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Meger AT, Spence MA, Sandhu M, Matthews D, Chen J, Jackson CJ, Raman S. Rugged fitness landscapes minimize promiscuity in the evolution of transcriptional repressors. Cell Syst 2024; 15:374-387.e6. [PMID: 38537640 DOI: 10.1016/j.cels.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 09/08/2023] [Accepted: 03/05/2024] [Indexed: 04/20/2024]
Abstract
How a protein's function influences the shape of its fitness landscape, smooth or rugged, is a fundamental question in evolutionary biochemistry. Smooth landscapes arise when incremental mutational steps lead to a progressive change in function, as commonly seen in enzymes and binding proteins. On the other hand, rugged landscapes are poorly understood because of the inherent unpredictability of how sequence changes affect function. Here, we experimentally characterize the entire sequence phylogeny, comprising 1,158 extant and ancestral sequences, of the DNA-binding domain (DBD) of the LacI/GalR transcriptional repressor family. Our analysis revealed an extremely rugged landscape with rapid switching of specificity, even between adjacent nodes. Further, the ruggedness arises due to the necessity of the repressor to simultaneously evolve specificity for asymmetric operators and disfavors potentially adverse regulatory crosstalk. Our study provides fundamental insight into evolutionary, molecular, and biophysical rules of genetic regulation through the lens of fitness landscapes.
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Affiliation(s)
- Anthony T Meger
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Matthew A Spence
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Mahakaran Sandhu
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Dana Matthews
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Jackie Chen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia; ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia; ARC Centre of Excellence for Innovations in Synthetic Biology, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
| | - Srivatsan Raman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Tsevelkhoroloo M, Shim SH, Lee CR, Hong SK, Hong YS. LacI-Family Transcriptional Regulator DagR Acts as a Repressor of the Agarolytic Pathway Genes in Streptomyces coelicolor A3(2). Front Microbiol 2021; 12:658657. [PMID: 33889146 PMCID: PMC8055832 DOI: 10.3389/fmicb.2021.658657] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/08/2021] [Indexed: 11/15/2022] Open
Abstract
Actinobacteria utilize various polysaccharides in the soil as carbon source by degrading them via extracellular hydrolytic enzymes. Agarose, a marine algal polysaccharide composed of D-galactose and 3,6-anhydro-L-galactose (AHG), is one of the carbon sources used by S. coelicolor A3(2). However, little is known about agar hydrolysis in S. coelicolor A3(2), except that the regulation of agar hydrolysis metabolism is strongly inhibited by glucose as in the catabolic pathways of other polysaccharides. In this study, we elucidated the role of DagR in regulating the expression of three agarase genes (dagA, dagB, and dagC) in S. coelicolor A3(2) by developing a dagR-deletion mutant (Δsco3485). We observed that the Δsco3485 mutant had increased mRNA level of the agarolytic pathway genes and 1.3-folds higher agarase production than the wild type strain, indicating that the dagR gene encodes a cluster-suited repressor. Electrophoretic mobility shift assay revealed that DagR bound to the upstream regions of the three agarase genes. DNase 1 footprinting analysis demonstrated that a palindromic sequence present in the upstream region of the three agarase genes was essential for DagR-binding. Uniquely, the DNA-binding activity of DagR was inhibited by AHG, one of the final degradation products of agarose. AHG-induced agarase production was not observed in the Δsco3485 mutant, as opposed to that in the wild type strain. Therefore, DagR acts as a repressor that binds to the promoter region of the agarase genes, inhibits gene expression at the transcriptional level, and is derepressed by AHG. This is the first report on the regulation of gene expression regarding agar metabolism in S. coelicolor A3(2).
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Affiliation(s)
- Maral Tsevelkhoroloo
- Department of Bioscience and Bioinformatics, Myong-Ji University, Yongin-si, South Korea
| | - So Heon Shim
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju-si, South Korea
| | - Chang-Ro Lee
- Department of Bioscience and Bioinformatics, Myong-Ji University, Yongin-si, South Korea
| | - Soon-Kwang Hong
- Department of Bioscience and Bioinformatics, Myong-Ji University, Yongin-si, South Korea
| | - Young-Soo Hong
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju-si, South Korea
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The relation between crosstalk and gene regulation form revisited. PLoS Comput Biol 2020; 16:e1007642. [PMID: 32097416 PMCID: PMC7059967 DOI: 10.1371/journal.pcbi.1007642] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 03/06/2020] [Accepted: 01/08/2020] [Indexed: 01/11/2023] Open
Abstract
Genes differ in the frequency at which they are expressed and in the form of regulation used to control their activity. In particular, positive or negative regulation can lead to activation of a gene in response to an external signal. Previous works proposed that the form of regulation of a gene correlates with its frequency of usage: positive regulation when the gene is frequently expressed and negative regulation when infrequently expressed. Such network design means that, in the absence of their regulators, the genes are found in their least required activity state, hence regulatory intervention is often necessary. Due to the multitude of genes and regulators, spurious binding and unbinding events, called “crosstalk”, could occur. To determine how the form of regulation affects the global crosstalk in the network, we used a mathematical model that includes multiple regulators and multiple target genes. We found that crosstalk depends non-monotonically on the availability of regulators. Our analysis showed that excess use of regulation entailed by the formerly suggested network design caused high crosstalk levels in a large part of the parameter space. We therefore considered the opposite ‘idle’ design, where the default unregulated state of genes is their frequently required activity state. We found, that ‘idle’ design minimized the use of regulation and thus minimized crosstalk. In addition, we estimated global crosstalk of S. cerevisiae using transcription factors binding data. We demonstrated that even partial network data could suffice to estimate its global crosstalk, suggesting its applicability to additional organisms. We found that S. cerevisiae estimated crosstalk is lower than that of a random network, suggesting that natural selection reduces crosstalk. In summary, our study highlights a new type of protein production cost which is typically overlooked: that of regulatory interference caused by the presence of excess regulators in the cell. It demonstrates the importance of whole-network descriptions, which could show effects missed by single-gene models. Genes differ in the frequency at which they are expressed and in the form of regulation used to control their activity. The basic level of regulation is mediated by different types of DNA-binding proteins, where each type regulates particular gene(s). We distinguish between two basic forms of regulation: positive—if a gene is activated by the binding of its regulatory protein, and negative—if it is active unless bound by its regulatory protein. Due to the multitude of genes and regulators, spurious binding and unbinding events, called “crosstalk”, could occur. How does the form of regulation, positive or negative, affect the extent of regulatory crosstalk? To address this question, we used a mathematical model integrating many genes and many regulators. As intuition suggests, we found that in most of the parameter space, crosstalk increased with the availability of regulators. We propose, that crosstalk is usually reduced when networks are designed such that minimal regulation is needed, which we call the ‘idle’ design. In other words: a frequently needed gene will use negative regulation and conversely, a scarcely needed gene will employ positive regulation. In both cases, the requirement for the regulators is minimized. In addition, we demonstrate how crosstalk can be calculated from available datasets and discuss the technical challenges in such calculation, specifically data incompleteness.
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Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nat Commun 2017; 8:216. [PMID: 28790313 PMCID: PMC5548793 DOI: 10.1038/s41467-017-00238-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 06/13/2017] [Indexed: 12/12/2022] Open
Abstract
Gene expression is controlled by networks of regulatory proteins that interact specifically with external signals and DNA regulatory sequences. These interactions force the network components to co-evolve so as to continually maintain function. Yet, existing models of evolution mostly focus on isolated genetic elements. In contrast, we study the essential process by which regulatory networks grow: the duplication and subsequent specialization of network components. We synthesize a biophysical model of molecular interactions with the evolutionary framework to find the conditions and pathways by which new regulatory functions emerge. We show that specialization of new network components is usually slow, but can be drastically accelerated in the presence of regulatory crosstalk and mutations that promote promiscuous interactions between network components.Gene networks evolve by transcription factor (TF) duplication and divergence of their binding site specificities, but little is known about the global constraints at play. Here, the authors study the coevolution of TFs and binding sites using a biophysical-evolutionary approach, and show that the emerging complex fitness landscapes strongly influence regulatory evolution with a role for crosstalk.
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Affiliation(s)
- Tamar Friedlander
- Institute of Science and Technology Austria, Am Campus 1, A-3400, Klosterneuburg, Austria.,The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture Hebrew University of Jerusalem, P.O. Box 12, Rehovot, 7610001, Israel
| | - Roshan Prizak
- Institute of Science and Technology Austria, Am Campus 1, A-3400, Klosterneuburg, Austria
| | - Nicholas H Barton
- Institute of Science and Technology Austria, Am Campus 1, A-3400, Klosterneuburg, Austria
| | - Gašper Tkačik
- Institute of Science and Technology Austria, Am Campus 1, A-3400, Klosterneuburg, Austria.
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Pieta L, Escudero FLG, Jacobus AP, Cheiran KP, Gross J, Moya MLE, Soares GLG, Margis R, Frazzon APG, Frazzon J. Comparative transcriptomic analysis of Listeria monocytogenes reveals upregulation of stress genes and downregulation of virulence genes in response to essential oil extracted from Baccharis psiadioides. ANN MICROBIOL 2017. [DOI: 10.1007/s13213-017-1277-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Liu S, Guo C, Dang Z, Liang X. Comparative proteomics reveal the mechanism of Tween80 enhanced phenanthrene biodegradation by Sphingomonas sp. GY2B. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 137:256-264. [PMID: 27984820 DOI: 10.1016/j.ecoenv.2016.12.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 12/04/2016] [Accepted: 12/09/2016] [Indexed: 05/22/2023]
Abstract
Previous study concerning the effects of surfactants on phenanthrene biodegradation focused on observing the changes of cell characteristics of Sphingomonas sp. GY2B. However, the impact of surfactants on the expression of bacterial proteins, controlling phenanthrene transport and catabolism, remains obscure. To overcome the knowledge gap, comparative proteomic approaches were used to investigate protein expressions of Sphingomonas sp. GY2B during phenanthrene biodegradation in the presence and absence of a nonionic surfactant, Tween80. A total of 23 up-regulated and 19 down-regulated proteins were detected upon Tween80 treatment. Tween80 could regulate ion transport (e.g. H+) in cell membrane to provide driving force (ATP) for the transmembrane transport of phenanthrene thus increasing its uptake and biodegradation by GY2B. Moreover, Tween80 probably increased GY2B vitality and growth by inducing the expression of peptidylprolyl isomerase to stabilize cell membrane, increasing the abundances of proteins involved in intracellular metabolic pathways (e.g. TCA cycle), as well as decreasing the abundances of translation/transcription-related proteins and cysteine desulfurase, thereby facilitating phenanthrene biodegradation. This study may facilitate a better understanding of the mechanisms that regulate surfactants-enhanced biodegradation of PAHs at the proteomic level.
