Identification and categorization of horizontally transferred genes in prokaryotic genomes

Horizontal gene transfer （HGT）, a process through which genomes acquire genetic materials from distantly related organisms, is believed to be one of the major forces in prokaryotic genome evolution.However, systematic investigation is still scarce to clarify two basic issues about HGT： （1） what types of genes are transferred; and （2） what influence HGT events over the organization and evolution of biological pathways. Genome-scale investigations of these two issues will advance the systematical understanding of HGT in the context of prokaryotic genome evolution. Having investigated 82 genomes, we constructed an HGT database across broad evolutionary timescales. We identified four function categories containing a high proportion of horizontally transferred genes： cell envelope, energy metabolism, regulatory functions, and transport/binding proteins. Such biased function distribution indicates that HGT is not completely random;instead, it is under high selective pressure, required by function restraints in organisms. Furthermore, we mapped the transferred genes onto the connectivity structure map of organism-specific pathways listed in Kyoto Encyclopedia of Genes and Genomes （KEGG）. Our results suggest that recruitment of transferred genes into pathways is also selectively constrained because of the tuned interaction between original pathway members. Pathway organization structures still conserve well through evolution even with the recruitment of horizontally transferred genes. Interestingly, in pathways whose organization were significantly affected by HGT events, the operon-like arrangement of transferred genes was found to be prevalent. Such results suggest that operon plays an essential and directional role in the integration of alien genes into pathways.     

Non contiguous-finished genome sequence and description of Enorma massiliensis gen. nov., sp. nov., a new member of the Family Coriobacteriaceae

Enorma massiliensis strain phI^T is the type strain of E. massiliensis gen. nov., sp. nov., the type species of a new genus within the family Coriobacteriaceae, Enorma gen. nov. This strain, whose genome is described here, was isolated from the fecal flora of a 26-year-old woman suffering from morbid obesity. E. massiliensis strain phI^T is a Gram-positive, obligately anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,280,571 bp long genome (1 chromosome but no plasmid) exhibits a G+C content of 62.0% and contains 1,901 protein-coding and 51 RNA genes, including 3 rRNA genes.     

Use of the EM algorithm to detect QTL affecting multiple-traits in an across half-sib family analysis

QTL detection experiments in livestock species commonly use the half-sib design. Each male is mated to a number of females, each female producing a limited number of progeny. Analysis consists of attempting to detect associations between phenotype and genotype measured on the progeny. When family sizes are limiting experimenters may wish to incorporate as much information as possible into a single analysis. However, combining information across sires is problematic because of incomplete linkage disequilibrium between the markers and the QTL in the population. This study describes formulæ for obtaining MLEs via the expectation maximization (EM) algorithm for use in a multiple-trait, multiple-family analysis. A model specifying a QTL with only two alleles, and a common within sire error variance is assumed. Compared to single-family analyses, power can be improved up to fourfold with multi-family analyses. The accuracy and precision of QTL location estimates are also substantially improved. With small family sizes, the multi-family, multi-trait analyses reduce substantially, but not totally remove, biases in QTL effect estimates. In situations where multiple QTL alleles are segregating the multi-family analysis will average out the effects of the different QTL alleles.     

Pulsed field gel electrophoresis and physical mapping of large DNA fragments in the Tm-2a region of chromosome 9 in tomato

Summary A method has been developed which allows the isolation of very high molecular weight DNA (>2 million bp) from leaf protoplasts of tomato (Lycopersicon esculentum). The DNA isolated in this manner was digested in agarose with rare-cutting restriction enzymes and separated by pulsed field gel electrophoresis. The size range of the reslting fragments was determined by hybridization to a number of single copy clones and the suitability of these enzymes for the mapping of large DNA fragments was evaluated. Furthermore, five genetically tightly linked single copy clones have been used to begin the construction of a physical map in a region of the genome containing the Tm-2a gene which confers resistance to tobacco mosaic virus. Two of the five clones were found to be on the same 560 kb SalI fragment and therefore are no further apart than that distance. The remaining three markers are distributed over at least 3 million bp, so that the total minimum physical distance of that cluster is at least 4 million bp. The results are discussed with respect to correlations between recombination frequencies and physical distance as well as physical mapping large regions of a complex plant genome like tomato.     

