Prokaryotic DNA Crossroads: Holliday Junction Formation and Resolution

Cells are continually exposed to a multitude of internal and external stressors, which give rise to various types of DNA damage. To protect the integrity of their genetic material, cells are equipped with a repertoire of repair proteins that engage in various repair mechanisms, facilitated by intricate networks of protein-protein and protein-DNA interactions. Among these networks is the homologous recombination (HR) system, a molecular repair mechanism conserved in all three domains of life. On one hand, HR ensures high-fidelity, template-dependent DNA repair, while on the other hand, it results in the generation of combinatorial genetic variations through allelic exchange. Despite substantial progress in understanding this pathway in bacteria, yeast, and humans, several critical questions remain unanswered, including the molecular processes leading to the exchange of DNA segments, the coordination of protein binding, conformational switching during branch migration, and the resolution of Holliday Junctions (HJs). This Review delves into our current understanding of the HR pathway in bacteria, shedding light on the roles played by various proteins or their complexes at different stages of HR. In the first part of this Review, we provide a brief overview of the end resection processes and the strand-exchange reaction, offering a concise depiction of the mechanisms that culminate in the formation of HJs. In the latter half, we expound upon the alternative methods of branch migration and HJ resolution more comprehensively and holistically, considering the historical research timelines. Finally, when we consolidate our knowledge about HR within the broader context of genome replication and the emergence of resistant species, it becomes evident that the HR pathway is indispensable for the survival of bacteria in diverse ecological niches.

Division of labor between SOS and PafBC in mycobacterial DNA repair and mutagenesis

DNA repair systems allow microbes to survive in diverse environments that compromise chromosomal integrity. Pathogens such as Mycobacterium tuberculosis must contend with the genotoxic host environment, which generates the mutations that underlie antibiotic resistance. Mycobacteria encode the widely distributed SOS pathway, governed by the LexA repressor, but also encode PafBC, a positive regulator of the transcriptional DNA damage response (DDR). Although the transcriptional outputs of these systems have been characterized, their full functional division of labor in survival and mutagenesis is unknown. Here, we specifically ablate the PafBC or SOS pathways, alone and in combination, and test their relative contributions to repair. We find that SOS and PafBC have both distinct and overlapping roles that depend on the type of DNA damage. Most notably, we find that quinolone antibiotics and replication fork perturbation are inducers of the PafBC pathway, and that chromosomal mutagenesis is codependent on PafBC and SOS, through shared regulation of the DnaE2/ImuA/B mutasome. These studies define the complex transcriptional regulatory network of the DDR in mycobacteria and provide new insight into the regulatory mechanisms controlling the genesis of antibiotic resistance in M. tuberculosis.

Mycobacterial Mutagenesis and Drug Resistance Are Controlled by Phosphorylation- and Cardiolipin-Mediated Inhibition of the RecA Coprotease

Infection with Mycobacterium tuberculosis continues to cause substantial human mortality, in part because of the emergence of antimicrobial resistance. Antimicrobial resistance in tuberculosis is solely the result of chromosomal mutations that modify drug activators or targets, yet the mechanisms controlling the mycobacterial DNA-damage response (DDR) remain incompletely defined. Here, we identify RecA serine 207 as a multifunctional signaling hub that controls the DDR in mycobacteria. RecA S207 is phosphorylated after DNA damage, which suppresses the emergence of antibiotic resistance by selectively inhibiting the LexA coprotease function of RecA without affecting its ATPase or strand exchange functions. Additionally, RecA associates with the cytoplasmic membrane during the mycobacterial DDR, where cardiolipin can specifically inhibit the LexA coprotease function of unmodified, but not S207 phosphorylated, RecA. These findings reveal that RecA S207 controls mutagenesis and antibiotic resistance in mycobacteria through phosphorylation and cardiolipin-mediated inhibition of RecA coprotease function.

