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Variation suggestive of horizontal gene transfer at a lipopolysaccharide (lps) biosynthetic locus in Xanthomonas oryzae pv. oryzae, the bacterial leaf blight pathogen of rice
Prabhu B Patil, Ramesh V Sonti
BMC Microbiology , 2004, DOI: 10.1186/1471-2180-4-40
Abstract: We report here the complete sequence of a 12.2 kb virulence locus of Xanthomonas oryzae pv. oryzae (Xoo) encoding six genes whose products are homologous to functions involved in LPS biosynthesis and transport. All six open reading frames (ORFs) have atypical G+C content and altered codon usage, which are the hallmarks of genomic islands that are acquired by horizontal gene transfer. The lps locus is flanked by highly conserved genes, metB and etfA, respectively encoding cystathionine gamma lyase and electron transport flavoprotein. Interestingly, two different sets of lps genes are present at this locus in the plant pathogens, Xanthomonas campestris pv. campestris (Xcc) and Xanthomonas axonopodis pv. citri (Xac). The genomic island is present in a number of Xoo strains from India and other Asian countries but is not present in two strains, one from India (BXO8) and another from Nepal (Nepal624) as well as the closely related rice pathogen, Xanthomonas oryzae pv. oryzicola (Xoor). TAIL-PCR analysis indicates that sequences related to Xac are present at the lps locus in both BXO8 and Nepal624. The Xoor strain has a hybrid lps gene cluster, with sequences at the metB and etfA ends, being most closely related to sequences from Xac and the tomato pathogen, Pseudomonas syringae pv. tomato respectively.This is the first report of hypervariation at an lps locus between different strains of a plant pathogenic bacterium. Our results indicate that multiple HGT events have occurred at this locus in the xanthomonad group of plant pathogens.LPS is an important constituent of the outer membrane of gram-negative bacteria. Variation in LPS composition can have profound consequences for these cells by potentially providing resistance against bacteriophages and antimicrobial compounds as well as facilitating evasion of the host immune system in animal pathogens. Extreme variation at LPS gene clusters has been reported in animal pathogenic bacteria. Recently, eleven highly divergent g
Horizontal Transfer and the Evolution of Host-Pathogen Interactions  [PDF]
Elena de la Casa-Esperón
International Journal of Evolutionary Biology , 2012, DOI: 10.1155/2012/679045
Abstract: Horizontal gene transfer has been long known in viruses and prokaryotes, but its importance in eukaryotes has been only acknowledged recently. Close contact between organisms, as it occurs between pathogens and their hosts, facilitates the occurrence of DNA transfer events. Once inserted in a foreign genome, DNA sequences have sometimes been coopted by pathogens to improve their survival or infectivity, or by hosts to protect themselves against the harm of pathogens. Hence, horizontal transfer constitutes a source of novel sequences that can be adopted to change the host-pathogen interactions. Therefore, horizontal transfer can have an important impact on the coevolution of pathogens and their hosts. 1. Introduction The evolution of pathogens and their hosts is often interpreted as an arms race: while hosts have developed multiple mechanisms to protect themselves, pathogens have generated diverse strategies to evade their hosts’ defenses. But pathogens and hosts have also evolved mechanisms that allow a mutualistic coexistence. During their coevolution, a relationship between pathogen and host has been established based on intricate and specialized molecular interactions. One of the possible outcomes of this long-standing and close relationship is the exchange of genetic material. Horizontal or lateral gene transfer (HT) is the nonsexual movement of genetic information between two organisms [1]. These sequences can be modified and adapted (i.e., coopted, domesticated) during the evolution of the recipient species to improve their own survival. When HT occurs between hosts and their pathogens (in one direction or the other), the acquired sequences can be coopted to affect how the two organisms interact with each other. Pathogens have developed an impressive array of strategies to avoid host defenses, including the interference or disruption of the host