1
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Garrett SC, Philippe C, Kim JG, Wei Y, Johnson KA, Olson S, Graveley BR, Terns MP. Investigation of CRISPR-Independent Phage Resistance Mechanisms Reveals a Role for FtsH in Phage Adsorption to Streptococcus thermophilus. J Bacteriol 2023; 205:e0048222. [PMID: 37255445 PMCID: PMC10294649 DOI: 10.1128/jb.00482-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 05/11/2023] [Indexed: 06/01/2023] Open
Abstract
Prokaryotes are under constant pressure from phage infection and thus have evolved multiple means of defense or evasion. While CRISPR-Cas constitutes a robust immune system and appears to be the predominant means of survival for Streptococcus thermophilus when facing lytic phage infection, other forms of phage resistance coexist in this species. Here, we show that S. thermophilus strains with deleted CRISPR-Cas loci can still give rise to phage-resistant clones following lytic phage challenge. Notably, non-CRISPR phage-resistant survivors had multiple mutations which would truncate or recode a membrane-anchored host protease, FtsH. Phage adsorption was dramatically reduced in FtsH mutants, implicating this protein in phage attachment. Phages were isolated which could bypass FtsH-based resistance through mutations predicted to alter tape measure protein translation. Together, these results identify key components in phage propagation that are subject to mutation in the molecular arms race between phage and host cell. IMPORTANCE Streptococcus thermophilus is an important organism for production of cultured dairy foods, but it is susceptible to lytic phages which can lead to failed products. Consequently, mechanisms for phage resistance are an active area of research. One such mechanism is CRISPR-Cas, and S. thermophilus is a model organism for the study of this form of adaptive immunity. Here, we expand on known mechanisms with our finding that spontaneous mutations in ftsH, a gene encoding a membrane-anchored protease, protected against phage infection by disrupting phage adsorption. In turn, mutations in phage tail protein genes allowed phages to overcome ftsH-based resistance. Our results identified components in phage propagation that are subject to mutation in the molecular arms race between phage and host.
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Affiliation(s)
- Sandra C. Garrett
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Cecile Philippe
- Department of Biochemistry and Molecular Biology, University of Georgia Athens, Athens, Georgia, USA
| | - Jenny G. Kim
- Department of Biochemistry and Molecular Biology, University of Georgia Athens, Athens, Georgia, USA
| | - Yunzhou Wei
- Department of Biochemistry and Molecular Biology, University of Georgia Athens, Athens, Georgia, USA
| | - Katie A. Johnson
- Department of Biochemistry and Molecular Biology, University of Georgia Athens, Athens, Georgia, USA
| | - Sara Olson
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Brenton R. Graveley
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Michael P. Terns
- Department of Biochemistry and Molecular Biology, University of Georgia Athens, Athens, Georgia, USA
- Department of Genetics, University of Georgia Athens, Athens, Georgia, USA
- Department of Microbiology, University of Georgia Athens, Athens, Georgia, USA
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2
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Shu S, Mi W. Regulatory mechanisms of lipopolysaccharide synthesis in Escherichia coli. Nat Commun 2022; 13:4576. [PMID: 35931690 PMCID: PMC9356133 DOI: 10.1038/s41467-022-32277-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 07/25/2022] [Indexed: 11/09/2022] Open
Abstract
Lipopolysaccharide (LPS) is an essential glycolipid and forms a protective permeability barrier for most Gram-negative bacteria. In E. coli, LPS levels are under feedback control, achieved by FtsH-mediated degradation of LpxC, which catalyzes the first committed step in LPS synthesis. FtsH is a membrane-bound AAA+ protease, and its protease activity toward LpxC is regulated by essential membrane proteins LapB and YejM. However, the regulatory mechanisms are elusive. We establish an in vitro assay to analyze the kinetics of LpxC degradation and demonstrate that LapB is an adaptor protein that utilizes its transmembrane helix to interact with FtsH and its cytoplasmic domains to recruit LpxC. Our YejM/LapB complex structure reveals that YejM is an anti-adaptor protein, competing with FtsH for LapB to inhibit LpxC degradation. Structural analysis unravels that LapB and LPS have overlapping binding sites in YejM. Thus, LPS levels control formation of the YejM/LapB complex to determine LpxC protein levels.
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Affiliation(s)
- Sheng Shu
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Wei Mi
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA. .,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA.
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3
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Ma C, Wang C, Luo D, Yan L, Yang W, Li N, Gao N. Structural insights into the membrane microdomain organization by SPFH family proteins. Cell Res 2022; 32:176-189. [PMID: 34975153 PMCID: PMC8807802 DOI: 10.1038/s41422-021-00598-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 11/09/2021] [Indexed: 02/03/2023] Open
Abstract
The lateral segregation of membrane constituents into functional microdomains, conceptually known as lipid raft, is a universal organization principle for cellular membranes in both prokaryotes and eukaryotes. The widespread Stomatin, Prohibitin, Flotillin, and HflK/C (SPFH) family proteins are enriched in functional membrane microdomains at various subcellular locations, and therefore were hypothesized to play a scaffolding role in microdomain formation. In addition, many SPFH proteins are also implicated in highly specific processes occurring on the membrane. However, none of these functions is understood at the molecular level. Here we report the structure of a supramolecular complex that is isolated from bacterial membrane microdomains and contains two SPFH proteins (HflK and HflC) and a membrane-anchored AAA+ protease FtsH. HflK and HflC form a circular 24-mer assembly, featuring a laterally segregated membrane microdomain (20 nm in diameter) bordered by transmembrane domains of HflK/C and a completely sealed periplasmic vault. Four FtsH hexamers are embedded inside this microdomain through interactions with the inner surface of the vault. These observations provide a mechanistic explanation for the role of HflK/C and their mitochondrial homologs prohibitins in regulating membrane-bound AAA+ proteases, and suggest a general model for the organization and functionalization of membrane microdomains by SPFH proteins.
