The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016: implications for DNA restriction and translocation activity

Among four types of bacterial restriction enzymes that cleave a foreign DNA depending on its methylation status, type I enzymes composed of three subunits are interesting because of their unique DNA cleavage and translocation mechanisms performed by the restriction subunit (HsdR). The elucidated N-terminal fragment structure of a putative HsdR subunit from Vibrio vulnificus YJ016 reveals three globular domains. The nucleolytic core within an N-terminal nuclease domain (NTD) is composed of one basic and three acidic residues, which include a metal-binding site. An ATP hydrolase (ATPase) site at the interface of two RecA-like domains (RDs) is located close to the probable DNA-binding site for translocation, which is far from the NTD nucleolytic core. Comparison of relative domain arrangements with other functionally related ATP and/or DNA complex structures suggests a possible translocation and restriction mechanism of the HsdR subunit. Furthermore, careful analysis of its sequence and structure implies that a linker helix connecting two RDs and an extended region within the nuclease domain may play a central role in switching the DNA translocation into the restriction activity.     

Conformational evaluation of labeled C3′‐O‐P‐13CH2‐O‐C4″ phosphonate internucleotide linkage,a phosphodiester isostere

Modified internucleotide linkage featuring the C3′‐O‐P‐CH₂‐O‐C4″ phosphonate grouping as an isosteric alternative to the phosphodiester C3′‐O‐P‐O‐CH₂‐C4″ bond was studied in order to learn more on its stereochemical arrangement, which we showed earlier to be of prime importance for the properties of the respective oligonucleotide analogues. Two approaches were pursued: First, the attempt to prepare the model dinucleoside phosphonate with ¹³C‐labeled CH₂ group present in the modified internucleotide linkage that would allow for a more detailed evaluation of the linkage conformation by NMR spectroscopy. Second, the use of ab initio calculations along with molecular dynamics (MD) simulations in order to observe the most populated conformations and specify main structural elements governing the conformational preferences. To deal with the former aim, a novel synthesis of key labeled reagent (CH₃O)₂P(O)¹³CH₂OH for dimer preparation had to be elaborated using aqueous ¹³C‐formaldehyde. The results from both approaches were compared and found consistent. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 514–529, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Septin 11 Restricts InlB-mediated Invasion by Listeria

Septins are filament-forming GTPases implicated in several cellular functions, including cytokinesis. We previously showed that SEPT2, SEPT9, and SEPT11 colocalize with several bacteria entering into mammalian non-phagocytic cells, and SEPT2 was identified as essential for this process. Here, we investigated the function of SEPT11, an interacting partner of SEPT9 whose function is still poorly understood. In uninfected HeLa cells, SEPT11 depletion by siRNA increased cell size but surprisingly did not affect actin filament formation or the colocalization of SEPT9 with actin filaments. SEPT11 depletion increased Listeria invasion, and incubating SEPT11-depleted cells with beads coated with the Listeria surface protein InlB also led to increased entry as compared with control cells. Strikingly, as shown by fluorescence resonance energy transfer, the InlB-mediated stimulation of Met signaling remained intact in SEPT11-depleted cells. Taken together, our results show that SEPT11 is not required for the bacterial entry process and rather restricts its efficacy. Because SEPT2 is essential for the InlB-mediated entry of Listeria, but SEPT11 is not, our findings distinguish the roles of different mammalian septins.Septins were discovered in the budding yeast Saccharomyces cerevisiae (1) where they organize into a ring at the mother-bud neck during cell division (2). Septins are GTPases of 30-65 kDa found in most eukaryotes, except plants, sharing an essential role in cytokinesis (3, 4). Fourteen septins have been identified in humans and classified on the basis of sequence identity into four distinct groups (3, 5). Septins from different groups polymerize into hetero-oligomeric protein complexes and filaments and may associate with cellular membranes, actin filaments, and microtubules (6, 7). Septins are increasingly regarded as novel cytoskeletal elements (8), but their role in post-mitotic events remains poorly understood.The crystal structure of the SEPT2-SEPT6-SEPT7 complex recently highlighted that septins, as opposed to actin and microtubules, form non-polar filaments (9). In the SEPT7-SEPT6-SEPT2-SEPT2-SEPT6-SEPT7 complex, SEPT2 has a central role in filament formation (9), whereas SEPT6 is thought to be replaceable with other SEPT6 group members, including SEPT11 (3). Widely expressed in mammalian tissues (10), SEPT11 may also be a substitute for SEPT6 in other mammalian septin complexes such as SEPT7-SEPT9-SEPT11 (10) or SEPT5-SEPT7-SEPT11 (11). Because other septins homologous to SEPT11 might compensate for its deficiency (12), the degree to which SEPT11 is required for septin filament structure and function is not yet known. Listeria monocytogenes is an invasive bacterium that enters into most mammalian cells in vitro through the interaction of the bacterial surface protein InlB with its host cellular receptor Met, the hepatocyte growth factor receptor (13). We originally identified SEPT9 associated with phagosomes containing latex beads coated with InlB (14). Given the association of septins with the cytoskeleton, and the importance of the cytoskeleton in bacterial invasion, we have started investigating septin function during infection of invasive bacteria in non-phagocytic cells. We have discovered that SEPT9, and its interacting partners SEPT2 and SEPT11, are recruited as 0.6-μm collars next to actin at the site of entry of invasive bacteria (15). Although functional studies using siRNA³ have revealed an essential role for SEPT2 in regulating bacterial entry, the role of SEPT11 has not yet been investigated. We thus addressed SEPT11 function in the context of Listeria infection.     

