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Pradhan UK, Meher PK, Naha S, Das R, Gupta A, Parsad R. ProkDBP: Toward more precise identification of prokaryotic DNA binding proteins. Protein Sci 2024; 33:e5015. [PMID: 38747369 PMCID: PMC11094783 DOI: 10.1002/pro.5015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/18/2024] [Accepted: 04/21/2024] [Indexed: 05/19/2024]
Abstract
Prokaryotic DNA binding proteins (DBPs) play pivotal roles in governing gene regulation, DNA replication, and various cellular functions. Accurate computational models for predicting prokaryotic DBPs hold immense promise in accelerating the discovery of novel proteins, fostering a deeper understanding of prokaryotic biology, and facilitating the development of therapeutics targeting for potential disease interventions. However, existing generic prediction models often exhibit lower accuracy in predicting prokaryotic DBPs. To address this gap, we introduce ProkDBP, a novel machine learning-driven computational model for prediction of prokaryotic DBPs. For prediction, a total of nine shallow learning algorithms and five deep learning models were utilized, with the shallow learning models demonstrating higher performance metrics compared to their deep learning counterparts. The light gradient boosting machine (LGBM), coupled with evolutionarily significant features selected via random forest variable importance measure (RF-VIM) yielded the highest five-fold cross-validation accuracy. The model achieved the highest auROC (0.9534) and auPRC (0.9575) among the 14 machine learning models evaluated. Additionally, ProkDBP demonstrated substantial performance with an independent dataset, exhibiting higher values of auROC (0.9332) and auPRC (0.9371). Notably, when benchmarked against several cutting-edge existing models, ProkDBP showcased superior predictive accuracy. Furthermore, to promote accessibility and usability, ProkDBP (https://iasri-sg.icar.gov.in/prokdbp/) is available as an online prediction tool, enabling free access to interested users. This tool stands as a significant contribution, enhancing the repertoire of resources for accurate and efficient prediction of prokaryotic DBPs.
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Affiliation(s)
- Upendra Kumar Pradhan
- Division of Statistical GeneticsICAR‐Indian Agricultural Statistics Research Institute, PUSANew DelhiIndia
| | - Prabina Kumar Meher
- Division of Statistical GeneticsICAR‐Indian Agricultural Statistics Research Institute, PUSANew DelhiIndia
| | - Sanchita Naha
- Division of Computer ApplicationsICAR‐Indian Agricultural Statistics Research Institute, PUSANew DelhiIndia
| | - Ritwika Das
- Division of Agricultural BioinformaticsICAR‐Indian Agricultural Statistics Research Institute, PUSANew DelhiIndia
| | - Ajit Gupta
- Division of Statistical GeneticsICAR‐Indian Agricultural Statistics Research Institute, PUSANew DelhiIndia
| | - Rajender Parsad
- ICAR‐Indian Agricultural Statistics Research Institute, PUSANew DelhiIndia
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2
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Gucwa K, Wons E, Wisniewska A, Jakalski M, Dubiak Z, Kozlowski LP, Mruk I. Lethal perturbation of an Escherichia coli regulatory network is triggered by a restriction-modification system's regulator and can be mitigated by excision of the cryptic prophage Rac. Nucleic Acids Res 2024; 52:2942-2960. [PMID: 38153127 PMCID: PMC11014345 DOI: 10.1093/nar/gkad1234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 12/29/2023] Open
Abstract
Bacterial gene regulatory networks orchestrate responses to environmental challenges. Horizontal gene transfer can bring in genes with regulatory potential, such as new transcription factors (TFs), and this can disrupt existing networks. Serious regulatory perturbations may even result in cell death. Here, we show the impact on Escherichia coli of importing a promiscuous TF that has adventitious transcriptional effects within the cryptic Rac prophage. A cascade of regulatory network perturbations occurred on a global level. The TF, a C regulatory protein, normally controls a Type II restriction-modification system, but in E. coli K-12 interferes with expression of the RacR repressor gene, resulting in de-repression of the normally-silent Rac ydaT gene. YdaT is a prophage-encoded TF with pleiotropic effects on E. coli physiology. In turn, YdaT alters expression of a variety of bacterial regulons normally controlled by the RcsA TF, resulting in deficient lipopolysaccharide biosynthesis and cell division. At the same time, insufficient RacR repressor results in Rac DNA excision, halting Rac gene expression due to loss of the replication-defective Rac prophage. Overall, Rac induction appears to counteract the lethal toxicity of YdaT. We show here that E. coli rewires its regulatory network, so as to minimize the adverse regulatory effects of the imported C TF. This complex set of interactions may reflect the ability of bacteria to protect themselves by having robust mechanisms to maintain their regulatory networks, and/or suggest that regulatory C proteins from mobile operons are under selection to manipulate their host's regulatory networks for their own benefit.
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Affiliation(s)
- Katarzyna Gucwa
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ewa Wons
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Aleksandra Wisniewska
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Marcin Jakalski
- 3P-Medicine Laboratory, Medical University of Gdansk, Debinki 7, 80-211 Gdansk, Poland
| | - Zuzanna Dubiak
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Lukasz Pawel Kozlowski
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Banacha 2, 02-097 Warsaw, Poland
| | - Iwona Mruk
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
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3
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Perez-Rueda E, Schellhorn HE, Kumar S. Editorial: Role of transcription factors and sigma factors in bacterial stress physiology. Front Microbiol 2023; 14:1291172. [PMID: 37869661 PMCID: PMC10588465 DOI: 10.3389/fmicb.2023.1291172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 09/25/2023] [Indexed: 10/24/2023] Open
Affiliation(s)
- Ernesto Perez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica del Estado de Yucatán, Mérida, Mexico
| | | | - Santosh Kumar
- Metabolic Engineering and Fermentation Science Group, Department of Food Science, University of Wisconsin-Madison, Madison, WI, United States
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4
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Somathilaka SS, Balasubramaniam S, Martins DP, Li X. Revealing gene regulation-based neural network computing in bacteria. BIOPHYSICAL REPORTS 2023; 3:100118. [PMID: 37649578 PMCID: PMC10462848 DOI: 10.1016/j.bpr.2023.100118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 07/26/2023] [Indexed: 09/01/2023]
Abstract
Bacteria are known to interpret a range of external molecular signals that are crucial for sensing environmental conditions and adapting their behaviors accordingly. These external signals are processed through a multitude of signaling transduction networks that include the gene regulatory network (GRN). From close observation, the GRN resembles and exhibits structural and functional properties that are similar to artificial neural networks. An in-depth analysis of gene expression dynamics further provides a new viewpoint of characterizing the inherited computing properties underlying the GRN of bacteria despite being non-neuronal organisms. In this study, we introduce a model to quantify the gene-to-gene interaction dynamics that can be embedded in the GRN as weights, converting a GRN to gene regulatory neural network (GRNN). Focusing on Pseudomonas aeruginosa, we extracted the GRNN associated with a well-known virulence factor, pyocyanin production, using an introduced weight extraction technique based on transcriptomic data and proving its computing accuracy using wet-lab experimental data. As part of our analysis, we evaluated the structural changes in the GRNN based on mutagenesis to determine its varying computing behavior. Furthermore, we model the ecosystem-wide cell-cell communications to analyze its impact on computing based on environmental as well as population signals, where we determine the impact on the computing reliability. Subsequently, we establish that the individual GRNNs can be clustered to collectively form computing units with similar behaviors to single-layer perceptrons with varying sigmoidal activation functions spatio-temporally within an ecosystem. We believe that this will lay the groundwork toward molecular machine learning systems that can see artificial intelligence move toward non-silicon devices, or living artificial intelligence, as well as giving us new insights into bacterial natural computing.
