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Certain LK, Way JC, Pezone MJ, Collins JJ. Using Engineered Bacteria to Characterize Infection Dynamics and Antibiotic Effects In Vivo. Cell Host Microbe 2017; 22:263-268.e4. [PMID: 28867388 DOI: 10.1016/j.chom.2017.08.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 05/17/2017] [Accepted: 08/01/2017] [Indexed: 12/31/2022]
Abstract
Synthetic biology has focused on engineering microbes to synthesize useful products or to serve as living diagnostics and therapeutics. Here we utilize a host-derived Escherichia coli strain engineered with a genetic toggle switch as a research tool to examine in vivo replicative states in a mouse model of chronic infection, and to compare in vivo and in vitro bacterial behavior. In contrast to the effect of antibiotics in vitro, we find that the fraction of actively dividing bacteria remains relatively high throughout the course of a chronic infection in vivo and increases in response to antibiotics. Moreover, the presence of non-dividing bacteria in vivo does not necessarily lead to an antibiotic-tolerant infection, in contrast to expectations from in vitro experiments. These results demonstrate the utility of engineered bacteria for querying pathogen behavior in vivo, and the importance of validating in vitro studies of antibiotic effects with in vivo models.
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Affiliation(s)
- Laura K Certain
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA; Division of Infectious Diseases, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA
| | - Jeffrey C Way
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA
| | - Matthew J Pezone
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA
| | - James J Collins
- Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Boston, MA 02115, USA; Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA; Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Synthetic Biology Center, MIT, Cambridge, MA 02139, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
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52
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Wang J, Liu Q, Feng J, Lv JP, Xie SL. Effect of high-doses pyrogallol on oxidative damage, transcriptional responses and microcystins synthesis in Microcystis aeruginosa TY001 (Cyanobacteria). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2016; 134P1:273-279. [PMID: 27643987 DOI: 10.1016/j.ecoenv.2016.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 09/06/2016] [Accepted: 09/10/2016] [Indexed: 06/06/2023]
Abstract
Severe eutrophication and harmful cyanobacterial blooms of freshwater ecosystems is a persistent environmental topic in recent decades. Pyrogallol (polyphenol) was confirmed to exhibit one of the most intensive inhibitory effects on the Microcystis aeruginosa. In this study, the expression of genes, release of microcystins (MCs) and antioxidant system of pyrogallol on Microcystis aeruginosa TY001 were investigated. The results revealed that the expression of stress response genes (prx, ftsH, grpE and fabZ) and DNA repair genes (recA and gyrB) were up-regulated. Meanwhile, the antioxidant enzymes, including superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD) activity, were increased, and the stress caused lipid peroxidation to occur and malondialdehyde (MDA) levels to change. Unexpectedly, the relative transcript abundance of microcystin synthesis genes (mcyB, mcyD and ntcA) and the contents of microcystins (MCs) significantly increased compared with the control in the culture medium. In conclusion, oxidative damage and DNA damage are the primary mechanisms for the allelopathic effect of pyrogallol on M. aeruginosa TY001.
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Affiliation(s)
- Jie Wang
- School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Qi Liu
- School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Jia Feng
- School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Jun-Ping Lv
- School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Shu-Lian Xie
- School of Life Science, Shanxi University, Taiyuan 030006, China.
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53
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Atas A, Seddon AM, Ford DC, Cooper IA, Wren BW, Oyston PCF, Karlyshev AV. YPTB3816 of Yersinia pseudotuberculosis strain IP32953 is a virulence-related metallo-oligopeptidase. BMC Microbiol 2016; 16:282. [PMID: 27887582 PMCID: PMC5124237 DOI: 10.1186/s12866-016-0900-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 11/17/2016] [Indexed: 12/03/2022] Open
Abstract
Background Although bacterial peptidases are known to be produced by various microorganisms, including pathogenic bacteria, their role in bacterial physiology is not fully understood. In particular, oligopeptidases are thought to be mainly involved in degradation of short peptides e.g. leader peptides released during classical protein secretion pathways. The aim of this study was to investigate effects of inactivation of an oligopeptidase encoding gene opdA gene of Yersinia pseudotuberculosis on bacterial properties in vivo and in vitro, and to test dependence of the enzymatic activity of the respective purified enzyme on the presence of different divalent cations. Results In this study we found that oligopeptidase OpdA of Yersinia pseudotuberculosis is required for bacterial virulence, whilst knocking out the respective gene did not have any effect on bacterial viability or growth rate in vitro. In addition, we studied enzymatic properties of this enzyme after expression and purification from E. coli. Using an enzyme depleted of contaminant divalent cations and different types of fluorescently labelled substrates, we found strong dependence of its activity on the presence of particular cations. Unexpectedly, Zn2+ showed stimulatory activity only at low concentrations, but inhibited the enzyme at higher concentrations. In contrast, Co2+, Ca2+ and Mn2+ stimulated activity at all concentrations tested, whilst Mg2+ revealed no effect on the enzyme activity at all concentrations used. Conclusions The results of this study provide valuable contribution to the investigation of bacterial peptidases in general, and that of metallo-oligopeptidases in particular. This is the first study demonstrating that opdA in Yersinia pseudotuberculsosis is required for pathogenicity. The data reported are important for better understanding of the role of OpdA-like enzymes in pathogenesis in bacterial infections. Characterisation of this protein may serve as a basis for the development of novel antibacterials based on specific inhibition of this peptidase activity. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0900-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ali Atas
- School of Life Sciences, Pharmacy and Chemistry; Faculty of Science, Engineering and Computing, Kingston University, Penrhyn Road, Kingston upon Thames, KT1 2EE, UK
| | - Alan M Seddon
- School of Life Sciences, Pharmacy and Chemistry; Faculty of Science, Engineering and Computing, Kingston University, Penrhyn Road, Kingston upon Thames, KT1 2EE, UK
| | - Donna C Ford
- Biomedical Sciences, DSTL Porton Down, Salisbury, Wiltshire, SP4 0JQ, UK
| | - Ian A Cooper
- Biomedical Sciences, DSTL Porton Down, Salisbury, Wiltshire, SP4 0JQ, UK
| | - Brendan W Wren
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Petra C F Oyston
- Biomedical Sciences, DSTL Porton Down, Salisbury, Wiltshire, SP4 0JQ, UK
| | - Andrey V Karlyshev
- School of Life Sciences, Pharmacy and Chemistry; Faculty of Science, Engineering and Computing, Kingston University, Penrhyn Road, Kingston upon Thames, KT1 2EE, UK.
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Tsai CH, Ho YH, Sung TC, Wu WF, Chen CS. Escherichia coli Proteome Microarrays Identified the Substrates of ClpYQ Protease. Mol Cell Proteomics 2016; 16:113-120. [PMID: 27864322 DOI: 10.1074/mcp.m116.065482] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Indexed: 01/12/2023] Open
Abstract
Proteolysis is a vital mechanism to regulate the cellular proteome in all kingdoms of life, and ATP-dependent proteases play a crucial role within this process. In Escherichia coli, ClpYQ is one of the primary ATP-dependent proteases. In addition to function with removals of abnormal peptides in the cells, ClpYQ degrades regulatory proteins if necessary and thus let cells adjust to various environmental conditions. In E. coli, SulA, RcsA, RpoH and TraJ as well as RNase R, have been identified as natural protein substrates of ClpYQ. ClpYQ contains ClpY and ClpQ. The ATPase ClpY is responsible for protein recognition, unfolding, and translocation into the catalytic core of ClpQ. In this study, we use an indirect identification strategy to screen possible ClpY targets with E. coli K12 proteome chips. The chip assay results showed that YbaB strongly bound to ClpY. We used yeast two-hybrid assay to confirm the interactions between ClpY and YbaB protein and determined the Kd between ClpY and YbaB by quartz crystal microbalance. Furthermore, we validated that YbaB was successfully degraded by ClpYQ protease activity using ClpYQ in vitro and in vivo degradation assay. These findings demonstrated the YbaB is a novel substrate of ClpYQ protease. This work also successfully demonstrated that with the use of recognition element of a protease can successfully screen its substrates by indirect proteome chip screening assay.
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Affiliation(s)
- Chih-Hsuan Tsai
- From the ‡Department of Agricultural Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan
| | - Yu-Hsuan Ho
- §Graduate Institute of Systems Biology and Bioinformatics, National Central University, No. 300, Jhongda Rd., Jhongli 32001, Taiwan.,¶Department of Biomedical Sciences and Engineering, National Central University, No. 300, Jhongda Rd., Jhongli 32001, Taiwan
| | - Tzu-Cheng Sung
- §Graduate Institute of Systems Biology and Bioinformatics, National Central University, No. 300, Jhongda Rd., Jhongli 32001, Taiwan.,¶Department of Biomedical Sciences and Engineering, National Central University, No. 300, Jhongda Rd., Jhongli 32001, Taiwan
| | - Whei-Fen Wu
- From the ‡Department of Agricultural Chemistry, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei 10617, Taiwan;
| | - Chien-Sheng Chen
- §Graduate Institute of Systems Biology and Bioinformatics, National Central University, No. 300, Jhongda Rd., Jhongli 32001, Taiwan; .,¶Department of Biomedical Sciences and Engineering, National Central University, No. 300, Jhongda Rd., Jhongli 32001, Taiwan
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55
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Gil F, Paredes-Sabja D. Acyldepsipeptide antibiotics as a potential therapeutic agent against Clostridium difficile recurrent infections. Future Microbiol 2016; 11:1179-89. [DOI: 10.2217/fmb-2016-0064] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Alternative antimicrobial therapies based on acyldepsipeptides may hold promising results, based on the fact that they have shown to efficiently eradicate persister cells, stationary cells and cell in biofilm structures of several pathogenic bacteria from the infected host. Clostridium difficile infection is considered the result of extensive hospital use of expanded-spectrum antibiotics, which cause dysbiosis of the intestinal microbiota, enhancing susceptibility to infection and persistence. Considering the urgent need for the development of novel and efficient antimicrobial strategies against C. difficile, we review the potential application to treat C. difficile infections of acyldepsipeptides family of antibiotics, its mechanism of action and current developmental stages.
