Abstract:
BACKGROUND:Ser/Thr/Tyr kinases (STYKs) commonly found in eukaryotes have been recently reported in many bacterial species. Recent studies elucidating their cellular functions have established their roles in bacterial growth and development. However functions of a large number of bacterial STYKs still remain elusive. The organisation of domains in a large dataset of bacterial STYKs has been investigated here in order to recognise variety in domain combinations which determine functions of bacterial STYKs. RESULTS:Using sensitive sequence and profile search methods, domain organisation of over 600 STYKs from 125 prokaryotic genomes have been examined. Kinase catalytic domains of STYKs tethered to a wide range of enzymatic domains such as phosphatases, HSP70, peptidyl prolyl isomerases, pectin esterases and glycoproteases have been identified. Such distinct preferences for domain combinations are not known to be present in either the Histidine kinase or the eukaryotic STYK families. Domain organisation of STYKs specific to certain groups of bacteria has also been noted in the current anlaysis. For example, Hydrophobin like domains in Mycobacterial STYK and penicillin binding domains in few STYKs of Gram-positive organisms and FHA domains in cyanobacterial STYKs. Homologues of characterised substrates of prokaryotic STYKs have also been identified. CONCLUSION:The domains and domain architectures of most of the bacterial STYKs identified are very different from the known domain organisation in STYKs of eukaryotes. This observation highlights distinct biological roles of bacterial STYKs compared to eukaryotic STYKs. Bacterial STYKs reveal high diversity in domain organisation. Some of the modular organisations conserved across diverse bacterial species suggests their central role in bacterial physiology. Unique domain architectures of few other groups of STYKs reveal recruitment of functions specific to the species.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Krupa A,Srinivasan Ndoi
10.1186/1471-2164-6-129keywords:
subject
Has Abstractpub_date
2005-09-19 00:00:00pages
129issn
1471-2164pii
1471-2164-6-129journal_volume
6pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:HPA axis plays a major role in physiological homeostasis. It is also involved in stress and adaptive response to the environment. In farm animals in general and specifically in pigs, breeding strategies have highly favored production traits such as lean growth rate, feed efficiency and prolificacy at the cos...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2118-8
更新日期:2015-11-17 00:00:00
abstract:BACKGROUND:Genomic imprinting is an evolutionary conserved mechanism of epigenetic gene regulation in placental mammals that results in silencing of one of the parental alleles. In order to decipher interactions between allele-specific DNA methylation of imprinted genes and evolutionary conservation, we performed a gen...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-649
更新日期:2010-11-22 00:00:00
abstract:BACKGROUND:Two strains of the silver fox (Vulpes vulpes), with markedly different behavioral phenotypes, have been developed by long-term selection for behavior. Foxes from the tame strain exhibit friendly behavior towards humans, paralleling the sociability of canine puppies, whereas foxes from the aggressive strain a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-482
更新日期:2011-10-03 00:00:00
abstract:BACKGROUND:Genetic association studies that seek to explain the inheritance of complex traits typically fail to explain a majority of the heritability of the trait under study. Thus, we are left with a gap in the map from genotype to phenotype. Several approaches have been used to fill this gap, including those that at...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6739-1
更新日期:2020-05-04 00:00:00
abstract:BACKGROUND:Biologists need to perform complex queries, often across a variety of databases. Typically, each data resource provides an advanced query interface, each of which must be learnt by the biologist before they can begin to query them. Frequently, more than one data source is required and for high-throughput ana...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-10-22
更新日期:2009-01-14 00:00:00
abstract:BACKGROUND:Moraxella catarrhalis is an important pathogen that often causes otitis media in children, a disease that is not currently vaccine preventable. Asymptomatic colonisation of the human upper respiratory tract is common and lack of clearance by the immune system is likely due to the emergence of seroresistant g...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2104-1
更新日期:2015-10-24 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs) exist pervasively across viruses, plants and animals and play important roles in the post-transcriptional regulation of genes. In the common carp, miRNA targets have not been investigated. In model species, single-nucleotide polymorphisms (SNPs) have been reported to impair or enhance miRN...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-413
