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Results for “Pathogen genomics”

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At least 145 records · Page 8Linked to original sources
PubMed1994

Digoxigenin-labelled molecular probe for the simultaneous detection of three potato pathogens: potato spindle tuber viroid (PSTVd), potato virus Y (PVY), and potato leafroll virus (PLRV).

A molecular probe, p3POT, was constructed of PSTVd, PVY, PLRV cDNA fragments introduced into pUC18 vector. Sequencing of the inserts revealed that cloned fragments covered conservative parts of pathogenic genomes. Dot-blot hybridization of digoxigenin-labelled construct to crude extracts from plants infected with different potato viruses proved high sensitivity and specificity of the p3POT probe. This makes p3POT probe an useful tool for the routine testing, and selection of virus-free potatoes.

DNA Probes↗
PubMed2003

Mycoplasma pneumoniae: a reduced-genome intracellular bacterial pathogen.

Mycoplasma pneumoniae has classically been considered an extracellular (or membrane-associated) organism. Nevertheless, the recently elucidated genomic structure of this pathogen strongly suggest that this organism may have been subjected to the process of reductive genetic evolution which is characteristic of intracellular bacteria. We studied the Mycoplasma pneumoniae RYC15989 strain, recovered from a pericardial biopsy sample from a patient with atypical pneumonia and acute pericarditis. The interaction of this strain with human hepatocytes Hep-G2 and mouse neuroblastoma N2-A cell lines was investigated. Confocal laser scanning microscopy and electronic microscopy evidence is presented of the intracellular location of fluorochrome-labelled Mycoplasma pneumoniae in cell lines infected with the organism in vitro. This finding provides preliminary evidence of cellular invasive capacity of Mycoplasma pneumoniae and casts some new light on the pathogenic potential of Mycoplasma pneumoniae in host infection.

Animals↗
PubMed2002

Genomic approaches to fungal pathogenicity.

Within a few years, the genome sequences of a large number of medically and agriculturally important fungi will be known. With this resource come the promises of genomic approaches to study pathogenicity and host-fungus interactions. Genomics is particularly attractive for these questions, as conventional genetic and biochemical approaches are limited in many pathogenic fungi. Recent work has applied signature-tagged mutagenesis and DNA microarray analysis to virulence studies in several fungal species, and novel approaches, such as protein arrays and genomic deletion libraries, are being developed in Saccharomyces cerevisiae and have significant potential in other fungi. High-throughput gene-discovery approaches should greatly increase our understanding of fungal pathogenesis.

Animals↗
PubMed2004

Complete DNA sequence of the linear mitochondrial genome of the pathogenic yeast Candida parapsilosis.

The complete sequence of the mitochondrial DNA of the opportunistic yeast pathogen Candida parapsilosis was determined. The mitochondrial genome is represented by linear DNA molecules terminating with tandem repeats of a 738-bp unit. The number of repeats varies, thus generating a population of linear DNA molecules that are heterogeneous in size. The length of the shortest molecules is 30,922 bp, whereas the longer molecules have expanded terminal tandem arrays (nx738 bp). The mitochondrial genome is highly compact, with less than 8% of the sequence corresponding to non-coding intergenic spacers. In silico analysis predicted genes encoding fourteen protein subunits of complexes of the respiratory chain and ATP synthase, rRNAs of the large and small subunits of the mitochondrial ribosome, and twenty-four transfer RNAs. These genes are organized into two transcription units. In addition, six intronic ORFs coding for homologues of RNA maturase, reverse transcriptase and DNA endonucleases were identified. In contrast to its overall molecular architecture, the coding sequences of the linear mitochondrial DNA of C. parapsilosis are highly similar to their counterparts in the circular mitochondrial genome of its close relative C. albicans. The complete sequence has implications for both mitochondrial DNA replication and the evolution of linear DNA genomes.

Base Sequence↗
PubMed2004

[Application of M-RAPD technique to obtain the genomic fingerprints of various pathogenic microbials].

OBJECTIVE: To obtain genomic fingerprints of different pathogenic microbials and make certain whether their patterns can be used in the identification of microbials by means of multiplex random amplified polymorphic DNA analysis (M-RAPD). METHODS: Arbitrary primers of 10 oligonucleotides were randomly grouped, and various microbials chromosomal DNA were amplified with three combinatorial primers at a special higher annealing temperature. The products were detected by 15 g/L agarose electrophoresis and the patterns were analyzed by the software of Gelworks 1d Intermediate. RESULTS: Specific and resistant DNA fingerprints for different pathogenic microbials with combinatorial primers were gained. The profiles were clear, well-distributed and the number was great. The products of the three primers included most products of every two primers and would appear with no relation to their length, but small products had more opportunity; three primers could provide information contents half as many again as that two primers could provide for the same pathogenic microbials. There were obvious differences among different drug-resistant strains and between the drug-resistant strains and the corresponding reference strains, but different strains of the same microorganism had more similarity than discrepancy. The analytic data of the software of Gelworks 1d Intermediate also support our results. CONCLUSION: M-RAPD is a simple and rapid technique for the identification of different kinds of pathogenic microbials, and it can provide rich genetic information.

