1
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Schwab S, Dame RT. Identification, characterization and classification of prokaryotic nucleoid-associated proteins. Mol Microbiol 2024. [PMID: 39039769 DOI: 10.1111/mmi.15298] [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: 04/22/2024] [Revised: 07/02/2024] [Accepted: 07/06/2024] [Indexed: 07/24/2024]
Abstract
Common throughout life is the need to compact and organize the genome. Possible mechanisms involved in this process include supercoiling, phase separation, charge neutralization, macromolecular crowding, and nucleoid-associated proteins (NAPs). NAPs are special in that they can organize the genome at multiple length scales, and thus are often considered as the architects of the genome. NAPs shape the genome by either bending DNA, wrapping DNA, bridging DNA, or forming nucleoprotein filaments on the DNA. In this mini-review, we discuss recent advancements of unique NAPs with differing architectural properties across the tree of life, including NAPs from bacteria, archaea, and viruses. To help the characterization of NAPs from the ever-increasing number of metagenomes, we recommend a set of cheap and simple in vitro biochemical assays that give unambiguous insights into the architectural properties of NAPs. Finally, we highlight and showcase the usefulness of AlphaFold in the characterization of novel NAPs.
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Affiliation(s)
- Samuel Schwab
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
| | - Remus T Dame
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
- Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands
- Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
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2
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Chaisupa P, Wright RC. State-of-the-art in engineering small molecule biosensors and their applications in metabolic engineering. SLAS Technol 2024; 29:100113. [PMID: 37918525 PMCID: PMC11314541 DOI: 10.1016/j.slast.2023.10.005] [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: 07/07/2023] [Revised: 10/18/2023] [Accepted: 10/25/2023] [Indexed: 11/04/2023]
Abstract
Genetically encoded biosensors are crucial for enhancing our understanding of how molecules regulate biological systems. Small molecule biosensors, in particular, help us understand the interaction between chemicals and biological processes. They also accelerate metabolic engineering by increasing screening throughput and eliminating the need for sample preparation through traditional chemical analysis. Additionally, they offer significantly higher spatial and temporal resolution in cellular analyte measurements. In this review, we discuss recent progress in in vivo biosensors and control systems-biosensor-based controllers-for metabolic engineering. We also specifically explore protein-based biosensors that utilize less commonly exploited signaling mechanisms, such as protein stability and induced degradation, compared to more prevalent transcription factor and allosteric regulation mechanism. We propose that these lesser-used mechanisms will be significant for engineering eukaryotic systems and slower-growing prokaryotic systems where protein turnover may facilitate more rapid and reliable measurement and regulation of the current cellular state. Lastly, we emphasize the utilization of cutting-edge and state-of-the-art techniques in the development of protein-based biosensors, achieved through rational design, directed evolution, and collaborative approaches.
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Affiliation(s)
- Patarasuda Chaisupa
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, United States
| | - R Clay Wright
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA 24061, United States; Translational Plant Sciences Center (TPSC), Virginia Tech, Blacksburg, VA 24061, United States.
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3
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Frumkin I, Laub MT. Selection of a de novo gene that can promote survival of Escherichia coli by modulating protein homeostasis pathways. Nat Ecol Evol 2023; 7:2067-2079. [PMID: 37945946 PMCID: PMC10697842 DOI: 10.1038/s41559-023-02224-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 09/12/2023] [Indexed: 11/12/2023]
Abstract
Cellular novelty can emerge when non-functional loci become functional genes in a process termed de novo gene birth. But how proteins with random amino acid sequences beneficially integrate into existing cellular pathways remains poorly understood. We screened ~108 genes, generated from random nucleotide sequences and devoid of homology to natural genes, for their ability to rescue growth arrest of Escherichia coli cells producing the ribonuclease toxin MazF. We identified ~2,000 genes that could promote growth, probably by reducing transcription from the promoter driving toxin expression. Additionally, one random protein, named Random antitoxin of MazF (RamF), modulated protein homeostasis by interacting with chaperones, leading to MazF proteolysis and a consequent loss of its toxicity. Finally, we demonstrate that random proteins can improve during evolution by identifying beneficial mutations that turned RamF into a more efficient inhibitor. Our work provides a mechanistic basis for how de novo gene birth can produce functional proteins that effectively benefit cells evolving under stress.
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Affiliation(s)
- Idan Frumkin
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael T Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Cambridge, MA, USA.
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4
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Zorz J, Paquette AJ, Gillis T, Kouris A, Khot V, Demirkaya C, De La Hoz Siegler H, Strous M, Vadlamani A. Coordinated proteome change precedes cell lysis and death in a mat-forming cyanobacterium. THE ISME JOURNAL 2023; 17:2403-2414. [PMID: 37914776 PMCID: PMC10689466 DOI: 10.1038/s41396-023-01545-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/12/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023]
Abstract
Cyanobacteria form dense multicellular communities that experience transient conditions in terms of access to light and oxygen. These systems are productive but also undergo substantial biomass turnover through cell death, supplementing heightened heterotrophic respiration. Here we use metagenomics and metaproteomics to survey the molecular response of a mat-forming cyanobacterium undergoing mass cell lysis after exposure to dark and anoxic conditions. A lack of evidence for viral, bacterial, or eukaryotic antagonism contradicts commonly held beliefs on the causative agent for cyanobacterial death during dense growth. Instead, proteogenomics data indicated that lysis likely resulted from a genetically programmed response triggered by a failure to maintain osmotic pressure in the wake of severe energy limitation. Cyanobacterial DNA was rapidly degraded, yet cyanobacterial proteins remained abundant. A subset of proteins, including enzymes involved in amino acid metabolism, peptidases, toxin-antitoxin systems, and a potentially self-targeting CRISPR-Cas system, were upregulated upon lysis, indicating possible involvement in the programmed cell death response. We propose this natural form of cell death could provide new pathways for controlling harmful algal blooms and for sustainable bioproduct production.