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Affiliation(s)
- Chengying Ma
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Chengkun Wang
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Dingyi Luo
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Lu Yan
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Wenxian Yang
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Ningning Li
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Ning Gao
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Centre for Life Sciences, School of Life Sciences, Peking University, Beijing, China ,grid.11135.370000 0001 2256 9319National Biomedical Imaging Center, Peking University, Beijing, China
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4
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Silveira CB, Luque A, Rohwer F. The landscape of lysogeny across microbial community density, diversity and energetics. Environ Microbiol 2021; 23:4098-4111. [PMID: 34121301 DOI: 10.1111/1462-2920.15640] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 12/11/2022]
Abstract
Lysogens are common at high bacterial densities, an observation that contrasts with the prevailing view of lysogeny as a low-density refugium strategy. Here, we review the mechanisms regulating lysogeny in complex communities and show that the additive effects of coinfections, diversity and host energic status yield a bimodal distribution of lysogeny as a function of microbial densities. At high cell densities (above 106 cells ml-1 or g-1 ) and low diversity, coinfections by two or more phages are frequent and excess energy availability stimulates inefficient metabolism. Both mechanisms favour phage integration and characterize the Piggyback-the-Winner dynamic. At low densities (below 105 cells ml-1 or g-1 ), starvation represses lytic genes and extends the time window for lysogenic commitment, resulting in a higher frequency of coinfections that cause integration. This pattern follows the predictions of the refugium hypothesis. At intermediary densities (between 105 and 106 cells ml-1 or g-1 ), encounter rates and efficient energy metabolism favour lysis. This may involve Kill-the-Winner lytic dynamics and induction. Based on these three regimes, we propose a framework wherein phage integration occurs more frequently at both ends of the host density gradient, with distinct underlying molecular mechanisms (coinfections and host metabolism) dominating at each extreme.
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Affiliation(s)
- Cynthia B Silveira
- Department of Biology, University of Miami, 1301 Memorial Drive, Coral Gables, FL, 33143, USA.,Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Sciences, University of Miami, 4600 Rickenbacker Causeway, Miami, FL, 33149, USA
| | - Antoni Luque
- Viral Information Institute, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA.,Department of Mathematics and Statistics, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA.,Computational Science Research Center, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA
| | - Forest Rohwer
- Viral Information Institute, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA.,Department of Biology, San Diego State University, 5500 Campanile Dr, San Diego, CA, 92182, USA
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5
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Samuels DS, Lybecker MC, Yang XF, Ouyang Z, Bourret TJ, Boyle WK, Stevenson B, Drecktrah D, Caimano MJ. Gene Regulation and Transcriptomics. Curr Issues Mol Biol 2020; 42:223-266. [PMID: 33300497 DOI: 10.21775/cimb.042.223] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Borrelia (Borreliella) burgdorferi, along with closely related species, is the etiologic agent of Lyme disease. The spirochete subsists in an enzootic cycle that encompasses acquisition from a vertebrate host to a tick vector and transmission from a tick vector to a vertebrate host. To adapt to its environment and persist in each phase of its enzootic cycle, B. burgdorferi wields three systems to regulate the expression of genes: the RpoN-RpoS alternative sigma factor cascade, the Hk1/Rrp1 two-component system and its product c-di-GMP, and the stringent response mediated by RelBbu and DksA. These regulatory systems respond to enzootic phase-specific signals and are controlled or fine- tuned by transcription factors, including BosR and BadR, as well as small RNAs, including DsrABb and Bb6S RNA. In addition, several other DNA-binding and RNA-binding proteins have been identified, although their functions have not all been defined. Global changes in gene expression revealed by high-throughput transcriptomic studies have elucidated various regulons, albeit technical obstacles have mostly limited this experimental approach to cultivated spirochetes. Regardless, we know that the spirochete, which carries a relatively small genome, regulates the expression of a considerable number of genes required for the transitions between the tick vector and the vertebrate host as well as the adaptation to each.
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Affiliation(s)
- D Scott Samuels
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Meghan C Lybecker
- Department of Biology, University of Colorado, Colorado Springs, CO 80918, USA
| | - X Frank Yang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Zhiming Ouyang
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Travis J Bourret
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE, 68105 USA
| | - William K Boyle
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE, 68105 USA
| | - Brian Stevenson
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky School of Medicine, Lexington, KY 40536, USA
| | - Dan Drecktrah
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Melissa J Caimano
- Departments of Medicine, Pediatrics, and Molecular Biology and Biophysics, UConn Health, Farmington, CT, USA
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6
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Quantification of Lysogeny Caused by Phage Coinfections in Microbial Communities from Biophysical Principles. mSystems 2020; 5:5/5/e00353-20. [PMID: 32934113 PMCID: PMC7498681 DOI: 10.1128/msystems.00353-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The association of temperate phages and bacterial hosts during lysogeny manipulates microbial dynamics from the oceans to the human gut. Lysogeny is well studied in laboratory models, but its environmental drivers remain unclear. Here, we quantified the probability of lysogenization caused by phage coinfections, a well-known trigger of lysogeny, in marine and gut microbial environments. Coinfections were quantified by developing a biophysical model that incorporated the traits of viral and bacterial communities. Lysogenization via coinfection was more frequent in highly productive environments like the gut, due to higher microbial densities and higher phage adsorption rates. At low cell densities, lysogenization occurred in bacteria with long duplication times. These results bridge the molecular understanding of lysogeny with the ecology of complex microbial communities. Temperate phages can associate with their bacterial host to form a lysogen, often modifying the phenotype of the host. Lysogens are dominant in the microbially dense environment of the mammalian gut. This observation contrasts with the long-standing hypothesis of lysogeny being favored at low microbial densities, such as in oligotrophic marine environments. Here, we hypothesized that phage coinfections—a well-understood molecular mechanism of lysogenization—increase at high microbial abundances. To test this hypothesis, we developed a biophysical model of coinfection for marine and gut microbiomes. The model stochastically sampled ranges of phage and bacterial concentrations, adsorption rates, lysogenic commitment times, and community diversity from each environment. In 90% of the sampled marine communities, less than 10% of the bacteria were predicted to be lysogenized via coinfection. In contrast, 25% of the sampled gut communities displayed more than 25% of lysogenization. The probability of lysogenization in the gut was a consequence of the higher densities and higher adsorption rates. These results suggest that, on average, coinfections can form two trillion lysogens in the human gut every day. In marine microbiomes, which were characterized by lower densities and phage adsorption rates, lysogeny via coinfection was still possible for communities with long lysogenic commitment times. Our study indicates that different physical factors causing coinfections can reconcile the traditional view of lysogeny at poor host growth (long commitment times) and the recent Piggyback-the-Winner framework proposing that lysogeny is favored in rich environments (high densities and adsorption rates). IMPORTANCE The association of temperate phages and bacterial hosts during lysogeny manipulates microbial dynamics from the oceans to the human gut. Lysogeny is well studied in laboratory models, but its environmental drivers remain unclear. Here, we quantified the probability of lysogenization caused by phage coinfections, a well-known trigger of lysogeny, in marine and gut microbial environments. Coinfections were quantified by developing a biophysical model that incorporated the traits of viral and bacterial communities. Lysogenization via coinfection was more frequent in highly productive environments like the gut, due to higher microbial densities and higher phage adsorption rates. At low cell densities, lysogenization occurred in bacteria with long duplication times. These results bridge the molecular understanding of lysogeny with the ecology of complex microbial communities.
