Survey of the number of two-component response regulator genes in the complete and annotated genome sequences of prokaryotes

Ashby, Mark K.

doi:10.1016/s0378-1097(04)00004-7

Cited by 65 publications

(48 citation statements)

References 11 publications

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“…The number of two-component systems (Fig. 3) agrees well with published data (11,34,38,93,94,102,106,118). The small differences result, in particular, from the integration of previously unrecognized, "atypical" HisKA domains, HisKA_2 (HWE) and HisKA_3 in a few proteins, and of ORFs detected on later sequenced plasmid genomes.…”

Section: Cyanobacterial Two-component Orf Repertoire: Structure and Fsupporting

confidence: 87%

“…Also presented is the percentage of the proteincoding capacity of the genome that is represented by twocomponent ORFs, as well as the ratio of the number of hybrid kinases to histidine kinases plus response regulators. For the nine complete annotated genomes, it is apparent that the total number of two-component genes is a function of the genome size, ecophysiology, and physiological properties of the organism, as has been noted in general for the Bacteria (11,38). Thus, about 3.5% of the coding capacity is taken up by twocomponent genes for the filamentous heterocystous strains.…”

Section: Distribution Of Two-component Orfsmentioning

confidence: 69%

“…The deduced sequences of two-component protein genes have been found to contain a number of other "sensory" domains, but precise functions for a large number of them still await definition (40). Surveys performed on complete annotated genomes of prokaryotes revealed that the differences in the total number of genes and the complexity of the ecophysiology of the bacterium and of its environment have an effect on the number of response regulators (11,38). The total number of all signal transduction proteins increases for most bacteria as a square of the genome size (38).…”

Section: Introductionmentioning

confidence: 99%

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Cyanobacterial Two-Component Proteins: Structure,Diversity, Distribution, andEvolution

Ashby

Houmard

2006

Microbiol Mol Biol Rev

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125

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SUMMARY A survey of the already characterized and potential two-component protein sequences that exist in the nine complete and seven partially annotated cyanobacterial genome sequences available (as of May 2005) showed that the cyanobacteria possess a much larger repertoire of such proteins than most other bacteria. By analysis of the domain structure of the 1,171 potential histidine kinases, response regulators, and hybrid kinases, many various arrangements of about thirty different modules could be distinguished. The number of two-component proteins is related in part to genome size but also to the variety of physiological properties and ecophysiologies of the different strains. Groups of orthologues were defined, only a few of which have representatives with known physiological functions. Based on comparisons with the proposed phylogenetic relationships between the strains, the orthology groups show that (i) a few genes, some of them clustered on the genome, have been conserved by all species, suggesting their very ancient origin and an essential role for the corresponding proteins, and (ii) duplications, fusions, gene losses, insertions, and deletions, as well as domain shuffling, occurred during evolution, leading to the extant repertoire. These mechanisms are put in perspective with the different genetic properties that cyanobacteria have to achieve genome plasticity. This review is designed to serve as a basis for orienting further research aimed at defining the most ancient regulatory mechanisms and understanding how evolution worked to select and keep the most appropriate systems for cyanobacteria to develop in the quite different environments that they have successfully colonized.

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Section: Cyanobacterial Two-component Orf Repertoire: Structure and Fsupporting

confidence: 87%

Section: Distribution Of Two-component Orfsmentioning

confidence: 69%

Section: Introductionmentioning

confidence: 99%

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Cyanobacterial Two-Component Proteins: Structure,Diversity, Distribution, andEvolution

Ashby

Houmard

2006

Microbiol Mol Biol Rev

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125

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“…Analyses of annotated bacterial genomes revealed that soil bacteria possess Ϸ50 TCSs per genome, which is far greater than the average for other bacteria (22). The soil bacterium P. putida KT2440 was shown to have 93 TCSs (8).…”

Section: Discussionmentioning

confidence: 99%

The TodS–TodT two-component regulatory system recognizes a wide range of effectors and works with DNA-bending proteins

