Closing gaps in the human genome using sequencing by synthesis

The most recent release of the finished human genome contains 260 euchromatic gaps (excluding chromosome Y). Recent work has helped explain a large number of these unresolved regions as 'structural' in nature. Another class of gaps is likely to be refractory to clone-based approaches, and cannot be approached in ways previously described. We present an approach for closing these gaps using 454 sequencing. As a proof of principle, we closed all three remaining non-structural gaps in chromosome 15.     

Crystal structure of a prokaryotic aspartyl tRNA-synthetase.

The crystal structure of Thermus thermophilus aspartyl tRNA-synthetase (AspRS) refined at 2.5 A resolution is described. This molecular structure is a textbook illustration of the modular organization of aminoacyl-tRNA synthetases. In addition to the three domains found in yeast AspRS, each monomer exhibits a module specific to prokaryotic enzymes, which corresponds to a helix-turn-helix motif in yeast AspRS, a domain implicated in the stabilization of the complex with tRNA. Its topology matches that of the histidine-containing phosphocarrier HPr which has been linked recently to another group of proteins containing the ferredoxin fold. We propose a more extensive alignment of these folds, which involves a circular permutation of the sequences and changes the point of entry of the whole domain. The C-terminal extension, another prokaryotic characteristic, leads to a significant increase in the network of interaction at the dimer interface. Some potential communication pathways suggest how a transfer of information between the two active sites of the homodimer might occur. Most of the residues involved belong to the class II-specific motifs in correlation with the dimeric state of nearly all class II enzymes. The T. thermophilus enzyme exhibits some features not found in any of the six other known AspRSs from mesophilic organisms.     

Relative Heterothallism and Production of Hybrid Perithecia by Auxotrophic Mutants of Glomerella cingulata from Apple

Glomerella cmgulata is a homothallic species but produces a ridge of fertile perithecia at a frontier between certain wild-type strains on agar. To account for the presence or absence of perithecia earlier workers suggested that alleles at A and B loci control the formation of perithecia at mycelial frontiers in + and – strains. We propose that G. cingulata actually demonstrates “relative heterothallism”. Of 7 induced nutritionally deficient mutants (auxotrophs) in 2 wild-type strains from apple, only one methionine (met-1) and one arginine (arg) mutant in only one wild-type strain gave a heavy ridge of perithecia at their junctures. Neither the met-l nor arg mutations have been identified as those in the A or B locus. The perithecia were either homozygous (selfs) for met-1 or arg, or heterozygous (hybrids). Paired met-1 and arg segregants from hybrid perirhecia as well as diauxotrophic strains from met-l or arg mutants also gave hybrids of selfs. Specific nutritional deficiencies in certain wild-type strains which can direct sexuality are not yet known. Genetic studies are now feasible in G. cingulata to define enzymatic factors responsible for pathogenicity.     

Flexibility in crosstalk between H2B ubiquitination and H3 methylation in vivo

Histone H2B ubiquitination is a dynamic modification that promotes methylation of histone H3K79 and H3K4. This crosstalk is important for the DNA damage response and has been implicated in cancer. Here, we show that in engineered yeast strains, ubiquitins tethered to every nucleosome promote H3K79 and H3K4 methylation from a proximal as well as a more distal site, but only if in a correct orientation. This plasticity indicates that the exact location of the attachment site, the native ubiquitin-lysine linkage and ubiquitination cycles are not critical for trans-histone crosstalk in vivo. The flexibility in crosstalk also indicates that other ubiquitination events may promote H3 methylation.     

Crystals of seryl-tRNA synthetase from Thermus thermophilus. Preliminary crystallographic data

Crystals have been obtained of seryl-tRNA synthetase from the extreme thermophile Thermus thermophilus, using mixed solutions of ammonium sulphate and methane pentane diol. The crystals are very stable and diffract to at least 2 A. The crystals are monoclinic (space group P21) with cell parameters a = 87.1 A, b = 126.9 A, c = 63.5 A and beta = 109.7 degrees.     

Effect of sodium channel abundance on Drosophila development, reproductive capacity and aging

The voltage-gated Na (+) channels (VGSC) are complex membrane proteins responsible for generation and propagation of the electrical signals through the brain, the skeletal muscle and the heart. The levels of sodium channels affect behavior and physical activity. This is illustrated by the maleless mutant allele (mle (napts)) in Drosophila, where the decreased levels of voltage-gated Na(+) channels cause temperature-sensitive paralysis. Here, we report that mle (napts) mutant flies exhibit developmental lethality, decreased fecundity and increased neurodegeneration. The negative effect of decreased levels of Na(+) channels on development and ts-paralysis was more pronounced at 18 and 29°C than at 25°C, suggesting particular sensitivity of the mle (napts) flies to temperatures above and below normal environmental conditions. Similarly, longevity of mle (napts) flies was unexpectedly short at 18 and 29°C compared with flies heterozygous for the mle (napts) mutation. Developmental lethality and neurodegeneration of mle (napts) flies was partially rescued by increasing the dosage of para, confirming a vital role of Na(+) channels in development, longevity and neurodegeneration of flies and their adaptation to temperatures.     

The ability of an attaching and effacing pathogen to trigger localized actin assembly contributes to virulence by promoting mucosal attachment

Enterohaemorrhagic Escherichia coli (EHEC) colonizes the intestine and causes bloody diarrhoea and kidney failure by producing Shiga toxin. Upon binding intestinal cells, EHEC triggers a change in host cell shape, generating actin ‘pedestals’ beneath bound bacteria. To investigate the importance of pedestal formation to disease, we infected genetically engineered mice incapable of supporting pedestal formation by an EHEC‐like mouse pathogen, or wild type mice with a mutant of that pathogen incapable of generating pedestals. We found that pedestal formation promotes attachment of bacteria to the intestinal mucosa and vastly increases the severity of Shiga toxin‐mediated disease.