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7
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The Bacteriophage Lambda CII Phenotypes for Complementation, Cellular Toxicity and Replication Inhibition Are Suppressed in cII-oop Constructs Expressing the Small RNA OOP. Viruses 2018. [PMID: 29518935 PMCID: PMC5869508 DOI: 10.3390/v10030115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The temperate bacteriophage lambda (λ) CII protein is a positive regulator of transcription from promoter pE, a component of the lysogenic response. The expression of cII was examined in vectors devoid of phage transcription-modulating elements. Their removal enabled evaluating if the expression of the small RNA OOP, on its own, could suppress CII activities, including complementing for a lysogenic response, cell toxicity and causing rapid cellular loss of ColE1 plasmids. The results confirm that OOP RNA expression from the genetic element pO-oop-to can prevent the ability of plasmid-encoded CII to complement for a lysogenic response, suggesting that it serves as a powerful regulatory pivot in λ development. Plasmids with a pO promoter sequence of 45 nucleotides (pO45), containing the −10 and −35 regions for oop, were non-functional; whereas, plasmids with pO94 prevented CII complementation, CII-dependent plasmid loss and suppressed CII toxicity, suggesting the pO promoter has an extended DNA sequence. All three CII activities were eliminated by the deletion of the COOH-terminal 20 amino acids of CII. Host mutations in the hflA locus, in pcnB and in rpoB influenced CII activities. These studies suggest that the COOH-terminal end of CII likely interacts with the β-subunit of RNA polymerase.
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8
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Lopes KL, Rodrigues RAO, Silva MC, Braga WGS, Silva-Filho MC. The Zinc-Finger Thylakoid-Membrane Protein FIP Is Involved With Abiotic Stress Response in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2018; 9:504. [PMID: 29720990 PMCID: PMC5915565 DOI: 10.3389/fpls.2018.00504] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 04/03/2018] [Indexed: 05/15/2023]
Abstract
Many plant genes have their expression modulated by stress conditions. Here, we used Arabidopsis FtsH5 protease, which expression is regulated by light stress, as bait in a yeast two-hybrid screen to search for new proteins involved in the stress response. As a result, we found FIP (FtsH5 Interacting Protein), which possesses an amino proximal cleavable transit peptide, a hydrophobic membrane-anchoring region, and a carboxyl proximal C4-type zinc-finger domain. In vivo experiments using FIP fused to green fluorescent protein (GFP) showed a plastid localization. This finding was corroborated by chloroplast import assays that showed FIP inserted in the thylakoid membrane. FIP expression was down-regulated in plants exposed to high light intensity, oxidative, salt, and osmotic stresses, whereas mutant plants expressing low levels of FIP were more tolerant to these abiotic stresses. Our data shows a new thylakoid-membrane protein involved with abiotic stress response in Arabidopsis thaliana.
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9
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Late-Arriving Signals Contribute Less to Cell-Fate Decisions. Biophys J 2017; 113:2110-2120. [PMID: 29117533 DOI: 10.1016/j.bpj.2017.09.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 08/14/2017] [Accepted: 09/05/2017] [Indexed: 11/24/2022] Open
Abstract
Gene regulatory networks are largely responsible for cellular decision-making. These networks sense diverse external signals and respond by adjusting gene expression, enabling cells to reach environment-dependent decisions crucial for their survival or reproduction. However, information-carrying signals may arrive at variable times. Besides the intrinsic strength of these signals, their arrival time (timing) may also carry information about the environment and can influence cellular decision-making in ways that are poorly understood. For example, it is unclear how the timing of individual phage infections affects the lysis-lysogeny decision of bacteriophage λ despite variable infection times being likely in the wild and even in laboratory conditions. In this work, we combine mathematical modeling with experimentation to address this question. We develop an experimentally testable theory, which reveals that late-infecting phages contribute less to cellular decision-making. This implies that infection delays lower the probability of lysogeny compared to simultaneous infections. Furthermore, we show that infection delays reduce lysogenization by providing insufficient CII for threshold crossing during the critical decision-making period. We find evidence for a cutoff time after which subsequent infections cannot influence the cellular decision. We derive an intuitive formula that approximates the probability of lysogeny for variable infection times by a time-weighted average of probabilities for simultaneous infections. We validate these theoretical predictions experimentally. Similar concepts and simplifying modeling approaches may help elucidate the mechanisms underlying other cellular decisions.
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10
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Amberg-Johnson K, Hari SB, Ganesan SM, Lorenzi HA, Sauer RT, Niles JC, Yeh E. Small molecule inhibition of apicomplexan FtsH1 disrupts plastid biogenesis in human pathogens. eLife 2017; 6:29865. [PMID: 28826494 PMCID: PMC5576918 DOI: 10.7554/elife.29865] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/17/2017] [Indexed: 12/21/2022] Open
Abstract
The malaria parasite Plasmodium falciparum and related apicomplexan pathogens contain an essential plastid organelle, the apicoplast, which is a key anti-parasitic target. Derived from secondary endosymbiosis, the apicoplast depends on novel, but largely cryptic, mechanisms for protein/lipid import and organelle inheritance during parasite replication. These critical biogenesis pathways present untapped opportunities to discover new parasite-specific drug targets. We used an innovative screen to identify actinonin as having a novel mechanism-of-action inhibiting apicoplast biogenesis. Resistant mutation, chemical-genetic interaction, and biochemical inhibition demonstrate that the unexpected target of actinonin in P. falciparum and Toxoplasma gondii is FtsH1, a homolog of a bacterial membrane AAA+ metalloprotease. PfFtsH1 is the first novel factor required for apicoplast biogenesis identified in a phenotypic screen. Our findings demonstrate that FtsH1 is a novel and, importantly, druggable antimalarial target. Development of FtsH1 inhibitors will have significant advantages with improved drug kinetics and multistage efficacy against multiple human parasites.
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Affiliation(s)
- Katherine Amberg-Johnson
- Department of Biochemistry, Stanford Medical School, Stanford, United States.,Microbiology and Immunology, Stanford Medical School, Stanford, United States
| | - Sanjay B Hari
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Suresh M Ganesan
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Hernan A Lorenzi
- Department of Infectious Disease, The J. Craig Venter Institute, Maryland, United States
| | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Ellen Yeh
- Department of Biochemistry, Stanford Medical School, Stanford, United States.,Microbiology and Immunology, Stanford Medical School, Stanford, United States.,Department of Pathology, Stanford Medical School, Stanford, United States
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11
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Bittner LM, Arends J, Narberhaus F. When, how and why? Regulated proteolysis by the essential FtsH protease in Escherichia coli. Biol Chem 2017; 398:625-635. [PMID: 28085670 DOI: 10.1515/hsz-2016-0302] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 01/09/2017] [Indexed: 11/15/2022]
Abstract
Cellular proteomes are dynamic and adjusted to permanently changing conditions by ATP-fueled proteolytic machineries. Among the five AAA+ proteases in Escherichia coli FtsH is the only essential and membrane-anchored metalloprotease. FtsH is a homohexamer that uses its ATPase domain to unfold and translocate substrates that are subsequently degraded without the need of ATP in the proteolytic chamber of the protease domain. FtsH eliminates misfolded proteins in the context of general quality control and properly folded proteins for regulatory reasons. Recent trapping approaches have revealed a number of novel FtsH substrates. This review summarizes the substrate diversity of FtsH and presents details on the surprisingly diverse recognition principles of three well-characterized substrates: LpxC, the key enzyme of lipopolysaccharide biosynthesis; RpoH, the alternative heat-shock sigma factor and YfgM, a bifunctional membrane protein implicated in periplasmic chaperone functions and cytoplasmic stress adaptation.
