Integrative and quantitative view of the CtrA regulatory network in a stalked budding bacterium.

Abstract:

:The Alphaproteobacteria show a remarkable diversity of cell cycle-dependent developmental patterns, which are governed by the conserved CtrA pathway. Its central component CtrA is a DNA-binding response regulator that is controlled by a complex two-component signaling network, mediating distinct transcriptional programs in the two offspring. The CtrA pathway has been studied intensively and was shown to consist of an upstream part that reads out the developmental state of the cell and a downstream part that integrates the upstream signals and mediates CtrA phosphorylation. However, the role of this circuitry in bacterial diversification remains incompletely understood. We have therefore investigated CtrA regulation in the morphologically complex stalked budding alphaproteobacterium Hyphomonas neptunium. Compared to relatives dividing by binary fission, H. neptunium shows distinct changes in the role and regulation of various pathway components. Most notably, the response regulator DivK, which normally links the upstream and downstream parts of the CtrA pathway, is dispensable, while downstream components such as the pseudokinase DivL, the histidine kinase CckA, the phosphotransferase ChpT and CtrA are essential. Moreover, CckA is compartmentalized to the nascent bud without forming distinct polar complexes and CtrA is not regulated at the level of protein abundance. We show that the downstream pathway controls critical functions such as replication initiation, cell division and motility. Quantification of the signal flow through different nodes of the regulatory cascade revealed that the CtrA pathway is a leaky pipeline and must involve thus-far unidentified factors. Collectively, the quantitative system-level analysis of CtrA regulation in H. neptunium points to a considerable evolutionary plasticity of cell cycle regulation in alphaproteobacteria and leads to hypotheses that may also hold in well-established model organisms such as Caulobacter crescentus.

journal_name

PLoS Genet

journal_title

PLoS genetics

authors

Leicht O,van Teeseling MCF,Panis G,Reif C,Wendt H,Viollier PH,Thanbichler M

doi

10.1371/journal.pgen.1008724

subject

Has Abstract

pub_date

2020-04-23 00:00:00

pages

e1008724

issue

4

eissn

1553-7390

issn

1553-7404

pii

PGENETICS-D-19-01258

journal_volume

16

pub_type

杂志文章
  • Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies.

    abstract::Exome sequencing has been widely used in detecting pathogenic nonsynonymous single nucleotide variants (SNVs) for human inherited diseases. However, traditional statistical genetics methods are ineffective in analyzing exome sequencing data, due to such facts as the large number of sequenced variants, the presence of ...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1004237

    authors: Wu J,Li Y,Jiang R

    更新日期:2014-03-20 00:00:00

  • Temporal and spatial regulation of protein cross-linking by the pre-assembled substrates of a Bacillus subtilis spore coat transglutaminase.

    abstract::In many cases protein assemblies are stabilized by covalent bonds, one example of which is the formation of intra- or intermolecular ε-(γ-glutamyl)lysil cross-links catalyzed by transglutaminases (TGases). Because of the potential for unwanted cross-linking reactions, the activities of many TGases have been shown to b...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1007912

    authors: Fernandes CG,Martins D,Hernandez G,Sousa AL,Freitas C,Tranfield EM,Cordeiro TN,Serrano M,Moran CP Jr,Henriques AO

    更新日期:2019-04-08 00:00:00

  • Multiple mechanisms regulate H3 acetylation of enhancers in response to thyroid hormone.

    abstract::Hormone-dependent activation of enhancers includes histone hyperacetylation and mediator recruitment. Histone hyperacetylation is mostly explained by a bimodal switch model, where histone deacetylases (HDACs) disassociate from chromatin, and histone acetyl transferases (HATs) are recruited. This model builds on decade...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1008770

    authors: Præstholm SM,Siersbæk MS,Nielsen R,Zhu X,Hollenberg AN,Cheng SY,Grøntved L

