Determination of the recognition sequence of Mycobacterium smegmatis topoisomerase I on mycobacterial genomic sequences

Sikder, Devanjan

doi:10.1093/nar/28.8.1830

Cited by 25 publications

(33 citation statements)

References 28 publications

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“…By comparison, a conserved T at position Ϫ4 was found in the cleavage sequences of E. coli, M. smegmatis, T. maritima topoisomerases I (23,27,29), and S. shibatae reverse gyrase (13). These results are consistent with the observation that the S. solfataricus topoisomerase and its archaeal homologues are phylogenetically more closely related to topoisomerases III than to topoisomerases I, whereas reverse gyrases are closely related to bacterial topoisomerases I (4).…”

Section: Discussionsupporting

confidence: 77%

“…The base preference of the enzyme at each position over a stretch of 6-bp sequence 5Ј to the site of strand scission (Ϫ7 to Ϫ2) renders the enzyme specific in oligonucleotide cleavage. Among characterized type I topoisomerases, only vaccinia virus topoisomerase I (a Topo IB enzyme) and M. smegmatis topoisomerase I have been shown to be highly specific in DNA cleavage (22,23). Most type I topoisomerases from prokaryotes are less stringent in cleavage target selection.…”

Section: Discussionmentioning

confidence: 99%

“…Most type I topoisomerases from prokaryotes are less stringent in cleavage target selection. E. coli, M. luteus topoisomerases I, and Sulfolobus shibatae reverse gyrase require only a C at position Ϫ4 for efficient cleavage (16,23,27). Because of its sequence specificity, the S. solfataricus topoisomerase presumably acts infrequently on the genomic DNA of S. solfataricus.…”

Section: Discussionmentioning

confidence: 99%

“…For example, E. coli and Micrococcus luteus topoisomerases I show a limited sequence preference (5Ј-CXXX2-3Ј) (27), whereas E. coli topoisomerase III and M. smegmatis topoisomerase I are more specific in cleavage (5Ј-CT2T-3Ј and 5Ј-CG/TCT2T-3Ј, respectively) (23,33). Analysis of the cleavage sequences of topoisomerases is of importance to the understanding of the molecular basis of the interaction between the enzymes and their DNA substrates.…”

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confidence: 99%

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DNA Topoisomerase III from the Hyperthermophilic Archaeon Sulfolobus solfataricus with Specific DNA Cleavage Activity

Dai

Wang

et al. 2003

J Bacteriol

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We report the production, purification, and characterization of a type IA DNA topoisomerase, previously designated topoisomerase I, from the hyperthermophilic archaeon Sulfolobus solfataricus. Topoisomerases are ubiquitous enzymes that participate in nearly all cellular activities involving DNA transactions (5, 31). Based on their catalytic mechanisms, topoisomerases are classified into two classes: type I enzymes, which generate a transient break on one DNA strand to allow the passage of the intact strand with a linking change of one in a single reaction cycle, and type II enzymes, which introduce a transient doublestranded break to allow the passage of another duplex DNA segment with a change in linking number by steps of two (5, 30). Each class of topoisomerases is further divided into two structurally and mechanistically distinct subfamilies on the basis of the polarity of enzyme attachment to the broken strands (i.e., IA, IB, IIA, and IIB). A cellular organism possesses multiple forms of topoisomerases. For example, Escherichia coli has two type IA enzymes (topoisomerases I and III) and two type IIA enzymes (gyrase and topoisomerase IV) (30). Humans carry two enzymes of each of the subfamilies IA (topoisomerases III␣ and III␤), IB (topoisomerase I and mitochondrial topoisomerase I), and IIA (topoisomerases II␣ and II␤) (31). Sulfolobus, a group of hyperthermophilic archaea, possesses two type IA enzymes (putative topoisomerase I, identified by gene annotation, and reverse gyrase) and a type IIB enzyme (topoisomerase VI) (2,8,10). It appears that all organisms have at least one type IA topoisomerase (31).E. coli DNA topoisomerase I is the most extensively studied representative of type IA enzymes. The E. coli enzyme is composed structurally of an N-terminal transesterification domain and a C-terminal DNA binding domain (1,17). The N-terminal domain has the active site tyrosine for DNA cleavage and is capable of forming a covalent adduct with single-stranded DNA. But this domain cannot relax negatively supercoiled DNA. The C-terminal domain consists of five copies of a zinc ribbon motif and is suspected to interact with the passing strand of DNA in the relaxation of negatively supercoiled DNA (1, 12). Each of the first three zinc ribbon motifs from the N terminus in this domain contains four cysteine residues at required sites and is likely to bind zinc (28). The fourth and fifth motifs have one and no cysteine residue, respectively. Sequence analysis of type IA topoisomerase-encoding genes has revealed a significant variation with respect to the copy number of zinc ribbon motifs (0 to 5) as well as the number of tetracysteine motifs in the enzymes (12). These data suggest that zinc ribbon motifs may not be required for DNA relaxation by at least some type IA topoisomerases. This suggestion is consistent with reports that zinc binding is not necessary for the relaxation activity of topoisomerases from Mycobacterium smegmatis and Thermotoga maritima (3,29).Although type IA topoisomerases share considerable seq...