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Affiliation(s)
- Lisa-Marie Bittner
- Microbial Biology, Ruhr University Bochum, Universitätsstr. 150, NDEF 06/783, D-44801 Bochum
| | - Jan Arends
- Microbial Biology, Ruhr University Bochum, Universitätsstr. 150, NDEF 06/783, D-44801 Bochum
| | - Franz Narberhaus
- Microbial Biology, Ruhr University Bochum, Universitätsstr. 150, NDEF 06/783, D-44801 Bochum
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12
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Increasing intracellular magnesium levels with the 31-amino acid MgtS protein. Proc Natl Acad Sci U S A 2017; 114:5689-5694. [PMID: 28512220 DOI: 10.1073/pnas.1703415114] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Synthesis of the 31-amino acid, inner membrane protein MgtS (formerly denoted YneM) is induced by very low Mg2+ in a PhoPQ-dependent manner in Escherichia coli Here we report that MgtS acts to increase intracellular Mg2+ levels and maintain cell integrity upon Mg2+ depletion. Upon development of a functional tagged derivative of MgtS, we found that MgtS interacts with MgtA to increase the levels of this P-type ATPase Mg2+ transporter under Mg2+-limiting conditions. Correspondingly, the effects of MgtS upon Mg2+ limitation are lost in a ∆mgtA mutant, and MgtA overexpression can suppress the ∆mgtS phenotype. MgtS stabilization of MgtA provides an additional layer of regulation of this tightly controlled Mg2+ transporter and adds to the list of small proteins that regulate inner membrane transporters.
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13
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Drecktrah D, Lybecker M, Popitsch N, Rescheneder P, Hall LS, Samuels DS. The Borrelia burgdorferi RelA/SpoT Homolog and Stringent Response Regulate Survival in the Tick Vector and Global Gene Expression during Starvation. PLoS Pathog 2015; 11:e1005160. [PMID: 26371761 PMCID: PMC4570706 DOI: 10.1371/journal.ppat.1005160] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 08/21/2015] [Indexed: 01/09/2023] Open
Abstract
As the Lyme disease bacterium Borrelia burgdorferi traverses its enzootic cycle, alternating between a tick vector and a vertebrate host, the spirochete must adapt and persist in the tick midgut under prolonged nutrient stress between blood meals. In this study, we examined the role of the stringent response in tick persistence and in regulation of gene expression during nutrient limitation. Nutritionally starving B. burgdorferi in vitro increased the levels of guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp), collectively referred to as (p)ppGpp, products of the bifunctional synthetase/hydrolase RelBbu (RelA/SpoT homolog). Conversely, returning B. burgdorferi to a nutrient-rich medium decreased (p)ppGpp levels. B. burgdorferi survival in ticks between the larval and nymph blood meals, and during starvation in vitro, was dependent on RelBbu. Furthermore, normal morphological conversion from a flat-wave shape to a condensed round body (RB) form during starvation was dependent on RelBbu; relBbu mutants more frequently formed RBs, but their membranes were compromised. By differential RNA sequencing analyses, we found that RelBbu regulates an extensive transcriptome, both dependent and independent of nutrient stress. The RelBbu regulon includes the glp operon, which is important for glycerol utilization and persistence in the tick, virulence factors and the late phage operon of the 32-kb circular plasmid (cp32) family. In summary, our data suggest that RelBbu globally modulates transcription in response to nutrient stress by increasing (p)ppGpp levels to facilitate B. burgdorferi persistence in the tick.
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Affiliation(s)
- Dan Drecktrah
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Meghan Lybecker
- Department of Biology, University of Colorado, Colorado Springs, Colorado, United States of America
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Niko Popitsch
- Oxford NIHR Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna & Medical University of Vienna, Vienna, Austria
| | - Philipp Rescheneder
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna & Medical University of Vienna, Vienna, Austria
| | - Laura S. Hall
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - D. Scott Samuels
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
- Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana, United States of America
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14
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Yoshioka-Nishimura M, Yamamoto Y. Quality control of Photosystem II: the molecular basis for the action of FtsH protease and the dynamics of the thylakoid membranes. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 137:100-6. [PMID: 24725639 DOI: 10.1016/j.jphotobiol.2014.02.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 02/17/2014] [Accepted: 02/17/2014] [Indexed: 01/20/2023]
Abstract
The reaction center-binding D1 protein of Photosystem II is damaged by excessive light, which leads to photoinhibition of Photosystem II. The damaged D1 protein is removed immediately by specific proteases, and a metalloprotease FtsH located in the thylakoid membranes is involved in the proteolytic process. According to recent studies on the distribution and organization of the protein complexes/supercomplexes in the thylakoid membranes, the grana of higher plant chloroplasts are crowded with Photosystem II complexes and light-harvesting complexes. For the repair of the photodamaged D1 protein, the majority of the active hexameric FtsH proteases should be localized in close proximity to the Photosystem II complexes. The unstacking of the grana may increase the area of the grana margin and facilitate easier access of the FtsH proteases to the damaged D1 protein. These results suggest that the structural changes of the thylakoid membranes by light stress increase the mobility of the membrane proteins and support the quality control of Photosystem II.
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Affiliation(s)
- Miho Yoshioka-Nishimura
- Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan.
| | - Yasusi Yamamoto
- Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
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15
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Roces C, Wegmann U, Campelo AB, García P, Rodríguez A, Martínez B. Lack of the host membrane protease FtsH hinders release of the Lactococcus lactis bacteriophage TP712. J Gen Virol 2013; 94:2814-2818. [PMID: 24018314 DOI: 10.1099/vir.0.057182-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The temperate bacteriophage TP712 was unable to plaque on Lactococcus lactis ΔftsH lacking the membrane protease FtsH and complementation in trans restored the WT phenotype. Absence of ftsH did not hinder phage adsorption, phage DNA delivery or activation of the lytic cycle. Thin sections revealed that TP712 virions appeared to be correctly assembled inside the ΔftsH host, but were not released. These virions were infective, demonstrating that a functional host FtsH is required by TP712 to proceed effectively with lysis of the host.
