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Tandon H, Sharma A, Wadhwa S, Varadarajan R, Singh R, Srinivasan N, Sandhya S. Bioinformatic and mutational studies of related toxin-antitoxin pairs in Mycobacterium tuberculosis predict and identify key functional residues. J Biol Chem 2019; 294:9048-9063. [PMID: 31018964 DOI: 10.1074/jbc.ra118.006814] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 04/23/2019] [Indexed: 12/17/2022] Open
Abstract
Mycobacterium tuberculosis possesses an unusually large representation of type II toxin-antitoxin (TA) systems, whose functions and targets are mostly unknown. To better understand the basis of their unique expansion and to probe putative functional similarities among these systems, here we computationally and experimentally investigated their sequence relationships. Bioinformatic and phylogenetic investigations revealed that 51 sequences of the VapBC toxin family group into paralogous sub-clusters. On the basis of conserved sequence fingerprints within paralogues, we predicted functional residues and residues at the putative TA interface that are useful to evaluate TA interactions. Substitution of these likely functional residues abolished the toxin's growth-inhibitory activity. Furthermore, conducting similarity searches in 101 mycobacterial and ∼4500 other prokaryotic genomes, we assessed the relative conservation of the M. tuberculosis TA systems and found that most TA orthologues are well-conserved among the members of the M. tuberculosis complex, which cause tuberculosis in animal hosts. We found that soil-inhabiting, free-living Actinobacteria also harbor as many as 12 TA pairs. Finally, we identified five novel putative TA modules in M. tuberculosis. For one of them, we demonstrate that overexpression of the putative toxin, Rv2514c, induces bacteriostasis and that co-expression of the cognate antitoxin Rv2515c restores bacterial growth. Taken together, our findings reveal that toxin sequences are more closely related than antitoxin sequences in M. tuberculosis Furthermore, the identification of additional TA systems reported here expands the known repertoire of TA systems in M. tuberculosis.
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Affiliation(s)
- Himani Tandon
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012 and
| | - Arun Sharma
- the Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, P. O. Box 4, Faridabad, Haryana-121001, India
| | - Saruchi Wadhwa
- the Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, P. O. Box 4, Faridabad, Haryana-121001, India
| | - Raghavan Varadarajan
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012 and
| | - Ramandeep Singh
- the Tuberculosis Research Laboratory, Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, P. O. Box 4, Faridabad, Haryana-121001, India
| | | | - Sankaran Sandhya
- From the Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012 and
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Veyron S, Peyroche G, Cherfils J. FIC proteins: from bacteria to humans and back again. Pathog Dis 2018; 76:4898014. [PMID: 29617857 DOI: 10.1093/femspd/fty012] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 02/21/2018] [Indexed: 01/18/2023] Open
Abstract
During the last decade, FIC proteins have emerged as a large family comprised of a variety of bacterial enzymes and a single member in animals. The air de famille of FIC proteins stems from a domain of conserved structure, which catalyzes the post-translational modification of proteins (PTM) by a phosphate-containing compound. In bacteria, examples of FIC proteins include the toxin component of toxin/antitoxin modules, such as Doc-Phd and VbhT-VbhA, toxins secreted by pathogenic bacteria to divert host cell processes, such as VopS, IbpA and AnkX, and a vast majority of proteins of unknown functions. FIC proteins catalyze primarily the transfer of AMP (AMPylation), but they are not restricted to this PTM and also carry out other modifications, for example by phosphocholine or phosphate. In a recent twist, animal FICD/HYPE was shown to catalyze both AMPylation and de-AMPylation of the endoplasmic reticulum BIP chaperone to regulate the unfolded protein response. FICD shares structural features with some bacterial FIC proteins, raising the possibility that bacteria also encode such dual activities. In this review, we discuss how structural, biochemical and cellular approaches have fertilized each other to understand the mechanism, regulation and function of FIC proteins from bacterial pathogens to humans.
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Affiliation(s)
- Simon Veyron
- CNRS and Ecole normale supérieure Paris-Saclay, 94235 Cachan, France
| | - Gérald Peyroche
- CNRS and Ecole normale supérieure Paris-Saclay, 94235 Cachan, France
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Abstract
Posttranslational modifications are covalent changes made to proteins that typically alter the function or location of the protein. AMPylation is an emerging posttranslational modification that involves the addition of adenosine monophosphate (AMP) to a protein. Like other, more well-studied posttranslational modifications, AMPylation is predicted to regulate the activity of the modified target proteins. However, the scope of this modification both in bacteria and in eukaryotes remains to be fully determined. In this review, we provide an up to date overview of the known AMPylating enzymes, the regulation of these enzymes, and the effect of this modification on target proteins.