defensive mechanisms and signaling cascades. For instance, vertebrate viruses can avoid detection and elimination by the host immune response by obstructing antigen presentation, blocking apoptosis, disrupting complement cascades, and mimicking or modulating cytokines and their receptors, among others [2, 3]. I will discuss how several of these strategies have been achieved through the acquisition and domestication of host genes. Hosts, in turn, can protect themselves from the deleterious effects of infections by two approaches: resistance and tolerance [4, 5]. Resistant traits reduce damage by limiting the pathogen growth and, therefore, the extent of the infection, sometimes eliminating the pathogen
Distributive Conjugal Transfer in Mycobacteria Generates Progeny with Meiotic-Like Genome-Wide Mosaicism, Allowing Mapping of a Mating Identity Locus  [PDF]
Todd A. Gray ,Janet A. Krywy,Jessica Harold,Michael J. Palumbo,Keith M. Derbyshire
PLOS Biology , 2013, DOI: 10.1371/journal.pbio.1001602
Abstract: Horizontal gene transfer (HGT) in bacteria generates variation and drives evolution, and conjugation is considered a major contributor as it can mediate transfer of large segments of DNA between strains and species. We previously described a novel form of chromosomal conjugation in mycobacteria that does not conform to classic oriT-based conjugation models, and whose potential evolutionary significance has not been evaluated. Here, we determined the genome sequences of 22 F1-generation transconjugants, providing the first genome-wide view of conjugal HGT in bacteria at the nucleotide level. Remarkably, mycobacterial recipients acquired multiple, large, unlinked segments of donor DNA, far exceeding expectations for any bacterial HGT event. Consequently, conjugal DNA transfer created extensive genome-wide mosaicism within individual transconjugants, which generated large-scale sibling diversity approaching that seen in meiotic recombination. We exploited these attributes to perform genome-wide mapping and introgression analyses to map a locus that determines conjugal mating identity in M. smegmatis. Distributive conjugal transfer offers a plausible mechanism for the predicted HGT events that created the genome mosaicism observed among extant Mycobacterium tuberculosis and Mycobacterium canettii species. Mycobacterial distributive conjugal transfer permits innovative genetic approaches to map phenotypic traits and confers the evolutionary benefits of sexual reproduction in an asexual organism.
Heterokaryon Incompatibility Is Suppressed Following Conidial Anastomosis Tube Fusion in a Fungal Plant Pathogen  [PDF]
Francine H. Ishikawa, Elaine A. Souza, Jun-ya Shoji, Lanelle Connolly, Michael Freitag, Nick D. Read, M. Gabriela Roca
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0031175
Abstract: It has been hypothesized that horizontal gene/chromosome transfer and parasexual recombination following hyphal fusion between different strains may contribute to the emergence of wide genetic variability in plant pathogenic and other fungi. However, the significance of vegetative (heterokaryon) incompatibility responses, which commonly result in cell death, in preventing these processes is not known. In this study, we have assessed this issue following different types of hyphal fusion during colony initiation and in the mature colony. We used vegetatively compatible and incompatible strains of the common bean pathogen Colletotrichum lindemuthianum in which nuclei were labelled with either a green or red fluorescent protein in order to microscopically monitor the fates of nuclei and heterokaryotic cells following hyphal fusion. As opposed to fusion of hyphae in mature colonies that resulted in cell death within 3 h, fusions by conidial anastomosis tubes (CAT) between two incompatible strains during colony initiation did not induce the vegetative incompatibility response. Instead, fused conidia and germlings survived and formed heterokaryotic colonies that in turn produced uninucleate conidia that germinated to form colonies with phenotypic features different to those of either parental strain. Our results demonstrate that the vegetative incompatibility response is suppressed during colony initiation in C. lindemuthianum. Thus, CAT fusion may allow asexual fungi to increase their genetic diversity, and to acquire new pathogenic traits.
