Bacillus subtilis is the best-characterized member of the Gram-positive bacteria. Its genome of 4,214,810 base pairs comprises 4,100 protein-coding genes. Of these protein-coding genes, 53% are represented once, while a quarter of the genome corresponds to several gene families that have been greatly expanded by gene duplication, the largest family containing 77 putative ATP-binding transport proteins. In addition, a large proportion of the genetic capacity is devoted to the utilization of a variety of carbon sources, including many plant-derived molecules. The identification of five signal peptidase genes, as well as several genes for components of the secretion apparatus, is important given the capacity of Bacillus strains to secrete large amounts of industrially important enzymes. Many of the genes are involved in the synthesis of secondary metabolites, including antibiotics, that are more typically associated with Streptomyces species. The genome contains at least ten prophages or remnants of prophages, indicating that bacteriophage infection has played an important evolutionary role in horizontal gene transfer, in particular in the propagation of bacterial pathogenesis.

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Data from the Genetic Association Information Network (GAIN) genome-wide association study (GWAS) in major depressive disorder (MDD) were used to explore previously reported candidate gene and single-nucleotide polymorphism (SNP) associations in MDD. A systematic literature search of candidate genes associated with MDD in case-control studies was performed before the results of the GAIN MDD study became available. Measured and imputed candidate SNPs and genes were tested in the GAIN MDD study encompassing 1738 cases and 1802 controls. Imputation was used to increase the number of SNPs from the GWAS and to improve coverage of SNPs in the candidate genes selected. Tests were carried out for individual SNPs and the entire gene using different statistical approaches, with permutation analysis as the final arbiter. In all, 78 papers reporting on 57 genes were identified, from which 92 SNPs could be mapped. In the GAIN MDD study, two SNPs were associated with MDD: C5orf20 (rs12520799; P = 0.038; odds ratio (OR) AT = 1.10, 95% CI 0.95-1.29; OR TT = 1.21, 95% confidence interval (CI) 1.01-1.47) and NPY (rs16139; P = 0.034; OR C allele = 0.73, 95% CI 0.55-0.97), constituting a direct replication of previously identified SNPs. At the gene level, TNF (rs76917; OR T = 1.35, 95% CI 1.13-1.63; P = 0.0034) was identified as the only gene for which the association with MDD remained significant after correction for multiple testing. For SLC6A2 (norepinephrine transporter (NET)) significantly more SNPs (19 out of 100; P = 0.039) than expected were associated while accounting for the linkage disequilibrium (LD) structure. Thus, we found support for involvement in MDD for only four genes. However, given the number of candidate SNPs and genes that were tested, even these significant may well be false positives. The poor replication may point to publication bias and false-positive findings in previous candidate gene studies, and may also be related to heterogeneity of the MDD phenotype as well as contextual genetic or environmental factors.

A gene bank from the chlorinated hydrocarbon-degrading bacterium Xanthobacter autotrophicus GJ10 was prepared in the broad-host-range cosmid vector pLAFR1. By using mutants impaired in dichloroethane utilization and strains lacking dehalogenase activities, several genes involved in 1,2-dichloroethane metabolism were isolated. The haloalkane dehalogenase gene dhLA was subcloned, and it was efficiently expressed from its own constitutive promoter in strains of a Pseudomonas sp., Escherichia coli, and a Xanthobacter sp. at levels up to 30% of the total soluble cellular protein. A 3-kilobase-pair BamHI DNA fragment on which the dhLA gene is localized was sequenced. The haloalkane dehalogenase gene was identified by the known N-terminal amino acid sequence of its product and found to encode a 310-amino-acid protein of molecular weight 35,143. Upstream of the dehalogenase gene, a good ribosome-binding site and two consensus E. coli promoter sequences were present.Xanthobacter spp. are nitrogen-fixing bacteria that are able to grow autotrophically with a mixture of hydrogen and oxygen as an energy source (33). A member of this genus that is able to utilize several halogenated hydrocarbons as carbon sources has been isolated (15). The organism was obtained from an enrichment culture with 1,2-dichloroethane, which is an environmentally important compound with a production volume larger than that of any other industrial halogenated chemical. The 1,2-dichloroethane-degrading bacterium, designated strain GJ10, was found to degrade 1,2-dichloroethane via 2-chloroethanol, 2-chloroacetaldehyde, and chloroacetic acid to glycolate ( Fig. 1) (13, 14). The dehalogenation steps in this sequence were found to be catalyzed by two different hydrolytic dehalogenases (14,17).Conversion of 1,2-dichloroethane was mediated by a haloalkane dehalogenase. This was the first enzyme found to catalyze hydrolytic dehalogenation of chlorinated hydrocarbons. The protein has been purified (17) and crystallized (26), and its three-dimensional structure is now under study. Chloroacetic acid hydrolysis was found to be mediated by a different enzyme. This haloacid dehalogenase has not been purified from strain GJ10, but much information is available about other dehalogenases of this class (22).So far, haloalkane dehalogenases are the only enzymes known to be capable of direct hydrolytic dehalogenation of chlorinated and brominated hydrocarbons, without the requirement for coenzymes or oxygen. The enzyme of X. autotrophicus GJ10 is constitutively expressed to 2 to 3% of the soluble cellular protein (13, 17). It has a remarkably broad substrate range which includes terminally halogenated alkanes with chain lengths up to 4 carbons for chlorinated and up to at least 10 carbons for brominated alkanes. Other haloalkane dehalogenases of broad substrate range have been found in gram-positive haloalkane-utilizing bacteria (11,28,35 So far, no information is available about the genetics of haloalkane-utilizing organisms. Since the system is attractive both for st...