Streptomyces Genome
Genome Architecture
from Ralph Kirby and Carton W. Chen writing in Streptomyces: Molecular Biology and Biotechnology
Linear replicons are relatively uncommon among bacteria and their preponderance among the Actinomycetales, and within the Streptomyces in particular, poses some interesting questions. These novel bacterial replicons are capped by terminal proteins that are covalently bound to the 5' ends of the linear DNA and these terminal structures are directly involved in replicating and protecting the ends of the linear genome. In addition and perhaps related to their linear nature, these genomes are among the largest bacterial chromosomes. As far as can be ascertained at present, these large genomes have a specific organizational structure in terms of their genes. The genome structure can be divided into a core region that is present syntenously in most Actinomycetales, two terminal regions that are highly variable throughout the explored Streptomyces and two regions to the left and right of the core region that contain many syntenous genes specific to the Streptomyces and not found in other Actinomycetales. Genome dynamics seems to be important to the Streptomyces with plasmid-chromosome interactions, horizontal gene transfer and interspecific recombination probably playing important roles in how these genomes to adapt to the diverse environment they reside in. Exploring the genome architecture of the Streptomyces helps our understanding of how and why the genus Streptomyces has a unique place in the evolution of the bacteria.
Further reading: Streptomyces: Molecular Biology and Biotechnology
from Ralph Kirby and Carton W. Chen writing in Streptomyces: Molecular Biology and Biotechnology
Linear replicons are relatively uncommon among bacteria and their preponderance among the Actinomycetales, and within the Streptomyces in particular, poses some interesting questions. These novel bacterial replicons are capped by terminal proteins that are covalently bound to the 5' ends of the linear DNA and these terminal structures are directly involved in replicating and protecting the ends of the linear genome. In addition and perhaps related to their linear nature, these genomes are among the largest bacterial chromosomes. As far as can be ascertained at present, these large genomes have a specific organizational structure in terms of their genes. The genome structure can be divided into a core region that is present syntenously in most Actinomycetales, two terminal regions that are highly variable throughout the explored Streptomyces and two regions to the left and right of the core region that contain many syntenous genes specific to the Streptomyces and not found in other Actinomycetales. Genome dynamics seems to be important to the Streptomyces with plasmid-chromosome interactions, horizontal gene transfer and interspecific recombination probably playing important roles in how these genomes to adapt to the diverse environment they reside in. Exploring the genome architecture of the Streptomyces helps our understanding of how and why the genus Streptomyces has a unique place in the evolution of the bacteria.
Further reading: Streptomyces: Molecular Biology and Biotechnology
Viral Sequences in Plant Genomes
Endogenous Viral Sequences in Plant Genomes
from Pierre-Yves Teycheney and Andrew D.W. Geering writing in Recent Advances in Plant Virology
Endogenous viral sequences from members of two virus families, the Caulimoviridae and Geminiviridae, have been discovered in several monocotyledonous and dicotyledonous plant species. For the most part, these sequences are replication-defective but those capable of causing infection have been discovered in tobacco (Nicotiana edwardsonii), petunia (Petunia hybrida) and banana and plantain (Musa spp.). Activation of endogenous caulimovirid sequences is one of the major impediments to international banana and plantain breeding efforts. Research on endogenous viral sequences in plants is still in its infancy, with little known about the contributions of these sequences to host and virus evolution, nor even a classification system adopted. On a practical note, problems still exist with differentially detecting viral genomic DNA in a host genetic background containing endogenous viral sequences, and a solution to the problem of activation of endogenous viral sequences in banana is still far away.
Further reading: Recent Advances in Plant Virology | Virology Publications
from Pierre-Yves Teycheney and Andrew D.W. Geering writing in Recent Advances in Plant Virology
Endogenous viral sequences from members of two virus families, the Caulimoviridae and Geminiviridae, have been discovered in several monocotyledonous and dicotyledonous plant species. For the most part, these sequences are replication-defective but those capable of causing infection have been discovered in tobacco (Nicotiana edwardsonii), petunia (Petunia hybrida) and banana and plantain (Musa spp.). Activation of endogenous caulimovirid sequences is one of the major impediments to international banana and plantain breeding efforts. Research on endogenous viral sequences in plants is still in its infancy, with little known about the contributions of these sequences to host and virus evolution, nor even a classification system adopted. On a practical note, problems still exist with differentially detecting viral genomic DNA in a host genetic background containing endogenous viral sequences, and a solution to the problem of activation of endogenous viral sequences in banana is still far away.
