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The diversity of bacterial pathogenicity mechanisms
Eugene Rosenberg
Genome Biology , 2005, DOI: 10.1186/gb-2005-6-5-320
Abstract: One of the remarkable features of the recent FEMS meeting on the molecular basis of bacterial pathogenesis was the novel ways in which genome sequences are now being used to study bacterial pathogens. In the 10 years since the first complete sequence of the genome of a pathogenic bacterium - that of Haemophilus influenzae - was published, the genomes of almost all the major human pathogens have been sequenced. The first and most obvious use of these data was comparative genome analysis in order to understand what distinguishes pathogenic from nonpathogenic strains. While this approach continues to be useful for discovering new genes that cause disease (virulence genes, which are possible targets for new antibacterial drugs) and clusters of virulence genes (pathogenicity islands) in the genome, and for providing clues to how pathogens have evolved, several new approaches to using genome data were presented at the meeting. These include the development of new vaccines (reverse vaccinology), uncovering new biosynthetic pathways, studying how bacteria adapt rapidly to new environments and the beginning of a comprehensive comparison of genomics and proteomics.Virulent strains of Escherichia coli can be divided into two classes: those that cause intestinal disease and those causing disease elsewhere in the body (extra-intestinal strains). Extra-intestinal E. coli (ExPEC strains) are the cause of a diverse spectrum of invasive human and animal infections, often leading to septicemia. Joerg Hacker (Institut für Molekulare Infektionsbiologie, Würzburg, Germany) reported the analysis of the genomes of a number of pathogenic and commensal E. coli strains. Each genome could be divided into the 'core genome' and the 'flexible gene pool'; the latter comprises up to one third of the entire genome. For example, the uropathogenic E. coli strain 536 contains six pathogenicity islands, comprising more than 500 kb in total. These islands show a characteristic genetic architecture and d
The genetic integrity of bacterial species: the core genome and the accessory genome, two different stories  [PDF]
Bo Segerman
Frontiers in Cellular and Infection Microbiology , 2012, DOI: 10.3389/fcimb.2012.00116
Abstract: Strains within a bacterial species typically have a set of conserved core genes and a variable set of accessory genes. The accessory genes often appear to move laterally between strains, thereby forming new trait combinations. Sometimes, genetic material also moves laterally between species, thereby resulting in diffuse borders between them. The growing number of genome sequences offers new possibilities to study these processes. Ten species for which abundant genomic data exists were here selected for analysis of the species border integrity. The average core genome similarities and relative core genome sizes (RCGSs) were determined for strain pairs within the species and for strain pairs crossing the species border. The variability within the species as well as the border integrity varies for different bacterial species. Some have very distinct borders while others are more or less indefinable. From the growing amount of genomic data, it becomes even clearer that the concept of bacterial species is, in many cases, far from absolute.
Defining the Estimated Core Genome of Bacterial Populations Using a Bayesian Decision Model  [PDF]
Andries J. van Tonder,Shilan Mistry,James E. Bray,Dorothea M. C. Hill,Alison J. Cody,Chris L. Farmer,Keith P. Klugman,Anne von Gottberg,Stephen D. Bentley,Julian Parkhill,Keith A. Jolley,Martin C. J. Maiden,Angela B. Brueggemann
PLOS Computational Biology , 2014, DOI: doi/10.1371/journal.pcbi.1003788
Abstract: The bacterial core genome is of intense interest and the volume of whole genome sequence data in the public domain available to investigate it has increased dramatically. The aim of our study was to develop a model to estimate the bacterial core genome from next-generation whole genome sequencing data and use this model to identify novel genes associated with important biological functions. Five bacterial datasets were analysed, comprising 2096 genomes in total. We developed a Bayesian decision model to estimate the number of core genes, calculated pairwise evolutionary distances (p-distances) based on nucleotide sequence diversity, and plotted the median p-distance for each core gene relative to its genome location. We designed visually-informative genome diagrams to depict areas of interest in genomes. Case studies demonstrated how the model could identify areas for further study, e.g. 25% of the core genes with higher sequence diversity in the Campylobacter jejuni and Neisseria meningitidis genomes encoded hypothetical proteins. The core gene with the highest p-distance value in C. jejuni was annotated in the reference genome as a putative hydrolase, but further work revealed that it shared sequence homology with beta-lactamase/metallo-beta-lactamases (enzymes that provide resistance to a range of broad-spectrum antibiotics) and thioredoxin reductase genes (which reduce oxidative stress and are essential for DNA replication) in other C. jejuni genomes. Our Bayesian model of estimating the core genome is principled, easy to use and can be applied to large genome datasets. This study also highlighted the lack of knowledge currently available for many core genes in bacterial genomes of significant global public health importance.