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Affiliation(s)
- Fernando Gil
- Microbiota–Host Interactions & Clostridia Research Group, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
| | - Daniel Paredes-Sabja
- Microbiota–Host Interactions & Clostridia Research Group, Departamento de Ciencias Biológicas, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
- Center for Bioinformatic & Integrative Biology, Facultad de Ciencias Biológicas, Universidad Andres Bello, Santiago, Chile
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56
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Zhao BB, Li XH, Zeng YL, Lu YJ. ClpP-deletion impairs the virulence of Legionella pneumophila and the optimal translocation of effector proteins. BMC Microbiol 2016; 16:174. [PMID: 27484084 PMCID: PMC4969725 DOI: 10.1186/s12866-016-0790-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/27/2016] [Indexed: 12/19/2022] Open
Abstract
Background The opportunistic bacterial pathogen Legionella pneumophila uses substrate effectors of Dot/Icm type IVB secretion system (T4BSS) to accomplish survival and replication in amoebae cells and mammalian alveolar macrophages. During the conversion between its highly resistant, infectious dormant form and vigorously growing, uninfectious replicative form, L. pneumophila utilizes a complicated regulatory network in which proteolysis may play a significant role. As a highly conserved core protease, ClpP is involved in various cellular processes as well as virulence in bacteria, and has been proved to be required for the expression of transmission traits and cell division of L. pneumophila. Results The clpP-deficient L. pneumophila strain failed to replicate and was digested in the first 3 h post-infection in mammalian cells J774A.1. Further investigation demonstrates that the clpP deficient mutant strain was unable to escape the endosome-lysosomal pathway in host cells. We also found that the clpP deficient mutant strain still expresses T4BSS components, induces contact-dependent cytotoxicity and translocate effector proteins RalF and LegK2, indicating that its T4BSS was overall functional. Interestingly, we further found that the translocation of several effector proteins is significantly reduced without ClpP. Conclusions The data indicate that ClpP plays an important role in regulating the virulence and effector translocation of Legionella pneumophila. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0790-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bei-Bei Zhao
- School of Life Sciences and Biomedical Center, Sun Yat-sen University, No. 135 Xingang road west, Guangzhou, 510275, China
| | - Xiang-Hui Li
- School of Life Sciences and Biomedical Center, Sun Yat-sen University, No. 135 Xingang road west, Guangzhou, 510275, China.,Present address: Jiangsu Information Institute of Science and Technology, Nanjing, 210042, China
| | - Yong-Lun Zeng
- School of Life Sciences and Biomedical Center, Sun Yat-sen University, No. 135 Xingang road west, Guangzhou, 510275, China.,Present address: School of Life Sciences, Centre for Cell and Developmental Biology, The Chinese University of Hong Kong, Hong Kong, 999077, China
| | - Yong-Jun Lu
- School of Life Sciences and Biomedical Center, Sun Yat-sen University, No. 135 Xingang road west, Guangzhou, 510275, China.
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57
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Encapsulation of multiple cargo proteins within recombinant Eut nanocompartments. Appl Microbiol Biotechnol 2016; 100:9187-9200. [PMID: 27450681 DOI: 10.1007/s00253-016-7737-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 07/07/2016] [Accepted: 07/10/2016] [Indexed: 01/08/2023]
Abstract
Spatial organization via encapsulation of enzymes within recombinant nanocompartments may increase efficiency in multienzyme cascades. Previously, we reported the encapsulation of single cargo proteins within nanocompartments in the heterologous host Escherichia coli. This was achieved by coexpression of the Salmonella enterica LT2 ethanolamine utilization bacterial microcompartment shell proteins EutS or EutSMNLK, with a signal sequence EutC1-19 cargo protein fusion. Optimization of this system, leading to the targeting of more than one cargo protein, requires an understanding of the encapsulation mechanism. In this work, we report that the signal sequence EutC1-19 targets cargo to the interior of nanocompartments via a hydrophobic interaction with a helix on shell protein EutS. We confirm that EutC1-19 does not interact with other Eut BMC shell proteins, EutMNLK. Furthermore, we show that a second signal sequence EutE1-21 interacts specifically with the same helix on EutS. Both signal sequences appear to compete for the same EutS helix to simultaneously colocalize two cargo proteins to the interior of recombinant nanocompartments. This work offers the first insights into signal sequence-shell protein interactions required for cargo sequestration within Eut BMCs. It also provides a basis for the future engineering of Eut nanocompartments as a platform for the potential colocalization of multienzyme cascades for synthetic biology applications.
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58
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Pressler K, Vorkapic D, Lichtenegger S, Malli G, Barilich BP, Cakar F, Zingl FG, Reidl J, Schild S. AAA+ proteases and their role in distinct stages along the Vibrio cholerae lifecycle. Int J Med Microbiol 2016; 306:452-62. [PMID: 27345492 DOI: 10.1016/j.ijmm.2016.05.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 05/09/2016] [Accepted: 05/24/2016] [Indexed: 12/29/2022] Open
Abstract
The facultative human pathogen Vibrio cholerae has to adapt to different environmental conditions along its lifecycle by means of transcriptional, translational and post-translational regulation. This study provides a first comprehensive analysis regarding the contribution of the cytoplasmic AAA+ proteases Lon, ClpP and HslV to distinct features of V. cholerae behaviour, including biofilm formation, motility, cholera toxin expression and colonization fitness in the mouse model. While absence of HslV did not yield to any altered phenotype compared to wildtype, absence of Lon or ClpP resulted in significantly reduced colonization in vivo. In addition, a Δlon deletion mutant showed altered biofilm formation and increased motility, which could be correlated with higher expression of V. cholerae flagella gene class IV. Concordantly, we could show by immunoblot analysis, that Lon is the main protease responsible for proteolytic control of FliA, which is required for class IV flagella gene transcription, but also downregulates virulence gene expression. FliA becomes highly sensitive to proteolytic degradation in absence of its anti-sigma factor FlgM, a scenario reported to occur during mucosal penetration due to FlgM secretion through the broken flagellum. Our results confirm that the high stability of FliA in the absence of Lon results in less cholera toxin and toxin corgulated pilus production under virulence gene inducing conditions and in the presence of a damaged flagellum. Thus, the data presented herein provide a molecular explanation on how V. cholerae can achieve full expression of virulence genes during early stages of colonization, despite FliA getting liberated from the anti-sigma factor FlgM.
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Affiliation(s)
- Katharina Pressler
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50, A-8010 Graz, Austria
| | - Dina Vorkapic
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50, A-8010 Graz, Austria
| | - Sabine Lichtenegger
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50, A-8010 Graz, Austria
| | - Gerald Malli
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50, A-8010 Graz, Austria
| | - Benjamin P Barilich
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50, A-8010 Graz, Austria
| | - Fatih Cakar
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50, A-8010 Graz, Austria
| | - Franz G Zingl
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50, A-8010 Graz, Austria
| | - Joachim Reidl
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50, A-8010 Graz, Austria
| | - Stefan Schild
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50, A-8010 Graz, Austria.
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Piri N, Kwong JMK, Gu L, Caprioli J. Heat shock proteins in the retina: Focus on HSP70 and alpha crystallins in ganglion cell survival. Prog Retin Eye Res 2016; 52:22-46. [PMID: 27017896 PMCID: PMC4842330 DOI: 10.1016/j.preteyeres.2016.03.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 03/14/2016] [Accepted: 03/22/2016] [Indexed: 10/22/2022]
Abstract
Heat shock proteins (HSPs) belong to a superfamily of stress proteins that are critical constituents of a complex defense mechanism that enhances cell survival under adverse environmental conditions. Cell protective roles of HSPs are related to their chaperone functions, antiapoptotic and antinecrotic effects. HSPs' anti-apoptotic and cytoprotective characteristics, their ability to protect cells from a variety of stressful stimuli, and the possibility of their pharmacological induction in cells under pathological stress make these proteins an attractive therapeutic target for various neurodegenerative diseases; these include Alzheimer's, Parkinson's, Huntington's, prion disease, and others. This review discusses the possible roles of HSPs, particularly HSP70 and small HSPs (alpha A and alpha B crystallins) in enhancing the survival of retinal ganglion cells (RGCs) in optic neuropathies such as glaucoma, which is characterized by progressive loss of vision caused by degeneration of RGCs and their axons in the optic nerve. Studies in animal models of RGC degeneration induced by ocular hypertension, optic nerve crush and axotomy show that upregulation of HSP70 expression by hyperthermia, zinc, geranyl-geranyl acetone, 17-AAG (a HSP90 inhibitor), or through transfection of retinal cells with AAV2-HSP70 effectively supports the survival of injured RGCs. RGCs survival was also stimulated by overexpression of alpha A and alpha B crystallins. These findings provide support for translating the HSP70- and alpha crystallin-based cell survival strategy into therapy to protect and rescue injured RGCs from degeneration associated with glaucomatous and other optic neuropathies.
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Affiliation(s)
- Natik Piri
- Stein Eye Institute, University of California, Los Angeles, CA 90095, USA; Brain Research Institute, University of California, Los Angeles, CA 90095, USA.
| | - Jacky M K Kwong
- Stein Eye Institute, University of California, Los Angeles, CA 90095, USA
| | - Lei Gu
- Stein Eye Institute, University of California, Los Angeles, CA 90095, USA
| | - Joseph Caprioli
- Stein Eye Institute, University of California, Los Angeles, CA 90095, USA; Brain Research Institute, University of California, Los Angeles, CA 90095, USA
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Kardon JR, Yien YY, Huston NC, Branco DS, Hildick-Smith GJ, Rhee KY, Paw BH, Baker TA. Mitochondrial ClpX Activates a Key Enzyme for Heme Biosynthesis and Erythropoiesis. Cell 2016; 161:858-67. [PMID: 25957689 DOI: 10.1016/j.cell.2015.04.017] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 01/15/2015] [Accepted: 03/13/2015] [Indexed: 12/21/2022]
Abstract
The mitochondrion maintains and regulates its proteome with chaperones primarily inherited from its bacterial endosymbiont ancestor. Among these chaperones is the AAA+ unfoldase ClpX, an important regulator of prokaryotic physiology with poorly defined function in the eukaryotic mitochondrion. We observed phenotypic similarity in S. cerevisiae genetic interaction data between mitochondrial ClpX (mtClpX) and genes contributing to heme biosynthesis, an essential mitochondrial function. Metabolomic analysis revealed that 5-aminolevulinic acid (ALA), the first heme precursor, is 5-fold reduced in yeast lacking mtClpX activity and that total heme is reduced by half. mtClpX directly stimulates ALA synthase in vitro by catalyzing incorporation of its cofactor, pyridoxal phosphate. This activity is conserved in mammalian homologs; additionally, mtClpX depletion impairs vertebrate erythropoiesis, which requires massive upregulation of heme biosynthesis to supply hemoglobin. mtClpX, therefore, is a widely conserved stimulator of an essential biosynthetic pathway and uses a previously unrecognized mechanism for AAA+ unfoldases.
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Affiliation(s)
- Julia R Kardon
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Yvette Y Yien
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nicholas C Huston
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Diana S Branco
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Gordon J Hildick-Smith
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kyu Y Rhee
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10065, USA; Division of Infectious Diseases, Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Barry H Paw
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Division of Hematology-Oncology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Tania A Baker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Abstract
This chapter describes the identification of the first prokaryotic ubiquitin-like protein modifier, Pup, which covalently attaches to proteins to target them for destruction by a bacterial proteasome in a manner akin to ubiquitin in eukaryotes. Despite using a proteasome as the end point for proteolysis, Pup and ubiquitin differ in sequence, structure and method of activation and conjugation to protein substrates. Pup is so far the only known posttranslational protein modifier in prokaryotes and its discovery opens the door to the possibility that others are present not only for proteolysis, but also to regulate protein function or localization. Here, we discuss the putative mechanism of activation and conjugation of Pup (termed "pupylation") to target proteins. In addition, because it is unclear whether or not Pup, like ubiquitin, is recycled or degraded during substrate targeting to the proteasome, we propose methods that may identify Pup deconjugation enzymes ("depupylases"). Finally, we outline future directions for Pup research and anti-tuberculosis drug discovery.