Further reading: Recent Advances in Plant Virology | Virology Publications
Serogroup B Meningococcus Vaccine
The First Vaccine Obtained Through Reverse Vaccinology: The Serogroup B Meningococcus Vaccine
from Jeannette Adu-Bobie, Beatrice Aricò, Marzia M. Giuliani and Davide Serruto writing in Vaccine Design: Innovative Approaches and Novel Strategies
Neisseria meningitidis was isolated over one hundred years when Anton Weicshelbaum identified the causative agent of cerebrospinal meningitis. Since its isolation in 1887, N. meningitidis has been recognized to cause endemic cases, case clusters, epidemics and pandemics of meningitis and devastating septicaemia. Despite over one century since its discovery, scientists have yet to identify a universal vaccine for this deadly bacterium. Although vaccines exist for several serogroups of pathogenic N. meningitidis, serotype B (MenB) has eluded scientists for decades, until the advent of genomics. The genome era has completely changed the way to design vaccines. The availability of the complete genome of microorganisms combined with a novel advanced technology has introduced a new prospective in vaccine research. This novel approach is now known as "Reverse Vaccinology" and N. meningitidis can be considered the first successful example of its application. A recent review describes the successful story of the development of the serogroup B vaccine, starting from the analysis of genome and finishing with the results obtained in clinical trials.
Further reading: Vaccine Design: Innovative Approaches and Novel Strategies | Neisseria: Molecular Mechanisms of Pathogenesis
from Jeannette Adu-Bobie, Beatrice Aricò, Marzia M. Giuliani and Davide Serruto writing in Vaccine Design: Innovative Approaches and Novel Strategies
Neisseria meningitidis was isolated over one hundred years when Anton Weicshelbaum identified the causative agent of cerebrospinal meningitis. Since its isolation in 1887, N. meningitidis has been recognized to cause endemic cases, case clusters, epidemics and pandemics of meningitis and devastating septicaemia. Despite over one century since its discovery, scientists have yet to identify a universal vaccine for this deadly bacterium. Although vaccines exist for several serogroups of pathogenic N. meningitidis, serotype B (MenB) has eluded scientists for decades, until the advent of genomics. The genome era has completely changed the way to design vaccines. The availability of the complete genome of microorganisms combined with a novel advanced technology has introduced a new prospective in vaccine research. This novel approach is now known as "Reverse Vaccinology" and N. meningitidis can be considered the first successful example of its application. A recent review describes the successful story of the development of the serogroup B vaccine, starting from the analysis of genome and finishing with the results obtained in clinical trials.
Further reading: Vaccine Design: Innovative Approaches and Novel Strategies | Neisseria: Molecular Mechanisms of Pathogenesis
Flagella of Salmonella
New insights into the role and formation of flagella in Salmonella
from Rasika M. Harshey writing in Salmonella: From Genome to Function
The flagellum of Salmonella enterica serovar Typhimurium is the best studied of all flagellar systems. The major function of the flagellum is to enable swimming and chemotaxis in liquid media, and swarming on surfaces. New structural information, along with biochemical, physicochemical and genetic analyses has greatly accelerated our understanding of the self-assembly of this highly sophisticated nano-machine. The study of swarming motility is a relatively new field, but has begun to reveal new roles for the flagellum, new functions for motility genes and new regulatory circuits that control the decision between motility and sessility. Morphological and functional similarities between flagella and needle complexes, discovery of partial flagellar structures that likely function in export rather than motility, and a rapidly accumulating genome database are gradually illuminating the evolutionary origins of the flagellum.
Further reading: Salmonella: From Genome to Function | Pili and Flagella
from Rasika M. Harshey writing in Salmonella: From Genome to Function
The flagellum of Salmonella enterica serovar Typhimurium is the best studied of all flagellar systems. The major function of the flagellum is to enable swimming and chemotaxis in liquid media, and swarming on surfaces. New structural information, along with biochemical, physicochemical and genetic analyses has greatly accelerated our understanding of the self-assembly of this highly sophisticated nano-machine. The study of swarming motility is a relatively new field, but has begun to reveal new roles for the flagellum, new functions for motility genes and new regulatory circuits that control the decision between motility and sessility. Morphological and functional similarities between flagella and needle complexes, discovery of partial flagellar structures that likely function in export rather than motility, and a rapidly accumulating genome database are gradually illuminating the evolutionary origins of the flagellum.
Further reading: Salmonella: From Genome to Function | Pili and Flagella
Fimbriae of Salmonella
Fimbrial signature arrangements in Salmonella
from Sean-Paul Nuccio, Nicholas R. Thomson, Maria C. Fookes and Andreas J. Bäumler writing in Salmonella: From Genome to Function
The complement of fimbrial operons held within a genome represents one of the key differentiating features of the sequenced Salmonella serovars and one of the single largest sources of genetic diversity. Generically described as filamentous non-flagellar surface appendages, fimbriae (also known as pili) typically imbue an adhesive trait to the cells expressing them. While much is known about the general biology of fimbrial assembly mechanisms, the role of these structures in Salmonella pathogenesis remains poorly characterized. Here we present fimbrial operon data gathered from the seventeen completed Salmonella genome sequences and discuss its implications in Salmonella pathogenesis and dissemination.