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Affiliation(s)
- Jackie Zorz
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada.
| | - Alexandre J Paquette
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
| | - Timber Gillis
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
| | - Angela Kouris
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
- Synergia Biotech Inc., Calgary, AB, Canada
| | - Varada Khot
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
| | - Cigdem Demirkaya
- Department of Chemical and Petroleum Engineering, University of Calgary, Calgary, AB, Canada
| | | | - Marc Strous
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
| | - Agasteswar Vadlamani
- Department of Earth, Energy, and Environment, University of Calgary, Calgary, AB, Canada
- Synergia Biotech Inc., Calgary, AB, Canada
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5
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Saha R, Bhattacharje G, De S, Das AK. Deciphering the conformational stability of MazE7 antitoxin in Mycobacterium tuberculosis from molecular dynamics simulation study. J Biomol Struct Dyn 2023:1-17. [PMID: 37965715 DOI: 10.1080/07391102.2023.2280675] [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: 07/24/2023] [Accepted: 11/01/2023] [Indexed: 11/16/2023]
Abstract
MazEF Toxin-antitoxin (TA) systems are associated with the persistent phenotype of the pathogen, Mycobacterium tuberculosis (Mtb), aiding their survival. Though extensively studied, the mode of action between the antitoxin-toxin and DNA of this family remains largely unclear. Here, the important interactions between MazF7 toxin and MazE7 antitoxin, and how MazE7 binds its promoter/operator region have been studied. To elucidate this, molecular dynamics (MD) simulation has been performed on MazE7, MazF7, MazEF7, MazEF7-DNA, and MazE7-DNA complexes to investigate how MazF7 and DNA affect the conformational change and dynamics of MazE7 antitoxin. This study demonstrated that the MazE7 dimer is disordered and one monomer (Chain C) attains stability after binding to the MazF7 toxin. Both the monomers (Chain C and Chain D) however are stabilized when MazE7 binds to DNA. MazE7 is also observed to sterically inhibit tRNA from binding to MazF7, thus suppressing its toxic activity. Comparative structural analysis performed on all the available antitoxins/antitoxin-toxin-DNA structures revealed MazEF7-DNA mechanism was similar to another TA system, AtaRT_E.coli. Simulation performed on the crystal structures of AtaR, AtaT, AtaRT, AtaRT-DNA, and AtaR-DNA showed that the disordered AtaR antitoxin attains stability by AtaT and DNA binding similar to MazE7. Based on these analyses it can thus be hypothesized that the disordered antitoxins enable tighter toxin and DNA binding thus preventing accidental toxin activation. Overall, this study provides crucial structural and dynamic insights into the MazEF7 toxin-antitoxin system and should provide a basis for targeting this TA system in combating Mycobacterium tuberculosis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Rituparna Saha
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Gourab Bhattacharje
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Soumya De
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
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6
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Roy TB, Sarma SP. Insights into the solution structure and transcriptional regulation of the MazE9 antitoxin in Mycobacterium tuberculosis. Proteins 2023. [PMID: 37737533 DOI: 10.1002/prot.26589] [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: 03/21/2023] [Revised: 08/21/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023]
Abstract
The present study endeavors to decode the details of the transcriptional autoregulation effected by the MazE9 antitoxin of the Mycobacterium tuberculosis MazEF9 toxin-antitoxin system. Regulation of this bicistronic operon at the level of transcription is a critical biochemical process that is key for the organism's stress adaptation and virulence. Here, we have reported the solution structure of the DNA binding domain of MazE9 and scrutinized the thermodynamic and kinetic parameters operational in its interaction with the promoter/operator region, specific to the mazEF9 operon. A HADDOCK model of MazE9 bound to its operator DNA has been calculated based on the information on interacting residues obtained from these studies. The thermodynamics and kinetics of the interaction of MazE9 with the functionally related mazEF6 operon indicate that the potential for intracellular cross-regulation is unlikely. An interesting feature of MazE9 is the cis ⇌ trans conformational isomerization of proline residues in the intrinsically disordered C-terminal domain of this antitoxin.
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Affiliation(s)
- Tanaya Basu Roy
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Siddhartha P Sarma
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
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7
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Structural and mutational analysis of MazE6-operator DNA complex provide insights into autoregulation of toxin-antitoxin systems. Commun Biol 2022; 5:963. [PMID: 36109664 PMCID: PMC9477884 DOI: 10.1038/s42003-022-03933-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/30/2022] [Indexed: 11/29/2022] Open
Abstract
Of the 10 paralogs of MazEF Toxin-Antitoxin system in Mycobacterium tuberculosis, MazEF6 plays an important role in multidrug tolerance, virulence, stress adaptation and Non Replicative Persistant (NRP) state establishment. The solution structures of the DNA binding domain of MazE6 and of its complex with the cognate operator DNA show that transcriptional regulation occurs by binding of MazE6 to an 18 bp operator sequence bearing the TANNNT motif (-10 region). Kinetics and thermodynamics of association, as determined by NMR and ITC, indicate that the nMazE6-DNA complex is of high affinity. Residues in N-terminal region of MazE6 that are key for its homodimerization, DNA binding specificity, and the base pairs in the operator DNA essential for the protein-DNA interaction, have been identified. It provides a basis for design of chemotherapeutic agents that will act via disruption of TA autoregulation, leading to cell death. The dimeric MazE6 antitoxin binds to a specific sequence in its cognate operator DNA for autoregulation, and the key residues for dimerization and DNA binding are identified.
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8
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Abstract
Despite their ubiquitous nature, few antisense RNAs have been functionally characterized, and this class of RNAs is considered by some to be transcriptional noise. Here, we report that an antisense RNA (asRNA), aMEF (antisense mazEF), functions as a dual regulator for the type II toxin-antitoxin (TA) system mazEF. Unlike type I TA systems and many other regulatory asRNAs, aMEF stimulates the synthesis and translation of mazEF rather than inhibition and degradation. Our data indicate that a double-stranded RNA intermediate and RNase III are not necessary for aMEF-dependent regulation of mazEF expression. The lack of conservation of asRNA promoters has been used to support the hypothesis that asRNAs are spurious transcriptional noise and nonfunctional. We demonstrate that the aMEF promoter is active and functional in Escherichia coli despite poor sequence conservation, indicating that the lack of promoter sequence conservation should not be correlated with functionality. IMPORTANCE Next-generation RNA sequencing of numerous organisms has revealed that transcription is widespread across the genome, termed pervasive transcription, and does not adhere to annotated gene boundaries. The function of pervasive transcription is enigmatic and has generated considerable controversy as to whether it is transcriptional noise or biologically relevant. Antisense transcription is one class of pervasive transcription that occurs from the DNA strand opposite an annotated gene. Relatively few pervasively transcribed asRNAs have been functionally characterized, and their regulatory roles or lack thereof remains unknown. It is important to study examples of these asRNAs and determine if they are functional regulators. In this study, we elucidate the function of an asRNA (aMEF) demonstrating that pervasive transcripts can be functional.