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Affiliation(s)
- Clara Roces
- DairySafe Group, Department of Technology and Biotechnology of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Villaviciosa, Asturias, Spain
| | - Udo Wegmann
- Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, United Kingdom
| | - Ana B Campelo
- DairySafe Group, Department of Technology and Biotechnology of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Villaviciosa, Asturias, Spain
| | - Pilar García
- DairySafe Group, Department of Technology and Biotechnology of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Villaviciosa, Asturias, Spain
| | - Ana Rodríguez
- DairySafe Group, Department of Technology and Biotechnology of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Villaviciosa, Asturias, Spain
| | - Beatriz Martínez
- DairySafe Group, Department of Technology and Biotechnology of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Villaviciosa, Asturias, Spain
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16
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Boehm M, Yu J, Krynicka V, Barker M, Tichy M, Komenda J, Nixon PJ, Nield J. Subunit organization of a synechocystis hetero-oligomeric thylakoid FtsH complex involved in photosystem II repair. THE PLANT CELL 2012; 24:3669-83. [PMID: 22991268 PMCID: PMC3480294 DOI: 10.1105/tpc.112.100891] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
FtsH metalloproteases are key components of the photosystem II (PSII) repair cycle, which operates to maintain photosynthetic activity in the light. Despite their physiological importance, the structure and subunit composition of thylakoid FtsH complexes remain uncertain. Mutagenesis has previously revealed that the four FtsH homologs encoded by the cyanobacterium Synechocystis sp PCC 6803 are functionally different: FtsH1 and FtsH3 are required for cell viability, whereas FtsH2 and FtsH4 are dispensable. To gain insights into FtsH2, which is involved in selective D1 protein degradation during PSII repair, we used a strain of Synechocystis 6803 expressing a glutathione S-transferase (GST)-tagged derivative (FtsH2-GST) to isolate FtsH2-containing complexes. Biochemical analysis revealed that FtsH2-GST forms a hetero-oligomeric complex with FtsH3. FtsH2 also interacts with FtsH3 in the wild-type strain, and a mutant depleted in FtsH3, like ftsH2(-) mutants, displays impaired D1 degradation. FtsH3 also forms a separate heterocomplex with FtsH1, thus explaining why FtsH3 is more important than FtsH2 for cell viability. We investigated the structure of the isolated FtsH2-GST/FtsH3 complex using transmission electron microscopy and single-particle analysis. The three-dimensional structural model obtained at a resolution of 26 Å revealed that the complex is hexameric and consists of alternating FtsH2/FtsH3 subunits.
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Affiliation(s)
- Marko Boehm
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jianfeng Yu
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Vendula Krynicka
- Institute of Microbiology, Academy of Sciences, 37981 Třeboň, Czech Republic
| | - Myles Barker
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Martin Tichy
- Institute of Microbiology, Academy of Sciences, 37981 Třeboň, Czech Republic
| | - Josef Komenda
- Institute of Microbiology, Academy of Sciences, 37981 Třeboň, Czech Republic
| | - Peter J. Nixon
- Division of Molecular Biosciences, Imperial College London, London SW7 2AZ, United Kingdom
- Address correspondence to
| | - Jon Nield
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
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17
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Abstract
Four different mechanisms have evolved in eubacteria to comply with changes in the environmental temperature. The underlying genetic mechanisms regulate gene expression at transcriptional, translational and posttranslational level. The high temperature response (HTR) is a reaction on increases in temperature and is mainly used by pathogenic bacteria when they enter their mammalian host. The temperature of 37°C causes induction of the virulent genes the products of which are only needed in this environment. The heat shock response (HSR) is induced by any sudden increase in temperature, allows the bacterial cell to adapt to this environmental stress factor and is shut off after adaptation. In a similar way the low temperature response (LTR) is a reaction to a new environment and leads to the constant expression of appropriate genes. In contrast, the cold shock response (CSR) includes turn off of the cold shock genes after adaptation to the low temperature. Sensors of temperature changes are specific DNA regions, RNA molecules or proteins and conformational changes have been identified as a common motif.
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18
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Langklotz S, Baumann U, Narberhaus F. Structure and function of the bacterial AAA protease FtsH. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1823:40-8. [PMID: 21925212 DOI: 10.1016/j.bbamcr.2011.08.015] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2011] [Revised: 08/24/2011] [Accepted: 08/30/2011] [Indexed: 10/17/2022]
Abstract
Proteolysis of regulatory proteins or key enzymes of biosynthetic pathways is a universal mechanism to rapidly adjust the cellular proteome to particular environmental needs. Among the five energy-dependent AAA(+) proteases in Escherichia coli, FtsH is the only essential protease. Moreover, FtsH is unique owing to its anchoring to the inner membrane. This review describes the structural and functional properties of FtsH. With regard to its role in cellular quality control and regulatory circuits, cytoplasmic and membrane substrates of the FtsH protease are depicted and mechanisms of FtsH-dependent proteolysis are discussed.
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Affiliation(s)
- Sina Langklotz
- Lehrstuhl für Biologie der Mikroorganismen, Ruhr-Universität Bochum, Germany
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19
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Bandyopadhyay K, Parua PK, Datta AB, Parrack P. Escherichia coli HflK and HflC can individually inhibit the HflB (FtsH)-mediated proteolysis of lambdaCII in vitro. Arch Biochem Biophys 2010; 501:239-43. [PMID: 20599668 DOI: 10.1016/j.abb.2010.06.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Revised: 06/14/2010] [Accepted: 06/25/2010] [Indexed: 11/25/2022]
Abstract
LambdaCII is the key protein that influences the lysis/lysogeny decision of lambda by activating several phage promoters. The effect of CII is modulated by a number of phage and host proteins including Escherichia coli HflK and HflC. These membrane proteins copurify as a tightly bound complex 'HflKC' that inhibits the HflB (FtsH)-mediated proteolysis of CII both in vitro and in vivo. Individual purification of HflK and HflC has not been possible so far, since each requires the presence of the other for proper folding. We report the first purification of HflK and HflC separately as active and functional proteins and show that each can interact with HflB on its own and each inhibits the proteolysis of CII. They also inhibit the proteolysis of E. coli sigma(32) by HflB. We show that at low concentrations each protein is dimeric, based on which we propose a scheme for the mutual interactions of HflB, HflK and HflC in a supramolecular HflBKC protease complex.
