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Singh PR, Dadireddy V, Udupa S, Kalladi SM, Shee S, Khosla S, Rajmani RS, Singh A, Ramakumar S, Nagaraja V. The Mycobacterium tuberculosis methyltransferase Rv2067c manipulates host epigenetic programming to promote its own survival. Nat Commun 2023; 14:8497. [PMID: 38129415 PMCID: PMC10739865 DOI: 10.1038/s41467-023-43940-6] [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: 04/28/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023] Open
Abstract
Mycobacterium tuberculosis has evolved several mechanisms to counter host defense arsenals for its proliferation. Here we report that M. tuberculosis employs a multi-pronged approach to modify host epigenetic machinery for its survival. It secretes methyltransferase (MTase) Rv2067c into macrophages, trimethylating histone H3K79 in a non-nucleosomal context. Rv2067c downregulates host MTase DOT1L, decreasing DOT1L-mediated nucleosomally added H3K79me3 mark on pro-inflammatory response genes. Consequent inhibition of caspase-8-dependent apoptosis and enhancement of RIPK3-mediated necrosis results in increased pathogenesis. In parallel, Rv2067c enhances the expression of SESTRIN3, NLRC3, and TMTC1, enabling the pathogen to overcome host inflammatory and oxidative responses. We provide the structural basis for differential methylation of H3K79 by Rv2067c and DOT1L. The structures of Rv2067c and DOT1L explain how their action on H3K79 is spatially and temporally separated, enabling Rv2067c to effectively intercept the host epigenetic circuit and downstream signaling.
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Affiliation(s)
- Prakruti R Singh
- Department of Microbiology & Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
- Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, India
| | | | - Shubha Udupa
- Department of Microbiology & Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Shashwath Malli Kalladi
- Department of Microbiology & Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Somnath Shee
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Sanjeev Khosla
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh (CSIR -IMTech), Chandigarh, India
| | - Raju S Rajmani
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | - Amit Singh
- Centre for Infectious Disease Research (CIDR), Department of Microbiology and Cell Biology, Indian Institute of Science (IISc), Bengaluru, India
| | | | - Valakunja Nagaraja
- Department of Microbiology & Cell Biology, Indian Institute of Science (IISc), Bengaluru, India.
- Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru, India.
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Li X, Lv J, Niu M, Liu S, Wu Y, Liu J, Xie J, Sun C, Wang YM. Characterization and Antibacterial Properties of Egg White Protein Films Loaded with ε-Polylysine: Evaluation of Their Degradability and Application. Foods 2023; 12:2431. [PMID: 37372641 DOI: 10.3390/foods12122431] [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: 05/29/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 06/29/2023] Open
Abstract
There is an ongoing trend to design new kinds of food packaging materials with excellent properties which are environmentally friendly enough. The aim of this study was to prepare and characterize egg white protein (EWP)-based composite films with and without ε-polylysine (Lys), as well as to compare their physical-chemical properties, structural properties, degradation and antibacterial properties. The results showed that with the addition of Lys, the composite films showed a decreasing tendency of the water permeability due to the enhanced interaction between proteins and water molecules. As indicated by the structural properties, stronger cross-linking and intermolecular interactions happened with increasing concentration of Lys. In addition, the composite films presented excellent antibacterial activities against Escherichia coli and Staphylococcus aureus on chilled pork in the presence of Lys. Therefore, our prepared films might be used as a freshness-keeping material with an application in meat preservation. The biodegradation evaluation demonstrated that the composite films were environmental-friendly and have potential applications in the field of food packaging.
