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Conversion of Gyrase to Topoisomerase IV

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Conversion of Gyrase to Topoisomerase IV COMMENTARY Evolutionary twist on topoisomerases: Conversion of gyrase to topoisomerase IV Keir C. Neuman1 Laboratory of Molecular Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892 ype II topoisomerases are essen- tial enzymes found in all cells, T where they maintain the topology of DNA in a well-defined state G segment (1). The defining activity of type II top- T segment oisomerases is an ATP-dependent pas- + 2 ATP (*) sage of a segment of dsDNA through a transient double-stranded break in a * * second segment of dsDNA (Fig. 1) (1, 2). Despite sharing the same core strand passage mechanism, different type II top- * oisomerases display dramatically different * substrate specificities and topological ac- -2 ADP tivities. The molecular basis for these dif- ferences and their evolutionary origins -2 P remains speculative. There is mounting i evidence that the differences are encoded in the poorly conserved C-terminal do- Gyrase Topo IV mains (CTDs) (3–6). Similarly, the high degree of homology among type II top- oisomerases is clear evidence that they are evolutionarily related, but the evolutionary pathway and the identity of the original type II topoisomerase are unknown (7). In PNAS, the article by Tretter et al. (8) provides biochemical, structural, and (–) evolutionary results showing the conver- sion of one type II topoisomerase into another. Their results enlarge our un- derstanding of the molecular and struc- tural basis governing the topological (–) (+) specificity and activity of type II topoisom- erases, illustrate how these features may have evolved from a common ancestor, and force reconsideration of notions con- Fig. 1. Core type II topoisomerase strand passage mechanism. (Upper, clockwise from top) Type II top- cerning the complement of essential oisomerase (blue, salmon, and yellow) binds gate segment DNA (green) and subsequently captures bacterial genes. a transfer segment DNA (pink to red denoting movement of the DNA ) followed by the binding of two ATP Bacteria typically possess two type molecules, which close the N-terminal gate (yellow). This is followed by double-strand cleavage of the gate strand and passage of the transfer strand across the cleaved DNA and through the enzyme. The transfer II topoisomerases: DNA gyrase, which strand and products of ATP hydrolysis are then released as the enzyme resets for another enzymatic cycle. maintains DNA in a slightly unwound This core strand passage mechanism is coupled with substrate specificity to achieve different topological (negatively supercoiled) state, and top- activities. Gyrase (Lower Left, blue, salmon, and yellow with purple GyrA CTD) wraps DNA around its GyrA oisomerase IV (Topo IV), which is pri- CTD, resulting in the formation of a left-handed DNA crossing, which is converted into a negative supercoil marily responsible for unlinking newly after passage of the transfer segment (red) through the gate segment (green). Topo IV (Lower Right, blue, replicated DNA (1). Gyrase is thought salmon, and yellow with purple ParC CTD) unlinks catenated DNA molecules and relaxes positive super- to be essential, because some bacteria coils more efficiently than negative supercoils. seem to lack Topo IV (7). These two en- – zymes are heterotetramers (A2:B2), share tively than negatively supercoiled DNA bated mechanism (9 11). Also under a great deal of sequence homology, and (Fig. 1). The determinants of substrate debate is the evolutionary order: did one perform the same core strand passage specificity for both topoisomerases have of the two type II topoisomerases evolve reaction (Fig. 1). However, the substrate been mapped to the CTDs of their GyrA from the other, and if so, what molecular selection and activity of the two enzymes and ParC domains (4–6). Removal of the determinants underlie the change in speci- are strikingly different. DNA gyrase CTDs results in type II topoisomerases ficity and topological activity? (GyrA2:GyrB2) introduces a right-handed that indiscriminately relax positively and wrap in the DNA, which, after strand pas- negatively supercoiled DNA and unlink sage, results in the introduction of nega- catenated DNA molecules (4, 5). The Author contributions: K.C.N. wrote the paper. tive supercoils (Fig. 1). Topo IV (ParC2: GyrA CTD is responsible for the wrap The author declares no conflict of interest. ParE2), in contrast, is an efficient deca- imposed on DNA by gyrase, whereas the See companion article on page 22055 in issue 51 of volume tenase that can also relax supercoiled ParC CTD slightly bends DNA and pro- 107. DNA, although it is more active on posi- vides substrate selection through a de- 1E-mail: [email protected]. www.pnas.org/cgi/doi/10.1073/pnas.1016041108 PNAS Early Edition | 1of2 Downloaded by guest on September 26, 2021 Tretter et al. (8) adopt an elegant ap- Following up on the evolutionary result in a true Topo IV, or are there proach to investigate the structural, bio- placement of A. aeolicus