comparative phylogenomics of pathogenic bacteria by microarray analysis CORD-Papers-2022-06-02 (Version 1)

Title: Comparative phylogenomics of pathogenic bacteria by microarray analysis
Abstract: DNA microarrays represent a powerful technology that enables whole-scale comparison of bacterial genomes. This coupled with new methods to model DNA microarray data is facilitating the development of robust comparative phylogenomics analyses. Such studies have dramatically increased our ability to differentiate between bacteria highlighting previously undetected genetic differences and population structures and providing new insight into virulence and evolution of bacterial pathogens. Recent results from such studies have generated insights into the evolution of bacterial pathogens the levels of diversity and plasticity in the genome of a species as well as the differences in virulence amongst pathogenic bacteria.
Published: 2005-08-24
Journal: Curr Opin Microbiol
DOI: 10.1016/j.mib.2005.08.012
DOI_URL: http://doi.org/10.1016/j.mib.2005.08.012
Author Name: Dorrell Nick
Author link: https://covid19-data.nist.gov/pid/rest/local/author/dorrell_nick
Author Name: Hinchliffe Stewart J
Author link: https://covid19-data.nist.gov/pid/rest/local/author/hinchliffe_stewart_j
Author Name: Wren Brendan W
Author link: https://covid19-data.nist.gov/pid/rest/local/author/wren_brendan_w
Author Name: Gottschalk, Gerhard
Author link: https://covid19-data.nist.gov/pid/rest/local/author/gottschalk_gerhard
Author Name: Schuster, Stephan C
Author link: https://covid19-data.nist.gov/pid/rest/local/author/schuster_stephan_c
sha: 86161746859c22d29da637d687deda287607c69d
license: no-cc
license_url: [no creative commons license associated]
source_x: Elsevier; Medline; PMC
source_x_url: https://www.elsevier.com/https://www.medline.com/https://www.ncbi.nlm.nih.gov/pubmed/
pubmed_id: 16125441
pubmed_id_url: https://www.ncbi.nlm.nih.gov/pubmed/16125441
pmcid: PMC7108221
pmcid_url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7108221
url: https://www.sciencedirect.com/science/article/pii/S1369527405001281 https://api.elsevier.com/content/article/pii/S1369527405001281 https://www.ncbi.nlm.nih.gov/pubmed/16125441/
has_full_text: TRUE
Keywords Extracted from Text Content: DNA Wren 621 Figure 1 8:620-626 Dorrell Microbiology 2005 Wren 625 www.sciencedirect.com Streptococcus (GAS) strains extraintestinal M. bovis Mycobacterum microti TTSS non-O1 Mycobacterium canettii S. aureus pan-array humans stomach human host proline-betaine transporter homolog RD3 human gastric pathogen H. pylori S. aureus strain Escherichia coli [1 gastrointestinal wellcharacterised M. chromosomal Neisseria meningitides [5 V. cholerae TTSS meninges P. aeruginosa genome. Neisseria species DNA lateral V. cholerae T, G Staphylococcus aureus [6] Y. pestis isolates S. aureus Salmonella species C. jejuni V. cholerae strains Y. pestis-specific human host [ bloodstream melting-temperature foci herd Campylobacter jejuni SET Cy3 Y. Neisseria gonorrhoeae subclones BCG strains E. coli surface parti-cularly M. microti strains N. meningitidis strains vitamin B12 receptor Neisseria meningitidis hosts immune system Y. pestis non-O1/non-O139 V. cholerae H. pylori Bacille Calmette-Guerin RD13 blood-brain barrier O139 strains genitourinary tract M. microti coronavirus UK Vibrio cholerae N. lactamica cellular Helicobacter pylori [3 O1 MSRA patients RDs RD1 non-O1/ non-O139 strains non-O139 V. cholerae M. cholera-free locations [9 gerbil gastritis non-O139 strains non-O1/non-O139 Mycobacterium bovis strains human clone nucleotide GBS M. bovis strains Neisseria lactamica tubercle bacilli cag Food Biotechnology
Extracted Text Content in Record: First 5000 Characters:DNA microarrays represent a powerful technology that enables whole-scale comparison of bacterial genomes. This, coupled with new methods to model DNA microarray data, is facilitating the development of robust comparative phylogenomics analyses. Such studies have dramatically increased our ability to differentiate between bacteria, highlighting previously undetected genetic differences and population structures and providing new insight into virulence and evolution of bacterial pathogens. Recent results from such studies have generated insights into the evolution of bacterial pathogens, the levels of diversity and plasticity in the genome of a species, as well as the differences in virulence amongst pathogenic bacteria. Comparative phylogenomics of pathogenic bacteria by microarray analysis Dorrell, Hinchliffe and Wren 621 Figure 1 Principles of comparative phylogenomics using DNA microarrays. For further details, see main body of text. www.sciencedirect.com Current Opinion in Microbiology 2005, 8:620-626 Comparative phylogenomics of pathogenic bacteria by microarray analysis Dorrell, Hinchliffe and Wren 625 www.sciencedirect.com Current Opinion in Microbiology 2005, 8:620-626 Traditional phylogenetic classification of bacteria to study evolutionary relatedness is based on the characterisation