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Affiliation(s)
- Shasha Liu
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
| | - Chuling Guo
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou 510006, PR China.
| | - Zhi Dang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, Guangzhou 510006, PR China.
| | - Xujun Liang
- School of Environment and Energy, South China University of Technology, Guangzhou 510006, PR China
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7
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Abstract
Epistatic interactions can frustrate and shape evolutionary change. Indeed, phenotypes may fail to evolve when essential mutations are only accessible through positive selection if they are fixed simultaneously. How environmental variability affects such constraints is poorly understood. Here, we studied genetic constraints in fixed and fluctuating environments using the Escherichia coli lac operon as a model system for genotype-environment interactions. We found that, in different fixed environments, all trajectories that were reconstructed by applying point mutations within the transcription factor-operator interface became trapped at suboptima, where no additional improvements were possible. Paradoxically, repeated switching between these same environments allows unconstrained adaptation by continuous improvements. This evolutionary mode is explained by pervasive cross-environmental tradeoffs that reposition the peaks in such a way that trapped genotypes can repeatedly climb ascending slopes and hence, escape adaptive stasis. Using a Markov approach, we developed a mathematical framework to quantify the landscape-crossing rates and show that this ratchet-like adaptive mechanism is robust in a wide spectrum of fluctuating environments. Overall, this study shows that genetic constraints can be overcome by environmental change and that cross-environmental tradeoffs do not necessarily impede but also, can facilitate adaptive evolution. Because tradeoffs and environmental variability are ubiquitous in nature, we speculate this evolutionary mode to be of general relevance.
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Afzal M, Shafeeq S, Manzoor I, Kuipers OP. GalR Acts as a Transcriptional Activator of galKT in the Presence of Galactose in Streptococcus pneumoniae. J Mol Microbiol Biotechnol 2015; 25:363-71. [PMID: 26544195 DOI: 10.1159/000439429] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We explored the regulatory mechanism of Leloir pathway genes in Streptococcus pneumoniae D39. Here, we demonstrate that the expression of galKT is galactose dependent. By microarray analysis and quantitative RT-PCR, we further show the role of the transcriptional regulator GalR, present upstream of galKT, as a transcriptional activator of galKT in the presence of galactose. Moreover, we predict a 19-bp regulatory site (5'-GATAGTTTAGTAAAATTTT-3') for the transcriptional regulator GalR in the promoter region of galK, which is also highly conserved in other streptococci. Growth comparison of D39 ΔgalK with the D39 wild type grown in the presence of galactose shows that galK is required for the proper growth of S. pneumoniae on galactose.
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Affiliation(s)
- Muhammad Afzal
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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9
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Afzal M, Shafeeq S, Manzoor I, Kuipers OP. Maltose-Dependent Transcriptional Regulation of the mal Regulon by MalR in Streptococcus pneumoniae. PLoS One 2015; 10:e0127579. [PMID: 26030923 PMCID: PMC4451989 DOI: 10.1371/journal.pone.0127579] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 04/16/2015] [Indexed: 12/25/2022] Open
Abstract
The maltose regulon (mal regulon) has previously been shown to consist of the mal gene cluster (malMP, malXCD and malAR operons) in Streptococcus pneumoniae. In this study, we have further elucidated the complete mal regulon in S. pneumoniae D39 using microarray analyses and β-galactosidase assays. In addition to the mal gene cluster, the complete mal regulon of S. pneumoniae D39 consists of a pullulanase (PulA), a glucosidase (DexB), a glucokinase (RokB), a PTS component (PtsG) and an amylase (AmyA2). Our microarray studies and β-galactosidase assays further showed that the LacI-family transcriptional regulator MalR represses the expression of the mal regulon in the absence of maltose. Furthermore, the role of the pleiotropic transcriptional regulator CcpA in the regulation of the mal regulon in the presence of maltose was explored. Our microarray analysis with a ΔccpA strain showed that CcpA only represses the expression of the malXCD operon and the pulA gene in the presence of maltose. Hence, we extend the mal regulon now consisting of pulA, dexB, rokB, ptsG and amyA2 in addition to malMP, malXCD and malAR operons.
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Affiliation(s)
- Muhammad Afzal
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Sulman Shafeeq
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Nobels väg 16, 17177, Stockholm, Sweden
| | - Irfan Manzoor
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Oscar P. Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
- * E-mail:
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Vujanac M, Iyer VS, Sengupta M, Ajdic D. Regulation of Streptococcus mutans PTS Bio by the transcriptional repressor NigR. Mol Oral Microbiol 2015; 30:280-94. [PMID: 25580872 DOI: 10.1111/omi.12093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2014] [Indexed: 11/29/2022]
Abstract
Streptococcus mutans is implicated in human dental caries, and the carbohydrate metabolism of this organism plays an important role in the formation of this disease. Carbohydrate transport and metabolism are essential for the survival of S. mutans in the oral cavity. It is known that a unique phosphoenolpyruvate-sugar phosphotransferase system PTS(B) (io) of S. mutans UA159 is expressed in sucrose-grown biofilms (Mol Oral Microbiol 28: 2013; 114). In this study we analyzed the transcriptional regulation of the operon (O(B) (io) ) encoding the PTS(B) (io) and showed that it was repressed by NigR, a LacI-like transcriptional regulator. Using electro-mobility shift assay, we described two operators to which NigR bound with different affinities. We also identified the transcriptional start site and showed that one of the operators overlaps with the promoter and presumably represses initiation of transcription. Mutational analyses revealed the key nucleotides in the operators required for high-affinity binding of NigR. PTS(B) (io) is expressed in S. mutans biofilms so understanding its regulation may provide improved strategies for caries treatment and prevention.
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Affiliation(s)
- M Vujanac
- Miller School of Medicine, University of Miami, Miami, FL, USA
| | - V S Iyer
- Miller School of Medicine, University of Miami, Miami, FL, USA
| | - M Sengupta
- Miller School of Medicine, University of Miami, Miami, FL, USA
| | - D Ajdic
- Miller School of Medicine, University of Miami, Miami, FL, USA
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Peroza EA, Ewald JC, Parakkal G, Skotheim JM, Zamboni N. A genetically encoded Förster resonance energy transfer sensor for monitoring in vivo trehalose-6-phosphate dynamics. Anal Biochem 2015; 474:1-7. [PMID: 25582303 DOI: 10.1016/j.ab.2014.12.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 12/22/2014] [Accepted: 12/29/2014] [Indexed: 11/18/2022]
Abstract
Trehalose-6-phosphate is a pivotal regulator of sugar metabolism, growth, and osmotic equilibrium in bacteria, yeasts, and plants. To directly visualize the intracellular levels of intracellular trehalose-6-phosphate, we developed a series of specific Förster resonance energy transfer (FRET) sensors for in vivo microscopy. We demonstrated real-time monitoring of regulation in the trehalose pathway of Escherichia coli. In Saccharomyces cerevisiae, we could show that the concentration of free trehalose-6-phosphate during growth on glucose is in a range sufficient for inhibition of hexokinase. These findings support the hypothesis of trehalose-6-phosphate as the effector of a negative feedback system, similar to the inhibition of hexokinase by glucose-6-phosphate in mammalian cells and controlling glycolytic flux.
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Affiliation(s)
- Estevão A Peroza
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Jennifer C Ewald
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Geetha Parakkal
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Nicola Zamboni
- Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
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Ravcheev DA, Khoroshkin MS, Laikova ON, Tsoy OV, Sernova NV, Petrova SA, Rakhmaninova AB, Novichkov PS, Gelfand MS, Rodionov DA. Comparative genomics and evolution of regulons of the LacI-family transcription factors. Front Microbiol 2014; 5:294. [PMID: 24966856 PMCID: PMC4052901 DOI: 10.3389/fmicb.2014.00294] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Accepted: 05/28/2014] [Indexed: 12/31/2022] Open
Abstract
DNA-binding transcription factors (TFs) are essential components of transcriptional regulatory networks in bacteria. LacI-family TFs (LacI-TFs) are broadly distributed among certain lineages of bacteria. The majority of characterized LacI-TFs sense sugar effectors and regulate carbohydrate utilization genes. The comparative genomics approaches enable in silico identification of TF-binding sites and regulon reconstruction. To study the function and evolution of LacI-TFs, we performed genomics-based reconstruction and comparative analysis of their regulons. For over 1300 LacI-TFs from over 270 bacterial genomes, we predicted their cognate DNA-binding motifs and identified target genes. Using the genome context and metabolic subsystem analyses of reconstructed regulons, we tentatively assigned functional roles and predicted candidate effectors for 78 and 67% of the analyzed LacI-TFs, respectively. Nearly 90% of the studied LacI-TFs are local regulators of sugar utilization pathways, whereas the remaining 125 global regulators control large and diverse sets of metabolic genes. The global LacI-TFs include the previously known regulators CcpA in Firmicutes, FruR in Enterobacteria, and PurR in Gammaproteobacteria, as well as the three novel regulators—GluR, GapR, and PckR—that are predicted to control the central carbohydrate metabolism in three lineages of Alphaproteobacteria. Phylogenetic analysis of regulators combined with the reconstructed regulons provides a model of evolutionary diversification of the LacI protein family. The obtained genomic collection of in silico reconstructed LacI-TF regulons in bacteria is available in the RegPrecise database (http://regprecise.lbl.gov). It provides a framework for future structural and functional classification of the LacI protein family and identification of molecular determinants of the DNA and ligand specificity. The inferred regulons can be also used for functional gene annotation and reconstruction of sugar catabolic networks in diverse bacterial lineages.