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Affiliation(s)
- Xin Li
- School of Life Sciences, Yantai University, Yantai 264005, China
| | - Jianhao Lv
- School of Life Sciences, Yantai University, Yantai 264005, China
| | - Minghao Niu
- School of Life Sciences, Yantai University, Yantai 264005, China
| | - Siqi Liu
- School of Life Sciences, Yantai University, Yantai 264005, China
| | - Yue Wu
- School of Life Sciences, Yantai University, Yantai 264005, China
| | - Jiahan Liu
- School of Life Sciences, Yantai University, Yantai 264005, China
| | - Jingwen Xie
- School of Life Sciences, Yantai University, Yantai 264005, China
| | - Chengfeng Sun
- School of Life Sciences, Yantai University, Yantai 264005, China
| | - Yue-Meng Wang
- School of Food and Biological Engineering, Yantai Institute of Technology, Yantai 264003, China
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3
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cKMT1 is a new lysine methyltransferase that methylates the ferredoxin-NADP(+) oxidoreductase (FNR) and regulates energy transfer in cyanobacteria. Mol Cell Proteomics 2023; 22:100521. [PMID: 36858286 PMCID: PMC10090440 DOI: 10.1016/j.mcpro.2023.100521] [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: 10/09/2022] [Revised: 02/20/2023] [Accepted: 02/24/2023] [Indexed: 03/03/2023] Open
Abstract
Lysine methylation is a conserved and dynamic regulatory post-translational modification performed by lysine methyltransferases (KMTs). KMTs catalyze the transfer of mono-, di-, or tri-methyl groups to substrate proteins and play a critical regulatory role in all domains of life. To date, only one KMT has been identified in cyanobacteria. Here, we tested all of the predicted KMTs in the cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis), and we biochemically characterized sll1526 that we termed cKMT1 (cyanobacterial lysine methyltransferase 1), and determined that it can catalyze lysine methylation both in vivo and in vitro. Loss of cKMT1 alters photosynthetic electron transfer in Synechocystis. We analyzed cKMT1-regulated methylation sites in Synechocystis using a timsTOF Pro instrument. We identified 305 class I lysine methylation sites within 232 proteins, and of these, 80 methylation sites in 58 proteins were hypomethylated in ΔcKMT1 cells. We further demonstrated that cKMT1 could methylate ferredoxin-NADP(+) oxidoreductase (FNR) and its potential sites of action on FNR were identified. Amino acid residues H118 and Y219 were identified as key residues in the putative active site of cKMT1 as indicated by structure simulation, site-directed mutagenesis, and KMT activity measurement. Using mutations that mimic the unmethylated forms of FNR, we demonstrated that the inability to methylate K139 residues results in a decrease in the redox activity of FNR and affects energy transfer in Synechocystis. Together, our study identified a new KMT in Synechocystis and elucidated a methylation-mediated molecular mechanism catalyzed by cKMT1 for the regulation of energy transfer in cyanobacteria.
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Helminiak L, Mishra S, Keun Kim H. Pathogenicity and virulence of Rickettsia. Virulence 2022; 13:1752-1771. [PMID: 36208040 PMCID: PMC9553169 DOI: 10.1080/21505594.2022.2132047] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/16/2022] [Accepted: 09/29/2022] [Indexed: 12/24/2022] Open
Abstract
Rickettsiae include diverse Gram-negative microbial species that exhibit obligatory intracellular lifecycles between mammalian hosts and arthropod vectors. Human infections with arthropod-borne Rickettsia continue to cause significant morbidity and mortality as recent environmental changes foster the proliferation of arthropod vectors and increased exposure to humans. However, the technical difficulties in working with Rickettsia have delayed our progress in understanding the molecular mechanisms involved in rickettsial pathogenesis and disease transmission. Recent advances in developing genetic tools for Rickettsia have enabled investigators to identify virulence genes, uncover molecular functions, and characterize host responses to rickettsial determinants. Therefore, continued efforts to determine virulence genes and their biological functions will help us understand the underlying mechanisms associated with arthropod-borne rickettsioses.
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Affiliation(s)
| | | | - Hwan Keun Kim
- Center for Infectious Diseases, Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, USA
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Tighilt L, Boulila F, De Sousa BFS, Giraud E, Ruiz-Argüeso T, Palacios JM, Imperial J, Rey L. The Bradyrhizobium Sp. LmicA16 Type VI Secretion System Is Required for Efficient Nodulation of Lupinus Spp. MICROBIAL ECOLOGY 2022; 84:844-855. [PMID: 34697646 DOI: 10.1007/s00248-021-01892-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/30/2021] [Indexed: 05/06/2023]
Abstract
Many bacteria of the genus Bradyrhizobium are capable of inducing nodules in legumes. In this work, the importance of a type VI secretion system (T6SS) in a symbiotic strain of the genus Bradyrhizobium is described. T6SS of Bradyrhizobium sp. LmicA16 (A16) is necessary for efficient nodulation with Lupinus micranthus and Lupinus angustifolius. A mutant in the gene vgrG, coding for a component of the T6SS nanostructure, induced less nodules and smaller plants than the wild-type (wt) strain and was less competitive when co-inoculated with the wt strain. A16 T6SS genes are organized in a 26-kb DNA region in two divergent gene clusters of nine genes each. One of these genes codes for a protein (Tsb1) of unknown function but containing a methyltransferase domain. A tsb1 mutant showed an intermediate symbiotic phenotype regarding vgrG mutant and higher mucoidity than the wt strain in free-living conditions. T6SS promoter fusions to the lacZ reporter indicate expression in nodules but not in free-living cells grown in different media and conditions. The analysis of nodule structure revealed that the level of nodule colonization was significantly reduced in the mutants with respect to the wt strain.
