1
|
Zhang R, Zhang CT. The impact of comparative genomics on infectious disease research. Microbes Infect 2006; 8:1613-22. [PMID: 16697228 DOI: 10.1016/j.micinf.2005.11.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2005] [Accepted: 11/30/2005] [Indexed: 12/31/2022]
Abstract
The past decade has witnessed a revolution in infectious disease research, fuelled by the accumulation of a huge amount of DNA sequence data. The avalanche of genome sequence information has largely promoted the development of comparative genomics, which exploits available genome sequences to perform either inter- or intra-species comparisons of bacterial genome contents, or performs comparisons between the human genome and those of other organisms. This review aims to summarize how comparative genomics is being extensively used in infectious disease research, such as in the studies to identify virulence determinants, antimicrobial drug targets, vaccine candidates and new markers for diagnostics. These applications hold considerable promise for alleviating the burden of infectious diseases in the coming years.
Collapse
Affiliation(s)
- Ren Zhang
- Department of Epidemiology and Biostatistics, Tianjin Cancer Institute and Hospital, Tianjin 300060, China
| | | |
Collapse
|
2
|
Abstract
Interpreting the functional content of a given genomic sequence is one of the central challenges of biology today. Perhaps the most promising approach to this problem is based on the comparative method of classic biology in the modern guise of sequence comparison. For instance, protein-coding regions tend to be conserved between species. Hence, a simple method for distinguishing a functional exon from the chance absence of stop codons is to investigate its homologue from closely related species. Predicting regulatory elements is even more difficult than exon prediction, but again, comparisons pinpointing conserved sequence motifs upstream of translation start sites are helping to unravel gene regulatory networks. In addition to interspecific studies, intraspecific sequence comparison yields insights into the evolutionary forces that have acted on a species in the past. Of particular interest here is the identification of selection events such as selective sweeps. Both intra- and interspecific sequence comparisons are based on a variety of computational methods, including alignment, phylogenetic reconstruction, and coalescent theory. This article surveys the biology and the central computational ideas applied in recent comparative genomics projects. We argue that the most fruitful method of understanding the functional content of genomes is to study them in the context of related genomic sequences. In particular, such a study may reveal selection, a fundamental pointer to biological relevance.
Collapse
Affiliation(s)
- Bernhard Haubold
- Fachbereich Biotechnologie & Bioinformatik, Fachhochschule Weihenstephan, 85350 Freising, Germany.
| | | |
Collapse
|
3
|
Cummings CA, Brinig MM, Lepp PW, van de Pas S, Relman DA. Bordetella species are distinguished by patterns of substantial gene loss and host adaptation. J Bacteriol 2004; 186:1484-92. [PMID: 14973121 PMCID: PMC344407 DOI: 10.1128/jb.186.5.1484-1492.2004] [Citation(s) in RCA: 151] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pathogens of the bacterial genus Bordetella cause respiratory disease in humans and animals. Although virulence and host specificity vary across the genus, the genetic determinants of this diversity remain unidentified. To identify genes that may underlie key phenotypic differences between these species and clarify their evolutionary relationships, we performed a comparative analysis of genome content in 42 Bordetella strains by hybridization of genomic DNA to a microarray representing the genomes of three Bordetella species and by subtractive hybridization. Here we show that B. pertussis and B. parapertussis are predominantly differentiated from B. bronchiseptica by large, species-specific regions of difference, many of which encode or direct synthesis of surface structures, including lipopolysaccharide O antigen, which may be important determinants of host specificity. The species also exhibit sequence diversity at a number of surface protein-encoding loci, including the fimbrial major subunit gene, fim2. Gene loss, rather than gene acquisition, accompanied by the proliferation of transposons, has played a fundamental role in the evolution of the pathogenic bordetellae and may represent a conserved evolutionary mechanism among other groups of microbial pathogens.
