A molecular mousetrap determines polarity of termination of DNA replication in E. coli

During chromosome synthesis in Escherichia coli, replication forks are blocked by Tus bound Ter sites on approach from one direction but not the other. To study the basis of this polarity, we measured the rates of dissociation of Tus from forked TerB oligonucleotides, such as would be produced by the replicative DnaB helicase at both the fork-blocking (nonpermissive) and permissive ends of the Ter site. Strand separation of a few nucleotides at the permissive end was sufficient to force rapid dissociation of Tus to allow fork progression. In contrast, strand separation extending to and including the strictly conserved G-C(6) base pair at the nonpermissive end led to formation of a stable locked complex. Lock formation specifically requires the cytosine residue, C(6). The crystal structure of the locked complex showed that C(6) moves 14 A from its normal position to bind in a cytosine-specific pocket on the surface of Tus.     

Mechanism of homologous recombination: mediators and helicases take on regulatory functions

Homologous recombination (HR) is an important mechanism for the repair of damaged chromosomes, for preventing the demise of damaged replication forks, and for several other aspects of chromosome maintenance. As such, HR is indispensable for genome integrity, but it must be regulated to avoid deleterious events. Mutations in the tumour-suppressor protein BRCA2, which has a mediator function in HR, lead to cancer formation. DNA helicases, such as Bloom's syndrome protein (BLM), regulate HR at several levels, in attenuating unwanted HR events and in determining the outcome of HR. Defects in BLM are also associated with the cancer phenotype. The past several years have witnessed dramatic advances in our understanding of the mechanism and regulation of HR.     

Emergence of distinct genetic variants in the population of primary Bartonella henselae isolates

Bartonella henselae isolates from different hosts display a marked genetic heterogeneity, as determined by pulsed-field gel electrophoresis (PFGE). The aim of the present study was to determine whether different genetic variants may coexist within the population of distinct B. henselae isolates and could be detected by PFGE. Three primary B. henselae isolates and the B. henselae reference strains ATCC 49793 and 49882 were subjected as single colony derived cultures in quadruplicate to PFGE analysis upon restriction with SmaI or NotI. Up to 4 fragment differences were found among the cultures obtained from each primary isolate, indicating the coexistence of genetic variants in the population of primary B. henselae isolates. The clonal relatedness of the genetic variants was confirmed by arbitrarily primed PCR and multi-locus sequence typing. In contrast to the primary isolates, no variants were detected among the single colony derived cultures of the high-passage ATCC strains. We hypothesized that the coexistence of different genetic variants may represent a feature that is restricted to primary or low-passage B. henselae isolates. The primary isolates were serially passed in vitro and then subjected as single colony derived cultures to PFGE analysis, which now revealed identical patterns among the quadruplicate cultures of each high-passage isolate. These results suggest that the population of a primary B. henselae isolate is composed of distinct genetic variants, which may disappear upon repeated passages on artificial culture media. Generation of genetic variants by B. henselae may represent an escape mechanism to circumvent the host specific immune responses.     

Proteomics gets faster and smarter

A report on the third annual joint meeting of the British Society for Proteome Research and the European Bioinformatics Institute, Hinxton, UK, 12-14 July 2006.     

Protein interactions of phosphatase and tensin homologue (PTEN) and its cancer-associated G20E mutant compared by using stable isotope labeling by amino acids in cell culture-based parallel affinity purification

The tumor suppressor PTEN (phosphatase and tensin homologue) negatively regulates the PI3K pathway through its lipid phosphatase activity and is one of the most commonly lost tumor suppressors in human cancers. Though the tumor suppressive function involves the lipid phosphatase-dependent and -independent activities of PTEN, the mechanism leading to the phosphatase-independent function of PTEN is understood poorly. Some PTEN mutants have lipid phosphatase activity but fail to suppress cell growth. Here, we use a cancer-associated mutant, G20E, to gain insight into the phosphatase-independent function of PTEN by investigating protein-protein interactions using MS-based stable isotope labeling by amino acids in cell culture (SILAC). A strategy named parallel affinity purification (PAP) and SILAC has been developed to prioritize interactors and to compare the interactions between wild-type and G20E PTEN. Clustering of the prioritized interactors acquired by the PAP-SILAC approach shows three distinct clusters: 1) wild-type-specific interactors, 2) interactors unique to the G20E mutant, and 3) proteins common to wild-type and mutant. These interactors are involved mainly in cell migration and apoptosis pathways. We further demonstrate that the wild-type-specific interactor, NUDTL16L1, is required for the regulatory function of wild-type PTEN in cell migration. These findings contribute to a better understanding of the mechanisms of the phosphatase-dependent and -independent functions of PTEN.     

Recombinant immunosuppressive protein from Pimpla hypochondrica venom (rVPr1) increases the susceptibility of Mamestra brassicae larvae to the fungal biological control agent, Beauveria bassiana

Although fungi are used to control a variety of insect pests, it is accepted that their usage could be increased if their efficacy was greater. The outcome of the interaction of a fungus and a pest insect may be influenced by a number of criteria, including the ability of the insect to mount effective immune responses against the pathogen. In view of this, we aimed to determine if a recombinant immunosuppressive wasp venom protein (rVPr1) can increase the susceptibility of larvae of the lepidopteran pest, Mamestra brassicae, to the fungal biological control agent, Beauveria bassiana. Bioassays indicated that when larvae were injected with 3.5 μl of rVPr1 and 100 B. bassiana conidia (combined injection assays), a significant reduction in survival of larvae occurred compared with each treatment on its own (P=0.006). Similar results were obtained when larvae were dipped in a solution containing 3 × 10(6) B. bassiana conidia per ml and then injected with 3.5 μl of rVPr1 2 days later (topical application assays), (P<0.001). These results indicate that rVPr1 can increase the efficacy of B. bassiana toward a lepidopteran pest, and are discussed within the context of insect immune responses and integrated pest management.     

Vitamin D receptor agonist doxercalciferol modulates dietary fat-induced renal disease and renal lipid metabolism

Diet-induced obesity (DIO) and insulin resistance in mice are associated with proteinuria, renal mesangial expansion, accumulation of extracellular matrix proteins, and activation of oxidative stress, proinflammatory cytokines, profibrotic growth factors, and the sterol regulatory element binding proteins, SREBP-1 and SREBP-2, that mediate increases in fatty acid and cholesterol synthesis. The purpose of the present study was to determine whether treatment of DIO mice with the vitamin D receptor (VDR) agonist doxercalciferol (1α-hydroxyvitamin D2) prevents renal disease. Our results indicate that treatment of DIO mice with the VDR agonist decreases proteinuria, podocyte injury, mesangial expansion, and extracellular matrix protein accumulation. The VDR agonist also decreases macrophage infiltration, oxidative stress, proinflammatory cytokines, and profibrotic growth factors. Furthermore, the VDR agonist also prevents the activation of the renin-angiotensin-aldosterone system including the angiotensin II type 1 receptor and the mineralocorticoid receptor. An additional novel finding of our study is that activation of VDR results in decreased accumulation of neutral lipids (triglycerides and cholesterol) and expression of adipophilin in the kidney by decreasing SREBP-1 and SREBP-2 expression and target enzymes that mediate fatty acid and cholesterol synthesis and increasing expression of the farnesoid X receptor. This study therefore demonstrates multiple novel effects of VDR activation in the kidney which prevent renal manifestations of DIO in the kidney.