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The Protease Locus of Francisella tularensis LVS Is Required for Stress Tolerance and Infection in the Mammalian Host. Infect Immun 2016; 84:1387-1402. [PMID: 26902724 DOI: 10.1128/iai.00076-16] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 02/12/2016] [Indexed: 02/05/2023] Open
Abstract
Francisella tularensis is the causative agent of tularemia and a category A potential agent of bioterrorism, but the pathogenic mechanisms of F. tularensis are largely unknown. Our previous transposon mutagenesis screen identified 95 lung infectivity-associated F. tularensis genes, including those encoding the Lon and ClpP proteases. The present study validates the importance of Lon and ClpP in intramacrophage growth and infection of the mammalian host by using unmarked deletion mutants of the F. tularensis live vaccine strain (LVS). Further experiments revealed that lon and clpP are also required for F. tularensis tolerance to stressful conditions. A quantitative proteomic comparison between heat-stressed LVS and the isogenic Lon-deficient mutant identified 29 putative Lon substrate proteins. The follow-up protein degradation experiments identified five substrates of the F. tularensis Lon protease (FTL578, FTL663, FTL1217, FTL1228, and FTL1957). FTL578 (ornithine cyclodeaminase), FTL663 (heat shock protein), and FTL1228 (iron-sulfur activator complex subunit SufD) have been previously described as virulence-associated factors in F. tularensis Identification of these Lon substrates has thus provided important clues for further understanding of the F. tularensis stress response and pathogenesis. The high-throughput approach developed in this study can be used for systematic identification of the Lon substrates in other prokaryotic and eukaryotic organisms.
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Abstract
Proteasomes are ATP-dependent, barrel-shaped proteases found in all three domains of life. In eukaryotes, proteins are typically targeted for degradation by posttranslational modification with the small protein ubiquitin. In 2008, the first bacterial protein modifier, Pup (prokaryotic ubiquitin-like protein), was identified in Mycobacterium tuberculosis. Functionally analogous to ubiquitin, conjugation with Pup serves as a signal for degradation by the mycobacterial proteasome. Proteolysis-dependent and -independent functions of the M. tuberculosis proteasome are essential for virulence of this successful pathogen. In this article we describe the discovery of the proteasome as a key player in tuberculosis pathogenesis and the biology and biochemistry of the Pup-proteasome system.
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Luan B, Huynh T, Li J, Zhou R. Nanomechanics of Protein Unfolding Outside a Generic Nanopore. ACS NANO 2016; 10:317-323. [PMID: 26655061 DOI: 10.1021/acsnano.5b04557] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Protein folding and unfolding have been the subject of active research for decades. Most of previous studies in protein unfolding were focused on temperature, chemical, and/or force (such as in atomic force microscopy (AFM)) induced denaturations. Recent studies on the functional roles of proteasomes (such as ClpXP) revealed a different unfolding process in cell, during which a target protein is mechanically unfolded and pulled into a confined, pore-like geometry for degradation. While the proteasome nanomachine has been extensively studied, the mechanism for unfolding proteins with the proteasome pore is still poorly understood. Here, we investigate the mechanical unfolding process of ubiquitin with (or really outside) a generic nanopore, and compare such process with that in the AFM pulling experiment. Unexpectedly, the required force for protein unfolding through a pore can be much smaller than that by the AFM. Simulation results also unveiled different nanomechanics, tearing fracture vs shearing friction, in these two distinct types of mechanical unfoldings.
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Affiliation(s)
- Binquan Luan
- Computational Biological Center, IBM Thomas J. Watson Research , Yorktown Heights, New York 10598, United States
| | - Tien Huynh
- Computational Biological Center, IBM Thomas J. Watson Research , Yorktown Heights, New York 10598, United States
| | - Jingyuan Li
- Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences , Beijing 100049, China
| | - Ruhong Zhou
- Computational Biological Center, IBM Thomas J. Watson Research , Yorktown Heights, New York 10598, United States
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65
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Joshi KK, Bergé M, Radhakrishnan SK, Viollier PH, Chien P. An Adaptor Hierarchy Regulates Proteolysis during a Bacterial Cell Cycle. Cell 2016; 163:419-31. [PMID: 26451486 DOI: 10.1016/j.cell.2015.09.030] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 07/01/2015] [Accepted: 09/02/2015] [Indexed: 11/30/2022]
Abstract
Regulated protein degradation is essential. The timed destruction of crucial proteins by the ClpXP protease drives cell-cycle progression in the bacterium Caulobacter crescentus. Although ClpXP is active alone, additional factors are inexplicably required for cell-cycle-dependent proteolysis. Here, we show that these factors constitute an adaptor hierarchy wherein different substrates are destroyed based on the degree of adaptor assembly. The hierarchy builds upon priming of ClpXP by the adaptor CpdR, which promotes degradation of one class of substrates and also recruits the adaptor RcdA to degrade a second class of substrates. Adding the PopA adaptor promotes destruction of a third class of substrates and inhibits degradation of the second class. We dissect RcdA to generate bespoke adaptors, identifying critical substrate elements needed for RcdA recognition and uncovering additional cell-cycle-dependent ClpXP substrates. Our work reveals how hierarchical adaptors and primed proteases orchestrate regulated proteolysis during bacterial cell-cycle progression.
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Affiliation(s)
- Kamal Kishore Joshi
- Department of Biochemistry and Molecular Biology, Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Matthieu Bergé
- Department of Microbiology and Molecular Medicine, Institute of Genetics & Genomics in Geneva (iGE3), University of Geneva Medical School, Geneva CH-1211, Switzerland
| | - Sunish Kumar Radhakrishnan
- Department of Microbiology and Molecular Medicine, Institute of Genetics & Genomics in Geneva (iGE3), University of Geneva Medical School, Geneva CH-1211, Switzerland
| | - Patrick Henri Viollier
- Department of Microbiology and Molecular Medicine, Institute of Genetics & Genomics in Geneva (iGE3), University of Geneva Medical School, Geneva CH-1211, Switzerland
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, Molecular and Cellular Biology Graduate Program, University of Massachusetts Amherst, Amherst, MA 01003, USA.
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66
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Chang CY, Hu HT, Tsai CH, Wu WF. The degradation of RcsA by ClpYQ(HslUV) protease in Escherichia coli. Microbiol Res 2016; 184:42-50. [PMID: 26856452 DOI: 10.1016/j.micres.2016.01.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 12/21/2015] [Accepted: 01/09/2016] [Indexed: 01/30/2023]
Abstract
In Escherichia coli, RcsA, a positive activator for transcription of cps (capsular polysaccharide synthesis) genes, is degraded by the Lon protease. In lon mutant, the accumulation of RcsA leads to overexpression of capsular polysaccharide. In a previous study, overproduction of ClpYQ(HslUV) protease represses the expression of cpsB∷lacZ, but there has been no direct observation demonstrating that ClpYQ degrades RcsA. By means of a MBP-RcsA fusion protein, we showed that RcsA activated cpsB∷lacZ expression and could be rapidly degraded by Lon protease in SG22622 (lon(+)). Subsequently, the comparative half-life experiments performed in the bacterial strains SG22623 (lon) and AC3112 (lon clpY clpQ) indicated that the RcsA turnover rate in AC3112 was relatively slow and RcsA was stable at 30°C or 41°C. In addition, ClpY could interact with RscA in an in vitro pull-down assay, and the more rapid degradation of RcsA was observed in the presence of ClpYQ protease at 41°C. Thus, we conclude that RcsA is indeed proteolized by ClpYQ protease.
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Affiliation(s)
- Chun-Yang Chang
- Department of Agricultural Chemistry, College of Bio-Resource and Agriculture, National Taiwan University, Taipei, Taiwan, ROC
| | - Hui-Ting Hu
- Department of Agricultural Chemistry, College of Bio-Resource and Agriculture, National Taiwan University, Taipei, Taiwan, ROC
| | - Chih-Hsuan Tsai
- Department of Agricultural Chemistry, College of Bio-Resource and Agriculture, National Taiwan University, Taipei, Taiwan, ROC
| | - Whei-Fen Wu
- Department of Agricultural Chemistry, College of Bio-Resource and Agriculture, National Taiwan University, Taipei, Taiwan, ROC.
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67
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Samanovic MI, Darwin KH. Game of 'Somes: Protein Destruction for Mycobacterium tuberculosis Pathogenesis. Trends Microbiol 2016; 24:26-34. [PMID: 26526503 PMCID: PMC4698092 DOI: 10.1016/j.tim.2015.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Revised: 09/25/2015] [Accepted: 10/05/2015] [Indexed: 01/12/2023]
Abstract
The proteasome system of Mycobacterium tuberculosis is required for causing disease. Proteasomes are multisubunit chambered proteases and, until recently, were only known to participate in adenosine triphosphate (ATP)-dependent proteolysis in bacteria. In this review, we discuss the latest advances in understanding how both ATP-dependent and ATP-independent proteasome-regulated pathways contribute to M. tuberculosis virulence.
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Affiliation(s)
- Marie I Samanovic
- New York University School of Medicine, Department of Microbiology, 550 First Avenue, MSB 236 New York, NY 10016, USA
| | - K Heran Darwin
- New York University School of Medicine, Department of Microbiology, 550 First Avenue, MSB 236 New York, NY 10016, USA.
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68
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Song C, Schmidt R, de Jager V, Krzyzanowska D, Jongedijk E, Cankar K, Beekwilder J, van Veen A, de Boer W, van Veen JA, Garbeva P. Exploring the genomic traits of fungus-feeding bacterial genus Collimonas. BMC Genomics 2015; 16:1103. [PMID: 26704531 PMCID: PMC4690342 DOI: 10.1186/s12864-015-2289-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 12/11/2015] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Collimonas is a genus belonging to the class of Betaproteobacteria and consists mostly of soil bacteria with the ability to exploit living fungi as food source (mycophagy). Collimonas strains differ in a range of activities, including swimming motility, quorum sensing, extracellular protease activity, siderophore production, and antimicrobial activities. RESULTS In order to reveal ecological traits possibly related to Collimonas lifestyle and secondary metabolites production, we performed a comparative genomics analysis based on whole-genome sequencing of six strains representing 3 recognized species. The analysis revealed that the core genome represents 43.1 to 52.7% of the genomes of the six individual strains. These include genes coding for extracellular enzymes (chitinase, peptidase, phospholipase), iron acquisition and type II secretion systems. In the variable genome, differences were found in genes coding for secondary metabolites (e.g. tripropeptin A and volatile terpenes), several unknown orphan polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS), nonribosomal peptide synthetase (NRPS) gene clusters, a new lipopeptide and type III and type VI secretion systems. Potential roles of the latter genes in the interaction with other organisms were investigated. Mutation of a gene involved in tripropeptin A biosynthesis strongly reduced the antibacterial activity against Staphylococcus aureus, while disruption of a gene involved in the biosynthesis of the new lipopeptide had a large effect on the antifungal/oomycetal activities. CONCLUSIONS Overall our results indicated that Collimonas genomes harbour many genes encoding for novel enzymes and secondary metabolites (including terpenes) important for interactions with other organisms and revealed genomic plasticity, which reflect the behaviour, antimicrobial activity and lifestylesof Collimonas spp.
