A conserved phenylalanine of motif IV in superfamily 2 helicases is required for cooperative, ATP-dependent binding of RNA substrates in DEAD-box proteins

We have identified a highly conserved phenylalanine in motif IV of the DEAD-box helicases that is important for their enzymatic activities. In vivo analyses of essential proteins in yeast showed that mutants of this residue had severe growth phenotypes. Most of the mutants also were temperature sensitive, which suggested that the mutations altered the conformational stability. Intragenic suppressors of the F405L mutation in yeast Ded1 mapped close to regions of the protein involved in ATP or RNA binding in DEAD-box crystal structures, which implicated a defect at this level. In vitro experiments showed that these mutations affected ATP binding and hydrolysis as well as strand displacement activity. However, the most pronounced effect was the loss of the ATP-dependent cooperative binding of the RNA substrates. Sequence analyses and an examination of the Protein Data Bank showed that the motif IV phenylalanine is conserved among superfamily 2 helicases. The phenylalanine appears to be an anchor that maintains the rigidity of the RecA-like domain. For DEAD-box proteins, the phenylalanine also aligns a highly conserved arginine of motif VI through van der Waals and cation-pi interactions, thereby helping to maintain the network of interactions that exist between the different motifs involved in ATP and RNA binding.     

The FSHD2 Gene SMCHD1 Is a Modifier of Disease Severity in Families Affected by FSHD1

Facioscapulohumeral muscular dystrophy type 1 (FSHD1) is caused by contraction of the D4Z4 repeat array on chromosome 4 to a size of 1–10 units. The residual number of D4Z4 units inversely correlates with clinical severity, but significant clinical variability exists. Each unit contains a copy of the DUX4 retrogene. Repeat contractions are associated with changes in D4Z4 chromatin structure that increase the likelihood of DUX4 expression in skeletal muscle, but only when the repeat resides in a genetic background that contains a DUX4 polyadenylation signal. Mutations in the structural maintenance of chromosomes flexible hinge domain containing 1 (SMCHD1) gene, encoding a chromatin modifier of D4Z4, also result in the increased likelihood of DUX4 expression in individuals with a rare form of FSHD (FSHD2). Because SMCHD1 directly binds to D4Z4 and suppresses somatic expression of DUX4, we hypothesized that SMCHD1 may act as a genetic modifier in FSHD1. We describe three unrelated individuals with FSHD1 presenting an unusual high clinical severity based on their upper-sized FSHD1 repeat array of nine units. Each of these individuals also carries a mutation in the SMCHD1 gene. Familial carriers of the FSHD1 allele without the SMCHD1 mutation were only mildly affected, suggesting a modifier effect of the SMCHD1 mutation. Knocking down SMCHD1 in FSHD1 myotubes increased DUX4 expression, lending molecular support to a modifier role for SMCHD1 in FSHD1. We conclude that FSHD1 and FSHD2 share a common pathophysiological pathway in which the FSHD2 gene can act as modifier for disease severity in families affected by FSHD1.     

iTILLING: A Personalized Approach to the Identification of Induced Mutations in Arabidopsis