type II top- additional evolutionary modifications of chemical, and evolutionary relationship oisomerase, which is near the point of di- the E. coli enzymes rendering a more between bacterial DNA gyrase and top- vergence between the ParC/GyrA CTD, complicated and subtle functional re- oisomerase IV. They identify an ancient Tretter et al. (8) show that the A. aeolicus lationship between gyrase and Topo IV? bacteria, Aquifex aeolicus, with a single GyrB subunit forms an active gyrase when A similar line of reasoning suggests that type II topoisomerase classified as a DNA mixed with Escherichia coli GyrA, whereas insertion of an appropriate GyrA box in gyrase based on sequence analysis but E. coli ParE mixed with E. coli GyrA is the A. aeolicus GyrA CTD should re- lacking the GyrA box essential for nega- inactive. Furthermore, substitution of the store gyrase activity. Finally, if Topo IV tive supercoiling (6). They crystalized the A. aeolicus GyrA CTD with the GyrA CTD evolved from gyrase, and more generally, A. aeolicus GyrA CTD, finding a six- containing an intact GyrA box from another an ancestral gyrase was the origin of bladed disk similar to other GyrA CTDs, all type II topoisomerases, the ATP re- except that the lack of the GyrA box re- quirement (2) of type II topoisomerases fi The picture that emerges sults in an open con guration of the may simply be a vestige of the ancestral disk resembling a ParC CTD (8). Thus, gyrase, which required the energy of A. aeolicus from this work is that structurally, the GyrA CTD ATP hydrolysis to perform the energeti- resembles a ParC CTD rather than a ca- a gyrase lacking the GyrA cally costly process of negatively super- nonical GyrA CTD. The biochemical fi coiling DNA. rami cations were determined by mea- box acts as a genuine In summary, the work by Tretter et al. suring the topological activity of A. fi aeolicus (8) rmly establishes the importance of the type II topoisomerase. The holo- Topo IV. CTDs in modulating and controlling the enzyme was unable to negatively supercoil activity of type II topoisomerases. The DNA, instead displaying robust decatena- current findings provide compelling bio- tion and supercoil relaxation suggestive hyperthermophilic species recapitulated chemical and evolutionary evidence for of Topo IV. The lack of gyrase activity is the negative supercoiling activity of gyrase. the direct conversion of a gyrase into a surprising, because it is a purportedly es- The authors accomplished a remarkable Topo IV. Moreover, the finding of a bac- sential bacterial gene. However, the A. achievement in converting the activity of terial species lacking gyrase questions aeolicus genome contains many genes a type II topoisomerase between two from archaea, among which the most hy- paralogs (gyrase and Topo IV). strict conservation of bacterial gyrase and perthermophilic species lack gyrase (12). The picture that emerges from this work points to a more sensitive criteria for de- Nevertheless, this finding forces recon- is that a gyrase lacking the GyrA box acts termining the identity of bacterial type II sideration of the absolute necessity of as a genuine Topo IV. Previously, it was topoisomerases based solely on their se- gyrase among bacteria. In an important unclear if Topo IV substrate preference quence. It is tempting to speculate that the extension of their biochemical character- and activity were encoded elsewhere in the CTDs may harbor additional regulatory ization of the A. aeolicus type II topoiso- ParC CTD. Now, a compelling case can functions besides the striking example merase, Tretter et al. (8) find that it be made for Topo IV activity arising from described here. Indeed, recent work has relaxed positively supercoiled DNA more the opening or a distortion of the GyrA shown that the condensin MukB physically efficiently than negatively supercoiled CTD. More generally, the chimera experi- interacts with the ParC CTD, stimulating DNA, a hallmark of Topo IV. This finding ments revealed how evolutionarily close the activity of Topo IV and coordinating provides a basis to define Topo IV sub- the A. aeolicus enzyme is to gyrase and the condensing and unlinking activities strate specificity at the molecular level and suggest a pathway through which Topo IV (13, 14). Further work on the modulation suggests that, in this instance, Topo IV evolved from the gyrase. of type II topoisomerase activity by the may have evolved directly from gyrase. This work raises a number of interesting CTDs will likely reveal additional insights This raises an interesting question: is the questions and suggests several lines of and surprises. substrate specificity of Topo IV (i.e., its additional inquiry. From a synthetic bi- preference for relaxing positive vs. nega- ology perspective, probing the generality ACKNOWLEDGMENTS. I thank Ashley Hardin for fi and reversibility of the findings should preperation of the gure. Work in my laboratory tive supercoils) an essential feature of the is supported by the intramural research program enzyme, or is it an evolutionary holdover prove fruitful.
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