of a limited number of genes, rRNA or signature sequences. However, owing to the acquisition of DNA through lateral gene transfer, the differences between closely related bacterial strains can be vast. By contrast, whole-genome sequencing comparisons allow a multitude of genes to be compared. Already, several bacterial species have had more than a single representative sequenced (e.g. Escherichia coli [1] , Campylobacter jejuni [2] , Helicobacter pylori [3] , Yersinia pestis [4] , Neisseria meningitides [5] , Staphylococcus aureus [6] and several Chlamydia species [7] ). Nevertheless, whole-scale genome sequencing remains an expensive endeavour and such comparisons are limited to only a handful of strains. DNA microarrays represent an alternative technology for whole-genome comparisons, enabling a 'bird's-eye view' of all the genes absent or present in a given genome compared to the reference genome on the microarray. Harnessing DNA microarray information through interrogative and robust algorithms has enabled a true 'comparative phlyogenomics' approach to be developed. Recent comparative phlyogenomics studies have been undertaken on increasingly large collections of strains of defined origin. One common feature of these studies is the unexpectedly large genetic diversity between strains of the same species, blurring our definition of species boundaries. Whole-genome comparisons typically identify sets of 'core genes', which are shared by all strains in a species, and 'accessory genes', which are present in one or more strains in a species and often result from gene acquisition. It is these differences that can often be used to identify genes and/or genetic islands related to 'gainof-function traits' in pathogenic strains. Uncovering the mechanisms behind this variability is fundamental in understanding and ultimately counteracting the threats posed by our old adversaries. This review will describe selected recent examples in which comparative phylogenomics using microarray data has provided new and often unexpected insights into the evolution, ecology, virulence and genome diversity of bacterial pathogens. Comparative phylogenomics studies involve analysis of the relative hybridisation capacity of sample bacterial DNA to reporter DNA elements that are bound to a microarray surface. DNA microarrays consist of minute samples of DNA (known as reporter elements) that are arrayed in a grid formation on a suitable medium. Each predicted coding sequence within a target genome or genomes is represented on the array by at least one specific reporter element. All DNA reporter elements are designed to minimise cross-hybridisation (hybridisation of DNA from one gene to reporter elements that represent other genes owing to sequence similarity) between spots. Sample genomic DNA from a test strain is labelled with a fluorescent marker (usually Cy3 or Cy5) and is competitively hybridised with genomic DNA from a control strain that has been labelled with a different fluorescent marker ( Figure 1 ). The control strain is usually DNA from the strain used to design the array, as this should hybridize to all reporter elements on the microarray. After washing to remove any unbound DNA, microarrays are scanned by a high-resolution fluorescence scanner, and the image obtained is analysed by specific software packages that are not discussed in this review. Control spots on the array and DNA 'spikes' in the labelling reaction can be used to aid normalisation of array data. A comparison of the levels of test and control DNA bound to each reporter element on the array can be performed and statistical methods are utilized to determine if the codi
Keywords Extracted from PMC Text: Neisseria meningitidis genitourinary tract C. jejuni M. microti strains Y. pestis isolates foci human cellular Y. pestis-specific patients http://bugs.sgul.ac.uk/ M. meninges M. bovis RD3 [19•, 20] O139 strains coronavirus Streptococcus (GAS) strains chromosomal DNA V. cholerae TTSS Staphylococcus aureus [6] S. aureus strain non-O1/non-O139 Helicobacter pylori [3 melting-temperature Y. humans RDs herd human gastric pathogen H. pylori Neisseria species BCG strains non-O139 V. cholerae GBS Cy3 human host non-O139 strains S. aureus pan-array N. meningitidis strains Neisseria meningitides [5 blood O1 extraintestinal [19•] brain barrier Mycobacterium canettii SET tubercle bacilli UK E. coli vitamin B12 receptor Mycobacterum microti RD1 Mycobacterium bovis strains P. aeruginosa genome. gerbil gastritis nucleotide Vibrio cholerae cholera-free locations [9 hosts immune system H. pylori non-O1/non-O139 V. cholerae proline-betaine transporter homolog cag lateral Neisseria lactamica M. microti Campylobacter jejuni T, G RD13 Neisseria gonorrhoeae Bacille Calmette-Guerin MSRA M. bovis strains V. cholerae strains human host [ S. aureus TTSS bloodstream non-O1 16• Escherichia coli [1 Y. pestis gastrointestinal N. lactamica V. cholerae surface clone subclones BμG@S stomach
