Abstract:
BACKGROUND:Protein effectors of pathogenicity are instrumental in modulating host immunity and disease resistance. The powdery mildew pathogen of grasses Blumeria graminis causes one of the most important diseases of cereal crops. B. graminis is an obligate biotrophic pathogen and as such has an absolute requirement to suppress or avoid host immunity if it is to survive and cause disease. RESULTS:Here we characterise a superfamily predicted to be the full complement of Candidates for Secreted Effector Proteins (CSEPs) in the fungal barley powdery mildew parasite B. graminis f.sp. hordei. The 491 genes encoding these proteins constitute over 7% of this pathogen's annotated genes and most were grouped into 72 families of up to 59 members. They were predominantly expressed in the intracellular feeding structures called haustoria, and proteins specifically associated with the haustoria were identified by large-scale mass spectrometry-based proteomics. There are two major types of effector families: one comprises shorter proteins (100-150 amino acids), with a high relative expression level in the haustoria and evidence of extensive diversifying selection between paralogs; the second type consists of longer proteins (300-400 amino acids), with lower levels of differential expression and evidence of purifying selection between paralogs. An analysis of the predicted protein structures underscores their overall similarity to known fungal effectors, but also highlights unexpected structural affinities to ribonucleases throughout the entire effector super-family. Candidate effector genes belonging to the same family are loosely clustered in the genome and are associated with repetitive DNA derived from retro-transposons. CONCLUSIONS:We employed the full complement of genomic, transcriptomic and proteomic analyses as well as structural prediction methods to identify and characterize the members of the CSEPs superfamily in B. graminis f.sp. hordei. Based on relative intron position and the distribution of CSEPs with a ribonuclease-like domain in the phylogenetic tree we hypothesize that the associated genes originated from an ancestral gene, encoding a secreted ribonuclease, duplicated successively by repetitive DNA-driven processes and diversified during the evolution of the grass and cereal powdery mildew lineage.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Pedersen C,Ver Loren van Themaat E,McGuffin LJ,Abbott JC,Burgis TA,Barton G,Bindschedler LV,Lu X,Maekawa T,Wessling R,Cramer R,Thordal-Christensen H,Panstruga R,Spanu PDdoi
10.1186/1471-2164-13-694subject
Has Abstractpub_date
2012-12-11 00:00:00pages
694issn
1471-2164pii
1471-2164-13-694journal_volume
13pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:In a previous genome-wide analysis of FXR binding to hepatic chromatin, we noticed that an extra nuclear receptor (NR) half-site was co-enriched close to the FXR binding IR-1 elements and we provided limited support that the monomeric LRH-1 receptor that binds to NR half-sites might function together with FX...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-51
更新日期:2012-02-01 00:00:00
abstract:BACKGROUND:Prokaryotic translation initiation involves the proper docking, anchoring, and accommodation of mRNA to the 30S ribosomal subunit. Three initiation factors (IF1, IF2, and IF3) and some ribosomal proteins mediate the assembly and activation of the translation initiation complex. Although the interaction betwe...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1808-6
更新日期:2015-08-14 00:00:00
abstract:BACKGROUND:The transcription factors peroxisome proliferator activated receptor γ (PPARγ) and CCAAT/enhancer binding protein α (C/EBPα) are key transcriptional regulators of adipocyte differentiation and function. We and others have previously shown that binding sites of these two transcription factors show a high degr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-152
更新日期:2011-03-16 00:00:00
abstract:BACKGROUND:Although the study of gene regulation via the action of specific microRNAs (miRNAs) has experienced a boom in recent years, the analysis of genome-wide interaction networks among miRNAs and respective targeted mRNAs has lagged behind. MicroRNAs simultaneously target many transcripts and fine-tune the express...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-725
更新日期:2013-10-22 00:00:00
abstract:BACKGROUND:The pattern of point mutation is important for studying mutational mechanisms, genome evolution, and diseases. Previous studies of mutation direction were largely based on substitution data from a limited number of loci. To date, there is no genome-wide analysis of mutation direction or methylation-dependent...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-316
更新日期:2006-12-13 00:00:00
abstract:BACKGROUND:A key developmental transformation in the life of all vertebrates is the transition to sexual maturity, whereby individuals are capable of reproducing for the first time. In the farming of Atlantic salmon, early maturation prior to harvest size has serious negative production impacts. RESULTS:We report geno...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5525-4