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Affiliation(s)
- Dmitry A Ravcheev
- Research Scientific Center for Bioinformatics, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia
| | - Matvei S Khoroshkin
- Research Scientific Center for Bioinformatics, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia
| | - Olga N Laikova
- Research Scientific Center for Bioinformatics, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia
| | - Olga V Tsoy
- Research Scientific Center for Bioinformatics, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia ; Faculty of Bioengineering and Bioinformatics, Moscow State University Moscow, Russia
| | - Natalia V Sernova
- Research Scientific Center for Bioinformatics, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia
| | - Svetlana A Petrova
- Research Scientific Center for Bioinformatics, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia ; Faculty of Bioengineering and Bioinformatics, Moscow State University Moscow, Russia
| | | | - Pavel S Novichkov
- Lawrence Berkeley National Laboratory, Genomics Division Berkeley, CA, USA
| | - Mikhail S Gelfand
- Research Scientific Center for Bioinformatics, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia
| | - Dmitry A Rodionov
- Research Scientific Center for Bioinformatics, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences Moscow, Russia ; Department of Bioinformatics, Sanford-Burnham Medical Research Institute La Jolla, CA, USA
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Small-molecule inhibitor of the Shigella flexneri master virulence regulator VirF. Infect Immun 2013; 81:4220-31. [PMID: 24002059 DOI: 10.1128/iai.00919-13] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
VirF is an AraC family transcriptional activator that is required for the expression of virulence genes associated with invasion and cell-to-cell spread by Shigella flexneri, including multiple components of the type three secretion system (T3SS) machinery and effectors. We tested a small-molecule compound, SE-1 (formerly designated OSSL_051168), which we had identified as an effective inhibitor of the AraC family proteins RhaS and RhaR, for its ability to inhibit VirF. Cell-based reporter gene assays with Escherichia coli and Shigella, as well as in vitro DNA binding assays with purified VirF, demonstrated that SE-1 inhibited DNA binding and transcription activation (likely by blocking DNA binding) by VirF. Analysis of mRNA levels using real-time quantitative reverse transcription-PCR (qRT-PCR) further demonstrated that SE-1 reduced the expression of the VirF-dependent virulence genes icsA, virB, icsB, and ipaB in Shigella. We also performed eukaryotic cell invasion assays and found that SE-1 reduced invasion by Shigella. The effect of SE-1 on invasion required preincubation of Shigella with SE-1, in agreement with the hypothesis that SE-1 inhibited the expression of VirF-activated genes required for the formation of the T3SS apparatus and invasion. We found that the same concentrations of SE-1 had no detectable effects on the growth or metabolism of the bacterial cells or the eukaryotic host cells, respectively, indicating that the inhibition of invasion was not due to general toxicity. Overall, SE-1 appears to inhibit transcription activation by VirF, exhibits selectivity toward AraC family proteins, and has the potential to be developed into a novel antibacterial agent.
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14
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Sullivan JT, Brown SD, Ronson CW. The NifA-RpoN regulon of Mesorhizobium loti strain R7A and its symbiotic activation by a novel LacI/GalR-family regulator. PLoS One 2013; 8:e53762. [PMID: 23308282 PMCID: PMC3538637 DOI: 10.1371/journal.pone.0053762] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 12/04/2012] [Indexed: 11/19/2022] Open
Abstract
Mesorhizobium loti is the microsymbiont of Lotus species, including the model legume L. japonicus. M. loti differs from other rhizobia in that it contains two copies of the key nitrogen fixation regulatory gene nifA, nifA1 and nifA2, both of which are located on the symbiosis island ICEMlSym(R7A). M. loti R7A also contains two rpoN genes, rpoN1 located on the chromosome outside of ICEMlSym(R7A) and rpoN2 that is located on ICEMlSym(R7A). The aims of the current work were to establish how nifA expression was activated in M. loti and to characterise the NifA-RpoN regulon. The nifA2 and rpoN2 genes were essential for nitrogen fixation whereas nifA1 and rpoN1 were dispensable. Expression of nifA2 was activated, possibly in response to an inositol derivative, by a novel regulator of the LacI/GalR family encoded by the fixV gene located upstream of nifA2. Other than the well-characterized nif/fix genes, most NifA2-regulated genes were not required for nitrogen fixation although they were strongly expressed in nodules. The NifA-regulated nifZ and fixU genes, along with nifQ which was not NifA-regulated, were required in M. loti for a fully effective symbiosis although they are not present in some other rhizobia. The NifA-regulated gene msi158 that encodes a porin was also required for a fully effective symbiosis. Several metabolic genes that lacked NifA-regulated promoters were strongly expressed in nodules in a NifA2-dependent manner but again mutants did not have an overt symbiotic phenotype. In summary, many genes encoded on ICEMlSym(R7A) were strongly expressed in nodules but not free-living rhizobia, but were not essential for symbiotic nitrogen fixation. It seems likely that some of these genes have functional homologues elsewhere in the genome and that bacteroid metabolism may be sufficiently plastic to adapt to loss of certain enzymatic functions.
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Affiliation(s)
- John T. Sullivan
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Steven D. Brown
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Clive W. Ronson
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- * E-mail:
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15
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Transcription factor family-based reconstruction of singleton regulons and study of the Crp/Fnr, ArsR, and GntR families in Desulfovibrionales genomes. J Bacteriol 2012; 195:29-38. [PMID: 23086211 DOI: 10.1128/jb.01977-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Accurate detection of transcriptional regulatory elements is essential for high-quality genome annotation, metabolic reconstruction, and modeling of regulatory networks. We developed a computational approach for reconstruction of regulons operated by transcription factors (TFs) from large protein families and applied this novel approach to three TF families in 10 Desulfovibrionales genomes. Phylogenetic analyses of 125 regulators from the ArsR, Crp/Fnr, and GntR families revealed that 65% of these regulators (termed reference TFs) are well conserved in Desulfovibrionales, while the remaining 35% of regulators (termed singleton TFs) are species specific and show a mosaic distribution. For regulon reconstruction in the group of singleton TFs, the standard orthology-based approach was inefficient, and thus, we developed a novel approach based on the simultaneous study of all homologous TFs from the same family in a group of genomes. As a result, we identified binding for 21 singleton TFs and for all reference TFs in all three analyzed families. Within each TF family we observed structural similarities between DNA-binding motifs of different reference and singleton TFs. The collection of reconstructed regulons is available at the RegPrecise database (http://regprecise.lbl.gov/RegPrecise/Desulfovibrionales.jsp).
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16
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Functional analysis of family GH36 α-galactosidases from Ruminococcus gnavus E1: insights into the metabolism of a plant oligosaccharide by a human gut symbiont. Appl Environ Microbiol 2012; 78:7720-32. [PMID: 22923411 DOI: 10.1128/aem.01350-12] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Ruminococcus gnavus belongs to the 57 most common species present in 90% of individuals. Previously, we identified an α-galactosidase (Aga1) belonging to glycoside hydrolase (GH) family 36 from R. gnavus E1 (M. Aguilera, H. Rakotoarivonina, A. Brutus, T. Giardina, G. Simon, and M. Fons, Res. Microbiol. 163:14-21, 2012). Here, we identified a novel GH36-encoding gene from the same strain and termed it aga2. Although aga1 showed a very simple genetic organization, aga2 is part of an operon of unique structure, including genes putatively encoding a regulator, a GH13, two phosphotransferase system (PTS) sequences, and a GH32, probably involved in extracellular and intracellular sucrose assimilation. The 727-amino-acid (aa) deduced Aga2 protein shares approximately 45% identity with Aga1. Both Aga1 and Aga2 expressed in Escherichia coli showed strict specificity for α-linked galactose. Both enzymes were active on natural substrates such as melibiose, raffinose, and stachyose. Aga1 and Aga2 occurred as homotetramers in solution, as shown by analytical ultracentrifugation. Modeling of Aga1 and Aga2 identified key amino acids which may be involved in substrate specificity and stabilization of the α-linked galactoside substrates within the active site. Furthermore, Aga1 and Aga2 were both able to perform transglycosylation reactions with α-(1,6) regioselectivity, leading to the formation of product structures up to [Hex](12) and [Hex](8), respectively. We suggest that Aga1 and Aga2 play essential roles in the metabolism of dietary oligosaccharides and could be used for the design of galacto-oligosaccharide (GOS) prebiotics, known to selectively modulate the beneficial gut microbiota.
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17
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Identification of the herboxidiene biosynthetic gene cluster in Streptomyces chromofuscus ATCC 49982. Appl Environ Microbiol 2012; 78:2034-8. [PMID: 22247174 DOI: 10.1128/aem.06904-11] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The 53-kb biosynthetic gene cluster for the novel anticholesterol natural product herboxidiene was identified in Streptomyces chromofuscus ATCC 49982 by genome sequencing and gene inactivation. In addition to herboxidiene, a biosynthetic intermediate, 18-deoxy-herboxidiene, was also isolated from the fermentation broth of S. chromofuscus ATCC 49982 as a minor metabolite.
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18
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Shelburne SA, Sahasrobhajane P, Suber B, Keith DB, Davenport MT, Horstmann N, Kumaraswami M, Olsen RJ, Brennan RG, Musser JM. Niche-specific contribution to streptococcal virulence of a MalR-regulated carbohydrate binding protein. Mol Microbiol 2011; 81:500-14. [PMID: 21645132 DOI: 10.1111/j.1365-2958.2011.07708.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Low G+C Gram-positive bacteria typically contain multiple LacI/GalR regulator family members, which often have highly similar amino-terminal DNA binding domains, suggesting significant overlap in target DNA sequences. The LacI/GalR family regulator catabolite control protein A (CcpA) is a global regulator of the Group A Streptococcus (GAS) transcriptome and contributes to GAS virulence in diverse infection sites. Herein, we studied the role of the maltose repressor (MalR), another LacI/GalR family member, in GAS global gene expression and virulence. MalR inactivation reduced GAS colonization of the mouse oropharynx but did not detrimentally affect invasive infection. The MalR transcriptome was limited to only 25 genes, and a highly conserved MalR DNA-binding sequence was identified. Variation of the MalR binding sequence significantly reduced MalR binding in vitro. In contrast, CcpA bound to the same DNA sequences as MalR but tolerated variation in the promoter sequences with minimal change in binding affinity. Inactivation of pulA, a MalR regulated gene which encodes a cell surface carbohydrate binding protein, significantly reduced GAS human epithelial cell adhesion and mouse oropharyngeal colonization but did not affect GAS invasive disease. These data delineate a molecular mechanism by which hierarchical regulation of carbon source utilization influences bacterial pathogenesis in a site-specific fashion.
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Affiliation(s)
- Samuel A Shelburne
- Department of Infectious Diseases, MD Anderson Cancer Center, Houston, TX 77030, USA.
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19
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Reshamwala SMS, Noronha SB. Biofilm formation in Escherichia coli cra mutants is impaired due to down-regulation of curli biosynthesis. Arch Microbiol 2011; 193:711-22. [PMID: 21559929 DOI: 10.1007/s00203-011-0708-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 01/18/2011] [Accepted: 04/13/2011] [Indexed: 11/25/2022]
Abstract
Cra is a pleiotropic regulatory protein that controls carbon and energy flux in enteric bacteria. Recent studies have shown that Cra also regulates other cell processes and influences biofilm formation. The purpose of the present study was to investigate the role of Cra in biofilm formation in Escherichia coli. Congo red-binding studies suggested that curli biosynthesis is impaired in cra mutants. Microarray analysis of wild-type and mutant E. coli cultivated in conditions promoting biofilm formation revealed that the curli biosynthesis genes, csgBAC and csgDEFG, are poorly expressed in the mutant, suggesting that transcription of genes required for curli production is regulated by Cra. Four putative Cra-binding sites were identified in the curli intergenic region, which were experimentally validated by performing electromobility shift assays. Site-directed mutagenesis of three Cra-binding sites in the promoter region of the csgDEFG operon suggests that Cra activates transcription of this operon upon binding to operator regions both downstream and upstream of the transcription start site. Based on the Cra-binding sites identified in this and other studies, the Cra consensus sequence is refined.