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Affiliation(s)
- Samitha S. Somathilaka
- VistaMilk Research Centre, Walton Institute for Information and Communication Systems Science, South East Technological University, Waterford, Ireland
- School of Computing, University of Nebraska-Lincoln, Lincoln, Nebraska
| | | | - Daniel P. Martins
- VistaMilk Research Centre, Walton Institute for Information and Communication Systems Science, South East Technological University, Waterford, Ireland
| | - Xu Li
- Department of Civil and Environmental Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska
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5
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Tyagi E, Singhvi N, Keshavam CC, Sangwan N, Gupta V, Bhimwal T, Seth R, Seth RK, Singh Y. Phylogenetic analysis and interactomics study unveil gene co-optive evolution of LysR-type transcription regulators across non-pathogenic, opportunistic, and pathogenic mycobacteria. 3 Biotech 2023; 13:168. [PMID: 37188288 PMCID: PMC10167064 DOI: 10.1007/s13205-023-03583-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 04/23/2023] [Indexed: 05/17/2023] Open
Abstract
Mycobacterial species is known for inhabiting various niches ranging from soil to harsh intracellular environment of animal hosts and their survival through constant changes. For survival and persistence, these organisms must quickly adapt by bringing shift in their metabolism. Metabolic shifts are brought by sensing the environmental cues usually by membrane localized sensor molecules. These signals are transmitted to regulators of various metabolic pathways leading to post-translational modifications of regulators ultimately resulting in altered metabolic state of the cell. Multiple regulatory mechanisms have been unearthed so far that play crucial role in adapting to these situations, and among them, the signal-dependent transcriptional regulators mediated responses are integral for the microbes to perceive environmental signals and generate appropriate adaptive responses. LysR-type transcriptional regulators (LTTRs) form the largest family of transcriptional regulators, which are present in all kingdoms of life. Their numbers vary among bacterial genera and even in different mycobacterial species. To understand the evolutionary aspect of pathogenicity based on LTTRs, we performed phylogenetic analysis of LTTRs encoded by several mycobacterial species representing non-pathogenic (NP), opportunistic (OP), and totally pathogenic (TP) mycobacteria. Our results showed that LTTRs of TP clustered separately from LTTRs of NP and OP mycobacteria. In addition, LTTRs frequency per Mb of genome was reduced in TP when compared with NP and OP. Further, the protein-protein interactions and degree-based network analysis showed concomitant increased interactions per LTTRs with increase in pathogenicity. These results suggested the increase in regulon of LTTRs during evolution of TP mycobacteria.
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Affiliation(s)
- Ekta Tyagi
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Nirjara Singhvi
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun, Uttarakhand 248001 India
| | | | - Nitika Sangwan
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Vipin Gupta
- Ministry of Environment Forest & Climate Change, Integrated Regional Office, Dehradun, 248001 India
| | - Tanisha Bhimwal
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Ranjana Seth
- Deshbandhu College, University of Delhi South Campus, New Delhi, 110019 India
| | | | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, 110007 India
- Present Address: Delhi School of Public Health, Institution of Eminence, University of Delhi, Delhi, 110007 India
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6
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Bettridge K, Harris FE, Yehya N, Xiao J. RNAP Promoter Search and Transcription Kinetics in Live E. coli Cells. J Phys Chem B 2023; 127:3816-3828. [PMID: 37098218 PMCID: PMC11212508 DOI: 10.1021/acs.jpcb.2c09142] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
Bacterial transcription has been studied extensively in vitro, which has provided detailed molecular mechanisms of transcription. The in vivo cellular environment, however, may impose different rules on transcription than the homogeneous and well-controlled in vitro environment. How an RNA polymerase (RNAP) molecule searches rapidly through vast nonspecific chromosomal DNA in the three-dimensional nucleoid space and identifies a specific promoter sequence remains elusive. Transcription kinetics in vivo could also be impacted by specific cellular environments including nucleoid organization and nutrient availability. In this work, we investigated the promoter search dynamics and transcription kinetics of RNAP in live E. coli cells. Using single-molecule tracking (SMT) and fluorescence recovery after photobleaching (FRAP) across different genetic, drug inhibition, and growth conditions, we observed that RNAP's promoter search is facilitated by nonspecific DNA interactions and is largely independent of nucleoid organization, growth condition, transcription activity, or promoter class. RNAP's transcription kinetics, however, are sensitive to these conditions and mainly modulated at the levels of actively engaged RNAP and the promoter escape rate. Our work establishes a foundation for further mechanistic studies of bacterial transcription in live cells.
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Affiliation(s)
- Kelsey Bettridge
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21287-0010, United States
| | - Frances E Harris
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21287-0010, United States
| | - Nicolás Yehya
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21287-0010, United States
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland 21287-0010, United States
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7
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Iyer MS, Pal A, Venkatesh KV. A Systems Biology Approach To Disentangle the Direct and Indirect Effects of Global Transcription Factors on Gene Expression in Escherichia coli. Microbiol Spectr 2023; 11:e0210122. [PMID: 36749045 PMCID: PMC10100776 DOI: 10.1128/spectrum.02101-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 01/19/2023] [Indexed: 02/08/2023] Open
Abstract
Delineating the pleiotropic effects of global transcriptional factors (TFs) is critical for understanding the system-wide regulatory response in a particular environment. Currently, with the availability of genome-wide TF binding and gene expression data for Escherichia coli, several gene targets can be assigned to the global TFs, albeit inconsistently. Here, using a systematic integrated approach with emphasis on metabolism, we characterized and quantified the direct effects as well as the growth rate-mediated indirect effects of global TFs using deletion mutants of FNR, ArcA, and IHF regulators (focal TFs) under glucose fermentative conditions. This categorization enabled us to disentangle the dense connections seen within the transcriptional regulatory network (TRN) and determine the exact nature of focal TF-driven epistatic interactions with other global and pathway-specific local regulators (iTFs). We extended our analysis to combinatorial deletions of these focal TFs to determine their cross talk effects as well as conserved patterns of regulatory interactions. Moreover, we predicted with high confidence several novel metabolite-iTF interactions using inferred iTF activity changes arising from the allosteric effects of the intracellular metabolites perturbed as a result of the absence of focal TFs. Further, using compendium level computational analyses, we revealed not only the coexpressed genes regulated by these focal TFs but also the coordination of the direct and indirect target expression in the context of the economy of intracellular metabolites. Overall, this study leverages the fundamentals of TF-driven regulation, which could serve as a better template for deciphering mechanisms underlying complex phenotypes. IMPORTANCE Understanding the pleiotropic effects of global TFs on gene expression and their relevance underlying a specific response in a particular environment has been challenging. Here, we distinguish the TF-driven direct effects and growth rate-mediated indirect effects on gene expression using single- and double-deletion mutants of FNR, ArcA, and IHF regulators under anaerobic glucose fermentation. Such dissection assists us in unraveling the precise nature of interactions existing between the focal TF(s) and several other TFs, including those altered by allosteric effects of intracellular metabolites. We were able to recapitulate the previously known metabolite-TF interactions and predict novel interactions with high confidence. Furthermore, we determined that the direct and indirect gene expression have a strong connection with each other when analyzed using the coexpressed- or coregulated-gene approach. Deciphering such regulatory patterns explicitly from the metabolism point of view would be valuable in understanding other unpredicted complex regulation existing in nature.