Low Effective Dispersal of Asexual Genotypes in Heterogeneous Landscapes by the Endemic Pathogen Penicillium marneffei  [PDF]
Matthew C Fisher ,William P Hanage,Sybren de Hoog,Elizabeth Johnson,Michael D Smith,Nicholas J White,Nongnuch Vanittanakom
PLOS Pathogens , 2005, DOI: 10.1371/journal.ppat.0010020
Abstract: Long-distance dispersal in microbial eukaryotes has been shown to result in the establishment of populations on continental and global scales. Such “ubiquitous dispersal” has been claimed to be a general feature of microbial eukaryotes, homogenising populations over large scales. However, the unprecedented sampling of opportunistic infectious pathogens created by the global AIDS pandemic has revealed that a number of important species exhibit geographic endemicity despite long-distance migration via aerially dispersed spores. One mechanism that might tend to drive such endemicity in the face of aerial dispersal is the evolution of niche-adapted genotypes when sexual reproduction is rare. Dispersal of such asexual physiological “species” will be restricted when natural habitats are heterogeneous, as a consequence of reduced adaptive variation. Using the HIV-associated endemic fungus Penicillium marneffei as our model, we measured the distribution of genetic variation over a variety of spatial scales in two host species, humans and bamboo rats. Our results show that, despite widespread aerial dispersal, isolates of P. marneffei show extensive spatial genetic structure in both host species at local and country-wide scales. We show that the evolution of the P. marneffei genome is overwhelmingly clonal, and that this is perhaps the most asexual fungus yet found. We show that clusters of genotypes are specific to discrete ecological zones and argue that asexuality has led to the evolution of niche-adapted genotypes, and is driving endemicity, by reducing this pathogen's potential to diversify in nature.
Low effective dispersal of asexual genotypes in heterogeneous landscapes by the endemic pathogen Penicillium marneffei.
Fisher Matthew C,Hanage William P,de Hoog Sybren,Johnson Elizabeth
PLOS Pathogens , 2005,
Abstract: Long-distance dispersal in microbial eukaryotes has been shown to result in the establishment of populations on continental and global scales. Such "ubiquitous dispersal" has been claimed to be a general feature of microbial eukaryotes, homogenising populations over large scales. However, the unprecedented sampling of opportunistic infectious pathogens created by the global AIDS pandemic has revealed that a number of important species exhibit geographic endemicity despite long-distance migration via aerially dispersed spores. One mechanism that might tend to drive such endemicity in the face of aerial dispersal is the evolution of niche-adapted genotypes when sexual reproduction is rare. Dispersal of such asexual physiological "species" will be restricted when natural habitats are heterogeneous, as a consequence of reduced adaptive variation. Using the HIV-associated endemic fungus Penicillium marneffei as our model, we measured the distribution of genetic variation over a variety of spatial scales in two host species, humans and bamboo rats. Our results show that, despite widespread aerial dispersal, isolates of P. marneffei show extensive spatial genetic structure in both host species at local and country-wide scales. We show that the evolution of the P. marneffei genome is overwhelmingly clonal, and that this is perhaps the most asexual fungus yet found. We show that clusters of genotypes are specific to discrete ecological zones and argue that asexuality has led to the evolution of niche-adapted genotypes, and is driving endemicity, by reducing this pathogen's potential to diversify in nature.
A Novel In Vitro Multiple-Stress Dormancy Model for Mycobacterium tuberculosis Generates a Lipid-Loaded, Drug-Tolerant, Dormant Pathogen
Chirajyoti Deb,Chang-Muk Lee,Vinod S. Dubey,Jaiyanth Daniel,Bassam Abomoelak,Tatiana D. Sirakova,Santosh Pawar,Linda Rogers,Pappachan E. Kolattukudy
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0006077
Abstract: Mycobacterium tuberculosis (Mtb) becomes dormant and phenotypically drug resistant when it encounters multiple stresses within the host. Inability of currently available drugs to kill latent Mtb is a major impediment to curing and possibly eradicating tuberculosis (TB). Most in vitro dormancy models, using single stress factors, fail to generate a truly dormant Mtb population. An in vitro model that generates truly dormant Mtb cells is needed to elucidate the metabolic requirements that allow Mtb to successfully go through dormancy, identify new drug targets, and to screen drug candidates to discover novel drugs that can kill dormant pathogen.