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Affiliation(s)
- Chunxu Song
- Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands.
| | - Ruth Schmidt
- Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands.
| | - Victor de Jager
- Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands.
| | - Dorota Krzyzanowska
- Laboratory of Biological Plant Protection, Intercollegiate Faculty of Biotechnology UG&MUG, Kladki 24, Gdansk, 80-822, Poland.
| | - Esmer Jongedijk
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands.
| | - Katarina Cankar
- Business Unit Bioscience, Plant Research International, Wageningen University and Research Centre, Wageningen, The Netherlands.
| | - Jules Beekwilder
- Business Unit Bioscience, Plant Research International, Wageningen University and Research Centre, Wageningen, The Netherlands.
| | - Anouk van Veen
- Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands.
| | - Wietse de Boer
- Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands.
| | - Johannes A van Veen
- Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands.
| | - Paolina Garbeva
- Netherlands Institute of Ecology, Department of Microbial Ecology, Droevendaalsesteeg 10, Wageningen, 6708 PB, The Netherlands.
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69
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Willrodt C, Hoschek A, Bühler B, Schmid A, Julsing MK. Decoupling production from growth by magnesium sulfate limitation boosts de novo limonene production. Biotechnol Bioeng 2015; 113:1305-14. [PMID: 26574166 DOI: 10.1002/bit.25883] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/08/2015] [Indexed: 01/23/2023]
Abstract
The microbial production of isoprenoids has recently developed into a prime example for successful bottom-up synthetic biology or top-down systems biology strategies. Respective fermentation processes typically rely on growing recombinant microorganisms. However, the fermentative production of isoprenoids has to compete with cellular maintenance and growth for carbon and energy. Non-growing but metabolically active E. coli cells were evaluated in this study as alternative biocatalyst configurations to reduce energy and carbon loss towards biomass formation. The use of non-growing cells in an optimized fermentation medium resulted in more than fivefold increased specific limonene yields on cell dry weight and glucose, as compared to the traditional growing-cell-approach. Initially, the stability of the resting-cell activity was limited. This instability was overcome via the optimization of the minimal fermentation medium enabling high and stable limonene production rates for up to 8 h and a high specific yield of ≥50 mg limonene per gram cell dry weight. Omitting MgSO4 from the fermentation medium was very promising to prohibit growth and allow high productivities. Applying a MgSO4 -limitation also improved limonene formation by growing cells during non-exponential growth involving a reduced biomass yield on glucose and a fourfold increase in specific limonene yields on biomass as compared to non-limited cultures. The control of microbial growth via the medium composition was identified as a key but yet underrated strategy for efficient isoprenoid production. Biotechnol. Bioeng. 2016;113: 1305-1314. © 2015 Wiley Periodicals, Inc.
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Affiliation(s)
- Christian Willrodt
- Department Solar Materials, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany.,Department of Biochemical and Chemical Engineering, Laboratory of Chemical Biotechnology, TU Dortmund University, Dortmund, Germany
| | - Anna Hoschek
- Department of Biochemical and Chemical Engineering, Laboratory of Chemical Biotechnology, TU Dortmund University, Dortmund, Germany
| | - Bruno Bühler
- Department of Biochemical and Chemical Engineering, Laboratory of Chemical Biotechnology, TU Dortmund University, Dortmund, Germany
| | - Andreas Schmid
- Department Solar Materials, Helmholtz Centre for Environmental Research (UFZ), Leipzig, Germany.
| | - Mattijs K Julsing
- Department of Biochemical and Chemical Engineering, Laboratory of Chemical Biotechnology, TU Dortmund University, Dortmund, Germany
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70
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Zhang Y, Maurizi MR. Mitochondrial ClpP activity is required for cisplatin resistance in human cells. Biochim Biophys Acta Mol Basis Dis 2015; 1862:252-64. [PMID: 26675528 DOI: 10.1016/j.bbadis.2015.12.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 11/05/2015] [Accepted: 12/04/2015] [Indexed: 02/07/2023]
Abstract
In human cells ClpP and ClpX are imported into the mitochondrial matrix, where they interact to form the ATP-dependent protease ClpXP and play a role in the mitochondrial unfolded protein response. We find that reducing the levels of mitochondrial ClpP or ClpX renders human cancer cells more sensitive to cisplatin, a widely used anti-cancer drug. Conversely, overexpression of HClpP desensitizes cells to cisplatin. Overexpression of inactive HClpP-S97A had no effect. Cisplatin resistance correlated with decreased cellular accumulation of cisplatin and decreased levels of diguanosine-cisplatin adducts in both mitochondrial and genomic DNA. In contrast, higher levels of cisplatin-DNA adducts were found in cells in which HClpP had been depleted. Changes in the levels of ClpP had no effect on the levels of CTR1, a copper transporter that contributes to cisplatin uptake. However, the levels of ATP7A and ATP7B, copper efflux pumps that help eliminate cisplatin from cells, were increased when HClpP was overexpressed. HClpP levels were elevated in cervical carcinoma cells (KB-CP20) and hepatoma cells (BEL-7404-CP20) independently selected for cisplatin resistance. The data indicate that robust HClpXP activity positively affects the ability of cells to efflux cisplatin and suggest that targeting HClpP or HClpX would offer a novel mechanism for sensitizing cancer cells to cisplatin.
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Affiliation(s)
- Yang Zhang
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Michael R Maurizi
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, United States.
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71
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Bradshaw N, Losick R. Asymmetric division triggers cell-specific gene expression through coupled capture and stabilization of a phosphatase. eLife 2015; 4. [PMID: 26465112 PMCID: PMC4714977 DOI: 10.7554/elife.08145] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 10/13/2015] [Indexed: 11/13/2022] Open
Abstract
Formation of a division septum near a randomly chosen pole during sporulation in Bacillus subtilis creates unequal sized daughter cells with dissimilar programs of gene expression. An unanswered question is how polar septation activates a transcription factor (σ(F)) selectively in the small cell. We present evidence that the upstream regulator of σ(F), the phosphatase SpoIIE, is compartmentalized in the small cell by transfer from the polar septum to the adjacent cell pole where SpoIIE is protected from proteolysis and activated. Polar recognition, protection from proteolysis, and stimulation of phosphatase activity are linked to oligomerization of SpoIIE. This mechanism for initiating cell-specific gene expression is independent of additional sporulation proteins; vegetative cells engineered to divide near a pole sequester SpoIIE and activate σ(F) in small cells. Thus, a simple model explains how SpoIIE responds to a stochastically-generated cue to activate σ(F) at the right time and in the right place.
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Affiliation(s)
- Niels Bradshaw
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
| | - Richard Losick
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
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72
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Parijat P, Batra JK. Role of DnaK in HspR-HAIR interaction of Mycobacterium tuberculosis. IUBMB Life 2015; 67:816-27. [PMID: 26442450 DOI: 10.1002/iub.1438] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 09/17/2015] [Indexed: 01/17/2023]
Abstract
Heat shock proteins (Hsps) are a highly conserved family of proteins. The regulation of expression of Hsps in Mycobacterium tuberculosis, is regulated both positively and negatively by alternate sigma factors and transcriptional DNA repressors, respectively. HspR is a negative regulator of expression of hsps, DnaK, ClpB, and Acr2 in M. tuberculosis. In this study, we expressed the M. tuberculosis HspR (MtHspR) in E. coli, and functionally characterized it. MtHspR independently bound to its putative cognate DNA, the HAIR element. MtHspR was found to exist in a dynamic mixture of dimeric and monomeric protein and presence of salt led to the formation of trimers which lacked the DNA binding activity. MtHspR was found to be heat stable with a Tm of 66°C. HspR-HAIR binding was stable upto 60°C suggesting that MtHspR is not the heat stress sensor. Mycobacterial DnaK was found to interact directly with MtHspR-HAIR complex in vitro in an ATP independent manner. The DnaK-HspR-HAIR binding pattern altered at high temperatures in the presence of aggregated α-casein substrate, suggesting that DnaK may indirectly be responding to heat stress in a feedback loop mechanism.
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Affiliation(s)
- Priyanka Parijat
- Immunochemistry Laboratory, National Institute of Immunology, New Delhi, India
| | - Janendra K Batra
- Immunochemistry Laboratory, National Institute of Immunology, New Delhi, India.,Centre for Molecular Medicine, National Institute of Immunology, New Delhi, India
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73
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An YJ, Na JH, Kim MI, Cha SS. Structural basis for the ATP-independent proteolytic activity of LonB proteases and reclassification of their AAA+ modules. J Microbiol 2015; 53:711-7. [PMID: 26428922 DOI: 10.1007/s12275-015-5417-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 09/14/2015] [Accepted: 09/14/2015] [Indexed: 11/24/2022]
Abstract
Lon proteases degrade defective or denature proteins as well as some folded proteins for the control of cellular protein quality. There are two types of Lon proteases, LonA and LonB. Each consists of two functional components: a protease component and an ATPase associated with various cellular activities (AAA+ module). Here, we report the 2.03 -resolution crystal structure of the isolated AAA+ module (iAAA+ module) of LonB from Thermococcus onnurineus NA1 (TonLonB). The iAAA+ module, having no bound nucleotide, adopts a conformation virtually identical to the ADP-bound conformation of AAA+ modules in the hexameric structure of TonLonB; this provides insights into the ATP-independent proteolytic activity observed in a LonB protease. Structural comparison of AAA+ modules between LonA and LonB revealed that the AAA+ modules of Lon proteases are separated into two distinct clades depending on their structural features. The AAA+ module of LonB belongs to the -H2 & Ins1 insert clade (HINS clade)- defined for the first time in this study, while the AAA+ module of LonA is a member of the HCLR clade.
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Affiliation(s)
- Young Jun An
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Ansan, 15627, Republic of Korea
| | - Jung-Hyun Na
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Ansan, 15627, Republic of Korea
| | - Myung-Il Kim
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Ansan, 15627, Republic of Korea
| | - Sun-Shin Cha
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Ansan, 15627, Republic of Korea. .,Department of Marine Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea. .,Department of Convergence Study on the Ocean Science and Technology, Ocean Science and Technology School, Korea Maritime and Ocean University, Pusan, 49112, Republic of Korea.
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74
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Pelzer A, Schwarz C, Knapp A, Wirtz A, Wilhelm S, Smits S, Schmitt L, Funken H, Jaeger KE. Functional expression, purification, and biochemical properties of subtilase SprP from Pseudomonas aeruginosa. Microbiologyopen 2015; 4:743-52. [PMID: 26175208 PMCID: PMC4618607 DOI: 10.1002/mbo3.275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 05/30/2015] [Accepted: 06/15/2015] [Indexed: 12/22/2022] Open
Abstract
The Pseudomonas aeruginosa genome encodes a variety of different proteolytic enzymes several of which play an important role as virulence factors. Interestingly, only two of these proteases are predicted to belong to the subtilase family and we have recently studied the physiological role of the subtilase SprP. Here, we describe the functional overexpression of SprP in Escherichia coli using a novel expression and secretion system. We show that SprP is autocatalytically activated by proteolysis and exhibits optimal activity at 50°C in a pH range of 7-8. We also demonstrate a significant increase in sprP promoter activity upon growth of P. aeruginosa at 43°C indicating a role for SprP in heat shock response.
