Comparative bacterial proteomics: analysis of the core genome concept

While comparative bacterial genomic studies commonly predict a set of genes indicative of common ancestry, experimental validation of the existence of this core genome requires extensive measurement and is typically not undertaken. Enabled by an extensive proteome database developed over six years, we have experimentally verified the expression of proteins predicted from genomic ortholog comparisons among 17 environmental and pathogenic bacteria. More exclusive relationships were observed among the expressed protein content of phenotypically related bacteria, which is indicative of the specific lifestyles associated with these organisms. Although genomic studies can establish relative orthologous relationships among a set of bacteria and propose a set of ancestral genes, our proteomics study establishes expressed lifestyle differences among conserved genes and proposes a set of expressed ancestral traits.     

Intraspecies variation in bacterial genomes: the need for a species genome concept

Bacterial populations are clonal. Their evolution involves not only divergence between orthologous genes but also gain of genes from other clones or species, which has only recently been widely appreciated through macrorestriction mapping, genomic subtraction and complete genome sequencing. Genes can also be lost in response to selection or by random mutation after becoming redundant. The bacterial genome is a dynamic structure and intraspecies variation needs to be included in genome analysis if we are to gain insight into the full species genome.     

Quantifying the variation in the effective population size within a genome

The effective population size (N(e)) is one of the most fundamental parameters in population genetics. It is thought to vary across the genome as a consequence of differences in the rate of recombination and the density of selected sites due to the processes of genetic hitchhiking and background selection. Although it is known that there is intragenomic variation in the effective population size in some species, it is not known whether this is widespread or how much variation in the effective population size there is. Here, we test whether the effective population size varies across the genome, between protein-coding genes, in 10 eukaryotic species by considering whether there is significant variation in neutral diversity, taking into account differences in the mutation rate between loci by using the divergence between species. In most species we find significant evidence of variation. We investigate whether the variation in N(e) is correlated to recombination rate and the density of selected sites in four species, for which these data are available. We find that N(e) is positively correlated to recombination rate in one species, Drosophila melanogaster, and negatively correlated to a measure of the density of selected sites in two others, humans and Arabidopsis thaliana. However, much of the variation remains unexplained. We use a hierarchical Bayesian analysis to quantify the amount of variation in the effective population size and show that it is quite modest in all species-most genes have an N(e) that is within a few fold of all other genes. Nonetheless we show that this modest variation in N(e) is sufficient to cause significant differences in the efficiency of natural selection across the genome, by demonstrating that the ratio of the number of nonsynonymous to synonymous polymorphisms is significantly correlated to synonymous diversity and estimates of N(e), even taking into account the obvious nonindependence between these measures.     

Automated bacterial genome analysis and annotation

More than 300 bacterial genome sequences are publicly available, and many more are scheduled to be completed and released in the near future. Converting this raw sequence information into a better understanding of the biology of bacteria involves the identification and annotation of genes, proteins and pathways. This processing is typically done using sequence annotation pipelines comprised of a variety of software modules and, in some cases, human experts. The reference databases, computational methods and knowledge that form the basis of these pipelines are constantly evolving, and thus there is a need to reprocess genome annotations on a regular basis. The combined challenge of revising existing annotations and extracting useful information from the flood of new genome sequences will necessitate more reliance on completely automated systems.     

Allelic variation at the level of intragenic recombination

This report examines five different naturally occurring alcohol dehydrogenase-1 alleles via the recombinational behavior of Adh1^- mutants induced within them. Twenty-two biochemically characterized Adh1^- mutants have been assessed for ability to recombine intragenically, using data generated by specifically staining for the presence of ADH in pollen grains. Each of the five naturally occurring Adh1 progenitor isoalleles appears unique. Allelic variation exists in (1) the rate of intragenic recombination sustained by an allele, and (2) the pattern of recombinational success or failure based on the ancestry of each mutant in a heteroallelic pair. In other words, we find quantitative and qualitative Adh1 allelic variation at the level of intragenic recombination. I have experimentally excluded several explanations for recombinational restriction. These results will be related to the structure, function and naturally occurring variability of the gene in higher organisms. Specifically, the "recon" (unit of recombination) has been resurrected as a potentially useful unit of natural selection. The reasonableness of several genres of hypotheses in evolutionary/population genetics, particularly those involving linkage disequilibrium, is called into question.     

Kinetic analysis of behavior of chemotactic bacterial population at the interface of two media

The behavior of a population of bacteria at the boundary with a chemotactically active water medium containing the sites of specific binding to cell receptors was analyzed. A kinetic model of chemotaxis was used for the analysis. Differences in the behavior of strains metabolizing and not metabolizing the substrate were revealed. Six phases of interface taxis were distinguished and characterized. The results of the analysis were confirmed by the densitometric data.     

Archaeal signal peptides--a comparative survey at the genome level

The correct delivery of noncytoplasmic proteins to locations both within and outside the cell depends on the appropriate targeting signals. Protein translocation across the bacterial plasma membrane and the eukaryal endoplasmic reticulum membrane relies on cleavable N-terminal signal peptides. Although the signal peptides of secreted proteins in Bacteria and Eukarya have been extensively studied at the sequence, structure, and functional levels, little is known of the nature of archaeal signal peptides. In this report, genome-based analysis was performed in an attempt to define the amino acid composition, length, and cleavage sites of various signal peptide classes in a wide range of archaeal species. The results serve to present a picture of the archaeal signal peptide, revealing the incorporation of bacterial, eukaryal, and archaeal traits.     