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Affiliation(s)
- Kaustav Bandyopadhyay
- Department of Biochemistry, Bose Institute P-1/12, C.I.T. Scheme VIIM, Kolkata 700 054, India
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20
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HflD, an Escherichia coli protein involved in the λ lysis–lysogeny switch, impairs transcription activation by λCII. Arch Biochem Biophys 2010; 493:175-83. [DOI: 10.1016/j.abb.2009.10.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2009] [Revised: 10/16/2009] [Accepted: 10/17/2009] [Indexed: 11/17/2022]
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21
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Avlund M, Dodd IB, Sneppen K, Krishna S. Minimal Gene Regulatory Circuits that Can Count like Bacteriophage Lambda. J Mol Biol 2009; 394:681-93. [DOI: 10.1016/j.jmb.2009.09.053] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Revised: 09/17/2009] [Accepted: 09/21/2009] [Indexed: 10/20/2022]
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22
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Narberhaus F, Obrist M, Führer F, Langklotz S. Degradation of cytoplasmic substrates by FtsH, a membrane-anchored protease with many talents. Res Microbiol 2009; 160:652-9. [DOI: 10.1016/j.resmic.2009.08.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Revised: 08/17/2009] [Accepted: 08/17/2009] [Indexed: 12/01/2022]
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23
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Parua PK, Datta AB, Parrack P. Specific hydrophobic residues in the 4 helix of CII are crucial for maintaining its tetrameric structure and directing the lysogenic choice. J Gen Virol 2009; 91:306-12. [DOI: 10.1099/vir.0.015040-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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24
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Matsushita-Ishiodori Y, Yamanaka K, Hashimoto H, Esaki M, Ogura T. Conserved aromatic and basic amino acid residues in the pore region ofCaenorhabditis elegansspastin play critical roles in microtubule severing. Genes Cells 2009; 14:925-40. [DOI: 10.1111/j.1365-2443.2009.01320.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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25
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Abstract
The Escherichia coli gene hflX was first identified as part of the hflA operon, mutations in which led to an increased frequency of lysogenization upon infection of the bacterium by the temperate coliphage lambda. Independent mutational studies have also indicated that the HflX protein has a role in transposition. Based on the sequence of its gene, HflX is predicted to be a GTP-binding protein, very likely a GTPase. We report here purification and characterization of the HflX protein. We also specifically examined its suggested functional roles mentioned above. Our results show that HflX is a monomeric protein with a high (30% to 40%) content of helices. It exhibits GTPase as well as ATPase activities, but it has no role in lambda lysogeny or in transposition.
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26
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Schumann W. Chapter 7 Temperature Sensors of Eubacteria. ADVANCES IN APPLIED MICROBIOLOGY 2009; 67:213-56. [DOI: 10.1016/s0065-2164(08)01007-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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27
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Polkinghorne A, Ziegler U, González-Hernández Y, Pospischil A, Timms P, Vaughan L. Chlamydophila pneumoniae HflX belongs to an uncharacterized family of conserved GTPases and associates with the Escherichia coli 50S large ribosomal subunit. MICROBIOLOGY-SGM 2008; 154:3537-3546. [PMID: 18957606 DOI: 10.1099/mic.0.2008/022137-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Predicted members of the HflX subfamily of phosphate-binding-loop guanosine triphosphatases (GTPases) are widely distributed in the bacterial kingdom but remain virtually uncharacterized. In an attempt to understand mechanisms used for regulation of growth and development in the chlamydiae, obligate intracellular and developmentally complex bacteria, we have begun investigations into chlamydial GTPases; we report here what appears to be the first analysis of a HflX family GTPase using a predicted homologue from Chlamydophila pneumoniae. In agreement with phylogenetic predictions for members of this GTPase family, purified recombinant Cp. pneumoniae HflX was specific for guanine nucleotides and exhibited a slow intrinsic GTPase activity when incubated with [gamma-(32)P]GTP. Using HflX-specific monoclonal antibodies, HflX could be detected by Western blotting and high-resolution confocal microscopy throughout the vegetative growth cycle of Cp. pneumoniae and, at early time points, appeared to partly localize to the membrane. Ectopic expression of Cp. pneumoniae HflX in Escherichia coli revealed co-sedimentation of HflX with the E. coli 50S large ribosomal subunit. The results of this work open up some intriguing possibilities for the role of GTPases belonging to this previously uncharacterized family of bacterial GTPases. Ribosome association is a feature shared by other important conserved GTPase families and more detailed investigations will be required to delineate the role of HflX in bacterial ribosome function.
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Affiliation(s)
- Adam Polkinghorne
- Institute of Veterinary Pathology, University of Zurich, Winterthurerstrasse 268, Zurich 8057, Switzerland
| | - Urs Ziegler
- Institute of Anatomy and Center for Microscopy and Image Analysis, University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | | | - Andreas Pospischil
- Institute of Veterinary Pathology, University of Zurich, Winterthurerstrasse 268, Zurich 8057, Switzerland
| | - Peter Timms
- Institute of Health and Biomedical Innovation and School of Life Sciences, Faculty of Science, Queensland University of Technology, Brisbane, Australia
| | - Lloyd Vaughan
- Institute of Veterinary Pathology, University of Zurich, Winterthurerstrasse 268, Zurich 8057, Switzerland
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28
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Dual role of FtsH in regulating lipopolysaccharide biosynthesis in Escherichia coli. J Bacteriol 2008; 190:7117-22. [PMID: 18776015 DOI: 10.1128/jb.00871-08] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In Escherichia coli, FtsH (HflB) is a membrane-bound, ATP-dependent metalloendoprotease belonging to the AAA family (ATPases associated with diverse cellular activities). FtsH has a limited spectrum of known substrates, including the transcriptional activator sigma32. FtsH is the only known E. coli protease that is essential, as it regulates the concentration of LpxC, which carries out the first committed step in the synthesis of lipid A. Here we identify a new FtsH substrate--3-deoxy-D-manno-octulosonate (KDO) transferase--which carries out the attachment of two KDO residues to the lipid A precursor (lipid IVA) to form the minimal essential structure of the lipopolysaccharide (LPS) (KDO2-lipid A). Thus, FtsH regulates the concentration of the lipid moiety of LPS (lipid A) as well as the sugar moiety (KDO-based core oligosaccharides), ensuring a balanced synthesis of LPS.
