Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus

Abstract

We present herein the first complete genome sequence of a thermophilic Bacillus-related species, Geobacillus kaustophilus HTA426, which is composed of a 3.54 Mb chromosome and a 47.9 kb plasmid, along with a comparative analysis with five other mesophilic bacillar genomes. Upon orthologous grouping of the six bacillar sequenced genomes, it was found that 1257 common orthologous groups composed of 1308 genes (37%) are shared by all the bacilli, whereas 839 genes (24%) in the G.kaustophilus genome were found to be unique to that species. We were able to find the first prokaryotic sperm protamine P1 homolog, polyamine synthase, polyamine ABC transporter and RNA methylase in the 839 unique genes; these may contribute to thermophily by stabilizing the nucleic acids. Contrasting results were obtained from the principal component analysis (PCA) of the amino acid composition and synonymous codon usage for highlighting the thermophilic signature of the G.kaustophilus genome. Only in the PCA of the amino acid composition were the Bacillus-related species located near, but were distinguishable from, the borderline distinguishing thermophiles from mesophiles on the second principal axis. Further analysis revealed some asymmetric amino acid substitutions between the thermophiles and the mesophiles, which are possibly associated with the thermoadaptation of the organism.

Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir

“…The genome of G. thermodenitrificans NG80-2 is composed of a 3,550,319-bp chromosome and a 57,693-bp plasmid, designated pLW1071, with mean G ϩ C contents of 49.0% and 39.8%, respectively (Table 1). Both the size and structure of the NG80-2 genome are similar to that of G. kaustophilus HTA426, the only other sequenced Geobacillus genome, which contains a 3,544,776-bp chromosome and a 47,890-bp plasmid (4). There are 3,499 predicted ORFs, 11 rRNA operons and 87 tRNA genes for all 20 aa, covering 86% of the genome (Table 1 and Fig.…”

“…Polyamines such as norspermine and norspermidine are commonly found in hyperthermophilic bacteria and are necessary for the hyperthermophilic phenotype of those bacteria (27). Spermine is the major type of polyamine in Geobacillus species, and has been implicated in thermophily in G. kaustophilus based on the presence of the ''unique'' genes encoding spermine/spermidine synthase and polyamine ABC transporters (4). Those unique genes were also found in NG80-2 (GT1637, GT0623-GT0626).…”

“…Those unique genes were also found in NG80-2 (GT1637, GT0623-GT0626). Takami et al (4) reported possible association of asymmetric amino acid substitutions (Arg, Ala, Gly, Val, and Pro are more frequently used in HTA426 than in mesophilic Bacillus strains) with thermoadaptation of G. kaustophilus HTA426. Similar amino acid substitution pattern was also observed in NG80-2 when compared with 7 sequenced Bacillus strains including 4 used to compare with HTA426 (SI Table 8), supporting the previous suggestion.…”

IcmF Is a Fusion between the Radical B12 Enzyme Isobutyryl-CoA Mutase and Its G-protein Chaperone

“…The genomic DNA of Geobacillus kaustophilus and Burkholderia xenovorans (formerly known as Burkholderia fungorum) were generous gifts from Hideto Takami (Japan Agency for Marine-Earth Science and Technology, Kanagawa, Japan) (18). The genomic DNA clone KNL023_G20 in the pTS1 plasmid containing the Nocardia farcinica icmF gene was obtained from Jun Ishikawa (National Institute of Infectious Diseases, Tokyo, Japan) (19).…”

Studies of the Activation Steps Concurrent to Ligand Binding in δOR and κOR Opioid Receptors Based on Molecular Dynamics Simulations

“…HutP also exists in five other Bacillus species, including B. anthracis [23], B. cereus [24], B. halodurans [25], B. thuringiensis [26] and Geobacillus kautophilus [27] with 60% sequence identity. Sequence comparisons with the other Bacillus HutPs revealed that the C-terminal amino acid residues are more conserved than the N-terminal residues.…”