Distinct Effector-binding Sites Enable Synergistic Transcriptional Activation by BenM, a LysR-type Regulator

Ezezika, Obidimma; Haddad, Sandra; Clark, Todd J.; Neidle, Ellen L.; Momany, Cory

doi:10.1016/j.jmb.2006.09.090

Cited by 93 publications

(187 citation statements)

References 43 publications

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“…It was later reclassified as a transcriptional activator and found to be part of a more complex regulatory network involving BenM. Both CatM and BenM activate the transcription of catBCIJFD but BenM additionally regulates expression of the benABCDE operon, which encodes proteins necessary for benzoate degradation (Collier et al, 1998;Ezezika et al, 2006Ezezika et al, , 2007. A larger subgroup of LTTRs that are associated with degradation of catechols and chlorinated aromatics has emerged in which CatM and BenM are classified.…”

Section: Lysr Family Transcriptional Regulatorsmentioning

confidence: 99%

Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins

2008

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The LysR family of transcriptional regulators represents the most abundant type of transcriptional regulator in the prokaryotic kingdom. Members of this family have a conserved structure with an Nterminal DNA-binding helix-turn-helix motif and a C-terminal co-inducer-binding domain. Despite considerable conservation both structurally and functionally, LysR-type transcriptional regulators (LTTRs) regulate a diverse set of genes, including those involved in virulence, metabolism, quorum sensing and motility. Numerous structural and transcriptional studies of members of the LTTR family are helping to unravel a compelling paradigm that has evolved from the original observations and conclusions that were made about this family of transcriptional regulators.

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Section: Lysr Family Transcriptional Regulatorsmentioning

confidence: 99%

Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins

2008

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“…Effector binding occurs in a small cleft formed between RD-I and RD-II (Fig. 1) and is a hallmark of the LTTR family (22,(70)(71)(72)(73)(74)(75)(76)(77)(78)(79)(80). A recent study using nondenaturing mass spectrometry has illustrated for the first time that an LTTR tetramer binds four molecules of its effector in a stepwise pattern while bound to DNA (81).…”

Section: Postranslational Regulation Of Cbbr Function: the Role Of Efmentioning

confidence: 99%

CbbR, the Master Regulator for Microbial Carbon Dioxide Fixation

Dangel

Tabita

2015

J Bacteriol

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Biological carbon dioxide fixation is an essential and crucial process catalyzed by both prokaryotic and eukaryotic organisms to allow ubiquitous atmospheric CO 2 to be reduced to usable forms of organic carbon. This process, especially the CalvinBassham-Benson (CBB) pathway of CO 2 fixation, provides the bulk of organic carbon found on earth. The enzyme ribulose 1,5-bisphosphate (RuBP) carboxylase/oxygenase (RubisCO) performs the key and rate-limiting step whereby CO 2 is reduced and incorporated into a precursor organic metabolite. This is a highly regulated process in diverse organisms, with the expression of genes that comprise the CBB pathway (the cbb genes), including RubisCO, specifically controlled by the master transcriptional regulator protein CbbR. Many organisms have two or more cbb operons that either are regulated by a single CbbR or employ a specific CbbR for each cbb operon. CbbR family members are versatile and accommodate and bind many different effector metabolites that influence CbbR's ability to control cbb transcription. Moreover, two members of the CbbR family are further posttranslationally modified via interactions with other transcriptional regulator proteins from two-component regulatory systems, thus augmenting CbbR-dependent control and optimizing expression of specific cbb operons. In addition to interactions with small effector metabolites and other regulator proteins, CbbR proteins may be selected that are constitutively active and, in some instances, elevate the level of cbb expression relative to wild-type CbbR. Optimizing CbbR-dependent control is an important consideration for potentially using microbes to convert CO 2 to useful bioproducts.

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“…While most LTTRs are thought to function as tetramers (54), only the LTTR CbnR crystallized as a tetramer (42); the other LTTR crystal structures all formed asymmetric dimers (40,41,57,(60)(61)(62)(63). Differences in oligomerization states may be due to differences in crystallization conditions or the absence of DNA-binding domains in some of the crystallized LTTRs (58). Sequence similarity between proposed LTTR oligomerization domains is low (58), suggesting that multiple weak interactions at relatively small interfaces contribute to oligomerization, rather than specific amino acid interactions (57).…”

Section: Discussionmentioning

confidence: 99%

“…We took advantage of the fact that crystal structures are highly conserved among LTTRs despite Ͻ20% overall sequence identity. Each monomer consists of a wHTH DBD, linker helix (LH), and two ␣/␤ domains, termed regulatory domain I (RD I) and regulatory domain II (RD II), enclosing a cavity postulated to be the effector binding domain (EBD) based on cocrystallization with effector molecules and on LTTR mutant studies (40,42,43,(57)(58)(59)(60)(61)(62). LTTRs can make either symmetric or asymmetric dimers.…”

Section: Screen For Nodd1 Alleles Showing Altered Responses To Luteolinmentioning

confidence: 99%

Isolation and Characterization of Mutant Sinorhizobium meliloti NodD1 Proteins with Altered Responses to Luteolin

et al. 2013

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c NodD1, a member of the NodD family of LysR-type transcriptional regulators (LTTRs), mediates nodulation (nod) gene expression in the soil bacterium Sinorhizobium meliloti in response to the plant-secreted flavonoid luteolin. We used genetic screens and targeted approaches to identify NodD1 residues that show altered responses to luteolin during the activation of nod gene transcription. Here we report four types of NodD1 mutants. Type I (NodD1 L69F, S104L, D134N, and M193I mutants) displays reduced or no activation of nod gene expression. Type II (NodD1 K205N) is constitutively active but repressed by luteolin. Type III (NodD1 L280F) demonstrates enhanced activity with luteolin compared to that of wild-type NodD1. Type IV (NodD1 D284N) shows moderate constitutive activity yet can still be induced by luteolin. In the absence of luteolin, many mutants display a low binding affinity for nod gene promoter DNA in vitro. Several mutants also show, as does wild-type NodD1, increased affinity for nod gene promoters with added luteolin. All of the NodD1 mutant proteins can homodimerize and heterodimerize with wild-type NodD1. Based on these data and the crystal structures of several LTTRs, we present a structural model of wildtype NodD1, identifying residues important for inducer binding, protein multimerization, and interaction with RNA polymerase at nod gene promoters.

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Distinct Effector-binding Sites Enable Synergistic Transcriptional Activation by BenM, a LysR-type Regulator

Cited by 93 publications

References 43 publications

Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins

Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins

CbbR, the Master Regulator for Microbial Carbon Dioxide Fixation

Isolation and Characterization of Mutant Sinorhizobium meliloti NodD1 Proteins with Altered Responses to Luteolin

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