更新日期:2012-08-21 00:00:00
abstract:BACKGROUND:Foraminiferan protists, which are significant players in most marine ecosystems, are also genetic innovators, harboring unique modifications to proteins that make up the basic eukaryotic cell machinery. Despite their ecological and evolutionary importance, foraminiferan genomes are poorly understood due to t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-169
更新日期:2011-03-31 00:00:00
abstract:BACKGROUND:Evolution leaves an imprint in species through genetic change. At the molecular level, evolutionary changes can be explored by studying ratios of nucleotide substitutions. The interplay among molecular evolution, derived phenotypes, and ecological ranges can provide insights into adaptive radiations. Caecili...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5694-1
更新日期:2019-05-09 00:00:00
abstract:BACKGROUND:White spot syndrome (WSS) is a viral disease that affects most of the commercially important shrimps and causes serious economic losses to the shrimp farming industry worldwide. However, little information is available in terms of the molecular mechanisms of the host-virus interaction. In this study, we used...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-120
更新日期:2007-05-16 00:00:00
abstract:MOTIVATION:Mass spectrometry is a complex technique used for large-scale protein profiling with clinical and pharmaceutical applications. While individual components in the system have been studied extensively, little work has been done to integrate various modules and evaluate them from a systems point of view. RESUL...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-S6-S2
更新日期:2012-01-01 00:00:00
abstract:BACKGROUND:Cryptocaryon irritans is an obligate parasitic ciliate protozoan that can infect various commercially important mariculture fish species and cause high lethality and economic loss. Current methods of controlling this parasite with chemicals or antibiotics are widely considered to be environmentally harmful. ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4565-5
更新日期:2018-03-12 00:00:00
abstract:BACKGROUND:With advances in next generation sequencing technology and analysis methods, single nucleotide variants (SNVs) and indels can be detected with high sensitivity and specificity in exome sequencing data. Recent studies have demonstrated the ability to detect disease-causing copy number variants (CNVs) in exome...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2374-2
更新日期:2016-01-14 00:00:00
abstract:BACKGROUND:Long non-coding RNAs (lncRNAs) are a new class of regulatory molecules with roles in diverse biological processes. While much effort has been invested in the analysis of lncRNAs from established plant models Arabidopsis, maize, and rice, almost nothing is known about lncRNAs from fruit crops, including those...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2014-2
更新日期:2015-10-19 00:00:00
abstract:BACKGROUND:Homologous recombination is the key process that generates genetic diversity and drives evolution. SPO11 protein triggers recombination by introducing DNA double stranded breaks at discreet areas of the genome called recombination hotspots. The hotspot locations are largely determined by the DNA binding spec...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-493
更新日期:2013-07-22 00:00:00
abstract:BACKGROUND:Genomic selection based on genotyping-by-sequencing (GBS) data could accelerate alfalfa yield gains, if it displayed moderate ability to predict parent breeding values. Its interest would be enhanced by predicting ability also for germplasm/reference populations other than those for which it was defined. Pre...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2212-y
更新日期:2015-12-01 00:00:00
abstract:BACKGROUND:Bacillus pumilus is a Gram-positive and endospore-forming bacterium broadly existing in a variety of environmental niches. Because it produces and secrets many industrially useful enzymes, a lot of studies have been done to understand the underlying mechanisms. Among them, scoC was originally identified as a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5671-8
更新日期:2019-04-30 00:00:00
abstract:BACKGROUND:Foxtail millet [Setaria italica (L.) P. Beauv.], a crop of historical importance in China, has been adopted as a model crop for studying C-4 photosynthesis, stress biology and biofuel traits. Construction of a high density genetic map and identification of stable quantitative trait loci (QTL) lay the foundat...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2628-z
更新日期:2016-05-04 00:00:00