Extracted PMC Text Content in Record: First 5000 Characters:Traditional phylogenetic classification of bacteria to study evolutionary relatedness is based on the characterisation of a limited number of genes, rRNA or signature sequences. However, owing to the acquisition of DNA through lateral gene transfer, the differences between closely related bacterial strains can be vast. By contrast, whole-genome sequencing comparisons allow a multitude of genes to be compared. Already, several bacterial species have had more than a single representative sequenced (e.g. Escherichia coli [1], Campylobacter jejuni [2], Helicobacter pylori [3], Yersinia pestis [4], Neisseria meningitides [5], Staphylococcus aureus [6] and several Chlamydia species [7]). Nevertheless, whole-scale genome sequencing remains an expensive endeavour and such comparisons are limited to only a handful of strains. DNA microarrays represent an alternative technology for whole-genome comparisons, enabling a 'bird's-eye view' of all the genes absent or present in a given genome compared to the reference genome on the microarray. Harnessing DNA microarray information through interrogative and robust algorithms has enabled a true 'comparative phlyogenomics' approach to be developed. Recent comparative phlyogenomics studies have been undertaken on increasingly large collections of strains of defined origin. One common feature of these studies is the unexpectedly large genetic diversity between strains of the same species, blurring our definition of species boundaries. Whole-genome comparisons typically identify sets of 'core genes', which are shared by all strains in a species, and 'accessory genes', which are present in one or more strains in a species and often result from gene acquisition. It is these differences that can often be used to identify genes and/or genetic islands related to 'gain-of-function traits' in pathogenic strains. Uncovering the mechanisms behind this variability is fundamental in understanding and ultimately counteracting the threats posed by our old adversaries. This review will describe selected recent examples in which comparative phylogenomics using microarray data has provided new and often unexpected insights into the evolution, ecology, virulence and genome diversity of bacterial pathogens. Comparative phylogenomics studies involve analysis of the relative hybridisation capacity of sample bacterial DNA to reporter DNA elements that are bound to a microarray surface. DNA microarrays consist of minute samples of DNA (known as reporter elements) that are arrayed in a grid formation on a suitable medium. Each predicted coding sequence within a target genome or genomes is represented on the array by at least one specific reporter element. All DNA reporter elements are designed to minimise cross-hybridisation (hybridisation of DNA from one gene to reporter elements that represent other genes owing to sequence similarity) between spots. Sample genomic DNA from a test strain is labelled with a fluorescent marker (usually Cy3 or Cy5) and is competitively hybridised with genomic DNA from a control strain that has been labelled with a different fluorescent marker (Figure 1 ). The control strain is usually DNA from the strain used to design the array, as this should hybridize to all reporter elements on the microarray. After washing to remove any unbound DNA, microarrays are scanned by a high-resolution fluorescence scanner, and the image obtained is analysed by specific software packages that are not discussed in this review. Control spots on the array and DNA 'spikes' in the labelling reaction can be used to aid normalisation of array data. A comparison of the levels of test and control DNA bound to each reporter element on the array can be performed and statistical methods are utilized to determine if the coding sequence in question is present, absent or highly divergent in the test strain. DNA microarrays often consist of gene fragments (reporter elements) amplified by polymerase chain reaction (PCR) that represent individual genes. Currently, up to 50 000 gene fragments can be spotted onto a single microscope slide using robotic technology. Advantages of this technology are: flexibility in the design of the array; the relative ease of production; and its relatively low cost. Multiple identical microarrays can be robotically printed in batches of over a hundred in a single run. Most of the cost in printing such arrays is caused by the synthesis of oligonucleotide primer pairs required for the amplification of target gene fragments. The use of clone libraries as the template for the amplification of PCR products can dramatically reduce this cost [8]. Oligonucleotide microarrays do not rely upon PCR amplification of gene targets, and areas of specificity within any gene sequence can be chosen for hybridisation analysis. However, the sequence of target DNA must be known before oligonucleotide synthesis. The two most frequently used formats are the Affymetrix and the Qiagen Operon systems.
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