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Kang J, Kang D, Yeom G, Park CJ. Molecular Diagnostic System Using Engineered Fusion Protein-Conjugated Magnetic Nanoparticles. Anal Chem 2021; 93:16804-16812. [PMID: 34886672 DOI: 10.1021/acs.analchem.1c03247] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
To effectively control the spread of new infectious diseases, there is a need for highly sensitive diagnostic methods to detect viral nucleic acids rapidly. This study outlines a universal and simple detection strategy that uses magnetic nanoparticles (MNPs) and a novel MagR-MazE fusion protein for molecular diagnostics to facilitate sensitive detection. This study has engineered a novel MNP conjugate that can be generated easily, without using many chemical reagents. The technique is a nucleic acid detection method, using MagR-MazE fusion protein-conjugated MNPs, where the results can be visualized with the naked eye, regardless of the oligonucleotide sequences of the target in the lateral flow assay. This method could sensitively detect polymerase chain reaction (PCR) products of 16S ribosomal RNA (rRNA) and the 2019-nCoV-N-positive control gene in 5 min. It shows a low limit of detection (LoD) of 0.013 ng/μL for dsDNA. It is simpler and more rapid, sensitive, and versatile than other techniques, making it suitable for point-of-care testing. The proposed detection system and MNP conjugation strategy using a fusion protein can be widely applied to various fields requiring rapid on-site diagnosis.
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Affiliation(s)
- Juyoung Kang
- SB BIOSCIENCE Co., Ltd., Daejeon34141, South Korea
| | - Donguk Kang
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
| | - Gyuho Yeom
- SB BIOSCIENCE Co., Ltd., Daejeon34141, South Korea
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju61005, South Korea
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10
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Song Y, Luo G, Zhu Y, Li T, Li C, He L, Zhao N, Zhao C, Yang J, Huang Q, Mu X, Tang X, Kang M, Wu S, He Y, Bao R. Pseudomonas aeruginosa antitoxin HigA functions as a diverse regulatory factor by recognizing specific pseudopalindromic DNA motifs. Environ Microbiol 2020; 23:1541-1558. [PMID: 33346387 DOI: 10.1111/1462-2920.15365] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 02/05/2023]
Abstract
Type II toxin-antitoxin (TA) systems modulate many essential cellular processes in prokaryotic organisms. Recent studies indicate certain type II antitoxins also transcriptionally regulate other genes, besides neutralizing toxin activity. Herein, we investigated the diverse transcriptional repression properties of type II TA antitoxin PaHigA from Pseudomonas aeruginosa. Biochemical and functional analyses showed that PaHigA recognized variable pseudopalindromic DNA sequences and repressed expression of multiple genes. Furthermore, we presented high resolution structures of apo-PaHigA, PaHigA-PhigBA and PaHigA-Ppa2440 complex, describing how the rearrangements of the HTH domain accounted for the different DNA-binding patterns among HigA homologues. Moreover, we demonstrated that the N-terminal loop motion of PaHigA was associated with its apo and DNA-bound states, reflecting a switch mechanism regulating HigA antitoxin function. Collectively, this work extends our understanding of how the PaHigB/HigA system regulates multiple metabolic pathways to balance the growth and stress response in P. aeruginosa and could guide further development of anti-TA oriented strategies for pathogen treatment.
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Affiliation(s)
- Yingjie Song
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Guihua Luo
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Yibo Zhu
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Tao Li
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Changcheng Li
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Lihui He
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Ninglin Zhao
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Chang Zhao
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Jing Yang
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Qin Huang
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Xingyu Mu
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Xinyue Tang
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Mei Kang
- Department of Laboratory medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Siying Wu
- Department of Laboratory medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yongxing He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Rui Bao
- Center of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
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11
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Flores-Bautista E, Hernandez-Guerrero R, Huerta-Saquero A, Tenorio-Salgado S, Rivera-Gomez N, Romero A, Ibarra JA, Perez-Rueda E. Deciphering the functional diversity of DNA-binding transcription factors in Bacteria and Archaea organisms. PLoS One 2020; 15:e0237135. [PMID: 32822422 PMCID: PMC7446807 DOI: 10.1371/journal.pone.0237135] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 07/20/2020] [Indexed: 11/18/2022] Open
Abstract
DNA-binding Transcription Factors (TFs) play a central role in regulation of gene expression in prokaryotic organisms, and similarities at the sequence level have been reported. These proteins are predicted with different abundances as a consequence of genome size, where small organisms contain a low proportion of TFs and large genomes contain a high proportion of TFs. In this work, we analyzed a collection of 668 experimentally validated TFs across 30 different species from diverse taxonomical classes, including Escherichia coli K-12, Bacillus subtilis 168, Corynebacterium glutamicum, and Streptomyces coelicolor, among others. This collection of TFs, together with 111 hidden Markov model profiles associated with DNA-binding TFs collected from diverse databases such as PFAM and DBD, was used to identify the repertoire of proteins putatively devoted to gene regulation in 1321 representative genomes of Archaea and Bacteria. The predicted regulatory proteins were posteriorly analyzed in terms of their genomic context, allowing the prediction of functions for TFs and their neighbor genes, such as genes involved in virulence, enzymatic functions, phosphorylation mechanisms, and antibiotic resistance. The functional analysis associated with PFAM groups showed diverse functional categories were significantly enriched in the collection of TFs and the proteins encoded by the neighbor genes, in particular, small-molecule binding and amino acid transmembrane transporter activities associated with the LysR family and proteins devoted to cellular aromatic compound metabolic processes or responses to drugs, stress, or abiotic stimuli in the MarR family. We consider that with the increasing data derived from new technologies, novel TFs can be identified and help improve the predictions for this class of proteins in complete genomes. The complete collection of experimentally characterized and predicted TFs is available at http://web.pcyt.unam.mx/EntrafDB/.