    更新日期:2020-05-26 00:00:00

  • In Vivo Senescence in the Sbds-Deficient Murine Pancreas: Cell-Type Specific Consequences of Translation Insufficiency.

    abstract::Genetic models of ribosome dysfunction show selective organ failure, highlighting a gap in our understanding of cell-type specific responses to translation insufficiency. Translation defects underlie a growing list of inherited and acquired cancer-predisposition syndromes referred to as ribosomopathies. We sought to i...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1005288

    authors: Tourlakis ME,Zhang S,Ball HL,Gandhi R,Liu H,Zhong J,Yuan JS,Guidos CJ,Durie PR,Rommens JM

    更新日期:2015-06-09 00:00:00

  • Genome-wide expression profiling of the Arabidopsis female gametophyte identifies families of small, secreted proteins.

    abstract::The female gametophyte of flowering plants, the embryo sac, develops within the diploid (sporophytic) tissue of the ovule. While embryo sac-expressed genes are known to be required at multiple stages of the fertilization process, the set of embryo sac-expressed genes has remained poorly defined. In particular, the set...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.0030171

    authors: Jones-Rhoades MW,Borevitz JO,Preuss D

    更新日期:2007-10-01 00:00:00

  • The genetic architecture of the genome-wide transcriptional response to ER stress in the mouse.

    abstract::Endoplasmic reticulum (ER) stress occurs when misfolded proteins accumulate in the ER. The cellular response to ER stress involves complex transcriptional and translational changes, important to the survival of the cell. ER stress is a primary cause and a modifier of many human diseases. A first step to understanding ...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1004924

    authors: Chow CY,Wang X,Riccardi D,Wolfner MF,Clark AG

    更新日期:2015-02-04 00:00:00

  • Genome-wide effects of long-term divergent selection.

    abstract::To understand the genetic mechanisms leading to phenotypic differentiation, it is important to identify genomic regions under selection. We scanned the genome of two chicken lines from a single trait selection experiment, where 50 generations of selection have resulted in a 9-fold difference in body weight. Analyses o...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1001188

    authors: Johansson AM,Pettersson ME,Siegel PB,Carlborg O

    更新日期:2010-11-04 00:00:00

  • Convergence of Light and ABA signaling on the ABI5 promoter.

    abstract::Light is one of the most important environmental cues regulating multiple aspects of plant growth and development, and abscisic acid (ABA) is a plant hormone that plays important roles during many phases of the plant life cycle and in plants' responses to various environmental stresses. How plants integrate the extern...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1004197

    authors: Xu D,Li J,Gangappa SN,Hettiarachchi C,Lin F,Andersson MX,Jiang Y,Deng XW,Holm M

    更新日期:2014-02-27 00:00:00

  • Sister centromere fusion during meiosis I depends on maintaining cohesins and destabilizing microtubule attachments.

    abstract::Sister centromere fusion is a process unique to meiosis that promotes co-orientation of the sister kinetochores, ensuring they attach to microtubules from the same pole during metaphase I. We have found that the kinetochore protein SPC105R/KNL1 and Protein Phosphatase 1 (PP1-87B) regulate sister centromere fusion in D...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1008072

    authors: Wang LI,Das A,McKim KS

    更新日期:2019-05-31 00:00:00

  • Mutations in MAB21L2 result in ocular Coloboma, microcornea and cataracts.

    abstract::Ocular coloboma results from abnormal embryonic development and is often associated with additional ocular and systemic features. Coloboma is a highly heterogeneous disorder with many cases remaining unexplained. Whole exome sequencing from two cousins affected with dominant coloboma with microcornea, cataracts, and s...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1005002

    authors: Deml B,Kariminejad A,Borujerdi RH,Muheisen S,Reis LM,Semina EV

    更新日期:2015-02-26 00:00:00

  • The monothiol glutaredoxin GrxD is essential for sensing iron starvation in Aspergillus fumigatus.

