The genome sequence of the plant pathogen Xylella fastidiosa. The Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and Analysis

Xylella fastidiosa is a fastidious, xylem-limited bacterium that causes a range of economically important plant diseases. Here we report the complete genome sequence of X. fastidiosa clone 9a5c, which causes citrus variegated chlorosis--a serious disease of orange trees. The genome comprises a 52.7% GC-rich 2,679,305-base-pair (bp) circular chromosome and two plasmids of 51,158 bp and 1,285 bp. We can assign putative functions to 47% of the 2,904 predicted coding regions. Efficient metabolic functions are predicted, with sugars as the principal energy and carbon source, supporting existence in the nutrient-poor xylem sap. The mechanisms associated with pathogenicity and virulence involve toxins, antibiotics and ion sequestration systems, as well as bacterium-bacterium and bacterium-host interactions mediated by a range of proteins. Orthologues of some of these proteins have only been identified in animal and human pathogens; their presence in X. fastidiosa indicates that the molecular basis for bacterial pathogenicity is both conserved and independent of host. At least 83 genes are bacteriophage-derived and include virulence-associated genes from other bacteria, providing direct evidence of phage-mediated horizontal gene transfer.     

Separation of the genetic loci for the H-Y antigen and for testis determination on human Y chromosome

The mammalian Y chromosome encodes a testis-determining factor (termed TDF in the human), a master regulator of sex differentiation. Embryos with a Y chromosome develop testes and become males whereas embryos lacking a Y chromosome develop ovaries and become females. Expression of H-Y, a minor histocompatibility antigen, may also be controlled by a gene on the Y chromosome, and it has been proposed that this antigen is the testis-determining factor. We have tested the postulated identity of H-Y and TDF in the human. H-Y typing with T cells was carried out on a series of sex-reversed humans (XX males and XY females), each shown by DNA hybridization to carry part but not all of the Y chromosome. This deletion analysis maps the gene for H-Y to the long arm or centromeric region of the human Y chromosome, far from the TDF locus, which maps to the distal short arm.     

Eukaryotic evolution: early origin of canonical introns

Spliceosomal introns, one of the hallmarks of eukaryotic genomes, were thought to have originated late in evolution and were assumed not to exist in eukaryotes that diverged early -- until the discovery of a single intron with an aberrant splice boundary in the primitive 'protozoan' Giardia. Here we describe introns from a close relative of Giardia, Carpediemonas membranifera, that have boundary sequences of the normal eukaryotic type, indicating that canonical introns are likely to have arisen very early in eukaryotic evolution.     

Structure of the bacteriophage phi29 DNA packaging motor

Motors generating mechanical force, powered by the hydrolysis of ATP, translocate double-stranded DNA into preformed capsids (proheads) of bacterial viruses and certain animal viruses. Here we describe the motor that packages the double-stranded DNA of the Bacillus subtilis bacteriophage phi29 into a precursor capsid. We determined the structure of the head-tail connector--the central component of the phi29 DNA packaging motor--to 3.2 A resolution by means of X-ray crystallography. We then fitted the connector into the electron densities of the prohead and of the partially packaged prohead as determined using cryo-electron microscopy and image reconstruction analysis. Our results suggest that the prohead plus dodecameric connector, prohead RNA, viral ATPase and DNA comprise a rotary motor with the head-prohead RNA-ATPase complex acting as a stator, the DNA acting as a spindle, and the connector as a ball-race. The helical nature of the DNA converts the rotary action of the connector into translation of the DNA.     

Implications for prediction and hazard assessment from the 2004 Parkfield earthquake

Obtaining high-quality measurements close to a large earthquake is not easy: one has to be in the right place at the right time with the right instruments. Such a convergence happened, for the first time, when the 28 September 2004 Parkfield, California, earthquake occurred on the San Andreas fault in the middle of a dense network of instruments designed to record it. The resulting data reveal aspects of the earthquake process never before seen. Here we show what these data, when combined with data from earlier Parkfield earthquakes, tell us about earthquake physics and earthquake prediction. The 2004 Parkfield earthquake, with its lack of obvious precursors, demonstrates that reliable short-term earthquake prediction still is not achievable. To reduce the societal impact of earthquakes now, we should focus on developing the next generation of models that can provide better predictions of the strength and location of damaging ground shaking.