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Affiliation(s)
- Emanuel Flores-Bautista
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida, Yucatán, México
| | - Rafael Hernandez-Guerrero
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida, Yucatán, México
| | - Alejandro Huerta-Saquero
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Ensenada, Baja California, México
| | - Silvia Tenorio-Salgado
- Tecnológico Nacional de México, Instituto Tecnológico de Mérida, Mérida, Yucatán, México
| | | | - Alba Romero
- Microbiota Host Interactions and Clostridia Research Group, Universidad Nacional Andrés Bello, Santiago de Chile, Chile
| | - Jose Antonio Ibarra
- Laboratorio de Genética Microbiana, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Ernesto Perez-Rueda
- Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Unidad Académica Yucatán, Mérida, Yucatán, México
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
- * E-mail:
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12
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Chen R, Zhou J, Sun R, Du C, Xie W. Conserved Conformational Changes in the Regulation of Mycobacterium tuberculosis MazEF-mt1. ACS Infect Dis 2020; 6:1783-1795. [PMID: 32485099 DOI: 10.1021/acsinfecdis.0c00048] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Toxin-antitoxin (TA) systems, which regulate many important cellular processes, are abundantly present in prokaryotic organisms. MazEF is a common type of TA system implicated in the formation of "persisters cells" of the pathogen Mycobacterium tuberculosis, which contains 10 such systems. However, the exact function and inhibition mode of each MazF protein are not quite understood. Here, we report four high-resolution crystal structures of MazF-mt1 in various forms, including one in complex with MazE-mt1. The toxin displayed two unique interlocked loops that allow the formation of a tight dimer. These loops would open upon interacting with the MazE-mt1 antitoxin mediated by the last two helices of MazE-mt1. With our structure-based design, a mutant that could bind to the antitoxin with an enhanced affinity was produced. Combined crystallographic and biochemical studies further revealed that the binding affinity of MazE-mt1 to MazF-mt1 was mainly attributed to its α3 helical region, while the terminal helix η1 contributes very little or even negatively to the association of the pair, in stark contrast to the MazEF-mt9 system. This study provides structural insight into the binding mode and the inhibition mechanism of the MazE/F-mt1 TA pair, which may reflect the functional differences between different TA systems.
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Affiliation(s)
- Ran Chen
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong 510006, People’s Republic of China
| | - Jie Zhou
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong 510006, People’s Republic of China
| | - Runlin Sun
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong 510006, People’s Republic of China
| | - Chaochao Du
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, 651 E. Dongfeng Road, Guangzhou, Guangdong 510060, People’s Republic of China
| | - Wei Xie
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong 510006, People’s Republic of China
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13
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Deep A, Tiwari P, Agarwal S, Kaundal S, Kidwai S, Singh R, Thakur KG. Structural, functional and biological insights into the role of Mycobacterium tuberculosis VapBC11 toxin-antitoxin system: targeting a tRNase to tackle mycobacterial adaptation. Nucleic Acids Res 2019; 46:11639-11655. [PMID: 30329074 PMCID: PMC6265470 DOI: 10.1093/nar/gky924] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 10/04/2018] [Indexed: 01/10/2023] Open
Abstract
Toxin–antitoxin (TA) systems are involved in diverse physiological processes in prokaryotes, but their exact role in Mycobacterium tuberculosis (Mtb) virulence and in vivo stress adaptation has not been extensively studied. Here, we demonstrate that the VapBC11 TA module is essential for Mtb to establish infection in guinea pigs. RNA-sequencing revealed that overexpression of VapC11 toxin results in metabolic slowdown, suggesting that modulation of the growth rate is an essential strategy for in vivo survival. Interestingly, overexpression of VapC11 resulted in the upregulation of chromosomal TA genes, suggesting the existence of highly coordinated crosstalk among TA systems. In this study, we also present the crystal structure of the VapBC11 heterooctameric complex at 1.67 Å resolution. Binding kinetic studies suggest that the binding affinities of toxin–substrate and toxin–antitoxin interactions are comparable. We used a combination of structural studies, molecular docking, mutational analysis and in vitro ribonuclease assays to enhance our understanding of the mode of substrate recognition by the VapC11 toxin. Furthermore, we have also designed peptide-based inhibitors to target VapC11 ribonuclease activity. Taken together, we propose that the structure-guided design of inhibitors against in vivo essential ribonucleases might be a novel strategy to hasten clearance of intracellular Mtb.
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Affiliation(s)
- Amar Deep
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh 160036, India
| | - Prabhakar Tiwari
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad Gurgaon Expressway, Faridabad 121001, India
| | - Sakshi Agarwal
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad Gurgaon Expressway, Faridabad 121001, India
| | - Soni Kaundal
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh 160036, India
| | - Saqib Kidwai
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad Gurgaon Expressway, Faridabad 121001, India
| | - Ramandeep Singh
- Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad Gurgaon Expressway, Faridabad 121001, India
| | - Krishan G Thakur
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh 160036, India
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14
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Vet S, Vandervelde A, Gelens L. Excitable dynamics through toxin-induced mRNA cleavage in bacteria. PLoS One 2019; 14:e0212288. [PMID: 30794601 PMCID: PMC6386449 DOI: 10.1371/journal.pone.0212288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/30/2019] [Indexed: 11/19/2022] Open
Abstract
Toxin-antitoxin (TA) systems in bacteria and archaea are small genetic elements consisting of the genes coding for an intracellular toxin and an antitoxin that can neutralize this toxin. In various cases, the toxins cleave the mRNA. In this theoretical work we use deterministic and stochastic modeling to explain how toxin-induced cleavage of mRNA in TA systems can lead to excitability, allowing large transient spikes in toxin levels to be triggered. By using a simplified network where secondary complex formation and transcriptional regulation are not included, we show that a two-dimensional, deterministic model captures the origin of such toxin excitations. Moreover, it allows to increase our understanding by examining the dynamics in the phase plane. By systematically comparing the deterministic results with Gillespie simulations we demonstrate that even though the real TA system is intrinsically stochastic, toxin excitations can be accurately described deterministically. A bifurcation analysis of the system shows that the excitable behavior is due to a nearby Hopf bifurcation in the parameter space, where the system becomes oscillatory. The influence of stress is modeled by varying the degradation rate of the antitoxin and the translation rate of the toxin. We find that stress increases the frequency of toxin excitations. The inclusion of secondary complex formation and transcriptional regulation does not fundamentally change the mechanism of toxin excitations. Finally, we show that including growth rate suppression and translational inhibition can lead to longer excitations, and even cause excitations in cases when the system would otherwise be non-excitable. To conclude, the deterministic model used in this work provides a simple and intuitive explanation of toxin excitations in TA systems.
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Affiliation(s)
- Stefan Vet
- Applied Physics Research Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels (IB2), VUB-ULB, Brussels, Belgium
- Unité de Chronobiologie théorique, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | | | - Lendert Gelens
- Applied Physics Research Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Laboratory of Dynamics in Biological Systems, KU Leuven, Leuven, Belgium
- * E-mail:
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15
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Yoon WS, Seok SH, Won HS, Cho T, Lee SJ, Seo MD. Structural changes of antitoxin HigA from Shigella flexneri by binding of its cognate toxin HigB. Int J Biol Macromol 2019; 130:99-108. [PMID: 30797012 DOI: 10.1016/j.ijbiomac.2019.02.111] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/19/2019] [Accepted: 02/19/2019] [Indexed: 11/17/2022]
Abstract
In toxin-antitoxin systems, many antitoxin proteins that neutralize their cognate toxin proteins also bind to DNA to repress transcription, and the DNA-binding affinity of the antitoxin is affected by its toxin. We solved crystal structures of the antitoxin HigA (apo-SfHigA) and its complex with the toxin HigB (SfHigBA) from Shigella flexneri. The apo-SfHigA shows a distinctive V-shaped homodimeric conformation with sequestered N-domains having a novel fold. SfHigBA appears as a heterotetramer formed by N-terminal dimerization of SfHigB-bound SfHigA molecules. The conformational change in SfHigA upon SfHigB binding is mediated by rigid-body movements of its C-domains, which accompanied an overall conformational change from wide V-shaped to narrow V-shaped dimer. Consequently, the two putative DNA-binding helices (α7 in each subunit) are repositioned to a conformation more compatible with canonical homodimeric DNA-binding proteins containing HTH motifs. Collectively, this study demonstrates a conformational change in an antitoxin protein, which occurs upon toxin binding and is responsible for regulating antitoxin DNA binding.