    abstract::Efficient adaptation to iron starvation is an essential virulence determinant of the most common human mold pathogen, Aspergillus fumigatus. Here, we demonstrate that the cytosolic monothiol glutaredoxin GrxD plays an essential role in iron sensing in this fungus. Our studies revealed that (i) GrxD is essential for gr...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1008379

    authors: Misslinger M,Scheven MT,Hortschansky P,López-Berges MS,Heiss K,Beckmann N,Heigl T,Hermann M,Krüger T,Kniemeyer O,Brakhage AA,Haas H

    更新日期:2019-09-16 00:00:00

  • Integrating molecular QTL data into genome-wide genetic association analysis: Probabilistic assessment of enrichment and colocalization.

    abstract::We propose a novel statistical framework for integrating the result from molecular quantitative trait loci (QTL) mapping into genome-wide genetic association analysis of complex traits, with the primary objectives of quantitatively assessing the enrichment of the molecular QTLs in complex trait-associated genetic vari...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1006646

    authors: Wen X,Pique-Regi R,Luca F

    更新日期:2017-03-09 00:00:00

  • Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs.

    abstract::We performed a genome-scale chromatin immunoprecipitation (ChIP)-chip comparison of two modifications (trimethylation of lysine 9 [H3me3K9] and trimethylation of lysine 27 [H3me3K27]) of histone H3 in Ntera2 testicular carcinoma cells and in three different anatomical sources of primary human fibroblasts. We found tha...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.0030089

    authors: O'Geen H,Squazzo SL,Iyengar S,Blahnik K,Rinn JL,Chang HY,Green R,Farnham PJ

    更新日期:2007-06-01 00:00:00

  • A nuclear calcium-sensing pathway is critical for gene regulation and salt stress tolerance in Arabidopsis.

    abstract::Salt stress is an important environmental factor that significantly limits crop productivity worldwide. Studies on responses of plants to salt stress in recent years have identified novel signaling pathways and have been at the forefront of plant stress biology and plant biology in general. Thus far, research on salt ...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1003755

    authors: Guan Q,Wu J,Yue X,Zhang Y,Zhu J

    更新日期:2013-08-01 00:00:00

  • Protein modularity of alternatively spliced exons is associated with tissue-specific regulation of alternative splicing.

    abstract::Recent comparative genomic analysis of alternative splicing has shown that protein modularity is an important criterion for functional alternative splicing events. Exons that are alternatively spliced in multiple organisms are much more likely to be an exact multiple of 3 nt in length, representing a class of "modular...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.0010034

    authors: Xing Y,Lee CJ

    更新日期:2005-09-01 00:00:00

  • Dynamics of Transcription Factor Binding Site Evolution.

    abstract::Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic ...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1005639

    authors: Tuğrul M,Paixão T,Barton NH,Tkačik G

    更新日期:2015-11-06 00:00:00

  • A single Ho-induced double-strand break at the MAT locus is lethal in Candida glabrata.

    abstract::Mating-type switching is a complex mechanism that promotes sexual reproduction in Saccharomycotina. In the model species Saccharomyces cerevisiae, mating-type switching is initiated by the Ho endonuclease that performs a site-specific double-strand break (DSB) at MAT, repaired by homologous recombination (HR) using on...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1008627

    authors: Maroc L,Zhou-Li Y,Boisnard S,Fairhead C

    更新日期:2020-10-15 00:00:00

  • Transcription and translation of the sigG gene is tuned for proper execution of the switch from early to late gene expression in the developing Bacillus subtilis spore.

    abstract::A cascade of alternative sigma factors directs developmental gene expression during spore formation by the bacterium Bacillus subtilis. As the spore develops, a tightly regulated switch occurs in which the early-acting sigma factor σF is replaced by the late-acting sigma factor σG. The gene encoding σG (sigG) is trans...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1007350

    authors: Mearls EB,Jackter J,Colquhoun JM,Farmer V,Matthews AJ,Murphy LS,Fenton C,Camp AH