Further reading: Salmonella: From Genome to Function | Pili and Flagella
from Sean-Paul Nuccio, Nicholas R. Thomson, Maria C. Fookes and Andreas J. Bäumler writing in Salmonella: From Genome to Function
The complement of fimbrial operons held within a genome represents one of the key differentiating features of the sequenced Salmonella serovars and one of the single largest sources of genetic diversity. Generically described as filamentous non-flagellar surface appendages, fimbriae (also known as pili) typically imbue an adhesive trait to the cells expressing them. While much is known about the general biology of fimbrial assembly mechanisms, the role of these structures in Salmonella pathogenesis remains poorly characterized. Here we present fimbrial operon data gathered from the seventeen completed Salmonella genome sequences and discuss its implications in Salmonella pathogenesis and dissemination.
Further reading: Salmonella: From Genome to Function | Pili and Flagella
Genomics and Pathogenesis of Salmonella
Genomics and Pathogenesis of Salmonella enterica serovars Typhi and Paratyphi A
from Kathryn E Holt, Tim T Perkins, Gordon Dougan and Robert A Kingsley writing in Salmonella: From Genome to Function
The genomics era has transformed the way that we can study bacterial pathogens. The availability of two complete and 17 draft genomes of S. Typhi has made it possible to study the phylogenetic structure of this pathogen in unparalleled resolution, monitor gene flux, accumulation of pseudogenes, neutral mutations and loci under selective pressure. We describe the molecular basis of Salmonella Typhi pathogenesis, in particular where genomics has contributed to our understanding in the past decade. Potentially important S. Typhi-specific virulence determinants include the Vi polysaccharide capsule, the type IV pilus, and a unique repertoire of fimbria. These may account for key differences in the disease outcome of this pathogen compared with non-typhoidal serotypes. Genome comparison with the closely related serotype S. Paratyphi A identifies a core set of pseudogenes, some of which emerged independently, that may define important features of genome degradation associated with host restriction and pathogenesis of invasive disease. Geo-phylogenetics of S. Typhi constructed from single nucleotide polymorphism data from high throughput draft genome sequences is now being applied to study molecular epidemiology in the field.
Further reading: Salmonella: From Genome to Function
from Kathryn E Holt, Tim T Perkins, Gordon Dougan and Robert A Kingsley writing in Salmonella: From Genome to Function
The genomics era has transformed the way that we can study bacterial pathogens. The availability of two complete and 17 draft genomes of S. Typhi has made it possible to study the phylogenetic structure of this pathogen in unparalleled resolution, monitor gene flux, accumulation of pseudogenes, neutral mutations and loci under selective pressure. We describe the molecular basis of Salmonella Typhi pathogenesis, in particular where genomics has contributed to our understanding in the past decade. Potentially important S. Typhi-specific virulence determinants include the Vi polysaccharide capsule, the type IV pilus, and a unique repertoire of fimbria. These may account for key differences in the disease outcome of this pathogen compared with non-typhoidal serotypes. Genome comparison with the closely related serotype S. Paratyphi A identifies a core set of pseudogenes, some of which emerged independently, that may define important features of genome degradation associated with host restriction and pathogenesis of invasive disease. Geo-phylogenetics of S. Typhi constructed from single nucleotide polymorphism data from high throughput draft genome sequences is now being applied to study molecular epidemiology in the field.
Further reading: Salmonella: From Genome to Function
Salmonella evolution
Evolutionary trends associated with niche specialization as modeled by whole genome analysis of egg-contaminating Salmonella enterica serovar Enteritidis
from Jean Guard, Devendra Shah, Cesar A. Morales and Doug Call writing in Salmonella: From Genome to Function
The mosaic nature of the Salmonella enterica genome facilitates its access to multiple environments. Many large scale genomic events have been described that contribute to the combinatorial complexity of the pathogenic Salmonellae. However, the impact of small scale genetic change occurring at the level of single nucleotide polymorphism (SNP) on the emergence of niche specialization is just now becoming appreciated. A recent review describes concepts behind the evolution that culminated in the remarkable ability of Salmonella enterica serovar Enteritidis to contaminate and survive in the internal content of eggs produced by otherwise healthy hens. Evidence suggests that combinations of SNPs facilitate niche specialization by Salmonella enterica. However, few typing methods incorporate unbiased strategies for their detection. Selection of appropriate biological assays for ranking SNPs and combinations of SNPs for their impact on the ability of Salmonella enterica to propagate outbreaks, pandemics and disease will be a significant challenge to improve the safety of the food supply.
