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Biosynthesis of storage compounds by Rhodococcus jostii RHA1 and global identification of genes involved in their metabolism.

Hernández MA, Mohn WW, Martínez E, Rost E, Alvarez AF, Alvarez HM - BMC Genomics (2008)

Bottom Line: Members of the genus Rhodococcus are frequently found in soil and other natural environments and are highly resistant to stresses common in those environments.Where possible, key amino acid residues in the above proteins (generally in active sites, effectors binding sites or substrate binding sites) were identified in order to support gene identification.An extensive capacity to synthesize and metabolize storage compounds appears to contribute versatility to RHA1 in its responses to environmental stresses.

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Affiliation: Centro Regional de Investigación y Desarrollo Científico Tecnológico, Facultad de Ciencias Naturales, Universidad Nacional de Patagonia San Juan Bosco, Km 4-Ciudad Universitaria, 9000 Comodoro Rivadavia, Chubut, Argentina. mahernandez@unpata.edu.ar

ABSTRACT

Background: Members of the genus Rhodococcus are frequently found in soil and other natural environments and are highly resistant to stresses common in those environments. The accumulation of storage compounds permits cells to survive and metabolically adapt during fluctuating environmental conditions. The purpose of this study was to perform a genome-wide bioinformatic analysis of key genes encoding metabolism of diverse storage compounds by Rhodococcus jostii RHA1 and to examine its ability to synthesize and accumulate triacylglycerols (TAG), wax esters, polyhydroxyalkanoates (PHA), glycogen and polyphosphate (PolyP).

Results: We identified in the RHA1 genome: 14 genes encoding putative wax ester synthase/acyl-CoA:diacylglycerol acyltransferase enzymes (WS/DGATs) likely involved in TAG and wax esters biosynthesis; a total of 54 genes coding for putative lipase/esterase enzymes possibly involved in TAG and wax ester degradation; 3 sets of genes encoding PHA synthases and PHA depolymerases; 6 genes encoding key enzymes for glycogen metabolism, one gene coding for a putative polyphosphate kinase and 3 putative exopolyphosphatase genes. Where possible, key amino acid residues in the above proteins (generally in active sites, effectors binding sites or substrate binding sites) were identified in order to support gene identification. RHA1 cells grown under N-limiting conditions, accumulated TAG as the main storage compounds plus wax esters, PHA (with 3-hydroxybutyrate and 3-hydroxyvalerate monomers), glycogen and PolyP. Rhodococcus members were previously known to accumulate TAG, wax esters, PHAs and polyP, but this is the first report of glycogen accumulation in this genus.

Conclusion: RHA1 possess key genes to accumulate diverse storage compounds. Under nitrogen-limiting conditions lipids are the principal storage compounds. An extensive capacity to synthesize and metabolize storage compounds appears to contribute versatility to RHA1 in its responses to environmental stresses.

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Alignment of PHA-synthase genes of R. jostii RHA1 and R. ruber. Amino acid residues that are conserved in all the known PHA synthases are indicated below the sequences (*). Conserved residues probably involved in catalysis are shown (●). Putative lipase box is indicated with a rectangle.
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Figure 1: Alignment of PHA-synthase genes of R. jostii RHA1 and R. ruber. Amino acid residues that are conserved in all the known PHA synthases are indicated below the sequences (*). Conserved residues probably involved in catalysis are shown (●). Putative lipase box is indicated with a rectangle.

Mentions: The three PHA synthases encoded in the genome of RHA1 have 37% to 39% sequence identity to R. ruber PHA synthase (Table 1). Multiple alignments of the primary structures of 59 PHA synthases from 45 different bacteria, including R. ruber, showed the presence of eight highly conserved amino acid residues, which are important for the enzyme function [15]. These eight highly conserved amino acid residues are also present in the three PHA synthases of RHA1 (Fig. 1). All PHA synthases additionally contain a putative lipase box, G-X-(S/C)-X-G, in which the essential active-site serine of the lipases is replaced with a cysteine in the PHA-synthases [43,44]. The PHA synthases encoded by phaC1 and phaC2 in RHA1 contain the lipase box G-X-C-X-G, while that encoded by phaC3 has a modified lipase box, where the first glycine of the motif is replaced by alanine. Three amino acid residues are proposed to be required for catalytic activity of PHA synthase, presumably forming a catalytic triad, which is found in enzymes belonging to the superfamily of α/β-hydrolases [15,43]. The conserved residues C-294, D-449 and H-477 of R. ruber PHA synthase were proposed to be involved in covalent catalysis during PHA biosynthesis [15]. The three PHA synthases of strain RHA1 all contain the same catalytic triad.