Lacal

Büsch

Guazzaroni

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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The TodS and TodT proteins form a previously unrecognized and highly specific two-component regulatory system in which the TodS sensor protein contains two input domains, each of which are coupled to a histidine kinase domain. This system regulates the expression of the genes involved in the degradation of toluene, benzene, and ethylbenzene through the toluene dioxygenase pathway. In contrast to the narrow substrate range of this catabolic pathway, the TodS effector profile is broad. TodS has basal autophosphorylation activity in vitro, which is enhanced by the presence of effectors. Toluene binds to TodS with high affinity (K d ‫؍‬ 684 ؎ 13 nM) and 1:1 stoichiometry. The analysis of the truncated variants of TodS reveals that toluene binds to the N-terminal input domain (K d ‫؍‬ 2.3 ؎ 0.1 M) but not to the C-terminal half. TodS transphosphorylates TodT, which binds to two highly similar DNA binding sites at base pairs ؊107 and ؊85 of the promoter. Integration host factor (IHF) plays a crucial role in the activation process and binds between the upstream TodT boxes and the ؊10 hexamer region. In an IHF-deficient background, expression from the tod promoter drops 8-fold. In vitro transcription assays confirmed the role determined in vivo for TodS, TodT, and IHF. A functional model is presented in which IHF favors the contact between the TodT activator, bound further upstream, and the ␣-subunit of RNA polymerase bound to the downstream promoter element. Once these contacts are established, the tod operon is efficiently transcribed.Pseudomonas ͉ sensor kinase ͉ toluene dioxygenase ͉ transcriptional regulator M any Pseudomonas putida strains are able to use benzene, toluene, and ethylbenzene as the sole carbon and energy source through the toluene dioxygenase (TOD) pathway (1). In this pathway, the aromatic hydrocarbons are oxidized to their corresponding substituted catechols, which are further metabolized to Krebs cycle intermediates (1, 2). The catabolic genes of the TOD pathway form the operon todXFC1C2BADEGIH, which is transcribed from a single promoter called P todX , located upstream from the todX gene (1-3). The todST genes are found downstream and form an independent operon that is expressed constitutively (2, 3).TodS and TodT have been proposed to form a two-component regulatory system (TCS) that regulates the tod catabolic operon in P. putida F1 (3). TodT shows all of the characteristics of a response regulator, whereas sequence-based domain predictions indicate that the 108-kDa TodS belongs to a family of sensor histidine kinases that have not been studied at the biochemical level. TodS is predicted to comprise two supradomains, each containing a PAS͞PAC sensory domain and a histidine kinase domain. The supradomains are separated by the receiver domain of a response regulator. In contrast to other histidine kinases, TodS apparently lacks transmembrane regions (3). The mode of action of this previously unrecognized type of histidine kinase has yet to be established. On the basis of moderate sequence simil...

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“…In fact, genes encoding TCSs are present in almost all bacteria and typically represent Յ1% of their genomes (1,2). TCSs are also present, although to a lesser extent, in archaea and eukaryotes such as fungi, slime molds, and plants (3,4).…”

mentioning

confidence: 99%

Bacterial sensor kinase TodS interacts with agonistic and antagonistic signals

Büsch

Lacal

Martos

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

105

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The TodS/TodT two-component system controls expression of the toluene dioxygenase (TOD) pathway for the metabolism of toluene in Pseudomonas putida DOT-T1E. TodS is a sensor kinase that ultimately controls tod gene expression through its cognate response regulator, TodT. We used isothermal titration calorimetry to study the binding of different compounds to TodS and related these findings to their capacity to induce gene expression in vivo. Agonistic compounds bound to TodS and induced gene expression in vivo. Toluene was a powerful agonist, but ortho-substitutions of toluene reduced or abolished in vivo responses, although TodS recognized o-xylene with high affinity. These compounds were called antagonists. We show that agonists and antagonists compete for binding to TodS both in vitro and in vivo. The failure of antagonists to induce gene expression in vivo correlated with their inability to stimulate TodS autophosphorylation in vitro. We propose intramolecular TodS signal transmission, not molecular recognition of compounds by TodS, to be the phenomenon that determines whether a given compound will lead to activation of expression of the tod genes. Molecular modeling identified residues F46, I74, F79, and I114 as being potentially involved in the binding of effector molecules. Alanine substitution mutants of these residues reduced affinities (2-to 345-fold) for both agonistic and antagonistic compounds. Our data indicate that determining the inhibitory activity of antagonists is a potentially fruitful alternative to design specific two-component system inhibitors for the development of new drugs to inhibit processes regulated by two-component systems.histidine kinases ͉ isothermal titration calorimetry ͉ Pseudomonas ͉ two-component systems ͉ aromatic hydrocarbons

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Survey of the number of two-component response regulator genes in the complete and annotated genome sequences of prokaryotes

Cited by 65 publications

References 11 publications

Cyanobacterial Two-Component Proteins: Structure,Diversity, Distribution, andEvolution

Cyanobacterial Two-Component Proteins: Structure,Diversity, Distribution, andEvolution

The TodS–TodT two-component regulatory system recognizes a wide range of effectors and works with DNA-bending proteins

Bacterial sensor kinase TodS interacts with agonistic and antagonistic signals

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