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Affiliation(s)
- Mahesh S. Iyer
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Ankita Pal
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - K. V. Venkatesh
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
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8
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Wisniewska A, Wons E, Potrykus K, Hinrichs R, Gucwa K, Graumann PL, Mruk I. Molecular basis for lethal cross-talk between two unrelated bacterial transcription factors - the regulatory protein of a restriction-modification system and the repressor of a defective prophage. Nucleic Acids Res 2022; 50:10964-10980. [PMID: 36271797 DOI: 10.1093/nar/gkac914] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/29/2022] [Accepted: 10/06/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial gene expression depends on the efficient functioning of global transcriptional networks, however their interconnectivity and orchestration rely mainly on the action of individual DNA binding proteins called transcription factors (TFs). TFs interact not only with their specific target sites, but also with secondary (off-target) sites, and vary in their promiscuity. It is not clear yet what mechanisms govern the interactions with secondary sites, and how such rewiring affects the overall regulatory network, but this could clearly constrain horizontal gene transfer. Here, we show the molecular mechanism of one such off-target interaction between two unrelated TFs in Escherichia coli: the C regulatory protein of a Type II restriction-modification system, and the RacR repressor of a defective prophage. We reveal that the C protein interferes with RacR repressor expression, resulting in derepression of the toxic YdaT protein. These results also provide novel insights into regulation of the racR-ydaST operon. We mapped the C regulator interaction to a specific off-target site, and also visualized C protein dynamics, revealing intriguing differences in single molecule dynamics in different genetic contexts. Our results demonstrate an apparent example of horizontal gene transfer leading to adventitious TF cross-talk with negative effects on the recipient's viability. More broadly, this study represents an experimentally-accessible model of a regulatory constraint on horizontal gene transfer.
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Affiliation(s)
- Aleksandra Wisniewska
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ewa Wons
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Katarzyna Potrykus
- Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Rebecca Hinrichs
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Philipps Universität Marburg, Germany.,Department of Chemistry, Philipps Universität Marburg, Hans-Meerwein-Strasse 6, 35032 Marburg, Germany
| | - Katarzyna Gucwa
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Peter L Graumann
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Philipps Universität Marburg, Germany.,Department of Chemistry, Philipps Universität Marburg, Hans-Meerwein-Strasse 6, 35032 Marburg, Germany
| | - Iwona Mruk
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
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9
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Andon JS, Lee B, Wang T. Enzyme directed evolution using genetically encodable biosensors. Org Biomol Chem 2022; 20:5891-5906. [PMID: 35437559 DOI: 10.1039/d2ob00443g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Directed evolution has been remarkably successful in identifying enzyme variants with new or improved properties, such as altered substrate scope or novel reactivity. Genetically encodable biosensors (GEBs), which convert the concentration of a small molecule ligand into an easily detectable output signal, have seen increasing application to enzyme directed evolution in the last decade. GEBs enable the use of high-throughput methods to assess enzyme activity of very large libraries, which can accelerate the search for variants with desirable activity. Here, we review different classes of GEBs and their properties in the context of enzyme evolution, how GEBs have been integrated into directed evolution workflows, and recent examples of enzyme evolution efforts utilizing GEBs. Finally, we discuss the advantages, challenges, and opportunities for using GEBs in the directed evolution of enzymes.
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Affiliation(s)
- James S Andon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - ByungUk Lee
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Tina Wang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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10
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Duarte-Velázquez I, de la Mora J, Ramírez-Prado JH, Aguillón-Bárcenas A, Tornero-Gutiérrez F, Cordero-Loreto E, Anaya-Velázquez F, Páramo-Pérez I, Rangel-Serrano Á, Muñoz-Carranza SR, Romero-González OE, Cardoso-Reyes LR, Rodríguez-Ojeda RA, Mora-Montes HM, Vargas-Maya NI, Padilla-Vaca F, Franco B. Escherichia coli transcription factors of unknown function: sequence features and possible evolutionary relationships. PeerJ 2022; 10:e13772. [PMID: 35880217 PMCID: PMC9308461 DOI: 10.7717/peerj.13772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/01/2022] [Indexed: 01/17/2023] Open
Abstract
Organisms need mechanisms to perceive the environment and respond accordingly to environmental changes or the presence of hazards. Transcription factors (TFs) are required for cells to respond to the environment by controlling the expression of genes needed. Escherichia coli has been the model bacterium for many decades, and still, there are features embedded in its genome that remain unstudied. To date, 58 TFs remain poorly characterized, although their binding sites have been experimentally determined. This study showed that these TFs have sequence variation at the third codon position G+C content but maintain the same Codon Adaptation Index (CAI) trend as annotated functional transcription factors. Most of these transcription factors are in areas of the genome where abundant repetitive and mobile elements are present. Sequence divergence points to groups with distinctive sequence signatures but maintaining the same type of DNA binding domain. Finally, the analysis of the promoter sequences of the 58 TFs showed A+T rich regions that agree with the features of horizontally transferred genes. The findings reported here pave the way for future research of these TFs that may uncover their role as spare factors in case of lose-of-function mutations in core TFs and trace back their evolutionary history.
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Affiliation(s)
- Isabel Duarte-Velázquez
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Javier de la Mora
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autonoma de Mexico, Mexico City, México
| | | | - Alondra Aguillón-Bárcenas
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Fátima Tornero-Gutiérrez
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Eugenia Cordero-Loreto
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Fernando Anaya-Velázquez
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Itzel Páramo-Pérez
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Ángeles Rangel-Serrano
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | | | | | - Luis Rafael Cardoso-Reyes
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | | | - Héctor Manuel Mora-Montes
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Naurú Idalia Vargas-Maya
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Felipe Padilla-Vaca
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
| | - Bernardo Franco
- Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México
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11
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Keshav A, Murarka P, Srivastava P. Bending is required for activation of dsz operon by the TetR family protein (DszGR). Gene 2022; 810:146061. [PMID: 34774682 DOI: 10.1016/j.gene.2021.146061] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 10/11/2021] [Accepted: 10/26/2021] [Indexed: 11/24/2022]
Abstract
The dsz operon responsible for the biodesulfurization of organosulfurs is under the control of a 385 bp long promoter. Recently, a TetR family protein was identified which served as an activator of operon. Here we report that the TetR family protein (WP_058249973.1), named DszGR can specifically activate the dsz operon. Direct binding of the DszGR to DNA was observed at single molecule level by AFM. It was found that the binding of DszGR to the promoter DNA induces a bend by about ∼40-50° degrees which may not be enough for the activation of the promoter. Thus, bendability in the promoter sequence was analyzed. The results show that the promoter has a curvature at around -235 and -200 bp with respect to dszA start codon. On mutating this region, a decrease in activity of the promoter was observed. Our results suggest that the DszGR protein binds to the upstream sequences and induces a bend, which is facilitated by further bending of the DNA which is required for dsz promoter activity. IHF binding site present in the promoter, and a significant reduction in desulphurization activity in the absence of either IHF subunits, suggested role of IHF in regulation of the dsz operon.