DNA Fingerprinting↗
PubMed1998

Comparison of the genome organization of pathogenic neisseriae.

Current efforts to completely sequence the meningococcal and gonocococcal genomes raise the question whether the lessons learned from the sequenced strains may be safely extrapolated to other members of these species, or whether, in view of the fact that Neisseriae are highly recombinogenic and exhibit a high degree of horizontal intra- and interspecies genetic transfer, only clone-specific conclusions are valid. From the known physical and genetic maps of each of two gonococcal and meningococcal strains, it would appear that both species exhibit a species-specific conservation in their genetic organization while the interspecies comparison revealed several rearrangements, although still with a high overall similarity. However, these data contrast with other evidence suggesting intra-species rearrangements, such as the nonconserved I-CeuI macrorestriction patterns of different meningococcal and other neisserial strains. Since I-CeuI cuts within the 23S-rRNA sequence, the restriction pattern should give reliable information on the distribution of rrn loci in the neisserial genomes. Further studies are warranted to answer these questions.

Genome, Bacterial↗
PubMed2005

The bioinformatics resource for oral pathogens.

Complete genomic sequences of several oral pathogens have been deciphered and multiple sources of independently annotated data are available for the same genomes. Different gene identification schemes and functional annotation methods used in these databases present a challenge for cross-referencing and the efficient use of the data. The Bioinformatics Resource for Oral Pathogens (BROP) aims to integrate bioinformatics data from multiple sources for easy comparison, analysis and data-mining through specially designed software interfaces. Currently, databases and tools provided by BROP include: (i) a graphical genome viewer (Genome Viewer) that allows side-by-side visual comparison of independently annotated datasets for the same genome; (ii) a pipeline of automatic data-mining algorithms to keep the genome annotation always up-to-date; (iii) comparative genomic tools such as Genome-wide ORF Alignment (GOAL); and (iv) the Oral Pathogen Microarray Database. BROP can also handle unfinished genomic sequences and provides secure yet flexible control over data access. The concept of providing an integrated source of genomic data, as well as the data-mining model used in BROP can be applied to other organisms. BROP can be publicly accessed at http://www.brop.org.

Bacteria↗
PubMed1994

Recombinant beet curly top virus genomes exhibit both parental and novel pathogenic phenotypes.

Recombinant genomes derived from the Logan and CFH strains of the geminivirus beet curly top virus (BCTV) have been constructed and analyzed for pathogenicity on Nicotiana benthamiana and sugar beet (Beta vulgaris L.). Infectivity assays indicated that the latent period on N. benthamiana was primarily determined by a DNA fragment bearing the leftward open reading frames (ORFs) L1, L2, L3, and L4. Recombinants bearing leftward ORFs from the CFH strain were characterized as having a short latent period (mean = 6-11 days), while the reciprocal recombinants bearing leftward ORFs from the Logan strain had latent periods defined as long (mean = 16-22 days). Infectivity assays on sugar beet indicated that certain recombinant BCTV genomes exhibited novel pathogenic properties not common to either wild type strain, including the loss of systemic movement and replication competency, or asymptomatic systemic infection of sugar beet. The results indicate that N. benthamiana is a more permissive host than sugar beet with respect to heterologous combinations of BCTV genes, and that pathogenicity and virulence of BCTV in sugar beet requires the interaction of certain viral gene products and/or cis-elements that have coevolved in the same strain.

Biological Transport↗
PubMed2001

Multiple pathogenic and benign genomic rearrangements occur at a 35 kb duplication involving the NEMO and LAGE2 genes.

The X-linked dominant and male-lethal disorder incontinentia pigmenti (IP) is caused by mutations in a gene called NEMO (IKK-gamma). We recently reported the structure of NEMO and demonstrated that most IP patients carry an identical deletion that arises due to misalignment between repeats. Affected male abortuses with the IP deletion had provided clues that a second, incomplete copy of NEMO was present in the genome. We have now identified clones containing this truncated copy (Delta NEMO) and incorporated them into a previously constructed physical contig in distal Xq28. Delta NEMO maps 22 kb distal to NEMO and only contains exons 3-10, confirming our proposed model. A sequence of 26 kb 3' of the NEMO coding sequence is also present in the same position relative to the Delta NEMO locus, bringing the total length of the duplication to 35.5 kb. The LAGE2 gene is also located within this duplicated region, and a similar but unique LAGE1 gene is located just distal to the duplicated loci. Mapping and sequence information indicated that the duplicated regions are in opposite orientation. Analysis of the great apes suggested that the NEMO/LAGE2 duplication occurred after divergence of the lineage leading to present day humans, chimpanzees and gorillas, approximately 10-15 million years ago. Intriguingly, despite this substantial evolutionary history, only 22 single nucleotide differences exist between the two copies over the entire 35.5 kb, making the duplications >99% identical. This high sequence identity and the inverted orientations of the two copies, along with duplications of smaller internal sections within each copy, predispose this region to various genomic alterations. We detected four rearrangements that involved NEMO, Delta NEMO or LAGE1 and LAGE2. The high sequence similarity between the two NEMO/LAGE2 copies may be due to frequent gene conversion, as we have detected evidence of sequence transfer between them. Together, these data describe an unusual and complex genomic region that is susceptible to various types of pathogenic and polymorphic rearrangements, including the recurrent lethal deletion associated with IP.