    更新日期:2018-04-27 00:00:00

  • Role of Pirh2 in mediating the regulation of p53 and c-Myc.

    abstract::Ubiquitylation is fundamental for the regulation of the stability and function of p53 and c-Myc. The E3 ligase Pirh2 has been reported to polyubiquitylate p53 and to mediate its proteasomal degradation. Here, using Pirh2 deficient mice, we report that Pirh2 is important for the in vivo regulation of p53 stability in r...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1002360

    authors: Hakem A,Bohgaki M,Lemmers B,Tai E,Salmena L,Matysiak-Zablocki E,Jung YS,Karaskova J,Kaustov L,Duan S,Madore J,Boutros P,Sheng Y,Chesi M,Bergsagel PL,Perez-Ordonez B,Mes-Masson AM,Penn L,Squire J,Chen X,Jurisica I

    更新日期:2011-11-01 00:00:00

  • Pervasive variation of transcription factor orthologs contributes to regulatory network evolution.

    abstract::Differences in transcriptional regulatory networks underlie much of the phenotypic variation observed across organisms. Changes to cis-regulatory elements are widely believed to be the predominant means by which regulatory networks evolve, yet examples of regulatory network divergence due to transcription factor (TF) ...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1005011

    authors: Nadimpalli S,Persikov AV,Singh M

    更新日期:2015-03-06 00:00:00

  • Time dependent genetic analysis links field and controlled environment phenotypes in the model C4 grass Setaria.

    abstract::Vertical growth of plants is a dynamic process that is influenced by genetic and environmental factors and has a pronounced effect on overall plant architecture and biomass composition. We have performed six controlled growth trials of an interspecific Setaria italica x Setaria viridis recombinant inbred line populati...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1006841

    authors: Feldman MJ,Paul RE,Banan D,Barrett JF,Sebastian J,Yee MC,Jiang H,Lipka AE,Brutnell TP,Dinneny JR,Leakey ADB,Baxter I

    更新日期:2017-06-23 00:00:00

  • Genomic ancestry of North Africans supports back-to-Africa migrations.

    abstract::North African populations are distinct from sub-Saharan Africans based on cultural, linguistic, and phenotypic attributes; however, the time and the extent of genetic divergence between populations north and south of the Sahara remain poorly understood. Here, we interrogate the multilayered history of North Africa by ...

    journal_title:PLoS genetics

    pub_type: 历史文章,杂志文章

    doi:10.1371/journal.pgen.1002397

    authors: Henn BM,Botigué LR,Gravel S,Wang W,Brisbin A,Byrnes JK,Fadhlaoui-Zid K,Zalloua PA,Moreno-Estrada A,Bertranpetit J,Bustamante CD,Comas D

    更新日期:2012-01-01 00:00:00

  • A systematic screen for morphological abnormalities during fission yeast sexual reproduction identifies a mechanism of actin aster formation for cell fusion.

    abstract::In non-motile fungi, sexual reproduction relies on strong morphogenetic changes in response to pheromone signaling. We report here on a systematic screen for morphological abnormalities of the mating process in fission yeast Schizosaccharomyces pombe. We derived a homothallic (self-fertile) collection of viable deleti...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1006721

    authors: Dudin O,Merlini L,Bendezú FO,Groux R,Vincenzetti V,Martin SG

    更新日期:2017-04-14 00:00:00

  • Correction: Methyl Farnesoate Plays a Dual Role in Regulating Drosophila Metamorphosis.

    abstract::[This corrects the article DOI: 10.1371/journal.pgen.1005038.]. ...

    journal_title:PLoS genetics

    pub_type: 已发布勘误

    doi:10.1371/journal.pgen.1006559

    authors: Wen D,Rivera-Perez C,Abdou M,Jia Q,He Q,Liu X,Zyaan O,Xu J,Bendena WG,Tobe SS,Noriega FG,Palli SR,Wang J,Li S