Collapse
Affiliation(s)
- C A Cummings
- Departments of Microbiology and Immunology. Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | | | | | | | | |
Collapse
|
4
|
Abstract
The sequencing of entire bacterial genomes is becoming increasingly routine, promising to revolutionise approaches to identifying putative antimicrobial drug targets. In silico methods can be used to identify putative gene products by comparing sequences of biochemically characterised enzymes and proteins with data produced by sequencing projects. Comparative genomics between a pathogenic bacterium versus nonpathogen as well as pathogen versus host can identify molecular targets that would be ideal for future investigation. The aim of these comparisons would be to identify genes that code for pathogenicity factors in the bacterium or genes essential for bacterial survival. The latter set of genes includes those that are nonfunctional or redundant in the host as well as genes absent from the host but essential in the pathogen. The products of these genes would be ideal targets for antimicrobial compounds. If compounds could be generated that disrupt the pathogen's ability to thrive but not affect the host, since there is a lack of the targeted protein, they could prove to be powerful therapeutics. An elegant example illustrating the power of comparative genomics involves comparison of the pathways of bacterial and eukaryotic aminoacyl-tRNA synthesis. Comparison of pathogenic bacterial genomes shows that many bacteria lack the genes encoding either one or two specific aminoacyl-tRNA synthetases, enzymes involved in ensuring correct aminoacylation of tRNA for subsequent translation of the genetic code. Bacteria have an alternative pathway by which amide aminoacyl-tRNAs are formed. Comparative genomics has demonstrated that this pathway is uniquely prokaryotic/archaeal and also relatively widely found in pathogenic bacteria, indicating the potential of the catalytic enzymes of the pathway as targets for novel antimicrobial drugs.
Collapse
Affiliation(s)
- Brian Fritz
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, Wisconsin, USA
| | | |
Collapse
|
5
|
Metzgar D, Liu L, Hansen C, Dybvig K, Wills C. Domain-level differences in microsatellite distribution and content result from different relative rates of insertion and deletion mutations. Genome Res 2002; 12:408-13. [PMID: 11875028 PMCID: PMC155286 DOI: 10.1101/gr.198602] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Microsatellites (short tandem polynucleotide repeats) are found throughout eukaryotic genomes at frequencies many orders of magnitude higher than the frequencies predicted to occur by chance. Most of these microsatellites appear to have evolved in a generally neutral manner. In contrast, microsatellites are generally absent from bacterial genomes except in locations where they provide adaptive functional variability, and these appear to have evolved under selection. We demonstrate a mutational bias towards deletion (repeat contraction) in a native chromosomal microsatellite of the bacterium Mycoplasma gallisepticum, through the collection and analysis of independent mutations in the absence of natural selection. Using this and similar existing data from two other bacterial species and four eukaryotic species, we find strong evidence that deletion biases resulting in repeat contraction are common in bacteria, while eukaryotic microsatellites generally experience unbiased mutation or a bias towards insertion (repeat expansion). This difference in mutational bias suggests that eukaryotic microsatellites should generally expand wherever selection does not exclude them, whereas bacterial microsatellites should be driven to extinction by mutational pressure wherever they are not maintained by selection. This is consistent with observed bacterial and eukaryotic microsatellite distributions. Hence, mutational biases that differ between eukaryotes and bacteria can account for many of the observed differences in microsatellite DNA content and distribution found in these two groups of organisms.
Collapse
Affiliation(s)
- David Metzgar
- Division of Biology, University of California at San Diego, San Diego, CA 92093-0116, USA.