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Affiliation(s)
- Aditi Keshav
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Pooja Murarka
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology Delhi, New Delhi, India
| | - Preeti Srivastava
- Department of Biochemical Engineering & Biotechnology, Indian Institute of Technology Delhi, New Delhi, India.
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12
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Pal A, Iyer MS, Srinivasan S, Narain Seshasayee AS, Venkatesh KV. Global pleiotropic effects in adaptively evolved Escherichia coli lacking CRP reveal molecular mechanisms that define the growth physiology. Open Biol 2022; 12:210206. [PMID: 35167766 PMCID: PMC8846999 DOI: 10.1098/rsob.210206] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Evolution facilitates emergence of fitter phenotypes by efficient allocation of cellular resources in conjunction with beneficial mutations. However, system-wide pleiotropic effects that redress the perturbations to the apex node of the transcriptional regulatory networks remain unclear. Here, we elucidate that absence of global transcriptional regulator CRP in Escherichia coli results in alterations in key metabolic pathways under glucose respiratory conditions, favouring stress- or hedging-related functions over growth-enhancing functions. Further, we disentangle the growth-mediated effects from the CRP regulation-specific effects on these metabolic pathways. We quantitatively illustrate that the loss of CRP perturbs proteome efficiency, as evident from metabolic as well as ribosomal proteome fractions, that corroborated with intracellular metabolite profiles. To address how E. coli copes with such systemic defect, we evolved Δcrp mutant in the presence of glucose. Besides acquiring mutations in the promoter of glucose transporter ptsG, the evolved populations recovered the metabolic pathways to their pre-perturbed state coupled with metabolite re-adjustments, which altogether enabled increased growth. By contrast to Δcrp mutant, the evolved strains remodelled their proteome efficiency towards biomass synthesis, albeit at the expense of carbon efficiency. Overall, we comprehensively illustrate the genetic and metabolic basis of pleiotropic effects, fundamental for understanding the growth physiology.
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Affiliation(s)
- Ankita Pal
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Mahesh S. Iyer
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sumana Srinivasan
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | | | - K. V. Venkatesh
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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13
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Wenholz DS, Miller M, Dawson C, Bhadbhade M, Black DS, Griffith R, Dinh H, Cain A, Lewis P, Kumar N. Inhibitors of bacterial RNA polymerase transcription complex. Bioorg Chem 2021; 118:105481. [PMID: 34801947 DOI: 10.1016/j.bioorg.2021.105481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 11/02/2021] [Accepted: 11/07/2021] [Indexed: 01/28/2023]
Abstract
A series of hybrid compounds that incorporated anthranilic acid with activated 1H-indoles through a glyoxylamide linker were designed to target bacterial RNA polymerase holoenzyme formation using computational docking. Synthesis, in vitro transcription inhibition assays, and biological testing of the hybrids identified a range of potent anti-transcription inhibitors with activity against a range of pathogenic bacteria with MICs as low as 3.1 μM. A structure activity relationship study identified the key structural components necessary for inhibition of both bacterial growth and transcription. Correlation of in vitro transcription inhibition activity with in vivo mechanism of action was established using fluorescence microscopy and resistance passaging using Gram-positive bacteria showed no resistance development over 30 days. Furthermore, no toxicity was observed from the compounds in a wax moth larvae model, establishing a platform for the development of a series of new antibacterial drugs with an established mode of action.
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Affiliation(s)
- Daniel S Wenholz
- School of Chemistry, UNSW Sydney, Kensington, NSW 2502, Australia
| | - Michael Miller
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Catherine Dawson
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Mohan Bhadbhade
- Mark Wainwright Analytical Centre, UNSW Sydney, NSW 2052, Australia
| | - David StC Black
- School of Chemistry, UNSW Sydney, Kensington, NSW 2502, Australia
| | - Renate Griffith
- School of Chemistry, UNSW Sydney, Kensington, NSW 2502, Australia
| | - Hue Dinh
- Department of Biological Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Amy Cain
- Department of Biological Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Peter Lewis
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia; School of Chemistry and Molecular Bioscience, University of Wollongong and Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Naresh Kumar
- School of Chemistry, UNSW Sydney, Kensington, NSW 2502, Australia.
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14
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Grimwade JE, Leonard AC. Blocking, Bending, and Binding: Regulation of Initiation of Chromosome Replication During the Escherichia coli Cell Cycle by Transcriptional Modulators That Interact With Origin DNA. Front Microbiol 2021; 12:732270. [PMID: 34616385 PMCID: PMC8488378 DOI: 10.3389/fmicb.2021.732270] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/18/2021] [Indexed: 11/25/2022] Open
Abstract
Genome duplication is a critical event in the reproduction cycle of every cell. Because all daughter cells must inherit a complete genome, chromosome replication is tightly regulated, with multiple mechanisms focused on controlling when chromosome replication begins during the cell cycle. In bacteria, chromosome duplication starts when nucleoprotein complexes, termed orisomes, unwind replication origin (oriC) DNA and recruit proteins needed to build new replication forks. Functional orisomes comprise the conserved initiator protein, DnaA, bound to a set of high and low affinity recognition sites in oriC. Orisomes must be assembled each cell cycle. In Escherichia coli, the organism in which orisome assembly has been most thoroughly examined, the process starts with DnaA binding to high affinity sites after chromosome duplication is initiated, and orisome assembly is completed immediately before the next initiation event, when DnaA interacts with oriC’s lower affinity sites, coincident with origin unwinding. A host of regulators, including several transcriptional modulators, targets low affinity DnaA-oriC interactions, exerting their effects by DNA bending, blocking access to recognition sites, and/or facilitating binding of DnaA to both DNA and itself. In this review, we focus on orisome assembly in E. coli. We identify three known transcriptional modulators, SeqA, Fis (factor for inversion stimulation), and IHF (integration host factor), that are not essential for initiation, but which interact directly with E. coli oriC to regulate orisome assembly and replication initiation timing. These regulators function by blocking sites (SeqA) and bending oriC DNA (Fis and IHF) to inhibit or facilitate cooperative low affinity DnaA binding. We also examine how the growth rate regulation of Fis levels might modulate IHF and DnaA binding to oriC under a variety of nutritional conditions. Combined, the regulatory mechanisms mediated by transcriptional modulators help ensure that at all growth rates, bacterial chromosome replication begins once, and only once, per cell cycle.
