Solution Structure of the C-Terminal Transcriptional Activator Domain of FixJ from Sinorhizobium meliloti and Its Recognition of the fixK Promoter,

Kurashima-Ito, Kaori; Kasai, Yuichi; Hosono, Kaito; Tamura, Koji; Oue, Soichi; Isogai, M.; Ito, Yutaka; Nakamura, H.; Shiro, Yoshitsugu

doi:10.1021/bi0509043

Cited by 20 publications

(21 citation statements)

References 43 publications

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“…Val 197 is the first residue in H4; this position is not conserved among SsrB family members. A positively charged residue (Arg or Lys) at this position in the crystal structures of the DNA complexes is shown to contact DNA and resides in the loop between H3 and H4 (17,18,20,21,23,35,36). Thus, we expect that this loop in SsrB also contacts DNA.…”

Section: Discussionmentioning

confidence: 96%

Structural and Functional Analysis of the C-terminal DNA Binding Domain of the Salmonella typhimurium SPI-2 Response Regulator SsrB

Carroll

Liao

Morgan

et al. 2009

Journal of Biological Chemistry

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In bacterial pathogenesis, virulence gene regulation is controlled by two-component regulatory systems. In Escherichia coli, the EnvZ/OmpR two-component system is best understood as regulating expression of outer membrane proteins, but in Salmonella enterica, OmpR activates transcription of the SsrA/B two-component system located on Salmonella pathogenicity island 2 (SPI-2). The response regulator SsrB controls expression of a type III secretory system in which effectors modify the vacuolar membrane and prevent its degradation via the endocytic pathway. Vacuolar modification enables Salmonella to survive and replicate in the macrophage phagosome and disseminate to the liver and spleen to cause systemic infection. The signals that activate EnvZ and SsrA are unknown but are related to the acidic pH encountered in the vacuole. Our previous work established that SsrB binds to regions of DNA that are AT-rich, with poor sequence conservation. Although SsrB is a major virulence regulator in Salmonella, very little is known regarding how it binds DNA and activates transcription. In the present work, we solved the structure of the C-terminal DNA binding domain of SsrB Salmonella infections occur in a wide variety of vertebrate hosts and continue to be a major health problem worldwide for humans. Salmonella infection requires at least two pathogenicity islands, Salmonella pathogenicity islands 1 and 2 (SPI-1 and SPI-2), 3 both of which encode type III secretion systems as well as secreted effectors, chaperones, and regulatory proteins (1-3). Genes located on SPI-1 are required for initial adherence to and invasion of intestinal epithelial cells (4). SPI-2 genes are required for intracellular survival, replication, and systemic infection of Salmonella (5, 6). SPI-2 consists of a 40-kb region located at 31 centisomes on the chromosome and contains ϳ32 genes (7). SPI-2 genes are organized into functional clusters encoding regulatory, structural genes, effectors, and chaperones. To date 10 promoters of SPI-2 genes and SPI-2 co-regulated genes have been identified (8 -10). These promoters, located upstream of the ssrA, ssrB, ssaB, sseA, ssaG, ssaM, sseI, srfN, sifA, and sifB genes, transcribe genes either individually or in large operons. Transcription from these promoters is activated by the SPI-2 encoded two-component signal transduction system, SsrA/SsrB (8, 11-13).Two-component signal transduction systems regulate gene expression in response to specific environmental signals (for review see Ref. 14). These systems represent the major paradigm for signal transduction in prokaryotes. They are frequently involved in regulating expression of virulence genes in pathogenic bacteria and are also present in the archaea, lower eukaryotes, and plants. In its simplest form, a two-component system contains a sensor kinase, often a membrane protein that functions in trans-membrane signaling, and a response regulator, usually a DNA-binding protein that regulates transcription. In Salmonella enterica serovar typhimurium, the SsrA/SsrB tw...

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Section: Discussionmentioning

confidence: 96%

Structural and Functional Analysis of the C-terminal DNA Binding Domain of the Salmonella typhimurium SPI-2 Response Regulator SsrB

Carroll

Liao

Morgan

et al. 2009

Journal of Biological Chemistry

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“…This attempt, however, did not result in the identification of a consensus "FixJ box," which made it impossible to distinguish putative direct FixJ targets from genes that are only indirectly regulated by FixJ. Likewise, the previous search for an "FixJ box" in S. meliloti had been inconclusive (23,41).…”

Section: Discussionmentioning

confidence: 98%

Comprehensive Assessment of the Regulons Controlled by the FixLJ-FixK₂-FixK₁Cascade inBradyrhizobium japonicum

