Role of Bound Zn(II) in the CadC Cd(II)/Pb(II)/Zn(II)-responsive Repressor

Kandegedara, Ashoka; Thiyagarajan, Saravanamuthu; Kondapalli, Kalyan C.; Stemmler, Timothy L.; Rosen, Barry P.

doi:10.1074/jbc.m809179200

Cited by 25 publications

(29 citation statements)

References 22 publications

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“…SmtB is one of the best-characterized members of this family of proteins. The Staphylococcus aureus pI258 cadmium repressor CadC, another characterized member of this family of proteins, shares 79% structural identity with SmtB (determined using SABERTOOTH [47]), with an RMSD of 2.3 Å in the positions of common atoms, despite only 48.4% sequence identity (48). Such dissimilar sequences sharing similar structures reinforces the view that the ArsR proteins are homodimeric molecules with an HTH DNA binding motif having a winged helix fold.…”

Section: Discussionmentioning

confidence: 49%

Regulatory Activities of Four ArsR Proteins in Agrobacterium tumefaciens 5A

Kang

Brame

Jetter

et al. 2016

Appl Environ Microbiol

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ArsR is a well-studied transcriptional repressor that regulates microbe-arsenic interactions. Most microorganisms have an arsR gene, but in cases where multiple copies exist, the respective roles or potential functional overlap have not been explored. We examined the repressors encoded by arsR1 and arsR2 (ars1 operon) and by arsR3 and arsR4 (ars2 operon) in Agrobacterium tumefaciens 5A. ArsR1 and ArsR4 are very similar in their primary sequences and diverge phylogenetically from ArsR2 and ArsR3, which are also quite similar to one another. Reporter constructs (lacZ) for arsR1, arsR2, and arsR4 were all inducible by As(III), but expression of arsR3 (monitored by reverse transcriptase PCR) was not influenced by As(III) and appeared to be linked transcriptionally to an upstream lysR-type gene. Experiments using a combination of deletion mutations and additional reporter assays illustrated that the encoded repressors (i) are not all autoregulatory as is typically known for ArsR proteins, (ii) exhibit variable control of each other's encoding genes, and (iii) exert variable control of other genes previously shown to be under the control of ArsR1. Furthermore, ArsR2, ArsR3, and ArsR4 appear to have an activator-like function for some genes otherwise repressed by ArsR1, which deviates from the well-studied repressor role of ArsR proteins. The differential regulatory activities suggest a complex regulatory network not previously observed in ArsR studies. The results indicate that fine-scale ArsR sequence deviations of the reiterated regulatory proteins apparently translate to different regulatory roles. IMPORTANCEGiven the significance of the ArsR repressor in regulating various aspects of microbe-arsenic interactions, it is important to assess potential regulatory overlap and/or interference when a microorganism carries multiple copies of arsR. This study explores this issue and shows that the four arsR genes in A. tumefaciens 5A, associated with two separate ars operons, encode proteins exhibiting various degrees of functional overlap with respect to autoregulation and cross-regulation, as well as control of other functional genes. In some cases, differences in regulatory activity are associated with only limited differences in protein primary structure. The experiments summarized herein also present evidence that ArsR proteins appear to have activator functions, representing novel regulatory activities for ArsR, previously known only to be a repressor. In reaction to arsenic in their environment, microorganisms orchestrate an organized response that may involve arsenite [As(III)] oxidation, arsenate [As(V)] reduction, or both. These redox reactions serve to detoxify or protect the organism or to generate energy, depending on the organism and the genes involved. Current models depict As(III) being taken up into the cell via aquaglyceroporins (e.g., reviewed in references 1, 2, and 3), where it then interacts with a DNA-binding repressor protein, ArsR, resulting in a conformational change in ArsR and causing it...