TILLING (for Targeting Induced Local Lesions IN Genomes) is a well-established method for identifying plants carrying point mutations in genes of interest. A traditional TILLING project requires a significant investment of time and resources to establish the mutant population and screening infrastructure. Here, we describe a modified TILLING procedure that substantially reduces the investment needed to perform mutation screening. Our motivation for developing iTILLING was to make it practical for individual laboratories to rapidly perform mutation screens using specialized genetic backgrounds. With iTILLING, M2 seeds are collected in bulk from the mutagenized population of plants, greatly reducing the labor needed to manage the mutant lines. Growth of the M2 seedlings for mutation screening, tissue collection, and DNA extraction are all performed in 96-well format. Mutations are then identified using high-resolution melt-curve analysis of gene-specific polymerase chain reaction products. Individual plants carrying mutations of interest are transferred from the 96-well growth plates to soil. One scientist can complete an iTILLING screen in less than 4 months. As a proof-of-principle test, we applied iTILLING to Arabidopsis (Arabidopsis thaliana) plants that were homozygous for the mekk1-1 (for MAPK/ERK kinase kinase 1) mutation and also carried a MEKK1 rescue construct. The goal of our screen was to identify mutations in the closely linked MEKK2 and MEKK3 loci. We obtained five mutations in MEKK2 and seven mutations in MEKK3, all located within 20 kb of the mekk1-1 T-DNA insertion. Using repeated iterations of the iTILLING process, mutations in three or more tandemly duplicated genes could be generated.The process of reverse genetics has been widely used by plant biologists to study gene function. In Arabidopsis (Arabidopsis thaliana), three approaches that have been used to generate populations of plants for reverse genetic analysis are insertional mutagenesis (Wisman et al., 1998; Alonso et al., 2003), fast neutron mutagenesis to induce deletions (Li et al., 2001), and chemical mutagenesis to induce point mutations (McCallum et al., 2000). In order to find individual plants carrying point mutations of interest, a process called TILLING (for Targeting Induced Local Lesions IN Genomes) was developed whereby genes are screened for mutations using a PCR-based assay (McCallum et al., 2000). Although originally developed for use with Arabidopsis, the TILLING process has been subsequently applied to a wide range of plants, including barley (Hordeum vulgare; Caldwell et al., 2004), Brassica napus (Wang et al., 2008), Brassica oleracea (Himelblau et al., 2009), Brassica rapa (Stephenson et al., 2010), Lotus japonicus (Perry et al., 2009), maize (Zea mays; Till et al., 2004), Medicago truncatula (Le Signor et al., 2009), oat (Avena sativa; Chawade et al., 2010), pea (Pisum sativum; Triques et al., 2007), potato (Solanum tuberosum; Elias et al., 2009), rice (Oryza sativa; Till et al., 2007), sorghum (Sorghum bicolor; Xin et al., 2008), soybean (Glycine max; Cooper et al., 2008), tomato (Solanum lycopersicum ; Gady et al., 2009), and wheat (Triticum aestivum; Dong et al., 2009). TILLING has also been used in Drosophila (Winkler et al., 2005), zebrafish (Wienholds et al., 2003), and Caenorhabditis elegans (Gilchrist et al., 2006).The chemical mutagen most commonly used to create the mutant populations used for TILLING is ethyl methanesulfonate (EMS). When working with plants, seeds are soaked in EMS to induce mutations throughout the genome. Mutagenized seeds are then planted on soil, and the resulting plants are grown to maturity to produce M2 seeds, which are collected from the plants individually or in small pools. Next, M2 seed samples from each individual plant are germinated and grown to produce tissue from which DNA can be extracted. The resulting large collection of ordered DNA samples and the corresponding M2 seeds constitute the infrastructure of a TILLING population. PCR-based screening can then be used to find individual plants in the population carrying mutations in genes of interest (McCallum et al., 2000). Once established, this type of TILLING infrastructure can serve the needs of an entire research community through a fee-for-service screening operation (Colbert et al., 2001; Martín et al., 2009).Several different strategies have been developed for identifying the mutations present in a TILLING population, but all of them involve detecting heteroduplex PCR products. A heteroduplex is formed when a mixture of wild-type and mutant PCR products are melted and reannealed, resulting in DNA duplexes that contain a single-base mismatch. TILLING was originally described using denaturing HPLC to identify mutations based on the differential retention times of heteroduplexes and homoduplexes in the chromatography column (McCallum et al., 2000). TILLING has since been modified so that endonucleases are used to cleave PCR products containing a heteroduplex. Cleavage products are then separated via gel electrophoresis to identify banding patterns indicative of mutations (Colbert et al., 2001).More recently, high-resolution melting analysis of PCR products has been used to identify heteroduplexes when performing TILLING (Dong et al., 2009; Gady et al., 2009). High-resolution melting analysis was originally developed for use in clinical settings to identify known single-nucleotide polymorphisms and small insertions/deletions potentially linked to genetic diseases (Erali et al., 2008). With high-resolution melting, the mismatch in a heteroduplex is visualized as a melting event that occurs more rapidly or at a lower temperature than the corresponding homoduplex. Montgomery et al. (2007) demonstrated that mutation scanning with high-resolution melting is a robust technique with greater than 95% sensitivity in distinguishing heteroduplexes from homoduplexes. It has also been observed that the sensitivity with which mutations in PCR products can be identified using DNA melting analysis depends on the resolution of the instrumentation used for collecting the melt-curve data (Zhou et al., 2005; Herrmann et al., 2006).Although traditional TILLING is a high-throughput method for mutation screening, the establishment of the initial screening population and the corresponding ordered DNA samples requires a substantial up-front investment of time and money. Because of this situation, TILLING resources are available for only two genetic backgrounds in Arabidopsis: wild-type Columbia-0 and Landsberg erecta (Greene et al., 2003; Martín et al., 2009). If a scientist is interested in identifying mutations in a more specialized genetic background, the costs associated with establishing a TILLING population can be prohibitive. Therefore, we were interested in determining if a modified version of the TILLING process could be developed that would substantially reduce the investment of time and resources necessary to perform mutation screening. The individualized TILLING procedure, or iTILLING, which we describe in this paper provides one solution to this challenge.     