Differential Regulation of Horizontally Acquired and Core Genome Genes by the Bacterial Modulator H-NS  [PDF]
Rosa C. Ba?os equal contributor,Aitziber Vivero equal contributor,Sonia Aznar,Jesús García,Miquel Pons,Cristina Madrid ,Antonio Juárez
PLOS Genetics , 2009, DOI: 10.1371/journal.pgen.1000513
Abstract: Horizontal acquisition of DNA by bacteria dramatically increases genetic diversity and hence successful bacterial colonization of several niches, including the human host. A relevant issue is how this newly acquired DNA interacts and integrates in the regulatory networks of the bacterial cell. The global modulator H-NS targets both core genome and HGT genes and silences gene expression in response to external stimuli such as osmolarity and temperature. Here we provide evidence that H-NS discriminates and differentially modulates core and HGT DNA. As an example of this, plasmid R27-encoded H-NS protein has evolved to selectively silence HGT genes and does not interfere with core genome regulation. In turn, differential regulation of both gene lineages by resident chromosomal H-NS requires a helper protein: the Hha protein. Tight silencing of HGT DNA is accomplished by H-NS-Hha complexes. In contrast, core genes are modulated by H-NS homoligomers. Remarkably, the presence of Hha-like proteins is restricted to the Enterobacteriaceae. In addition, conjugative plasmids encoding H-NS variants have hitherto been isolated only from members of the family. Thus, the H-NS system in enteric bacteria presents unique evolutionary features. The capacity to selectively discriminate between core and HGT DNA may help to maintain horizontally transmitted DNA in silent form and may give these bacteria a competitive advantage in adapting to new environments, including host colonization.
Plastic architecture of bacterial genome revealed by comparative genomics of Photorhabdus variants
Sophie Gaudriault, Sylvie Pages, Anne Lanois, Christine Laroui, Corinne Teyssier, Estelle Jumas-Bilak, Alain Givaudan
Genome Biology , 2008, DOI: 10.1186/gb-2008-9-7-r117
Abstract: We used a combination of macrorestriction and DNA microarray experiments to perform a comparative genomic study of different P. luminescens TT01 variants. Prolonged culturing of TT01 strain and a genomic variant, collected from the laboratory-maintained symbiotic nematode, generated bacterial lineages composed of primary and secondary phenotypic variants and colonial variants. The primary phenotypic variants exhibit several characteristics that are absent from the secondary forms. We identify substantial plasticity of the genome architecture of some variants, mediated mainly by deletions in the 'flexible' gene pool of the TT01 reference genome and also by genomic amplification. We show that the primary or secondary phenotypic variant status is independent from global genomic architecture and that the bacterial lineages are genomic lineages. We focused on two unusual genomic changes: a deletion at a new recombination hotspot composed of long approximate repeats; and a 275 kilobase single block duplication belonging to a new class of genomic duplications.Our findings demonstrate that major genomic variations occur in Photorhabdus clonal populations. The phenotypic consequences of these genomic changes are cryptic. This study provides insight into the field of bacterial genome architecture and further elucidates the role played by clonal genomic variation in bacterial genome evolution.Comparative genomics, in the study of different bacterial genera, species, and strains, leads to the definition of two DNA pools in bacterial genomes: a set of genes shared by all genomes in a taxa, namely the 'core' genome; and a set of genes containing mobile and accessory genetic elements, termed the 'flexible' gene pool. Both intergenomic and intragenomic rearrangements occur in this 'flexible' gene pool [1]. Changes in the 'flexible' gene pool are considered to be the motor of bacterial diversification and evolution [2-4].However, comparative genomic analyses of genomic variants with
