Abstract:
BACKGROUND:Rice blast disease is caused by the filamentous Ascomycetous fungus Magnaporthe oryzae and results in significant annual rice yield losses worldwide. Infection by this and many other fungal plant pathogens requires the development of a specialized infection cell called an appressorium. The molecular processes regulating appressorium formation are incompletely understood. RESULTS:We analyzed genome-wide gene expression changes during spore germination and appressorium formation on a hydrophobic surface compared to induction by cAMP. During spore germination, 2,154 (approximately 21%) genes showed differential expression, with the majority being up-regulated. During appressorium formation, 357 genes were differentially expressed in response to both stimuli. These genes, which we refer to as appressorium consensus genes, were functionally grouped into Gene Ontology categories. Overall, we found a significant decrease in expression of genes involved in protein synthesis. Conversely, expression of genes associated with protein and amino acid degradation, lipid metabolism, secondary metabolism and cellular transportation exhibited a dramatic increase. We functionally characterized several differentially regulated genes, including a subtilisin protease (SPM1) and a NAD specific glutamate dehydrogenase (Mgd1), by targeted gene disruption. These studies revealed hitherto unknown findings that protein degradation and amino acid metabolism are essential for appressorium formation and subsequent infection. CONCLUSION:We present the first comprehensive genome-wide transcript profile study and functional analysis of infection structure formation by a fungal plant pathogen. Our data provide novel insight into the underlying molecular mechanisms that will directly benefit efforts to identify fungal pathogenicity factors and aid the development of new disease management strategies.
journal_name
Genome Bioljournal_title
Genome biologyauthors
Oh Y,Donofrio N,Pan H,Coughlan S,Brown DE,Meng S,Mitchell T,Dean RAdoi
10.1186/gb-2008-9-5-r85subject
Has Abstractpub_date
2008-01-01 00:00:00pages
R85issue
5eissn
1474-7596issn
1474-760Xpii
gb-2008-9-5-r85journal_volume
9pub_type
杂志文章相关文献
GENOME BIOLOGY文献大全abstract:BACKGROUND:The chromodomain helicase DNA-binding family of ATP-dependent chromatin remodeling factors play essential roles during eukaryote growth and development. They are recruited by specific transcription factors and regulate the expression of developmentally important genes. Here, we describe an unexpected role in...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1226-y
更新日期:2017-05-31 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: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:BACKGROUND:Francisella tularensis subspecies tularensis and holarctica are pathogenic to humans, whereas the two other subspecies, novicida and mediasiatica, rarely cause disease. To uncover the factors that allow subspecies tularensis and holarctica to be pathogenic to humans, we compared their genome sequences with t...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2007-8-6-r102
更新日期:2007-01-01 00:00:00
abstract:BACKGROUND:We propose that a computerized, internet-based graphical description language for systems biology will be essential for describing, archiving and analyzing complex problems of biological function in health and disease. RESULTS:We outline here a conceptual basis for designing such a language and describe Bio...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2001-2-4-research0012
更新日期:2001-01-01 00:00:00
abstract::Proteins of the phytochrome superfamily of red/far-red light receptors have a variety of biological roles in plants, algae, bacteria and fungi and demonstrate a diversity of spectral sensitivities and output signaling mechanisms. Over the past few years the first three-dimensional structures of phytochrome light-sensi...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2008-9-8-230
更新日期:2008-01-01 00:00:00
abstract::In most eukaryotes, histones, which are the major structural components of chromatin, are expressed as a family of sequence variants encoded by multiple genes. Because different histone variants can contribute to a distinct or unique nucleosomal architecture, this heterogeneity can be exploited to regulate a wide rang...
journal_title:Genome biology
pub_type: 杂志文章,评审
doi:10.1186/gb-2001-2-7-reviews0006
更新日期:2001-01-01 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:Seed germination involves progression from complete metabolic dormancy to a highly active, growing seedling. Many factors regulate germination and these interact extensively, forming a complex network of inputs that control the seed-to-seedling transition. Our understanding of the direct regulation of gene e...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1302-3
更新日期:2017-09-15 00:00:00
abstract::Single-cell analysis technologies are essential tools in research and clinical diagnostics. These methods include flow cytometry, mass cytometry, and other microfluidics-based technologies. Most laboratories that employ these methods maintain large repositories of antibodies. These ever-growing collections of antibodi...