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Affiliation(s)
- Julia E Grimwade
- Microbial Genetics Laboratory, Biological Sciences Program, Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, United States
| | - Alan C Leonard
- Microbial Genetics Laboratory, Biological Sciences Program, Department of Biomedical and Chemical Engineering and Sciences, Florida Institute of Technology, Melbourne, FL, United States
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15
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Cazier AP, Blazeck J. Advances in promoter engineering: novel applications and predefined transcriptional control. Biotechnol J 2021; 16:e2100239. [PMID: 34351706 DOI: 10.1002/biot.202100239] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/08/2022]
Abstract
Synthetic biology continues to progress by relying on more robust tools for transcriptional control, of which promoters are the most fundamental component. Numerous studies have sought to characterize promoter function, determine principles to guide their engineering, and create promoters with stronger expression or tailored inducible control. In this review, we will summarize promoter architecture and highlight recent advances in the field, focusing on the novel applications of inducible promoter design and engineering towards metabolic engineering and cellular therapeutic development. Additionally, we will highlight how the expansion of new, machine learning techniques for modeling and engineering promoter sequences are enabling more accurate prediction of promoter characteristics. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Andrew P Cazier
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst St. NW, Atlanta, Georgia, 30332, USA
| | - John Blazeck
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 311 Ferst St. NW, Atlanta, Georgia, 30332, USA
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16
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Wurihan W, Weber AM, Gong Z, Lou Z, Sun S, Zhou J, Fan H. GrgA overexpression inhibits Chlamydia trachomatis growth through sigma 66- and sigma 28-dependent mechanisms. Microb Pathog 2021; 156:104917. [PMID: 33940135 DOI: 10.1016/j.micpath.2021.104917] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 01/21/2023]
Abstract
The obligate intracellular bacterium Chlamydia trachomatis is an important human pathogen with a biphasic developmental cycle comprised of an infectious elementary body (EB) and a replicative reticulate body (RB). Whereas σ66, the primary sigma factor, is necessary for transcription of most chlamydial genes throughout the developmental cycle, σ28 is required for expression of some late genes. We previously showed that the Chlamydia-specific transcription factor GrgA physically interacts with both of these sigma factors and activates transcription from σ66- and σ28-dependent promoters in vitro. Here, we investigated the organismal functions of GrgA. We show that overexpression of GrgA slows EB-to-RB conversion, decreases RB proliferation, and reduces progeny EB production. In contrast, overexpression of a GrgA variant without the σ28-binding domain shows significantly less severe inhibitory effects, while overexpression of a variant without the σ66-binding domain demonstrates no adverse effects. These findings indicate that GrgA plays important roles in the expression regulation of both σ66-dependent genes and σ28-dependent genes during the chlamydial developmental cycle.
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Affiliation(s)
- Wurihan Wurihan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Alec M Weber
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Zheng Gong
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Zhongzi Lou
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, Piscataway, NJ, 08854, USA; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Samantha Sun
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Jizhang Zhou
- Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, China
| | - Huizhou Fan
- Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, Piscataway, NJ, 08854, USA.
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17
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Serdyukov DS, Goryachkovskaya TN, Mescheryakova IA, Kuznetsov SA, Popik VM, Peltek SE. Fluorescent bacterial biosensor E. coli/pTdcR-TurboYFP sensitive to terahertz radiation. BIOMEDICAL OPTICS EXPRESS 2021; 12:705-721. [PMID: 33680537 PMCID: PMC7901329 DOI: 10.1364/boe.412074] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 05/05/2023]
Abstract
A fluorescent biosensor E. coli/pTdcR-TurboYFP sensitive to terahertz (THz) radiation was developed via transformation of Escherichia coli (E. coli) cells with plasmid, in which the promotor of the tdcR gene controls the expression of yellow fluorescent protein TurboYFP. The biosensor was exposed to THz radiation in various vessels and nutrient media. The threshold and dynamics of fluorescence were found to depend on irradiation conditions. Heat shock or chemical stress yielded the absence of fluorescence induction. The biosensor is applicable to studying influence of THz radiation on the activity of tdcR promotor that is involved in the transport and metabolism of threonine and serine in E. coli.
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Affiliation(s)
- Danil S. Serdyukov
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, 630090, Russia
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, 630090, Russia
- Institute of Laser Physics of the Siberian Branch of the Russian Academy of Sciences, 15B Lavrentiev Aven., Novosibirsk, 630090, Russia
| | - Tatiana N. Goryachkovskaya
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, 630090, Russia
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, 630090, Russia
| | - Irina A. Mescheryakova
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, 630090, Russia
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, 630090, Russia
| | - Sergei A. Kuznetsov
- Physics Department of Novosibirsk State University, 2 Pirogov Str., Novosibirsk, 630090, Russia
- Technological Design Institute of Applied Microelectronics — Novosibirsk Branch of Rzhanov Institute of Semiconductor Physics of the Siberian Branch of the Russian Academy of Sciences, 2/1 Lavrentiev Aven., Novosibirsk, 630090, Russia
| | - Vasiliy M. Popik
- Budker Institute of Nuclear Physics of the Siberian Branch of the Russian Academy of Sciences, 11 Lavrentiev Aven., Novosibirsk, 630090, Russia
| | - Sergey E. Peltek
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, 630090, Russia
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, 630090, Russia
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18
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Widespread Strain-Specific Distinctions in Chromosomal Binding Dynamics of a Highly Conserved Escherichia coli Transcription Factor. mBio 2020; 11:mBio.01058-20. [PMID: 32576674 PMCID: PMC7315121 DOI: 10.1128/mbio.01058-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial gene regulation is governed by often hundreds of transcription factors (TFs) that bind directly to targets on the chromosome. Global studies of TFs usually make assumptions that regulatory targets within model strains will be conserved between members of the same species harboring common genetic targets. We recently discovered that YhaJ of Escherichia coli is crucial for virulence in two different pathotypes but binds to distinct regions of their genomes and regulates no common genes. This surprising result leads to strain-specific mechanisms of virulence regulation, but the implications for other E. coli pathotypes or commensals were unclear. Here, we report that heterogenous binding of YhaJ is widespread within the E. coli species. We analyzed the global YhaJ binding dynamics of four evolutionarily distinct E. coli isolates under two conditions, revealing 78 significant sites on the core genome as well as horizontally acquired loci. Condition-dependent dosage of YhaJ correlated with the number of occupied sites in vivo but did not significantly alter its enrichment at regions bound in both conditions, explaining the availability of this TF to occupy accessory sites in response to the environment. Strikingly, only ∼15% of YhaJ binding sites were common to all strains. Furthermore, differences in enrichment of uncommon sites were observed largely in chromosomal regions found in all strains and not explained exclusively by binding to strain-specific horizontally acquired elements or mutations in the DNA binding sequence. This observation suggests that intraspecies distinctions in TF binding dynamics are a widespread phenomenon and represent strain-specific gene regulatory potential.IMPORTANCE In bacterial cells, hundreds of transcription factors coordinate gene regulation and thus are a major driver of cellular processes. However, the immense diversity in bacterial genome structure and content makes deciphering regulatory networks challenging. This is particularly apparent for the model organism Escherichia coli as evolution has driven the emergence of species members with highly distinct genomes, which occupy extremely different niches in nature. While it is well-known that transcription factors must integrate horizontally acquired DNA into the regulatory network of the cell, the extent of regulatory diversity beyond single model strains is unclear. We have explored this concept in four evolutionarily distinct E. coli strains and show that a highly conserved transcription factor displays unprecedented diversity in chromosomal binding sites. Importantly, this diversity is not restricted to strain-specific DNA or mutation in binding sites. This observation suggests that strain-specific regulatory networks are potentially widespread within individual bacterial species.
