Abstract:
BACKGROUND:Pseudomonas aeruginosa is a ubiquitous environmental bacterium and an important opportunistic human pathogen. Generally, the acquisition of genes in the form of pathogenicity islands distinguishes pathogenic isolates from nonpathogens. We therefore sequenced a highly virulent strain of P. aeruginosa, PA14, and compared it with a previously sequenced (and less pathogenic) strain, PAO1, to identify novel virulence genes. RESULTS:The PA14 and PAO1 genomes are remarkably similar, although PA14 has a slightly larger genome (6.5 megabses [Mb]) than does PAO1 (6.3 Mb). We identified 58 PA14 gene clusters that are absent in PAO1 to determine which of these genes, if any, contribute to its enhanced virulence in a Caenorhabditis elegans pathogenicity model. First, we tested 18 additional diverse strains in the C. elegans model and observed a wide range of pathogenic potential; however, genotyping these strains using a custom microarray showed that the presence of PA14 genes that are absent in PAO1 did not correlate with the virulence of these strains. Second, we utilized a full-genome nonredundant mutant library of PA14 to identify five genes (absent in PAO1) required for C. elegans killing. Surprisingly, although these five genes are present in many other P. aeruginosa strains, they do not correlate with virulence in C. elegans. CONCLUSION:Genes required for pathogenicity in one strain of P. aeruginosa are neither required for nor predictive of virulence in other strains. We therefore propose that virulence in this organism is both multifactorial and combinatorial, the result of a pool of pathogenicity-related genes that interact in various combinations in different genetic backgrounds.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Lee DG,Urbach JM,Wu G,Liberati NT,Feinbaum RL,Miyata S,Diggins LT,He J,Saucier M,Déziel E,Friedman L,Li L,Grills G,Montgomery K,Kucherlapati R,Rahme LG,Ausubel FMdoi
10.1186/gb-2006-7-10-r90subject
Has Abstractpub_date
2006-01-01 00:00:00pages
R90issue
10eissn
1474-7596issn
1474-760Xpii
gb-2006-7-10-r90journal_volume
7pub_type
杂志文章相关文献
GENOME BIOLOGY文献大全abstract:BACKGROUND:MicroRNAs (miRNAs) are a class of small, non-coding regulatory RNAs that regulate gene expression by guiding target mRNA cleavage or translational inhibition. So far, identification of miRNAs has been limited to a few model plant species, such as Arabidopsis, rice and Populus, whose genomes have been sequenc...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-6-r96
更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:The regulatory mechanisms underlying tissue specificity are a crucial part of the development and maintenance of multicellular organisms. A genome-wide analysis of promoters in the context of gene-expression patterns in tissue surveys provides a means of identifying the general principles for these mechanism...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2005-6-4-r33
更新日期:2005-01-01 00:00:00
abstract::Understanding the functional impact of genomic variants is a major goal of modern genetics and personalized medicine. Although many synonymous and non-coding variants act through altering the efficiency of pre-mRNA splicing, it is difficult to predict how these variants impact pre-mRNA splicing. Here, we describe a ma...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1437-x
更新日期:2018-06-01 00:00:00
abstract:BACKGROUND:Growth rate is central to the development of cells in all organisms. However, little is known about the impact of changing growth rates. We used continuous cultures to control growth rate and studied the transcriptional program of the model eukaryote Saccharomyces cerevisiae, with generation times varying be...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2006-7-11-r107
更新日期:2006-01-01 00:00:00
abstract:BACKGROUND:Genome editing of malaria parasites is key to the generation of live attenuated parasites used in experimental vaccination approaches. DNA repair in Plasmodium generally occurs only through homologous recombination. This has been used to generate transgenic parasites that lack one to three genes, leading to ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-015-0811-1
更新日期:2015-11-17 00:00:00
abstract::Recent genomic studies showing abnormalities in the fibroblast growth factor system in the postmortem brains of people with major depressive disorder support previous indications of a role for growth factors in mood disorders. Similar molecular pathways, volumetric changes, and the effects of exercise on mood suggest ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2005-6-4-215
更新日期:2005-01-01 00:00:00
