Complete genome sequence of the thermophilic Acidobacteria, Pyrinomonas methylaliphatogenes type strain K22 T

The P. methylaliphatogenes K22
^T
genome assembly has a size of 3.79 Mb with a %G?+?C content of 59.3, both of which
are comparable with the genomes of other sequenced Acidobacteria 24]. It possesses complete citric acid and pentose phosphate cycles. A complete electron
transport pathway with an F-type ATPase, NADH dehydrogenase and cytochrome C complex,
and the presence of genes encoding superoxide dismutase (PYK22_00483-00484) and catalase
(PYK22_02691) are consistent with the observed aerobic phenotype. Genes encoding outer
membrane secretion (for example, a type II secretion system, PYK22_02507-02511) and
protein assembly (Bam complex, PYK22_02371 01777) are present, confirming the observed
Gram-negative cell wall structure 4]. Interestingly, P. methylaliphatogenes K22
^T
possesses a near-complete complement of flagella encoding-genes (possibly missing
the proximal rod flgF gene) despite having no observed motility. Key genes for all autotrophic carbon fixation
pathways were absent. However, it was previously noted that while P. methylaliphatogenes K22
^T
was unable to fix carbon, additional CO
₂
to the headspace while growing heterotrophically improved growth 4]. The presence of phosphoenolpyruvate carboxylase and isocitrate dehydrogenase confirmed
the ability of P. methylaliphatogenes K22
^T
to supplement carbon anapleurotically. No genes encoding the ability to fix dinitrogen
gas were found, again confirming previous phenotypic observations. Interestingly,
the genome contains a gene cluster encoding a group 5-type [NiFe] hydrogenase (PYK22_03058-03084)
similar to that found in Mycobacterium smegmatis 25]; this may confer an ability to oxidize tropospheric concentrations of hydrogen for
cell maintenance.

Previous phenotypic characterization of P. methylaliphatogenes K22
^T
indicated that it possessed a heterotrophic phenotype with the ability to grow on
a range of simple carbohydrates. The P. methylaliphatogenes K22
^T
genome encodes for a large number of beta-glucosidase and exoglucanase-acting glycosyl
hydrolases, reflecting its ability to grow on primarily simple oligosaccharides such
as cellobiose, sucrose, and maltose. A single C6 endoglucanase-acting glycosyl hydrolase
(PYK22_03181) was identified in the genome despite having no reported growth on complex
or crystalline cellulose as energy sources 4]. Two endo-1,4-beta-xylanases genes confer an ability to grow on xylan and xanthan
gum.

Transporters encoded in the P. methylaliphatogenes K22
^T
genome mainly belong to the ABC-type transporter superfamily and the major facilitator
superfamily. This is consistent with previous study of acidobacterial genomes, which
suggest these transporters types were adapted for low-nutrient conditions 26]. ABC transporters in P. methylaliphatogenes K22
^T
appear to be involved in the transport of carbohydrates (and derivatives) such as
ribose, D-xylose, lipopolysaccharide (rfbAB, e.g. PYK22_01076-77, PYK22_01839-40, PYK22_02287-88), and lipo-oligosaccharide (nodJI, PYK22_00778 and PYK22_00785). These reflect the carbohydrate and polypeptide utilizing
phenotype of the bacterium. Pyrinomonas methylaliphatogenes K22
^T
also possesses putative ABC transporters targeting amino acid cysteine, oligopeptides
(oppABCDF, e.g. the PYK22_01277-281 cluster), and lipoproteins (lolCDE, PYK22_02373-4). Nitrogen assimilation is facilitated via an ammonia permease (PYK22_02853),
the importation of oligopeptides by an oppABCDF ABC transporter system (similar to the system in Salmonella typhimurium 27]), and major facilitator superfamily nitrate/nitrite permeases (PYK22_00018 PYK22_00946).
Additionally, the P. methylaliphatogenes K22
^T
genome contained a cluster of genes tonB-exbB-exbD-exbD (PYK22_00991-94) associated with siderophore transport in some other acidobacterial
species 26]. However, genes involved in siderophore synthesis, polyketide synthase, and nonribosomal
peptide synthetase were not found, suggesting that it scavenges siderophores produced
by other bacteria.

Based upon 16S rRNA gene sequence similarity, the most closely related and cultivated
strain to P. methylaliphatogenes K22
^T
is C. thermophilum B
^T28] (Fig. 1). The sequence similarity (~86 %) indicates that the two strains may belong to the
same subdivision based on taxonomic sequence identity thresholds calculated for other
prokaryotic taxa 29]. This phylogenetic dissimilarity between the two strains is also reflected in a comparison
of the genomic content and the different metabolic modes of existence (chemoheterotrophic
P. methylaliphatogenes K22
^T
vs. photoheterotrophic C. thermophilum B
^T
) of the two strains. For example, the C. thermophilum B
^T
genome encodes for genes for chlorosomes, bacteriochlorophyll pigments a and c and a pigment protein complex for phototrophic growth, whereas no genes encoding
for phototrophy were found in K22
^T
. The C. thermophilum B
^T
genome also contained significantly more COGs (15 vs 50) related to signal transduction
kinases (COG0515 and COG0642) than were encoded in P. methylaliphatogenes K22
^T
. Conversely, P. methylaliphatogenes K22
^T
contained more genes related to amino acid utilization, such as amino acid transporters
(COG0531) and amidohydrolases (COG1228), reflecting its ability to grow using proteinaceous
media as the carbon and energy source. While both species possess carbohydrate-related
metabolisms, the P. methylaliphatogenes K22
^T
genome encodes a much larger number of glycosyltransferases (COG0438 and COG0463)
and beta-glucosidase-related glycosidases (COG1472) than that of C. thermophilum B
^T
.