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Affiliation(s)
- Alexander Pelzer
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Duesseldorf, Forschungszentrum Juelich, D-52426, Juelich, Germany
| | - Christian Schwarz
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstr. 1, D-40225, Duesseldorf, Germany
| | - Andreas Knapp
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Duesseldorf, Forschungszentrum Juelich, D-52426, Juelich, Germany
| | - Astrid Wirtz
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Duesseldorf, Forschungszentrum Juelich, D-52426, Juelich, Germany
| | - Susanne Wilhelm
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Duesseldorf, Forschungszentrum Juelich, D-52426, Juelich, Germany
| | - Sander Smits
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstr. 1, D-40225, Duesseldorf, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich-Heine-University Duesseldorf, Universitaetsstr. 1, D-40225, Duesseldorf, Germany
| | - Horst Funken
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Duesseldorf, Forschungszentrum Juelich, D-52426, Juelich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich-Heine-University Duesseldorf, Forschungszentrum Juelich, D-52426, Juelich, Germany.,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Juelich GmbH, D-52426, Juelich, Germany
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75
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Li Q, Xie L, Long Q, Mao J, Li H, Zhou M, Xie J. Proteasome Accessory Factor C (pafC) Is a novel gene Involved in Mycobacterium Intrinsic Resistance to broad-spectrum antibiotics--Fluoroquinolones. Sci Rep 2015; 5:11910. [PMID: 26139381 PMCID: PMC4490553 DOI: 10.1038/srep11910] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 06/09/2015] [Indexed: 12/17/2022] Open
Abstract
Antibiotics resistance poses catastrophic threat to global public health. Novel insights into the underlying mechanisms of action will inspire better measures to control drug resistance. Fluoroquinolones are potent and widely prescribed broad-spectrum antibiotics. Bacterial protein degradation pathways represent novel druggable target for the development of new classes of antibiotics. Mycobacteria proteasome accessory factor C (pafC), a component of bacterial proteasome, is involved in fluoroquinolones resistance. PafC deletion mutants are hypersensitive to fluoroquinolones, including moxifloxacin, norfloxacin, ofloxacin, ciprofloxacin, but not to other antibiotics such as isoniazid, rifampicin, spectinomycin, chloramphenicol, capreomycin. This phenotype can be restored by complementation. The pafC mutant is hypersensitive to H2O2 exposure. The iron chelator (bipyridyl) and a hydroxyl radical scavenger (thiourea) can abolish the difference. The finding that pafC is a novel intrinsic selective resistance gene provided new evidence for the bacterial protein degradation pathway as druggable target for the development of new class of antibiotics.
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Affiliation(s)
- Qiming Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Longxiang Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Quanxin Long
- 1] Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China [2] The Second Affiliated Hospital and the Key Laboratory of Molecular Biology of Infectious Diseases of the Ministry of Education, Chongqing Medical University, 1 Medical Road, Yuzhong District, Chongqing, 400016, China
| | - Jinxiao Mao
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Hui Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Mingliang Zhou
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, Chongqing 400715, China
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76
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Affiliation(s)
- Ratnesh Chandra Mishra
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Anil Grover
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
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77
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Cheng J, Wang H, Xu X, Wang L, Tian B, Hua Y. Characteristics of dr1790 disruptant and its functional analysis in Deinococcus radiodurans. Braz J Microbiol 2015; 46:601-11. [PMID: 26273280 PMCID: PMC4507557 DOI: 10.1590/s1517-838246220131018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 12/19/2014] [Indexed: 11/22/2022] Open
Abstract
Deinococcus radiodurans (DR) is an extremophile that is well
known for its resistance to radiation, oxidants and desiccation. The gene
dr1790 of D. radiodurans
was predicted to encode a yellow-related protein. The primary objective of the
present study was to characterize the biological function of the DR1790 protein,
which is a member of the ancient yellow/major royal jelly (MRJ) protein family,
in prokaryotes. Fluorescence labeling demonstrated that the yellow-related
protein encoded by dr1790 is a membrane protein. The deletion
of the dr1790 gene decreased the cell growth rate and
sensitivity to hydrogen peroxide and radiation and increased the membrane
permeability of D. radiodurans. Transcript
profiling by microarray and RT-PCR analyses of the dr1790
deletion mutant suggested that some genes that are involved in protein secretion
and transport were strongly suppressed, while other genes that are involved in
protein quality control, such as chaperones and proteases, were induced. In
addition, the expression of genes with predicted functions that are involved in
antioxidant systems, electron transport, and energy metabolism was significantly
altered through the disruption of dr1790. Moreover, the results
of proteomic analyses using 2-DE and MS also demonstrated that DR1790
contributed to D. radiodurans survival. Taken
together, these results indicate that the DR1790 protein from the ancient yellow
protein family plays a pleiotropic role in the survival of prokaryotic cells and
contributes to the extraordinary resistance of D. radiodurans
against oxidative and radiation stresses.
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Affiliation(s)
- Jianhui Cheng
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hu Wang
- Institute of Ageing Research, Hangzhou Normal University, Hangzhou, China, Institute of Ageing Research, Hangzhou Normal University, Hangzhou, China
| | - Xin Xu
- Zhejiang University, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Liangyan Wang
- Zhejiang University, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Bing Tian
- Zhejiang University, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Yuejin Hua
- Zhejiang University, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
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78
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Xu X, Niu Y, Liang K, Wang J, Li X, Yang Y. Heat shock transcription factor δ³² is targeted for degradation via an ubiquitin-like protein ThiS in Escherichia coli. Biochem Biophys Res Commun 2015; 459:240-245. [PMID: 25721662 DOI: 10.1016/j.bbrc.2015.02.087] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 02/13/2015] [Indexed: 01/09/2023]
Abstract
The posttranslational modification of proteins with ubiquitin and ubiquitin-like proteins (UBLs) plays an important role in eukaryote biology, through which substrate proteins are targeted for degradation by the proteasome. Prokaryotes have been thought to degrade proteins by an ubiquitin independent pathway. Here, we show that ThiS, an ubiquitin-like protein, is covalently attached to δ(32) and at least 27 other proteins, leading to their subsequent degradation by proteases, in a similar manner to the ubiquitin-proteasome system (UPS) in eukaryotes. Molecular biology and biochemical studies confirm that specific lysine sites in δ(32) can be modified by ThiS. The results presented here establish a new model for δ(32) degradation and show that Escherichia coli uses a small-protein modifier to control protein stability.
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Affiliation(s)
- Xibing Xu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Yulong Niu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Ke Liang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Jianmei Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Xufeng Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China
| | - Yi Yang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610064, China.
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79
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Krishnakumar S, Gaudana SB, Digmurti MG, Viswanathan GA, Chetty M, Wangikar PP. Influence of mixotrophic growth on rhythmic oscillations in expression of metabolic pathways in diazotrophic cyanobacterium Cyanothece sp. ATCC 51142. BIORESOURCE TECHNOLOGY 2015; 188:145-152. [PMID: 25736893 DOI: 10.1016/j.biortech.2015.02.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 02/05/2015] [Accepted: 02/06/2015] [Indexed: 06/04/2023]
Abstract
This study investigates the influence of mixotrophy on physiology and metabolism by analysis of global gene expression in unicellular diazotrophic cyanobacterium Cyanothece sp. ATCC 51142 (henceforth Cyanothece 51142). It was found that Cyanothece 51142 continues to oscillate between photosynthesis and respiration in continuous light under mixotrophy with cycle time of ∼ 13 h. Mixotrophy is marked by an extended respiratory phase compared with photoautotrophy. It can be argued that glycerol provides supplementary energy for nitrogen fixation, which is derived primarily from the glycogen reserves during photoautotrophy. The genes of NDH complex, cytochrome c oxidase and ATP synthase are significantly overexpressed in mixotrophy during the day compared to autotrophy with synchronous expression of the bidirectional hydrogenase genes possibly to maintain redox balance. However, nitrogenase complex remains exclusive to nighttime metabolism concomitantly with uptake hydrogenase. This study throws light on interrelations between metabolic pathways with implications in design of hydrogen producer strains.
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Affiliation(s)
- S Krishnakumar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sandeep B Gaudana
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Madhuri G Digmurti
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Ganesh A Viswanathan
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Madhu Chetty
- School of Information Technology, Federation University Australia, Gippsland Campus, VIC 3841, Australia
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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80
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Song C, Sundqvist G, Malm E, de Bruijn I, Kumar A, van de Mortel J, Bulone V, Raaijmakers JM. Lipopeptide biosynthesis in Pseudomonas fluorescens is regulated by the protease complex ClpAP. BMC Microbiol 2015; 15:29. [PMID: 25885431 PMCID: PMC4332742 DOI: 10.1186/s12866-015-0367-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 01/29/2015] [Indexed: 11/10/2022] Open
Abstract
Background Lipopeptides (LP) are structurally diverse compounds with potent surfactant and broad-spectrum antibiotic activities. In Pseudomonas and other bacterial genera, LP biosynthesis is governed by large multimodular nonribosomal peptide synthetases (NRPS). To date, relatively little is known about the regulatory genetic network of LP biosynthesis. Results This study provides evidence that the chaperone ClpA, together with the serine protease ClpP, regulates the biosynthesis of the LP massetolide in Pseudomonas fluorescens SS101. Whole-genome transcriptome analyses of clpA and clpP mutants showed their involvement in the transcription of the NRPS genes massABC and the transcriptional regulator massAR. In addition, transcription of genes associated with cell wall and membrane biogenesis, energy production and conversion, amino acid transport and metabolism, and pilus assembly were altered by mutations in clpA and clpP. Proteome analysis allowed the identification of additional cellular changes associated to clpA and clpP mutations. The expression of proteins of the citrate cycle and the heat shock proteins DnaK and DnaJ were particularly affected. Combined with previous findings, these results suggest that the ClpAP complex regulates massetolide biosynthesis via the pathway-specific, LuxR-type regulator MassAR, the heat shock proteins DnaK and DnaJ, and proteins of the TCA cycle. Conclusions Combining transcriptome and proteome analyses provided new insights into the regulation of LP biosynthesis in P. fluorescens and led to the identification of specific missing links in the regulatory pathways. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0367-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chunxu Song
- Laboratory of Phytopathology, Wageningen University, 6708 PB, Wageningen, the Netherlands. .,Department of Microbial Ecology, Netherlands Institute of Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, the Netherlands.
| | - Gustav Sundqvist
- Division of Glycoscience, Royal Institute of Technology (KTH), AlbaNova University Centre, SE-106 91, Stockholm, Sweden.
| | - Erik Malm
- Division of Glycoscience, Royal Institute of Technology (KTH), AlbaNova University Centre, SE-106 91, Stockholm, Sweden.
| | - Irene de Bruijn
- Department of Microbial Ecology, Netherlands Institute of Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, the Netherlands.
| | - Aundy Kumar
- Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Judith van de Mortel
- Laboratory of Phytopathology, Wageningen University, 6708 PB, Wageningen, the Netherlands. .,Current address: HAS University of Applied Sciences, 5911 KJ, Venlo, the Netherlands.
| | - Vincent Bulone
- Division of Glycoscience, Royal Institute of Technology (KTH), AlbaNova University Centre, SE-106 91, Stockholm, Sweden.
| | - Jos M Raaijmakers
- Laboratory of Phytopathology, Wageningen University, 6708 PB, Wageningen, the Netherlands. .,Department of Microbial Ecology, Netherlands Institute of Ecology, Droevendaalsesteeg 10, 6708 PB, Wageningen, the Netherlands.