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Affiliation(s)
- Won-Su Yoon
- Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi 16499, Republic of Korea; College of Pharmacy and Research Institute of Pharmaceutical Science and Technology (RIPST), Ajou University, Suwon, Gyeonggi 16499, Republic of Korea
| | - Seung-Hyeon Seok
- College of Pharmacy and Research Institute of Pharmaceutical Science and Technology (RIPST), Ajou University, Suwon, Gyeonggi 16499, Republic of Korea
| | - Hyung-Sik Won
- Department of Biotechnology, Research Institute (RIBHS) and College of Biomedical & Health Science, Konkuk University, Chungju, Chungbuk 27478, Republic of Korea
| | - Taehwan Cho
- Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi 16499, Republic of Korea; College of Pharmacy and Research Institute of Pharmaceutical Science and Technology (RIPST), Ajou University, Suwon, Gyeonggi 16499, Republic of Korea
| | - Sang Jae Lee
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Min-Duk Seo
- Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi 16499, Republic of Korea; College of Pharmacy and Research Institute of Pharmaceutical Science and Technology (RIPST), Ajou University, Suwon, Gyeonggi 16499, Republic of Korea.
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16
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Nikolic N. Autoregulation of bacterial gene expression: lessons from the MazEF toxin-antitoxin system. Curr Genet 2019; 65:133-138. [PMID: 30132188 PMCID: PMC6343021 DOI: 10.1007/s00294-018-0879-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/13/2018] [Accepted: 08/14/2018] [Indexed: 11/30/2022]
Abstract
Autoregulation is the direct modulation of gene expression by the product of the corresponding gene. Autoregulation of bacterial gene expression has been mostly studied at the transcriptional level, when a protein acts as the cognate transcriptional repressor. A recent study investigating dynamics of the bacterial toxin-antitoxin MazEF system has shown how autoregulation at both the transcriptional and post-transcriptional levels affects the heterogeneity of Escherichia coli populations. Toxin-antitoxin systems hold a crucial but still elusive part in bacterial response to stress. This perspective highlights how these modules can also serve as a great model system for investigating basic concepts in gene regulation. However, as the genomic background and environmental conditions substantially influence toxin activation, it is important to study (auto)regulation of toxin-antitoxin systems in well-defined setups as well as in conditions that resemble the environmental niche.
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Affiliation(s)
- Nela Nikolic
- Institute of Science and Technology (IST) Austria, 3400, Klosterneuburg, Austria.
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17
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Roy M, Kundu A, Bhunia A, Das Gupta S, De S, Das AK. Structural characterization of VapB46 antitoxin from
Mycobacterium tuberculosis
: insights into VapB46–
DNA
binding. FEBS J 2019; 286:1174-1190. [DOI: 10.1111/febs.14737] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Revised: 10/24/2018] [Accepted: 12/17/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Madhurima Roy
- Department of Biotechnology Indian Institute of Technology Kharagpur India
| | - Anirban Kundu
- Department of Biotechnology Indian Institute of Technology Kharagpur India
| | | | | | - Soumya De
- School of Bioscience Indian Institute of Technology Kharagpur India
| | - Amit Kumar Das
- Department of Biotechnology Indian Institute of Technology Kharagpur India
- School of Bioscience Indian Institute of Technology Kharagpur India
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18
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Walling LR, Butler JS. Toxins targeting transfer RNAs: Translation inhibition by bacterial toxin-antitoxin systems. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1506. [PMID: 30296016 DOI: 10.1002/wrna.1506] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/07/2018] [Accepted: 08/13/2018] [Indexed: 01/09/2023]
Abstract
Prokaryotic toxin-antitoxin (TA) systems are composed of a protein toxin and its cognate antitoxin. These systems are abundant in bacteria and archaea and play an important role in growth regulation. During favorable growth conditions, the antitoxin neutralizes the toxin's activity. However, during conditions of stress or starvation, the antitoxin is inactivated, freeing the toxin to inhibit growth and resulting in dormancy. One mechanism of growth inhibition used by several TA systems results from targeting transfer RNAs (tRNAs), either through preventing aminoacylation, acetylating the primary amino group, or endonucleolytic cleavage. All of these mechanisms inhibit translation and result in growth arrest. Many of these toxins only act on a specific tRNA or a specific subset of tRNAs; however, more work is necessary to understand the specificity determinants of these toxins. For the toxins whose specificity has been characterized, both sequence and structural components of the tRNA appear important for recognition by the toxin. Questions also remain regarding the mechanisms used by dormant bacteria to resume growth after toxin induction. Rescue of stalled ribosomes by transfer-messenger RNAs, removal of acetylated amino groups from tRNAs, or ligation of cleaved RNA fragments have all been implicated as mechanisms for reversing toxin-induced dormancy. However, the mechanisms of resuming growth after induction of the majority of tRNA targeting toxins are not yet understood. This article is categorized under: Translation > Translation Regulation RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition.