abstract:BACKGROUND:Shotgun sequencing of environmental DNA is an essential technique for characterizing uncultivated microbes in situ. However, the taxonomic and functional assignment of the obtained sequence fragments remains a pressing problem. RESULTS:Existing algorithms are largely optimized for speed and coverage; in con...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-461
更新日期:2010-08-05 00:00:00
abstract:BACKGROUND:Fluorescence of dyes bound to double-stranded PCR products has been utilized extensively in various real-time quantitative PCR applications, including post-amplification dissociation curve analysis, or differentiation of amplicon length or sequence composition. Despite the current era of whole-genome sequenc...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-544
更新日期:2008-11-17 00:00:00
abstract:BACKGROUND:Transmembrane β-barrel proteins are a special class of transmembrane proteins which play several key roles in human body and diseases. Due to experimental difficulties, the number of transmembrane β-barrel proteins with known structures is very small. Over the years, a number of learning-based methods have b...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-S2-S5
更新日期:2012-04-12 00:00:00
abstract:BACKGROUND:Avian infectious bronchitis virus (IBV) is a gamma coronavirus that severely affects the poultry industry worldwide. Long non-coding RNAs (lncRNAs), a subset of non-coding RNAs with a length of more than 200 nucleotides, have been recently recognized as pivotal factors in the pathogenesis of viral infections...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07359-3
更新日期:2021-01-20 00:00:00
abstract:BACKGROUND:The ascomycete fungus Zymoseptoria tritici (synonyms: Mycosphaerella graminicola, Septoria tritici) is a major pathogen of wheat that causes the economically important foliar disease Septoria tritici blotch. Despite its importance as a pathogen, little is known about the reaction of this fungus to light. To ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06899-y
更新日期:2020-07-25 00:00:00
abstract:BACKGROUND:Closely related species of the carp family (Cyprinidae) have evolved distinctive abilities to survive under cold stress, but molecular mechanisms underlying the generation of cold resistance remain largely unknown. In this study, we compared transcriptomic profiles of two carp species to identify key factors...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06946-8
更新日期:2020-08-05 00:00:00
abstract:BACKGROUND:This paper presents a retrospective statistical study on the newly-released data set by the Stanley Neuropathology Consortium on gene expression in bipolar disorder and schizophrenia. This data set contains gene expression data as well as limited demographic and clinical data for each subject. Previous studi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-531
更新日期:2008-11-07 00:00:00
abstract:BACKGROUND:Comparative genomics has emerged as a promising means of unravelling the molecular networks underlying complex traits such as drought tolerance. Here we assess the genotype-dependent component of the drought-induced transcriptome response in two poplar genotypes differing in drought tolerance. Drought-induce...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-630
更新日期:2010-11-12 00:00:00
abstract:BACKGROUND:Cold tolerance is a key determinant of the geographical distribution range of a plant species and crop production. Cold acclimation can enhance freezing-tolerance of plant species through a period of exposure to low nonfreezing temperatures. As a subtropical evergreen broadleaf plant, oil-tea camellia demons...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3570-4
更新日期:2017-02-28 00:00:00
abstract:BACKGROUND:Among viruses, bacteriophages are a group of special interest due to their capacity of infecting bacteria that are important for biotechnology and human health. Composting is a microbial-driven process in which complex organic matter is converted into humus-like substances. In thermophilic composting, the de...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3729-z
更新日期:2017-05-04 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs) are small non-coding RNAs that regulate genes at the post-transcriptional level in spatiotemporal manner. Several miRNAs are identified as prognostic and diagnostic markers in many human cancers. Estimation of the temporal activities of the miRNAs is an important step in the way to underst...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2260-3
更新日期:2015-12-18 00:00:00
abstract:BACKGROUND:The hard clam or northern quahog, Mercenaria mercenaria, is one of the most valuable seafood products in the United States representing the first marine resource in some Northeastern states. Severe episodes of hard clam mortality have been consistently associated with infections caused by a thraustochytrid p...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-245
更新日期:2014-03-28 00:00:00