Phylogenetic analysis of phn transporters of Achromobacter insolitus LCu2

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Abstract

Phosphonates are alternative phosphorus sources for bacteria. The genome of Achromobacter insolitus strain LCu2 contains three predicted phn clusters of ABC-type phosphonate transporters into the cell. To understand the functional, evolutionary, and ecological role of the phn clusters, phylogenetic analysis of substrate-binding PhnD proteins from strain LCu2 with their homologs in other Achromobacter species and in closely related genera of the family Alcaligenaceae was carried out. The PhnD transporters formed three separate clusters, which indicated the differences in their structural composition. PhnD1 and PhnD2 were present in the genomes of all Achromobacter species and grouped separately from those of other members of the family Alcaligenaceae, which indicated vertical inheritance of the phnD1 and phnD2 genes and their involvement in the life-supporting processes. PhnD3 was found in the genomes of seven Achromobacter species. The phnD3 gene was probably acquired via horizontal transfer or duplication and is induced during adaptation to changing environmental conditions. Maintenance of three structurally different clusters of the phn transporters is probably ecologically advantageous to A. insolitus LCu2, providing for phosphorus retrieval from synthetic and natural organophosphonates as well as other sources.

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About the authors

Ye. V. Kryuchkova

Saratov Scientific Centre, Russian Academy of Sciences

Author for correspondence.
Email: kryu-lena@yandex.ru

Institute of Biochemistry and Physiology of Plants and Microorganisms

Russian Federation, Saratov

G. L. Burygin

Saratov Scientific Centre, Russian Academy of Sciences; Saratov State University; Saratov State University of Genetics, Biotechnology and Engineering Named after N.I. Vavilov

Email: kryu-lena@yandex.ru

Institute of Biochemistry and Physiology of Plants and Microorganisms

Russian Federation, Saratov; Saratov; Saratov

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2. Fig. 1. Phylogenetic analysis of amino acid sequences of PhnD transporters of bacteria of the genus Achromobacter and some representatives of the family Alcaligenaceae. PhnD sequences of the strain A. insolitus LCu2 are indicated by stars; curly brackets correspond to the boundaries of clusters formed by the proteins PhnD1, PhnD2, PhnD3; structural organizations of ABC cassettes of phn transporters in the genomes of Achromobacter, including A. insolitus LCu2, are shown on the right; phnD is marked in green.

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3. Fig. S1. Multiple alignment of PhnD1 from different bacteria relative to the reference protein from E. coli (3P7I) (3P7I) E. coli UTI89; (Q1R3F7) E. coli UTI89; (WP_207408615.1) Bordetella petrii; (WP_276287551.1) Cupriavidus basilensis; (QQV13938.1) Achromobacter xylosoxidans; (QEK91627) Achromobacter insolitus LCu2; (WP_062683200.1) Achromobacter denitrificans. “*” ‒ identical amino acids; “:” ‒ amino acids of the same class; “.” ‒ part of amino acids of the same class; conserved motifs are marked in peach; amino acid residues responsible for the formation of hydrogen bonds between the substrate (2-aminoethylphosphonate) and the protein from E. coli (3P7I) are marked with asterisks (Alicea et al., 2011). Alicea I., Marvin J. S., Miklos A. E., Ellington A. D., Looger L. L., Schreiter E. R. Structure of the Escherichia coli phosphonate binding protein PhnD and rationally optimized phosphonate biosensors // J. Mol. Biol. 2011. V. 414. P. 356‒369.

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