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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0269

PubMed

23674154, Appl Microbiol Biotechnol. 2014 Feb;98(3):1185-94. doi: 10.1007/s00253-013-4969-8. Epub 2013 May 15.

Characterization method

RT-PCR

Genomic accession number

NC_017943.1

Nucelotide position range

25887-44810

Substrate

chitin

Loci

HFX_RS15565-HFX_RS15635

Species

Haloferax mediterranei/2252

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

ugpC HFX_RS15565 WP_004056420.1 0 - 1131 (-) NC_017943.1:25887-27018 -
- HFX_RS15570 WP_014732644.1 1300 - 2527 (+) NC_017943.1:27187-28414 -
- HFX_RS15575 WP_004056418.1 2576 - 3284 (+) NC_017943.1:28463-29171 -
- HFX_RS15580 WP_004056417.1 3330 - 3705 (+) NC_017943.1:29217-29592 -
nagZ HFX_RS15585 WP_004056416.1 3802 - 5395 (-) NC_017943.1:29689-31282 3.2.1.52
- HFX_RS15590 WP_004056415.1 5491 - 6403 (-) NC_017943.1:31378-32290 -
- HFX_RS15595 WP_014732645.1 6404 - 7382 (-) NC_017943.1:32291-33269 -
- HFX_RS15600 WP_004056413.1 7533 - 8850 (-) NC_017943.1:33420-34737 -
dgoD HFX_RS15605 WP_004056412.1 9001 - 10153 (+) NC_017943.1:34888-36040 4.2.1.6
- HFX_RS15610 WP_004056411.1 10219 - 10963 (+) NC_017943.1:36106-36850 -
- HFX_RS15615 WP_004056410.1 10981 - 12052 (-) NC_017943.1:36868-37939 -
- HFX_RS19805 WP_137685702.1 12031 - 12235 (+) NC_017943.1:37918-38122 -
- HFX_RS15620 WP_004056409.1 12378 - 13797 (-) NC_017943.1:38265-39684 -
- HFX_RS15625 WP_004056408.1 13851 - 15294 (-) NC_017943.1:39738-41181 -
- HFX_RS15630 WP_014732646.1 15290 - 17003 (-) NC_017943.1:41177-42890 -
- HFX_RS15635 WP_004056406.1 17301 - 18924 (-) NC_017943.1:43188-44811 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

ugpC 1 - 1131 (-) TC: gnl|TC-DB|Q8TZQ3|3.A.1.1.16 Yes
- 1301 - 2527 (+) other Yes
- 2577 - 3284 (+) STP: STP|PIG-L Yes
- 3331 - 3705 (+) other Yes
nagZ 3803 - 5395 (-) CAZyme: GH3 Yes
- 5492 - 6403 (-) TC: gnl|TC-DB|G4FGN6|3.A.1.1.41 Yes
- 6405 - 7382 (-) TC: gnl|TC-DB|Q72H67|3.A.1.1.25 Yes
- 7534 - 8850 (-) STP: STP|SBP_bac_1 Yes
dgoD 9002 - 10153 (+) other Yes
- 10220 - 10963 (+) TF: DBD-Pfam|HTH_5,DBD-SUPERFAMILY|0040266 Yes
- 10982 - 12052 (-) other Yes
- 12032 - 12235 (+) other Yes
- 12379 - 13797 (-) other Yes
- 13852 - 15294 (-) CAZyme: CBM5 Yes
- 15291 - 17003 (-) CAZyme: CBM5|GH18 Yes
- 17302 - 18924 (-) CAZyme: CBM5|GH18 Yes

PUL ID

PUL0269

PubMed

23674154, Appl Microbiol Biotechnol. 2014 Feb;98(3):1185-94. doi: 10.1007/s00253-013-4969-8. Epub 2013 May 15.

Title

Characterization of genes for chitin catabolism in Haloferax mediterranei.

Author

Hou J, Han J, Cai L, Zhou J, Lu Y, Jin C, Liu J, Xiang H

Abstract

Chitin is the second most abundant natural polysaccharide after cellulose. But degradation of chitin has never been reported in haloarchaea. In this study, we revealed that Haloferax mediterranei, a metabolically versatile haloarchaeon, could utilize colloidal or powdered chitin for growth and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) accumulation, and the gene cluster (HFX_5025-5039) for the chitin catabolism pathway was experimentally identified. First, reverse transcription polymerase chain reaction results showed that the expression of the genes encoding the four putative chitinases (ChiAHme, ChiBHme, ChiCHme, and ChiDHme, HFX_5036-5039), the LmbE-like deacetylase (DacHme, HFX_5027), and the glycosidase (GlyAHme, HFX_5029) was induced by colloidal or powdered chitin, and chiA Hme, chiB Hme, and chiC Hme were cotranscribed. Knockout of chiABC Hme or chiD Hme had a significant effect on cell growth and PHBV production when chitin was used as the sole carbon source, and the chiABCD Hme knockout mutant lost the capability to utilize chitin. Knockout of dac Hme or glyA Hme also decreased PHBV accumulation on chitin. These results suggested that ChiABCDHme, DacHme, and GlyAHme were indeed involved in chitin degradation in H. mediterranei. Additionally, the chitinase assay showed that each chitinase possessed hydrolytic activity toward colloidal or powdered chitin, and the major product of colloidal chitin hydrolysis by ChiABCDHme was diacetylchitobiose, which was likely further degraded to monosaccharides by DacHme, GlyAHme, and other related enzymes for both cell growth and PHBV biosynthesis. Taken together, this study revealed the genes and enzymes involved in chitin catabolism in haloarchaea for the first time and indicated the potential of H. mediterranei as a whole-cell biocatalyst in chitin bioconversion.