Mycobacterium tuberculosis RuvX is a Holliday junction resolvase formed by dimerisation of the monomeric YqgF nuclease domain

The Mycobacterium tuberculosis genome possesses homologues of the ruvC and yqgF genes that encode putative Holliday junction (HJ) resolvases. However, their gene expression profiles and enzymatic properties have not been experimentally defined. Here we report that expression of ruvC and yqgF is induced in response to DNA damage. Protein-DNA interaction assays with purified M. tuberculosis RuvC (MtRuvC) and YqgF (MtRuvX) revealed that both associate preferentially with HJ DNA, albeit with differing affinities. Although both MtRuvC and MtRuvX cleaved HJ DNA in vitro, the latter displayed robust HJ resolution activity by symmetrically related, paired incisions. MtRuvX showed a higher binding affinity for the HJ structure over other branched recombination and replication intermediates. An MtRuvX(D28N) mutation, eliminating one of the highly conserved catalytic residues in this class of endonucleases, dramatically reduced its ability to cleave HJ DNA. Furthermore, a unique cysteine (C38) fulfils a crucial role in HJ cleavage, consistent with disulfide-bond mediated dimerization being essential for MtRuvX activity. In contrast, E. coli YqgF is monomeric and exhibits no branched DNA binding or cleavage activity. These results fit with a functional modification of YqgF in M. tuberculosis so that it can act as a dimeric HJ resolvase analogous to that of RuvC.

Structural studies on Mycobacterium tuberculosis RecA: molecular plasticity and interspecies variability

Structures of crystals of Mycobacterium tuberculosis RecA, grown and analysed under different conditions, provide insights into hitherto underappreciated details of molecular structure and plasticity. In particular, they yield information on the invariant and variable features of the geometry of the P-loop, whose binding to ATP is central for all the biochemical activities of RecA. The strengths of interaction of the ligands with the P-loop reveal significant differences. This in turn affects the magnitude of the motion of the 'switch' residue, Gln195 in M. tuberculosis RecA, which triggers the transmission of ATP-mediated allosteric information to the DNA binding region. M. tuberculosis RecA is substantially rigid compared with its counterparts from M. smegmatis and E. coli, which exhibit concerted internal molecular mobility. The interspecies variability in the plasticity of the two mycobacterial proteins is particularly surprising as they have similar sequence and 3D structure. Details of the interactions of ligands with the protein, characterized in the structures reported here, could be useful for design of inhibitors against M. tuberculosis RecA.

Suramin is a potent and selective inhibitor of Mycobacterium tuberculosis RecA protein and the SOS response: RecA as a potential target for antibacterial drug discovery

OBJECTIVES

In eubacteria, RecA is essential for recombinational DNA repair and for stalled replication forks to resume DNA synthesis. Recent work has implicated a role for RecA in the development of antibiotic resistance in pathogenic bacteria. Consequently, our goal is to identify and characterize small-molecule inhibitors that target RecA both in vitro and in vivo.

METHODS

We employed ATPase, DNA strand exchange and LexA cleavage assays to elucidate the inhibitory effects of suramin on Mycobacterium tuberculosis RecA. To gain insights into the mechanism of suramin action, we directly visualized the structure of RecA nucleoprotein filaments by atomic force microscopy. To determine the specificity of suramin action in vivo, we investigated its effect on the SOS response by pull-down and western blot assays as well as for its antibacterial activity.

RESULTS

We show that suramin is a potent inhibitor of DNA strand exchange and ATPase activities of bacterial RecA proteins with IC(50) values in the low micromolar range. Additional evidence shows that suramin inhibits RecA-catalysed proteolytic cleavage of the LexA repressor. The mechanism underlying such inhibitory actions of suramin involves its ability to disassemble RecA-single-stranded DNA filaments. Notably, suramin abolished ciprofloxacin-induced recA gene expression and the SOS response and augmented the bactericidal action of ciprofloxacin.