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29
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Licht S, Lee I. Resolving individual steps in the operation of ATP-dependent proteolytic molecular machines: from conformational changes to substrate translocation and processivity. Biochemistry 2008; 47:3595-605. [PMID: 18311925 DOI: 10.1021/bi800025g] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Clp, Lon, and FtsH proteases are proteolytic molecular machines that use the free energy of ATP hydrolysis to unfold protein substrates and processively present them to protease active sites. Here we review recent biochemical and structural studies relevant to the mechanism of ATP-dependent processive proteolysis. Despite the significant structural differences among the Clp, Lon, and FtsH proteases, these enzymes share important mechanistic features. In these systems, mechanistic studies have provided evidence for ATP binding and hydrolysis-driven conformational changes that drive translocation of substrates, which has significant implications for the processive mechanism of proteolysis. These studies indicate that the nucleotide (ATP, ADP, or nonhydrolyzable ATP analogues) occupancy of the ATPase binding sites can influence the binding mode and/or binding affinity for protein substrates. A general mechanism is proposed in which the communication between ATPase active sites and protein substrate binding regions coordinates a processive cycle of substrate binding, translocation, proteolysis, and product release.
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Affiliation(s)
- Stuart Licht
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA.
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30
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Rokney A, Kobiler O, Amir A, Court DL, Stavans J, Adhya S, Oppenheim AB. Host responses influence on the induction of lambda prophage. Mol Microbiol 2008; 68:29-36. [PMID: 18298445 PMCID: PMC2327240 DOI: 10.1111/j.1365-2958.2008.06119.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Inactivation of bacteriophage lambda CI repressor leads almost exclusively to lytic development. Prophage induction can be initiated either by DNA damage or by heat treatment of a temperature-sensitive repressor. These two treatments also cause a concurrent activation of either the host SOS or heat-shock stress responses respectively. We studied the effects of these two methods of induction on the lytic pathway by monitoring the activation of different lambda promoters, and found that the lambda genetic network co-ordinates information from the host stress response networks. Our results show that the function of the CII transcriptional activator, which facilitates the lysogenic developmental pathway, is not observed following either method of induction. Mutations in the cro gene restore the CII function irrespective of the induction method. Deletion of the heat-shock protease gene ftsH can also restore CII function following heat induction but not following SOS induction. Our findings highlight the importance of the elimination of CII function during induction as a way to ensure an efficient lytic outcome. We also show that, despite the common inhibitory effect on CII function, there are significant differences in the heat- and SOS-induced pathways leading to the lytic cascade.
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Affiliation(s)
- Assaf Rokney
- Department of Molecular Genetics and Biotechnology, The Hebrew University-Hadassah Medical School, Jerusalem, Israel.
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31
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Inobe T, Matouschek A. Protein targeting to ATP-dependent proteases. Curr Opin Struct Biol 2008; 18:43-51. [PMID: 18276129 DOI: 10.1016/j.sbi.2007.12.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Revised: 12/21/2007] [Accepted: 12/26/2007] [Indexed: 11/27/2022]
Abstract
ATP-dependent proteases control diverse cellular processes by degrading specific regulatory proteins. Recent work has shown that protein substrates are specifically transferred to ATP-dependent proteases through different routes. These routes can function in parallel or independently. In all of these targeting mechanisms, it can be useful to separate two steps: substrate binding to the protease and initiation of degradation.
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Affiliation(s)
- Tomonao Inobe
- Department of Biochemistry, Molecular Biology and Cell Biology, 2205 Tech Drive, Hogan 2-100 Northwestern University, Evanston, IL, USA
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32
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Srinivasan R, Rajeswari H, Ajitkumar P. Analysis of degradation of bacterial cell division protein FtsZ by the ATP-dependent zinc-metalloprotease FtsH in vitro. Microbiol Res 2008; 163:21-30. [PMID: 16638632 DOI: 10.1016/j.micres.2006.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2005] [Revised: 02/13/2006] [Accepted: 03/06/2006] [Indexed: 11/30/2022]
Abstract
The identity of protease(s), which would degrade bacterial cell division protein FtsZ in vivo, remains unknown. However, we had earlier demonstrated that Escherichia coli metalloprotease FtsH degrades E. coli cell division protein FtsZ in an ATP- and Zn(2+)-dependent manner in vitro. In this study, we examined FtsH protease-mediated degradation of FtsZ in vitro in detail using seven different deletion mutants of FtsZ as the substrates, which lack different extents of specific regions at the N- or C-terminus. FtsH protease assay in vitro on these mutants revealed that FtsH could degrade all the seven deletion mutants irrespective of the deletions or the extent of deletions at the N- or C-terminus. These observations indicated that neither the N-terminus nor the C-terminus was required for the degradation of FtsZ, like already known in the case of the FtsH substrate sigma(32) protein. The recombinant clones expressing full-length FtsZ protein and FtsZ deletion mutant proteins would be useful in investigating the possibility of FtsZ as a potential in vivo substrate for FtsH in ftsH-null cells carrying ftsH suppressor function and ectopically expressed FtsH protease.
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Affiliation(s)
- Ramanujam Srinivasan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
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33
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Abstract
Temperature is an important physical stress factor sensed by bacteria and used to regulate gene expression. Three different macromolecules have been identified being able to sense temperature: DNA, mRNA and proteins. Depending on the induction mechanism, two different pathways have to be distinguished, namely the heat shock response and the high temperature response. While the heat shock response is induced by temperature increments and is transient, the high temperature response needs a specific temperature to become induced and proceeds as long as cells are exposed to that temperature. The heat shock response is induced by denatured proteins and aimed to prevent formation of protein aggregates by refolding or degradation, and the high temperature response is mainly used by pathogenic bacteria to detect entry into a mammalian host followed by induction of their virulence genes. All known high temperature sensors are present in two alternative conformations depending on the temperature. Heat shock sensors are either molecular chaperones or proteases which keep either a positive transcriptional regulator inactive or a negative regulator active or do not attack the regulator, respectively, under physiological conditions. Denatured proteins either titrate the molecular chaperones or activate the protease. The evolution of the different temperature sensors is discussed.
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Affiliation(s)
- Wolfgang Schumann
- Institute of Genetics, University of Bayreuth, D-95440 Bayreuth, Germany.
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34
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Srinivasan R, Ajitkumar P. Bacterial cell division protein FtsZ is stable against degradation by AAA family protease FtsH in Escherichia coli cells. J Basic Microbiol 2007; 47:251-9. [PMID: 17518418 DOI: 10.1002/jobm.200610236] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We have found that FtsH protease of Escherichia coli could degrade E. coli cell division protein FtsZ in an ATP- and Zn(2+)-dependent manner in vitro and that the degradation did not show specificity for the N-terminus or C-terminus of FtsZ, like in the case of degradation of its conventional substrate sigma(32) protein. In continuation of these observations, in the present study, we examined whether FtsH would affect the stability and turnover of FtsZ in vivo. We found that FtsZ levels were not elevated in E. coli AR754 (ftsH1 ts) cells at nonpermissive temperature as compared to the levels in an FtsH-active isogenic AR753 strain. Neither did FtsH degrade ectopically expressed FtsZ in AR754 strain nor did ectopic expression of FtsH reduced FtsZ levels in E. coli AR5090 ftsH null strain (ftsH::kan, sfhC21). Pulse chase experiments in AR754 and AR5090 strains showed that there were no compensatory changes in FtsZ turnover, in case FtsZ degradation had occurred. Even under cell division arrested conditions, wherein FtsZ was not required, FtsH protease did not degrade unutilized FtsZ. These experiments demonstrate that either FtsH protease may not have a role in regulating the levels of FtsZ in vivo under the conditions tested or that some cellular component(s) might be stabilising FtsZ against FtsH protease.
