Functional analysis of DNA replication fork reversal catalyzed by Mycobacterium tuberculosis RuvAB proteins

Initially discovered in Escherichia coli, RuvAB proteins are ubiquitous in bacteria and play a dual role as molecular motor proteins responsible for branch migration of the Holliday junction(s) and reversal of stalled replication forks. Despite mounting genetic evidence for a crucial role of RuvA and RuvB proteins in reversal of stalled replication forks, the mechanistic aspects of this process are still not fully understood. Here, we elucidate the ability of Mycobacterium tuberculosis RuvAB (MtRuvAB) complex to catalyze the reversal of replication forks using a range of DNA replication fork substrates. Our studies show that MtRuvAB, unlike E. coli RuvAB, is able to drive replication fork reversal via the formation of Holliday junction intermediates, suggesting that RuvAB-catalyzed fork reversal involves concerted unwinding and annealing of nascent leading and lagging strands. We also demonstrate the reversal of replication forks carrying hemi-replicated DNA, indicating that MtRuvAB complex-catalyzed fork reversal is independent of symmetry at the fork junction. The fork reversal reaction catalyzed by MtRuvAB is coupled to ATP hydrolysis, is processive, and culminates in the formation of an extended reverse DNA arm. Notably, we found that sequence heterology failed to impede the fork reversal activity of MtRuvAB. We discuss the implications of these results in the context of recognition and processing of varied types of replication fork structures by RuvAB proteins.     

Crystal structures of Mycobacterium smegmatis RecA and its nucleotide complexes

The crystal structures of Mycobacterium smegmatis RecA (RecA(Ms)) and its complexes with ADP, ATPgammaS, and dATP show that RecA(Ms) has an expanded binding site like that in Mycobacterium tuberculosis RecA, although there are small differences between the proteins in their modes of nucleotide binding. Nucleotide binding is invariably accompanied by the movement of Gln 196, which appears to provide the trigger for transmitting the effect of nucleotide binding to the DNA-binding loops. These observations provide a framework for exploring the known properties of the RecA proteins.     

Primitive neuroectodermal tumor of the kidney. A report of two cases diagnosed by fine needle aspiration cytology

BACKGROUND: Primitive neurocetodermal tumors (PNETs) constitute a family of neoplasms of presumed neuroectrodermal origin most often presenting as bone or soft tissue masses. There are very few reported cases of PNET of the kidney and none diagnosed by fine needle aspiration cytology (FNAC), to the best of our knowledge, in the world literature. We present two cases of renal PNET diagnosed on cytology. CASES: Two patients with renal masses were diagnosed as having PNET on FNAC. Cytologically the tumors showed a dispersed population of malignant small round cells with focal rosette formation and perivascular arrangement of tumor cells. Immunohistochemistry on the cell blocks in both cases showed strong membrane positivity for CD99 (MIC2). Cytogenetic studies in both cases showed the characteristic t(11;22)(q24;q12) translocation, with additional chromosomal abnormalities in case 2. CONCLUSION: PNET of the kidney is a distinct entity and can be diagnosed on fine needle aspiration smears and confirmed with immunohistochemistry and cytogenetic studies. A diagnosis of PNET must be included in the differential diagnosis of renal masses in adolescents and young adults.     

Inhibition of Rho protein stimulates iNOS expression in rat vascular smooth muscle cells

Inducible nitric oxide synthase (iNOS) in vascular smooth muscle cells (VSMCs) is upregulated in arterial injury and plays a role in regulating VSMC proliferation and restenosis. Inflammatory cytokines [e.g., interleukin-1beta (IL-1beta)] released during vascular injury induce iNOS. Small GTP-binding proteins of the Ras superfamily play a major role in IL-1beta-dependent signaling pathways. In this study, we examined the role of Rho GTPases in regulating iNOS expression in VSMCs. Treatment of VSMCs with mevastatin, which inhibits isoprenylation of Rho and other small GTP-binding proteins, produced significantly higher amounts of IL-1beta-evoked NO and iNOS protein compared with control. Similarly, bacterial toxins [Toxin B from Clostridium difficile and C3 ADP-ribosyl transferase (C3) toxin from Clostridium botulinium] that specifically inactivate Rho proteins increased NOS products (NO and citrulline) and iNOS expression. Toxin B increased the activity of iNOS promoter-reporter construct in VSMCs. Both toxins enhanced IL-1beta-stimulated iNOS expression and NO production. These data demonstrate for the first time that inhibition of Rho induces iNOS and suggest a role for Rho protein in IL-1beta-stimulated NO production in VSMCs.     

The RecA intein of Mycobacterium tuberculosis promotes cleavage of ectopic DNA sites. Implications for the dispersal of inteins in natural populations

The RecA intein of Mycobacterium tuberculosis, a novel double-stranded DNA endonuclease, requires both Mn(2+) and ATP for efficient cleavage of the inteinless recA allele. In this study, we show that Mg(2+) alone was sufficient to stimulate PI-MtuI to cleave double-stranded DNA at ectopic sites. In the absence of Mg(2+), PI-MtuI formed complexes with topologically different forms of DNA containing ectopic recognition sequences with equal affinity but failed to cleave DNA. We observed that PI-MtuI was able to inflict double-strand breaks robustly within the ectopic recognition sequence to generate either a blunt end or 1-2-nucleotide 3'-hydroxyl overhangs. Mutational analyses of the presumptive metal ion-binding ligands (Asp(122), Asp(222), and Glu(220)) together with immunoprecipitation assays provided compelling evidence to link both the Mg(2+)- and Mn(2+) and ATP-dependent endonuclease activities to PI-MtuI. The kinetic mechanism of PI-MtuI promoted cleavage of ectopic DNA sites proceeded through a sequential mechanism with transient accumulation of nicked circular duplex DNA as an intermediate. Together, these data suggest that PI-MtuI, like group II introns, might mediate ectopic DNA transposition and hence its lateral transfer in natural populations.     

