Abstract:
BACKGROUND:Mitogen-activated protein kinases (MAPKs) are key regulators of immune responses in animals and plants. In Arabidopsis, perception of microbe-associated molecular patterns (MAMPs) activates the MAPKs MPK3, MPK4 and MPK6. Increasing information depicts the molecular events activated by MAMPs in plants, but the specific and cooperative contributions of the MAPKs in these signalling events are largely unclear. RESULTS:In this work, we analyse the behaviour of MPK3, MPK4 and MPK6 mutants in early and late immune responses triggered by the MAMP flg22 from bacterial flagellin. A genome-wide transcriptome analysis reveals that 36% of the flg22-upregulated genes and 68% of the flg22-downregulated genes are affected in at least one MAPK mutant. So far MPK4 was considered as a negative regulator of immunity, whereas MPK3 and MPK6 were believed to play partially redundant positive functions in defence. Our work reveals that MPK4 is required for the regulation of approximately 50% of flg22-induced genes and we identify a negative role for MPK3 in regulating defence gene expression, flg22-induced salicylic acid accumulation and disease resistance to Pseudomonas syringae. Among the MAPK-dependent genes, 27% of flg22-upregulated genes and 76% of flg22-downregulated genes require two or three MAPKs for their regulation. The flg22-induced MAPK activities are differentially regulated in MPK3 and MPK6 mutants, both in amplitude and duration, revealing a highly interdependent network. CONCLUSIONS:These data reveal a new set of distinct functions for MPK3, MPK4 and MPK6 and indicate that the plant immune signalling network is choreographed through the interplay of these three interwoven MAPK pathways.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Frei dit Frey N,Garcia AV,Bigeard J,Zaag R,Bueso E,Garmier M,Pateyron S,de Tauzia-Moreau ML,Brunaud V,Balzergue S,Colcombet J,Aubourg S,Martin-Magniette ML,Hirt Hdoi
10.1186/gb-2014-15-6-r87subject
Has Abstractpub_date
2014-06-30 00:00:00pages
R87issue
6eissn
1474-7596issn
1474-760Xpii
gb-2014-15-6-r87journal_volume
15pub_type
杂志文章相关文献
GENOME BIOLOGY文献大全abstract::A report of the fifth annual Personal Genomes and Medical Genomics meeting, held at Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA, November 14-17, 2012. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2012-13-12-324
更新日期:2012-12-19 00:00:00
abstract::The 3.5-day-old blastocyst-stage mouse embryo consists of two tissues and contains approximately 60 cells. This tiny structure has now been observed to express nearly 600 genes in a sex-specific fashion, including at least one gene (Rhox/Pem) expressed only in females from their paternal X chromosome. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2006-7-2-205
更新日期:2006-01-01 00:00:00
abstract::A large number of histone modifications has been implicated in the regulation of gene expression. Together, these modifications have the potential to form a complex combinatorial regulatory code. Genome-wide mapping approaches provide new opportunities to decipher this code, but they may suffer from systematic biases....
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2005-6-6-113
更新日期:2005-01-01 00:00:00
abstract:BACKGROUND:Complete genomic sequences of closely related organisms, such as the chlamydiae, afford the opportunity to assess significant strain differences against a background of many shared characteristics. The chlamydiae are ubiquitous intracellular parasites that are important pathogens of humans and other organism...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2002-3-9-research0051
更新日期:2002-08-29 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::Linking biochemical genetic data to the reference genome for the laboratory mouse is important for comparative physiology and for developing mouse models of human biology and disease. We describe here a new database of curated metabolic pathways for the laboratory mouse called MouseCyc http://mousecyc.jax.org. MouseCy...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2009-10-8-r84
更新日期:2009-01-01 00:00:00
abstract:BACKGROUND:Tumors comprise a complex microenvironment of interacting malignant and stromal cell types. Much of our understanding of the tumor microenvironment comes from in vitro studies isolating the interactions between malignant cells and a single stromal cell type, often along a single pathway. RESULT:To develop a...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02019-x
更新日期:2020-05-07 00:00:00
abstract::How viruses evolve within hosts can dictate infection outcomes; however, reconstructing this process is challenging. We evaluate our multiplexed amplicon approach, PrimalSeq, to demonstrate how virus concentration, sequencing coverage, primer mismatches, and replicates influence the accuracy of measuring intrahost vir...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-018-1618-7
更新日期:2019-01-08 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:BACKGROUND:Light and carbon are two essential signals influencing plant growth and development. Little is known about how carbon and light signaling pathways intersect or influence one another to affect gene expression. RESULTS:Microarrays are used to investigate carbon and light signaling interactions at a genome-wid...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2004-5-2-r10
更新日期:2004-01-01 00:00:00
abstract:BACKGROUND:Developmental programs are implemented by regulatory interactions between Transcription Factors (TFs) and their target genes, which remain poorly understood. While recent studies have focused on regulatory cascades of TFs that govern early development, little is known about how the ultimate effectors of cell...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2013-14-8-r86
更新日期:2013-08-23 00:00:00
abstract:BACKGROUND:Understanding the design logic of living systems requires the understanding and comparison of proteomes. Proteomes define the commonalities between organisms more precisely than genomic sequences. Because uncertainties remain regarding the accuracy of proteomic data, several issues need to be resolved before...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2008-9-11-r167
更新日期:2008-01-01 00:00:00
