Genome-wide survey of two-component signal transduction systems in the plant growth-promoting bacterium Azospirillum.


BACKGROUND:Two-component systems (TCS) play critical roles in sensing and responding to environmental cues. Azospirillum is a plant growth-promoting rhizobacterium living in the rhizosphere of many important crops. Despite numerous studies about its plant beneficial properties, little is known about how the bacterium senses and responds to its rhizospheric environment. The availability of complete genome sequenced from four Azospirillum strains (A. brasilense Sp245 and CBG 497, A. lipoferum 4B and Azospirillum sp. B510) offers the opportunity to conduct a comprehensive comparative analysis of the TCS gene family. RESULTS:Azospirillum genomes harbour a very large number of genes encoding TCS, and are especially enriched in hybrid histidine kinases (HyHK) genes compared to other plant-associated bacteria of similar genome sizes. We gained further insight into HyHK structure and architecture, revealing an intriguing complexity of these systems. An unusual proportion of TCS genes were orphaned or in complex clusters, and a high proportion of predicted soluble HKs compared to other plant-associated bacteria are reported. Phylogenetic analyses of the transmitter and receiver domains of A. lipoferum 4B HyHK indicate that expansion of this family mainly arose through horizontal gene transfer but also through gene duplications all along the diversification of the Azospirillum genus. By performing a genome-wide comparison of TCS, we unraveled important 'genus-defining' and 'plant-specifying' TCS. CONCLUSIONS:This study shed light on Azospirillum TCS which may confer important regulatory flexibility. Collectively, these findings highlight that Azospirillum genomes have broad potential for adaptation to fluctuating environments.


BMC Genomics


BMC genomics


Borland S,Oudart A,Prigent-Combaret C,Brochier-Armanet C,Wisniewski-Dyé F




Has Abstract


2015-10-22 00:00:00










  • A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data.

    abstract:BACKGROUND:In research laboratories using DNA-microarrays, usually a number of researchers perform experiments, each generating possible sources of error. There is a need for a quick and robust method to assess data quality and sources of errors in DNA-microarray experiments. To this end, a novel and cost-effective val...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: van Hijum SA,de Jong A,Baerends RJ,Karsens HA,Kramer NE,Larsen R,den Hengst CD,Albers CJ,Kok J,Kuipers OP

    更新日期:2005-05-20 00:00:00

  • Genome-wide signatures of local adaptation among seven stoneflies species along a nationwide latitudinal gradient in Japan.

    abstract:BACKGROUND:Environmental heterogeneity continuously produces a selective pressure that results in genomic variation among organisms; understanding this relationship remains a challenge in evolutionary biology. Here, we evaluated the degree of genome-environmental association of seven stonefly species across a wide geog...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Gamboa M,Watanabe K

    更新日期:2019-01-24 00:00:00

  • Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea.

    abstract:BACKGROUND:Mobile genetic elements (MGEs) play an essential role in genome rearrangement and evolution, and are widely used as an important genetic tool. RESULTS:In this article, we present genetic maps of recently active Insertion Sequence (IS) elements, the simplest form of MGEs, for all sequenced cyanobacteria and ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Zhou F,Olman V,Xu Y

    更新日期:2008-01-24 00:00:00

  • Fine mapping and RNA-Seq unravels candidate genes for a major QTL controlling multiple fiber quality traits at the T1 region in upland cotton.

    abstract:BACKGROUND:Improving fiber quality is a major challenge in cotton breeding, since the molecular basis of fiber quality traits is poorly understood. Fine mapping and candidate gene prediction of quantitative trait loci (QTL) controlling cotton fiber quality traits can help to elucidate the molecular basis of fiber quali...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Liu D,Zhang J,Liu X,Wang W,Liu D,Teng Z,Fang X,Tan Z,Tang S,Yang J,Zhong J,Zhang Z

    更新日期:2016-04-19 00:00:00

  • Comparative genomics of koala, cattle and sheep strains of Chlamydia pecorum.

    abstract:BACKGROUND:Chlamydia pecorum is an important pathogen of domesticated livestock including sheep, cattle and pigs. This pathogen is also a key factor in the decline of the koala in Australia. We sequenced the genomes of three koala C. pecorum strains, isolated from the urogenital tracts and conjunctiva of diseased koala...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Bachmann NL,Fraser TA,Bertelli C,Jelocnik M,Gillett A,Funnell O,Flanagan C,Myers GS,Timms P,Polkinghorne A

    更新日期:2014-08-08 00:00:00

  • Comparative analysis of function and interaction of transcription factors in nematodes: extensive conservation of orthology coupled to rapid sequence evolution.