CONCLUSIONS

Our findings suggest a strategy to chemically disrupt the vital processes controlled by RecA and hence the promise of small molecules for use against drug-susceptible as well as drug-resistant strains of M. tuberculosis for better infection control and the development of new therapies.

Profile of blood donors and reasons for deferral in coastal South India

BACKGROUND

A blood transfusion is a life-saving procedure in many instances. An adequate supply of safe blood is ensured by exercising donor deferral criteria and screening for Transfusion Transmitted Infections (TTI). The aim of this paper is to study the profile of blood donors and reasons for donor deferral in coastal South India.

METHOD

The study was conducted at a tertiary care hospital in Mangalore. All those who donated between 1 January 2008 and 31 December 2008 were included in the study. Data was collected using a pre-tested semi-structured proforma and analysed using SPSS version 11.5.

RESULTS

Most of the donors were under the age of 25 (42.92%). Donors were predominantly male (95.20%). In terms of occupation, most subjects were students (28.01%) followed by businessmen (18.61%). Slightly more than three-quarters of the donors (77.20%) were replacement donors. The main reasons for deferral were consumption of medication in the past 72 hours (15.15%), hypertension (13.18%), a low haemoglobin level (12.34%) and alcohol intake in the past 72 hours (12.20%). Among the TTIs identified, most samples were positive for Hepatitis B surface Antigen - HBsAg (0.87%) or tested positive for Anti-Hepatitis C (HCV antibodies (0.36%).

CONCLUSION

From the study it was concluded that the majority of the donor population was young and educated. The reason for donation was mainly replacement rather than voluntary. This issue needs to be addressed by exercising proactive measures to increase the number of voluntary, nonremunerated, low-risk donors.

Ferroelectric and Magnetic Properties of Hot-Pressed BiFeO3-PVDF Composite Films

The ferroelectric and magnetic properties of hot-pressed BiFeO3- (BFO) polyvinylidene fluoride (PVDF) composite films have been studied. The BiFeO3 (BFO) ceramics have been synthesized by a rapid liquid phase sintering technique. The X-ray diffraction (XRD) studies revealed that the impure phase observed in pure BFO ceramics was significantly reduced in the composite films. The presence of both ferroelectric and magnetic hysteresis loops confirms the multiferroic nature of the composite films at room temperature. A well-saturated ferroelectric hysteresis loop with a remanent polarization (Pr)∼4.8 μC-cm-2 and coercive field (Ec)∼1.55 kV/cm has been observed in composite thin films at room temperature. The magnetic hysteresis loops were traced at room temperature with SQUID. The remanent magnetization (Mr)∼3.0×10−3 emu/gm and coercive field (Hc)∼0.99 kOe was observed in the composite film. The magnetic polarization of the composite films has found to be enhanced as compared to pure BFO and correlated to reduction in BFO impure peak intensity.

Effect of administration and withdrawal of oral contraceptive pills on serum lipids and lipoproteins

We studied the effects of oral contraceptive pills (OCP) supplied by the Govt of India in its Family Welfare Campaign, on serum lipid levels of women. The OCP, containing 30 micrograms ethinyl estradiol and 1 mg of norethisterone acetate were administered to the women for six months continuously and serum lipid levels were estimated after three and six months of the treatment. There were no significant changes in serum cholesterol, high density lipoprotein (HDL), low density lipoprotein (LDL), serum triglycerides and very low density lipoprotein (VLDL). In a simultaneous study we also measured serum lipid levels at 3 and 6 months after withdrawal of the pills in women who had been receiving OCP containing 50 micrograms of ethinyl estradiol and 0.5 mg of one of the progesterones for the past 1 1/2 to 2 years continuously. Only serum LDL level fell significantly (P less than 0.01) on 3 months withdrawal period. It is concluded that 6 months of usage of the OCP marketed by the Govt. of India does not affect the serum lipid profile.