Proteomics-based confirmation of protein expression and correction of annotation errors in the Brucella abortus genome
Julie Lamontagne, Maxime Béland, Anik Forest, Alexandra C?té-Martin, Najib Nassif, Fadi Tomaki, Ignacio Moriyón, Edgardo Moreno, Eustache Paramithiotis
BMC Genomics , 2010, DOI: 10.1186/1471-2164-11-300
Abstract: The proteomic data was compiled from several independent comparative studies of Brucella abortus that used either outer membrane blebs, cytosols, or whole bacteria grown in media, as well as intracellular bacteria recovered at different times following macrophage infection. We identified a total of 621 bacterial proteins that were differentially expressed in a condition-specific manner. For 305 of these proteins we provide the first experimental evidence of their expression. Using a custom-built protein sequence database, we uncovered 7 annotation errors. We provide experimental evidence of expression of 5 genes that were originally annotated as non-expressed pseudogenes, as well as start site annotation errors for 2 other genes.An essential element for ensuring correct functional studies is the correspondence between reported genome sequences and subsequent proteomics studies. In this study, we have used proteomics evidence to confirm expression of multiple proteins previously considered to be putative, as well as correct annotation errors in the genome of Brucella abortus strain 2308.Brucella species bacteria are gram negative alpha proteobacteria superbly adapted for survival in intracellular environments. They infect a wide range of mammals, including essentially all economically important domestic mammals, many wild species, and humans. Brucellosis is the largest bacterial zoonosis in the world [1-3]. In humans, untreated brucellosis is a long lasting disease characterized by recurrent fever episodes and clinical manifestations that include spondylitis, severe headaches, joint or abdominal pain, endocarditis, and meningoencephalitis. In severe non-treated cases brucellosis can cause death [1-3].Seven terrestrial Brucella species have been defined: Brucella melitensis, Brucella abortus, Brucella suis, Brucella ovis, Brucella canis, Brucella neotomae and Brucella microti which infect goats, cattle, pigs, sheep, dogs, desert wood rats and common voles, respectivel
The Core Proteome and Pan Proteome of Salmonella Paratyphi A Epidemic Strains  [PDF]
Li Zhang, Di Xiao, Bo Pang, Qian Zhang, Haijian Zhou, Lijuan Zhang, Jianzhong Zhang, Biao Kan
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0089197
Abstract: Comparative proteomics of the multiple strains within the same species can reveal the genetic variation and relationships among strains without the need to assess the genomic data. Similar to comparative genomics, core proteome and pan proteome can also be obtained within multiple strains under the same culture conditions. In this study we present the core proteome and pan proteome of four epidemic Salmonella Paratyphi A strains cultured under laboratory culture conditions. The proteomic information was obtained using a Two-dimensional gel electrophoresis (2-DE) technique. The expression profiles of these strains were conservative, similar to the monomorphic genome of S. Paratyphi A. Few strain-specific proteins were found in these strains. Interestingly, non-core proteins were found in similar categories as core proteins. However, significant fluctuations in the abundance of some core proteins were also observed, suggesting that there is elaborate regulation of core proteins in the different strains even when they are cultured in the same environment. Therefore, core proteome and pan proteome analysis of the multiple strains can demonstrate the core pathways of metabolism of the species under specific culture conditions, and further the specific responses and adaptations of the strains to the growth environment.