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Section: Discussionsupporting

confidence: 77%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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DNA Topoisomerase III from the Hyperthermophilic Archaeon Sulfolobus solfataricus with Specific DNA Cleavage Activity

Dai

Wang

et al. 2003

J Bacteriol

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“…Microhomologyindependent illegitimate recombination is promoted by topoisomerases, when the nicking and cloning reactions are separated and act on unrelated DNA ends (2,5,32,54). Although topoisomerases generally do not have strong sequence specificity (83), several of the topoisomerases and also RuvC have AA or TT at or close to their cleavage sites (3,71,74,83,94), as found here. Some topoisomerases also break and join sin- (83), which could fuse the transforming single strand to resident DNA.…”

Section: Discussionsupporting

confidence: 56%

Impact of mutS Inactivation on Foreign DNA Acquisition by Natural Transformation in Pseudomonas stutzeri

Meier

Wackernagel

2005

J Bacteriol

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In prokaryotic mismatch repair the MutS protein and its homologs recognize the mismatches. The mutS gene of naturally transformable Pseudomonas stutzeri ATCC 17587 (genomovar 2) was identified and characterized. The deduced amino acid sequence (859 amino acids; 95.6 kDa) displayed protein domains I to IV and a mismatchbinding motif similar to those in MutS of Escherichia coli. A mutS::aac mutant showed 20-to 163-fold-greater spontaneous mutability. Transformation experiments with DNA fragments of rpoB containing single nucleotide changes (providing rifampin resistance) indicated that mismatches resulting from both transitions and transversions were eliminated with about 90% efficiency in mutS ؉ . The mutS ؉ gene of strain ATCC 17587 did not complement an E. coli mutant but partially complemented a P. stutzeri JM300 mutant (genomovar 4). The declining heterogamic transformation by DNA with 0.1 to 14.6% sequence divergence was partially alleviated by mutS::aac, indicating that there was a 14 to 16% contribution of mismatch repair to sexual isolation. Expression of mutS ؉ from a multicopy plasmid eliminated autogamic transformation and greatly decreased heterogamic transformation, suggesting that there is strong limitation of MutS in the wild type for marker rejection. Remarkably, mutS::aac altered foreign DNA acquisition by homology-facilitated illegitimate recombination (HFIR) during transformation, as follows: (i) the mean length of acquired DNA was increased in transformants having a net gain of DNA, (ii) the HFIR events became clustered (hot spots) and less dependent on microhomologies, which may have been due to topoisomerase action, and (iii) a novel type of transformants (14%) had integrated foreign DNA with no loss of resident DNA. We concluded that in P. stutzeri upregulation of MutS could enforce sexual isolation and downregulation could increase foreign DNA acquisition and that MutS affects mechanisms of HFIR.In all organisms repair of DNA is an essential process for maintaining DNA integrity and for avoiding mutations. Misincorporated bases remaining after DNA replication or spontaneous base modification in DNA produce mismatches which are repaired by an excision-type mechanism provided by the mismatch repair (MMR) system (11, 56). MMR proteins were first identified in Streptococcus pneumoniae, and the best-characterized MMR proteins are those in Escherichia coli (11,55). In prokaryotes MutS initiates the repair by recognition and binding to the mismatch; this is followed by a search together with MutL on both sides of the mismatch for a site from where excision can be initiated (30). The ubiquity of MutS homologs in all three biological kingdoms (19) underscores the importance of MutS in maintaining the genetic stability of cellular genomes (26). In bacteria loss of the mismatch repair capacity results in mutator strains with increased spontaneous mutation frequencies (23). Such mutator strains have been found among environmental, commensal, and pathogenic isolates of Pseudomonas aeruginosa (59), E. c...

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A novel bipartite mode of binding of M. smegmatis topoisomerase I to its recognition sequence

Sikder

Nagaraja

2001

Journal of Molecular Biology

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We have investigated interaction of Mycobacterium smegmatis topoisomerase I at its specific recognition sequence. DNase I footprinting demonstrates a large region of protection on both the scissile and non-scissile strands of DNA. Methylation protection and interference analyses reveal base-specific contacts within the recognition sequence. Missing contact analyses reveal additional interactions with the residues in both single and double-stranded DNA, and hence underline the role for the functional groups associated with those bases. These interactions are supplemented by phosphate contacts in the scissile strand. Conformation specific probes reveal protein-induced structural distortion of the DNA helix at the T-A-T-A sequence 11 bp upstream to the recognition sequence. Based on these footprinting analyses that define parameters of topoisomerase I-DNA interactions, a model of topoisomerase I binding to its substrate is presented. Within the large protected region of 30 bp, the enzyme makes direct contact at two locations in the scissile strand, one around the cleavage site and the other 8-12 bases upstream. Thus the enzyme makes asymmetric recognition of DNA and could carry out DNA relaxation by either of the two proposed mechanisms: enzyme bridged and restricted rotation.

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Determination of the recognition sequence of Mycobacterium smegmatis topoisomerase I on mycobacterial genomic sequences

Cited by 25 publications

References 28 publications

DNA Topoisomerase III from the Hyperthermophilic Archaeon Sulfolobus solfataricus with Specific DNA Cleavage Activity

DNA Topoisomerase III from the Hyperthermophilic Archaeon Sulfolobus solfataricus with Specific DNA Cleavage Activity

Impact of mutS Inactivation on Foreign DNA Acquisition by Natural Transformation in Pseudomonas stutzeri

A novel bipartite mode of binding of M. smegmatis topoisomerase I to its recognition sequence

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