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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0291

PubMed

29453395, Sci Rep. 2018 Feb 16;8(1):3177. doi: 10.1038/s41598-018-21534-3.

Characterization method

electrophoretic mobility shift assay,qPCR

Genomic accession number

CP014225.1

Nucelotide position range

2260803-2272654

Substrate

lactose

Loci

ompL- yihO- yihP- yihQ- yihR- yihS- yihT- yihU- yihV- yihW+

Species

Escherichia coli/562

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

ompL AW869_11135 AMC96743.1 0 - 693 (-) CP014225.1:2260803-2261496 -
- AW869_11140 AMC96744.1 760 - 2164 (-) CP014225.1:2261563-2262967 -
- AW869_11145 AMC96745.1 2206 - 3592 (-) CP014225.1:2263009-2264395 -
- AW869_11150 AMC96746.1 3637 - 5674 (-) CP014225.1:2264440-2266477 -
- AW869_11155 AMC96747.1 5872 - 6775 (-) CP014225.1:2266675-2267578 -
- AW869_11160 AMC96748.1 6912 - 8154 (-) CP014225.1:2267715-2268957 -
- AW869_11165 AMC96749.1 8170 - 9049 (-) CP014225.1:2268973-2269852 -
- AW869_11170 AMC96750.1 9072 - 9969 (-) CP014225.1:2269875-2270772 -
- AW869_11175 AMC96751.1 10136 - 11033 (+) CP014225.1:2270939-2271836 -
- AW869_11180 AMC96752.1 11066 - 11852 (+) CP014225.1:2271869-2272655 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

ompL 1 - 693 (-) TC: gnl|TC-DB|P76773|1.B.35.2.2 Yes
- 761 - 2164 (-) TC: gnl|TC-DB|P32137|2.A.2.3.9 Yes
- 2207 - 3592 (-) TC: gnl|TC-DB|P32137|2.A.2.3.9 Yes
- 3638 - 5674 (-) CAZyme: GH31 Yes
- 5873 - 6775 (-) CDS No
- 6913 - 8154 (-) CDS No
- 8171 - 9049 (-) CDS No
- 9073 - 9969 (-) CDS No
- 10137 - 11033 (+) STP: STP|PfkB No
- 11067 - 11852 (+) TF: DBD-Pfam|HTH_DeoR,DBD-SUPERFAMILY|0043758 No

PUL ID

PUL0291

PubMed

29453395, Sci Rep. 2018 Feb 16;8(1):3177. doi: 10.1038/s41598-018-21534-3.

Title

The genes of the sulphoquinovose catabolism in Escherichia coli are also associated with a previously unknown pathway of lactose degradation.

Author

Kaznadzey A, Shelyakin P, Belousova E, Eremina A, Shvyreva U, Bykova D, Emelianenko V, Korosteleva A, Tutukina M, Gelfand MS

Abstract

Comparative genomics analysis of conserved gene cassettes demonstrated resemblance between a recently described cassette of genes involved in sulphoquinovose degradation in Escherichia coli K-12 MG1655 and a Bacilli cassette linked with lactose degradation. Six genes from both cassettes had similar functions related to carbohydrate metabolism, namely, hydrolase, aldolase, kinase, isomerase, transporter, and transcription factor. The Escherichia coli sulphoglycolysis cassette was thus predicted to be associated with lactose degradation. This prediction was confirmed experimentally: expression of genes coding for aldolase (yihT), isomerase (yihS), and kinase (yihV) was dramatically increased during growth on lactose. These genes were previously shown to be activated during growth on sulphoquinovose, so our observation may indicate multi-functional capabilities of the respective proteins. Transcription starts for yihT, yihV and yihW were mapped in silico, in vitro and in vivo. Out of three promoters for yihT, one was active only during growth on lactose. We further showed that switches in yihT transcription are controlled by YihW, a DeoR-family transcription factor in the Escherichia coli cassette. YihW acted as a carbon source-dependent dual regulator involved in sustaining the baseline growth in the absence of lac-operon, with function either complementary, or opposite to a global regulator of carbohydrate metabolism, cAMP-CRP.