abstract:BACKGROUND:Host-associated microbiomes, the microorganisms occurring inside and on host surfaces, influence evolutionary, immunological, and ecological processes. Interactions between host and microbiome affect metabolism and contribute to host adaptation to changing environments. Meta-analyses of host-associated bacte...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1908-8
更新日期:2020-02-03 00:00:00
abstract:BACKGROUND:A large fraction of the human genome is attributable to L1 retrotransposon sequences. Not only do L1s themselves make up a significant portion of the genome, but L1-encoded proteins are thought to be responsible for the transposition of other repetitive elements and processed pseudogenes. In addition, L1s ca...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2003-4-5-r30
更新日期:2003-01-01 00:00:00
abstract:BACKGROUND:Protein domains display a range of structural diversity, with numerous additions and deletions of secondary structural elements between related domains. We have observed a small number of cases of surprising large-scale deletions of core elements of structural domains. We propose a new concept called domain ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-015-0655-8
更新日期:2015-04-30 00:00:00
abstract:BACKGROUND:The wealth of genomic data in bacteria is helping microbiologists understand the factors involved in gene innovation. Among these, the expansion and reduction of gene families appears to have a fundamental role in this, but the factors influencing gene family size are unclear. RESULTS:The relative content o...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2004-5-4-r27
更新日期:2004-01-01 00:00:00
abstract::DNA arrays are valuable tools in molecular biology laboratories. Their rapid acceptance was aided by the release of plans for a pin-spotting microarrayer by researchers at Stanford. Inkjet microarraying is a flexible, complementary technique that allows the synthesis of arrays of any oligonucleotide sequences de novo....
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2004-5-8-r58
更新日期:2004-01-01 00:00:00
abstract:BACKGROUND:Understanding the embryonic stem cell (ESC) fate decision between self-renewal and proper differentiation is important for developmental biology and regenerative medicine. Attention has focused on mechanisms involving histone modifications, alternative pre-messenger RNA splicing, and cell-cycle progression. ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1512-3
更新日期:2018-09-14 00:00:00
abstract:BACKGROUND:Cultivable archaeal species are assigned to two phyla -- the Crenarchaeota and the Euryarchaeota -- by a number of important genetic differences, and this ancient split is strongly supported by phylogenetic analysis. The recently described hyperthermophile Nanoarchaeum equitans, harboring the smallest cellul...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2005-6-5-r42
更新日期:2005-01-01 00:00:00
abstract:BACKGROUND:Altering the biochemical makeup of chromatin by the incorporation of histone variants during development represents a key mechanism in regulating gene expression. The histone variant H2A.B, H2A.B.3 in mice, appeared late in evolution and is most highly expressed in the testis. In the mouse, it is encoded by ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1633-3
更新日期:2019-01-31 00:00:00
abstract::Levels of transcripts sharing microRNA response elements are co-regulated. These RNA-RNA interactions imply that combinations of microRNAs modulate cell-specific transcript networks. ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2011-12-11-132
更新日期:2011-11-21 00:00:00
abstract::Pooled CRISPR screens allow researchers to interrogate genetic causes of complex phenotypes at the genome-wide scale and promise higher specificity and sensitivity compared to competing technologies. Unfortunately, two problems exist, particularly for CRISPRi/a screens: variability in guide efficiency and large rare o...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1538-6
更新日期:2018-10-08 00:00:00
abstract:BACKGROUND:The recent availability of genome sequences has provided unparalleled insights into the broad-scale patterns of transposable element (TE) sequences in eukaryotic genomes. Nevertheless, the difficulties that TEs pose for genome assembly and annotation have prevented detailed, quantitative inferences about the...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2006-7-11-r112
更新日期:2006-01-01 00:00:00
abstract:BACKGROUND:The lifelong accumulation of somatic mutations underlies age-related phenotypes and cancer. Mutagenic forces are thought to shape the genome of aging cells in a tissue-specific way. Whole genome analyses of somatic mutation patterns, based on both types and genomic distribution of variants, can shed light on...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1892-z