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Affiliation(s)
- L Tighilt
- Laboratoire d'Ecologie Microbienne, Faculté Des Sciences de La Nature Et de La Vie, Université de Bejaia, 06000, Bejaia, Algeria
- Centro de Biotecnología Y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación Y Tecnología Agraria Y Alimentaria (INIA), Campus de Montegancedo, 28223, Madrid, Spain
| | - F Boulila
- Laboratoire d'Ecologie Microbienne, Faculté Des Sciences de La Nature Et de La Vie, Université de Bejaia, 06000, Bejaia, Algeria
| | - B F S De Sousa
- Centro de Biotecnología Y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación Y Tecnología Agraria Y Alimentaria (INIA), Campus de Montegancedo, 28223, Madrid, Spain
- Departamento de Biotecnología Y Biología Vegetal, ETSI Agronómica, Alimentaria Y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - E Giraud
- IRD, Laboratoire Des Symbioses Tropicales Et Méditerranéennes (LSTM), UMR IRD/SupAgro/INRA/Université de Montpellier/CIRAD, TA-A82/J-Campus International de Baillarguet, 34398Cedex 5, Montpellier, France
| | - T Ruiz-Argüeso
- Centro de Biotecnología Y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación Y Tecnología Agraria Y Alimentaria (INIA), Campus de Montegancedo, 28223, Madrid, Spain
- Departamento de Biotecnología Y Biología Vegetal, ETSI Agronómica, Alimentaria Y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - J M Palacios
- Centro de Biotecnología Y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación Y Tecnología Agraria Y Alimentaria (INIA), Campus de Montegancedo, 28223, Madrid, Spain
- Departamento de Biotecnología Y Biología Vegetal, ETSI Agronómica, Alimentaria Y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain
| | - J Imperial
- Centro de Biotecnología Y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación Y Tecnología Agraria Y Alimentaria (INIA), Campus de Montegancedo, 28223, Madrid, Spain
- Instituto de Ciencias Agrarias, CSIC, 28006, Madrid, Spain
| | - L Rey
- Centro de Biotecnología Y Genómica de Plantas, Universidad Politécnica de Madrid (UPM), Instituto Nacional de Investigación Y Tecnología Agraria Y Alimentaria (INIA), Campus de Montegancedo, 28223, Madrid, Spain.
- Departamento de Biotecnología Y Biología Vegetal, ETSI Agronómica, Alimentaria Y de Biosistemas, Universidad Politécnica de Madrid, 28040, Madrid, Spain.
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Parada C, Neri-Badillo IC, Vallecillo AJ, Segura E, Silva-Miranda M, Guzmán-Gutiérrez SL, Ortega PA, Coronado-Aceves EW, Cancino-Villeda L, Torres-Larios A, Aceves Sánchez MDJ, Flores Valdez MA, Espitia C. New Insights into the Methylation of Mycobacterium tuberculosis Heparin Binding Hemagglutinin Adhesin Expressed in Rhodococcus erythropolis. Pathogens 2021; 10:pathogens10091139. [PMID: 34578171 PMCID: PMC8467707 DOI: 10.3390/pathogens10091139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 08/19/2021] [Accepted: 08/30/2021] [Indexed: 12/02/2022] Open
Abstract
In recent years, knowledge of the role that protein methylation is playing on the physiopathogenesis of bacteria has grown. In Mycobacterium tuberculosis, methylation of the heparin binding hemagglutinin adhesin modulates the immune response, making this protein a subunit vaccine candidate. Through its C-terminal lysine-rich domain, this surface antigen interacts with heparan sulfate proteoglycans present in non-phagocytic cells, leading to extrapulmonary dissemination of the pathogen. In this study, the adhesin was expressed as a recombinant methylated protein in Rhodococcus erythropolis L88 and it was found associated to lipid droplets when bacteria were grown under nitrogen limitation. In order to delve into the role methylation could have in host–pathogen interactions, a comparative analysis was carried out between methylated and unmethylated protein produced in Escherichia coli. We found that methylation had an impact on lowering protein isoelectric point, but no differences between the proteins were found in their capacity to interact with heparin and A549 epithelial cells. An important finding was that HbhA is a Fatty Acid Binding Protein and differences in the conformational stability of the protein in complex with the fatty acid were observed between methylated and unmethylated protein. Together, these results suggest that the described role for this mycobacteria protein in lipid bodies formation could be related to its capacity to transport fatty acids. Obtained results also provide new clues about the role HbhA methylation could have in tuberculosis and point out the importance of having heterologous expression systems to obtain modified proteins.