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Section: Discussionmentioning

confidence: 49%

Regulatory Activities of Four ArsR Proteins in Agrobacterium tumefaciens 5A

Kang

Brame

Jetter

et al. 2016

Appl Environ Microbiol

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“…CadC consists of two different metal ion sites, site 1 and site 2 (4 sites in total per homodimer). Site 1 is a thiol-rich mononuclear metal ion binding site, whereas site 2 consists of two metal ion sites at the homodimer interface [10,11]. Site 1 is responsible for the regulatory role of CadC whereas site 2 has been shown by mutagenesis studies to not be necessary for the correct biological function [10].…”

Section: Coordination Chemistry Of Cd(ii) In Cadcmentioning

confidence: 98%

Natural and Artificial Proteins Containing Cadmium

Peacock

Pecoraro

2012

Metal Ions in Life Sciences

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This chapter describes an approach using designed proteins to understand the structure, spectroscopy, and dynamics of proteins that bind Cd(II). We will show that three-stranded coiled coils (3SCCs) based on the parent peptides TRI (Ac-G(LKALEEK)(4)G-NH(2)) or GRAND (Ac-G(LKALEEK)(5)G-NH(2)) have been essential for understanding how Cd(II) binds to thiolate-rich environments in proteins. Examples are given correlating physical properties such as the binding constants or deprotonation constants relating to structure. We present a scale that relates (113)Cd NMR chemical shifts to structures extracted from (111m)Cd PAC experiments. In addition, we describe motional processes that help transport from the helical interface of proteins into the hydrophobic interior of helical bundles. These studies help clarify the chemistry of Cd(II) in relation to metal-regulated gene expression and detoxification.

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“…In the ArsR/SmtB proteins, metal binding triggers conformational changes that result in derepression of gene expression by driving repositioning of the helix-turn-helix DNA interaction motif (26)(27)(28)(29)(31)(32)(33). This movement results in a switch from a "closed" DNA-binding structure to an "open" low-affinity conformation of the homodimer.…”

Section: Discussionmentioning

confidence: 99%

“…A search of the Protein Data Bank using the DALI server (30) identifies BigR, HylU, and CadC as the closest structural relatives of NolR (Fig. S1 B-D) with Z-scores of 14.4-14.9 and 2.0-2.7 Å rmsd for 95-97 Cα atoms (26,(31)(32)(33). The major differences between these proteins occur in the length and positioning of the N-terminal α-helical region at the dimerization interface ( Fig.…”

Section: Resultsmentioning

confidence: 99%

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Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR

Lee

Krishnan

Jez

2014

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

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The symbiosis between rhizobial microbes and host plants involves the coordinated expression of multiple genes, which leads to nodule formation and nitrogen fixation. As part of the transcriptional machinery for nodulation and symbiosis across a range of Rhizobium, NolR serves as a global regulatory protein. Here, we present the X-ray crystal structures of NolR in the unliganded form and complexed with two different 22-base pair (bp) double-stranded operator sequences (oligos AT and AA). Structural and biochemical analysis of NolR reveals protein-DNA interactions with an asymmetric operator site and defines a mechanism for conformational switching of a key residue (Gln56) to accommodate variation in target DNA sequences from diverse rhizobial genes for nodulation and symbiosis. This conformational switching alters the energetic contributions to DNA binding without changes in affinity for the target sequence. Two possible models for the role of NolR in the regulation of different nodulation and symbiosis genes are proposed. To our knowledge, these studies provide the first structural insight on the regulation of genes involved in the agriculturally and ecologically important symbiosis of microbes and plants that leads to nodule formation and nitrogen fixation.transcription factor | protein structure T he symbiosis between rhizobial bacteria from the Rhizobium, Sinorhizobium, Mesorhizobium, Azorhizobium, and Bradyrhizobium genera and leguminous plants leads to the formation of root nodules (1, 2). These plant organs are specialized for nitrogen fixation and assimilation and are of major ecological and agricultural importance. For example, nitrogen-fixing nodules account for one quarter of total nitrogen fixed globally each year (3). The development of nitrogen-fixing nodules by rhizobia involves a variety of interactions between the plant and microbe; however, at the center of this process are a set of nod (nodulation) genes required for the synthesis of oligosaccharide-nodulation factors, for determining host-plant specificity, and for optimizing the efficiency of symbiosis (4-6). Successful interaction between the rhizobium and host plant requires expression of both positive and negative transcriptional control of genes related to nodulation and symbiosis (7,8

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Role of Bound Zn(II) in the CadC Cd(II)/Pb(II)/Zn(II)-responsive Repressor

Cited by 25 publications

References 22 publications

Regulatory Activities of Four ArsR Proteins in Agrobacterium tumefaciens 5A

Regulatory Activities of Four ArsR Proteins in Agrobacterium tumefaciens 5A

Natural and Artificial Proteins Containing Cadmium

Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR

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