Gyrase, reverse

Fig. 2. Homology of chromatin remodeling ATPases to DNA translocases. Motifs I-III, V, and VI in the Sf2 helicase signature in the Swi/Snf superfamily (including yeast Motlp, Radl6p and Rad54p) are aligned and compared with the motifs in reverse gyrase Sf2-like signature and the PerA helicase Sfl signature. The conserved elements of the latter two are taken from Refs. [192] and [333], respectively.

Rodriguez, A.C. and Stock, D. (2002) Crystal structure of reverse gyrase insights into the positive supercoiling of DNA. EMBO J. 21, 418 26. 

Rodriguez, A.C. (2002) Studies of a positive supercoiling machine. Nucleotide hydrolysis and a multifunctional latch in the mechatrism of reverse gyrase. J. Biol. Chem. 277, 29865-29873. 

CARNOSINE SYNTHETASE CHAPERONES CHOLINE KINASE CHOLOYL-CoA SYNTHETASE COBALAMIN ADENOSYLTRANSFERASE 4-COUMAROYL-CoA SYNTHETASE CREATINE KINASE CTP SYNTHETASE CYTIDYLATE KINASE 2-DEHYDRO-3-DEOXYGLUCONOKINASE DEHYDROGLUCONOKINASE DEOXYADENOSINE KINASE DEOXYADENYLATE KINASE DEOXYCYTIDINE KINASE (DEOXYjNUCLEOSIDE MONOPHOSPHATE KINASE DEOXYTHYMIDINE KINASE DEPHOSPHO-CoA KINASE DETHIOBIOTIN SYNTHASE DIACYLGLYCEROL KINASE DIHYDROFOLATE SYNTHETASE DNA GYRASES DNA REVERSE GYRASE ETHANOLAMINE KINASE EXONUCLEASE V... 

DNA (CYTOSINE-5-)-METHYLTRANSEERASE DNA, exonucleolytic cleavage, PHOSPHODLESTERASES DNA GLYCOSYLA.SES DNA GYRASES DNA REVERSE GYRASE DNA LIGASES... 

DNA OXIDATIVE DAMAGE AND REPAIR PHOTOREACTIVATION DNA Reverse gyrase,... 

The energy source for the process is provided by cleavage of ATP. DNA gyrase untwists relaxed circular dsDNA one turn at a time and reseals the cut ends. A reverse gyrase from certain bacteria twists the relaxed DNA more tightly. In both cases the change causes the DNA to form superhelical turns.67193-197 These may be either solenoidal or plectonemically interwound (as a twisted thread Fig. 5-18). 

Thermostabilization of double-stranded DNA is provided by base pairing (1) and base stacking (see Reference 27 and references therein) complemented by positive supercoiling by reverse gyrase [in hyperthermophiles (8, 9, 28)] and by stabilization via interactions with histone-like proteins (29, 30). The relative contribution of base paring and base stacking into the thermostability of double-stranded DNA has been a subject of extensive studies for more than four decades (1, 27, 31). We will consider here this question, based on the results of recent experimental and computational works (31, 32). 

Bouthier de la Tour C, Portemer C, Huber R, Forterre P, Duguet M. Reverse gyrase in thermophilic eubacteria. J. Bac-teriol. 1991 173 3921-3923. 

An enzyme which may specifically prevent heat denaturation of DNA is thought to be the reverse gyrase [38-41]. Although not specific for archaea, this enzyme seems to be specific for thermophilic prokaryotes (archaea as well as bacteria). The reverse gyrase introduces positive supercoils into double-stranded, covalently closed DNA. But as mentioned by Bouthier de la Tour et al. [41], there is no direct evidence for the involvement of this type of supercoiling in the stability of DNA at high temperature . 

A DNA-dependent ATPase activity was found associated with the purified enzyme [77]. In contrast, an ATP-independent relaxation activity detected in partially purified fractions of reverse gyrase [74] was absent from completely purified fractions and probably corresponds to a distinct DNA topoisomerase (see below). A reverse gyrase with similar structure and properties was purified later by Slezarev[78] from another extremely thermophilic archaebacterium, Desulfurococcus amylolyticus[7S],... 

How does a type I DNA topoisomerase, such as reverse gyrase, catalyze DNA supercoiling Slezarev and Kozyavkin [82] suggested that reverse gyrase binds onto... 

Structure and properties very similar to that in archaebacteria has been recently purified from Calderobacterium hydrogenophilum [Mikulik, personal communication] which belongs to a group of extreme thermophilic eubacteria distinct from the Thermococcales. Table 1 summarizes the distribution of reverse gyrase in prokaryotes. 

The excellent correlation between the presence of reverse gyrase and the extreme thermophilic phenotype, both in archaebacteria and in eubacteria (Table 1) strongly suggests that reverse gyrase helps to maintain the DNA in a suitable conformation at... 

Data are from references [89,91,92] and from Mikulik (personal communication) for Calderobacterium hydrogenophilum. Reverse gyrase activity has not been detected in moderately thermophilic and mesophilic eubacteria from the genera Bacillus and Thermus [89]. In all cells lacking reverse gyrase activity, except Halobacterium halobium, one can detect an ATP-independent relaxation activity. 

Abbreviations RvG act., reverse-gyrase activity +, detection of ATP-dependent positive supercoiling in crude extract ND, not detected (see also Fig. 7) e, euryarchaeota c, crenarchaeota Topt, optimal growth temperature. 

Finally, the composite helicase-topoisomerase structure of reverse gyrase suggests that this unusual enzyme could also be involved in any one of the mechanisms which requires the concerted action of such activities [Duguet, M., personal communication]. 

In their first paper, Kikuchi and Asai [72] reported that S. acidocaldarius contained, besides a reverse gyrase, one ATP-independent and two ATP-dependent thermophilic DNA topoisomerases (including one DNA gyrase). However, their purification procedure lacked a step to remove DNA, so that at least one of the ATP-dependent topoisomerases probably corresponded to the reverse gyrase copurifying with DNA (discussed in ref [74]). Later work did not confirm the presence of a classical gyrase but demonstrated the presence of at least one type II DNA topoisomerase, and probably one ATP-independent type I DNA topoisomerase in Sulfolobus and in other thermophilic archaebacteria. 

A type II DNA topoisomerase has been detected by Kikuchi and coworkers in S. acidocaldarius [95]. This enzyme seems to be much less abundant and active than reverse gyrase. It exhibits the usual ATP requirement of type II DNA topoisomerases (in the millimolar range) and can relax either negatively or positively supercoiled DNA. 

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