Genome analysis and reconstruction of metabolic pathways of amino acids and betaine degradation in the haloalkaliphilic bacteria Anoxynatronum sibiricum

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Abstract

The genome of the haloalkaliphilic anaerobic microorganism Anoxynatronum sibiricum Z-7981T isolated earlier from the Nizhneye Beloye soda lake (Republic of Buryatia, Russia) was analyzed. The ability of the organism to use betaine as an electron acceptor in the Stickland reaction was revealed. The introduction of betaine into the medium not only stimulated growth on amino acids used by A. sibiricum individually, but also allowed identifying additional amino acids, growth on which was not possible without the acceptor. Based on the genomic characteristics and experimental growth data, metabolic schemes of amino acid degradation in the presence and absence of betaine were proposed. Schemes for threonine, glutamate and lysine when used together with betaine were compiled for the first time. For all amino acids used, the qualitative and quantitative composition of the metabolic products was determined and the stoichiometric substrate/product ratios were obtained. Balance equations for the identified variants of the Stickland reaction, including those previously not described in the literature, have been compiled.

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About the authors

E. N. Detkova

FRC “Fundamentals of Biotechnology” of the RAS

Email: kevbrin@inmi.ru

S. N. Winogradsky Institute of Microbiology

Russian Federation, Moscow, 119071

Yu. V. Boltyanskaya

FRC “Fundamentals of Biotechnology” of the RAS

Email: kevbrin@inmi.ru

S. N. Winogradsky Institute of Microbiology

Russian Federation, Moscow, 119071

N. V. Pimenov

FRC “Fundamentals of Biotechnology” of the RAS

Email: kevbrin@inmi.ru

S. N. Winogradsky Institute of Microbiology

Russian Federation, Moscow, 119071

A. V. Mardanov

FRC “Fundamentals of Biotechnology” of the RAS

Email: kevbrin@inmi.ru

K. G. Skryabin Institute of Bioengineering

Russian Federation, Moscow, 119071

V. V. Kevbrin

FRC “Fundamentals of Biotechnology” of the RAS

Author for correspondence.
Email: kevbrin@inmi.ru

S. N. Winogradsky Institute of Microbiology

Russian Federation, Moscow, 119071

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Supplementary files

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2. Fig. 1. Proposed metabolic scheme of threonine and serine degradation in A. sibiricum Z-7981T: a – without betaine; b – with betaine. BRC – betaine reductase complex. Substrates and products are shown in bold. Designations of genes and corresponding enzymes are given in Table S2 (supplementary materials).

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3. Fig. 2. Proposed metabolic scheme of glutamate degradation in A. sibiricum Z-7981T: a – without betaine; b – with betaine. Substrates and products are shown in bold. Designations of genes and corresponding enzymes are given in Table S2 (supplementary materials).

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4. Fig. 3. Proposed metabolic scheme of aspartate degradation by A. sibiricum Z-7981T. Substrates and products are shown in bold. Gene and enzyme designations are given in Table S2 (Supplementary Material).

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5. Fig. 4. Proposed metabolic scheme of lysine degradation in A. sibiricum Z-7981T: a – without betaine; b – with betaine. Substrates and products are shown in bold. Designations of genes and corresponding enzymes are given in Table S2 (supplementary materials).

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6. Fig. 5. Urea cycle during arginine degradation in A. sibiricum Z-7981T. Substrates and products are shown in bold. Gene and enzyme designations are given in Table S2 (Supplementary Material).

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7. Fig. 6. Proposed metabolic scheme of alanine, leucine, isoleucine, valine, phenylalanine, and methionine degradation in the presence of betaine for A. sibiricum Z-7981T. Substrates and products are shown in bold. Gene and enzyme designations are given in Table S2 (Supplementary Material).

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8. Additional materials
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