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Affiliation(s)
- Shamlan M S Reshamwala
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, Maharashtra, 400076, India
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20
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Huguet-Tapia JC, Badger JH, Loria R, Pettis GS. Streptomyces turgidiscabies Car8 contains a modular pathogenicity island that shares virulence genes with other actinobacterial plant pathogens. Plasmid 2011; 65:118-24. [DOI: 10.1016/j.plasmid.2010.11.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2010] [Revised: 11/02/2010] [Accepted: 11/08/2010] [Indexed: 10/18/2022]
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21
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Hübner S, Declerck N, Diethmaier C, Le Coq D, Aymerich S, Stülke J. Prevention of cross-talk in conserved regulatory systems: identification of specificity determinants in RNA-binding anti-termination proteins of the BglG family. Nucleic Acids Res 2011; 39:4360-72. [PMID: 21278164 PMCID: PMC3105407 DOI: 10.1093/nar/gkr021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Each family of signal transduction systems requires specificity determinants that link individual signals to the correct regulatory output. In Bacillus subtilis, a family of four anti-terminator proteins controls the expression of genes for the utilisation of alternative sugars. These regulatory systems contain the anti-terminator proteins and a RNA structure, the RNA anti-terminator (RAT) that is bound by the anti-terminator proteins. We have studied three of these proteins (SacT, SacY, and LicT) to understand how they can transmit a specific signal in spite of their strong structural homology. A screen for random mutations that render SacT capable to bind a RNA structure recognized by LicT only revealed a substitution (P26S) at one of the few non-conserved residues that are in contact with the RNA. We have randomly modified this position in SacT together with another non-conserved RNA-contacting residue (Q31). Surprisingly, the mutant proteins could bind all RAT structures that are present in B. subtilis. In a complementary approach, reciprocal amino acid exchanges have been introduced in LicT and SacY at non-conserved positions of the RNA-binding site. This analysis revealed the key role of an arginine side-chain for both the high affinity and specificity of LicT for its cognate RAT. Introduction of this Arg at the equivalent position of SacY (A26) increased the RNA binding in vitro but also resulted in a relaxed specificity. Altogether our results suggest that this family of anti-termination proteins has evolved to reach a compromise between RNA binding efficacy and specific interaction with individual target sequences.
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Affiliation(s)
- Sebastian Hübner
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Grisebach strasse 8, D-37077 Göttingen, Germany
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22
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Dawid A, Kiviet DJ, Kogenaru M, de Vos M, Tans SJ. Multiple peaks and reciprocal sign epistasis in an empirically determined genotype-phenotype landscape. CHAOS (WOODBURY, N.Y.) 2010; 20:026105. [PMID: 20590334 DOI: 10.1063/1.3453602] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Insight into the ruggedness of adaptive landscapes is central to understanding the mechanisms and constraints that shape the course of evolution. While empirical data on adaptive landscapes remain scarce, a handful of recent investigations have revealed genotype-phenotype and genotype-fitness landscapes that appeared smooth and single peaked. Here, we used existing in vivo measurements on lac repressor and operator mutants in Escherichia coli to reconstruct the genotype-phenotype map that details the repression value of this regulatory system as a function of two key repressor residues and four key operator base pairs. We found that this landscape is multipeaked, harboring in total 19 distinct optima. Analysis showed that all direct evolutionary pathways between peaks involve significant dips in the repression value. Consistent with earlier predictions, we found reciprocal sign epistatic interactions at the repression minimum of the most favorable paths between two peaks. These results suggest that the occurrence of multiple peaks and reciprocal epistatic interactions may be a general feature in coevolving systems like the repressor-operator pair studied here.
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Affiliation(s)
- Alexandre Dawid
- AMOLF Institute, Science Park 104, 1098 XG Amsterdam, The Netherlands
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23
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Pokusaeva K, Neves AR, Zomer A, O'Connell-Motherway M, MacSharry J, Curley P, Fitzgerald GF, van Sinderen D. Ribose utilization by the human commensal Bifidobacterium breve UCC2003. Microb Biotechnol 2009; 3:311-23. [PMID: 21255330 PMCID: PMC3815373 DOI: 10.1111/j.1751-7915.2009.00152.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Growth of Bifidobacterium breve UCC2003 on ribose leads to the transcriptional induction of the rbsACBDK gene cluster. Generation and phenotypic analysis of an rbsA insertion mutant established that the rbs gene cluster is essential for ribose utilization, and that its transcription is likely regulated by a LacI‐type regulator encoded by rbsR, located immediately upstream of rbsA. Gel mobility shift assays using purified RbsRHis indicate that the promoter upstream of rbsABCDK is negatively controlled by RbsRHis binding to an 18 bp inverted repeat and that RbsRHis binding activity is modulated by d‐ribose. The rbsK gene of the rbs operon of B. breve UCC2003 was shown to specify a ribokinase (EC 2.7.1.15), which specifically directs its phosphorylating activity towards d‐ribose, converting this pentose sugar to ribose‐5‐phosphate.
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Affiliation(s)
- Karina Pokusaeva
- Alimentary Pharmabiotic Centre, Department of Microbiology, University College Cork, Western Road, Cork, Ireland
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24
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Carlson PE, Carr KA, Janes BK, Anderson EC, Hanna PC. Transcriptional profiling of Bacillus anthracis Sterne (34F2) during iron starvation. PLoS One 2009; 4:e6988. [PMID: 19768119 PMCID: PMC2742718 DOI: 10.1371/journal.pone.0006988] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Accepted: 08/06/2009] [Indexed: 12/31/2022] Open
Abstract
Lack of available iron is one of many environmental challenges that a bacterium encounters during infection and adaptation to iron starvation is important for the pathogen to efficiently replicate within the host. Here we define the transcriptional response of B. anthracis Sterne (34F2) to iron depleted conditions. Genome-wide transcript analysis showed that B. anthracis undergoes considerable changes in gene expression during growth in iron-depleted media, including the regulation of known and candidate virulence factors. Two genes encoding putative internalin proteins were chosen for further study. Deletion of either gene (GBAA0552 or GBAA1340) resulted in attenuation in a murine model of infection. This attenuation was amplified in a double mutant strain. These data define the transcriptional changes induced during growth in low iron conditions and illustrate the potential of this dataset in the identification of putative virulence determinants for future study.
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Affiliation(s)
- Paul E. Carlson
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Katherine A. Carr
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Brian K. Janes
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Erica C. Anderson
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
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25
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Herrera-Herrera JA, Pérez-Avalos O, Salgado LM, Ponce-Noyola T. Cyclic AMP regulates the biosynthesis of cellobiohydrolase in Cellulomonas flavigena growing in sugar cane bagasse. Arch Microbiol 2009; 191:745-50. [PMID: 19701743 DOI: 10.1007/s00203-009-0502-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Revised: 08/06/2009] [Accepted: 08/10/2009] [Indexed: 10/20/2022]
Abstract
Cellulomonas flavigena produces a battery of cellulase components that act concertedly to degrade cellulose. The addition of cAMP to repressed C. flavigena cultures released catabolic repression, while addition of cAMP to induced C. flavigena cultures led to a cellobiohydrolase hyperproduction. Exogenous cAMP showed positive regulation on cellobiohydrolase production in C. flavigena grown on sugar cane bagasse. A C. flavigena cellobiohydrolase gene was cloned (named celA), which coded for a 71- kDa enzyme. Upstream, a repressor celR1, identified as a 38 kDa protein, was monitored by use of polyclonal antibodies.
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26
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Nentwich SS, Brinkrolf K, Gaigalat L, Hüser AT, Rey DA, Mohrbach T, Marin K, Pühler A, Tauch A, Kalinowski J. Characterization of the LacI-type transcriptional repressor RbsR controlling ribose transport in Corynebacterium glutamicum ATCC 13032. MICROBIOLOGY-SGM 2009; 155:150-164. [PMID: 19118356 DOI: 10.1099/mic.0.020388-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The gene products of the rbsRACBD (rbs) operon of C. glutamicum (cg1410-cg1414) encode a ribose-specific ATP-binding cassette (ABC) transport system and its corresponding regulatory protein (RbsR). Deletion of the structural genes rbsACBD prohibited ribose uptake. Deletion of the regulatory gene rbsR resulted in an increased mRNA level of the whole operon. Analysis of the promoter region of the rbs operon by electrophoretic mobility shift assays identified a catabolite-responsive element (cre)-like sequence as the RbsR-binding site. Additional RbsR-binding sites were identified in front of the recently characterized uriR operon (uriR-rbsK1-uriT-uriH) and the ribokinase gene rbsK2. In vitro, the repressor RbsR bound to its targets in the absence of an effector. A probable negative effector of RbsR in vivo is ribose 5-phosphate or a derivative thereof, since in a ribokinase (rbsK1 rbsK2) double mutant, no derepression of the rbs operon in the presence of ribose was observed. Analysis of the ribose stimulon in the C. glutamicum wild-type revealed transcriptional induction of the uriR and rbs operons as well as of the rbsK2 gene. The inconsistency between the existence of functional RbsR-binding sites upstream of the ribokinase genes, their transcriptional induction during growth on ribose, and the missing induction in the rbsR mutant suggested the involvement of a second transcriptional regulator. Simultaneous deletion of the regulatory genes rbsR and uriR finally demonstrated a transcriptional co-control of the rbs and uriR operons and the rbsK2 gene by both regulators, RbsR and UriR, which were furthermore shown to recognize the same cognate DNA sequences in the operators of their target genes.