Dynamic and structural scalings of the complexation between pDNA and bPEI in semidilute and low‐salt solutions

Using a combination of static and dynamic laser light scattering, we investigated the complexation of a supercoiled plasmid DNA (pDNA, 10⁴ bp) and a branched polyethyleneimine (bPEI, M_w = 25 kD) in semidilute and low‐salt aqueous solutions. Our results unearth some scaling laws for dynamic and structural properties of the resultant complexes (polyplexes) with different bPEI:pDNA (N:P) molar ratios. Namely, the average scattering intensity (<I>) and the average linewidth of the Rayleigh peak (<Γ>) are scaled to the scattering vector (q) as <I> ∝ q or <Γ> ∝ q, where α_S and α_D are two N:P dependent scaling exponents. The N:P ratio strongly affects the complexation. When N:P < 2.0, the motions of the negatively charged and extended pDNA chains and the polyplexes are highly correlated so that they behave like a transient network with a fractal dimension. As the N:P ratio increases, nearly all of pDNA chains condensed and the overall charge of the polyplexes reverses to slightly positive, resulting in a turbid dispersion of large loose aggregates made of smaller, but more compact, polyplexes. Further increase of N:P finally disrupts large loose aggregates, leading to a homogeneous transparent dispersion of the polyplexes. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 571–577, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

28-nor-oleanane-type triterpene saponins from Camellia japonica and their inhibitory activity on LPS-induced NO production in macrophage RAW264.7 cells

Four new 28-nor-oleanane-type triterpene oligoglycosides, camellenodiol 3-O-β-D-galactopyranosyl(1→2)[β-D-xylopyranosyl(1→2)-β-D-galactopyranosyl(1→3)]-β-D-glucuronopyranoside (2), camellenodiol 3-O-4'-O-acetyl-β-D-galactopyranosyl(1→2)[β-D-xylopyranosyl(1→2)-β-D-galactopyranosyl(1→3)]-β-D-glucuronopyranoside (4), camellenodiol 3-O-(β-D-galactopyranosyl(1→2)[β-D-xylopyranosyl(1→2)-β-D-galactopyranosyl(1→3)]-6'-methoxy-β-D- glucuronopyranoside (5), and maragenin II 3-O-(β-D-galactopyranosyl(1→2)[β-D-xylopyranosyl(1→2)-β-D-galactopyranosyl(1→3)]-6'-methoxy-β-D-glucuronopyranoside (6), along with two known compounds, (1 and 3), were isolated from the stem bark of Camellia japonica. Their chemical structures were established mainly by 2D NMR techniques and mass spectrometry. The isolated compounds showed inhibitory effects on NO production in RAW264.7 macrophages.     

The CYCLIN-A CYCA1;2/TAM Is Required for the Meiosis I to Meiosis II Transition and Cooperates with OSD1 for the Prophase to First Meiotic Division Transition

Meiosis halves the chromosome number because its two divisions follow a single round of DNA replication. This process involves two cell transitions, the transition from prophase to the first meiotic division (meiosis I) and the unique meiosis I to meiosis II transition. We show here that the A-type cyclin CYCA1;2/TAM plays a major role in both transitions in Arabidopsis. A series of tam mutants failed to enter meiosis II and thus produced diploid spores and functional diploid gametes. These diploid gametes had a recombined genotype produced through the single meiosis I division. In addition, by combining the tam-2 mutation with AtSpo11-1 and Atrec8, we obtained plants producing diploid gametes through a mitotic-like division that were genetically identical to their parents. Thus tam alleles displayed phenotypes very similar to that of the previously described osd1 mutant. Combining tam and osd1 mutations leads to a failure in the prophase to meiosis I transition during male meiosis and to the production of tetraploid spores and gametes. This suggests that TAM and OSD1 are involved in the control of both meiotic transitions.     

A mathematical model of mitochondrial swelling

Background

Salmonid alphavirus (SAV) is a widespread pathogen in European aquaculture of salmonid fish. Distinct viral subtypes have been suggested based on sequence comparisons and some of these have different geographical distributions. In Norway, only SAV subtype 3 have so far been identified. Little is known about viral mechanisms important for pathogenesis and transmission. Tools for detailed exploration of SAV genomes are therefore needed.