Further reading: Salmonella: From Genome to Function
from Jean Guard, Devendra Shah, Cesar A. Morales and Doug Call writing in Salmonella: From Genome to Function
The mosaic nature of the Salmonella enterica genome facilitates its access to multiple environments. Many large scale genomic events have been described that contribute to the combinatorial complexity of the pathogenic Salmonellae. However, the impact of small scale genetic change occurring at the level of single nucleotide polymorphism (SNP) on the emergence of niche specialization is just now becoming appreciated. A recent review describes concepts behind the evolution that culminated in the remarkable ability of Salmonella enterica serovar Enteritidis to contaminate and survive in the internal content of eggs produced by otherwise healthy hens. Evidence suggests that combinations of SNPs facilitate niche specialization by Salmonella enterica. However, few typing methods incorporate unbiased strategies for their detection. Selection of appropriate biological assays for ranking SNPs and combinations of SNPs for their impact on the ability of Salmonella enterica to propagate outbreaks, pandemics and disease will be a significant challenge to improve the safety of the food supply.
Further reading: Salmonella: From Genome to Function
Salmonella genomes
Comparison of Salmonella genomes
from Ye Feng, Wei-Qiao Liu, Kenneth E. Sanderson, and Shu-Lin Liu writing in Salmonella: From Genome to Function:
Salmonella contains over 2600 known lineages, each with distinct biological characteristics, including differences in the niche in which they dwell and the nature of diseases they may cause in their hosts. Genomic sequence analysis is beginning to reveal the genetic basis that determines the phenotypic differences among them. Comparison of eight sequenced genomes of Salmonella subgroup I lineages, which infect warm-blooded animals including humans, demonstrates that these pathogens share about 90% of their genes (the "core" genome), with the remaining ca. 10% genes being unique to each of the lineages (the "accessory" genome). Prophages and Salmonella Pathogenicity Islands (SPIs) are the main components of the accessory genome. Insertion of large DNA segments, such as SPI7 in S. Typhi, may disrupt physical balance of the genome between replication origin and terminus and rearrangements of the genome, such as inversions or translocations mediated by homologous sites (rrn operons, prophages, IS200, etc.) may accelerate rebalancing of the genome. Laterally transferred genes are the main driving force in Salmonella evolution and speciation; evidence exists indicating that mismatch repair genes may spontaneously regulate bacterial mutability through allele conversion to facilitate or inhibit incorporation of foreign DNA. Further studies may help elucidate the genetic basis of distinct pathogeneses and host ranges among the Salmonella pathogens.
Further reading: Salmonella: From Genome to Function
from Ye Feng, Wei-Qiao Liu, Kenneth E. Sanderson, and Shu-Lin Liu writing in Salmonella: From Genome to Function:
Salmonella contains over 2600 known lineages, each with distinct biological characteristics, including differences in the niche in which they dwell and the nature of diseases they may cause in their hosts. Genomic sequence analysis is beginning to reveal the genetic basis that determines the phenotypic differences among them. Comparison of eight sequenced genomes of Salmonella subgroup I lineages, which infect warm-blooded animals including humans, demonstrates that these pathogens share about 90% of their genes (the "core" genome), with the remaining ca. 10% genes being unique to each of the lineages (the "accessory" genome). Prophages and Salmonella Pathogenicity Islands (SPIs) are the main components of the accessory genome. Insertion of large DNA segments, such as SPI7 in S. Typhi, may disrupt physical balance of the genome between replication origin and terminus and rearrangements of the genome, such as inversions or translocations mediated by homologous sites (rrn operons, prophages, IS200, etc.) may accelerate rebalancing of the genome. Laterally transferred genes are the main driving force in Salmonella evolution and speciation; evidence exists indicating that mismatch repair genes may spontaneously regulate bacterial mutability through allele conversion to facilitate or inhibit incorporation of foreign DNA. Further studies may help elucidate the genetic basis of distinct pathogeneses and host ranges among the Salmonella pathogens.
Further reading: Salmonella: From Genome to Function
Metagenomics Book Review
I am pleased to provide the following excerpt from a book review of Metagenomics: Theory, Methods and Applications:
"the book is recommended for life science researchers and all students in biology and medicine wishing to learn more about this new and very interesting field" from Arzneimittelforschung/Drug Research (2010) 60: 226-227 read more ...
"the book is recommended for life science researchers and all students in biology and medicine wishing to learn more about this new and very interesting field" from Arzneimittelforschung/Drug Research (2010) 60: 226-227 read more ...
 | Edited by: Diana Marco "an excellent resource for students, researchers, and scientists ... a valuable resource on the newly evolving biological field of metagenomics, making contributions to ecology, biodiversity, bioremediation, bioprospection of natural products, medicine, and other disciplines." (Doodys)ISBN: 978-1-904455-54-7 Publisher: Caister Academic Press Publication Date: January 2010 Cover: Hardback |