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Affiliation(s)
- Svenja S Nentwich
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Karina Brinkrolf
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Lars Gaigalat
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Andrea T Hüser
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Daniel A Rey
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Tobias Mohrbach
- Institut für Biochemie, Universität zu Köln, Zülpicher Strasse 47, 50674 Köln, Germany
| | - Kay Marin
- Institut für Biochemie, Universität zu Köln, Zülpicher Strasse 47, 50674 Köln, Germany
| | - Alfred Pühler
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Andreas Tauch
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstrasse 27, 33615 Bielefeld, Germany
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27
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Brinkrolf K, Plöger S, Solle S, Brune I, Nentwich SS, Hüser AT, Kalinowski J, Pühler A, Tauch A. The LacI/GalR family transcriptional regulator UriR negatively controls uridine utilization of Corynebacterium glutamicum by binding to catabolite-responsive element (cre)-like sequences. Microbiology (Reading) 2008; 154:1068-1081. [DOI: 10.1099/mic.0.2007/014001-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Karina Brinkrolf
- International NRW Graduate School in Bioinformatics and Genome Research, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Svenja Plöger
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Sandra Solle
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Iris Brune
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Svenja S. Nentwich
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Andrea T. Hüser
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Alfred Pühler
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Andreas Tauch
- Institut für Genomforschung und Systembiologie, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
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Gao YG, Yao M, Itou H, Zhou Y, Tanaka I. The structures of transcription factor CGL2947 from Corynebacterium glutamicum in two crystal forms: a novel homodimer assembling and the implication for effector-binding mode. Protein Sci 2007; 16:1878-86. [PMID: 17766384 PMCID: PMC2206975 DOI: 10.1110/ps.072976907] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Among the transcription factors, the helix-turn-helix (HTH) GntR family comprised of FadR, HutC, MocR, YtrA, AraR, and PlmA subfamilies regulates the most varied biological processes. Generally, proteins belonging to this family contain an N-terminal DNA-binding domain and a C-terminal effector-binding/oligomerization domain. The members of the YtrA subfamily are much shorter than other members of this family, with chain lengths of 120-130 residues with about 50 residues located in the C-terminal domain. Because of this length, the mode of dimerization and the ability to bind effectors by the C-terminal domain are puzzling. Here, we first report the structure of the transcription factor CGL2947 from Corynebacterium glutamicum, which belongs to the YtrA family. The monomer is composed of a DNA-binding domain containing a winged HTH motif in the N terminus and two helices (alpha4 and alpha5) with a fishhook-shaped arrangement in the C terminus. Helices alpha4 and alpha5 of two monomers intertwine together to form a novel homodimer assembly. The effector-accommodating pocket with 2-methyl-2,4-pentanediol (MPD) docked was located, and it was suggested to represent a novel mode of effector binding. The structures in two crystal forms (MPD-free and -bound in the proposed effector-binding pocket) were solved. The structural variations have implications regarding how the effector-induced conformational change modulates DNA affinity for YtrA family members.
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Affiliation(s)
- Yong-Gui Gao
- Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0810, Japan
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Goulas TK, Goulas AK, Tzortzis G, Gibson GR. Molecular cloning and comparative analysis of four β-galactosidase genes from Bifidobacterium bifidum NCIMB41171. Appl Microbiol Biotechnol 2007; 76:1365-72. [PMID: 17684740 DOI: 10.1007/s00253-007-1099-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2007] [Revised: 06/25/2007] [Accepted: 06/25/2007] [Indexed: 11/30/2022]
Abstract
Bifidobacterium bifidum NCIMB41171 carries four genes encoding different beta-galactosidases. One of them, named bbgIII, consisted of an open reading frame of 1,935 amino acid (a.a.) residues encoding a protein with a multidomain structure, commonly identified on cell wall bound enzymes, having a signal peptide, a membrane anchor, FIVAR domains, immunoglobulin Ig-like and discoidin-like domains. The other three genes, termed bbgI, bbgII and bbgIV, encoded proteins of 1,291, 689 and 1,052 a.a. residues, respectively, which were most probably intracellularly located. Two cases of protein evolution between strains of the same species were identified when the a.a. sequences of the BbgI and BbgIII were compared with homologous proteins from B. bifidum DSM20215. The homologous proteins were found to be differentiated at the C-terminal a.a. part either due to a single nucleotide insertion or to a whole DNA sequence insertion, respectively. The bbgIV gene was located in a gene organisation surrounded by divergently transcribed genes putatively for sugar transport (galactoside-symporter) and gene regulation (LacI-transcriptional regulator), a structure that was found to be highly conserved in B. longum, B. adolescentis and B. infantis, suggesting optimal organisation shared amongst those species.
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Affiliation(s)
- Theodoros K Goulas
- Department of Food Biosciences, School of Chemistry, Food Biosciences and Pharmacy, The University of Reading, Whiteknights, Reading RG6 6AP, UK.
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31
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Benanti EL, Chivers PT. The N-terminal arm of the Helicobacter pylori Ni2+-dependent transcription factor NikR is required for specific DNA binding. J Biol Chem 2007; 282:20365-75. [PMID: 17522054 DOI: 10.1074/jbc.m702982200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The Ni(2+)-dependent transcription factor NikR is widespread among microbes. The two experimentally characterized NikR orthologs, from Helicobacter pylori and Escherichia coli, display vastly different regulatory capabilities in response to increased intracellular Ni(2+). Here, we demonstrate that the nine-residue N-terminal arm present in H. pylori NikR plays a critical role in the expanded regulatory capabilities of this NikR family member. Specifically, the N-terminal arm is required to inhibit NikR binding to low affinity and nonspecific DNA sequences and is also linked to a cation requirement for NikR binding to the nixA promoter. Site-directed mutagenesis and arm-truncation variants of NikR indicate that two residues, Asp-7 and Asp-8, are linked to the cation requirement for binding. Pro-4 and Lys-6 are required for maximal DNA binding affinity of the full-length protein to both the nixA and ureA promoters. The N-terminal arm is highly variable among NikR family members, and these results suggest that it is an adaptable structural feature that can tune the regulatory capabilities of NikR to the nickel physiology of the microbe in which it is found.
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Affiliation(s)
- Erin L Benanti
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
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Casabon I, Couture M, Vaillancourt K, Vadeboncoeur C. Synthesis of HPr(Ser-P)(His-P) by enzyme I of the phosphoenolpyruvate: sugar phosphotransferase system of Streptococcus salivarius. Biochemistry 2006; 45:6692-702. [PMID: 16716080 DOI: 10.1021/bi060278p] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
HPr is a protein of the bacterial phosphoenolpyruvate:sugar phosphotransferase transport system (PTS). In Gram-positive bacteria, HPr can be phosphorylated on Ser(46) by HPr(Ser) kinase/phosphorylase (HPrK/P) and on His(15) by enzyme I (EI) of the PTS. In vitro studies have shown that phosphorylation on one residue greatly inhibits the second phosphorylation. However, streptococci contain significant amounts of HPr(Ser-P)(His approximately P) during exponential growth, and recent studies suggest that phosphorylation of HPr(Ser-P) by EI is involved in the recycling of HPr(Ser-P)(His approximately P). We report in this paper a study on the phosphorylation of Streptococcus salivarius HPr, HPr(Ser-P), and HPr(S46D) by EI. Our results indicate that (i) the specificity constant (k(cat)/K(m)) of EI for HPr(Ser-P) at pH 7.9 was approximately 5000-fold smaller than that observed for HPr, (ii) no metabolic intermediates were able to stimulate HPr(Ser-P) phosphorylation, (iii) the rate of HPr phosphorylation decreased at pHs below 6.5, while that of HPr(Ser-P) increased and was almost 10-fold higher at pH 6.1 than at pH 7.9, (iv) HPr(S46D), a mutated HPr alleged to mimic HPr(Ser-P), was also phosphorylated more efficiently under acidic conditions, and, lastly, (v) phosphorylation of Bacillus subtilis HPr(Ser-P) by B. subtilis EI was also stimulated at acidic pH. Our results suggest that the high levels of HPr(Ser-P)(His approximately P) in streptococci result from the combination of two factors, a high physiological concentration of HPr(Ser-P) and stimulation of HPr(Ser-P) phosphorylation by EI at acidic pH, an intracellular condition that occurs in response to the acidification of the external medium during growth of the culture.
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Affiliation(s)
- Israël Casabon
- Groupe de Recherche en Ecologie Buccale (GREB), Faculté de Médecine Dentaire, and Département de Biochimie et de Microbiologie, Faculté des Sciences et de Génie, Université Laval, Quebec City, Quebec, Canada G1K 7P4
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Poelwijk FJ, Kiviet DJ, Tans SJ. Evolutionary potential of a duplicated repressor-operator pair: simulating pathways using mutation data. PLoS Comput Biol 2006; 2:e58. [PMID: 16733549 PMCID: PMC1464816 DOI: 10.1371/journal.pcbi.0020058] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2006] [Accepted: 04/12/2006] [Indexed: 02/06/2023] Open
Abstract
Ample evidence has accumulated for the evolutionary importance of duplication events. However, little is known about the ensuing step-by-step divergence process and the selective conditions that allow it to progress. Here we present a computational study on the divergence of two repressors after duplication. A central feature of our approach is that intermediate phenotypes can be quantified through the use of in vivo measured repression strengths of Escherichia coli lac mutants. Evolutionary pathways are constructed by multiple rounds of single base pair substitutions and selection for tight and independent binding. Our analysis indicates that when a duplicated repressor co-diverges together with its binding site, the fitness landscape allows funneling to a new regulatory interaction with early increases in fitness. We find that neutral mutations do not play an essential role, which is important for substantial divergence probabilities. By varying the selective pressure we can pinpoint the necessary ingredients for the observed divergence. Our findings underscore the importance of coevolutionary mechanisms in regulatory networks, and should be relevant for the evolution of protein-DNA as well as protein-protein interactions. The evolution of a new trait critically depends on the existence of a path of viable intermediates. Generally speaking, fitness decreasing steps in this path hamper evolution, whereas fitness increasing steps accelerate it. Unfortunately, intermediates are hard to catch in action since they occur only transiently, which is why they have largely been neglected in evolutionary studies. The novelty of this study is that intermediate phenotypes can be predicted using published measurements of Escherichia coli mutants. Using this approach, the evolution of a small genetic network is simulated by computer. Following the duplication of one of its components, a new protein-DNA interaction develops via the accumulation of point mutations and selection. The resulting paths reveal a high potential to obtain a new regulatory interaction, in which neutral drift plays an almost negligible role. This study provides a mechanistic rationale for why such rapid divergence can occur and under which minimal selective conditions. In addition it yields a quantitative prediction for the minimum number of essential mutations.