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Affiliation(s)
- Amanda K. Casey
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard NA5.120F, Dallas, Texas 75390-9148, United States
| | - Kim Orth
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard NA5.120F, Dallas, Texas 75390-9148, United States
- Howard Hughes Medical Institute, 6000 Harry Hines Boulevard NA5.120F, Dallas, Texas 75390-9148, United States
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Harms A, Stanger FV, Dehio C. Biological Diversity and Molecular Plasticity of FIC Domain Proteins. Annu Rev Microbiol 2016; 70:341-60. [PMID: 27482742 DOI: 10.1146/annurev-micro-102215-095245] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The ubiquitous proteins with FIC (filamentation induced by cyclic AMP) domains use a conserved enzymatic machinery to modulate the activity of various target proteins by posttranslational modification, typically AMPylation. Following intensive study of the general properties of FIC domain catalysis, diverse molecular activities and biological functions of these remarkably versatile proteins are now being revealed. Here, we review the biological diversity of FIC domain proteins and summarize the underlying structure-function relationships. The original and most abundant genuine bacterial FIC domain proteins are toxins that use diverse molecular activities to interfere with bacterial physiology in various, yet ill-defined, biological contexts. Host-targeted virulence factors have evolved repeatedly out of this pool by exaptation of the enzymatic FIC domain machinery for the manipulation of host cell signaling in favor of bacterial pathogens. The single human FIC domain protein HypE (FICD) has a specific function in the regulation of protein stress responses.
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Affiliation(s)
- Alexander Harms
- Focal Area Infection Biology, Biozentrum, University of Basel, CH-4056 Basel, Switzerland; , ,
| | - Frédéric V Stanger
- Focal Area Infection Biology, Biozentrum, University of Basel, CH-4056 Basel, Switzerland; , , .,Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, CH-4056 Basel, Switzerland.,*Current address: Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Christoph Dehio
- Focal Area Infection Biology, Biozentrum, University of Basel, CH-4056 Basel, Switzerland; , ,
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Sharma A, Gilbert JA, Lal R. (Meta)genomic insights into the pathogenome of Cellulosimicrobium cellulans. Sci Rep 2016; 6:25527. [PMID: 27151933 PMCID: PMC4858710 DOI: 10.1038/srep25527] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/14/2016] [Indexed: 11/17/2022] Open
Abstract
Despite having serious clinical manifestations, Cellulosimicrobium cellulans remain under-reported with only three genome sequences available at the time of writing. Genome sequences of C. cellulans LMG16121, C. cellulans J36 and Cellulosimicrobium sp. strain MM were used to determine distribution of pathogenicity islands (PAIs) across C. cellulans, which revealed 49 potential marker genes with known association to human infections, e.g. Fic and VbhA toxin-antitoxin system. Oligonucleotide composition-based analysis of orthologous proteins (n = 791) across three genomes revealed significant negative correlation (P < 0.05) between frequency of optimal codons (Fopt) and gene G+C content, highlighting the G+C-biased gene conversion (gBGC) effect across Cellulosimicrobium strains. Bayesian molecular-clock analysis performed on three virulent PAI proteins (Fic; D-alanyl-D-alanine-carboxypeptidase; transposase) dated the divergence event at 300 million years ago from the most common recent ancestor. Synteny-based annotation of hypothetical proteins highlighted gene transfers from non-pathogenic bacteria as a key factor in the evolution of PAIs. Additonally, deciphering the metagenomic islands using strain MM’s genome with environmental data from the site of isolation (hot-spring biofilm) revealed (an)aerobic respiration as population segregation factor across the in situ cohorts. Using reference genomes and metagenomic data, our results highlight the emergence and evolution of PAIs in the genus Cellulosimicrobium.
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Affiliation(s)
| | - Jack A Gilbert
- Biosciences Division (BIO), Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, USA.,Department of Surgery, University of Chicago, 5841 S Maryland Ave, Chicago, IL, USA.,Marine Biological Laboratory, Woods Hole, MA, USA
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, India
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Abstract
Fic proteins are a family of proteins characterized by the presence of a conserved FIC domain that is involved in the modification of protein substrates by the addition of phosphate-containing compounds, including AMP and other nucleoside monophosphates, phosphocholine and phosphate. Fic proteins are widespread in bacteria, and various pathogenic species secrete Fic proteins as toxins that mediate post-translational modifications of host cell proteins, to interfere with cytoskeletal, trafficking, signalling or translation pathways in the host cell. In this Review, we discuss the current knowledge of the structure, function and regulation of Fic proteins and consider important areas for future research.