Results

Infectious cDNA clones in which a genome of subtype 3 SAV is under the control of a CMV promoter were constructed. The clones were designed to express proteins that are putatively identical to those previously reported for the SAVH20/03 strain. A polyclonal antiserum was raised against a part of the E2 glycoprotein in order to detect expression of the subgenomic open reading frame (ORF) encoding structural viral proteins. Transfection of the cDNA clone revealed the expression of the E2 protein by IFAT, and in serial passages of the supernatant the presence of infectious recombinant virus was confirmed through RT-PCR, IFAT and the development of a cytopathic effect similar to that seen during infection with wild type SAV. Confirmation that the recovered virus originated from the infectious plasmid was done by sequence identification of an introduced genetic tag. The recombinant virus was infectious also when an additional ORF encoding an EGFP reporter gene under the control of a second subgenomic alphavirus promoter was added. Finally, we used the system to study the effect of selected point mutations on infectivity in Chinook salmon embryo cells. While introduced mutations in nsP2₁₉₇, nsP3₂₆₃ and nsP3₃₂₃ severely reduced infectivity, a serine to proline mutation in E2₂₀₆ appeared to enhance the virus titer production.

Conclusion

We have constructed infectious clones for SAV based on a subtype 3 genome. The clones may serve as a platform for further functional studies.     

Gcg-XTEN: An Improved Glucagon Capable of Preventing Hypoglycemia without Increasing Baseline Blood Glucose

Objective

While the majority of current diabetes treatments focus on reducing blood glucose levels, hypoglycemia represents a significant risk associated with insulin treatment. Glucagon plays a major regulatory role in controlling hypoglycemia in vivo, but its short half-life and hyperglycemic effects prevent its therapeutic use for non-acute applications. The goal of this study was to identify a modified form of glucagon suitable for prophylactic treatment of hypoglycemia without increasing baseline blood glucose levels.

Methodology/Principal Findings

Through application of the XTEN technology, we report the construction of a glucagon fusion protein with an extended exposure profile (Gcg-XTEN). The in vivo half-life of the construct was tuned to support nightly dosing through design and testing in cynomolgus monkeys. Efficacy of the construct was assessed in beagle dogs using an insulin challenge to induce hypoglycemia. Dose ranging of Gcg-XTEN in fasted beagle dogs demonstrated that the compound was biologically active with a pharmacodynamic profile consistent with the designed half-life. Prophylactic administration of 0.6 nmol/kg Gcg-XTEN to dogs conferred resistance to a hypoglycemic challenge at 6 hours post-dose without affecting baseline blood glucose levels. Consistent with the designed pharmacokinetic profile, hypoglycemia resistance was not observed at 12 hours post-dose. Importantly, the solubility and stability of the glucagon peptide were also significantly improved by fusion to XTEN.

Conclusions/Significance

The data show that Gcg-XTEN is effective in preventing hypoglycemia without the associated hyperglycemia expected for unmodified glucagon. While the plasma clearance of this Gcg-XTEN has been optimized for overnight dosing, specifically for the treatment of nocturnal hypoglycemia, constructs with significantly longer exposure profiles are feasible. Such constructs may have multiple applications such as allowing for more aggressive insulin treatment regimens, treating hypoglycemia due to insulin-secreting tumors, providing synergistic efficacy in combination therapies with long-acting GLP1 analogs, and as an appetite suppressant for treatment of obesity. The improved physical properties of the Gcg-XTEN molecule may also allow for novel delivery systems not currently possible with native glucagon.     

The beta domain is required for Vps4p oligomerization into a functionally active ATPase

Endocytic and biosynthetic trafficking pathways to the lysosome/vacuole converge at the prevacuolar endosomal compartment. During transport through this compartment, integral membrane proteins that are destined for delivery to the lysosome/vacuole lumen undergo multivesicular body (MVB) sorting into internal vesicles formed by invagination of the endosomal limiting membrane. Vps4 is an AAA family ATPase which plays a key role in MVB sorting and facilitates transport through endosomes. It possesses an N-terminal microtubule interacting and trafficking domain required for recruitment to endosomes and an AAA domain with an ATPase catalytic site. The recently solved 3D structure revealed a beta domain, which protrudes from the AAA domain, and a final C-terminal alpha-helix. However, the in vivo roles of these domains are not known. In this study, we have identified motifs in these domains that are highly conserved between yeast and human Vps4. We have mutated these motifs and studied the effect on yeast Vps4p function in vivo and in vitro. We show that the beta domain of the budding yeast Vps4p is not required for recruitment to endosomes, but is essential for all Vps4p endocytic functions in vivo. We also show that the beta domain is required for Vps4p homotypic interaction and for full ATPase activity. In addition, it is required for interaction with Vta1p, which works in concert with Vps4p in vivo. Our studies suggest that assembly of a Vps4p oligomeric complex with full ATPase activity that interacts with Vta1p is essential for normal endosome function.