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Affiliation(s)
- Cristina Parada
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
| | - Isabel Cecilia Neri-Badillo
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
| | - Antonio J. Vallecillo
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
- Facultad de Ciencias Agropecuarias, Universidad de Cuenca, Cuenca 010220, Ecuador
| | - Erika Segura
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
| | - Mayra Silva-Miranda
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
- Consejo Nacional de Ciencia y Tecnología, CONACyT, Ciudad de México 03940, Mexico
| | - Silvia Laura Guzmán-Gutiérrez
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
- Consejo Nacional de Ciencia y Tecnología, CONACyT, Ciudad de México 03940, Mexico
| | - Paola A. Ortega
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
| | - Enrique Wenceslao Coronado-Aceves
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
| | - Laura Cancino-Villeda
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
| | - Alfredo Torres-Larios
- Department of Biochemistry and Structural Biology, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico;
| | - Michel de Jesús Aceves Sánchez
- Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Guadalajara 44270, Mexico; (M.d.J.A.S.); (M.A.F.V.)
| | - Mario Alberto Flores Valdez
- Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, A.C., Guadalajara 44270, Mexico; (M.d.J.A.S.); (M.A.F.V.)
| | - Clara Espitia
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico; (C.P.); (I.C.N.-B.); (A.J.V.); (E.S.); (M.S.-M.); (S.L.G.-G.); (P.A.O.); (E.W.C.-A.); (L.C.-V.)
- Correspondence:
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Engström P, Burke TP, Tran CJ, Iavarone AT, Welch MD. Lysine methylation shields an intracellular pathogen from ubiquitylation and autophagy. SCIENCE ADVANCES 2021; 7:eabg2517. [PMID: 34172444 PMCID: PMC8232902 DOI: 10.1126/sciadv.abg2517] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 05/12/2021] [Indexed: 05/05/2023]
Abstract
Many intracellular pathogens avoid detection by their host cells. However, it remains unknown how they avoid being tagged by ubiquitin, an initial step leading to antimicrobial autophagy. Here, we show that the intracellular bacterial pathogen Rickettsia parkeri uses two protein-lysine methyltransferases (PKMTs) to modify outer membrane proteins (OMPs) and prevent their ubiquitylation. Mutants deficient in the PKMTs were avirulent in mice and failed to grow in macrophages because of ubiquitylation and autophagic targeting. Lysine methylation protected the abundant surface protein OmpB from ubiquitin-dependent depletion from the bacterial surface. Analysis of the lysine-methylome revealed that PKMTs modify a subset of OMPs, including OmpB, by methylation at the same sites that are modified by host ubiquitin. These findings show that lysine methylation is an essential determinant of rickettsial pathogenesis that shields bacterial proteins from ubiquitylation to evade autophagic targeting.