| | | | | | | | | |
Collapse
|
6
|
Abstract
Infectious diseases remain a major cause of deaths and disabilities in the world, the majority of which are caused by bacteria. Although immunisation is the most cost effective and efficient means to control microbial diseases, vaccines are not yet available to prevent many major bacterial infections. Examples include dysentery (shigellosis), gonorrhoea, trachoma, gastric ulcers and cancer (Helicobacter pylori). Improved vaccines are needed to combat some diseases for which current vaccines are inadequate. Tuberculosis, for example, remains rampant throughout most countries in the world and represents a global emergency heightened by the pandemic of HIV. The availability of complete genome sequences has dramatically changed the opportunities for developing novel and improved vaccines and facilitated the efficiency and rapidity of their development. Complete genomic databases provide an inclusive catalogue of all potential candidate vaccines for any bacterial pathogen. In conjunction with adjunct technologies, including bioinformatics, random mutagenesis, microarrays, and proteomics, a systematic and comprehensive approach to identifying vaccine discovery can be undertaken. Genomics must be used in conjunction with population biology to ensure that the vaccine can target all pathogenic strains of a species. A proof in principle of the utility of genomics is provided by the recent exploitation of the complete genome sequence of Neisseria meningitidis group B.
Collapse
Affiliation(s)
- Richard Moxon
- Molecular Infectious Diseases Group, Weatherall Institute of Molecular Medicine and University of Oxford Department of Paediatrics, John Radcliffe Hospital, Oxford UK
| | | |
Collapse
|
7
|
Burchmore R, Janssen CS, Turner CM. After the genome--where next? Mol Biochem Parasitol 2001; 118:129-31. [PMID: 11738702 DOI: 10.1016/s0166-6851(01)00364-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- R Burchmore
- Division of Infection and Immunity, Institute of Biomedical and Life Sciences, Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK
| | | | | |
Collapse
|
8
|
van Lin LH, Pace T, Janse CJ, Birago C, Ramesar J, Picci L, Ponzi M, Waters AP. Interspecies conservation of gene order and intron-exon structure in a genomic locus of high gene density and complexity in Plasmodium. Nucleic Acids Res 2001; 29:2059-68. [PMID: 11353075 PMCID: PMC55447 DOI: 10.1093/nar/29.10.2059] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A 13.6 kb contig of chromosome 5 of Plasmodium berghei, a rodent malaria parasite, has been sequenced and analysed for its coding potential. Assembly and comparison of this genomic locus with the orthologous locus on chromosome 10 of the human malaria Plasmodium falciparum revealed an unexpectedly high level of conservation of the gene organisation and complexity, only partially predicted by current gene-finder algorithms. Adjacent putative genes, transcribed from complementary strands, overlap in their untranslated regions, introns and exons, resulting in a tight clustering of both regulatory and coding sequences, which is unprecedented for genome organisation of PLASMODIUM: In total, six putative genes were identified, three of which are transcribed in gametocytes, the precursor cells of gametes. At least in the case of two multiple exon genes, alternative splicing and alternative transcription initiation sites contribute to a flexible use of the dense information content of this locus. The data of the small sample presented here indicate the value of a comparative approach for Plasmodium to elucidate structure, organisation and gene content of complex genomic loci and emphasise the need to integrate biological data of all Plasmodium species into the P.falciparum genome database and associated projects such as PlasmodB to further improve their annotation.
Collapse
Affiliation(s)
- L H van Lin
- Department of Parasitology, Leiden University Medical Centre, PO Box 9600, 2300 RC Leiden, The Netherlands
| | | | | | | | | | | | | | | |
Collapse
|
9
|
Abstract
As bacterial resistance to currently used antibiotics increases, so too must efforts to identify novel agents and strategies for the prevention and treatment of bacterial infection. In the past, antimicrobial drug discovery efforts have focused on eradicating infection by either cidal or static agents, resulting in clearance of the bacterium from the infected host. To this end, drug discovery targets have been those proteins or processes essential for bacterial cell viability. However, inhibition of the interaction between the bacterium and its host may also be a target. During establishment of an infection, pathogenic bacteria use carefully regulated pathways of conditional gene expression to transition from a free-living form to one that must adapt to the host milieu. This transition requires the regulated production of both extracellular and cell-surface molecules, often termed virulence factors. As the biological imperatives of the invading organism change during the course of an infection, the expression of these factors is altered in response to environmental cues. These may be changes in the host environment, for example, pH, metabolites, metal ions, osmolarity, and temperature. Alternatively, effector molecules produced by the bacterium to sense changing cell density can also lead to changes in virulence gene expression. Although the mechanisms of pathogenesis among different bacteria vary, the principles of virulence are generally conserved. Bacterial virulence may therefore offer unique opportunities to inhibit the establishment of infection or alter its course as a method of antimicrobial chemotherapy.
