Characterization of novel Brown midrib 6 mutations affecting lignin biosynthesis in sorghum

The presence of lignin reduces the quality of lignocellulosic biomass for forage materials and feedstock for biofuels. In C4 grasses,the brown midrib phenotype has been linked to mutations to genes in the monolignol biosynthesis pathway. For example,the Bmr6 gene in sorghum(Sorghum bicolor) has been previously shown to encode cinnamyl alcohol dehydrogenase(CAD),which catalyzes the final step of the monolignol biosynthesis pathway. Mutations in this gene have been shown to reduce the abundance of lignin,enhance digestibility,and improve saccharification efficiencies and ethanol yields. Nine sorghum lines harboring five different bmr6 alleles were identified in an EMS-mutagenized TILLING population. DNA sequencing of Bmr6 revealed that the majority of the mutations impacted evolutionarily conserved amino acids while three-dimensional structural modeling predicted that all of these alleles interfered with the enzyme's ability to bind with its NADPH cofactor. All of the new alleles reduced in vitro CAD activity levels and enhanced glucose yields following saccharification. Further,many of these lines were associated with higher reductions in acid detergent lignin compared to lines harboring the previously characterized bmr6-ref allele. These bmr6 lines represent new breeding tools for manipulating biomass composition to enhance forage and feedstock quality.     

Exploring the Functional Complementation between Grp94 and Hsp90

Grp94 and Hsp90 are the ER and cytoplasmic paralog members, respectively, of the hsp90 family of molecular chaperones. The structural and biochemical differences between Hsp90 and Grp94 that allow each paralog to efficiently chaperone its particular set of clients are poorly understood. The two paralogs exhibit a high degree of sequence similarity, yet also display significant differences in their quaternary conformations and ATPase activity. In order to identify the structural elements that distinguish Grp94 from Hsp90, we characterized the similarities and differences between the two proteins by testing the ability of Hsp90/Grp94 chimeras to functionally substitute for the wild-type chaperones in vivo. We show that the N-terminal domain or the combination of the second lobe of the Middle domain plus the C-terminal domain of Grp94 can functionally substitute for their yeast Hsp90 counterparts but that the equivalent Hsp90 domains cannot functionally replace their counterparts in Grp94. These results also identify the interface between the Middle and C-terminal domains as an important structural unit within the Hsp90 family.     

Mechanism of the interaction of beta(2)-glycoprotein I with negatively charged phospholipid membranes.

In an attempt to understand the multifunctional involvement of beta(2)-glycoprotein I (beta(2)GPI) in autoimmune diseases, thrombosis, atherosclerosis, and inflammatory processes, substantial interest is focused on the interaction of beta(2)GPI with negatively charged ligands, in particular, with acidic phospholipids. In this study, unilamellar vesicles composed of cardiolipin were used as in vitro membrane system to test and further refine a model of interaction based on the crystal structure of beta(2)GPI. The data suggest that beta(2)GPI anchors to the membrane surface with its hydrophobic loop adjacent to the positively charged lysine rich region in domain V. Subsequently, beta(2)GPI penetrates the membrane interfacial headgroup region as indicated by a restriction of the lipid side chain mobility, but without formation of a nonbilayer lipid phase. A structural rearrangement of beta(2)GPI upon lipid binding was detected by microcalorimetry and may result in the exposure of cryptic epitopes located in the complement control protein domains. This lipid-dependent conformational change may induce oligomerization of beta(2)GPI and promote intermolecular associations. Thus, the aggregation tendency of beta(2)GPI may serve as the basis for the formation of a molecular link between cells but may also be an essential feature for binding of autoantibodies and hence determine the role of beta(2)GPI in autoimmune diseases.     

Structural basis for VIPP1 oligomerization and maintenance of thylakoid membrane integrity

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Genome-Wide Identification of Genes Conferring Energy Related Resistance to a Synthetic Antimicrobial Peptide (Bac8c)

A fundamental issue in the design and development of antimicrobials is the lack of understanding of complex modes of action and how this complexity affects potential pathways for resistance evolution. Bac8c (RIWVIWRR-NH₂) is an 8 amino acid antimicrobial peptide (AMP) that has been shown to have enhanced activity against a range of pathogenic Gram-positive and Gram-negative bacteria, as well as yeast. We have previously demonstrated that Bac8c appears to interfere with multiple targets, at least in part through the disruption of cytoplasmic membrane related functions, and that resistance to this peptide does not easily develop using standard laboratory methods. Here, we applied a genomics approach, SCalar Analysis of Library Enrichement (SCALEs), to map the effect of gene overexpression onto Bac8c resistance in parallel for all genes and gene combinations (up to ∼ 10 adjacent genes) in the E. coli genome (a total of ∼ 500,000 individual clones were mapped). Our efforts identified an elaborate network of genes for which overexpression leads to low-level resistance to Bac8c (including biofilm formation, multi-drug transporters, etc). This data was analyzed to provide insights into the complex relationships between mechanisms of action and potential routes by which resistance to this synthetic AMP can develop.     