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Affiliation(s)
- Lauren R Walling
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York
| | - J Scott Butler
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York.,Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York.,Center for RNA Biology, University of Rochester Medical Center, Rochester, New York
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19
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Nikolic N, Bergmiller T, Vandervelde A, Albanese TG, Gelens L, Moll I. Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations. Nucleic Acids Res 2018; 46:2918-2931. [PMID: 29432616 PMCID: PMC5888573 DOI: 10.1093/nar/gky079] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Revised: 12/30/2017] [Accepted: 01/27/2018] [Indexed: 01/24/2023] Open
Abstract
The MazF toxin sequence-specifically cleaves single-stranded RNA upon various stressful conditions, and it is activated as a part of the mazEF toxin-antitoxin module in Escherichia coli. Although autoregulation of mazEF expression through the MazE antitoxin-dependent transcriptional repression has been biochemically characterized, less is known about post-transcriptional autoregulation, as well as how both of these autoregulatory features affect growth of single cells during conditions that promote MazF production. Here, we demonstrate post-transcriptional autoregulation of mazF expression dynamics by MazF cleaving its own transcript. Single-cell analyses of bacterial populations during ectopic MazF production indicated that two-level autoregulation of mazEF expression influences cell-to-cell growth rate heterogeneity. The increase in growth rate heterogeneity is governed by the MazE antitoxin, and tuned by the MazF-dependent mazF mRNA cleavage. Also, both autoregulatory features grant rapid exit from the stress caused by mazF overexpression. Time-lapse microscopy revealed that MazF-mediated cleavage of mazF mRNA leads to increased temporal variability in length of individual cells during ectopic mazF overexpression, as explained by a stochastic model indicating that mazEF mRNA cleavage underlies temporal fluctuations in MazF levels during stress.
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Affiliation(s)
- Nela Nikolic
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Tobias Bergmiller
- Institute of Science and Technology Austria (IST Austria), 3400 Klosterneuburg, Austria
| | - Alexandra Vandervelde
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium
| | - Tanino G Albanese
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Lendert Gelens
- Laboratory of Dynamics in Biological Systems, Department of Cellular and Molecular Medicine, University of Leuven, 3000 Leuven, Belgium
| | - Isabella Moll
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna BioCenter (VBC), 1030 Vienna, Austria
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20
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He C, Zheng S, Zhang J, Li W, Fu Y. Hunting for the “Sweet Spot”: Effects of Contiguous Guanines and Strand Lengths on the Catalytic Performance of DNA-Based Peroxidase Mimetics. Catal Letters 2018. [DOI: 10.1007/s10562-018-2356-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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21
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OxyR of Haemophilus parasuis is a global transcriptional regulator important in oxidative stress resistance and growth. Gene 2018; 643:107-116. [DOI: 10.1016/j.gene.2017.12.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 12/05/2017] [Accepted: 12/07/2017] [Indexed: 11/17/2022]
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22
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Physical and Functional Interplay between MazF 1Bif and Its Noncognate Antitoxins from Bifidobacterium longum. Appl Environ Microbiol 2017; 83:AEM.03232-16. [PMID: 28213540 DOI: 10.1128/aem.03232-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 02/09/2017] [Indexed: 11/20/2022] Open
Abstract
Bifidobacterium longum strain JDM301, a widely used commercial strain in China, encodes at least two MazEF-like modules and one RelBE-like toxin-antitoxin (TA) system in its chromosome, designated MazE1F1Bif, MazE2F2Bif, and RelBEBif, respectively. Bacterial TA systems play an important role in several stress responses, but the relationship between these TA systems is largely unknown. In this study, the interactions between MazF1Bif and MazE2Bif or RelBBif were assessed in B. longum strain JDM301. MazF1Bif caused the degradation of tufABif mRNA, and its toxicity was inhibited by forming a protein complex with its cognate antitoxin, MazE1Bif Notably, MazF1Bif toxicity was also partially neutralized when jointly expressed with noncognate antitoxin MazE2Bif or RelBBif Our results show that the two noncognate antitoxins also inhibited mRNA degradation caused by MazF1Bif toxin. Furthermore, the physical interplay between MazF1Bif and its noncognate antitoxins was confirmed by immunoprecipitation. These results suggest that MazF1Bif can arrest cell growth and that MazF1Bif toxicity can be neutralized by its cognate and noncognate antitoxins. These results imply that JDM301 uses a sophisticated toxin-antitoxin interaction network to alter its physiology when coping with environmental stress.IMPORTANCE Although toxin-antitoxin (TA) systems play an important role in several stress responses, the regulatory mechanisms of multiple TA system homologs in the bacterial genome remain largely unclear. In this study, the relationships between MazE1F1Bif and the other two TA systems of Bifidobacterium longum strain JDM301 were explored, and the interactions between MazF1Bif and MazE2Bif or RelBBif were characterized. In addition, the mRNA degradation activity of MazF1Bif was demonstrated. In particular, the interaction of the toxin with noncognate antitoxins was shown, even between different TA families (MazF1Bif toxin and RelBBif antitoxin) in JDM301. This work provides insight into the regulatory mechanisms of TA systems implicated in the stress responses of bifidobacteria.
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23
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Turnbull KJ, Gerdes K. HicA toxin of Escherichia coli derepresses hicAB transcription to selectively produce HicB antitoxin. Mol Microbiol 2017; 104:781-792. [PMID: 28266056 DOI: 10.1111/mmi.13662] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2017] [Indexed: 12/13/2022]
Abstract
Antitoxins encoded by type II toxin - antitoxin (TA) modules neutralize cognate toxins by direct protein - protein contact and in addition, regulate TA operon transcription by binding to operators in the promoter regions. On top of the simple negative feed-back regulation, canonical type II TA operons are regulated by a mechanism called 'Conditional Cooperativity'(CC). In CC, the cellular toxin:antitoxin (T:A) ratio controls the transcription-rate such that low T:A ratios favour repression and high T:A ratios favour de-repression of TA operon transcription. Here a new molecular mechanism that secures selective synthesis of antitoxin in the presence of excess toxin was unravelled. The hicAB locus of E. coli K-12 encodes HicA mRNase and HicB antitoxin. It was shown that hicAB is transcribed by two promoters, an upstream one that is activated by CRP-cAMP and competence factor Sxy and a downstream one that is autorepressed solely by HicB. Excess HicA destabilizes the HicB•operator complex in vitro and consistently, activates hicAB transcription in vivo. Remarkably, the hicAB transcript synthesized from the HicB-controlled promoter produces HicB but not HicA. Thus, the HicA-mediated derepression of hicAB transcription provides a mechanism that conditionally and selectively stimulates synthesis of HicB antitoxin under conditions of excess HicA toxin.