Horizontal gene transfer may explain variation in θs  [PDF]
Rohan Maddamsetti,Philip J. Hatcher,Stéphane Cruveiller,Claudine Médigue,Jeffrey E. Barrick,Richard E. Lenski
Quantitative Biology , 2012,
Abstract: Martincorena et al. estimated synonymous diversity ({\theta}s = 2N{\mu}) across 2,930 orthologous gene alignments from 34 Escherichia coli genomes, and found substantial variation among genes in the density of synonymous polymorphisms. They argue that this pattern reflects variation in the mutation rate per nucleotide ({\mu}) among genes. However, the effective population size (N) is not necessarily constant across the genome. In particular, different genes may have different histories of horizontal gene transfer (HGT), whereas Martincorena et al. used a model with random recombination to calculate {\theta}s. They did filter alignments in an effort to minimize the effects of HGT, but we doubt that any procedure can completely eliminate HGT among closely related genomes, such as E. coli living in the complex gut community. Here we show that there is no significant variation among genes in rates of synonymous substitutions in a long-term evolution experiment with E. coli and that the per-gene rates are not correlated with {\theta}s estimates from genome comparisons. However, there is a significant association between {\theta}s and HGT events. Together, these findings imply that {\theta}s variation reflects different histories of HGT, not local optimization of mutation rates to reduce the risk of deleterious mutations as proposed by Martincorena et al.
A genetic code alteration generates a proteome of high diversity in the human pathogen Candida albicans
Ana C Gomes, Isabel Miranda, Raquel M Silva, Gabriela R Moura, Benjamin Thomas, Alexandre Akoulitchev, Manuel AS Santos
Genome Biology , 2007, DOI: 10.1186/gb-2007-8-10-r206
Abstract: Here we used an unusual decoding of leucine CUG codons as serine in the main human fungal pathogen Candida albicans to elucidate the global impact of genetic code alterations on the proteome. We show that C. albicans decodes CUG codons ambiguously and tolerates partial reversion of their identity from serine back to leucine on a genome-wide scale.Such codon ambiguity expands the proteome of this human pathogen exponentially and is used to generate important phenotypic diversity. This study highlights novel features of C. albicans biology and unanticipated roles for codon ambiguity in the evolution of the genetic code.Since the elucidation of the genetic code in the 1960s, 24 alterations in codon identity have been recorded in prokaryotic and eukaryotic translation systems. These alterations involve redefinition of identity of both sense and nonsense codons and codon unassignment (codons vanished from genomes) [1]. Furthermore, artificial expansion of the genetic code to incorporate non-natural amino acids [2-4] and natural incorporation of selenocysteine (Sec; 21st amino acid) and pyrrolysine (22nd amino acid) have also been reported [5,6]. Sec is incorporated in both prokaryotic and eukaryotic selenoproteins through reprogramming of UGA stop codons by novel translation elongation factors (selenoprotein translation factor B prokaryotes, elongation factor [EF]-Sec, and selenium-binding protein 2 eukaryotes), a new tRNA (tRNASec), and a Sec mRNA insertion element [7]. L-pyrrolysine insertion occurs in the archeon Methanosarcina barkeri through reprogramming of the UAG stop codon by a pyrrolysine insertion sequence in the methylamine methyltransferase mRNA [8]. The flexibility of the genetic code is further exemplified by the absence of glutamine and asparagine aminoacyl-tRNA synthetases in several mitochondria and archaeal and bacterial species. In those particular cases, aminoacylation of tRNAGln and tRNAAsn is accomplished by an ATP-dependent transamidation reaction
Identification of urdbean genotypes with horizontal resistance to Colletotrichum truncatum, a leaf spot pathogen  [cached]
RAJAN SHARMA and R.P. KAUSHAL
Indian Phytopathology , 2012,
Abstract: Horizontal resistance to Colletotrichum truncatum in 12 selected lines of Vigna mungo was studied on the basis of components of disease resistance viz., incubation period, lesion size, lesion number per leaf and spore intensity. Based on these components, HPBU 71 was the most promising genotype possessing resistance to the majority of the pathogen isolates. HPBU 125 and Palampur 93 also showed comparatively more resistance to the eleven pathogen isolates collected from different V. mungo growing areas of Himachal Pradesh, India.
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