A single codon insertion in PICALM is associated with development of familial subvalvular aortic stenosis in Newfoundland dogs

Familial subvalvular aortic stenosis (SAS) is one of the most common congenital heart defects in dogs and is an inherited defect of Newfoundlands, golden retrievers and human children. Although SAS is known to be inherited, specific genes involved in Newfoundlands with SAS have not been defined. We hypothesized that SAS in Newfoundlands is inherited in an autosomal dominant pattern and caused by a single genetic variant. We studied 93 prospectively recruited Newfoundland dogs, and 180 control dogs of 30 breeds. By providing cardiac screening evaluations for Newfoundlands we conducted a pedigree evaluation, genome-wide association study and RNA sequence analysis to identify a proposed pattern of inheritance and genetic loci associated with the development of SAS. We identified a three-nucleotide exonic insertion in phosphatidylinositol-binding clathrin assembly protein (PICALM) that is associated with the development of SAS in Newfoundlands. Pedigree evaluation best supported an autosomal dominant pattern of inheritance and provided evidence that equivocally affected individuals may pass on SAS in their progeny. Immunohistochemistry demonstrated the presence of PICALM in the canine myocardium and area of the subvalvular ridge. Additionally, small molecule inhibition of clathrin-mediated endocytosis resulted in developmental abnormalities within the outflow tract (OFT) of Xenopus laevis embryos. The ability to test for presence of this PICALM insertion may impact dog-breeding decisions and facilitate reduction of SAS disease prevalence in Newfoundland dogs. Understanding the role of PICALM in OFT development may aid in future molecular and genetic investigations into other congenital heart defects of various species.     

Cocoon-spinning larvae of Oriental fruit moth and Indianmeal moth do not produce aggregation pheromone

1 Mature larvae of the Oriental fruit moth (OFM) Grapholita molesta (Lepidoptera: Tortricidae) and the Indianmeal moth (IMM) Plodia interpunctella (Lepidoptera: Pyralidae) leave their food source in search of suitable pupation sites in which to spin cocoons. These sites are typically well-concealed cracks and crevices within the environment. Such cocooning behaviour is also observed in larvae of the codling moth (CM) Cydia pomonella (Lepidoptera: Tortricidae), which aggregate prior to pupation in response to a pheromone blend produced by cocoon-spinning conspecific larvae.
2 In laboratory experiments, we tested whether cocoon-spinning OFM and IMM larvae produce aggregation pheromones and whether CM larvae are cross-attracted to closely-related OFM larvae.
3 Fifth-instar OFM and IMM larvae were not attracted to, or arrested by, cocoon-spinning conspecifics. Moreover, fifth-instar CM larvae were not cross-attracted to either cocoon-spinning OFM or IMM larvae.
4 Analyses of volatiles released from cocoon-spinning OFM and IMM larvae revealed that both OFM and IMM lack components that are present in the aggregation pheromone of CM larvae. This information may help explain why CM larvae are not cross-attracted to cocooning OFM or IMM larvae.     

Does aggregation behavior of codling moth larvae,Cydia pomonella,increase the risk of parasitism by Mastrus ridibundus?

Mastrus ridibundus is a specialist hymenopteran parasitoid that parasitizes last-instar larvae or prepupae of the codling moth, Cydia pomonella. Foraging females eavesdrop on an aggregation pheromone produced by cocooning larvae. We investigated whether larvae that cocoon in aggregation experience a greater rate of parasitism than larvae that cocoon in isolation. In wind tunnel experiments, 10 larvae in aggregations were more readily located by female M. ridibundus than 10 larvae well separated from each other. Similarly, aggregations of 30 larvae were more attractive to female M. ridibundus than those of 3 larvae. In cage experiments, larval cocooning in aggregation or isolation had no effect on the mean rate of parasitism and the mean number of eggs deposited per parasitized host. In Petri-dish experiments, the location of larvae within an aggregation significantly affected their rate of parasitism, with those in the center of an aggregation completely shielded from parasitism. Our data suggest that aggregation behavior by C. pomonella larvae does not appear to increase the rate of parasitism. The increased risk of aggregated larvae to be detected by M. ridibundus is likely offset by diluted parasitism risk and structural refugia effects that larvae in aggregation experience. As an egg-limited parasitoid, female M. ridibundus can parasitize on average only one larva in an aggregation, with the likelihood of parasitism for each larva being inversely proportional to the number of larvae in that aggregation.