Structural studies on MtRecA-nucleotide complexes: insights into DNA and nucleotide binding and the structural signature of NTP recognition

RecA protein plays a crucial role in homologous recombination and repair of DNA. Central to all activities of RecA is its binding to Mg+2-ATP. The active form of the protein is a helical nucleoprotein filament containing the nucleotide cofactor and single-stranded DNA. The stability and structure of the helical nucleoprotein filament formed by RecA are modulated by nucleotide cofactors. Here we report crystal structures of a MtRecA-ADP complex, complexes with ATPS in the presence and absence of magnesium as well as a complex with dATP and Mg+2. Comparison with the recently solved crystal structures of the apo form as well as a complex with ADP-AlF4 confirms an expansion of the P-loop region in MtRecA, compared to its homologue in Escherichia coli, correlating with the reduced affinity of MtRecA for ATP. The ligand bound structures reveal subtle variations in nucleotide conformations among different nucleotides that serve in maintaining the network of interactions crucial for nucleotide binding. The nucleotide binding site itself, however, remains relatively unchanged. The analysis also reveals that ATPS rather than ADP-AlF4 is structurally a better mimic of ATP. From among the complexed structures, a definition for the two DNA-binding loops L1 and L2 has clearly emerged for the first time and provides a basis to understand DNA binding by RecA. The structural information obtained from these complexes correlates well with the extensive biochemical data on mutants available in the literature, contributing to an understanding of the role of individual residues in the nucleotide binding pocket, at the molecular level. Modeling studies on the mutants again point to the relative rigidity of the nucleotide binding site. Comparison with other NTP binding proteins reveals many commonalties in modes of binding by diverse members in the structural family, contributing to our understanding of the structural signature of NTP recognition

Allergic Mastocytic Gastroenteritis and Colitis: An Unexplained Etiology in Chronic Abdominal Pain and Gastrointestinal Dysmotility

Abdominal pain, bloating, early satiety, and changes in bowel habits are common presenting symptoms in individuals with functional GI disorders. Emerging data suggests that these symptoms may be associated with mast cell excess and/or mast cell instability in the GI tract. The aim of this retrospective study was to evaluate the contribution of mast cells to the aforementioned symptoms in individuals with a history of atopic disease. A retrospective chart review of individuals seen in a university GI practice was conducted and twenty-four subjects were identified. The majority had abdominal pain, early satiety, and nocturnal awakening. 66.7% and 37.5% had a history of environmental and/or food allergy. Solid gastric emptying was increased as were the mean number of mast cells reported on biopsies from the stomach, small bowel, and colon (>37/hpf) by CD117 staining. Mean whole blood histamine levels were uniformly elevated. This study suggests that in individuals with these characteristics, consideration should be given to staining their gastrointestinal biopsies for mast cells as this may provide them with relatively non-toxic but highly targeted treatment options. Allergic gastroenteritis and colitis may represent a third type of GI mast cell disorder along with mast cell activation syndrome and mastocytic enterocolitis

Shoaling of Metapenaeus dobsoni in the inshore waters of Malpe

Along the Dakshina Kannada cost the monsoon months (June-August) in every year are usually observed as closed season by the mechanised fishing boats. During this time a variety of artisanal crafts and gears are operated by the local fishermen

Crystallographic identification of an ordered C-terminal domain and a second nucleotide-binding site in RecA: new insights into allostery

RecA protein is a crucial and central component of the homologous recombination and DNA repair machinery. Despite numerous studies on the protein, several issues concerning its action, including the allosteric regulation mechanism have remained unclear. Here we report, for the first time, a crystal structure of a complex of Mycobacterium smegmatis RecA (MsRecA) with dATP, which exhibits a fully ordered C-terminal domain, with a second dATP molecule bound to it. ATP binding is an essential step for all activities of RecA, since it triggers the formation of active nucleoprotein filaments. In the crystal filament, dATP at the first site communicates with a dATP of the second site of an adjacent subunit, through conserved residues, suggesting a new route for allosteric regulation. In addition, subtle but definite changes observed in the orientation of the nucleotide at the first site and in the positions of the segment preceding loop L2 as well as in the segment 102–105 situated between the 2 nt, all appear to be concerted and suggestive of a biological role for the second bound nucleotide

Transmission of Cowpea Mild Mottle Virus by Bemisia tabaci in a Nonpersistent Manner

In studies in India, individual adults of Bemisia tabaci (Gennadius) acquired cowpea mild mottle virus (CMMV) after an acquisition feed on infected soyabean plants and transmitted it within 5 min to healthy soyabean plants. Starvation before the acquisition feed had no influence on transmission, but starvation after the acquisition feed decreased transmission frequency. Irrespective of the length of the acquisition feed, the ability to transmit CMMV was retained for only 4 successive inoculation access periods of 5 min each, but adults that lost the ability to transmit the virus could acquire and transmit it again. CMMV was not detected by enzyme-linked immunosorbent assay in adults that had been provided with access to infected plants for 1-8 h