Diffusion ordered spectroscopy as a complement to size exclusion chromatography in oligosaccharide analysis

A series of N-acetyl-chitooligosaccharides (GlcNAc)(1-6) have been studied by a nuclear magnetic resonance (NMR) method, diffusion ordered spectroscopy (DOSY). DOSY has also been applied to two additional synthetic related oligosaccharides [GlcNH(2)-(GlcNAc)(4) and GlcNH(2)-(GlcNAc)(2)-GlcNAcSO(3)Na]. A plot of the log of the determined diffusion coefficients (logD) of (GlcNAc)(n) versus the log of molecular weight was linear (6 points, R(2) = 0.995). The molecular weights of the two synthetic chitin derivatives could be estimated to within 10% error. The processed NMR data of all the chitooligosaccharides was also plotted in a polyacrylamide gel-like format to aid visual interpretation. Moreover, the logD value of the NMR signal resonances of a chitin-binding protein (hevein) changed as a function of a given titrated ligand, (GlcNAc)(6). Evidence for a 2:1 hevein:(GlcNAc)(6) complex is detected by DOSY at high hevein:(GlcNAc)(6) ratios. This data is consistent with published analytical ultracentrifugation and isothermal titration calorimetry data. A 1:1 complex is preferred at higher ligand concentrations. DOSY can complement size exclusion chromatography in carbohydrate research with the advantage that oligosaccharides are more readily detected by NMR.     

Identification of short 'eukaryotic' Okazaki fragments synthesized from a prokaryotic replication origin

Although archaeal genomes encode proteins similar to eukaryotic replication factors, the hyperthermophilic archaeon Pyrococcus abyssi replicates its circular chromosome at a high rate from a single origin (oriC) as in Bacteria. In further elucidating the mechanism of archaeal DNA replication, we have studied the elongation step of DNA replication in vivo. We have detected, in two main archaeal phyla, short RNA-primed replication intermediates whose structure and length are very similar to those of eukaryotic Okazaki fragments. Mapping of replication initiation points further showed that discontinuous DNA replication in P. abyssi starts at a well-defined site within the oriC recently identified in this hyperthermophile. Short Okazaki fragments and a high replication speed imply a very efficient turnover of Okazaki fragments in Archaea. Archaea therefore have a unique replication system showing mechanistic similarities to both Bacteria and Eukarya.     