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81
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Jaskólska M, Gerdes K. CRP-dependent positive autoregulation and proteolytic degradation regulate competence activator Sxy of Escherichia coli. Mol Microbiol 2015; 95:833-45. [PMID: 25491382 DOI: 10.1111/mmi.12901] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/02/2014] [Indexed: 12/23/2022]
Abstract
Natural competence, the ability of bacteria to take up exogenous DNA and incorporate it into their chromosomes, is in most bacteria a transient phenomenon under complex genetic and environmental control. In the Gram-negative bacteria Haemophilus influenzae and Vibrio cholerae, the master regulator Sxy/TfoX controls competence development. Although not known to be naturally competent, Escherichia coli possesses a Sxy homologue and a competence regulon containing the genes required for DNA uptake. Here, we show that in contrast to other characterised Gamma-proteobacteria, E. coli Sxy is positively autoregulated at the level of transcription by a mechanism that requires cAMP receptor protein (CRP), cyclic AMP (cAMP) and a CRP-S site in the sxy promoter. Similarly, we found no evidence that Sxy expression in E. coli was regulated at the translational level. However, our analysis revealed that Sxy is an unstable protein and that its cellular level is negatively regulated at the post-translational level via degradation by Lon protease. Interestingly, in the Gram-positive model organism Bacillus subtilis, the competence master regulator ComK is also positively autoregulated at the level of transcription and negatively regulated by proteolysis. Together, these findings reveal striking similarities between the competence regulons of a Gram-positive and a Gram-negative bacterium.
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Affiliation(s)
- Milena Jaskólska
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
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82
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Abstract
Microorganisms live in fluctuating environments, requiring stress response pathways to resist environmental insults and stress. These pathways dynamically monitor cellular status, and mediate adaptive changes by remodeling the proteome, largely accomplished by remodeling transcriptional networks and protein degradation. The complementarity of fast, specific proteolytic degradation and slower, broad transcriptomic changes gives cells the mechanistic repertoire to dynamically adjust cellular processes and optimize response behavior. Together, this enables cells to minimize the 'cost' of the response while maximizing the ability to survive environmental stress. Here we highlight recent progress in our understanding of transcriptional networks and proteolysis that illustrates the design principles used by bacteria to generate the complex behaviors required to resist stress.
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83
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Adaptor-mediated Lon proteolysis restricts Bacillus subtilis hyperflagellation. Proc Natl Acad Sci U S A 2014; 112:250-5. [PMID: 25538299 DOI: 10.1073/pnas.1417419112] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Lon AAA+ protease is a highly conserved intracellular protease that is considered an anticancer target in eukaryotic cells and a crucial virulence regulator in bacteria. Lon degrades both damaged, misfolded proteins and specific native regulators, but how Lon discriminates among a large pool of candidate targets remains unclear. Here we report that Bacillus subtilis LonA specifically degrades the master regulator of flagellar biosynthesis SwrA governed by the adaptor protein swarming motility inhibitor A (SmiA). SmiA-dependent LonA proteolysis is abrogated upon microbe-substrate contact causing SwrA protein levels to increase and elevate flagellar density above a critical threshold for swarming motility atop solid surfaces. Surface contact-dependent cellular differentiation in bacteria is rapid, and regulated proteolysis may be a general mechanism of transducing surface stimuli.
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84
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Kwong JMK, Gu L, Nassiri N, Bekerman V, Kumar-Singh R, Rhee KD, Yang XJ, Hauswirth WW, Caprioli J, Piri N. AAV-mediated and pharmacological induction of Hsp70 expression stimulates survival of retinal ganglion cells following axonal injury. Gene Ther 2014; 22:138-45. [PMID: 25427613 PMCID: PMC4320032 DOI: 10.1038/gt.2014.105] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 10/15/2014] [Accepted: 10/20/2014] [Indexed: 12/23/2022]
Abstract
We evaluated the effect of AAV2- and 17-AAG (17-N -allylamino-17-demethoxygeldanamycin)-mediated upregulation of Hsp70 expression on the survival of retinal ganglion cells (RGCs) injured by optic nerve crush (ONC). AAV2-Hsp70 expression in the retina was primarily observed in the ganglion cell layer. Approximately 75% of all transfected cells were RGCs. RGC survival in AAV2-Hsp70 injected animals was increased by an average of 110% 2 weeks after the axonal injury compared to the control. The increase in cell numbers was not even across the retinas with a maximum effect of approximately 306% observed in the inferior quadrant. 17-AAG-mediated expression of Hsp70 has been associated with cell protection in various models of neurodegenerative diseases. We show here that a single intravitreal injection of 17-AAG (0.2 ug/ul) results in an increased survival of ONC injured RGCs by approximately 49% compared to the vehicle-treated animals. Expression of Hsp70 in retinas of 17-AAG-treated animals was upregulated approximately by 2-fold compared to control animals. Our data support the idea that the upregulation of Hsp70 has a beneficial effect on the survival of injured RGCs, and the induction of this protein could be viewed as a potential neuroprotective strategy for optic neuropathies.
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Affiliation(s)
- J M K Kwong
- Jules Stein Eye Institute, UCLA, Los Angeles, CA, USA
| | - L Gu
- Jules Stein Eye Institute, UCLA, Los Angeles, CA, USA
| | - N Nassiri
- Jules Stein Eye Institute, UCLA, Los Angeles, CA, USA
| | - V Bekerman
- Jules Stein Eye Institute, UCLA, Los Angeles, CA, USA
| | - R Kumar-Singh
- Department of Ophthalmology, Tufts University School of Medicine, Boston, MA, USA
| | - K D Rhee
- Jules Stein Eye Institute, UCLA, Los Angeles, CA, USA
| | - X-J Yang
- Jules Stein Eye Institute, UCLA, Los Angeles, CA, USA
| | - W W Hauswirth
- Department of Ophthalmology, University of Florida, Gainesville, FL, USA
| | - J Caprioli
- Jules Stein Eye Institute, UCLA, Los Angeles, CA, USA
| | - N Piri
- Jules Stein Eye Institute, UCLA, Los Angeles, CA, USA
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85
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Kaushik S, Sowdhamini R. Distribution, classification, domain architectures and evolution of prolyl oligopeptidases in prokaryotic lineages. BMC Genomics 2014; 15:985. [PMID: 25407321 PMCID: PMC4522959 DOI: 10.1186/1471-2164-15-985] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 10/09/2014] [Indexed: 11/30/2022] Open
Abstract
Background Prolyl oligopeptidases (POPs) are proteolytic enzymes, widely distributed in all the kingdoms of life. Bacterial POPs are pharmaceutically important enzymes, yet their functional and evolutionary details are not fully explored. Therefore, current analysis is aimed at understanding the distribution, domain architecture, probable biological functions and gene family expansion of POPs in bacterial and archaeal lineages. Results Exhaustive sequence analysis of 1,202 bacterial and 91 archaeal genomes revealed ~3,000 POP homologs, with only 638 annotated POPs. We observed wide distribution of POPs in all the analysed bacterial lineages. Phylogenetic analysis and co-clustering of POPs of different phyla suggested their common functions in all the prokaryotic species. Further, on the basis of unique sequence motifs we could classify bacterial POPs into eight subtypes. Analysis of coexisting domains in POPs highlighted their involvement in protein-protein interactions and cellular signaling. We proposed significant extension of this gene family by characterizing 39 new POPs and 158 new α/β hydrolase members. Conclusions Our study reflects diversity and functional importance of POPs in bacterial species. Many genomes with multiple POPs were identified with high sequence variations and different cellular localizations. Such anomalous distribution of POP genes in different bacterial genomes shows differential expansion of POP gene family primarily by multiple horizontal gene transfer events. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-985) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Swati Kaushik
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore, 560065, India. .,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, 94158, USA.
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore, 560065, India.
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86
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Carney DW, Compton CL, Schmitz KR, Stevens JP, Sauer RT, Sello JK. A simple fragment of cyclic acyldepsipeptides is necessary and sufficient for ClpP activation and antibacterial activity. Chembiochem 2014; 15:2216-20. [PMID: 25212124 PMCID: PMC4343535 DOI: 10.1002/cbic.201402358] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Indexed: 12/30/2022]
Abstract
The development of new antibacterial agents, particularly those with unique biological targets, is essential to keep pace with the inevitable emergence of drug resistance in pathogenic bacteria. We identified the minimal structural component of the cyclic acyldepsipeptide (ADEP) antibiotics that exhibits antibacterial activity. We found that N-acyldifluorophenylalanine fragments function via the same mechanism of action as ADEPs, as evidenced by the requirement of ClpP for the fragments' antibacterial activity, the ability of fragments to activate Bacillus subtilis ClpP in vitro, and the capacity of an N-acyldifluorophenylalanine affinity matrix to capture ClpP from B. subtilis cell lysates. N-acyldifluorophenylalanine fragments are much simpler in structure than the full ADEPs and are also highly amenable to structural diversification. Thus, the stage has been set for the development of non-peptide activators of ClpP that can be used as antibacterial agents.
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Affiliation(s)
- Daniel W. Carney
- Department of Chemistry, Brown University, 324 Brook Street, Providence, RI 02912
| | - Corey L. Compton
- Department of Chemistry, Brown University, 324 Brook Street, Providence, RI 02912
| | - Karl R. Schmitz
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
| | - Julia P. Stevens
- Department of Chemistry, Brown University, 324 Brook Street, Providence, RI 02912
| | - Robert T. Sauer
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139
| | - Jason K. Sello
- Department of Chemistry, Brown University, 324 Brook Street, Providence, RI 02912
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87
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Role of adaptor TrfA and ClpPC in controlling levels of SsrA-tagged proteins and antitoxins in Staphylococcus aureus. J Bacteriol 2014; 196:4140-51. [PMID: 25225270 DOI: 10.1128/jb.02222-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Staphylococcus aureus responds to changing extracellular environments in part by adjusting its proteome through alterations of transcriptional priorities and selective degradation of the preexisting pool of proteins. In Bacillus subtilis, the proteolytic adaptor protein MecA has been shown to play a role in assisting with the proteolytic degradation of proteins involved in competence and the oxidative stress response. However, the targets of TrfA, the MecA homolog in S. aureus, have not been well characterized. In this work, we investigated how TrfA assists chaperones and proteases to regulate the proteolysis of several classes of proteins in S. aureus. By fusing the last 3 amino acids of the SsrA degradation tag to Venus, a rapidly folding yellow fluorescent protein, we obtained both fluorescence-based and Western blot assay-based evidence that TrfA and ClpCP are the adaptor and protease, respectively, responsible for the degradation of the SsrA-tagged protein in S. aureus. Notably, the impact of TrfA on degradation was most prominent during late log phase and early stationary phase, due in part to a combination of transcriptional regulation and proteolytic degradation of TrfA by ClpCP. We also characterized the temporal transcriptional regulation governing TrfA activity, wherein Spx, a redox-sensitive transcriptional regulator degraded by ClpXP, activates trfA transcription while repressing its own promoter. Finally, the scope of TrfA-mediated proteolysis was expanded by identifying TrfA as the adaptor that works with ClpCP to degrade antitoxins in S. aureus. Together, these results indicate that the adaptor TrfA adds temporal nuance to protein degradation by ClpCP in S. aureus.
