Mapping the
            <i>Sinorhizobium meliloti</i>
            1021 solute-binding protein-dependent transportome

Mauchline, Tim H.; Fowler, Jane E.; East, Alison K.; Sartor, Andrea L.; Zaheer, Rahat; Hosie, Arthur H.F.; Poole, Philip S.; Finan, Turlough M.

doi:10.1073/pnas.0606673103

Cited by 137 publications

(159 citation statements)

References 51 publications

Supporting

Mentioning

147

Contrasting

Unclassified

Order By: Relevance

“…One of the sites is located upstream of pcaD and corresponds to the binding site characterized in this study. The second site is located upstream of an ABC-type transport system whose expression is induced by protocatechuate (24). It seems likely that this transport system is dedicated to the uptake of protocatechuate, and we are pursuing studies to determine whether this system in fact transports protocatechuate and whether expression of this system is regulated by PcaQ.…”

Section: Discussionmentioning

confidence: 99%

Binding Site Determinants for the LysR-Type Transcriptional Regulator PcaQ in the Legume Endosymbiont Sinorhizobium meliloti

2008

View full text Add to dashboard Cite

LysR-type transcriptional regulators represent one of the largest groups of prokaryotic regulators described to date. In the gram-negative legume endosymbiont Sinorhizobium meliloti, enzymes involved in the protocatechuate branch of the ␤-ketoadipate pathway are encoded within the pcaDCHGB operon, which is subject to regulation by the LysR-type protein PcaQ. In this work, purified PcaQ was shown to bind strongly (equilibrium dissociation constant, 0.54 nM) to a region at positions ؊78 to ؊45 upstream of the pcaD transcriptional start site. Within this region, we defined a PcaQ binding site with dyad symmetry that is required for regulation of pcaD expression in vivo and for binding of PcaQ in vitro. We also demonstrated that PcaQ participates in negative autoregulation by monitoring expression of pcaQ via a transcriptional fusion to lacZ. Although pcaQ homologues are present in many ␣-proteobacteria, this work describes the first reported purification of this regulator, as well as characterization of its binding site, which is conserved in Agrobacterium tumefaciens, Rhizobium leguminosarum, Rhizobium etli, and Mesorhizobium loti.In a soil environment, plant-derived aromatic acids represent significant carbon and energy sources. The first step in the metabolism of these compounds involves their conversion into either protocatechuate or catechol, which is subsequently metabolized to tricarboxylic acid intermediates via the ␤-ketoadipate pathway (18). This metabolic pathway has been documented in many members of the family Rhizobiaceae (23,35,(38)(39)(40), suggesting that the ␤-ketoadipate pathway is important for the survival of these soil-dwelling microorganisms.Sinorhizobium meliloti is a gram-negative, soil-dwelling bacterium that participates in a symbiotic relationship with the legume alfalfa through the establishment of nitrogen-fixing root nodules. Enzymes involved in the protocatechuate branch of the ␤-ketoadipate pathway in S. meliloti are encoded within the pcaDCHGB and pcaIJF operons, which are subject to regulation by products encoded by pcaQ and pcaR, respectively (23). The regulator encoded by pcaQ is a member of the LysR-type transcriptional regulator (LTTR) superfamily, and PcaQ homologues are present in many species of ␣-proteobacteria (3,4,7,23,34,36,37).LysR-type regulators comprise one of the largest groups of prokaryotic transcriptional regulators characterized to date; these proteins regulate a diverse range of regulons, including genes whose products are involved in nitrogen and carbon fixation, biofilm formation, the oxidative stress response, bacterial virulence, and the catabolism of various compounds, including aromatic acids (10,16,19,22,23,28,34,46,47,51,55,57). LTTR proteins consist of a conserved helix-turn-helix DNA binding motif located in the N-terminal portion of the polypeptide, whereas the C terminus includes an inducer binding site. As a general rule, LTTRs act as transcriptional activators by inducing expression of a target gene(s) upon interaction with a coeffector molecule,...

show abstract

Section: Discussionmentioning

confidence: 99%

Binding Site Determinants for the LysR-Type Transcriptional Regulator PcaQ in the Legume Endosymbiont Sinorhizobium meliloti

2008

View full text Add to dashboard Cite

show abstract

“…The recent completion of genome-sequencing projects in several rhizobial and bradyrhizobial species enables us to analyze global postgenomic approaches to bacteria, including the analysis of transcriptomes, systematic mutant libraries, ORFeomes, proteomes, transportomes (Mauchline et al, 2006) and metabolomes, toward the further development of functional genomics (MacLean et al, 2007). In this study, we aimed to reveal bradyrhizobial genomic regions relevant to symbiotic nitrogen fixation by using statistical model analysis to correlate variable genomic regions with symbiotic phenotypes of the host plants.…”