journal_title:Genome biology
pub_type: 信件
doi:10.1186/s13059-016-1006-0
更新日期:2016-06-29 00:00:00
abstract::The eXtensible Genome Data Broker (xGDB) provides a software infrastructure consisting of integrated tools for the storage, display, and analysis of genome features in their genomic context. Common features include gene structure annotations, spliced alignments, mapping of repetitive sequence, and microarray probes, b...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2006-7-11-r111
更新日期:2006-01-01 00:00:00
abstract::Circular RNAs (circRNAs) are a new class of non-polyadenylated non-coding RNAs that may play important roles in many biological processes. Here we develop a single-cell universal poly(A)-independent RNA sequencing (SUPeR-seq) method to sequence both polyadenylated and non-polyadenylated RNAs from individual cells. Thi...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-015-0706-1
更新日期:2015-07-23 00:00:00
abstract:BACKGROUND:The binding of transcription factors to specific locations in the genome is integral to the orchestration of transcriptional regulation in cells. To characterize transcription factor binding site function on a large scale, we predicted and mutagenized 455 binding sites in human promoters. We carried out func...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2012-13-9-r50
更新日期:2012-09-26 00:00:00
abstract::Trans-splicing is an unusual process in which two separate RNA strands are spliced together to yield a mature mRNA. We present a novel computational approach which has an overall accuracy of 82% and can predict 92% of known trans-splicing sites. We have applied our method to chromosomes 1 and 3 of Leishmania major, wi...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2005-6-11-r95
更新日期:2005-01-01 00:00:00
abstract::The explosive growth in taxonomic metagenome profiling methods over the past years has created a need for systematic comparisons using relevant performance criteria. The Open-community Profiling Assessment tooL (OPAL) implements commonly used performance metrics, including those of the first challenge of the initiativ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1646-y
更新日期:2019-03-04 00:00:00
abstract:BACKGROUND:Pseudogenes reveal ancestral gene functions. Some obligate intracellular bacteria, such as Mycobacterium leprae and Rickettsia spp., carry substantial fractions of pseudogenes. Until recently, horizontal gene transfers were considered to be rare events in obligate host-associated bacteria. RESULTS:We presen...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2008-9-2-r42
更新日期:2008-01-01 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: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:BACKGROUND:Hemiascomycetous yeasts have intron-poor genomes with very few cases of alternative splicing. Most of the reported examples result from intron retention in Saccharomyces cerevisiae and some have been shown to be functionally significant. Here we used transcriptome-wide approaches to evaluate the mechanisms u...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2010-11-6-r65
更新日期:2010-01-01 00:00:00
abstract::A report on the Wellcome Trust/Cold Spring Harbor Genome Informatics meeting, Cold Spring Harbor, USA, 7-11 May 2003. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2003-4-9-336
更新日期:2003-01-01 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::We present a graph-based method for the analysis of repeat families in a repeat library. We build a repeat domain graph that decomposes a repeat library into repeat domains, short subsequences shared by multiple repeat families, and reveals the mosaic structure of repeat families. Our method recovers documented mosaic...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2006-7-1-r7
更新日期:2006-01-01 00:00:00
abstract:BACKGROUND:Gene expression signatures indicative of tumor proliferative capacity and tumor-immune cell interactions have emerged as principal biology-driven predictors of breast cancer outcomes. How these signatures relate to one another in biological and prognostic contexts remains to be clarified. RESULTS:To investi...
journal_title:Genome biology
pub_type: 杂志文章,随机对照试验
doi:10.1186/gb-2013-14-4-r34
更新日期:2013-04-29 00:00:00
abstract:BACKGROUND:Circular RNAs are a class of endogenous RNAs with various functions in eukaryotic cells. Worthy of note, circular RNAs play a critical role in cancer. Currently, nothing is known about their role in head and neck squamous cell carcinoma (HNSCC). The identification of circular RNAs in HNSCC might become usefu...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-017-1368-y
更新日期:2017-12-20 00:00:00
abstract::We describe here a CRISPR simultaneous and wide-editing induced by a single system (SWISS), in which RNA aptamers engineered in crRNA scaffold recruit their cognate binding proteins fused with cytidine deaminase and adenosine deaminase to Cas9 nickase target sites to generate multiplexed base editing. By using paired ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-02051-x
更新日期:2020-06-16 00:00:00
abstract:BACKGROUND:Gene loss, inversions, translocations, and other chromosomal rearrangements vary among species, resulting in different rates of structural genome evolution. Major chromosomal rearrangements are rare in most eukaryotes, giving large regions with the same genes in the same order and orientation across species....
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2011-12-5-r45
更新日期:2011-01-01 00:00:00
abstract::A report on the 23rd Fungal Genetics Conference, Pacific Grove, USA, 15-20 March 2005. ...
journal_title:Genome biology
pub_type:
doi:10.1186/gb-2005-6-8-336
更新日期:2005-01-01 00:00:00
abstract:BACKGROUND:Single-cell transcriptomics is rapidly advancing our understanding of the cellular composition of complex tissues and organisms. A major limitation in most analysis pipelines is the reliance on manual annotations to determine cell identities, which are time-consuming and irreproducible. The exponential growt...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-019-1795-z
更新日期:2019-09-09 00:00:00
abstract:BACKGROUND:Polyploidy is ubiquitous in eukaryotic plant and fungal lineages, and it leads to the co-existence of several copies of similar or related genomes in one nucleus. In plants, polyploidy is considered a major factor in successful domestication. However, polyploidy challenges chromosome folding architecture in ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/s13059-020-01998-1
更新日期:2020-04-29 00:00:00
abstract::A report of the second annual Beyond the Genome conference held on the 19-22 September 2011 at The Universities at Shady Grove, Rockville, Maryland, USA, where increases in computing that may help make personal genomics a reality were a major focus. ...
journal_title:Genome biology
pub_type: 杂志文章
doi:10.1186/gb-2011-12-10-308
更新日期:2011-10-24 00:00:00