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Affiliation(s)
- Patrik Engström
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Thomas P Burke
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Cuong J Tran
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Anthony T Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Matthew D Welch
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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McGinn J, Lamason RL. The enigmatic biology of rickettsiae: recent advances, open questions and outlook. Pathog Dis 2021; 79:ftab019. [PMID: 33784388 PMCID: PMC8035066 DOI: 10.1093/femspd/ftab019] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/26/2021] [Indexed: 02/05/2023] Open
Abstract
Rickettsiae are obligate intracellular bacteria that can cause life-threatening illnesses and are among the oldest known vector-borne pathogens. Members of this genus are extraordinarily diverse and exhibit a broad host range. To establish intracellular infection, Rickettsia species undergo complex, multistep life cycles that are encoded by heavily streamlined genomes. As a result of reductive genome evolution, rickettsiae are exquisitely tailored to their host cell environment but cannot survive extracellularly. This host-cell dependence makes for a compelling system to uncover novel host-pathogen biology, but it has also hindered experimental progress. Consequently, the molecular details of rickettsial biology and pathogenesis remain poorly understood. With recent advances in molecular biology and genetics, the field is poised to start unraveling the molecular mechanisms of these host-pathogen interactions. Here, we review recent discoveries that have shed light on key aspects of rickettsial biology. These studies have revealed that rickettsiae subvert host cells using mechanisms that are distinct from other better-studied pathogens, underscoring the great potential of the Rickettsia genus for revealing novel biology. We also highlight several open questions as promising areas for future study and discuss the path toward solving the fundamental mysteries of this neglected and emerging human pathogen.
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Affiliation(s)
- Jon McGinn
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Rebecca L Lamason
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
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9
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Lemfack MC, Brandt W, Krüger K, Gurowietz A, Djifack J, Jung JP, Hopf M, Noack H, Junker B, von Reuß S, Piechulla B. Reaction mechanism of the farnesyl pyrophosphate C-methyltransferase towards the biosynthesis of pre-sodorifen pyrophosphate by Serratia plymuthica 4Rx13. Sci Rep 2021; 11:3182. [PMID: 33542330 PMCID: PMC7862628 DOI: 10.1038/s41598-021-82521-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/18/2021] [Indexed: 11/25/2022] Open
Abstract
Classical terpenoid biosynthesis involves the cyclization of the linear prenyl pyrophosphate precursors geranyl-, farnesyl-, or geranylgeranyl pyrophosphate (GPP, FPP, GGPP) and their isomers, to produce a huge number of natural compounds. Recently, it was shown for the first time that the biosynthesis of the unique homo-sesquiterpene sodorifen by Serratia plymuthica 4Rx13 involves a methylated and cyclized intermediate as the substrate of the sodorifen synthase. To further support the proposed biosynthetic pathway, we now identified the cyclic prenyl pyrophosphate intermediate pre-sodorifen pyrophosphate (PSPP). Its absolute configuration (6R,7S,9S) was determined by comparison of calculated and experimental CD-spectra of its hydrolysis product and matches with those predicted by semi-empirical quantum calculations of the reaction mechanism. In silico modeling of the reaction mechanism of the FPP C-methyltransferase (FPPMT) revealed a SN2 mechanism for the methyl transfer followed by a cyclization cascade. The cyclization of FPP to PSPP is guided by a catalytic dyad of H191 and Y39 and involves an unprecedented cyclopropyl intermediate. W46, W306, F56, and L239 form the hydrophobic binding pocket and E42 and H45 complex a magnesium cation that interacts with the diphosphate moiety of FPP. Six additional amino acids turned out to be essential for product formation and the importance of these amino acids was subsequently confirmed by site-directed mutagenesis. Our results reveal the reaction mechanism involved in methyltransferase-catalyzed cyclization and demonstrate that this coupling of C-methylation and cyclization of FPP by the FPPMT represents an alternative route of terpene biosynthesis that could increase the terpenoid diversity and structural space.
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Affiliation(s)
- Marie Chantal Lemfack
- Institute of Biological Sciences, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany.
| | - Wolfgang Brandt
- Department of Bioorganic Chemistry, Leibniz-Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Germany.