Collapse
Affiliation(s)
- L E Alksne
- Infectious Diseases Department, Wyeth-Ayerst Research, 401 North Middletown Road, Pearl River, NY 10965, USA
| | | |
Collapse
|
10
|
Metzgar D, Wills C. Evolutionary changes in mutation rates and spectra and their influence on the adaptation of pathogens. Microbes Infect 2000; 2:1513-22. [PMID: 11099938 DOI: 10.1016/s1286-4579(00)01306-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The evolutionary tuning of mutational processes may play a key role in prokaryotic evolution, particularly among pathogens. In this paper we review the evidence that genetic systems controlling the rate and spectrum of heritable mutations have evolved to optimize levels of adaptive variation and rates of genetic change.
Collapse
Affiliation(s)
- D Metzgar
- Department of Biology, Mail Code 0116, University of California at San Diego, La Jolla, CA 92093-0116, USA.
| | | |
Collapse
|
11
|
Moxon R, Tang C. Challenge of investigating biologically relevant functions of virulence factors in bacterial pathogens. Philos Trans R Soc Lond B Biol Sci 2000; 355:643-56. [PMID: 10874737 PMCID: PMC1692766 DOI: 10.1098/rstb.2000.0605] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Recent innovations have increased enormously the opportunities for investigating the molecular basis of bacterial pathogenicity, including the availability of whole-genome sequences, techniques for identifying key virulence genes, and the use of microarrays and proteomics. These methods should provide powerful tools for analysing the patterns of gene expression and function required for investigating host-microbe interactions in vivo. But, the challenge is exacting. Pathogenicity is a complex phenotype and the reductionist approach does not adequately address the eclectic and variable outcomes of host-microbe interactions, including evolutionary dynamics and ecological factors. There are difficulties in distinguishing bacterial 'virulence' factors from the many determinants that are permissive for pathogenicity, for example those promoting general fitness. A further practical problem for some of the major bacterial pathogens is that there are no satisfactory animal models or experimental assays that adequately reflect the infection under investigation. In this review, we give a personal perspective on the challenge of characterizing how bacterial pathogens behave in vivo and discuss some of the methods that might be most relevant for understanding the molecular basis of the diseases for which they are responsible. Despite the powerful genomic, molecular, cellular and structural technologies available to us, we are still struggling to come to grips with the question of 'What is a pathogen?'
Collapse
Affiliation(s)
- R Moxon
- Oxford University, Department of Paediatrics, John Radcliffe Hospital, UK.
| | | |
Collapse
|
12
|
Drysdale R, Bayraktaroglu L. Current awareness. Yeast 2000; 17:159-66. [PMID: 10900461 PMCID: PMC2448328 DOI: 10.1155/2000/907141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In order to keep subscribers up-to-date with the latest developments in their field, this current awareness service is provided by John Wiley & Sons and contains newly-published material on comparative and functional genomics. Each bibliography is divided into 16 sections. 1 Reviews & symposia; 2 General; 3 Large-scale sequencing and mapping; 4 Genome evolution; 5 Comparative genomics; 6 Gene families and regulons; 7 Pharmacogenomics; 8 Large-scale mutagenesis programmes; 9 Functional complementation; 10 Transcriptomics; 11 Proteomics; 12 Protein structural genomics; 13 Metabolomics; 14 Genomic approaches to development; 15 Technological advances; 16 Bioinformatics. Within each section, articles are listed in alphabetical order with respect to author. If, in the preceding period, no publications are located relevant to any one of these headings, that section will be omitted
Collapse
Affiliation(s)
- R Drysdale
- FlyBase-Cambridge, Department of Genetics, University of Cambridge, UK
| | | |
Collapse
|
13
|
|