Animals↗
PubMed2002

Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157.

We have sequenced the genome of Shigella flexneri serotype 2a, the most prevalent species and serotype that causes bacillary dysentery or shigellosis in man. The whole genome is composed of a 4 607 203 bp chromosome and a 221 618 bp virulence plasmid, designated pCP301. While the plasmid shows minor divergence from that sequenced in serotype 5a, striking characteristics of the chromosome have been revealed. The S.flexneri chromosome has, astonishingly, 314 IS elements, more than 7-fold over those possessed by its close relatives, the non-pathogenic K12 strain and enterohemorrhagic O157:H7 strain of Escherichia coli. There are 13 translocations and inversions compared with the E.coli sequences, all involve a segment larger than 5 kb, and most are associated with deletions or acquired DNA sequences, of which several are likely to be bacteriophage-transmitted pathogenicity islands. Furthermore, S.flexneri, resembling another human-restricted enteric pathogen, Salmonella typhi, also has hundreds of pseudogenes compared with the E.coli strains. All of these could be subjected to investigations towards novel preventative and treatment strategies against shigellosis.

Amino Acid Sequence↗
PubMed2003

Uncovering genomic differences in human pathogenic Yersinia enterocolitica.

To map out genomic differences between highly pathogenic Yersinia enterocolitica WA-314C biogroup 1B, serotype O:8 strain and low-pathogenic Y. enterocolitica Y-108C biogroup 4, serotype O:3 strain we have applied a method of suppression subtractive hybridization (SSH). In total, 428 WA-314-specific and 83 Y-108-specific sequences were uncovered by SSH. Among them were DNA fragments with similarity to known genes from several groups: (1) genes involved in O-antigen biosynthesis, (2) host-specific restriction-modification systems, (3) systems of iron and heme acquisition and storage, (4) flagellar biogenesis genes, (5) putative virulence factors, (6) drug resistance genes, and (7) mobile elements. Mapped out genomic differences may be applied in identification and development of novel therapeutic strategies for the treatment of enteropathogenic Yersinia.

Animals↗
PubMed2002

Comparative genomics of microbial pathogens and symbionts.

We are interested in quantifying the contribution of gene acquisition, loss, expansion and rearrangements to the evolution of microbial genomes. Here, we discuss factors influencing microbial genome divergence based on pair-wise genome comparisons of closely related strains and species with different lifestyles. A particular focus is on intracellular pathogens and symbionts of the genera Rickettsia, Bartonella and BUCHNERA: Extensive gene loss and restricted access to phage and plasmid pools may provide an explanation for why single host pathogens are normally less successful than multihost pathogens. We note that species-specific genes tend to be shorter than orthologous genes, suggesting that a fraction of these may represent fossil-orfs, as also supported by multiple sequence alignments among species. The results of our genome comparisons are placed in the context of phylogenomic analyses of alpha and gamma proteobacteria. We highlight artefacts caused by different rates and patterns of mutations, suggesting that atypical phylogenetic placements can not a priori be taken as evidence for horizontal gene transfer events. The flexibility in genome structure among free-living microbes contrasts with the extreme stability observed for the small genomes of aphid endosymbionts, in which no rearrangements or inflow of genetic material have occurred during the past 50 millions years (1). Taken together, the results suggest that genomic stability correlate with the content of repeated sequences and mobile genetic elements, and thereby indirectly with bacterial lifestyles.

Alphaproteobacteria↗
PubMed1999

Sequence and analysis of the genome of a baculovirus pathogenic for Lymantria dispar.