Section: Discussionmentioning

confidence: 99%

Genomic comparison of Bradyrhizobium japonicum strains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members

et al. 2008

View full text Add to dashboard Cite

Comparative genomic hybridization (CGH) was performed with nine strains of Bradyrhizobium japonicum (a symbiotic nitrogen-fixing bacterium associated with soybean) and eight other members of the Bradyrhizobiaceae by DNA macroarray of B. japonicum USDA110. CGH clearly discriminated genomic variations in B. japonicum strains, but similar CGH patterns were observed in other members of the Bradyrhizobiaceae. The most variable regions were 14 genomic islands (4-97 kb) and low G þ C regions on the USDA110 genome, some of which were missing in several strains of B. japonicum and other members of the Bradyrhizobiaceae. The CGH profiles of B. japonicum were classified into three genome types: 110, 122 and 6. Analysis of DNA sequences around the boundary regions showed that at least seven genomic islands were missing in genome type 122 as compared with type 110. Phylogenetic analysis for internal transcribed sequences revealed that strains belonging to genome types 110 and 122 formed separate clades. Thus genomic islands were horizontally inserted into the ancestor genome of type 110 after divergence of the type 110 and 122 strains. To search for functional relationships of variable genomic islands, we conducted linear models of the correlation between the existence of genomic regions and the parameters associated with symbiotic nitrogen fixation in soybean. Variable genomic regions including genomic islands were associated with the enhancement of symbiotic nitrogen fixation in B. japonicum USDA110.

show abstract

“…Furthermore, we identified putative PcaQ DNA-binding sites located upstream of genes encoding ABC-type transport systems in 10 members of the a-proteobacteria, including S. meliloti. Expression of one of these ABC-type transport systems (encoded by smb20568-smb20784 in S. meliloti) has previously been shown to be upregulated by growth with protocatechuate (Mauchline et al, 2006). As we show herein that the smb20568-smb20784 gene cluster is required for growth with protocatechuate, we designate these genes pcaMNVWX.…”

Section: Prediction Of Putative Pcaq-binding Sites In Proteobacteriamentioning

confidence: 99%

The LysR-type PcaQ protein regulates expression of a protocatechuate-inducible ABC-type transport system in Sinorhizobium meliloti

et al. 2011

View full text Add to dashboard Cite

The LysR protein PcaQ regulates the expression of genes encoding products relevant to the degradation of the aromatic acid protocatechuate (3,4-dihydroxybenzoate), and we have previously defined a PcaQ DNA-binding site located upstream of the target pcaDCHGB operon in Sinorhizobium meliloti. In this work, we show that PcaQ also regulates the expression of the S. meliloti smb20568-smb20787-smb20786-smb20785-smb20784 gene cluster, which is predicted to encode an ABC transport system. ABC transport systems have not been shown before to transport protocatechuate, and we have designated this gene cluster pcaMNVWX. The transcriptional start site of pcaM was mapped, and the predicted PcaQ DNA-binding site was located at −73 to −58 relative to this site. Results from electrophoretic mobility shift assays with purified PcaQ and from expression assays indicated that PcaQ activates expression of the transport system in the presence of protocatechuate. To investigate this transport system further, we generated a pcaM deletion mutant (predicted to encode the substrate-binding protein) and introduced a polar insertion mutation into pcaN, a gene that is predicted to encode a permease. These mutants grew poorly on protocatechuate, presumably because they fail to transport protocatechuate. Genome analyses revealed PcaQ-like DNA-binding sites encoded upstream of ABC transport systems in other members of the α-proteobacteria, and thus it appears likely that these systems are involved in the uptake of protocatechuate.

show abstract

Mapping the Sinorhizobium meliloti 1021 solute-binding protein-dependent transportome

Cited by 137 publications

References 51 publications

Binding Site Determinants for the LysR-Type Transcriptional Regulator PcaQ in the Legume Endosymbiont Sinorhizobium meliloti

Binding Site Determinants for the LysR-Type Transcriptional Regulator PcaQ in the Legume Endosymbiont Sinorhizobium meliloti

Genomic comparison of Bradyrhizobium japonicum strains with different symbiotic nitrogen-fixing capabilities and other Bradyrhizobiaceae members

The LysR-type PcaQ protein regulates expression of a protocatechuate-inducible ABC-type transport system in Sinorhizobium meliloti

Contact Info

Product

Resources

About