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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0081

PubMed

31133029, BMC Microbiol. 2019 May 27;19(1):112. doi: 10.1186/s12866-019-1487-6.

Characterization method

qRT-PCR,microarray

Genomic accession number

BA000032.2

Nucelotide position range

67900-82169

Substrate

oligogalacturonide

Loci

VPA0076-VPA0088

Species

Vibrio parahaemolyticus/670

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

VPA0076 - BAC61419.1 0 - 798 (-) BA000032.2:67900-68698 -
VPA0077 - BAC61420.1 1038 - 1800 (+) BA000032.2:68938-69700 -
VPA0078 - BAC61421.1 1818 - 2343 (+) BA000032.2:69718-70243 -
VPA0079 - BAC61422.1 2350 - 2671 (+) BA000032.2:70250-70571 -
VPA0080 - BAC61423.1 2711 - 3347 (+) BA000032.2:70611-71247 -
VPA0081 - BAC61424.1 3423 - 4335 (+) BA000032.2:71323-72235 -
VPA0082 - BAC61425.1 4433 - 5363 (+) BA000032.2:72333-73263 -
VPA0083 - BAC61426.1 5374 - 5998 (+) BA000032.2:73274-73898 -
VPA0084 - BAC61427.1 6183 - 7923 (-) BA000032.2:74083-75823 -
VPA0085 - BAC61428.1 8052 - 8730 (+) BA000032.2:75952-76630 -
VPA0086 - BAC61429.1 8745 - 10974 (+) BA000032.2:76645-78874 -
VPA0087 - BAC61430.1 11274 - 13047 (+) BA000032.2:79174-80947 -
VPA0088 - BAC61431.1 13103 - 14270 (+) BA000032.2:81003-82170 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 798 (-) TF: DBD-Pfam|MarR,DBD-SUPERFAMILY|0040266 No
- 1039 - 1800 (+) CDS No
- 1819 - 2343 (+) CDS No
- 2351 - 2671 (+) STP: STP|AraC_binding No
- 2712 - 3347 (+) CDS No
- 3424 - 4335 (+) CDS No
- 4434 - 5363 (+) STP: STP|PfkB No
- 5375 - 5998 (+) CDS No
- 6184 - 7923 (-) TC: gnl|TC-DB|A3UWQ9|2.A.21.3.12 Yes
- 8053 - 8730 (+) TC: gnl|TC-DB|A6TDJ4|1.B.35.1.7 Yes
- 8746 - 10974 (+) CAZyme: PL9_1 Yes
- 11275 - 13047 (+) TC: gnl|TC-DB|A3UWQ9|2.A.21.3.12 Yes
- 13104 - 14270 (+) CAZyme: PL22_1|PL22 Yes

PUL ID

PUL0081

PubMed

31133029, BMC Microbiol. 2019 May 27;19(1):112. doi: 10.1186/s12866-019-1487-6.

Title

Carbohydrate metabolic systems present on genomic islands are lost and gained in Vibrio parahaemolyticus.

Author

Regmi A, Boyd EF

Abstract

BACKGROUND: Utilizing unique carbohydrates or utilizing them more efficiently help bacteria expand and colonize new niches. Horizontal gene transfer (HGT) of catabolic systems is a powerful mechanism by which bacteria can acquire new phenotypic traits that can increase survival and fitness in different niches. In this work, we examined carbon catabolism diversity among Vibrio parahaemolyticus, a marine species that is also an important human and fish pathogen. RESULTS: Phenotypic differences in carbon utilization between Vibrio parahaemolyticus strains lead us to examine genotypic differences in this species and the family Vibrionaceae in general. Bioinformatics analysis showed that the ability to utilize D-galactose was present in all V. parahaemolyticus but at least two distinct transporters were present; a major facilitator superfamily (MFS) transporter and a sodium/galactose transporter (SGLT). Growth and genetic analyses demonstrated that SGLT was a more efficient transporter of D-galactose and was the predominant type among strains. Phylogenetic analysis showed that D-galactose gene galM was acquired multiples times within the family Vibrionaceae and was transferred between distantly related species. The ability to utilize D-gluconate was universal within the species. Deletion of eda (VP0065), which encodes aldolase, a key enzyme in the Entner-Doudoroff (ED) pathway, reached a similar biomass to wild type when grown on D-gluconate as a sole carbon source. Two additional eda genes were identified, VPA1708 (eda2) associated with a D-glucuronate cluster and VPA0083 (eda3) that clustered with an oligogalacturonide (OGA) metabolism cluster. EDA2 and EDA3 were variably distributed among the species. A metabolic island was identified that contained citrate fermentation, L-rhamnose and OGA metabolism clusters as well as a CRISPR-Cas system. Phylogenetic analysis showed that CitF and RhaA had a limited distribution among V. parahaemolyticus, and RhaA was acquired at least three times. Within V. parahaemolyticus, two different regions contained the gene for L-arabinose catabolism and most strains had the ability to catabolism this sugar. CONCLUSION: Our data suggest that horizontal transfer of metabolic systems among Vibrionaceae is an important source of metabolic diversity. This work identified four EDA homologues suggesting that the ED pathway plays a significant role in metabolism. We describe previously uncharacterized metabolism islands that were hotspots for the gain and loss of functional modules likely mediated by transposons.