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Affiliation(s)
- Frank J Poelwijk
- FOM Institute for Atomic and Molecular Physics (AMOLF), Amsterdam, Netherlands
| | - Daniel J Kiviet
- FOM Institute for Atomic and Molecular Physics (AMOLF), Amsterdam, Netherlands
| | - Sander J Tans
- FOM Institute for Atomic and Molecular Physics (AMOLF), Amsterdam, Netherlands
- * To whom correspondence should be addressed. E-mail:
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Krell T, Molina-Henares AJ, Ramos JL. The IclR family of transcriptional activators and repressors can be defined by a single profile. Protein Sci 2006; 15:1207-13. [PMID: 16597823 PMCID: PMC2242505 DOI: 10.1110/ps.051857206] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
In the last decade enormous advances in life sciences have been possible due to the information obtained from DNA sequencing projects. The optimal interpretation and analysis of genome sequence data requires the precise annotation and classification of proteins deduced from open reading frames, which is usually done with the help of family-specific signatures. Here we report a novel profile for the IclR type of transcriptional activators and repressors. In contrast to profiles for other families of transcriptional regulators, the new IclR profile is located outside the helix-turn-helix DNA-binding motif. We provide evidence that the new profile is more specific than any of the existing signatures for this family of regulators. More than 500 representatives of this family were identified with this profile. A database on bacterial regulators (http://www.bactregulators.org) was built to compile and regroup the sequences with the aid of the new profile.
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Affiliation(s)
- Tino Krell
- Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
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Molina-Henares AJ, Krell T, Eugenia Guazzaroni M, Segura A, Ramos JL. Members of the IclR family of bacterial transcriptional regulators function as activators and/or repressors. FEMS Microbiol Rev 2006; 30:157-86. [PMID: 16472303 DOI: 10.1111/j.1574-6976.2005.00008.x] [Citation(s) in RCA: 158] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Members of the IclR family of regulators are proteins with around 250 residues. The IclR family is best defined by a profile covering the effector binding domain. This is supported by structural data and by a number of mutants showing that effector specificity lies within a pocket in the C-terminal domain. These regulators have a helix-turn-helix DNA binding motif in the N-terminal domain and bind target promoters as dimers or as a dimer of dimers. This family comprises regulators acting as repressors, activators and proteins with a dual role. Members of the IclR family control genes whose products are involved in the glyoxylate shunt in Enterobacteriaceae, multidrug resistance, degradation of aromatics, inactivation of quorum-sensing signals, determinants of plant pathogenicity and sporulation. No clear consensus exists on the architecture of DNA binding sites for IclR activators: the MhpR binding site is formed by a 15-bp palindrome, but the binding sites of PcaU and PobR are three perfect 10-bp sequence repetitions forming an inverted and a direct repeat. IclR-type positive regulators bind their promoter DNA in the absence of effector. The mechanism of repression differs among IclR-type regulators. In most of them the binding sites of RNA polymerase and the repressor overlap, so that the repressor occludes RNA polymerase binding. In other cases the repressor binding site is distal to the RNA polymerase, so that the repressor destabilizes the open complex.
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Affiliation(s)
- Antonio J Molina-Henares
- Consejo Superior de Investigaciones Científicas, Estación Experimental del Zaidín, Department of Biochemistry and Molecular and Cellular Biology of Plants, Granada, Spain
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Brune I, Brinkrolf K, Kalinowski J, Pühler A, Tauch A. The individual and common repertoire of DNA-binding transcriptional regulators of Corynebacterium glutamicum, Corynebacterium efficiens, Corynebacterium diphtheriae and Corynebacterium jeikeium deduced from the complete genome sequences. BMC Genomics 2005; 6:86. [PMID: 15938759 PMCID: PMC1180825 DOI: 10.1186/1471-2164-6-86] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2005] [Accepted: 06/07/2005] [Indexed: 11/10/2022] Open
Abstract
Background The genus Corynebacterium includes Gram-positive microorganisms of great biotechnologically importance, such as Corynebacterium glutamicum and Corynebacterium efficiens, as well as serious human pathogens, such as Corynebacterium diphtheriae and Corynebacterium jeikeium. Although genome sequences of the respective species have been determined recently, the knowledge about the repertoire of transcriptional regulators and the architecture of global regulatory networks is scarce. Here, we apply a combination of bioinformatic tools and a comparative genomic approach to identify and characterize a set of conserved DNA-binding transcriptional regulators in the four corynebacterial genomes. Results A collection of 127 DNA-binding transcriptional regulators was identified in the C. glutamicum ATCC 13032 genome, whereas 103 regulators were detected in C. efficiens YS-314, 63 in C. diphtheriae NCTC 13129 and 55 in C. jeikeium K411. According to amino acid sequence similarities and protein structure predictions, the DNA-binding transcriptional regulators were grouped into 25 regulatory protein families. The common set of DNA-binding transcriptional regulators present in the four corynebacterial genomes consists of 28 proteins that are apparently involved in the regulation of cell division and septation, SOS and stress response, carbohydrate metabolism and macroelement and metal homeostasis. Conclusion This work describes characteristic features of a set of conserved DNA-binding transcriptional regulators present within the corynebacterial core genome. The knowledge on the physiological function of these proteins should not only contribute to our understanding of the regulation of gene expression but will also provide the basis for comprehensive modeling of transcriptional regulatory networks of these species.
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Affiliation(s)
- Iris Brune
- Institut für Genomforschung, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstr. 25, D-33615 Bielefeld, Germany
| | - Karina Brinkrolf
- Institut für Genomforschung, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstr. 25, D-33615 Bielefeld, Germany
- International NRW Graduate School in Bioinformatics and Genome Research, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstr. 25, D-33615 Bielefeld, Germany
| | - Jörn Kalinowski
- Institut für Genomforschung, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstr. 25, D-33615 Bielefeld, Germany
| | - Alfred Pühler
- Lehrstuhl für Genetik, Fakultät für Biologie, Universität Bielefeld, Universitätsstr. 25, D-33615 Bielefeld, Germany
| | - Andreas Tauch
- Institut für Genomforschung, Centrum für Biotechnologie, Universität Bielefeld, Universitätsstr. 25, D-33615 Bielefeld, Germany
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Pérez-Rueda E, Collado-Vides J, Segovia L. Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea. Comput Biol Chem 2004; 28:341-50. [PMID: 15556475 DOI: 10.1016/j.compbiolchem.2004.09.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2004] [Revised: 09/13/2004] [Accepted: 09/15/2004] [Indexed: 11/21/2022]
Abstract
We have addressed the distribution and abundance of 75 transcription factor (TF) families in complete genomes from 90 different bacterial and archaeal species. We found that the proportion of TFs increases with genome size. The deficit of TFs in some genomes might be compensated by the presence of proteins organizing and compacting DNA, such as histone-like proteins. Nine families are represented in all the bacteria and archaea we analyzed, whereas 17 families are specific to bacteria, providing evidence for regulon specialization at an early stage of evolution between the bacterial and archeal lineages. Ten of the 17 families identified in bacteria belong exclusively to the proteobacteria defining a specific signature for this taxonomical group. In bacteria, 10 families are lost mostly in intracellular pathogens and endosymbionts, while 9 families seem to have been horizontally transferred to archaea. The winged helix-turn-helix (HTH) is by far the most abundant structure (motif) in prokaryotes, and might have been the earliest HTH motif to appear as shown by its distribution and abundance in both bacterial and archaeal cellular domains. Horizontal gene transfer and lineage-specific gene losses suggest a progressive elimination of TFs in the course of archaeal and bacterial evolution. This analysis provides a framework for discussing the selective forces directing the evolution of the transcriptional machinery in prokaryotes.
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Affiliation(s)
- Ernesto Pérez-Rueda
- Facultad de Ciencias, UAEM, Av. Universidad 1001, CP. 62210, Col. Chamilpa, Cuernavaca, Morelos, México.
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Dellaire G, Nisman R, Eskiw CH, Bazett-Jones DP. In situ imaging and isolation of proteins using dsDNA oligonucleotides. Nucleic Acids Res 2004; 32:e165. [PMID: 15562000 PMCID: PMC534643 DOI: 10.1093/nar/gnh164] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
As proteomics initiatives mature, the need will arise for the multiple visualization of proteins and supramolecular complexes within their true context, in situ. Single-stranded DNA and RNA aptamers can be used for low resolution imaging of cellular receptors and cytoplasmic proteins by light microscopy (LM). These techniques, however, cannot be applied to the imaging of nuclear antigens as these single-stranded aptamers bind endogenous RNA and DNA with high affinity. To overcome this problem, we have developed a novel method for the in situ detection of proteins using double-stranded DNA oligonucleotides. To demonstrate this system we have utilized the prokaryotic DNA-binding proteins LacI and TetR as peptide tags to image fusion proteins in situ using dsDNA oligonucleotides encoding either the Lac or Tet operator. Using fluorescent and fluorogold dsDNA oligonucleotides, we localized within the nucleus a TetR-PML fusion protein within promyelocytic leukaemia protein (PML) bodies by LM and a LacI-SC35 fusion protein within nuclear speckles by correlative light and electron microscopy (LM/EM). Isolation of LacI-SC35 was also accomplished by using biotinylated dsDNA and streptavidin sepharose. The use of dsDNA oligonucleotides should complement existing aptamer in situ detection techniques by allowing the multiple detection and localization of nuclear proteins in situ and at high resolution.
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Affiliation(s)
- Graham Dellaire
- Programme in Cell Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, Ontario, Canada M5G 1X8
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Vaillancourt K, LeMay JD, Lamoureux M, Frenette M, Moineau S, Vadeboncoeur C. Characterization of a galactokinase-positive recombinant strain of Streptococcus thermophilus. Appl Environ Microbiol 2004; 70:4596-603. [PMID: 15294791 PMCID: PMC492372 DOI: 10.1128/aem.70.8.4596-4603.2004] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2004] [Accepted: 04/21/2004] [Indexed: 11/20/2022] Open
Abstract
The lactic acid bacterium Streptococcus thermophilus is widely used by the dairy industry for its ability to transform lactose, the primary sugar found in milk, into lactic acid. Unlike the phylogenetically related species Streptococcus salivarius, S. thermophilus is unable to metabolize and grow on galactose and thus releases substantial amounts of this hexose into the external medium during growth on lactose. This metabolic property may result from the inability of S. thermophilus to synthesize galactokinase, an enzyme of the Leloir pathway that phosphorylates intracellular galactose to generate galactose-1-phosphate. In this work, we report the complementation of Gal(-) strain S. thermophilus SMQ-301 with S. salivarius galK, the gene that codes for galactokinase, and the characterization of recombinant strain SMQ-301K01. The recombinant strain, which was obtained by transformation of strain SMQ-301 with pTRKL2TK, a plasmid bearing S. salivarius galK, grew on galactose with a generation time of 55 min, which was almost double the generation time on lactose. Data confirmed that (i) the ability of SMQ-301K01 to grow on galactose resulted from the expression of S. salivarius galK and (ii) transcription of the plasmid-borne galK gene did not require GalR, a transcriptional regulator of the gal and lac operons, and did not interfere with the transcription of these operons. Unexpectedly, recombinant strain SMQ-301K01 still expelled galactose during growth on lactose, but only when the amount of the disaccharide in the medium exceeded 0.05%. Thus, unlike S. salivarius, the ability to metabolize galactose was not sufficient for S. thermophilus to simultaneously metabolize the glucose and galactose moieties of lactose. Nevertheless, during growth in milk and under time-temperature conditions that simulated those used to produce mozzarella cheese, the recombinant Gal(+) strain grew and produced acid more rapidly than the Gal(-) wild-type strain.