et al. 2008

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Symbiotic N 2 fixation in Bradyrhizobium japonicum is controlled by a complex transcription factor network. Part of it is a hierarchically arranged cascade in which the two-component regulatory system FixLJ, in response to a moderate decrease in oxygen concentration, activates the fixK 2 gene. The FixK 2 protein then activates not only a number of genes essential for microoxic respiration in symbiosis (fixNOQP and fixGHIS) but also further regulatory genes (rpoN 1 , nnrR, and fixK 1 ). The results of transcriptome analyses described here have led to a comprehensive and expanded definition of the FixJ, FixK 2 , and FixK 1 regulons, which, respectively, consist of 26, 204, and 29 genes specifically regulated in microoxically grown cells. Most of these genes are subject to positive control. Particular attention was addressed to the FixK 2 -dependent genes, which included a bioinformatics search for putative FixK 2 binding sites on DNA (FixK 2 boxes). Using an in vitro transcription assay with RNA polymerase holoenzyme and purified FixK 2 as the activator, we validated as direct targets eight new genes. Interestingly, the adjacent but divergently oriented fixK 1 and cycS genes shared the same FixK 2 box for the activation of transcription in both directions. This recognition site may also be a direct target for the FixK 1 protein, because activation of the cycS promoter required an intact fixK 1 gene and either microoxic or anoxic, denitrifying conditions. We present evidence that cycS codes for a c-type cytochrome which is important, but not essential, for nitrate respiration. Two other, unexpected results emerged from this study: (i) specifically FixK 1 seemed to exert a negative control on genes that are normally activated by the N 2 fixation-specific transcription factor NifA, and (ii) a larger number of genes are expressed in a FixK 2 -dependent manner in endosymbiotic bacteroids than in culture-grown cells, pointing to a possible symbiosisspecific control.

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“…The C-terminal DNA-binding domain of FruA is similar to that of FixJ, which is structurally similar to that of NarL and Spo0A (37). For each of these well-studied response regulators, phosphorylation of the N-terminal receiver domain enhances DNA binding by the C-terminal helix-turn-helix-containing domain, although the effects on dimerization (i.e., in solution versus on the DNA) can be different and the sequence and arrangement of recognition sites in target promoters are different (1,37,43,44,59). Identification of a histidine protein kinase capable of producing phosphorylated FruA in vitro is an important goal of future studies in order to better understand the mechanism of transcriptional activation by FruA.…”

Section: Figmentioning

confidence: 91%

Regulation of the Myxococcus xanthus C-Signal-Dependent Ω4400 Promoter by the Essential Developmental Protein FruA

Yoder-Himes

Kroos

2006

J Bacteriol

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The bacterium Myxococcus xanthus employs extracellular signals to coordinate aggregation and sporulation during multicellular development. Extracellular, contact-dependent signaling that involves the CsgA protein (called C-signaling) activates FruA, a putative response regulator that governs a branched signaling pathway inside cells. One branch regulates cell movement, leading to aggregation. The other branch regulates gene expression, leading to sporulation. C-signaling is required for full expression of most genes induced after 6 h into development, including the gene identified by Tn5 lac insertion ⍀4400. To determine if FruA is a direct regulator of ⍀4400 transcription, a combination of in vivo and in vitro experiments was performed. ⍀4400 expression was abolished in a fruA mutant. The DNA-binding domain of FruA bound specifically to DNA upstream of the promoter ؊35 region in vitro. Mutations between bp ؊86 and ؊77 greatly reduced binding. One of these mutations had been shown previously to reduce ⍀4400 expression in vivo and make it independent of C-signaling. For the first time, chromatin immunoprecipitation (ChIP) experiments were performed on M. xanthus. The ChIP experiments demonstrated that FruA is associated with the ⍀4400 promoter region late in development, even in the absence of C-signaling. Based on these results, we propose that FruA directly activates ⍀4400 transcription to a moderate level prior to C-signaling and, in response to C-signaling, binds near bp ؊80 and activates transcription to a higher level. Also, the highly localized effects of mutations between bp ؊86 and ؊77 on DNA binding in vitro, together with recently published footprints, allow us to predict a consensus binding site of GTCG/CGA/G for the FruA DNA-binding domain.

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Solution Structure of the C-Terminal Transcriptional Activator Domain of FixJ from Sinorhizobium meliloti and Its Recognition of the fixK Promoter^,

Cited by 20 publications

References 43 publications

Structural and Functional Analysis of the C-terminal DNA Binding Domain of the Salmonella typhimurium SPI-2 Response Regulator SsrB

Structural and Functional Analysis of the C-terminal DNA Binding Domain of the Salmonella typhimurium SPI-2 Response Regulator SsrB

Comprehensive Assessment of the Regulons Controlled by the FixLJ-FixK₂-FixK₁Cascade inBradyrhizobium japonicum

Regulation of the Myxococcus xanthus C-Signal-Dependent Ω4400 Promoter by the Essential Developmental Protein FruA

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Solution Structure of the C-Terminal Transcriptional Activator Domain of FixJ from Sinorhizobium meliloti and Its Recognition of the fixK Promoter,

Cited by 20 publications

References 43 publications

Structural and Functional Analysis of the C-terminal DNA Binding Domain of the Salmonella typhimurium SPI-2 Response Regulator SsrB

Structural and Functional Analysis of the C-terminal DNA Binding Domain of the Salmonella typhimurium SPI-2 Response Regulator SsrB

Comprehensive Assessment of the Regulons Controlled by the FixLJ-FixK2-FixK1Cascade inBradyrhizobium japonicum

Regulation of the Myxococcus xanthus C-Signal-Dependent Ω4400 Promoter by the Essential Developmental Protein FruA

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Solution Structure of the C-Terminal Transcriptional Activator Domain of FixJ from Sinorhizobium meliloti and Its Recognition of the fixK Promoter^,

Comprehensive Assessment of the Regulons Controlled by the FixLJ-FixK₂-FixK₁Cascade inBradyrhizobium japonicum