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Affiliation(s)
- Kathryn J Turnbull
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, DK-2200, Denmark
| | - Kenn Gerdes
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, DK-2200, Denmark
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24
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Kato F, Yabuno Y, Yamaguchi Y, Sugai M, Inouye M. Deletion of mazF increases Staphylococcus aureus biofilm formation in an ica-dependent manner. Pathog Dis 2017; 75:3063887. [DOI: 10.1093/femspd/ftx026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 03/07/2017] [Indexed: 11/12/2022] Open
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25
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Srikumar A, Krishna PS, Sivaramakrishna D, Kopfmann S, Hess WR, Swamy MJ, Lin-Chao S, Prakash JSS. The Ssl2245-Sll1130 Toxin-Antitoxin System Mediates Heat-induced Programmed Cell Death in Synechocystis sp. PCC6803. J Biol Chem 2017; 292:4222-4234. [PMID: 28104802 DOI: 10.1074/jbc.m116.748178] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 01/17/2017] [Indexed: 12/13/2022] Open
Abstract
Two putative heat-responsive genes, ssl2245 and sll1130, constitute an operon that also has characteristics of a toxin-antitoxin system, thus joining several enigmatic features. Closely related orthologs of Ssl2245 and Sll1130 exist in widely different bacteria, which thrive under environments with large fluctuations in temperature and salinity, among which some are thermo-epilithic biofilm-forming cyanobacteria. Transcriptome analyses revealed that the clustered regularly interspaced short palindromic repeats (CRISPR) genes as well as several hypothetical genes were commonly up-regulated in Δssl2245 and Δsll1130 mutants. Genes coding for heat shock proteins and pilins were also induced in Δsll1130 We observed that the majority of cells in a Δsll1130 mutant strain remained unicellular and viable after prolonged incubation at high temperature (50 °C). In contrast, the wild type formed large cell clumps of dead and live cells, indicating the attempt to form biofilms under harsh conditions. Furthermore, we observed that Sll1130 is a heat-stable ribonuclease whose activity was inhibited by Ssl2245 at optimal temperatures but not at high temperatures. In addition, we demonstrated that Ssl2245 is physically associated with Sll1130 by electrostatic interactions, thereby inhibiting its activity at optimal growth temperature. This association is lost upon exposure to heat, leaving Sll1130 to exhibit its ribonuclease activity. Thus, the activation of Sll1130 leads to the degradation of cellular RNA and thereby heat-induced programmed cell death that in turn supports the formation of a more resistant biofilm for the surviving cells. We suggest to designate Ssl2245 and Sll1130 as MazE and MazF, respectively.
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Affiliation(s)
- Afshan Srikumar
- From the Department of Biotechnology and Bioinformatics, School of Life Sciences and
| | - Pilla Sankara Krishna
- From the Department of Biotechnology and Bioinformatics, School of Life Sciences and
| | | | - Stefan Kopfmann
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany, and
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, D-79104 Freiburg, Germany, and
| | - Musti J Swamy
- School of Chemistry, University of Hyderabad, Hyderabad 500046, India
| | - Sue Lin-Chao
- Institute of Molecular Biology, Academia Sinica, Taipei 115, Taiwan
| | - Jogadhenu S S Prakash
- From the Department of Biotechnology and Bioinformatics, School of Life Sciences and
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26
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The Arginine Pairs and C-Termini of the Sso7c4 from Sulfolobus solfataricus Participate in Binding and Bending DNA. PLoS One 2017; 12:e0169627. [PMID: 28068385 PMCID: PMC5222340 DOI: 10.1371/journal.pone.0169627] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 12/20/2016] [Indexed: 11/19/2022] Open
Abstract
The Sso7c4 from Sulfolobus solfataricus forms a dimer, which is believed to function as a chromosomal protein involved in genomic DNA compaction and gene regulation. Here, we present the crystal structure of wild-type Sso7c4 at a high resolution of 1.63 Å, showing that the two basic C-termini are disordered. Based on the fluorescence polarization (FP) binding assay, two arginine pairs, R11/R22' and R11'/R22, on the top surface participate in binding DNA. As shown in electron microscopy (EM) images, wild-type Sso7c4 compacts DNA through bridging and bending interactions, whereas the binding of C-terminally truncated proteins rigidifies and opens DNA molecules, and no compaction of the DNA occurs. Moreover, the FP, EM and fluorescence resonance energy transfer (FRET) data indicated that the two basic and flexible C-terminal arms of the Sso7c4 dimer play a crucial role in binding and bending DNA. Sso7c4 has been classified as a repressor-like protein because of its similarity to Escherichia coli Ecrep 6.8 and Ecrep 7.3 as well as Agrobacterium tumefaciens ACCR in amino acid sequence. Based on these data, we proposed a model of the Sso7c4-DNA complex using a curved DNA molecule in the catabolite activator protein-DNA complex. The DNA end-to-end distance measured with FRET upon wild-type Sso7c4 binding is almost equal to the distance measured in the model, which supports the fidelity of the proposed model. The FRET data also confirm the EM observation showing that the binding of wild-type Sso7c4 reduces the DNA length while the C-terminal truncation does not. A functional role for Sso7c4 in the organization of chromosomal DNA and/or the regulation of gene expression through bridging and bending interactions is suggested.
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27
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Yang J, Zhou K, Liu P, Dong Y, Gao Z, Zhang J, Liu Q. Structural insight into the E. coli HigBA complex. Biochem Biophys Res Commun 2016; 478:1521-7. [DOI: 10.1016/j.bbrc.2016.08.131] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 08/23/2016] [Indexed: 12/16/2022]
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28
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Chan WT, Espinosa M, Yeo CC. Keeping the Wolves at Bay: Antitoxins of Prokaryotic Type II Toxin-Antitoxin Systems. Front Mol Biosci 2016; 3:9. [PMID: 27047942 PMCID: PMC4803016 DOI: 10.3389/fmolb.2016.00009] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/04/2016] [Indexed: 12/21/2022] Open
Abstract
In their initial stages of discovery, prokaryotic toxin-antitoxin (TA) systems were confined to bacterial plasmids where they function to mediate the maintenance and stability of usually low- to medium-copy number plasmids through the post-segregational killing of any plasmid-free daughter cells that developed. Their eventual discovery as nearly ubiquitous and repetitive elements in bacterial chromosomes led to a wealth of knowledge and scientific debate as to their diversity and functionality in the prokaryotic lifestyle. Currently categorized into six different types designated types I–VI, type II TA systems are the best characterized. These generally comprised of two genes encoding a proteic toxin and its corresponding proteic antitoxin, respectively. Under normal growth conditions, the stable toxin is prevented from exerting its lethal effect through tight binding with the less stable antitoxin partner, forming a non-lethal TA protein complex. Besides binding with its cognate toxin, the antitoxin also plays a role in regulating the expression of the type II TA operon by binding to the operator site, thereby repressing transcription from the TA promoter. In most cases, full repression is observed in the presence of the TA complex as binding of the toxin enhances the DNA binding capability of the antitoxin. TA systems have been implicated in a gamut of prokaryotic cellular functions such as being mediators of programmed cell death as well as persistence or dormancy, biofilm formation, as defensive weapons against bacteriophage infections and as virulence factors in pathogenic bacteria. It is thus apparent that these antitoxins, as DNA-binding proteins, play an essential role in modulating the prokaryotic lifestyle whilst at the same time preventing the lethal action of the toxins under normal growth conditions, i.e., keeping the proverbial wolves at bay. In this review, we will cover the diversity and characteristics of various type II TA antitoxins. We shall also look into some interesting deviations from the canonical type II TA systems such as tripartite TA systems where the regulatory role is played by a third party protein and not the antitoxin, and a unique TA system encoding a single protein with both toxin as well as antitoxin domains.