Plant genome evolution: lessons from comparative genomics at the DNA level

Angiosperm genomes show tremendous variability in genome size and chromosome number. Nevertheless, comparative genetic mapping has revealed genome collinearity of closely related species. Sequence-based comparisons were used to assess the conservation of gene arrangements. Numerous small rearrangements, insertions/deletions, duplications, inversions and translocations have been detected. Importantly, comparative sequence analyses have unambiguously shown micro-collinearity of distantly related plant species. Duplications and subsequent gene loss have been identified as a particular important factor in the evolution of plant genomes.     

Genetic variation of the Siberian tit Parus cinctus populations at the regional level: a mitochondrial sequence analysis

We studied the matrilinear genetic structure of the Siberian tit Parus cinctus by sequencing 911 bp of the mitochondrial control region of 56 birds from Fennoscandia and 3 from Yakutia, central Siberia, representing subspecies P. c. lapponicus and P. c. cinctus , respectively. One major haplotype comprised 35.7% of all birds and was present in all Fennoscandian populations. Sequence variation of 5 museum specimens from Norway fitted with the pattern of the present-day birds. The nucleotide diversity was 0.00205±0.00025 in the Fennoscandian population and no population structuring was detected. The star-like phylogeny suggests a recent expansion of the population size in the evolutionary time scale. A modern decline of the population size from 200 000 pairs to 50 000 pairs in Finland has resulted from cutting and fragmentation of old-growth forests, but the effects of this could not yet be detected in the mtDNA pattern. However, the nucleotide diversity differed among populations being the highest at Kuusamo, close to the Russian border. Conceivably, the gene flow maintained by the substantial migration of Siberian tits is sufficient to prevent differentiation of local populations in Fennoscandia. Presumably the large conservation areas in NE Finland and on the Russian side of the border contribute to the high genetic variation observed in the Kuusamo population. Comparison of the mtDNA phylogeny of the Siberian tit with the phylogenies of the great tit, the blue tit and the willow tit showed that the Siberian tit and some other non-migratory species of the foliage gleaning guild share similar post glacial histories in the western palaearctic.     

中国人群参考基因组及基因组变异图谱资源库

随着人类基因组计划和国际千人基因组计划的实施,已公开数百个中国人个体的全基因组数据。建立高精度的中国人群参考基因组序列,发现并解析中国人群特有的序列变异,是我国未来精准医学研究的基础。为满足未来精准医学研究中国人基因组数据持续增长的科学管理和深入研究的需求,中国科学院北京基因组研究所发展并建立了基于中国人群全基因组测序数据的虚拟中国人基因组数据库(Virtual Chinese Genome Database, VCGDB)和中国人群基因组变异数据库(Genome Variation Map, GVM),面向国内外用户提供数据检索、共享、下载和在线分析服务。本文重点介绍了这两个数据库的特点和功能,以及未来发展与应用前景,以期为中国人群参考基因组及基因组变异图谱资源库的推广使用、发展完善提供有益信息。     

Use of bacterial DNA-methylases for structuro-functional analysis of the eukaryotic genome

Bacterial DNA-methylases with known recognition sites (RS) were used as probes for structural-and-functional analysis of eukaryotic genome. Adenine and cytosine DNA-methylases recognizing 4 to 6-member unique and degenerative nucleotide sequences having a symmetrical and asymmetrical structure were used for probing. The use of a set of methylases enabled the selection of a probe that was the most sensitive for the given pathology. Thus, severe hypothyrosis was found to be associated with changes in the acceptor capacity of liver DNA in the heterologous++ methylation reaction as could be evidenced from testing by two probes, CCCC and GAATGC. In the cells of chicken liver hepatoma MC29, the acceptor capacity of DNA during GGA methylation appeared to be altered in the greatest degree. DNA-methylases with degenerative SR are weakly specific probes for the study of structural changes (methylation) of the animal genome.     

Construction of a Helicobacter pylori genome map and demonstration of diversity at the genome level.

Genomic DNA from 30 strains of Helicobacter pylori was subjected to pulsed-field gel electrophoresis (PFGE) after digestion with NotI and NruI. The genome sizes of the strains ranged from 1.6 to 1.73 Mb, with an average size of 1.67 Mb. By using NotI and NruI, a circular map of H. pylori UA802 (1.7 Mb) which contained three copies of 16S and 23S rRNA genes was constructed. An unusual feature of the H. pylori genome was the separate location of at least two copies of 16S and 23S rRNA genes. Almost all strains had different PFGE patterns after NotI and NruI digestion, suggesting that the H. pylori genome possesses a considerable degree of genetic variability. However, three strains from different sites (the fundus, antrum, and body of the stomach) within the same patient gave identical PFGE patterns. The genomic pattern of individual isolates remained constant during multiple subcultures in vitro. The reason for the genetic diversity observed among H. pylori strains remains to be explained.     