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88
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Knudsen GM, Nielsen MB, Thomsen LE, Aabo S, Rychlik I, Olsen JE. The role of ClpP, RpoS and CsrA in growth and filament formation of Salmonella enterica serovar Typhimurium at low temperature. BMC Microbiol 2014; 14:208. [PMID: 25123657 PMCID: PMC4236599 DOI: 10.1186/s12866-014-0208-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 07/21/2014] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Salmonellae are food-borne pathogens of great health and economic importance. To pose a threat to humans, Salmonellae normally have to cope with a series of stressful conditions in the food chain, including low temperature. In the current study, we evaluated the importance of the Clp proteolytic complex and the carbon starvation protein, CsrA, for the ability of Salmonella Typhimurium to grow at low temperature. RESULTS A clpP mutant was severely affected in growth and formed pin point colonies at 10°C. Contrary to this, rpoS and clpP/rpoS mutants were only slightly affected. The clpP mutant formed cold resistant suppressor mutants at a frequency of 2.5 × 10(-3) and these were found not to express RpoS. Together these results indicated that the impaired growth of the clpP mutant was caused by high level of RpoS. Evaluation by microscopy of the clpP mutant revealed that it formed filamentous cells when grown at 10°C, and this phenotype too, disappered when rpoS was mutated in parallel indicating a RpoS-dependency. A csrA (sup) mutant was also growth attenuated a low temperature. An rpoS/csrA (sup) double mutant was also growth attenuated, indicating that the phenotype of the csrA mutant was independent from RpoS. CONCLUSIONS The cold sensitivity of clpP mutant was associated with increased levels of RpoS and probably caused by toxic levels of RpoS. Although a csrA mutant also accumulated high level of RpoS, growth impairment caused by lack of csrA was not related to RpoS levels in a similar way.
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Affiliation(s)
| | | | | | | | | | - John Elmerdahl Olsen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, Frederiksberg C 1870, Denmark.
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89
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Chan CM, Hahn E, Zuber P. Adaptor bypass mutations of Bacillus subtilis spx suggest a mechanism for YjbH-enhanced proteolysis of the regulator Spx by ClpXP. Mol Microbiol 2014; 93:426-38. [PMID: 24942655 DOI: 10.1111/mmi.12671] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2014] [Indexed: 12/28/2022]
Abstract
The global regulator, Spx, is under proteolytic control exerted by the adaptor YjbH and ATP-dependent protease ClpXP in Bacillus subtilis. While YjbH is observed to bind the Spx C-terminus, YjbH shows little affinity for ClpXP, indicating adaptor activity that does not operate by tethering. Chimeric proteins derived from B. subtilis AbrB and the Spx C-terminus showed that a 28-residue C-terminal section of Spx (AbrB28), but not the last 12 or 16 residues (AbrB12, AbrB16), was required for YjbH interaction and for ClpXP proteolysis, although the rate of AbrB28 proteolysis was not affected by YjbH addition. The result suggested that the YjbH-targeted 28 residue segment of the Spx C-terminus bears a ClpXP-recognition element(s) that is hidden in the intact Spx protein. Residue substitutions in the conserved helix α6 of the C-terminal region generated Spx substrates that were degraded by ClpXP at accelerated rates compared to wild-type Spx, and showed reduced dependency on the YjbH activity. The residue substitutions also weakened the interaction between Spx and YjbH. The results suggest a model in which YjbH, through interaction with residues of helix α6, exposes the C-terminus of Spx for recognition and proteolysis by ClpXP.
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Affiliation(s)
- Chio Mui Chan
- Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health & Science University, Portland, OR, USA
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90
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Hou XH, Zhang JQ, Song XY, Ma XB, Zhang SY. Contribution of ClpP to stress tolerance and virulence properties of Streptococcus mutans. J Basic Microbiol 2014; 54:1222-32. [PMID: 24979467 DOI: 10.1002/jobm.201300747] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 03/18/2014] [Indexed: 11/06/2022]
Abstract
Abilities to tolerate environmental stresses and to form biofilms on teeth surface are key virulence attributes of Streptococcus mutans, the primary causative agent of human dental caries. ClpP, the chief intracellular protease of S. mutans, along with ATPases degrades altered proteins that might be toxic for bacteria, and thus plays important roles in stress response. To further understand the roles of ClpP in stress response of S. mutans, a ClpP deficient strain was constructed and used for general stress tolerance, autolysis, mutacins production, and virulence assays. Here, we demonstrated that inactivation of ClpP in S. mutans resulted in a sensitive phenotype to several environmental stresses, including acid, cold, thermal, and oxidative stresses. The ClpP deficient strain displayed slow growth rates, poor growth yields, formation of long chains, increased clumping in broth, and reduced capacity to form biofilms in presence of glucose. Mutacins production and autolysis of S. mutans were also impaired by mutation of clpP. Animals study showed that clpP mutation increased virulence of S. mutans but not significant. However, enhanced abilities to survive lethal acid and to form biofilm in sucrose were observed in ClpP deficient strain. Our findings revealed a broad impact of ClpP on several virulence properties of S. mutans and highlighted the relevance of ClpP proteolysis with progression of diseases caused by S. mutans.
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Affiliation(s)
- Xiang-Hua Hou
- Department of Clinical Laboratory, The First Affiliated Hospital of Xiamen University, Xiamen, China
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91
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Wurtmann EJ, Ratushny AV, Pan M, Beer KD, Aitchison JD, Baliga NS. An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation. Mol Microbiol 2014; 92:369-82. [PMID: 24612392 PMCID: PMC4060883 DOI: 10.1111/mmi.12564] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2014] [Indexed: 01/27/2023]
Abstract
It is known that environmental context influences the degree of regulation at the transcriptional and post-transcriptional levels. However, the principles governing the differential usage and interplay of regulation at these two levels are not clear. Here, we show that the integration of transcriptional and post-transcriptional regulatory mechanisms in a characteristic network motif drives efficient environment-dependent state transitions. Through phenotypic screening, systems analysis, and rigorous experimental validation, we discovered an RNase (VNG2099C) in Halobacterium salinarum that is transcriptionally co-regulated with genes of the aerobic physiologic state but acts on transcripts of the anaerobic state. Through modelling and experimentation we show that this arrangement generates an efficient state-transition switch, within which RNase-repression of a transcriptional positive autoregulation (RPAR) loop is critical for shutting down ATP-consuming active potassium uptake to conserve energy required for salinity adaptation under aerobic, high potassium, or dark conditions. Subsequently, we discovered that many Escherichia coli operons with energy-associated functions are also putatively controlled by RPAR indicating that this network motif may have evolved independently in phylogenetically distant organisms. Thus, our data suggest that interplay of transcriptional and post-transcriptional regulation in the RPAR motif is a generalized principle for efficient environment-dependent state transitions across prokaryotes.
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Affiliation(s)
| | - Alexander V. Ratushny
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Seattle Biomedical Research Institute, Seattle, WA, 98109, USA
| | - Min Pan
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | | | - John D. Aitchison
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Seattle Biomedical Research Institute, Seattle, WA, 98109, USA
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92
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Hong EJ, Park JS, Kim Y, Lee HS. Role of Corynebacterium glutamicum sprA encoding a serine protease in glxR-mediated global gene regulation. PLoS One 2014; 9:e93587. [PMID: 24691519 PMCID: PMC3972247 DOI: 10.1371/journal.pone.0093587] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 03/05/2014] [Indexed: 11/19/2022] Open
Abstract
The global regulator glxR of Corynebacterium glutamicum is involved in many cellular activities. Considering its role, the GlxR protein likely interacts with other proteins to obtain, maintain, and control its activity. To isolate proteins interacting with GlxR, we used a two-hybrid system with GlxR as the bait. Subsequently, the partner, a subtilisin-like serine protease, was isolated from a C. glutamicum genomic library. Unlike glxR, which showed constitutive expression, the expression of sprA, encoding a serine protease, was maximal in the log phase. Purified His6-SprA protein underwent self-proteolysis and proteolyzed purified GlxR. The proteolytic action of SprA on GlxR was not observed in the presence of cyclic adenosine monophosphate, which modulates GlxR activity. The C. glutamicum sprA deletion mutant (ΔsprA) and sprA-overexpressing (P180-sprA) strains showed reduced growth. The activity of isocitrate dehydrogenase (a tricarboxylic acid cycle enzyme) in these strains decreased to 30–50% of that in the wild-type strain. In the P180-sprA strain, proteins involved in diverse cellular functions such as energy and carbon metabolism (NCgl2809), nitrogen metabolism (NCgl0049), methylation reactions (NCgl0719), and peptidoglycan biosynthesis (NCgl1267), as well as stress, starvation, and survival (NCgl0938) were affected and showed decreased transcription. Taken together, these data suggest that SprA, as a serine protease, performs a novel regulatory role not only in glxR-mediated gene expression but also in other areas of cell physiology. In addition, the tight control of SprA and GlxR availability may indicate their importance in global gene regulation.
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Affiliation(s)
- Eun-Ji Hong
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-ro, Sejong-si, Korea
| | - Joon-Song Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-ro, Sejong-si, Korea
| | - Younhee Kim
- Department of Oriental Medicine, Semyung University, Checheon, Chungbuk, Korea
| | - Heung-Shick Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong-ro, Sejong-si, Korea
- * E-mail:
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93
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Ambro Ľ, Pevala V, Ondrovičová G, Bellová J, Kunová N, Kutejová E, Bauer J. Mutations to a glycine loop in the catalytic site of human Lon changes its protease, peptidase and ATPase activities. FEBS J 2014; 281:1784-97. [PMID: 24520911 DOI: 10.1111/febs.12740] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 12/05/2013] [Accepted: 01/30/2014] [Indexed: 11/28/2022]
Abstract
UNLABELLED Lon, also called protease La, is an ATP-dependent protease present in all kingdoms of life. It is involved in protein quality control and several regulatory processes. Eukaryotic Lon possesses three domains, an N-terminal domain, an ATPase domain and a proteolytic domain. It requires ATP hydrolysis to digest larger, intact proteins, but can cleave small, fluorogenic peptides such as Glu-Ala-Ala-Phe-MNA by only binding, but not hydrolyzing, ATP. Both ATPase and peptidase activities can be stimulated by the binding of a larger protein substrate, such as β-casein. To better understand its mechanism of action, we have prepared several point mutants of four conserved residues of human Lon (G893A, G893P, G894A, G894P, G894S, G893A-G894A, G893P-G894A, G893A-G894P, T880V, W770A, W770P) and studied their ATPase, protease and peptidase activities. Our results show that mutations to Gly894 enhance its basal ATPase activity but do not change its β-casein-stimulated activity. The loop containing Gly893 and Gly894, which flanks Lon's proteolytic active site, therefore appears to be involved in the conformational change that occurs upon substrate binding. Furthermore, mutations to Trp770 have the same general effects on the ATPase activity as mutations to Gly893, indicating that Trp770 is involved in ATPase stimulation. We have also established that this loop does not need to move in order to cleave small, fluorogenic peptides, but does move during the digestion of β-casein. Finally, we also noted that Lon's ability to digest small peptides can be inhibited by moderate ATP concentrations. DATABASE Lon (Endopeptidase La), EC 4.4.21.53 STRUCTURED DIGITAL ABSTRACT: • hLonP cleaves beta casein by protease assay (1, 2, 3, 4, 5, 6) • hLon and hLon bind by cross-linking study (View interaction).