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Affiliation(s)
- Wai Ting Chan
- Molecular Microbiology and Infection Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - Manuel Espinosa
- Molecular Microbiology and Infection Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - Chew Chieng Yeo
- Faculty of Medicine, Biomedical Research Centre, Universiti Sultan Zainal Abidin Kuala Terengganu, Malaysia
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Sekar K, Gentile AM, Bostick JW, Tyo KEJ. N-Terminal-Based Targeted, Inducible Protein Degradation in Escherichia coli. PLoS One 2016; 11:e0149746. [PMID: 26900850 PMCID: PMC4765774 DOI: 10.1371/journal.pone.0149746] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 02/04/2016] [Indexed: 11/18/2022] Open
Abstract
Dynamically altering protein concentration is a central activity in synthetic biology. While many tools are available to modulate protein concentration by altering protein synthesis rate, methods for decreasing protein concentration by inactivation or degradation rate are just being realized. Altering protein synthesis rates can quickly increase the concentration of a protein but not decrease, as residual protein will remain for a while. Inducible, targeted protein degradation is an attractive option and some tools have been introduced for higher organisms and bacteria. Current bacterial tools rely on C-terminal fusions, so we have developed an N-terminal fusion (Ntag) strategy to increase the possible proteins that can be targeted. We demonstrate Ntag dependent degradation of mCherry and beta-galactosidase and reconfigure the Ntag system to perform dynamic, exogenously inducible degradation of a targeted protein and complement protein depletion by traditional synthesis repression. Model driven analysis that focused on rates, rather than concentrations, was critical to understanding and engineering the system. We expect this tool and our model to enable inducible protein degradation use particularly in metabolic engineering, biological study of essential proteins, and protein circuits.
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Affiliation(s)
- Karthik Sekar
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States of America
| | - Andrew M. Gentile
- Master of Biotechnology Program, Northwestern University, Evanston, IL, United States of America
| | - John W. Bostick
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States of America
- Department of Pathology, Northwestern University, Chicago, IL, United States of America
- Department of Microbiology-Immunology, Northwestern University, Chicago, IL, United States of America
| | - Keith E. J. Tyo
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States of America
- * E-mail:
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Alva V, Söding J, Lupas AN. A vocabulary of ancient peptides at the origin of folded proteins. eLife 2015; 4:e09410. [PMID: 26653858 PMCID: PMC4739770 DOI: 10.7554/elife.09410] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 12/13/2015] [Indexed: 01/01/2023] Open
Abstract
The seemingly limitless diversity of proteins in nature arose from only a few thousand domain prototypes, but the origin of these themselves has remained unclear. We are pursuing the hypothesis that they arose by fusion and accretion from an ancestral set of peptides active as co-factors in RNA-dependent replication and catalysis. Should this be true, contemporary domains may still contain vestiges of such peptides, which could be reconstructed by a comparative approach in the same way in which ancient vocabularies have been reconstructed by the comparative study of modern languages. To test this, we compared domains representative of known folds and identified 40 fragments whose similarity is indicative of common descent, yet which occur in domains currently not thought to be homologous. These fragments are widespread in the most ancient folds and enriched for iron-sulfur- and nucleic acid-binding. We propose that they represent the observable remnants of a primordial RNA-peptide world.
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Affiliation(s)
- Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Johannes Söding
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Andrei N Lupas
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
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Wessner F, Lacoux C, Goeders N, Fouquier d'Hérouel A, Matos R, Serror P, Van Melderen L, Repoila F. Regulatory crosstalk between type I and type II toxin-antitoxin systems in the human pathogen Enterococcus faecalis. RNA Biol 2015; 12:1099-108. [PMID: 26305399 DOI: 10.1080/15476286.2015.1084465] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
We discovered a chromosomal locus containing 2 toxin-antitoxin modules (TAs) with an antisense transcriptional organization in the E. faecalis clinical isolate V583. These TAs are homologous to the type I txpA-ratA system and the type II mazEF, respectively. We have shown that the putative MazF is toxic for E. coli and triggers RNA degradation, and its cognate antitoxin MazE counteracts toxicity. The second module, adjacent to mazEF, expresses a toxin predicted to belong to the TxpA type I family found in Firmicutes, and the antisense RNA antidote, RatA. Genomic analysis indicates that the cis-association of mazEF and txpA-ratA modules has been favored during evolution, suggesting a selective advantage for this TA organization in the E. faecalis species. We showed regulatory interplays between the 2 modules, involving transcription control and RNA stability. Remarkably, our data reveal that MazE and MazEF have a dual transcriptional activity: they act as autorepressors and activate ratA transcription, most likely in a direct manner. RatA controls txpA RNA levels through stability. Our data suggest a pivotal role of MazEF in the coordinated expression of mazEF and txpA-ratA modules in V583. To our knowledge, this is the first report describing a crosstalk between type I and II TAs.
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Affiliation(s)
- Françoise Wessner
- a INRA UMR1319 Micalis ; Jouy-en-Josas , France.,b AgroParisTech, UMR Micalis ; Jouy-en-Josas , France
| | - Caroline Lacoux
- a INRA UMR1319 Micalis ; Jouy-en-Josas , France.,b AgroParisTech, UMR Micalis ; Jouy-en-Josas , France
| | - Nathalie Goeders
- c Université Libre de Bruxelles, Faculté des Sciences, Institut de Biologie et Médecine Moléculaire ; Gosselies , Belgium
| | | | - Renata Matos
- a INRA UMR1319 Micalis ; Jouy-en-Josas , France.,b AgroParisTech, UMR Micalis ; Jouy-en-Josas , France
| | - Pascale Serror
- a INRA UMR1319 Micalis ; Jouy-en-Josas , France.,b AgroParisTech, UMR Micalis ; Jouy-en-Josas , France
| | - Laurence Van Melderen
- c Université Libre de Bruxelles, Faculté des Sciences, Institut de Biologie et Médecine Moléculaire ; Gosselies , Belgium
| | - Francis Repoila
- a INRA UMR1319 Micalis ; Jouy-en-Josas , France.,b AgroParisTech, UMR Micalis ; Jouy-en-Josas , France
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