    abstract:BACKGROUND:Much of the morphological diversity in eukaryotes results from differential regulation of gene expression in which transcription factors (TFs) play a central role. The nematode Caenorhabditis elegans is an established model organism for the study of the roles of TFs in controlling the spatiotemporal pattern ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Haerty W,Artieri C,Khezri N,Singh RS,Gupta BP

    更新日期:2008-08-27 00:00:00

  • The genome sequencing of an albino Western lowland gorilla reveals inbreeding in the wild.

    abstract:BACKGROUND:The only known albino gorilla, named Snowflake, was a male wild born individual from Equatorial Guinea who lived at the Barcelona Zoo for almost 40 years. He was diagnosed with non-syndromic oculocutaneous albinism, i.e. white hair, light eyes, pink skin, photophobia and reduced visual acuity. Despite previo...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Prado-Martinez J,Hernando-Herraez I,Lorente-Galdos B,Dabad M,Ramirez O,Baeza-Delgado C,Morcillo-Suarez C,Alkan C,Hormozdiari F,Raineri E,Estellé J,Fernandez-Callejo M,Valles M,Ritscher L,Schöneberg T,de la Calle-Mustienes E

    更新日期:2013-05-31 00:00:00

  • Comparative genomics and evolution of the HSP90 family of genes across all kingdoms of organisms.

    abstract:BACKGROUND:HSP90 proteins are essential molecular chaperones involved in signal transduction, cell cycle control, stress management, and folding, degradation, and transport of proteins. HSP90 proteins have been found in a variety of organisms suggesting that they are ancient and conserved. In this study we investigate ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Chen B,Zhong D,Monteiro A

    更新日期:2006-06-17 00:00:00

  • Dosage sensitivity of X-linked genes in human embryonic single cells.

    abstract:BACKGROUND:During the evolution of mammalian sex chromosomes, the degeneration of Y-linked homologs has led to a dosage imbalance between X-linked and autosomal genes. The evolutionary resolution to such dosage imbalance, as hypothesized by Susumu Ohno fifty years ago, should be doubling the expression of X-linked gene...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Yang JR,Chen X

    更新日期:2019-01-14 00:00:00

  • Genome-wide analysis of NBS-encoding disease resistance genes in Cucumis sativus and phylogenetic study of NBS-encoding genes in Cucurbitaceae crops.

    abstract:BACKGROUND:Plant nucleotide-binding site (NBS)-leucine-rich repeat (LRR) proteins encoded by resistance genes play an important role in the responses of plants to various pathogens, including viruses, bacteria, fungi, and nematodes. In this study, a comprehensive analysis of NBS-encoding genes within the whole cucumber...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Wan H,Yuan W,Bo K,Shen J,Pang X,Chen J

    更新日期:2013-02-19 00:00:00

  • De novo sequencing and transcriptome analysis of the desert shrub, Ammopiptanthus mongolicus, during cold acclimation using Illumina/Solexa.

    abstract:BACKGROUND:Ammopiptanthus mongolicus (Maxim. ex Kom.) Cheng f., an evergreen broadleaf legume shrub, is distributed in Mid-Asia where the temperature can be as low as -30°C during the winter. Although A. mongolicus is an ideal model to study the plant response to cold stress, insufficient genomic resources for this spe...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Pang T,Ye CY,Xia X,Yin W

    更新日期:2013-07-18 00:00:00

  • Analysis of salivary transcripts and antigens of the sand fly Phlebotomus arabicus.

    abstract:BACKGROUND:Sand fly saliva plays an important role in blood feeding and Leishmania transmission as it was shown to increase parasite virulence. On the other hand, immunity to salivary components impedes the establishment of infection. Therefore, it is most desirable to gain a deeper insight into the composition of sali...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Hostomská J,Volfová V,Mu J,Garfield M,Rohousová I,Volf P,Valenzuela JG,Jochim RC

    更新日期:2009-06-25 00:00:00

  • Transcriptome analysis reveals the time of the fourth round of genome duplication in common carp (Cyprinus carpio).

    abstract:BACKGROUND:Common carp (Cyprinus carpio) is thought to have undergone one extra round of genome duplication compared to zebrafish. Transcriptome analysis has been used to study the existence and timing of genome duplication in species for which genome sequences are incomplete. Large-scale transcriptome data for the com...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Wang JT,Li JT,Zhang XF,Sun XW