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Affiliation(s)
- Craig R Roy
- Yale University School of Medicine, New Haven, Connecticut 06536, USA
| | - Jacqueline Cherfils
- Laboratoire de Biologie et Pharmacologie Appliquée, Centre National de la Recherche Scientifique-Ecole Normale Supérieure Cachan, 61 Avenue du Président Wilson, 94235 Cachan, France
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Lewallen DM, Sreelatha A, Dharmarajan V, Madoux F, Chase P, Griffin PR, Orth K, Hodder P, Thompson PR. Inhibiting AMPylation: a novel screen to identify the first small molecule inhibitors of protein AMPylation. ACS Chem Biol 2014; 9:433-42. [PMID: 24274060 DOI: 10.1021/cb4006886] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Enzymatic transfer of the AMP portion of ATP to substrate proteins has recently been described as an essential mechanism of bacterial infection for several pathogens. The first AMPylator to be discovered, VopS from Vibrio parahemolyticus, catalyzes the transfer of AMP onto the host GTPases Cdc42 and Rac1. Modification of these proteins disrupts downstream signaling events, contributing to cell rounding and apoptosis, and recent studies have suggested that blocking AMPylation may be an effective route to stop infection. To date, however, no small molecule inhibitors have been discovered for any of the AMPylators. Therefore, we developed a fluorescence-polarization-based high-throughput screening assay and used it to discover the first inhibitors of protein AMPylation. Herein we report the discovery of the first small molecule VopS inhibitors (e.g., calmidazolium, GW7647, and MK886) with Ki's ranging from 6 to 50 μM and upward of 30-fold selectivity versus HYPE, the only known human AMPylator.
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Affiliation(s)
- Daniel M. Lewallen
- Department of Chemistry, The Scripps Research Institute, Scripps Florida, 120 Scripps Way, Jupiter, Florida 33458, United States
| | - Anju Sreelatha
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Venkatasubramanian Dharmarajan
- Department
of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, 120 Scripps Way, Jupiter, Florida 33458, United States
| | - Franck Madoux
- Lead Identification, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Peter Chase
- Lead Identification, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Patrick R. Griffin
- Department
of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, 120 Scripps Way, Jupiter, Florida 33458, United States
| | - Kim Orth
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Peter Hodder
- Lead Identification, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Paul R. Thompson
- Department of Chemistry, The Scripps Research Institute, Scripps Florida, 120 Scripps Way, Jupiter, Florida 33458, United States
- The Kellogg School of Science and Technology, The Scripps Research Institute, Scripps Florida, Jupiter, Florida, United States
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Cruz JW, Rothenbacher FP, Maehigashi T, Lane WS, Dunham CM, Woychik NA. Doc toxin is a kinase that inactivates elongation factor Tu. J Biol Chem 2014; 289:7788-98. [PMID: 24448800 DOI: 10.1074/jbc.m113.544429] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The Doc toxin from bacteriophage P1 (of the phd-doc toxin-antitoxin system) has served as a model for the family of Doc toxins, many of which are harbored in the genomes of pathogens. We have shown previously that the mode of action of this toxin is distinct from the majority derived from toxin-antitoxin systems: it does not cleave RNA; in fact P1 Doc expression leads to mRNA stabilization. However, the molecular triggers that lead to translation arrest are not understood. The presence of a Fic domain, albeit slightly altered in length and at the catalytic site, provided a clue to the mechanism of P1 Doc action, as most proteins with this conserved domain inactivate GTPases through addition of an adenylyl group (also referred to as AMPylation). We demonstrated that P1 Doc added a single phosphate group to the essential translation elongation factor and GTPase, elongation factor (EF)-Tu. The phosphorylation site was at a highly conserved threonine, Thr-382, which was blocked when EF-Tu was treated with the antibiotic kirromycin. Therefore, we have established that Fic domain proteins can function as kinases. This distinct enzymatic activity exhibited by P1 Doc also solves the mystery of the degenerate Fic motif unique to the Doc family of toxins. Moreover, we have established that all characterized Fic domain proteins, even those that phosphorylate, target pivotal GTPases for inactivation through a post-translational modification at a single functionally critical acceptor site.
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Affiliation(s)
- Jonathan W Cruz
- From the Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, and Rutgers Cancer Institute of New Jersey, Piscataway, New Jersey 08854
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Gao N, Shearwin K, Mack J, Finzi L, Dunlap D. Purification of bacteriophage lambda repressor. Protein Expr Purif 2013; 91:30-6. [PMID: 23831434 DOI: 10.1016/j.pep.2013.06.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 06/10/2013] [Accepted: 06/17/2013] [Indexed: 01/06/2023]
Abstract
Bacteriophage lambda repressor controls the lysogeny/lytic growth switch after infection of E. coli by lambda phage. In order to study in detail the looping of DNA mediated by the protein, tag-free repressor and a loss-of-cooperativity mutant were expressed in E.coli and purified by (1) ammonium sulfate fractionation, (2) anion-exchange chromatography and (3) heparin affinity chromatography. This method employs more recently developed and readily available chromatography resins to produce highly pure protein in good yield. In tethered particle motion looping assays and atomic force microscopy "footprinting" assays, both the wild-type protein and a C-terminal His-tagged variant, purified using immobilized metal affinity chromatography, bound specifically to high affinity sites to mediate loop formation. In contrast the G147D loss-of-cooperativity mutant bound specifically but did not secure loops.
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Affiliation(s)
- Ning Gao
- Physics Department, Emory University, 400 Dowman Dr., Atlanta, GA 30322, United States
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