| | - Katja Krüger
- Institute of Biological Sciences, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany.,Department of Internal Medicine I, University Hospital RWTH Aachen, 52074, Aachen, Germany
| | - Alexandra Gurowietz
- Department of Bioorganic Chemistry, Leibniz-Institute of Plant Biochemistry, Weinberg 3, 06120, Halle, Germany.,Institute of Biology, Martin-Luther-Universität Halle-Wittenberg, Weinberg 10, 06120, Halle (Saale), Germany
| | - Jacky Djifack
- Institute of Biological Sciences, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany.,PIMAN Consultants, 12 Rue Barthelemy Danjou, 92100, Boulogne-Billancourt, France
| | - Jan-Philip Jung
- Institute of Biological Sciences, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany
| | - Marius Hopf
- Institute of Biological Sciences, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany.,Duale Hochschule Gera-Eisenach, Weg der Freundschaft 4, 07546, Gera, Germany
| | - Heiko Noack
- Institute of Pharmacy/Biosynthesis of Active Substances, Hoher Weg 8, 06120, Halle (Saale), Germany
| | - Björn Junker
- Institute of Pharmacy/Biosynthesis of Active Substances, Hoher Weg 8, 06120, Halle (Saale), Germany
| | - Stephan von Reuß
- Laboratory of Bioanalytical Chemistry, Institute of Chemistry, University of Neuchatel, Avenue de Bellevaux 51, 2000, Neuchâtel, Switzerland
| | - Birgit Piechulla
- Institute of Biological Sciences, University of Rostock, Albert-Einstein-Straße 3, 18059, Rostock, Germany
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10
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Sartor P, Bock J, Hennecke U, Thierbach S, Fetzner S. Modification of the Pseudomonas aeruginosa toxin 2-heptyl-1-hydroxyquinolin-4(1H)-one and other secondary metabolites by methyltransferases from mycobacteria. FEBS J 2020; 288:2360-2376. [PMID: 33064871 DOI: 10.1111/febs.15595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 09/22/2020] [Accepted: 10/12/2020] [Indexed: 11/26/2022]
Abstract
The opportunistic pathogen Pseudomonas aeruginosa, one of the most prevalent species in infections of the cystic fibrosis lung, produces a range of secondary metabolites, among them the respiratory toxin 2-heptyl-1-hydroxyquinolin-4(1H)-one (2-heptyl-4-hydroxyquinoline N-oxide, HQNO). Cultures of the emerging cystic fibrosis pathogen Mycobacteroides abscessus detoxify HQNO by methylating the N-hydroxy moiety. In this study, the class I methyltransferase MAB_2834c and its orthologue from Mycobacterium tuberculosis, Rv0560c, were identified as HQNO O-methyltransferases. The P. aeruginosa exoproducts 4-hydroxyquinolin-2(1H)-one (DHQ), 2-heptylquinolin-4(1H)-one (HHQ), and 2-heptyl-3-hydroxyquinolin-4(1H)-one (the 'Pseudomonas quinolone signal', PQS), some structurally related (iso)quinolones, and the flavonol quercetin were also methylated; however, HQNO was by far the preferred substrate. Both enzymes converted a benzimidazole[1,2-a]pyridine-4-carbonitrile-based compound, representing the scaffold of antimycobacterial substances, to an N-methylated derivative. We suggest that these promiscuous methyltransferases, newly termed as heterocyclic toxin methyltransferases (Htm), are involved in cellular response to chemical stress and possibly contribute to resistance of mycobacteria toward antimicrobial natural compounds as well as drugs. Thus, synthetic antimycobacterial agents may be designed to be unamenable to methyl transfer. ENZYMES: S-adenosyl-l-methionine:2-heptyl-1-hydroxyquinolin-4(1H)-one O-methyl-transferase, EC 2.1.1.
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Affiliation(s)
- Pascal Sartor
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Germany
| | - Jonathan Bock
- Organic Chemistry Research Group, Department of Chemistry and Department of Bioengineering Sciences, Vrije Universiteit Brussels, Belgium
| | - Ulrich Hennecke
- Organic Chemistry Research Group, Department of Chemistry and Department of Bioengineering Sciences, Vrije Universiteit Brussels, Belgium
| | - Sven Thierbach
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Germany
| | - Susanne Fetzner
- Institute for Molecular Microbiology and Biotechnology, University of Münster, Germany
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11
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Forrest S, Welch M. Arming the troops: Post-translational modification of extracellular bacterial proteins. Sci Prog 2020; 103:36850420964317. [PMID: 33148128 PMCID: PMC10450907 DOI: 10.1177/0036850420964317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Protein secretion is almost universally employed by bacteria. Some proteins are retained on the cell surface, whereas others are released into the extracellular milieu, often playing a key role in virulence. In this review, we discuss the diverse types and potential functions of post-translational modifications (PTMs) occurring to extracellular bacterial proteins.