Microbial Community Composition Affects Soil Fungistasis

Most soils inhibit fungal germination and growth to a certain extent, a phenomenon known as soil fungistasis. Previous observations have implicated microorganisms as the causal agents of fungistasis, with their action mediated either by available carbon limitation (nutrient deprivation hypothesis) or production of antifungal compounds (antibiosis hypothesis). To obtain evidence for either of these hypotheses, we measured soil respiration and microbial numbers (as indicators of nutrient stress) and bacterial community composition (as an indicator of potential differences in the composition of antifungal components) during the development of fungistasis. This was done for two fungistatic dune soils in which fungistasis was initially fully or partly relieved by partial sterilization treatment or nutrient addition. Fungistasis development was measured as restriction of the ability of the fungi Chaetomium globosum, Fusarium culmorum, Fusarium oxysporum, and Trichoderma harzianum to colonize soils. Fungistasis did not always reappear after soil treatments despite intense competition for carbon, suggesting that microbial community composition is important in the development of fungistasis. Both microbial community analysis and in vitro antagonism tests indicated that the presence of pseudomonads might be essential for the development of fungistasis. Overall, the results lend support to the antibiosis hypothesis.     

Evolutionary Rate and Genetic Heterogeneity of Human T-Cell Lymphotropic Virus Type II (HTLV-II) Using Isolates from European Injecting Drug Users

Seven new Italian and two new British HTLV-II isolates were obtained from injecting drug users and the entire long terminal repeat (LTR) region was sequenced. Restriction analysis showed that all the Italian isolates are of the IIb subtype, whereas the British isolates are of the IIa subtype. To understand whether the further differentiation of each two principal HTLV-II subtypes in several subgroups could be statistically supported by phylogenetic analysis, the neighbor-joining, parsimony, and maximum likelihood methods were used. The separation between IIa and IIb is very well supported by all three methods. At least two phylogenetic subgroups exist within the HTLV-IIa and at least three within the HTLV-IIb subtype. In the present analysis, no statistical support was obtained for additional phylogroups. Two particular subgroups seem interesting because they include all European and North American injecting drug user strains within the IIa and IIb subtypes, respectively. These data confirm that European HTLV-II infection among drug users is probably derived from North America. They also suggest that though a certain differentiation by restriction analysis in different subgroups is possible, carefully interpreted phylogenetic analyses remain necessary. Using the likelihood ratio test, a molecular clock for the drug user strains was calibrated. A fixation rate between 1.08 × 10⁻⁴ and 2.7 × 10⁻⁵ nucleotide substitutions per site per year was calculated for the IIa and IIb injecting drug user strains. This is the lowest fixation rate so far reported for RNA viruses, including for HIV, which typically range between 10⁻² and 10⁻⁴.     

Constitutive activation of G-proteins by polycystin-1 is antagonized by polycystin-2.

Polycystin-1 (PC1), a 4,303-amino acid integral membrane protein of unknown function, interacts with polycystin-2 (PC2), a 968-amino acid alpha-type channel subunit. Mutations in their respective genes cause autosomal dominant polycystic kidney disease. Using a novel heterologous expression system and Ca(2+) and K(+) channels as functional biosensors, we found that full-length PC1 functioned as a constitutive activator of G(i/o)-type but not G(q)-type G-proteins and modulated the activity of Ca(2+) and K(+) channels via the release of Gbetagamma subunits. PC1 lacking the N-terminal 1811 residues replicated the effects of full-length PC1. These effects were independent of regulators of G-protein signaling proteins and were lost in PC1 mutants lacking a putative G-protein binding site. Co-expression with full-length PC2, but not a C-terminal truncation mutant, abrogated the effects of PC1. Our data provide the first experimental evidence that full-length PC1 acts as an untraditional G-protein-coupled receptor, activity of which is physically regulated by PC2. Thus, our study strongly suggests that mutations in PC1 or PC2 that distort the polycystin complex would initiate abnormal G-protein signaling in autosomal dominant polycystic kidney disease.