Microbicide surface nano-structures

Abstract

The prevention of infectious diseases is a global challenge where multidrug-resistant bacteria or “superbugs” pose a serious threat to worldwide public health. Microtopographic surfaces have attracted much attention as they represent a biomimetic and nontoxic surface antibacterial strategy to replace biocides. The antimicrobial effect of such natural and biomimetic surface nanostructures involves a physical approach which eradicates bacteria via the structural features of the surfaces without any release of biocides or chemicals. These recent developments present a significant proof-of-concept and a powerful tool in which cellular adhesion and death caused by a physical approach, can be controlled by the micro/nanotopology of such surfaces. This represents an innovative direction of development of clean, effective and nonresistant antimicrobial surfaces. The minireview will cover novel approaches for the construction of nanostructures on surfaces in order to create antimicrobial surface in an environmentally friendly, nontoxic manner.     

What Can Medicine Learn from the Human DNA Sequence?

The cooperation of biochemistry with clinical medicine consists of two overlapping temporal phases. Phase 1 of the cooperation, which still is not finished, is characterized by joint work on the pathogenesis and diagnostics of systemic metabolic diseases, whereas in phase 2 the cooperation on tissue and cell specific as well as on molecular diseases is prevailing. In view of the conceptual revolution and shift in paradigm, which biochemistry and medicine are presently experiencing, the content of cooperation between the two disciplines will profoundly change. It will become deeply influenced by the results of the research into the human genome and human proteome. Biochemistry will strongly be occupied to relate the thousands of protein coding genes to the structure and function of the encoded proteins, and medicine will be concerned in finding new protein markers for diagnostics, to identify novel drug targets, and to investigate, for example, the proteomes of the variety of tumors to aid tumor classification, to mention only a few areas of interest which medicine will have in the progress of human genome research. The review summarizes the recent achievements in sequencing the human DNA as published in February 2001 by the International Human Genome Sequencing Consortium and Celera Genomics and discusses their significance in respect to the further development of molecular, in particular genetic, medicine as an interdisciplinary field of the modern clinical sciences. Only biochemistry can provide the conceptual and experimental basis for the causal understanding of biological mechanisms as encoded in the genome of an organism.     

A physical map and clone bank of the black pine (Pinus thunbergii) chloroplast genome

Black pine chloroplast DNA is 119,707 bp long. The physical map is shown and the genes are listed. Plasmid clones covering the entire DNA sequence have been ordered and available upon request.     

Thiol Peroxidase Deficiency Leads to Increased Mutational Load and Decreased Fitness in Saccharomyces cerevisiae

Thiol peroxidases are critical enzymes in the redox control of cellular processes that function by reducing low levels of hydroperoxides and regulating redox signaling. These proteins were also shown to regulate genome stability, but how their dysfunction affects the actual mutations in the genome is not known. Saccharomyces cerevisiae has eight thiol peroxidases of glutathione peroxidase and peroxiredoxin families, and the mutant lacking all these genes (∆8) is viable. In this study, we employed two independent ∆8 isolates to analyze the genome-wide mutation spectrum that results from deficiency in these enzymes. Deletion of these genes was accompanied by a dramatic increase in point mutations, many of which clustered in close proximity and scattered throughout the genome, suggesting strong mutational bias. We further subjected multiple lines of wild-type and ∆8 cells to long-term mutation accumulation, followed by genome sequencing and phenotypic characterization. ∆8 lines showed a significant increase in nonrecurrent point mutations and indels. The original ∆8 cells exhibited reduced growth rate and decreased life span, which were further reduced in all ∆8 mutation accumulation lines. Although the mutation spectrum of the two independent isolates was different, similar patterns of gene expression were observed, suggesting the direct contribution of thiol peroxidases to the observed phenotypes. Expression of a single thiol peroxidase could partially restore the growth phenotype of ∆8 cells. This study shows how deficiency in nonessential, yet critical and conserved oxidoreductase function, leads to increased mutational load and decreased fitness.     

Within-population structure highlighted by differential introgression across semipermeable barriers to gene flow in Anguilla marmorata

In the marine environment, differential gene exchange between partially reproductively isolated taxa can result in introgression that extends over long distances due to high larval dispersal potential. However, the degree to which this process contributes to interlocus variance of genetic differentiation within introgressed populations remains unclear. Using a genome-scan approach in the Indo-Pacific eel Anguilla marmorata, we investigated the degree of interpopulation genetic differentiation, the rate of introgression, and within-population genetic patterns at 858 AFLP markers genotyped in 1117 individuals. Three divergent populations were identified based on clustering analysis. Genetic assignments of individuals revealed the existence of different types of hybrids that tended to co-occur with parental genotypes in three population contact zones. Highly variable levels of genetic differentiation were found between populations across the AFLP markers, and reduced rates of introgression were shown at some highly differentiated loci. Gene flow across semipermeable genetic barriers was shown to generate spatial introgression patterns at some loci which define within-population structure over long distances. These results suggest that differential introgression in subdivided populations may be relevant when interpreting spatial variation patterns displayed by outlying loci in other marine fish populations.