A Reference Pan-Genome Approach to Comparative Bacterial Genomics: Identification of Novel Epidemiological Markers in Pathogenic Campylobacter  [PDF]
Guillaume Méric, Koji Yahara, Leonardos Mageiros, Ben Pascoe, Martin C. J. Maiden, Keith A. Jolley, Samuel K. Sheppard
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0092798
Abstract: The increasing availability of hundreds of whole bacterial genomes provides opportunities for enhanced understanding of the genes and alleles responsible for clinically important phenotypes and how they evolved. However, it is a significant challenge to develop easy-to-use and scalable methods for characterizing these large and complex data and relating it to disease epidemiology. Existing approaches typically focus on either homologous sequence variation in genes that are shared by all isolates, or non-homologous sequence variation - focusing on genes that are differentially present in the population. Here we present a comparative genomics approach that simultaneously approximates core and accessory genome variation in pathogen populations and apply it to pathogenic species in the genus Campylobacter. A total of 7 published Campylobacter jejuni and Campylobacter coli genomes were selected to represent diversity across these species, and a list of all loci that were present at least once was compiled. After filtering duplicates a 7-isolate reference pan-genome, of 3,933 loci, was defined. A core genome of 1,035 genes was ubiquitous in the sample accounting for 59% of the genes in each isolate (average genome size of 1.68 Mb). The accessory genome contained 2,792 genes. A Campylobacter population sample of 192 genomes was screened for the presence of reference pan-genome loci with gene presence defined as a BLAST match of ≥70% identity over ≥50% of the locus length - aligned using MUSCLE on a gene-by-gene basis. A total of 21 genes were present only in C. coli and 27 only in C. jejuni, providing information about functional differences associated with species and novel epidemiological markers for population genomic analyses. Homologs of these genes were found in several of the genomes used to define the pan-genome and, therefore, would not have been identified using a single reference strain approach.
Beyond the genome to tissue proteomics
Lance A Liotta, Emanuel F Petricoin
Breast Cancer Research , 1999, DOI: 10.1186/bcr23
Abstract: Progress in these three phases of molecular medicine is largely driven by new technologies. The development of polymerase chain reaction, high throughput sequencing, and bioinformatics has been a driving force in the first phase. In the second phase, microhybridization arrays applied to genetic analysis and gene expression [1] is a powerful new tool that has entered the commercial sector, and is becoming widely available to researchers. As more genes are identified, it is likely that specialized arrays will be offered that are specific for a tissue type (eg mammary gland chip), physiologic process (eg apoptosis chip, angiogenesis chip, invasion chip) or class of genes (eg suppressor gene chip, oncogene chip).Whereas DNA is an information archive, proteins do all the work of the cell. The existence of a given DNA sequence does not guarantee the synthesis of a corresponding protein [2,3]. The DNA sequence is also not sufficient to describe protein structure, function, and cellular location. This is because protein complexity and versatility stems from context-dependent post-translational processes such as phosphorylation, sulfation, and glycosylation. Moreover, the DNA code does not provide information about how proteins link together into networks and functional machines in the cell. In fact, the activation of a protein signal pathway causing a cell to migrate, die, or initiate division can immediately take place before any changes occur in DNA/RNA gene expression. Consequently, the technology to drive the molecular medicine revolution into the third phase is emerging from protein analytic methods.The term 'proteome', which denotes all the proteins expressed by a genome, was first coined in late 1994 at the Siena two-dimensional gel electrophoresis meeting [4]. Proteomics is proclaimed as the next step after genomics. A goal of investigators in this exciting field is to assemble a complete library of all of the proteins. Only a small percentage of the proteome has be
Core Proteome of the Minimal Cell: Comparative Proteomics of Three Mollicute Species  [PDF]
Gleb Y. Fisunov, Dmitry G. Alexeev, Nicolay A. Bazaleev, Valentina G. Ladygina, Maria A. Galyamina, Ilya G. Kondratov, Nadezhda A. Zhukova, Marina V. Serebryakova, Irina A. Demina, Vadim M. Govorun
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0021964
Abstract: Mollicutes (mycoplasmas) have been recognized as highly evolved prokaryotes with an extremely small genome size and very limited coding capacity. Thus, they may serve as a model of a ‘minimal cell’: a cell with the lowest possible number of genes yet capable of autonomous self-replication. We present the results of a comparative analysis of proteomes of three mycoplasma species: A. laidlawii, M. gallisepticum, and M. mobile. The core proteome components found in the three mycoplasma species are involved in fundamental cellular processes which are necessary for the free living of cells. They include replication, transcription, translation, and minimal metabolism. The members of the proteome core seem to be tightly interconnected with a number of interactions forming core interactome whether or not additional species-specific proteins are located on the periphery. We also obtained a genome core of the respective organisms and compared it with the proteome core. It was found that the genome core encodes 73 more proteins than the proteome core. Apart of proteins which may not be identified due to technical limitations, there are 24 proteins that seem to not be expressed under the optimal conditions.
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