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Affiliation(s)
- Katy Vaillancourt
- Groupe de Recherche en Ecologie Buccale, Département de Biochimie et de Microbiologie, Faculté des Sciences et de Génie, and Faculté de Médecine Dentaire, Université Laval, Quebec City, Quebec, Canada G1K 7P4
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Zheng Y, Roberts RJ, Kasif S. Segmentally variable genes: a new perspective on adaptation. PLoS Biol 2004; 2:E81. [PMID: 15094797 PMCID: PMC387263 DOI: 10.1371/journal.pbio.0020081] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2003] [Accepted: 01/20/2004] [Indexed: 11/30/2022] Open
Abstract
Genomic sequence variation is the hallmark of life and is key to understanding diversity and adaptation among the numerous microorganisms on earth. Analysis of the sequenced microbial genomes suggests that genes are evolving at many different rates. We have attempted to derive a new classification of genes into three broad categories: lineage-specific genes that evolve rapidly and appear unique to individual species or strains; highly conserved genes that frequently perform housekeeping functions; and partially variable genes that contain highly variable regions, at least 70 amino acids long, interspersed among well-conserved regions. The latter we term segmentally variable genes (SVGs), and we suggest that they are especially interesting targets for biochemical studies. Among these genes are ones necessary to deal with the environment, including genes involved in host–pathogen interactions, defense mechanisms, and intracellular responses to internal and environmental changes. For the most part, the detailed function of these variable regions remains unknown. We propose that they are likely to perform important binding functions responsible for protein–protein, protein–nucleic acid, or protein–small molecule interactions. Discerning their function and identifying their binding partners may offer biologists new insights into the basic mechanisms of adaptation, context-dependent evolution, and the interaction between microbes and their environment. Segmentally variable genes show a mosaic pattern of one or more rapidly evolving, variable regions. Discerning their function may provide new insights into the forces that shape genome diversity and adaptation
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Affiliation(s)
- Yu Zheng
- Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, USA.
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Bertram R, Schlicht M, Mahr K, Nothaft H, Saier MH, Titgemeyer F. In silico and transcriptional analysis of carbohydrate uptake systems of Streptomyces coelicolor A3(2). J Bacteriol 2004; 186:1362-73. [PMID: 14973030 PMCID: PMC344420 DOI: 10.1128/jb.186.5.1362-1373.2004] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Streptomyces coelicolor is the prototype for the investigation of antibiotic-producing and differentiating actinomycetes. As soil bacteria, streptomycetes can metabolize a wide variety of carbon sources and are hence vested with various specific permeases. Their activity and regulation substantially determine the nutritional state of the cell and, therefore, influence morphogenesis and antibiotic production. We have surveyed the genome of S. coelicolor A3(2) to provide a thorough description of the carbohydrate uptake systems. Among 81 ATP-binding cassette (ABC) permeases that are present in the genome, we found 45 to encode a putative solute binding protein, an essential feature for carbohydrate permease function. Similarity analysis allowed the prediction of putative ABC systems for transport of cellobiose and cellotriose, alpha-glucosides, lactose, maltose, maltodextrins, ribose, sugar alcohols, xylose, and beta-xylosides. A novel putative bifunctional protein composed of a substrate binding and a membrane-spanning moiety is likely to account for ribose or ribonucleoside uptake. Glucose may be incorporated by a proton-driven symporter of the major facilitator superfamily while a putative sodium-dependent permease of the solute-sodium symporter family may mediate uptake of galactose and a facilitator protein of the major intrinsic protein family may internalize glycerol. Of the predicted gene clusters, reverse transcriptase PCRs showed active gene expression in 8 of 11 systems. Together with the previously surveyed permeases of the phosphotransferase system that accounts for the uptake of fructose and N-acetylglucosamine, the genome of S. coelicolor encodes at least 53 potential carbohydrate uptake systems.
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Affiliation(s)
- Ralph Bertram
- Lehrstuhl für Mikrobiologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91058 Erlangen, Germany
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Barrangou R, Altermann E, Hutkins R, Cano R, Klaenhammer TR. Functional and comparative genomic analyses of an operon involved in fructooligosaccharide utilization by Lactobacillus acidophilus. Proc Natl Acad Sci U S A 2003; 100:8957-62. [PMID: 12847288 PMCID: PMC166420 DOI: 10.1073/pnas.1332765100] [Citation(s) in RCA: 184] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Lactobacillus acidophilus is a probiotic organism that displays the ability to use prebiotic compounds such as fructooligosaccharides (FOS), which stimulate the growth of beneficial commensals in the gastrointestinal tract. However, little is known about the mechanisms and genes involved in FOS utilization by Lactobacillus species. Analysis of the L. acidophilus NCFM genome revealed an msm locus composed of a transcriptional regulator of the LacI family, a four-component ATP-binding cassette (ABC) transport system, a fructosidase, and a sucrose phosphorylase. Transcriptional analysis of this operon demonstrated that gene expression was induced by sucrose and FOS but not by glucose or fructose, suggesting some specificity for nonreadily fermentable sugars. Additionally, expression was repressed by glucose but not by fructose, suggesting catabolite repression via two cre-like sequences identified in the promoter-operator region. Insertional inactivation of the genes encoding the ABC transporter substrate-binding protein and the fructosidase reduced the ability of the mutants to grow on FOS. Comparative analysis of gene architecture within this cluster revealed a high degree of synteny with operons in Streptococcus mutans and Streptococcus pneumoniae. However, the association between a fructosidase and an ABC transporter is unusual and may be specific to L. acidophilus. This is a description of a previously undescribed gene locus involved in transport and catabolism of FOS compounds, which can promote competition of beneficial microorganisms in the human gastrointestinal tract.
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Affiliation(s)
- Rodolphe Barrangou
- Genomic Sciences Program and Southeast Dairy Foods Research Center, North Carolina State University, Raleigh, NC 27695, USA
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43
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Trindade MI, Abratt VR, Reid SJ. Induction of sucrose utilization genes from Bifidobacterium lactis by sucrose and raffinose. Appl Environ Microbiol 2003; 69:24-32. [PMID: 12513973 PMCID: PMC152442 DOI: 10.1128/aem.69.1.24-32.2003] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The probiotic organism Bifidobacterium lactis was isolated from a yoghurt starter culture with the aim of analyzing its use of carbohydrates for the development of prebiotics. A sucrose utilization gene cluster of B. lactis was identified by complementation of a gene library in Escherichia coli. Three genes, encoding a sucrose phosphorylase (ScrP), a GalR-LacI-type transcriptional regulator (ScrR), and a sucrose transporter (ScrT), were identified by sequence analysis. The scrP gene was expressed constitutively from its own promoter in E. coli grown in complete medium, and the strain hydrolyzed sucrose in a reaction that was dependent on the presence of phosphates. Primer extension experiments with scrP performed by using RNA isolated from B. lactis identified the transcriptional start site 102 bp upstream of the ATG start codon, immediately adjacent to a palindromic sequence resembling a regulator binding site. In B. lactis, total sucrase activity was induced by the presence of sucrose, raffinose, or oligofructose in the culture medium and was repressed by glucose. RNA analysis of the scrP, scrR, and scrT genes in B. lactis indicated that expression of these genes was influenced by transcriptional regulation and that all three genes were similarly induced by sucrose and raffinose and repressed by glucose. Analysis of the sucrase activities of deletion constructs in heterologous E. coli indicated that ScrR functions as a positive regulator.
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Affiliation(s)
- Marla I Trindade
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch 7701, South Africa
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Jensen JB, Peters NK, Bhuvaneswari TV. Redundancy in periplasmic binding protein-dependent transport systems for trehalose, sucrose, and maltose in Sinorhizobium meliloti. J Bacteriol 2002; 184:2978-86. [PMID: 12003938 PMCID: PMC135073 DOI: 10.1128/jb.184.11.2978-2986.2002] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have identified a cluster of six genes involved in trehalose transport and utilization (thu) in Sinorhizobium meliloti. Four of these genes, thuE, -F, -G, and -K, were found to encode components of a binding protein-dependent trehalose/maltose/sucrose ABC transporter. Their deduced gene products comprise a trehalose/maltose-binding protein (ThuE), two integral membrane proteins (ThuF and ThuG), and an ATP-binding protein (ThuK). In addition, a putative regulatory protein (ThuR) was found divergently transcribed from the thuEFGK operon. When the thuE locus was inactivated by gene replacement, the resulting S. meliloti strain was impaired in its ability to grow on trehalose, and a significant retardation in growth was seen on maltose as well. The wild type and the thuE mutant were indistinguishable for growth on glucose and sucrose. This suggested a possible overlap in function of the thuEFGK operon with the aglEFGAK operon, which was identified as a binding protein-dependent ATP-binding transport system for sucrose, maltose, and trehalose. The K(m)s for trehalose transport were 8 +/- 1 nM and 55 +/- 5 nM in the uninduced and induced cultures, respectively. Transport and growth experiments using mutants impaired in either or both of these transport systems show that these systems form the major transport systems for trehalose, maltose, and sucrose. By using a thuE'-lacZ fusion, we show that thuE is induced only by trehalose and not by cellobiose, glucose, maltopentaose, maltose, mannitol, or sucrose, suggesting that the thuEFGK system is primarily targeted toward trehalose. The aglEFGAK operon, on the other hand, is induced primarily by sucrose and to a lesser extent by trehalose. Tests for root colonization, nodulation, and nitrogen fixation suggest that uptake of disaccharides can be critical for colonization of alfalfa roots but is not important for nodulation and nitrogen fixation per se.
