Genomic and phenotypic comparison of polyhydroxyalkanoates producing strains of genus Caldimonas/ Schlegelella

Abstract

Polyhydroxyalkanoates (PHAs) have emerged as an environmentally friendly alternative to conventional polyesters. In this study, we present a comprehensive analysis of the genomic and phenotypic characteristics of three non-model thermophilic bacteria known for their ability to produce PHAs: Schlegelella aquatica LMG 23380^T, Caldimonas thermodepolymerans DSM 15264, and C. thermodepolymerans LMG 21645 and the results were compared with the type strain C. thermodepolymerans DSM 15344^T. We have assembled the first complete genomes of these three bacteria and performed the structural and functional annotation. This analysis has provided valuable insights into the biosynthesis of PHAs and has allowed us to propose a comprehensive scheme of carbohydrate metabolism in the studied bacteria. Through phylogenomic analysis, we have confirmed the synonymity between Caldimonas and Schlegelella genera, and further demonstrated that S. aquatica and S. koreensis, currently classified as orphan species, belong to the Caldimonas genus.

Keywords: Caldimonas; DSM 15264; DSM 15344T; LMG 21645; LMG 23380T; Next-Generation Industrial Biotechnology; PHAs; Schlegelella; de novo assembly.

Graphical abstract

Fig. 1

Relative abundances of genes in particular clusters of orthologous groups (COGs) categories in the Schlegelella aquatica (Sa) LMG 23380^T, Caldimonas thermodepolymerans (Ct) DSM 15264 and LMG 21645, and reference type strain DSM 15344^T.

Fig. 2

Phylogenomic tree representing placement of Schlegelella aquatica LMG 23880^T and Caldimonas thermodepolymerans DSM 15264 and LMG 21645 (highlighted in red). Bacteria placed in the Caldimonas genus are highlighted with the rectangle. The tree was constructed using the Phylophlan internal database of circa 400 genes conserved across bacterial domain. The values represent the bootstrap support based on 100 replicates.

Fig. 3

Genes involved in carbohydrate metabolism forming xyl and gts operons across Schlegelella aquatica (Sa) LMG 23880^T, Caldimonas thermodepolymerans (Ct) DSM 15264 and LMG 21645, and the reference type strain DSM 15344^T.

Fig. 4

Schematic illustration of proposed carbohydrate metabolism in studied Caldimonas/Schlegelella strains. Xylose isomerase pathway (formed by XylA xylose isomerase and XylB xylulokinase) and the pentose phosphate pathway are shown using brown arrows, the Embden-Meyerhof-Parnas pathway is shown with orange arrows, and the Entner-Doudoroff pathway with magenta arrows. Abbreviations (enzymes): Eda, 2-keto-3-deoxy-6-phosphogluconate aldolase; Edd, 6-phosphogluconate dehydratase; Eno, phosphopyruvate hydratase; Fba, fructose-1,6-biphosphate aldolase; Fbp, fructose-1,6-biphosphatase; Gap, glyceraldehyde-3-phosphate dehydrogenase; Gcd, glucose dehydrogenase; Gnd, 6-phosphogluconate dehydrogenase; Pdh, pyruvate dehydrogenase; Pgi, glucose-6-phosphate isomerase; Pgk, phosphoglycerate kinase; Pgl, 6-phosphogluconolactonase; Pgm, phosphoglycerate mutase; PhaA, acetyl-CoA acetyltransferase (3-ketothiolase); PhaB, acetoacetyl-CoA reductase; PhaC, poly(3-hydroxyalkanoate) polymerase; Pyk, pyruvate kinase; Rpe, ribulose-5-phosphate 3-epimerase; RpiA, ribose-5-phosphate isomerase; Tal, transaldolase; Tkt, transketolase; Tpi, triosephosphate isomerase; Zwf glucose-6-phosphate dehydrogenase. Abbreviations (metabolites): AA-CoA, acetoacetyl coenzyme A; Acetyl-CoA, acetyl coenzyme A; DHPA, dihydroxyacetone phosphate; E4P, erythrose 4-phosphate; FBP, fructose 1,6-biphosphate; F6P, fructose 6-phosphate; GLL, glucono-δ-lactone; GLN, gluconate; G3P glyceraldehyde 3-phosphate; G6P, glucose 6-phosphate; 3HB-CoA, 3-hydroxybutyryl coenzyme A; KDPG, 2-keto-3-deoxy-6-phosphogluconate; 2KG, 2-ketogluconate; 2KG-6 P, 2-ketogluconate 6-phosphate; NADH, reduced nicotinamide adenine dinucleotide; NADPH, reduced nicotinamide adenine dinucleotide phosphate; PEP, phosphoenolpyruvate; 3PG, 3-phosphoglycerate; 6PG, 6-phosphogluconate; PHB, poly-3-hydroxybutyrate; R5P, ribose 5-phosphate; Ru5P, ribulose 5-phosphate; S7P, seduheptulose 7-phosphate; XLN, xylonate; X5P, xylulose 5-phosphate. GtsABCD and XylFGH stand for mannose/glucose and xylose ABC transporter, respectively. Note that xylose isomerase pathway and b-glucosidase are not present in S. aquatica.