Biosynthesis of storage compounds by Rhodococcus jostii RHA1 and global identification of genes involved in their metabolism.

Hernández MA, Mohn WW, Martínez E, Rost E, Alvarez AF, Alvarez HM - BMC Genomics (2008)

Alignment of PHA-synthase genes of R. jostii RHA1 and R. ruber. Amino acid residues that are conserved in all the known PHA synthases are indicated below the sequences (*). Conserved residues probably involved in catalysis are shown (●). Putative lipase box is indicated with a rectangle.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2667194&req=5

Figure 1: Alignment of PHA-synthase genes of R. jostii RHA1 and R. ruber. Amino acid residues that are conserved in all the known PHA synthases are indicated below the sequences (*). Conserved residues probably involved in catalysis are shown (●). Putative lipase box is indicated with a rectangle.
Mentions: The three PHA synthases encoded in the genome of RHA1 have 37% to 39% sequence identity to R. ruber PHA synthase (Table 1). Multiple alignments of the primary structures of 59 PHA synthases from 45 different bacteria, including R. ruber, showed the presence of eight highly conserved amino acid residues, which are important for the enzyme function [15]. These eight highly conserved amino acid residues are also present in the three PHA synthases of RHA1 (Fig. 1). All PHA synthases additionally contain a putative lipase box, G-X-(S/C)-X-G, in which the essential active-site serine of the lipases is replaced with a cysteine in the PHA-synthases [43,44]. The PHA synthases encoded by phaC1 and phaC2 in RHA1 contain the lipase box G-X-C-X-G, while that encoded by phaC3 has a modified lipase box, where the first glycine of the motif is replaced by alanine. Three amino acid residues are proposed to be required for catalytic activity of PHA synthase, presumably forming a catalytic triad, which is found in enzymes belonging to the superfamily of α/β-hydrolases [15,43]. The conserved residues C-294, D-449 and H-477 of R. ruber PHA synthase were proposed to be involved in covalent catalysis during PHA biosynthesis [15]. The three PHA synthases of strain RHA1 all contain the same catalytic triad.

Bottom Line: Members of the genus Rhodococcus are frequently found in soil and other natural environments and are highly resistant to stresses common in those environments.Where possible, key amino acid residues in the above proteins (generally in active sites, effectors binding sites or substrate binding sites) were identified in order to support gene identification.An extensive capacity to synthesize and metabolize storage compounds appears to contribute versatility to RHA1 in its responses to environmental stresses.

View Article: PubMed Central - HTML - PubMed

Affiliation: Centro Regional de Investigación y Desarrollo Científico Tecnológico, Facultad de Ciencias Naturales, Universidad Nacional de Patagonia San Juan Bosco, Km 4-Ciudad Universitaria, 9000 Comodoro Rivadavia, Chubut, Argentina. mahernandez@unpata.edu.ar

ABSTRACT

Background: Members of the genus Rhodococcus are frequently found in soil and other natural environments and are highly resistant to stresses common in those environments. The accumulation of storage compounds permits cells to survive and metabolically adapt during fluctuating environmental conditions. The purpose of this study was to perform a genome-wide bioinformatic analysis of key genes encoding metabolism of diverse storage compounds by Rhodococcus jostii RHA1 and to examine its ability to synthesize and accumulate triacylglycerols (TAG), wax esters, polyhydroxyalkanoates (PHA), glycogen and polyphosphate (PolyP).

Results: We identified in the RHA1 genome: 14 genes encoding putative wax ester synthase/acyl-CoA:diacylglycerol acyltransferase enzymes (WS/DGATs) likely involved in TAG and wax esters biosynthesis; a total of 54 genes coding for putative lipase/esterase enzymes possibly involved in TAG and wax ester degradation; 3 sets of genes encoding PHA synthases and PHA depolymerases; 6 genes encoding key enzymes for glycogen metabolism, one gene coding for a putative polyphosphate kinase and 3 putative exopolyphosphatase genes. Where possible, key amino acid residues in the above proteins (generally in active sites, effectors binding sites or substrate binding sites) were identified in order to support gene identification. RHA1 cells grown under N-limiting conditions, accumulated TAG as the main storage compounds plus wax esters, PHA (with 3-hydroxybutyrate and 3-hydroxyvalerate monomers), glycogen and PolyP. Rhodococcus members were previously known to accumulate TAG, wax esters, PHAs and polyP, but this is the first report of glycogen accumulation in this genus.

Conclusion: RHA1 possess key genes to accumulate diverse storage compounds. Under nitrogen-limiting conditions lipids are the principal storage compounds. An extensive capacity to synthesize and metabolize storage compounds appears to contribute versatility to RHA1 in its responses to environmental stresses.

Show MeSH
Related in: MedlinePlus