abstract:BACKGROUND:Retroviral elements are pervasively transcribed and dynamically regulated during development. While multiple histone- and DNA-modifying enzymes have broadly been associated with their global silencing, little is known about how the many diverse retroviral families are each selectively recognized. RESULTS:He...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2014-15-4-r58
更新日期:2014-04-30 00:00:00
abstract:BACKGROUND:Genome structures are dynamic and non-randomly organized in the nucleus of higher eukaryotes. To maximize the accuracy and coverage of three-dimensional genome structural models, it is important to integrate all available sources of experimental information about a genome's organization. It remains a major c...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1264-5
更新日期:2017-07-31 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:Although genetic or epigenetic alterations have been shown to affect the three-dimensional organization of genomes, the utility of chromatin conformation in the classification of human disease has never been addressed. RESULTS:Here, we explore whether chromatin conformation can be used to classify human leu...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2014-15-4-r60
更新日期:2014-04-30 00:00:00
abstract::The mechanistic details of most disease-causing mutations remain poorly explored within the context of regulatory networks. We present a high-resolution three-dimensional integrated regulatory network (iRegNet3D) in the form of a web tool, where we resolve the interfaces of all known transcription factor (TF)-TF, TF-D...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-016-1138-2
更新日期:2017-01-18 00:00:00
abstract::Somatic evolution of malignant cells produces tumors composed of multiple clonal populations, distinguished in part by rearrangements and copy number changes affecting chromosomal segments. Whole genome sequencing mixes the signals of sampled populations, diluting the signals of clone-specific aberrations, and complic...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1267-2
更新日期:2017-07-27 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::Numerous methods have been developed to analyse RNA sequencing (RNA-seq) data, but most rely on the availability of a reference genome, making them unsuitable for non-model organisms. Here we present superTranscripts, a substitute for a reference genome, where each gene with multiple transcripts is represented by a si...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1284-1
更新日期:2017-08-04 00:00:00
abstract::Completion of fungal, plant and human genomes paved the way to the identification of erythrocytic rhesus proteins and their kidney homologs as ammonium transporters. ...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2001-2-3-reviews1010
更新日期:2001-01-01 00:00:00
abstract:BACKGROUND:While the song of all songbirds is controlled by the same neural circuit, the hormone dependence of singing behavior varies greatly between species. For this reason, songbirds are ideal organisms to study ultimate and proximate mechanisms of hormone-dependent behavior and neuronal plasticity. RESULTS:We pre...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-014-0578-9
更新日期:2015-01-29 00:00:00
abstract:BACKGROUND:Evolutionary centromere repositioning and human analphoid neocentromeres occurring in clinical cases are, very likely, two stages of the same phenomenon whose properties still remain substantially obscure. Chromosome 13 is the chromosome with the highest number of neocentromeres. We reconstructed the mammali...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2006-7-10-r91
更新日期:2006-01-01 00:00:00
abstract:BACKGROUND:Recent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant species. The Amborella genome is a unique reference for understanding the evolution of angiosperm genomes becau...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2011-12-5-r48
更新日期:2011-01-01 00:00:00
abstract::A report of the 6th Georgia Tech-Oak Ridge National Lab International Conference on Bioinformatics 'In silico Biology: Gene Discovery and Systems Genomics', Atlanta, USA, 15-17 November, 2007. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2008-9-2-302
更新日期:2008-01-01 00:00:00
abstract:BACKGROUND:Simple sequence repeats (SSRs) in DNA have been traditionally thought of as functionally unimportant and have been studied mainly as genetic markers. A recent handful of studies have shown, however, that SSRs in different positions of a gene can play important roles in determining protein function, genetic d...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2006-7-2-r14
更新日期:2006-01-01 00:00:00
abstract:BACKGROUND:The recent reports of two circular RNAs (circRNAs) with strong potential to act as microRNA (miRNA) sponges suggest that circRNAs might play important roles in regulating gene expression. However, the global properties of circRNAs are not well understood. RESULTS:We developed a computational pipeline to ide...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-014-0409-z
更新日期:2014-07-29 00:00:00
abstract:BACKGROUND:RNA splicing is a key post-transcriptional mechanism that generates protein diversity and contributes to the fine-tuning of gene expression, which may facilitate adaptation to environmental challenges. Here, we employ a systems approach to study alternative splicing changes upon enteric infection in females ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1918-6
更新日期:2020-01-17 00:00:00
abstract::We describe a bioinformatic tool, Tumor Aberration Prediction Suite (TAPS), for the identification of allele-specific copy numbers in tumor samples using data from Affymetrix SNP arrays. It includes detailed visualization of genomic segment characteristics and iterative pattern recognition for copy number identificati...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2011-12-10-r108
更新日期:2011-10-24 00:00:00
abstract:BACKGROUND:Foodborne outbreaks of Salmonella remain a pressing public health concern. We recently detected a large outbreak of Salmonella enterica serovar Enteritidis phage type 14b affecting more than 30 patients in our hospital. This outbreak was linked to community, national and European-wide cases. Hospital patient...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-015-0677-2
更新日期:2015-05-30 00:00:00