更新日期:2019-02-15 00:00:00
abstract:BACKGROUND:RNA amplification is necessary for profiling gene expression from small tissue samples. Previous studies have shown that the T7 based amplification techniques are reproducible but may distort the true abundance of targets. However, the consequences of such distortions on the ability to detect biological vari...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-252
更新日期:2006-10-09 00:00:00
abstract:BACKGROUND:The transformation of a developing epithelium into an adult structure is a complex process, which often involves coordinated changes in cell proliferation, metabolism, adhesion, and shape. To identify genetic mechanisms that control epithelial differentiation, we analyzed the temporal patterns of gene expres...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-498
更新日期:2012-09-20 00:00:00
abstract:BACKGROUND:Enterohemorrhagic Escherichia coli (EHEC) are zoonotic agents associated with outbreaks worldwide. Growth of EHEC strains in ground beef could be inhibited by background microbiota that is present initially at levels greater than that of the pathogen E. coli. However, how the microbiota outcompetes the patho...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3957-2
更新日期:2017-08-03 00:00:00
abstract:BACKGROUND:The regenerative response of Schwann cells after peripheral nerve injury is a critical process directly related to the pathophysiology of a number of neurodegenerative diseases. This SC injury response is dependent on an intricate gene regulatory program coordinated by a number of transcription factors and m...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-84
更新日期:2013-02-06 00:00:00
abstract:BACKGROUND:During eukaryotic genome evolution, tandem gene duplication is the most frequent event giving rise to clustered gene families. However, how expression divergence between tandemly duplicated genes has emerged and maintained remain unclear. In particular, it is unknown if epigenetic regulators have been involv...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-S1-S8
更新日期:2014-01-01 00:00:00
abstract:BACKGROUND:Magnesium (Mg)-deficiency is frequently observed in Citrus plantations and is responsible for the loss of productivity and poor fruit quality. Knowledge on the effects of Mg-deficiency on upstream targets is scarce. Seedlings of 'Xuegan' [Citrus sinensis (L.) Osbeck] were irrigated with Mg-deficient (0 mM Mg...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1462-z
更新日期:2015-03-31 00:00:00
abstract:BACKGROUND:The membrane protein CD46, a ubiquitous cell surface pathogen receptor, can bind Streptococcus to trigger cell autophagy, which is a critical step in the control of infection. RESULTS:In this study, we found a new splice variant designated CD46 transcript variant (CD46-TV). The splice variant is characteriz...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-630
更新日期:2014-07-28 00:00:00
abstract:BACKGROUND:Infectious laryngotracheitis virus (ILTV; gallid herpesvirus 1) infection causes high mortality and huge economic losses in the poultry industry. To protect chickens against ILTV infection, chicken-embryo origin (CEO) and tissue-culture origin (TCO) vaccines have been used. However, the transmission of vacci...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-143
更新日期:2012-04-24 00:00:00
abstract:BACKGROUND:The phytoflagellated protozoan, Euglena gracilis, has been proposed as an attractive feedstock for the accumulation of valuable compounds such as β-1,3-glucan, also known as paramylon, and wax esters. The production of wax esters proceeds under anaerobic conditions, designated as wax ester fermentation. In s...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2540-6
更新日期:2016-03-03 00:00:00
abstract:BACKGROUND:Carrot (Daucus carota) is a major food crop in the US and worldwide. Its capacity for storage and its lifecycle as a biennial make it an attractive species for the introduction of foreign genes, especially for oral delivery of vaccines and other therapeutic proteins. Until recently efforts to express recombi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-222
更新日期:2006-08-31 00:00:00
abstract:BACKGROUND:The ability to rapidly map millions of oligonucleotide fragments to a reference genome is crucial to many high throughput genomic technologies. RESULTS:We propose an intuitive and efficient algorithm, titled extreme MApping of OligoNucleotide (xMAN), to rapidly map millions of oligonucleotide fragments to a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-S1-S20
更新日期:2008-01-01 00:00:00
abstract:BACKGROUND:A systems toxicology investigation comparing and integrating transcriptomic and proteomic results was conducted to develop holistic effects characterizations for the wildlife bird model, Northern bobwhite (Colinus virginianus) dosed with the explosives degradation product 2-amino-4,6-dinitrotoluene (2A-DNT)....