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19
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Singhvi N, Gupta V, Singh P, Prakash O, Bechthold A, Singh Y, Lal R. Prediction of Transcription Factors and Their Involvement in Regulating Rifamycin Production in Amycolatopsis mediterranei S699. Indian J Microbiol 2020; 60:310-317. [PMID: 32655198 DOI: 10.1007/s12088-020-00868-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/03/2020] [Indexed: 12/16/2022] Open
Abstract
Amycolatopsis mediterranei S699 produces rifamycin B and successors of this strain are in use for the industrial production of rifamycin B. Semisynthetic derivatives of rifamycin B are used against Mycobacterium tuberculosis that causes tuberculosis. Although the rifamycin biosynthetic gene cluster was characterized two decades ago, the regulation of rifamycin B biosynthesis in Amycolatopsis mediterranei S699 is poorly understood. In this study, we analysed the genome and proteome of Amycolatopsis mediterranei S699 and identified 1102 transcription factors which comprise about 10% of the total genome. Using interactomics approaches we delineated 30 unique transcription factors directly involved in secondary metabolism that regulate rifamycin B biosynthesis. We also predict the role of RifN as hub in controlling the regulation of other genes involved in rifamycin biosynthesis. RifN is important for maintaining the integrity of the rifamycin-network. Thus, these transcription factor can be exploited to improve rifamycin B production in Amycolatopsis mediterranei S699.
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Affiliation(s)
- Nirjara Singhvi
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Vipin Gupta
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Priya Singh
- Department of Zoology, University of Delhi, Delhi, 110007 India.,Present Address: Acharya Narendra Dev College, University of Delhi, New Delhi, 110019 India
| | - Om Prakash
- National Centre for Cell Sciences, Pune, Maharashtra 411007 India
| | - Andreas Bechthold
- Pharmaceutical Biology and Biotechnology, Institute of Pharmaceutical Sciences, Albert-Ludwigs University, 79104 Freiburg, Germany
| | - Yogendra Singh
- Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Rup Lal
- The Energy and Resources Institute, Darbari Seth Block, IHC Complex, New Delhi, 110033 India
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20
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Suter DM. Transcription Factors and DNA Play Hide and Seek. Trends Cell Biol 2020; 30:491-500. [PMID: 32413318 DOI: 10.1016/j.tcb.2020.03.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 01/12/2023]
Abstract
Transcription factors (TFs) bind to specific DNA motifs to regulate the expression of target genes. To reach their binding sites, TFs diffuse in 3D and perform local motions such as 1D sliding, hopping, or intersegmental transfer. TF-DNA interactions depend on multiple parameters, such as the chromatin environment, TF partitioning into distinct subcellular regions, and cooperativity with other DNA-binding proteins. In this review, how current understanding of the search process has initially been shaped by prokaryotic studies is discussed, as well as what is known about the parameters regulating TF search efficiency in the context of the complex eukaryotic chromatin landscape.
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Affiliation(s)
- David M Suter
- Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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21
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An improved bind-n-seq strategy to determine protein-DNA interactions validated using the bacterial transcriptional regulator YipR. BMC Microbiol 2020; 20:1. [PMID: 31896348 PMCID: PMC6941359 DOI: 10.1186/s12866-019-1672-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 12/03/2019] [Indexed: 11/10/2022] Open
Abstract
Background Interactions between transcription factors and DNA lie at the centre of many biological processes including DNA recombination, replication, repair and transcription. Most bacteria encode diverse proteins that act as transcription factors to regulate various traits. Several technologies for identifying protein–DNA interactions at the genomic level have been developed. Bind-n-seq is a high-throughput in vitro method first deployed to analyse DNA interactions associated with eukaryotic zinc-finger proteins. The method has three steps (i) binding protein to a randomised oligonucleotide DNA target library, (ii) deep sequencing of bound oligonucleotides, and (iii) a computational algorithm to define motifs among the sequences. The classical Bind-n-seq strategy suffers from several limitations including a lengthy wet laboratory protocol and a computational algorithm that is difficult to use. We introduce here an improved, rapid, and simplified Bind-n-seq protocol coupled with a user-friendly downstream data analysis and handling algorithm, which has been optimized for bacterial target proteins. We validate this new protocol by showing the successful characterisation of the DNA-binding specificities of YipR (YajQ interacting protein regulator), a well-known transcriptional regulator of virulence genes in the bacterial phytopathogen Xanthomonas campestris pv. campestris (Xcc). Results The improved Bind-n-seq approach identified several DNA binding motif sequences for YipR, in particular the CCCTCTC motif, which were located in the promoter regions of 1320 Xcc genes. Informatics analysis revealed that many of these genes regulate functions associated with virulence, motility, and biofilm formation and included genes previously found involved in virulence. Additionally, electromobility shift assays show that YipR binds to the promoter region of XC_2633 in a CCCTCTC motif-dependent manner. Conclusion We present a new and rapid Bind-n-seq protocol that should be useful to investigate DNA-binding proteins in bacteria. The analysis of YipR DNA binding using this protocol identifies a novel DNA sequence motif in the promoter regions of target genes that define the YipR regulon.
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22
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Distinct intraspecies virulence mechanisms regulated by a conserved transcription factor. Proc Natl Acad Sci U S A 2019; 116:19695-19704. [PMID: 31501343 PMCID: PMC6765310 DOI: 10.1073/pnas.1903461116] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Bacterial pathogens emerge by adapting mechanisms of virulence, differentiating them from their nonpathogenic progenitor. Virulence factors are often encoded on accessory genomic elements not part of the core genome and therefore must be integrated into the regulatory architecture of the cell. Here, we show that a highly conserved transcription factor in Escherichia coli has been relieved of a common purpose and adapted to regulate virulence pleiotropically in 2 distinct genetic backgrounds. This leads to enhanced virulence of both intestinal enterohemorrhagic E. coli and extraintestinal uropathogenic E. coli by exclusive mechanisms. These findings challenge the assumption that conserved transcription factors regulate common pathways maintained within a species and suggest that transcriptional repurposing creates new primary roles on an individual basis. Tailoring transcriptional regulation to coordinate the expression of virulence factors in tandem with the core genome is a hallmark of bacterial pathogen evolution. Bacteria encode hundreds of transcription factors forming the base-level control of gene regulation. Moreover, highly homologous regulators are assumed to control conserved genes between members within a species that harbor the same genetic targets. We have explored this concept in 2 Escherichia coli pathotypes that employ distinct virulence mechanisms that facilitate specification of a different niche within the host. Strikingly, we found that the transcription factor YhaJ actively regulated unique gene sets between intestinal enterohemorrhagic E. coli (EHEC) and extraintestinal uropathogenic E. coli (UPEC), despite being very highly conserved. In EHEC, YhaJ directly activates expression of type 3 secretion system components and effectors. Alternatively, YhaJ enhances UPEC virulence regulation by binding directly to the phase-variable type 1 fimbria promoter, driving its expression. Additionally, YhaJ was found to override the universal GAD acid tolerance system but exclusively in EHEC, thereby indirectly enhancing type 3 secretion pleiotropically. These results have revealed that within a species, conserved regulators are actively repurposed in a “personalized” manner to benefit particular lifestyles and drive virulence via multiple distinct mechanisms.
