A second NAD+-dependent DNA ligase (LigB) in Escherichia coli

Sriskanda, Verl

doi:10.1093/nar/29.24.4930

Cited by 43 publications

(43 citation statements)

References 25 publications

(25 reference statements)

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“…ExoI and the RecJ single-strand 59 exonuclease could be imagined to contribute by extending single-strand nicks to gaps, but recJ mutations showed little effect on duplication rate. The ligB gene encodes a nonessential homolog of the standard DNA ligase (ligA) (Sriskanda and Shuman 2001) and made no significant contribution to duplication formation.…”

Section: Testing the Role Of Other Recombination/repair Functions In mentioning

confidence: 99%

Recombination and Annealing Pathways Compete for Substrates in Making rrn Duplications in Salmonella enterica

et al. 2014

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Tandem genetic duplications arise frequently between the seven directly repeated 5.5-kb rrn loci that encode ribosomal RNAs in Salmonella enterica. The closest rrn genes, rrnB and rrnE, flank a 40-kb region that includes the purHD operon. Duplications of purHD arise by exchanges between rrn loci and form at a high rate (10 23 /cell/division) that remains high in strains blocked for early steps in recombination (recA, recB, and/or recF), but drops 30-fold in mutants blocked for later Holliday junction resolution (ruvC recG). The duplication defect of a ruvC recG mutant was fully corrected by an added mutation in any one of the recA, recB, or recF genes. To explain these results, we propose that early recombination defects activate an alternative single-strand annealing pathway for duplication formation. In wild-type cells, rrn duplications form primarily by the action of RecFORA on single-strand gaps. Double-strand breaks cannot initiate rrn duplications because rrn loci lack Chi sites, which are essential for recombination between two separated rrn sequences. A recA or recF mutation allows unrepaired gaps to accumulate such that different rrn loci can provide single-strand rrn sequences that lack the RecA coating that normally inhibits annealing. A recB mutation activates annealing by allowing double-strand ends within rrn to avoid digestion by RecBCD and provide a new source of rrn ends for use in annealing. The equivalent high rates of rrn duplication by recombination and annealing pathways may reflect a limiting economy of gaps and breaks arising in heavily transcribed, palindrome-rich rrn sequences.

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Section: Testing the Role Of Other Recombination/repair Functions In mentioning

confidence: 99%

Recombination and Annealing Pathways Compete for Substrates in Making rrn Duplications in Salmonella enterica

et al. 2014

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“…In the E. coli genome ligB was identified by virtue of its sequence similarity with the primary NAD ϩ -dependent ligA, and ligB homologues were also detected in Yersinia and Salmonella (28,29). For E. coli LigB the NAD ϩ -dependent nick-joining activity was demonstrated, but the specific activity was only 1% that of LigA (28). Thus, the precise function of LigB still has to be elucidated; however, LigB cannot compensate for the loss of LigA.…”

Section: Specific Inhibition Of Nadmentioning

confidence: 99%

Specific and Potent Inhibition of NAD+-dependent DNA Ligase by Pyridochromanones

Brötz‐Oesterhelt

Knezevic

Bartel

et al. 2003

Journal of Biological Chemistry

115

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Pyridochromanones were identified by high throughput screening as potent inhibitors of NAD ؉ -dependent DNA ligase from Escherichia coli. Further characterization revealed that eubacterial DNA ligases from Gramnegative and Gram-positive sources were inhibited at nanomolar concentrations. In contrast, purified human DNA ligase I was not affected (IC 50 > 75 M), demonstrating remarkable specificity for the prokaryotic target. The binding mode is competitive with the eubacteriaspecific cofactor NAD ؉ , and no intercalation into DNA was detected. Accordingly, the compounds were bactericidal for the prominent human pathogen Staphylococcus aureus in the low g/ml range, whereas eukaryotic cells were not affected up to 60 g/ml. The hypothesis that inhibition of DNA ligase is the antibacterial principle was proven in studies with a temperature-sensitive ligase-deficient E. coli strain. This mutant was highly susceptible for pyridochromanones at elevated temperatures but was rescued by heterologous expression of human DNA ligase I. A physiological consequence of ligase inhibition in bacteria was massive DNA degradation, as visualized by fluorescence microscopy of labeled DNA. In summary, the pyridochromanones demonstrate that diverse eubacterial DNA ligases can be addressed by a single inhibitor without affecting eukaryotic ligases or other DNA-binding enzymes, which proves the value of DNA ligase as a novel target in antibacterial therapy.Multiple drug resistance among bacterial pathogens is spreading even in developed countries and has made many currently available antibiotics ineffective (1). As a consequence the number of reports on therapy failures increases and treatment costs rise, causing a growing public health problem. Thus, the search for novel antibacterial classes with innovative mechanisms of action is crucial to keep pace with the innate adaptability of the bacterial population. From the information revealed by sequencing more than 80 bacterial genomes, many novel target ideas have emerged in the last decade. However, even classical target areas such as cell wall, protein, or DNA synthesis contain many vital reactions not exploited in antibacterial therapy so far.DNA ligases are promising target candidates because they are indispensable for many fundamental processes in DNA metabolism including the linkage of Okazaki fragments during replication, recombination processes, and repair pathways requiring resynthesis of DNA (2, 3). Their crucial function is emphasized by the fact that eukaryotic cells contain several isoenzymes and that viruses encode their own ligases (3, 4). The reaction catalyzed by the DNA ligases, the joining of nicked DNA strands, proceeds in three sequential nucleotidyl transfer reactions (2). The first step is the nucleophilic attack by the active site lysine on the AMP moiety of a cofactor, resulting in a covalent enzyme-AMP intermediate. The AMP is then transferred to the 5Ј-phosphate end of the nicked duplex DNA and finally released when the ligase catalyzes the attack by the adjacent...