The genome of the Lymantria dispar multinucleocapsid nucleopolyhedrovirus (LdMNPV) was sequenced and analyzed. It is composed of 161,046 bases with a G + C content of 57.5% and contains 163 putative open reading frames (ORFs) of >/=150 nucleotides. Homologs were found to 95 of the 155 genes predicted for the Autographa californica MNPV (AcMNPV) genome. More than 9% of the LdMNPV genome was occupied by 16 repeated genes related to AcMNPV ORF2. Readily identifiable homologs of several genes that have been reported to play important roles in the AcMNPV life cycle are not present; these include ie-2, a transcriptional transactivator, and gp64, a major envelope glycoprotein of the nonoccluded form of the virus. A number of genes lacking in AcMNPV but present in other baculoviruses were identified; these include two viral enhancing factor homologs, a second copy of a conotoxin-like gene, and a dutpase homolog. Although a single gene predicted to encode a large subunit of ribonucleotide reductase was found, two different copies of the small subunit gene were present. In addition, homologs of genes not previously reported for baculoviruses were identified, including a predicted protein with homology to DNA ligases and another that has motifs most closely related to a yeast mitochondrial helicase. Thirteen homologous regions (hrs) containing 54 repeated sequences that include 30-bp imperfect palindromes were identified. The imperfect palindromes are related to those from other baculoviruses.

Amino Acid Sequence↗
PubMed2000

Gene conservation and loss in the mutS-rpoS genomic region of pathogenic Escherichia coli.

The extent and nature of DNA polymorphism in the mutS-rpoS region of the Escherichia coli genome were assessed in 21 strains of enteropathogenic E. coli (EPEC) and enterohemorrhagic E. coli (EHEC) and in 6 strains originally isolated from natural populations. The intervening region between mutS and rpoS was amplified by long-range PCR, and the resulting amplicons varied substantially in length (7.8 to 14.2 kb) among pathogenic groups. Restriction maps based on five enzymes and sequence analysis showed that strains of the EPEC 1, EPEC 2, and EHEC 2 groups have a long mutS-rpoS region composed of a approximately 6.0-kb DNA segment found in strain K-12 and a novel DNA segment ( approximately 2.9 kb) located at the 3' end of rpoS. The novel segment contains three genes (yclC, pad1, and slyA) that occur in E. coli O157:H7 and related strains but are not found in K-12 or members of the ECOR group A. Phylogenetic analysis of the common sequences indicates that the long intergenic region is ancestral and at least two separate deletion events gave rise to the shorter regions characteristic of the E. coli O157:H7 and K-12 lineages.

Adenosine Triphosphatases↗
PubMed2003

Genetic and molecular characterization of a dental pathogen using genome-wide approaches.

Actinobacillus actinomycetemcomitans causes periodontitis, a costly chronic infection that affects a large number of patients. The pathogenesis of this dental infection is a multifactorial process that results in a serious degenerative disease of the periodontium. Although significant progress has been achieved after the identification of this Gram-negative bacterium as the etiological agent of this infection, much remains to be done to understand in detail the bacterial factors and host-pathogen interactions involved in the pathogenesis of this disease. Classic research approaches have resulted in the identification of important virulence factors and cellular processes, although they have provided a rather narrow picture of some of the steps of this complex process. In contrast, a much wider picture could be obtained with the application of tools such as bioinformatics and genomics. These tools will provide global information regarding the differential expression of genes encoding factors and processes that lead to the pathogenesis of this disease. Furthermore, comparative genomics has the potential of helping us to understand the emergence and evolution of this human pathogen. This genome-wide approach should provide a more complete picture of the pathogenesis process of this disease, and will facilitate the development of efficient diagnostic, preventive, and therapeutic measures for this disease.

Actinobacillus Infections↗
PubMed2006

Genomic clusters, putative pathogen recognition molecules, and antimicrobial genes are induced by infection of C. elegans with M. nematophilum.

The interaction between the nematode Caenorhabditis elegans and a Gram-positive bacterial pathogen, Microbacterium nematophilum, provides a model for an innate immune response in nematodes. This pathogen adheres to the rectal and post-anal cuticle of the worm, causing slowed growth, constipation, and a defensive swelling response of rectal hypodermal cells. To explore the genomic responses that the worm activates after pathogenic attack we used microarray analysis of transcriptional changes induced after 6-h infection, comparing virulent with avirulent infection. We defined 89 genes with statistically significant expression changes of at least twofold, of which 68 were up-regulated and 21 were down-regulated. Among the former, those encoding C-type lectin domains were the most abundant class. Many of the 89 genes exhibit genomic clustering, and we identified one large cluster of 62 genes, of which most were induced in response to infection. We tested 41 of the induced genes for involvement in immunity using mutants or RNAi, finding that six of these are required for the swelling response and five are required more generally for defense. Our results indicate that C-type lectins and other putative pathogen-recognition molecules are important for innate immune defense in C. elegans. We also found significant induction of genes encoding lysozymes, proteases, and defense-related proteins, as well as various domains of unknown function. The genes induced during infection by M. nematophilum appear largely distinct from genes induced by other pathogens, suggesting that C. elegans mounts pathogen-specific responses to infection.

Animals↗