Reverse gyrase from hyperthermophiles: probable transfer of a thermoadaptation trait from Archaea to Bacteria

Abstract

The hyperthermophilic bacterium Thermotoga maritima MSB8 possesses a reverse gyrase whose enzymatic properties are very similar to those of archaeal reverse gyrases. It catalyzes the positive supercoiling of the DNA in an Mg 2؉ -and ATP-dependent process. Its optimal temperature of activity is around 90°C, and it is highly thermostable. We have cloned and DNA sequenced the corresponding gene (T. maritima topR). This is the first report describing the analysis of a gene encoding a reverse gyrase in bacteria. The T. maritima topR gene codes for a protein of 1,104 amino acids with a deduced molecular weight of 128,259, a value in agreement with that estimated from the denaturing gel electrophoresis of the purified enzyme. Like its archaeal homologs, the T. maritima reverse gyrase exhibits helicase and topoisomerase domains, and its sequence matches very well the consensus sequence for six reverse gyrases now available. Phylogenetic analysis shows that all reverse gyrases, including the T. maritima enzyme, form a very homogeneous group, distinct from the type I 5 topoisomerases of the TopA subfamily, for which we have previously isolated a representative gene in T. What are the molecular mechanisms involved in the adaptation of life to elevated temperatures? In terms of DNA dynamics, part of the answer was provided by the discovery in thermophilic organisms of a particular topoisomerase, the reverse gyrase, that modifies the topological state of DNA by introducing positive supercoils in an ATP-dependent process (14). It was suggested that overlinking could compensate for the effect of temperature on DNA structure (16). The enzyme is widely distributed in thermophilic archaea (6,8). The first reverse gyrase characterized was isolated from the hyperthermophilic archaeum Sulfolobus acidocaldarius (23,33). Mechanistic studies showed that it is transiently linked to the DNA by a 5Ј phosphotyrosyl bond (22,24), classifying it in the type I 5Ј topoisomerase family as proposed by Roca (38). Sequence analysis further showed that it is a single polypeptide containing putative helicase and topoisomerase domains located in the amino-and carboxy-terminal, respectively, parts of the protein (9). The helicase domain exhibits motifs found in DNA and RNA helicases, and the topoisomerase domain exhibits a significant similarity with the 5Ј topoisomerase I (protein ) from Escherichia coli. From all of these data, a mechanism of reverse gyration involving the concerted action of two such domains was proposed (9, 14).To date, four other archaeal reverse gyrase genes have been sequenced: from Sulfolobus shibatae (21), Methanopyrus kandleri (26), Pyrococcus furiosus (3), and Methanococcus jannaschii (7). A comparative analysis of reverse gyrases from two members of the order Sulfolobales (S. acidocaldarius and S. shibatae) and M. kandleri with the other type I topoisomerases of the 5Ј family (21) showed that the reverse gyrases constitute a new group within this family distinct from the previously described TopA and TopB groups, represent...

Identification and Characterization of Human Archaemetzincin-1 and -2, Two Novel Members of a Family of Metalloproteases Widely Distributed in Archaea

“…Only AMZ2b genes and AMZ2 from bacterial M. xanthus stand outside these groups. Interestingly, AMZ2 from A. aeolicus groups with AMZs from archaeal organisms, suggesting a relatively late lateral gene transfer event from Archaea to bacteria as was previously proposed for other A. aeolicus genes (28,29). Finally, data from this analysis were fitted to a taxonomic tree to construct a model that could explain the evolution of AMZ genes (Fig.…”

Global extent of horizontal gene transfer

“…We found a few marginal preferences (P Ͻ 0.001) for subcategories of molecular functions such as helicase activity (GO:0004386) at the second taxonomic range, nucleic acid binding (GO:0003676) at the third range, oxidoreductase activity (GO:0016491) at the fourth range, and a marginal preference for extracellular region (GO:0005576) at the third and fourth ranges in the GO cellular component category. These data reconfirmed previous observations that HGT was biased toward cell surface and DNA binding functions (17) and, for example, that the helicase domain integrated into reverse gyrase has undergone HGT (29), but the biases are marginal. Thus, as a first approximation, our estimation suggests that HGT is nearly neutral to all Fig.…”

Insights into thermoadaptation and the evolution of mesophily from the bacterial phylum Thermotogae

“…The increased heat protection provided by this enzyme may be linked to a role in the DNA damage response, possibly through recruitment to lesions (Perugino et al 2009;Lulchev and Klostermeier 2014). Interestingly, cultivated hyperthermophilic isolates from both the Thermotogae and the Aquificae have acquired their reverse gyrase genes from Archaea by lateral gene transfer (LGT), suggesting that hyperthermophily may have been acquired by Bacteria from Archaea (Forterre et al 2000;Brochier-Armanet and Forterre 2006).…”