    更新日期:2012-03-19 00:00:00

  • Syntenic relationships between cucumber (Cucumis sativus L.) and melon (C. melo L.) chromosomes as revealed by comparative genetic mapping.

    abstract:BACKGROUND:Cucumber, Cucumis sativus L. (2n = 2 × = 14) and melon, C. melo L. (2n = 2 × = 24) are two important vegetable species in the genus Cucumis (family Cucurbitaceae). Both species have an Asian origin that diverged approximately nine million years ago. Cucumber is believed to have evolved from melon through chr...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Li D,Cuevas HE,Yang L,Li Y,Garcia-Mas J,Zalapa J,Staub JE,Luan F,Reddy U,He X,Gong Z,Weng Y

    更新日期:2011-08-05 00:00:00

  • Overlapping genes in the human and mouse genomes.

    abstract:BACKGROUND:Increasing evidence suggests that overlapping genes are much more common in eukaryotic genomes than previously thought. In this study we identified and characterized the overlapping genes in a set of 13,484 pairs of human-mouse orthologous genes. RESULTS:About 10% of the genes under study are overlapping ge...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Sanna CR,Li WH,Zhang L

    更新日期:2008-04-14 00:00:00

  • Comparative analysis of the predicted secretomes of Rosaceae scab pathogens Venturia inaequalis and V. pirina reveals expanded effector families and putative determinants of host range.

    abstract:BACKGROUND:Fungal plant pathogens belonging to the genus Venturia cause damaging scab diseases of members of the Rosaceae. In terms of economic impact, the most important of these are V. inaequalis, which infects apple, and V. pirina, which is a pathogen of European pear. Given that Venturia fungi colonise the sub-cuti...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Deng CH,Plummer KM,Jones DAB,Mesarich CH,Shiller J,Taranto AP,Robinson AJ,Kastner P,Hall NE,Templeton MD,Bowen JK

    更新日期:2017-05-02 00:00:00

  • Evidence of uneven selective pressure on different subsets of the conserved human genome; implications for the significance of intronic and intergenic DNA.

    abstract:BACKGROUND:Human genetic variation produces the wide range of phenotypic differences that make us individual. However, little is known about the distribution of variation in the most conserved functional regions of the human genome. We examined whether different subsets of the conserved human genome have been subjected...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Davidson S,Starkey A,MacKenzie A

    更新日期:2009-12-16 00:00:00

  • A systematic analysis of protein palmitoylation in Caenorhabditis elegans.

    abstract:BACKGROUND:Palmitoylation is a reversible post-translational protein modification which involves the addition of palmitate to cysteine residues. Palmitoylation is catalysed by the DHHC family of palmitoyl-acyl transferases (PATs) and reversibility is conferred by palmitoyl-protein thioesterases (PPTs). Mutations in gen...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Edmonds MJ,Morgan A

    更新日期:2014-10-02 00:00:00

  • Complete genomic sequence of the Vibrio alginolyticus bacteriophage Vp670 and characterization of the lysis-related genes, cwlQ and holA.

    abstract:BACKGROUND:Biocontrol of bacterial pathogens by bacteriophages (phages) represents a promising strategy. Vibrio alginolyticus, a gram-negative bacterium, is a notorious pathogen responsible for the loss of economically important farmed marine animals. To date, few V. alginolyticus phages have been successfully isolated...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Luo P,Yun L,Li Y,Tian Y,Liu Q,Huang W,Hu C

    更新日期:2018-10-11 00:00:00

  • PLAIDOH: a novel method for functional prediction of long non-coding RNAs identifies cancer-specific LncRNA activities.

    abstract:BACKGROUND:Long non-coding RNAs (lncRNAs) exhibit remarkable cell-type specificity and disease association. LncRNA's functional versatility includes epigenetic modification, nuclear domain organization, transcriptional control, regulation of RNA splicing and translation, and modulation of protein activity. However, mos...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Pyfrom SC,Luo H,Payton JE

    更新日期:2019-02-15 00:00:00

  • Differential control of Zap1-regulated genes in response to zinc deficiency in Saccharomyces cerevisiae.

    abstract:BACKGROUND:The Zap1 transcription factor is a central player in the response of yeast to changes in zinc status. We previously used transcriptome profiling with DNA microarrays to identify 46 potential Zap1 target genes in the yeast genome. In this new study, we used complementary methods to identify additional Zap1 ta...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Wu CY,Bird AJ,Chung LM,Newton MA,Winge DR,Eide DJ

    更新日期:2008-08-01 00:00:00

  • A modified sequence capture approach allowing standard and methylation analyses of the same enriched genomic DNA sample.

