAZyme: CBM6 Yes

PUL ID

PUL0443

PubMed

28069559, J Proteomics. 2017 Mar 6;156:63-74. doi: 10.1016/j.jprot.2017.01.003. Epub 2017 Jan 6.

Title

Proteomic insights into mannan degradation and protein secretion by the forest floor bacterium Chitinophaga pinensis.

Author

Larsbrink J, Tuveng TR, Pope PB, Bulone V, Eijsink VG, Brumer H, McKee LS

Abstract

Together with fungi, saprophytic bacteria are central to the decomposition and recycling of biomass in forest environments. The Bacteroidetes phylum is abundant in diverse habitats, and several species have been shown to be able to deconstruct a wide variety of complex carbohydrates. The genus Chitinophaga is often enriched in hotspots of plant and microbial biomass degradation. We present a proteomic assessment of the ability of Chitinophaga pinensis to grow on and degrade mannan polysaccharides, using an agarose plate-based method of protein collection to minimise contamination with exopolysaccharides and proteins from lysed cells, and to reflect the realistic setting of growth on a solid surface. We show that select Polysaccharide Utilisation Loci (PULs) are expressed in different growth conditions, and identify enzymes that may be involved in mannan degradation. By comparing proteomic and enzymatic profiles, we show evidence for the induced expression of enzymes and PULs in cells grown on mannan polysaccharides compared with cells grown on glucose. In addition, we show that the secretion of putative biomass-degrading enzymes during growth on glucose comprises a system for nutrient scavenging, which employs constitutively produced enzymes. SIGNIFICANCE OF THIS STUDY: Chitinophaga pinensis belongs to a bacterial genus which is prominent in microbial communities in agricultural and forest environments, where plant and fungal biomass is intensively degraded. Such degradation is hugely significant in the recycling of carbon in the natural environment, and the enzymes responsible are of biotechnological relevance in emerging technologies involving the deconstruction of plant cell wall material. The bacterium has a comparatively large genome, which includes many uncharacterised carbohydrate-active enzymes. We present the first proteomic assessment of the biomass-degrading machinery of this species, focusing on mannan, an abundant plant cell wall hemicellulose. Our findings include the identification of several novel enzymes, which are promising targets for future biochemical characterisation. In addition, the data indicate the expression of specific Polysaccharide Utilisation Loci, induced in the presence of different growth substrates. We also highlight how a constitutive secretion of enzymes which deconstruct microbial biomass likely forms part of a nutrient scavenging process.