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23
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Structural and DNA-binding studies of the PadR-like transcriptional regulator BC1756 from Bacillus cereus. Biochem Biophys Res Commun 2019; 515:607-613. [PMID: 31178139 DOI: 10.1016/j.bbrc.2019.05.141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 05/22/2019] [Indexed: 02/03/2023]
Abstract
Transcription factors that belong to the PadR family play an essential role in the transcriptional regulation of diverse biological processes by recognizing their cognate palindromic DNA sequences. Bacillus cereus harbors a gene that encodes a PadR-like protein (bcPLP; BC1756). bcPLP has not been structurally characterized, and it remains unelucidated how bcPLP interacts with a specific DNA sequence to function as a transcription factor. To provide structural insights into DNA recognition by bcPLP, we performed a structural study and a DNA-binding analysis of bcPLP. The crystal structure of bcPLP was determined at 1.92 Å resolution. bcPLP consists of two domains, an N-terminal domain (NTD) and a C-terminal domain (CTD), and forms a homodimer mainly using the CTD. In the structure, bcPLP contains a highly positively charged elongated patch in the NTD that serves as a putative DNA-binding site. Indeed, an electrophoresis mobility shift assay and a fluorescence polarization assay showed that bcPLP specifically recognizes a palindromic DNA sequence upstream of the bcPLP-encoding region. Moreover, based on our mutagenesis and modeling studies, we demonstrate that bcPLP interacts with dsDNA primarily using the Y19, Y41, P64, and K66 residues in the NTD.
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24
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Fernández‐Cabezón L, Cros A, Nikel PI. Evolutionary Approaches for Engineering Industrially Relevant Phenotypes in Bacterial Cell Factories. Biotechnol J 2019; 14:e1800439. [DOI: 10.1002/biot.201800439] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/08/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Lorena Fernández‐Cabezón
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark 2800 Kongens Lyngby Denmark
| | - Antonin Cros
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark 2800 Kongens Lyngby Denmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark 2800 Kongens Lyngby Denmark
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25
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Liu FY, Lo SC, Shu CC. The Reaction of Dimerization by Itself Reduces the Noise Intensity of the Protein Monomer. Sci Rep 2019; 9:3405. [PMID: 30833660 PMCID: PMC6399348 DOI: 10.1038/s41598-019-39611-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/29/2019] [Indexed: 12/22/2022] Open
Abstract
Because of the small particle number of intracellular species participating in genetic circuits, stochastic fluctuations are inevitable. This intracellular noise is detrimental to precise regulation. To maintain the proper function of a cell, some natural motifs attenuate the noise at the protein level. In many biological systems, the protein monomer is used as a regulator, but the protein dimer also exists. In the present study, we demonstrated that the dimerization reaction reduces the noise intensity of the protein monomer. Compared with two common noise-buffering motifs, the incoherent feedforward loop (FFL) and negative feedback control, the coefficient of variation (COV) in the case of dimerization was 25% less. Furthermore, we examined a system with direct interaction between proteins and other ligands. Both the incoherent FFL and negative feedback control failed to buffer the noise, but the dimerization was effective. Remarkably, the formation of only one protein dimer was sufficient to cause a 7.5% reduction in the COV.
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Affiliation(s)
- Feng-You Liu
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei City, Taiwan R.O.C
| | - Shih-Chiang Lo
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei City, Taiwan R.O.C
| | - Che-Chi Shu
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei City, Taiwan R.O.C..
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26
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Girardin RC, Bai G, He J, Sui H, McDonough KA. AbmR (Rv1265) is a novel transcription factor of Mycobacterium tuberculosis that regulates host cell association and expression of the non-coding small RNA Mcr11. Mol Microbiol 2018; 110:811-830. [PMID: 30207611 PMCID: PMC6282994 DOI: 10.1111/mmi.14126] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/07/2018] [Accepted: 09/09/2018] [Indexed: 12/11/2022]
Abstract
Gene regulatory networks used by Mycobacterium tuberculosis (Mtb) during infection include many genes of unknown function, confounding efforts to determine their roles in Mtb biology. Rv1265 encodes a conserved hypothetical protein that is expressed during infection and in response to elevated levels of cyclic AMP. Here, we report that Rv1265 is a novel auto‐inhibitory ATP‐binding transcription factor that upregulates expression of the small non‐coding RNA Mcr11, and propose that Rv1265 be named ATP‐binding mcr11regulator (AbmR). AbmR directly and specifically bound DNA, as determined by electrophoretic mobility shift assays, and this DNA‐binding activity was enhanced by AbmR’s interaction with ATP. Genetic knockout of abmR in Mtb increased abmR promoter activity and eliminated growth phase‐dependent increases in mcr11 expression during hypoxia. Mutagenesis identified arginine residues in the carboxy terminus that are critical for AbmR’s DNA‐binding activity and gene regulatory function. Limited similarity to other DNA‐ or ATP‐binding domains suggests that AbmR belongs to a novel class of DNA‐ and ATP‐binding proteins. AbmR was also found to form large organized structures in solution and facilitate the serum‐dependent association of Mtb with human lung epithelial cells. These results indicate a potentially complex role for AbmR in Mtb biology.
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Affiliation(s)
- Roxie C Girardin
- Department of Biomedical Sciences, School of Public Health, University at Albany, PO Box 22002, Albany, NY, 12201-2002, USA
| | - Guangchun Bai
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, USA
| | - Jie He
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Haixin Sui
- Department of Biomedical Sciences, School of Public Health, University at Albany, PO Box 22002, Albany, NY, 12201-2002, USA.,Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Kathleen A McDonough
- Department of Biomedical Sciences, School of Public Health, University at Albany, PO Box 22002, Albany, NY, 12201-2002, USA.,Wadsworth Center, New York State Department of Health, Albany, NY, USA
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27
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Pinheiro J, Lisboa J, Pombinho R, Carvalho F, Carreaux A, Brito C, Pöntinen A, Korkeala H, dos Santos NM, Morais-Cabral JH, Sousa S, Cabanes D. MouR controls the expression of the Listeria monocytogenes Agr system and mediates virulence. Nucleic Acids Res 2018; 46:9338-9352. [PMID: 30011022 PMCID: PMC6182135 DOI: 10.1093/nar/gky624] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 06/25/2018] [Accepted: 06/28/2018] [Indexed: 12/11/2022] Open
Abstract
The foodborne pathogen Listeria monocytogenes (Lm) causes invasive infection in susceptible animals and humans. To survive and proliferate within hosts, this facultative intracellular pathogen tightly coordinates the expression of a complex regulatory network that controls the expression of virulence factors. Here, we identified and characterized MouR, a novel virulence regulator of Lm. Through RNA-seq transcriptomic analysis, we determined the MouR regulon and demonstrated how MouR positively controls the expression of the Agr quorum sensing system (agrBDCA) of Lm. The MouR three-dimensional structure revealed a dimeric DNA-binding transcription factor belonging to the VanR class of the GntR superfamily of regulatory proteins. We also showed that by directly binding to the agr promoter region, MouR ultimately modulates chitinase activity and biofilm formation. Importantly, we demonstrated by in vitro cell invasion assays and in vivo mice infections the role of MouR in Lm virulence.