DNA-Binding Activities of Hop1 Protein, a Synaptonemal Complex Component from Saccharomyces cerevisiae

The meiosis-specific HOP1 gene is important both for crossing over between homologs and for production of viable spores. hop1 diploids fail to assemble synaptonemal complex (SC), which normally provides the framework for meiotic synapsis. Immunochemical methods have shown that the 70-kDa HOP1 product is a component of the SC. To assess its molecular function, we have purified Hop1 protein to homogeneity and shown that it forms dimers and higher oligomers in solution. Consistent with the zinc-finger motif in its sequence, the purified protein contained about 1 mol equivalent of zinc whereas mutant protein lacking a conserved cysteine within this motif did not. Electrophoretic gel mobility shift assays with different forms of M13 DNA showed that Hop1 binds more readily to linear duplex DNA and negatively superhelical DNA than to nicked circular duplex DNA and even more weakly to single-stranded DNA. Linear duplex DNA binding was enhanced by the addition of Zn²⁺, was stronger for longer DNA fragments, and was saturable to about 55 bp/protein monomer. Competitive inhibition of this binding by added oligonucleotides suggests preferential affinity for G-rich sequences and weaker binding to poly(dA-dT). Nuclear extracts of meiotic cells caused exonucleolytic degradation of linear duplex DNA if the extracts were prepared from hop1 mutants; addition of purified Hop1 conferred protection against this degradation. These findings suggest that Hop1 acts in meiotic synapsis by binding to sites of double-strand break formation and helping to mediate their processing in the pathway to meiotic recombination.     

Active nucleoprotein filaments of single-stranded binding protein and recA protein on single-stranded DNA have a regular repeating structure.

When E. coli single-stranded DNA binding protein (SSB) coats single-stranded DNA (ssDNA) in the presence of 1 mM MgCl2 it inhibits the subsequent binding of recA protein, whereas SSB binding to ssDNA in 12 mM MgCl2 promotes the binding of recA protein. These two conditions correspond respectively to those which produce 'smooth' and 'beaded' forms of ssDNA-SSB filaments. By gel filtration and immunoprecipitation we observed active nucleoprotein filaments of recA protein and SSB on ssDNA that contained on average 1 monomer of recA protein per 4 nucleotides and 1 monomer of SSB per 20-22 nucleotides. Filaments in such a mixture, when digested with micrococcal nuclease produced a regular repeating pattern, approximately every 70-80 nucleotides, that differed from the pattern observed when only recA protein was bound to the ssDNA. We conclude that the beaded ssDNA-SSB nucleoprotein filament readily binds recA protein and forms an intermediate that is active in the formation of joint molecules and can retain substantially all of the SSB that was originally bound.     

Characterization and comparison of the soluble and membrane-bound cyclic AMP-dependent protein kinase from swine kidney

The catalytic subunits of adenosine 3′:5′ monophosphate-dependent protein kinase (ATP:protein transferase, E.C. 2.7.1.1.37) from the soluble and membrane fractions of swine kidney were purified to homogeneity by a new procedure and their structural, kinetic and immunological properties were compared. The specific activities of the purified enzymes were 2.35 and 2.6 µmol/min/mg of protein, with histone as the substrate. Both preparations contained a single polypeptide chain, and only one band was observed upon polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. The molecular weight of both enzymes determined by gel electrophoresis was 42 000 ± 1000, and sedimentation equilibrium yielded a value of 41000 ± 800. Analysis by sedimentation velocity showed the presence of a single peak with and S_20,w of 3.1 ± 0.2 for each preparation. The amino acid compositions are very similar, and each enzyme contains about one residue of cysteine which is essential for enzymatic activity. ATP and Mg²⁺ protect both enzymes from inhibition by thiol specific reagents to the same extent. The catalytic subunits have similar apparent K m's for protein substrates. The enzymes exhibit single completely confluent precipitin lines when examined by immunodiffusion and the particulate catalytic subunit competitively displaces the soluble ¹²⁵I-catalytic subunit in homologous radioimmunoassays. The soluble and particulate ¹²⁵I-catalytic subunits bind to the regulatory subunits in the washed plasma membranes with attendent loss of kinase activity, which could be reversed by cyclic AMP. The results of experiments with kidney cortex slices treated with parathyroid hormone, epinephrine or dibutyryl cyclic AMP showed the translocation of phosphotransferase activity from the cytosol to the particulate membrane fraction. Taken collectively, these observations suggest that only one form of the catalytic subunit of cyclic AMP-dependent protein kinase is present in swine kidney, and that it may exchange between the cytosol and membrane fractions in response to specific physiological signals.