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“…LigA is also essential in Salmonella typhimurium, Bacillus subtilis, and Staphylococcus aureus (10 -12). Some bacteria, including E. coli, S. typhimurium, Shigella flexneri, Yersinia pestis, and Pseudomonas putida, have a second NAD ϩ -dependent ligase (13), the function of which is not known.…”

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Biochemical and Genetic Analysis of the Four DNA Ligases of Mycobacteria

Gong

Martins

Bongiorno

et al. 2004

Journal of Biological Chemistry

129

142

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Mycobacterium tuberculosis encodes an NAD ؉ -dependent DNA ligase (LigA) plus three distinct ATP-dependent ligase homologs (LigB, LigC, and LigD). Here we purify and characterize the multiple DNA ligase enzymes of mycobacteria and probe genetically whether the ATP-dependent ligases are required for growth of M. tuberculosis. We find significant differences in the reactivity of mycobacterial ligases with a nicked DNA substrate, whereby LigA and LigB display vigorous nick sealing activity in the presence of NAD ؉ and ATP, respectively, whereas LigC and LigD, which have ATPspecific adenylyltransferase activity, display weak nick joining activity and generate high levels of the DNA- DNA ligases are grouped into two families, ATP-dependent ligases and NAD ϩ -dependent ligases, according to their nucleotide substrate requirement (1, 2). The ligase reaction entails three nucleotidyl transfer steps (1). In the first step, attack by ligase on the ␣ phosphorus of ATP or NAD ϩ results in release of PP i or NMN and formation of a covalent ligase-adenylate intermediate. In the second step, the AMP is transferred to the 5Ј end of the 5Ј phosphate-terminated DNA strand to form DNA-adenylate (AppDNA). In the third step, ligase catalyzes attack by a DNA 3Ј-OH on DNA-adenylate to join the two polynucleotides and liberate AMP. ATP-dependent DNA ligases are found in all three domains of life (Bacteria, Archaea, and Eukarya), whereas the NAD ϩ -dependent enzymes are present only in bacteria and entomopoxviruses (1-7).All known bacteria encode a highly conserved NAD ϩ -dependent DNA ligase (LigA). A conditional mutant of Escherichia coli LigA results in growth arrest at the restrictive temperature; thus LigA is essential in E. coli (8,9). LigA is also essential in Salmonella typhimurium, Bacillus subtilis, and Staphylococcus aureus (10 -12). Some bacteria, including E. coli, S. typhimurium, Shigella flexneri, Yersinia pestis, and Pseudomonas putida, have a second NAD ϩ -dependent ligase (13), the function of which is not known.The presumption that bacteria encode only NAD ϩ -dependent DNA ligases was overturned by the demonstration in 1997 of an ATP-dependent ligase in the respiratory pathogen Haemophilus influenzae (5). The 268-amino acid (aa) 1 H. influenzae ligase consists of a minimized catalytic domain. ATP-dependent ligase homologues coexist with NAD ϩ -dependent enzymes in several other bacterial species, including major human pathogens such as Neisseria meningitidis, Y. pestis, Vibrio cholerae, Pseudomonas aeruginosa, and Mycobacterium tuberculosis (3,14,15).Remarkably, M. tuberculosis encodes three distinct ATP-dependent ligase homologues (LigB, LigC, and LigD) plus an NAD ϩ -dependent ligase (LigA) (Fig. 1) (16). To begin to understand the rationale for this plethora of ligases in a single bacterium, we have produced and characterized recombinant versions of the mycobacterial DNA ligase enzymes and probed genetically the essentiality or dispensability of the ATP-dependent ligases for growth of M. tuberculosis. EXPERIMENTAL ...

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A second NAD+-dependent DNA ligase (LigB) in Escherichia coli

Cited by 43 publications

References 25 publications

Recombination and Annealing Pathways Compete for Substrates in Making rrn Duplications in Salmonella enterica

Recombination and Annealing Pathways Compete for Substrates in Making rrn Duplications in Salmonella enterica

Specific and Potent Inhibition of NAD+-dependent DNA Ligase by Pyridochromanones

Biochemical and Genetic Analysis of the Four DNA Ligases of Mycobacteria

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