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Affiliation(s)
- Ľuboš Ambro
- Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia
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94
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DnaJ-promoted binding of DnaK to multiple sites on σ32 in the presence of ATP. J Bacteriol 2014; 196:1694-703. [PMID: 24532774 DOI: 10.1128/jb.01197-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Escherichia coli DnaK chaperone system is a canonical heat shock protein 70 (Hsp70) chaperone system comprising Hsp70, Hsp40, and a nucleotide exchange factor. Although Hsp40 is known to facilitate the effective binding of Hsp70 to substrates, the role of Hsp40 in Hsp70-substrate interactions has not yet been fully elucidated. Using the E. coli heat shock transcription factor σ(32) as a substrate in the DnaK chaperone system, we here provide new insight into the Hsp70-substrate interaction. When DnaK-σ(32) complexes formed under various conditions were analyzed by gel filtration, several DnaK-σ(32) complexes with different molecular masses were detected. The results indicated that multiple DnaK molecules simultaneously bind to σ(32), even though it has been suggested that DnaK interacts with σ(32) at a molar ratio of 1:1. Two σ(32) mutants, L201D σ(32) and I54A σ(32), which have reduced affinities for DnaK and DnaJ (Hsp40), respectively, were used to further characterize DnaK-σ(32) complex formation. Pulldown assays demonstrated that the affinity of I54A σ(32) for DnaK was similar to that of wild-type σ(32) in the absence of DnaJ, whereas L201D σ(32) exhibited an extremely low affinity for DnaK. However, in the presence of ATP and DnaJ, the yield of DnaK eluted with L201D σ(32) was much higher than that eluted with I54A σ(32). These results indicate that there are multiple DnaK binding sites on σ(32) and that DnaJ strongly promotes DnaK binding to any site in the presence of ATP, regardless of the intrinsic affinity of DnaK for the site.
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95
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Conditional, temperature-induced proteolytic regulation of cyanobacterial RNA helicase expression. J Bacteriol 2014; 196:1560-8. [PMID: 24509313 DOI: 10.1128/jb.01362-13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Conditional proteolysis is a crucial process regulating the abundance of key regulatory proteins associated with the cell cycle, differentiation pathways, or cellular response to abiotic stress in eukaryotic and prokaryotic organisms. We provide evidence that conditional proteolysis is involved in the rapid and dramatic reduction in abundance of the cyanobacterial RNA helicase, CrhR, in response to a temperature upshift from 20 to 30°C. The proteolytic activity is not a general protein degradation response, since proteolysis is only present and/or functional in cells grown at 30°C and is only transiently active at 30°C. Degradation is also autoregulatory, since the CrhR proteolytic target is required for activation of the degradation machinery. This suggests that an autoregulatory feedback loop exists in which the target of the proteolytic machinery, CrhR, is required for activation of the system. Inhibition of translation revealed that only elongation is required for induction of the temperature-regulated proteolysis, suggesting that translation of an activating factor was already initiated at 20°C. The results indicate that Synechocystis responds to a temperature shift via two independent pathways: a CrhR-independent sensing and signal transduction pathway that regulates induction of crhR expression at low temperature and a CrhR-dependent conditional proteolytic pathway at elevated temperature. The data link the potential for CrhR RNA helicase alteration of RNA secondary structure with the autoregulatory induction of conditional proteolysis in the response of Synechocystis to temperature upshift.
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96
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Polysaccharides and proteins added to flowing drinking water at microgram-per-liter levels promote the formation of biofilms predominated by bacteroidetes and proteobacteria. Appl Environ Microbiol 2014; 80:2360-71. [PMID: 24487544 DOI: 10.1128/aem.04105-13] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biopolymers are important substrates for heterotrophic bacteria in (ultra)oligotrophic freshwater environments, but information about their utilization at microgram-per-liter levels by attached freshwater bacteria is lacking. This study aimed at characterizing biopolymer utilization in drinking-water-related biofilms by exposing such biofilms to added carbohydrates or proteins at 10 μg C liter(-1) in flowing tap water for up to 3 months. Individually added amylopectin was not utilized by the biofilms, whereas laminarin, gelatin, and caseinate were. Amylopectin was utilized during steady-state biofilm growth with simultaneously added maltose but not with simultaneously added acetate. Biofilm formation rates (BFR) at 10 μg C liter(-1) per substrate were ranked as follows, from lowest to highest: blank or amylopectin (≤6 pg ATP cm(-2) day(-1)), gelatin or caseinate, laminarin, maltose, acetate alone or acetate plus amylopectin, and maltose plus amylopectin (980 pg ATP cm(-2) day(-1)). Terminal restriction fragment length polymorphism (T-RFLP) and 16S rRNA gene sequence analyses revealed that the predominant maltose-utilizing bacteria also dominated subsequent amylopectin utilization, indicating catabolic repression and (extracellular) enzyme induction. The accelerated BFR with amylopectin in the presence of maltose probably resulted from efficient amylopectin binding to and hydrolysis by inductive enzymes attached to the bacterial cells. Cytophagia, Flavobacteriia, Gammaproteobacteria, and Sphingobacteriia grew during polysaccharide addition, and Alpha-, Beta-, and Gammaproteobacteria, Cytophagia, Flavobacteriia, and Sphingobacteriia grew during protein addition. The succession of bacterial populations in the biofilms coincided with the decrease in the specific growth rate during biofilm formation. Biopolymers can clearly promote biofilm formation at microgram-per-liter levels in drinking water distribution systems and, depending on their concentrations, might impair the biological stability of distributed drinking water.
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97
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Schnappinger D, Ehrt S. Regulated Expression Systems for Mycobacteria and Their Applications. Microbiol Spectr 2014; 2:03. [PMID: 25485177 PMCID: PMC4254785 DOI: 10.1128/microbiolspec.mgm2-0018-2013] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Indexed: 11/20/2022] Open
Abstract
For bacterial model organisms like Escherichia coli and Bacillus subtilis genetic tools to experimentally manipulate the activity of individual genes existed for decades. But for genetically less tractable yet medically important bacteria such as M. tuberculosis such tools have rarely been available. More recently several groups developed genetic switches that function efficiently in M. tuberculosis and other mycobacteria. Together these systems utilize six different transcription factors, eight different regulated promoters, and three different regulatory principles. Here we describe their design features, review their main applications, and discuss advantages and disadvantages of regulating transcription, translation, or protein stability for controlling gene activities in bacteria.
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Affiliation(s)
- Dirk Schnappinger
- Department of Microbiology and Immunology, Weill Medical College, and Program in Molecular Biology, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10065
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Medical College, and Program in Immunology and Microbial Pathogenesis, Weill Graduate School of Medical Sciences of Cornell University, New York, NY 10065
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98
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Konovalova A, Søgaard-Andersen L, Kroos L. Regulated proteolysis in bacterial development. FEMS Microbiol Rev 2013; 38:493-522. [PMID: 24354618 DOI: 10.1111/1574-6976.12050] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 09/03/2013] [Accepted: 10/14/2013] [Indexed: 11/30/2022] Open
Abstract
Bacteria use proteases to control three types of events temporally and spatially during the processes of morphological development. These events are the destruction of regulatory proteins, activation of regulatory proteins, and production of signals. While some of these events are entirely cytoplasmic, others involve intramembrane proteolysis of a substrate, transmembrane signaling, or secretion. In some cases, multiple proteolytic events are organized into pathways, for example turnover of a regulatory protein activates a protease that generates a signal. We review well-studied and emerging examples and identify recurring themes and important questions for future research. We focus primarily on paradigms learned from studies of model organisms, but we note connections to regulated proteolytic events that govern bacterial adaptation, biofilm formation and disassembly, and pathogenesis.
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Affiliation(s)
- Anna Konovalova
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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99
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Guyet A, Gominet M, Benaroudj N, Mazodier P. Regulation of the clpP1clpP2 operon by the pleiotropic regulator AdpA in Streptomyces lividans. Arch Microbiol 2013; 195:831-41. [PMID: 24196782 DOI: 10.1007/s00203-013-0918-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 06/26/2013] [Accepted: 07/26/2013] [Indexed: 11/28/2022]
Abstract
Insertion of an apramycin resistance cassette in the clpP1clpP2 operon (encoding the ClpP1 and ClpP2 peptidase subunits) affects morphological and physiological differentiation of Streptomyces lividans. Another key factor controlling Streptomyces differentiation is the pleiotropic transcriptional regulator AdpA. We have identified a spontaneous missense mutation (-1 frameshift) in the adpA (bldH) open reading frame in a clpP1clpP2 mutant that led to the synthesis of a non-functional AdpA protein. Electrophoretic mobility shift assays showed that AdpA bound directly to clpP1clpP2 promoter region. Quantitative real-time PCR analysis showed that AdpA regulated the clpP1clpP2 operon expression at specific growth times. In vitro, AdpA and ClgR, a transcriptional activator of clpP1clpP2 operon and other genes, were able to bind simultaneously to clpP1 promoter, which suggests that AdpA binding to clpP1 promoter did not affect that of ClgR. This study allowed to uncover an interplay between the ClpP peptidases and AdpA in S. lividans.
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Affiliation(s)
- Aurélie Guyet
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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100
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Ricci V, Blair JMA, Piddock LJV. RamA, which controls expression of the MDR efflux pump AcrAB-TolC, is regulated by the Lon protease. J Antimicrob Chemother 2013; 69:643-50. [PMID: 24169580 PMCID: PMC3922155 DOI: 10.1093/jac/dkt432] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES RamA regulates the AcrAB-TolC multidrug efflux system. Using Salmonella Typhimurium, we investigated the stability of RamA and its impact on antibiotic resistance. METHODS To detect RamA, we introduced ramA::3XFLAG::aph into plasmid pACYC184 and transformed this into Salmonella Typhimurium SL1344ramA::cat and lon::aph mutants. An N-terminus-deleted mutant [pACYC184ramA(Δ2-21)::3XFLAG::aph] in which the first 20 amino acids of RamA were deleted was also constructed. To determine the abundance and half-life of FLAG-tagged RamA, we induced RamA with chlorpromazine (50 mg/L) and carried out western blotting using anti-FLAG antibody. Susceptibility to antibiotics and phenotypic characterization of the lon mutant was also carried out. RESULTS We show that on removal of chlorpromazine, a known inducer of ramA, the abundance of RamA decreased to pre-induced levels. However, in cells lacking functional Lon, we found that the RamA protein was not degraded. We also demonstrated that the 21 amino acid residues of the RamA N-terminus are required for recognition by the Lon protease. Antimicrobial susceptibility and phenotypic tests showed that the lon mutant was more susceptible to fluoroquinolone antibiotics, was filamentous when observed by microscopy and grew poorly, but showed no difference in motility or the ability to form a biofilm. There was also no difference in the ability of the lon mutant to invade human intestinal cells (INT-407). CONCLUSIONS In summary, we show that the ATP-dependent Lon protease plays an important role in regulating the expression of RamA and therefore multidrug resistance via AcrAB-TolC in Salmonella Typhimurium.
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Affiliation(s)
- Vito Ricci
- Antimicrobials Research Group, School of Immunity and Infection and Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
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