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Affiliation(s)
- Suzanne Forrest
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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12
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Kuiper EG, Dey D, LaMore PA, Owings JP, Prezioso SM, Goldberg JB, Conn GL. Substrate recognition by the Pseudomonas aeruginosa EF-Tu-modifying methyltransferase EftM. J Biol Chem 2019; 294:20109-20121. [PMID: 31753919 DOI: 10.1074/jbc.ra119.011213] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/20/2019] [Indexed: 01/09/2023] Open
Abstract
The opportunistic bacterial pathogen Pseudomonas aeruginosa is a leading cause of serious infections in individuals with cystic fibrosis, compromised immune systems, or severe burns. P. aeruginosa adhesion to host epithelial cells is enhanced by surface-exposed translation elongation factor EF-Tu carrying a Lys-5 trimethylation, incorporated by the methyltransferase EftM. Thus, the EF-Tu modification by EftM may represent a target to prevent P. aeruginosa infections in vulnerable individuals. Here, we extend our understanding of EftM activity by defining the molecular mechanism by which it recognizes EF-Tu. Acting on the observation that EftM can bind to EF-Tu lacking its N-terminal peptide (encompassing the Lys-5 target site), we generated an EftM homology model and used it in protein/protein docking studies to predict EftM/EF-Tu interactions. Using site-directed mutagenesis of residues in both proteins, coupled with binding and methyltransferase activity assays, we experimentally validated the predicted protein/protein interface. We also show that EftM cannot methylate the isolated N-terminal EF-Tu peptide and that binding-induced conformational changes in EftM are likely needed to enable placement of the first 5-6 amino acids of EF-Tu into a conserved peptide-binding channel in EftM. In this channel, a group of residues that are highly conserved in EftM proteins position the N-terminal sequence to facilitate Lys-5 modification. Our findings reveal that EftM employs molecular strategies for substrate recognition common among both class I (Rossmann fold) and class II (SET domain) methyltransferases and pave the way for studies seeking a deeper understanding of EftM's mechanism of action on EF-Tu.
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Affiliation(s)
- Emily G Kuiper
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322.,Graduate Program in Biochemistry, Cell and Developmental Biology (BCDB), Graduate Division of Biological and Biomedical Sciences (GDBBS), Emory University, Atlanta, Georgia 30322
| | - Debayan Dey
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Paige A LaMore
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Joshua P Owings
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, and Emory Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, Georgia 30322
| | - Samantha M Prezioso
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, and Emory Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, Georgia 30322.,Graduate Program in Microbiology and Molecular Genetics (MMG), Graduate Division of Biological and Biomedical Sciences (GDBBS), Emory University, Atlanta, Georgia 30322
| | - Joanna B Goldberg
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, and Emory Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, Georgia 30322.,Graduate Program in Microbiology and Molecular Genetics (MMG), Graduate Division of Biological and Biomedical Sciences (GDBBS), Emory University, Atlanta, Georgia 30322.,Emory Antibiotic Resistance Center (ARC), Emory University School of Medicine, Atlanta, Georgia 30322
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322 .,Graduate Program in Biochemistry, Cell and Developmental Biology (BCDB), Graduate Division of Biological and Biomedical Sciences (GDBBS), Emory University, Atlanta, Georgia 30322.,Emory Antibiotic Resistance Center (ARC), Emory University School of Medicine, Atlanta, Georgia 30322
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13
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Outer Membrane Protein OmpB Methylation May Mediate Bacterial Virulence. Trends Biochem Sci 2017; 42:936-945. [PMID: 29037863 DOI: 10.1016/j.tibs.2017.09.005] [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: 08/07/2017] [Revised: 09/16/2017] [Accepted: 09/20/2017] [Indexed: 12/29/2022]
Abstract
Methylation of outer membrane proteins (OMPs) has been implicated in bacterial virulence. Lysine methylation in rickettsial OmpB is correlated with rickettsial virulence, and N- and O-methylations are also observed in virulence-relevant OMPs from several pathogenic bacteria that cause typhus, leptospirosis, tuberculosis, and anaplasmosis. We summarize recent findings on the structure of methylated OmpB, biochemical characterization, and crystal structures of OmpB methyltransferases. Native rickettsial OmpB purified from highly virulent strains contains multiple clusters of trimethyllysine, in contrast with mostly monomethyllysine, and no trimethyllysine is found in an avirulent strain. Crystal structure of the methyltransferases reveals mechanistic insights for catalysis, and a working model is discussed for this unusual post-translational modification.
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