Social heterosis and the maintenance of genetic diversity at the genome level

Social heterosis is when individuals in groups or neighbourhoods receive a mutualistic benefit from across‐individual genetic diversity. Although it can be a viable evolutionary mechanism to maintain allelic diversity at a given locus, its efficacy at maintaining genome‐wide diversity is in question when multiple loci are being simultaneously selected. Therefore, we modelled social heterosis in a population of haploid genomes of two‐ or three‐linked loci. With such linkages, social heterosis decreases gametic diversity, but maintains allelic diversity. Genomes tend to survive as complimentary pairs, with alternate alleles at each locus (e.g. the pair AbC and aBc). The outcomes of selection appear similar to fitness epistasis but are novel in the sense that phenotypic interactions occur across rather than within individuals. The model’s results strongly suggest that strong linkage across gene loci actually increases the probability that social heterosis maintains significant genetic diversity at the level of the genome.     

Bacterial genome mapper: A comparative bacterial genome mapping tool

Recently, next generation sequencing (NGS) technologies have led to a revolutionary increase in sequencing speed and costefficacy. Consequently, a vast number of contigs from many recently sequenced bacterial genomes remain to be accurately mapped and annotated, requiring the development of more convenient bioinformatics programs. In this paper, we present a newly developed web-based bioinformatics program, Bacterial Genome Mapper, which is suitable for mapping and annotating contigs that have been assembled from bacterial genome sequence raw data. By constructing a multiple alignment map between target contig sequences and two reference bacterial genome sequences, this program also provides very useful comparative genomics analysis of draft bacterial genomes. AVAILABILITY: The database is available for free at http://mbgm.kribb.re.kr.     

Compositional variation in bacterial genes and proteins with potential expression level

Usage of guanine and cytosine at three codon sites in eubacterial genes vary distinctly with potential expressivity, as predicted by Codon Adaptation Index (CAI). In bacteria with moderate/high GC-content, G(3) follows a biphasic relationship, while C(3) increases with CAI. In AT-rich bacteria, correlation of CAI is negative with G(3), but non-specific with C(3). Correlations of CAI with residues encoded by G-starting codons are positive, while with those by C-starting codons are usually negative/random. Average Size/Complexity Score and aromaticity of gene-products decrease with CAI, confirming general validity of cost-minimization principle in free-living eubacteria. Alcoholicity of bacterial gene-products usually decreases with expressivity.     

Inherited variation at the epigenetic level: paramutation from the plant to the mouse

In contrast with a wide definition of the 'epigenetic variation', including all changes in gene expression that do not result from the alteration of the gene structure, a more restricted class had been defined, initially in plants, under the name 'paramutation'. It corresponds to epigenetic modifications distinct from the regulatory interactions of the cell differentiation pathways, mitotically stable and sexually transmitted with non-Mendelian patterns. This class of epigenetic changes appeared for some time restricted to the plant world, but examples progressively accumulated of epigenetic inheritance in organisms ranging from mice to humans. Occurrence of paramutation in the mouse and possible mechanisms were then established in the paradigmatic case of a mutant phenotype maintained and hereditarily transmitted by wild-type homozygotes. Together with the recent findings in plants indicative of a necessary step of RNA amplification in the reference maize paramutation, the mouse studies point to a new role of RNA, as an inducer and hereditary determinant of epigenetic variation. Given the known presence of a wide range of RNAs in human spermatozoa, as well as a number of unexplained cases of familial disease predisposition and transgenerational maintenance, speculations can be extended to possible roles of RNA-mediated inheritance in human biology and pathology.     

DNA microarray analysis of genome dynamics in Yersinia pestis: insights into bacterial genome microevolution and niche adaptation

Genomics research provides an unprecedented opportunity for us to probe into the pathogenicity and evolution of the world's most deadly pathogenic bacterium, Yersinia pestis, in minute detail. In our present work, extensive microarray analysis in conjunction with PCR validation revealed that there are considerable genome dynamics, due to gene acquisition and loss, in natural populations of Y. pestis. We established a genomotyping system to group homologous isolates of Y. pestis, based on profiling or gene acquisition and loss in their genomes, and then drew an outline of parallel microevolution of the Y. pestis genome. The acquisition of a number of genomic islands and plasmids most likely induced Y. pestis to evolve rapidly from Yersinia pseudotuberculosis to a new, deadly pathogen. Horizontal gene acquisition also plays a key role in the dramatic evolutionary segregation of Y. pestis lineages (biovars and genomovars). In contrast to selective genome expansion by gene acquisition, genome reduction occurs in Y. pestis through the loss of DNA regions. We also theorized about the links between niche adaptation and genome microevolution. The transmission, colonization, and expansion of Y. pestis in the natural foci of endemic plague are parallel and directional and involve gradual adaptation to the complex of interactions between the environment, the hosts, and the pathogen itself. These adaptations are based on the natural selections against the accumulation of genetic changes within genome. Our data strongly support that the modern plague originated from Yunnan Province in China, due to the arising of biovar orientalis from biovar antiqua rather than mediaevalis.