    更新日期:2017-01-20 00:00:00

  • Intronic Alus influence alternative splicing.

    abstract::Examination of the human transcriptome reveals higher levels of RNA editing than in any other organism tested to date. This is indicative of extensive double-stranded RNA (dsRNA) formation within the human transcriptome. Most of the editing sites are located in the primate-specific retrotransposed element called Alu. ...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1000204

    authors: Lev-Maor G,Ram O,Kim E,Sela N,Goren A,Levanon EY,Ast G

    更新日期:2008-09-26 00:00:00

  • Binding of NF-κB to nucleosomes: effect of translational positioning, nucleosome remodeling and linker histone H1.

    abstract::NF-κB is a key transcription factor regulating the expression of inflammatory responsive genes. How NF-κB binds to naked DNA templates is well documented, but how it interacts with chromatin is far from being clear. Here we used a combination of UV laser footprinting, hydroxyl footprinting and electrophoretic mobility...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1003830

    authors: Lone IN,Shukla MS,Charles Richard JL,Peshev ZY,Dimitrov S,Angelov D

    更新日期:2013-01-01 00:00:00

  • Heritability informed power optimization (HIPO) leads to enhanced detection of genetic associations across multiple traits.

    abstract::Genome-wide association studies have shown that pleiotropy is a common phenomenon that can potentially be exploited for enhanced detection of susceptibility loci. We propose heritability informed power optimization (HIPO) for conducting powerful pleiotropic analysis using summary-level association statistics. We find ...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1007549

    authors: Qi G,Chatterjee N

    更新日期:2018-10-05 00:00:00

  • A point mutation decouples the lipid transfer activities of microsomal triglyceride transfer protein.

    abstract::Apolipoprotein B-containing lipoproteins (B-lps) are essential for the transport of hydrophobic dietary and endogenous lipids through the circulation in vertebrates. Zebrafish embryos produce large numbers of B-lps in the yolk syncytial layer (YSL) to move lipids from yolk to growing tissues. Disruptions in B-lp produ...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1008941

    authors: Wilson MH,Rajan S,Danoff A,White RJ,Hensley MR,Quinlivan VH,Recacha R,Thierer JH,Tan FJ,Busch-Nentwich EM,Ruddock L,Hussain MM,Farber SA

    更新日期:2020-08-06 00:00:00

  • Common Cell Shape Evolution of Two Nasopharyngeal Pathogens.

    abstract::Respiratory infectious diseases are the third cause of worldwide death. The nasopharynx is the portal of entry and the ecological niche of many microorganisms, of which some are pathogenic to humans, such as Neisseria meningitidis and Moraxella catarrhalis. These microbes possess several surface structures that intera...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1005338

    authors: Veyrier FJ,Biais N,Morales P,Belkacem N,Guilhen C,Ranjeva S,Sismeiro O,Péhau-Arnaudet G,Rocha EP,Werts C,Taha MK,Boneca IG

    更新日期:2015-07-10 00:00:00

  • Re-sequencing expands our understanding of the phenotypic impact of variants at GWAS loci.

    abstract::Genome-wide association studies (GWAS) have identified >500 common variants associated with quantitative metabolic traits, but in aggregate such variants explain at most 20-30% of the heritable component of population variation in these traits. To further investigate the impact of genotypic variation on metabolic trai...

    journal_title:PLoS genetics

    pub_type: 杂志文章

    doi:10.1371/journal.pgen.1004147

    authors: Service SK,Teslovich TM,Fuchsberger C,Ramensky V,Yajnik P,Koboldt DC,Larson DE,Zhang Q,Lin L,Welch R,Ding L,McLellan MD,O'Laughlin M,Fronick C,Fulton LL,Magrini V,Swift A,Elliott P,Jarvelin MR,Kaakinen M,McCarthy

    更新日期:2014-01-30 00:00:00