    abstract:BACKGROUND:Bread wheat has a large complex genome that makes whole genome resequencing costly. Therefore, genome complexity reduction techniques such as sequence capture make re-sequencing cost effective. With a high-quality draft wheat genome now available it is possible to design capture probe sets and to use them to...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Olohan L,Gardiner LJ,Lucaci A,Steuernagel B,Wulff B,Kenny J,Hall N,Hall A

    更新日期:2018-04-13 00:00:00

  • The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum.

    abstract:BACKGROUND:Marine diatoms constitute a major component of eukaryotic phytoplankton and stand at the crossroads of several evolutionary lineages. These microalgae possess peculiar genomic features and novel combinations of genes acquired from bacterial, animal and plant ancestors. Furthermore, they display both DNA meth...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Rogato A,Richard H,Sarazin A,Voss B,Cheminant Navarro S,Champeimont R,Navarro L,Carbone A,Hess WR,Falciatore A

    更新日期:2014-08-20 00:00:00

  • Characterization of the small RNA component of the transcriptome from grain and sweet sorghum stems.

    abstract:BACKGROUND:Sorghum belongs to the tribe of the Andropogoneae that includes potential biofuel crops like switchgrass, Miscanthus and successful biofuel crops like corn and sugarcane. However, from a genomics point of view sorghum has compared to these other species a simpler genome because it lacks the additional rounds...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Calviño M,Bruggmann R,Messing J

    更新日期:2011-07-08 00:00:00

  • Assisted clustering of gene expression data using ANCut.

    abstract:BACKGROUND:In biomedical research, gene expression profiling studies have been extensively conducted. The analysis of gene expression data has led to a deeper understanding of human genetics as well as practically useful models. Clustering analysis has been a critical component of gene expression data analysis and can ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Teran Hidalgo SJ,Wu M,Ma S

    更新日期:2017-08-16 00:00:00

  • Comparative profiling of the transcriptional response to infection in two species of Drosophila by short-read cDNA sequencing.

    abstract:BACKGROUND:Homology-based comparisons of the genes involved in innate immunity across many insect taxa with fully sequenced genomes has revealed a striking pattern of gene gain and loss, particularly among genes that encode proteins involved in clearing pathogens (effectors). However, limited functional annotation in n...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Sackton TB,Clark AG

    更新日期:2009-06-07 00:00:00

  • Culture-independent genomic characterisation of Candidatus Chlamydia sanzinia, a novel uncultivated bacterium infecting snakes.

    abstract:BACKGROUND:Recent molecular studies have revealed considerably more diversity in the phylum Chlamydiae than was previously thought. Evidence is growing that many of these novel chlamydiae may be important pathogens in humans and animals. A significant barrier to characterising these novel chlamydiae is the requirement ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Taylor-Brown A,Bachmann NL,Borel N,Polkinghorne A

    更新日期:2016-09-05 00:00:00

  • Transcriptional response of Mexican axolotls to Ambystoma tigrinum virus (ATV) infection.

    abstract:BACKGROUND:Very little is known about the immunological responses of amphibians to pathogens that are causing global population declines. We used a custom microarray gene chip to characterize gene expression responses of axolotls (Ambystoma mexicanum) to an emerging viral pathogen, Ambystoma tigrinum virus (ATV). RESU...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Cotter JD,Storfer A,Page RB,Beachy CK,Voss SR

    更新日期:2008-10-20 00:00:00

  • Visualizing spatiotemporal dynamics of apoptosis after G1 arrest by human T cell leukemia virus type 1 Tax and insights into gene expression changes using microarray-based gene expression analysis.

    abstract:BACKGROUND:Human T cell leukemia virus type 1 (HTLV-1) Tax is a potent activator of viral and cellular gene expression that interacts with a number of cellular proteins. Many reports show that Tax is capable of regulating cell cycle progression and apoptosis both positively and negatively. However, it still remains to ...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Arainga M,Murakami H,Aida Y

    更新日期:2012-06-22 00:00:00

  • Inferring linkage disequilibrium from non-random samples.

    abstract:BACKGROUND:Linkage disequilibrium (LD) plays a fundamental role in population genetics and in the current surge of studies to screen for subtle genetic variants affecting complex traits. Methods widely implemented in LD analyses require samples to be randomly collected, which, however, are usually ignored and thus rais...

    journal_title:BMC genomics

    pub_type: 杂志文章


    authors: Wang M,Jia T,Jiang N,Wang L,Hu X,Luo Z

    更新日期:2010-05-26 00:00:00