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Affiliation(s)
- Jorge Pinheiro
- Group of Molecular Microbiology, IBMC – Institute for Molecular and Cell Biology; i3S – Institute for Research and Innovation in Health, Porto 4200-135, Portugal
- ICBAS- Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto 4200-135, Portugal
| | - Johnny Lisboa
- Group of Fish Immunology & Vaccinology, IBMC – Institute for Molecular and Cell Biology; i3S – Institute for Research and Innovation in Health, Porto 4200-135, Portugal
| | - Rita Pombinho
- Group of Molecular Microbiology, IBMC – Institute for Molecular and Cell Biology; i3S – Institute for Research and Innovation in Health, Porto 4200-135, Portugal
- ICBAS- Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto 4200-135, Portugal
| | - Filipe Carvalho
- Group of Molecular Microbiology, IBMC – Institute for Molecular and Cell Biology; i3S – Institute for Research and Innovation in Health, Porto 4200-135, Portugal
- ICBAS- Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto 4200-135, Portugal
| | - Alexis Carreaux
- Group of Molecular Microbiology, IBMC – Institute for Molecular and Cell Biology; i3S – Institute for Research and Innovation in Health, Porto 4200-135, Portugal
- SDV - UFR Sciences Du Vivant: Université Paris Diderot-Paris 7, Paris 75013, France
| | - Cláudia Brito
- Group of Molecular Microbiology, IBMC – Institute for Molecular and Cell Biology; i3S – Institute for Research and Innovation in Health, Porto 4200-135, Portugal
- ICBAS- Instituto de Ciências Biomédicas Abel Salazar, University of Porto, Porto 4200-135, Portugal
| | - Anna Pöntinen
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki 00014, Finland
| | - Hannu Korkeala
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki 00014, Finland
| | - Nuno M S dos Santos
- Group of Fish Immunology & Vaccinology, IBMC – Institute for Molecular and Cell Biology; i3S – Institute for Research and Innovation in Health, Porto 4200-135, Portugal
| | - João H Morais-Cabral
- Group of Structural Biochemistry, IBMC – Institute for Molecular and Cell Biology; i3S – Institute for Research and Innovation in Health, Porto 4200-135, Portugal
| | - Sandra Sousa
- Group of Molecular Microbiology, IBMC – Institute for Molecular and Cell Biology; i3S – Institute for Research and Innovation in Health, Porto 4200-135, Portugal
| | - Didier Cabanes
- Group of Molecular Microbiology, IBMC – Institute for Molecular and Cell Biology; i3S – Institute for Research and Innovation in Health, Porto 4200-135, Portugal
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28
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Kim Y, Chhor G, Tsai CS, Fox G, Chen CS, Winans NJ, Jedrzejczak R, Joachimiak A, Winans SC. X-ray crystal structures of the pheromone-binding domains of two quorum-hindered transcription factors, YenR of Yersinia enterocolitica and CepR2 of Burkholderia cenocepacia. Proteins 2017; 85:1831-1844. [PMID: 28614901 DOI: 10.1002/prot.25336] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/08/2017] [Accepted: 06/12/2017] [Indexed: 12/17/2022]
Abstract
The ability of LuxR-type proteins to regulate transcription is controlled by bacterial pheromones, N-acylhomoserine lactones (AHLs). Most LuxR-family proteins require their cognate AHLs for activity, and some of them require AHLs for folding and stability, and for protease-resistance. However, a few members of this family are able to fold, dimerize, bind DNA, and regulate transcription in the absence of AHLs; moreover, these proteins are antagonized by their cognate AHLs. One such protein is YenR of Yersinia enterocolitica, which is antagonized by N-3-oxohexanoyl-l-homoserine lactone (OHHL). This pheromone is produced by the OHHL synthase, a product of the adjacent yenI gene. Another example is CepR2 of Burkholderia cenocepacia, which is antagonized by N-octanoyl-l-homoserine lactone (OHL), whose synthesis is directed by the cepI gene of the same bacterium. Here, we describe the high-resolution crystal structures of the AHL binding domains of YenR and CepR2. YenR was crystallized in the presence and absence of OHHL. While this ligand does not cause large scale changes in the YenR structure, it does alter the orientation of several highly conserved YenR residues within and near the pheromone-binding pocket, which in turn caused a significant movement of a surface-exposed loop.
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Affiliation(s)
- Youngchang Kim
- Midwest Center for Structural Genomics, Biosciences, Argonne National Laboratory, Argonne, Illinois, 60439.,Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois, 60439
| | - Gekleng Chhor
- Midwest Center for Structural Genomics, Biosciences, Argonne National Laboratory, Argonne, Illinois, 60439
| | - Ching-Sung Tsai
- Department of Microbiology, Cornell University, Ithaca, New York, 14853
| | - Gabriel Fox
- Department of Microbiology, Cornell University, Ithaca, New York, 14853
| | - Chia-Sui Chen
- Department of Microbiology, Cornell University, Ithaca, New York, 14853
| | - Nathan J Winans
- Department of Microbiology, Cornell University, Ithaca, New York, 14853
| | - Robert Jedrzejczak
- Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois, 60439
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Biosciences, Argonne National Laboratory, Argonne, Illinois, 60439.,Structural Biology Center, Biosciences, Argonne National Laboratory, Argonne, Illinois, 60439.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, 60637
| | - Stephen C Winans
- Department of Microbiology, Cornell University, Ithaca, New York, 14853
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29
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Bacterial Transcription as a Target for Antibacterial Drug Development. Microbiol Mol Biol Rev 2016; 80:139-60. [PMID: 26764017 DOI: 10.1128/mmbr.00055-15] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Transcription, the first step of gene expression, is carried out by the enzyme RNA polymerase (RNAP) and is regulated through interaction with a series of protein transcription factors. RNAP and its associated transcription factors are highly conserved across the bacterial domain and represent excellent targets for broad-spectrum antibacterial agent discovery. Despite the numerous antibiotics on the market, there are only two series currently approved that target transcription. The determination of the three-dimensional structures of RNAP and transcription complexes at high resolution over the last 15 years has led to renewed interest in targeting this essential process for antibiotic development by utilizing rational structure-based approaches. In this review, we describe the inhibition of the bacterial transcription process with respect to structural studies of RNAP, highlight recent progress toward the discovery of novel transcription inhibitors, and suggest additional potential antibacterial targets for rational drug design.
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30
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Camsund D, Lindblad P. Engineered transcriptional systems for cyanobacterial biotechnology. Front Bioeng Biotechnol 2014; 2:40. [PMID: 25325057 PMCID: PMC4181335 DOI: 10.3389/fbioe.2014.00040] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 09/15/2014] [Indexed: 11/13/2022] Open
Abstract
Cyanobacteria can function as solar-driven biofactories thanks to their ability to perform photosynthesis and the ease with which they are genetically modified. In this review, we discuss transcriptional parts and promoters available for engineering cyanobacteria. First, we go through special cyanobacterial characteristics that may impact engineering, including the unusual cyanobacterial RNA polymerase, sigma factors and promoter types, mRNA stability, circadian rhythm, and gene dosage effects. Then, we continue with discussing component characteristics that are desirable for synthetic biology approaches, including decoupling, modularity, and orthogonality. We then summarize and discuss the latest promoters for use in cyanobacteria regarding characteristics such as regulation, strength, and dynamic range and suggest potential uses. Finally, we provide an outlook and suggest future developments that would advance the field and accelerate the use of cyanobacteria for renewable biotechnology.
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Affiliation(s)
- Daniel Camsund
- Science for Life Laboratory, Microbial Chemistry, Department of Chemistry - Ångström, Uppsala University , Uppsala , Sweden
| | - Peter Lindblad
- Science for Life Laboratory, Microbial Chemistry, Department of Chemistry - Ångström, Uppsala University , Uppsala , Sweden
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