更新日期:2019-12-18 00:00:00
abstract:BACKGROUND:Methods of microarray analysis that suit experimentalists using the technology are vital. Many methodologies discard the quantitative results inherent in cDNA microarray comparisons or cannot be flexibly applied to multifactorial experimental design. Here we present a flexible, quantitative Bayesian framewor...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2002-3-12-research0071
更新日期:2002-01-01 00:00:00
abstract::A report on the 18th Congress of the European Society for Evolutionary Biology (ESEB), Aarhus, Denmark, 20-25 August, 2001. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2001-2-11-reports4026
更新日期:2001-01-01 00:00:00
abstract:BACKGROUND:While CRISPR-Cas systems hold tremendous potential for engineering the human genome, it is unclear how well each system performs against one another in both non-homologous end joining (NHEJ)-mediated and homology-directed repair (HDR)-mediated genome editing. RESULTS:We systematically compare five different...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1445-x
更新日期:2018-05-29 00:00:00
abstract::High-throughput technologies have enabled the systematic identification and characterization of most, or possibly all, of the components governing segmentation in the fruit fly Drosophila. What have we learned? ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2008-9-2-207
更新日期:2008-01-01 00:00:00
abstract:BACKGROUND:Although 2,061 proteins of Pyrococcus horikoshii OT3, a hyperthermophilic archaeon, have been predicted from the recently completed genome sequence, the majority of proteins show no similarity to those from other organisms and are thus hypothetical proteins of unknown function. Because most proteins operate ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2005-6-12-r98
更新日期:2005-01-01 00:00:00
abstract:BACKGROUND:The identification of causal genes from genome-wide association studies (GWAS) is the next important step for the translation of genetic findings into biologically meaningful mechanisms of disease and potential therapeutic targets. Using novel chromatin interaction detection techniques and allele specific as...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-016-1078-x
更新日期:2016-11-01 00:00:00
abstract::In predicting hierarchical protein function annotations, such as terms in the Gene Ontology (GO), the simplest approach makes predictions for each term independently. However, this approach has the unfortunate consequence that the predictor may assign to a single protein a set of terms that are inconsistent with one a...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2008-9-s1-s6
更新日期:2008-01-01 00:00:00
abstract::Derived from the maize Mu1 transposon, RescueMu provides strategies for maize gene discovery and mutant phenotypic analysis. 9.92 Mb of gene-enriched sequences next to RescueMu insertion sites were co-assembled with expressed sequence tags and analyzed. Multiple plasmid recoveries identified probable germinal insertio...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2004-5-10-r82
更新日期:2004-01-01 00:00:00
abstract::Protein kinases are critical to cellular signalling and post-translational gene regulation, but their biological substrates are difficult to identify. We show that cyclin-dependent kinase (CDK) consensus motifs are frequently clustered in CDK substrate proteins. Based on this, we introduce a new computational strategy...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-2-r23
更新日期:2007-01-01 00:00:00
abstract::A recent study reveals a surprisingly high degree of change in the occupancy patterns of two transcription factors in the livers of five vertebrates. ...
journal_title:Genome biology
pub_type: 评论,杂志文章
doi:10.1186/gb-2010-11-6-122
更新日期:2010-01-01 00:00:00
abstract:BACKGROUND:Concepts of orthology and paralogy are become increasingly important as whole-genome comparison allows their identification in complete genomes. Functional specificity of proteins is assumed to be conserved among orthologs and is different among paralogs. We used this assumption to identify residues which de...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2002-3-3-preprint0002
更新日期:2002-01-01 00:00:00
abstract:BACKGROUND:Whole genome sequencing of marine cyanobacteria has revealed an unprecedented degree of genomic variation and streamlining. With a size of 1.66 megabase-pairs, Prochlorococcus sp. MED4 has the most compact of these genomes and it is enigmatic how the few identified regulatory proteins efficiently sustain the...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2005-6-9-r73
更新日期:2005-01-01 00:00:00