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

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

Author information

1
A. A. Kharkevich Institute for Information Transmission Problems, RAS, Bolshoy Karetny per. 19, Moscow, 127051, Russia.
2
N. I. Vavilov Institute of General Genetics, RAS, ul. Gubkina 3, Moscow, 119991, Russia.
3
M. V. Lomonosov Moscow State University, Vorobievy Gory 1-73, Moscow, 119991, Russia.
4
The University of Edinburgh, Alexander Crum Brown Rd, Edinburgh, Scotland, EH9 3FF, UK.
5
Institute of Cell Biophysics, RAS, Institutskaya 3, Pushchino, 142290, Russia.
6
Novosibirsk State University, ul. Pirogova 2, Novosibirsk, 630090, Russia.
7
Institute of Cell Biophysics, RAS, Institutskaya 3, Pushchino, 142290, Russia. m.tutukina@skoltech.ru.
8
Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, 143028, Russia. m.tutukina@skoltech.ru.
9
Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, 143028, Russia.
10
Faculty of Computer Science, Higher School of Economics, Kochnovsky pr. 3, Moscow, 125319, Russia.

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.

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