Homologous recombination in mycobacteria

In recent years, considerable effort and resources have been expended to develop targeted gene delivery methods, and generation of auxotrophic mutants of mycobacteria. The results of these studies suggest that mycobacteria exhibit a wide range of recombination rates, which vary from loci to loci. Here we review the methods developed for allele exchange and targeted gene disruption as well as the mechanistic aspects of homologous recombination in mycobacteria. The results of whole genome, functional and structural analyses of Mycobacterium tuberculosis and Mycobacterium smegmatis RecA and SSB proteins provide insights into variations of the prototypic Escherichia coli paradigm. This variation of a common theme might allow mycobacteria to function in their natural but complex physiological environments

Isolation and characterization of a geminivirus causing yellow mosaic disease of horsegram (Macrotyloma uniflorum (Lam.) Verdc.) in India.

Horsegram yellow mosaic disease was shown to be caused by a geminivirus; horsegram yellow mosaic virus (HYMV). The virus could not be transmitted by mechanical sap inoculation. Leaf dip and purified virus preparations showed geminate virus particles, measuring 15-18 * 30 nm. An antiserum for HYMV was produced and in enzyme-linked immunosorbent assay (ELISA) and immunosorbent electron microscopy (ISEM) tests HYMV was detected in leaf extracts of fieldinfected bambara groundnut, french bean, groundnut, limabean, mungbean, pigeonpea and soybean showing yellow mosaic symptoms. Bemisia tabaci fed on purified HYMV through a parafilm membrane transmitted the virus to all the hosts listed above but not to Ageratum conyzoides, okra, cassava, cowpea, Croton bonplandianus, Lab-lab purpureus, Malvastrum coromandalianum and tomato. No reaction was obtained in ELISA and ISEM tests between HYMV antibodies and extracts of plants diseased by whitefly-transmitted agents in India such as A. conyzoides yellow mosaic, okra yellow vein mosaic, C. bonplandianus, yellow vein mosaic, M. coromandalianum yellow vein mosaic, tomato leaf curl and cassava mosaic. HYMV was also not found to be related serologically to bean golden mosaic, virus

An unusual catch of sharks in a purse seine at Malpe, Karnataka

An unusual catch of sharks in a purse seine fishery at Malpe on the Dakshlna Kannada coast in Karnataka On 10-10-1990 was observed. A single purse seine boat landed approximately 3.5 tonnes of sharks together with the seerflsh Scomberomorous commerson, (400 kg), catfish Tachysurus serratus (100 kg) and the kingfish Rachycentron canadus (100 kg) . The sharks were identified as the black-tip shark Carcharhtnus limbatus

Saccharomyces cerevisiae Mre11 is a high-affinity G4 DNA-binding protein and a G-rich DNA-specific endonuclease: implications for replication of telomeric DNA

In Saccharomyces cerevisiae, Mre11p/Rad50p/Xrs2p (MRX) complex plays a vital role in several nuclear processes including cellular response to DNA damage, telomere length maintenance, cell cycle checkpoint control and meiotic recombination. Telomeres are comprised of tandem repeats of G-rich DNA and are incorporated into non-nucleosomal chromatin. Although the structure of the yeast telomeric DNA is poorly understood, it has been suggested that the G-rich sequences can fold into G4 DNA, which has been shown to inhibit DNA synthesis by telomerase. However, little is known about the factors and mechanistic aspects of the generation of appropriate termini for DNA synthesis by telomerase. Here, we show that S.cerevisiae Mre11 protein (ScMre11p) possesses substantially higher binding affinity for G4 DNA, over single- or double-stranded DNA, and binding was inhibited by poly(dG) or porphyrin. Binding of ScMre11p to G4 DNA was most robust, compared with G2′ DNA and the resulting protein–DNA complexes were strikingly very resistant to dissociation by NaCl. Remarkably, binding of ScMre11p to G4 DNA and G-rich single-stranded DNA was accompanied by the endonucleolytic cleavage at sites flanking the array of G residues and G-quartets in Mn(2+)-dependent manner. Collectively, these results suggest that ScMre11p is likely to play a major role in generating appropriate substrates for DNA synthesis by telomerase and telomere-binding proteins. We discuss the implications of these findings with regard to telomere length maintenance by telomerase-dependent and independent mechanisms

On a fin whale stranded at Someswara, South Kanara

A huge whale was observed floating near the shore at Ullal was dragged away from the shore into the sea for about 15-20 km and released by the trawler fishermen. But the whale was swept shoreward by strong waves and was stranded at Someswara beach which identified was Balaenoptera physalis. Morphometry were recorded and had Total length (tip of the lowerjaw to tipofthefluke) 1,402 cm Distance between flipper base to origin of fluke 1,037cm and Distance from origin of fluke to genito-anal slit 457cms. The whale was a female with prominent genital opening with maximum girth at the region of flippers