Comparative genomics of Thermus thermophilus: Plasticity of the megaplasmid and its contribution to a thermophilic lifestyle

Sequence analysis and characterizations of two novel plasmids isolated from Thermus sp. 4C

Two novel plasmids, named pS4C and pL4C, were isolated from the thermophilic bacterium Thermus sp. 4C. The pS4C with a length of 5015bp and 58.25% of G+C content, contains 9 putative open reading frames (ORFs). The larger plasmid, pL4C, consisting of 21,248bp, has a G+C content of 68.60% and 34 putative ORFs. Both plasmids encode their own replication protein. The ORF 22 of pL4C and the ORF 4 of pS4C encode proteins with high sequence similarities to integrase (97%) and transposase (97%), respectively, which are both involved in DNA rearrangement and exchange. Furthermore, sequence analysis of pL4C also showed that several plasmid-encoded genes may be involved in DNA modification and repair, such as DNA G:T-mismatch repair endonuclease and micrococcal nuclease-like protein. These proteins may be involved in raising the repair efficiency and other minor editing needs. Interestingly, the elimination of plasmids significantly lowered the growth temperature of Thermus sp. 4C. Few reports dealing with the DNA repair enzymes on the plasmid from Thermus strains were published so far.

Extrachromosomal element capture and the evolution of multiple replication origins in archaeal chromosomes

In all three domains of life, DNA replication begins at specialized loci termed replication origins. In bacteria, replication initiates from a single, clearly defined site. In contrast, eukaryotic organisms exploit a multitude of replication origins, dividing their genomes into an array of short contiguous units. Recently, the multiple replication origin paradigm has also been demonstrated within the archaeal domain of life, with the discovery that the hyperthermophilic archaeon Sulfolobus has three replication origins. However, the evolutionary mechanism driving the progression from single to multiple origin usage remains unclear. Here, we demonstrate that Aeropyrum pernix, a distant relative of Sulfolobus, has two origins. Comparison with the Sulfolobus origins provides evidence for evolution of replicon complexity by capture of extrachromosomal genetic elements. We additionally identify a previously unrecognized candidate archaeal initiator protein that is distantly related to eukaryotic Cdt1. Our data thus provide evidence that horizontal gene transfer, in addition to its well-established role in contributing to the information content of chromosomes, may fundamentally alter the manner in which the host chromosome is replicated.

Transcription activation mediated by a cyclic AMP receptor protein from Thermus thermophilus HB8

The extremely thermophilic bacterium Thermus thermophilus HB8, which belongs to the phylum Deinococcus-Thermus, has an open reading frame encoding a protein belonging to the cyclic AMP (cAMP) receptor protein (CRP) family present in many bacteria. The protein named T. thermophilus CRP is highly homologous to the CRP family proteins from the phyla Firmicutes, Actinobacteria, and Cyanobacteria, and it forms a homodimer and interacts with cAMP. CRP mRNA and intracellular cAMP were detected in this strain, which did not drastically fluctuate during cultivation in a rich medium. The expression of several genes was altered upon disruption of the T. thermophilus CRP gene. We found six CRP-cAMP-dependent promoters in in vitro transcription assays involving DNA fragments containing the upstream regions of the genes exhibiting decreased expression in the CRP disruptant, indicating that the CRP is a transcriptional activator. The consensus T. thermophilus CRP-binding site predicted upon nucleotide sequence alignment is 5'-(C/T)NNG(G/T)(G/T)C(A/C)N(A/T)NNTCACAN(G/C)(G/C)-3'. This sequence is unique compared with the known consensus binding sequences of CRP family proteins. A putative -10 hexamer sequence resides at 18 to 19 bp downstream of the predicted T. thermophilus CRP-binding site. The CRP-regulated genes found in this study comprise clustered regularly interspaced short palindromic repeat (CRISPR)-associated (cas) ones, and the genes of a putative transcriptional regulator, a protein containing the exonuclease III-like domain of DNA polymerase, a GCN5-related acetyltransferase homolog, and T. thermophilus-specific proteins of unknown function. These results suggest a role for cAMP signal transduction in T. thermophilus and imply the T. thermophilus CRP is a cAMP-responsive regulator.