Proteome of HU-Lacking E. coli Studied by Means of 2D Gel Electrophoresis


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Abstract

Histone-like protein HU is a dimeric nucleoid-associated protein (NAP). HU is the most conserved NAP. It binds nonspecifically to duplex DNA with a preference for targeting nicked and bent DNA. HU limits the architecture of the bacterial nucleoid and its deletion is lethal for Bacillus subtilis and Mycoplasma genitalium which do not contain other NAPs. E. coli lacking HU is viable but has numerous growth defects. The effects of the HU protein on gene expression is known from microarray analysis and HU regulons were identified. In HU-deficient E. coli, absence of this DNA architectural protein causes a disorder in gene regulation; on the other hand, E. coli growth under standard conditions is almost unaltered in the absence of HU. To understand how the bacterium confronts the chromosomal disorder, we performed proteome analysis to compare protein abundances in cells containing the HU protein or not. Comparison of the proteomic profile of wild-type and HU-deficient E. coli shows how the altered gene expression influences the protein content. We show that proteome profile changes are very similar to the gene expression profile changes in HU-deficient E. coli. Several exceptions show that proteome studies are very important.

About the authors

D. E. Kamashev

Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences; Sechenov First Moscow State Medical University

Author for correspondence.
Email: dkamashev@gmail.com
Russian Federation, Moscow, 117997; Moscow, 119146

T. V. Rakitina

Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences; National Research Center Kurchatov Institute

Email: dkamashev@gmail.com
Russian Federation, Moscow, 117997; Moscow, 123098

D. S. Matyushkina

Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency

Email: dkamashev@gmail.com
Russian Federation, Moscow, 119435

D. V. Evsyutina

Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency

Email: dkamashev@gmail.com
Russian Federation, Moscow, 119435

A. A. Vanyushkina

Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency

Email: dkamashev@gmail.com
Russian Federation, Moscow, 119435

Yu. K. Agapova

National Research Center Kurchatov Institute

Email: dkamashev@gmail.com
Russian Federation, Moscow, 123098

V. E. Anisimova

Sechenov First Moscow State Medical University

Email: dkamashev@gmail.com
Russian Federation, Moscow, 119146

A. L. Drobyshev

Sechenov First Moscow State Medical University

Email: dkamashev@gmail.com
Russian Federation, Moscow, 119146

I. O. Butenko

Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency

Email: dkamashev@gmail.com
Russian Federation, Moscow, 119435

O. V. Pobeguts

Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency

Email: dkamashev@gmail.com
Russian Federation, Moscow, 119435

G. Y. Fisunov

Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency

Email: dkamashev@gmail.com
Russian Federation, Moscow, 119435

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