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1798-4
更新日期:2015-08-07 00:00:00
abstract:BACKGROUND:Laboratory evolution is an important tool for developing robust yeast strains for bioethanol production since the biological basis behind combined tolerance requires complex alterations whose proper regulation is difficult to achieve by rational metabolic engineering. Previously, we reported on the evolved i...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1737-4
更新日期:2015-07-09 00:00:00
abstract:BACKGROUND:Floral transition is a critical event in the life cycle of a flowering plant as it determines its reproductive success. Despite extensive studies of specific genes that regulate this process, the global changes in transcript expression profiles at the point when a vegetative meristem transitions into an infl...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1688-9
更新日期:2015-06-18 00:00:00
abstract:BACKGROUND:Sequencing of the approximately 1.7 billion bases of the zebrafish genome is currently underway. To date, few high resolution genetic maps exist for the zebrafish genome, based mainly on single nucleotide polymorphisms (SNPs) and short microsatellite repeats. The desire to construct a higher resolution genet...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-347
更新日期:2010-06-01 00:00:00
abstract:BACKGROUND:Micro (mi)RNAs are important regulators of plant development. Across plant lineages, Dicer-like 1 (DCL1) proteins process long ds-like structures to produce micro (mi) RNA duplexes in a stepwise manner. These miRNAs are incorporated into Argonaute (AGO) proteins and influence expression of RNAs that have seq...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1049
更新日期:2014-12-02 00:00:00
abstract:BACKGROUND:The beta-defensin gene cluster (DEFB) at chromosome 8p23.1 is one of the most copy number (CN) variable regions of the human genome. Whereas individual DEFB CNs have been suggested as independent genetic risk factors for several diseases (e.g. psoriasis and Crohn's disease), the role of multisite sequence va...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-252
更新日期:2010-04-19 00:00:00
abstract:BACKGROUND:The technological revolution in next-generation sequencing has brought unprecedented opportunities to study any organism of interest at the genomic or transcriptomic level. Transcriptome assembly is a crucial first step for studying the molecular basis of phenotypes of interest using RNA-Sequencing (RNA-Seq)...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2923-8
更新日期:2016-07-27 00:00:00
abstract:BACKGROUND:Avian pathogenic Escherichia coli (APEC) causes colibacillosis, which results in significant economic losses to the poultry industry worldwide. However, the diversity between isolates remains poorly understood. Here, a total of 272 APEC isolates collected from the United Kingdom (UK), Italy and Germany were ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3289-7
更新日期:2016-11-22 00:00:00
abstract:BACKGROUND:Most members of the serpin family of proteins are potent, irreversible inhibitors of specific serine or cysteine proteinases. Inhibitory serpins are distinguished from members of other families of proteinase inhibitors by their metastable structure and unique suicide-substrate mechanism. Animal serpins exert...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-449
更新日期:2012-09-04 00:00:00
abstract:BACKGROUND:Teleost intestine is crucial for seawater acclimation by sensing osmolality of imbibed seawater and regulating drinking and water/ion absorption. Regulatory genes for transforming intestinal function have not been identified. A transcriptomic approach was used to search for such genes in the intestine of eur...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1134
更新日期:2014-12-18 00:00:00
abstract:BACKGROUND:The NBS disease-related gene family coordinates the inherent immune system in plants in response to pathogen infections. Previous studies have identified NBS-encoding genes in Pyrus bretschneideri ('Dangshansuli', an Asian pear) and Pyrus communis ('Bartlett', a European pear) genomes, but the patterns of ge...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07226-1
更新日期:2020-11-19 00:00:00
abstract:BACKGROUND:Bifidobacteria are commonly found as part of the microbiota of the gastrointestinal tract (GIT) of a broad range of hosts, where their presence is positively correlated with the host's health status. In this study, we assessed the genomes of thirteen representatives of Bifidobacterium breve, which is not onl...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-170
更新日期:2014-03-01 00:00:00
abstract:BACKGROUND:The Abeta-binding alcohol dehydrogenase/17beta-hydroxysteroid dehydrogenase type 10 (ABAD/HSD10) is an enzyme involved in pivotal metabolic processes and in the mitochondrial dysfunction seen in the Alzheimer's disease. Here we use comparative genomic analyses to study the evolution of the HADH2 gene encodin...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-202
更新日期:2006-08-09 00:00:00