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Affiliation(s)
- John Beck Jensen
- Department of Biology, Faculty of Science, University of Tromsø, N-9037 Tromsø, Norway
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Rigali S, Derouaux A, Giannotta F, Dusart J. Subdivision of the helix-turn-helix GntR family of bacterial regulators in the FadR, HutC, MocR, and YtrA subfamilies. J Biol Chem 2002; 277:12507-15. [PMID: 11756427 DOI: 10.1074/jbc.m110968200] [Citation(s) in RCA: 288] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Haydon and Guest (Haydon, D. J, and Guest, J. R. (1991) FEMS Microbiol. Lett. 63, 291-295) first described the helix-turn-helix GntR family of bacterial regulators. They presented them as transcription factors sharing a similar N-terminal DNA-binding (d-b) domain, but they observed near-maximal divergence in the C-terminal effector-binding and oligomerization (E-b/O) domain. To elucidate this C-terminal heterogeneity, structural, phylogenetic, and functional analyses were performed on a family that now comprises about 270 members. Our comparative study first focused on the C-terminal E-b/O domains and next on DNA-binding domains and palindromic operator sequences, has classified the GntR members into four subfamilies that we called FadR, HutC, MocR, and YtrA. Among these subfamilies a degree of similarity of about 55% was observed throughout the entire sequence. Structure/function associations were highlighted although they were not absolutely stringent. The consensus sequences deduced for the DNA-binding domain were slightly different for each subfamily, suggesting that fusion between the D-b and E-b/O domains have occurred separately, with each subfamily having its own D-b domain ancestor. Moreover, the compilation of the known or predicted palindromic cis-acting elements has highlighted different operator sequences according to our subfamily subdivision. The observed C-terminal E-b/O domain heterogeneity was therefore reflected on the DNA-binding domain and on the cis-acting elements, suggesting the existence of a tight link between the three regions involved in the regulating process.
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Affiliation(s)
- Sébastien Rigali
- Centre d'Ingénierie des Protéines, Université de Liège, Institut de Chimie B6, Sart-Tilman, B-4000 Liège, Belgium.
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Marasco R, Muscariello L, Rigano M, Sacco M. Mutational analysis of the bglH catabolite-responsive element (cre) in Lactobacillus plantarum. FEMS Microbiol Lett 2002; 208:143-6. [PMID: 11934508 DOI: 10.1111/j.1574-6968.2002.tb11074.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Catabolite repression of the Lactobacillus plantarum bglH gene is mediated by the catabolite control protein A (CcpA). Here we show that the binding site for the protein is a catabolite-responsive element (cre) sequence overlapping the start site of transcription. Two single and one double base substitutions in the cre sequence caused derepression of a plasmid-borne bglH-cat transcriptional fusion in L. plantarum cells grown on glucose. Analysis of the single mutations indicates that the G and C nucleotide residues in positions 2 and 13, respectively, of the 14-bp cre sequence are required for catabolite repression.
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Affiliation(s)
- Rosangela Marasco
- Facoltà di Scienze MM FF NN, Università degli Studi del Sannio, via Caio Ponzio Telesino 11, 82100, Benevento, Italy
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Schmidt H, Zhang WL, Hemmrich U, Jelacic S, Brunder W, Tarr PI, Dobrindt U, Hacker J, Karch H. Identification and characterization of a novel genomic island integrated at selC in locus of enterocyte effacement-negative, Shiga toxin-producing Escherichia coli. Infect Immun 2001; 69:6863-73. [PMID: 11598060 PMCID: PMC100065 DOI: 10.1128/iai.69.11.6863-6873.2001] [Citation(s) in RCA: 128] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2001] [Accepted: 08/15/2001] [Indexed: 11/20/2022] Open
Abstract
The selC tRNA gene is a common site for the insertion of pathogenicity islands in a variety of bacterial enteric pathogens. We demonstrate here that Escherichia coli that produces Shiga toxin 2d and does not harbor the locus of enterocyte effacement (LEE) contains, instead, a novel genomic island. In one representative strain (E. coli O91:H(-) strain 4797/97), this island is 33,014 bp long and, like LEE in E. coli O157:H7, is integrated 15 bp downstream of selC. This E. coli O91:H(-) island contains genes encoding a novel serine protease, termed EspI; an adherence-associated locus, similar to iha of E. coli O157:H7; an E. coli vitamin B12 receptor (BtuB); an AraC-type regulatory module; and four homologues of E. coli phosphotransferase proteins. The remaining sequence consists largely of complete and incomplete insertion sequences, prophage sequences, and an intact phage integrase gene that is located directly downstream of the chromosomal selC. Recombinant EspI demonstrates serine protease activity using pepsin A and human apolipoprotein A-I as substrates. We also detected Iha-reactive protein in outer membranes of a recombinant clone and 10 LEE-negative, Shiga toxin-producing E. coli (STEC) strains by immunoblot analysis. Using PCR analysis of various STEC, enteropathogenic E. coli, enterotoxigenic E. coli, enteroaggregative E. coli, uropathogenic E. coli, and enteroinvasive E. coli strains, we detected the iha homologue in 59 (62%) of 95 strains tested. In contrast, espI and btuB were present in only two (2%) and none of these strains, respectively. We conclude that the newly described island occurs exclusively in a subgroup of STEC strains that are eae negative and contain the variant stx(2d )gene.
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Affiliation(s)
- H Schmidt
- Institut für Hygiene und Mikrobiologie der Universität Würzburg, Würzburg, Germany.
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Eon S, Culard F, Sy D, Charlier M, Spotheim-Maurizot M. Radiation disrupts protein-DNA complexes through damage to the protein. The lac repressor-operator system. Radiat Res 2001; 156:110-7. [PMID: 11418079 DOI: 10.1667/0033-7587(2001)156[0110:rdpdct]2.0.co;2] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Eon, S., Culard, F., Sy, D., Charlier, M. and Spotheim-Maurizot, M. Radiation Disrupts Protein-DNA Complexes through Damage to the Protein. The lac Repressor-Operator System. Radiat. Res. 156, 110-117 (2001). Binding of a protein to its cognate DNA sequence is a key step in the regulation of gene expression. If radiation damage interferes with protein-DNA recognition, the entire regulation process may be perturbed. We have studied the effect of gamma rays on a model regulatory system, the E. coli lactose repressor-operator complex. We have observed the disruption of the complex upon irradiation in aerated solution. The complex is completely restored by the addition of nonirradiated repressor, but not by the addition of nonirradiated DNA. Thus radiation disrupts the DNA-protein complex by affecting the binding ability of the protein. This interpretation is supported by the dramatic loss of binding ability of a free irradiated repressor toward nonirradiated DNA. Interestingly, the dose necessary for the disruption of the irradiated complex is higher than that for inducing the complete loss of the binding ability of the free irradiated repressor. This may be due to the protection of key amino acids by the bound DNA. As seen from calculations of the accessibility of amino acids to radiolytic OH(.), the protection is due to both masking and conformational effects.
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Affiliation(s)
- S Eon
- Centre de Biophysique Moléculaire-CNRS, Rue Charles-Sadron, F-45071 Orléans Cedex 2, France
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Saier MH. Phylogenetic approaches to the identification and characterization of protein families and superfamilies. MICROBIAL & COMPARATIVE GENOMICS 2001; 1:129-50. [PMID: 9689209 DOI: 10.1089/mcg.1996.1.129] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
With the advent of megabase genome sequencing, the need for computational analyses increases exponentially. Sequencing errors must be corrected, encoded proteins must be identified, functions must be assigned to these proteins, and distant phylogenetic relationships must be recognized in order to maximize the yield of information obtainable from genome sequencing projects. Both the computer and the human brain have their limitations, but using them in combination, the biologist can vastly extend his or her analytic capabilities. Computer techniques can be used to estimate protein structure, function, biogenesis, and evolution. In this review, the application of available computer programs to several protein families, particularly transport, receptor, and transcriptional regulatory protein families, illustrate our current capabilities and limitations. Although some multidomain protein families are evolutionarily homogeneous, others have mosaic origins. Evidence concerning the nature and frequency of occurrence of domain shuffling, splicing, fusion, deletion, and duplication during evolution of specific protein families is evaluated. It is shown that specific families of enzymes, receptors, transport proteins, and transcriptional regulatory proteins share a common evolutionary origin, frequently diverging in function because of domain splicing and ligation. Some large families arose gradually over evolutionary time, whereas others developed suddenly, due to bursts of intragenic or intergenic (or both) duplication events occurring over relatively short periods of time. It is argued that energy coupling to transport was a late occurrence, superimposed on preexisting mechanisms of solute facilitation. It is also shown that several transport protein families have evolved independently of each other, employing different routes, at different times in evolutionary history, to give topologically similar transmembrane protein complexes.
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Affiliation(s)
- M H Saier
- Department of Biology, University of California at San Diego, La Jolla, USA
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Jankovic I, Egeter O, Brückner R. Analysis of catabolite control protein A-dependent repression in Staphylococcus xylosus by a genomic reporter gene system. J Bacteriol 2001; 183:580-6. [PMID: 11133951 PMCID: PMC94913 DOI: 10.1128/jb.183.2.580-586.2001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2000] [Accepted: 10/27/2000] [Indexed: 11/20/2022] Open
Abstract
A single-copy reporter system for Staphylococcus xylosus has been developed, that uses a promoterless version of the endogenous beta-galactosidase gene lacH as a reporter gene and that allows integration of promoters cloned in front of lacH into the lactose utilization gene cluster by homologous recombination. The system was applied to analyze carbon catabolite repression of S. xylosus promoters by the catabolite control protein CcpA. To test if lacH is a suitable reporter gene, beta-galactosidase activities directed by two promoters known to be subject to CcpA regulation were measured. In these experiments, repression of the malRA maltose utilization operon promoter and autoregulation of the ccpA promoters were confirmed, proving the applicability of the system. Subsequently, putative CcpA operators, termed catabolite-responsive elements (cres), from promoter regions of several S. xylosus genes were tested for their ability to confer CcpA regulation upon a constitutive promoter, P(vegII). For that purpose, cre sequences were placed at position +3 or +4 within the transcribed region of P(vegII). Measurements of beta-galactosidase activities in the presence or absence of glucose yielded repression ratios between two- and eightfold. Inactivation of ccpA completely abolished glucose-dependent regulation. Therefore, the tested cres functioned as operator sites for CcpA. With promoters exclusively regulated by CcpA, signal transduction leading to CcpA activation in S. xylosus was examined. Glucose-dependent regulation was measured in a set of isogenic mutants showing defects in genes encoding glucose kinase GlkA, glucose uptake protein GlcU, and HPr kinase HPrK. GlkA and GlcU deficiency diminished glucose-dependent CcpA-mediated repression, but loss of HPr kinase activity abolished regulation. These results clearly show that HPr kinase provides the essential signal to activate CcpA in S. xylosus. Glucose uptake protein GlcU and glucose kinase GlkA participate in activation, but they are not able to trigger CcpA-mediated regulation independently from HPr kinase.
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Affiliation(s)
- I Jankovic
- Mikrobielle Genetik, Universität Tübingen, D-72076 Tübingen, Germany
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