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Affiliation(s)
- Ramanujam Srinivasan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore - 560012, India
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35
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Halder S, Datta AB, Parrack P. Probing the antiprotease activity of lambdaCIII, an inhibitor of the Escherichia coli metalloprotease HflB (FtsH). J Bacteriol 2007; 189:8130-8. [PMID: 17890311 PMCID: PMC2168696 DOI: 10.1128/jb.00820-07] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The CIII protein encoded by the temperate coliphage lambda acts as an inhibitor of the ubiquitous Escherichia coli metalloprotease HflB (FtsH). This inhibition results in the stabilization of transcription factor lambdaCII, thereby helping the phage to lysogenize the host bacterium. LambdaCIII, a small (54-residue) protein of unknown structure, also protects sigma(32), another specific substrate of HflB. In order to understand the details of the inhibitory mechanism of CIII, we cloned and expressed the protein with an N-terminal six-histidine tag. We also synthesized and studied a 28-amino-acid peptide, CIIIC, encompassing the central 14 to 41 residues of CIII that exhibited antiproteolytic activity. Our studies show that CIII exists as a dimer under native conditions, aided by an intersubunit disulfide bond, which is dispensable for dimerization. Unlike CIII, CIIIC resists digestion by HflB. While CIII binds to HflB, it does not bind to CII. On the basis of these results, we discuss various mechanisms for the antiproteolytic activity of CIII.
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Affiliation(s)
- Sabyasachi Halder
- Department of Biochemistry, Bose Institute, P-1/12, CIT Scheme VIIM, Kolkata 700054, India
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36
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Obrist M, Milek S, Klauck E, Hengge R, Narberhaus F. Region 2.1 of the Escherichia coli heat-shock sigma factor RpoH (σ
32) is necessary but not sufficient for degradation by the FtsH protease. Microbiology (Reading) 2007; 153:2560-2571. [PMID: 17660420 DOI: 10.1099/mic.0.2007/007047-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The cellular level of the Escherichia coli heat-shock sigma factor RpoH (sigma32) is negatively controlled by chaperone-mediated proteolysis through the essential metalloprotease FtsH. Point mutations in the highly conserved region 2.1 stabilize RpoH in vivo. To assess the importance of this turnover element, hybrid proteins were constructed between E. coli RpoH and Bradyrhizobium japonicum RpoH1, a stable RpoH protein that differs from region 2.1 of E. coli RpoH at several positions. Nine amino acids forming a putative alpha-helix were exchanged between the two proteins. Both hybrids were active sigma factors and showed intermediate protein stability. Introduction of RpoH region 2.1 into the general stress sigma factor RpoS, which is a substrate of the ClpXP protease, did not render RpoS susceptible to FtsH. Hence, region 2.1 alone is not sufficient to confer FtsH sensitivity to other proteins. Region 2.1 is not a major chaperone-binding site since DnaK and DnaJ bound efficiently to all RpoH variants. The in vivo stability of the mutated RpoH proteins correlated with their stability in a purified in vitro degradation system, suggesting that region 2.1 might be directly involved in the interaction with the FtsH protease.
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Affiliation(s)
- Markus Obrist
- Institute of Microbial Biology, Ruhr University Bochum, D-44780 Bochum, Germany
- Institute of Microbiology, ETH Zürich, Switzerland
| | - Sonja Milek
- Institute of Microbial Biology, Ruhr University Bochum, D-44780 Bochum, Germany
| | | | - Regine Hengge
- Institute of Microbiology, Free University Berlin, Germany
| | - Franz Narberhaus
- Institute of Microbial Biology, Ruhr University Bochum, D-44780 Bochum, Germany
- Institute of Microbiology, ETH Zürich, Switzerland
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37
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Komayama K, Khatoon M, Takenaka D, Horie J, Yamashita A, Yoshioka M, Nakayama Y, Yoshida M, Ohira S, Morita N, Velitchkova M, Enami I, Yamamoto Y. Quality control of Photosystem II: cleavage and aggregation of heat-damaged D1 protein in spinach thylakoids. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1767:838-46. [PMID: 17543883 DOI: 10.1016/j.bbabio.2007.05.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2006] [Revised: 04/30/2007] [Accepted: 05/01/2007] [Indexed: 01/02/2023]
Abstract
Moderate heat stress (40 degrees C, 30 min) on spinach thylakoids induced cleavage of the D1 protein, producing an N-terminal 23-kDa fragment, a C-terminal 9-kDa fragment, and aggregation of the D1 protein. A homologue of Arabidopsis FtsH2 protease, which is responsible for degradation of the damaged D1 protein, was abundant in the stroma thylakoids. Two processes occurred in the thylakoids in response to heat stress: dephosphorylation of the D1 protein in the stroma thylakoids, and aggregation of the phosphorylated D1 protein in the grana. Heat stress also induced the release of the extrinsic PsbO, P and Q proteins from Photosystem II, which affected D1 degradation and aggregation significantly. The cleavage and aggregation of the D1 protein appear to be two alternative processes influenced by protein phosphorylation/dephosphorylation, distribution of FtsH, and intactness of the thylakoids.
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Affiliation(s)
- Keisuke Komayama
- Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
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38
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Kobiler O, Rokney A, Oppenheim AB. Phage lambda CIII: a protease inhibitor regulating the lysis-lysogeny decision. PLoS One 2007; 2:e363. [PMID: 17426811 PMCID: PMC1838920 DOI: 10.1371/journal.pone.0000363] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2006] [Accepted: 03/21/2007] [Indexed: 11/18/2022] Open
Abstract
The ATP-dependent protease FtsH (HflB) complexed with HflKC participates in post-translational control of the lysis-lysogeny decision of bacteriophage lambda by rapid degradation of lambda CII. Both phage-encoded proteins, the CII transcription activator and the CIII polypeptide, are required for efficient lysogenic response. The conserved CIII is both an inhibitor and substrate of FtsH. Here we show that the protease inhibitor CIII is present as oligomeric amphipathic alpha helical structures and functions as a competitive inhibitor of FtsH by preventing binding of the CII substrate. We identified single alanine substitutions in CIII that abolish its activity. We characterize a dominant negative effect of a CIII mutant. Thus, we suggest that CIII oligomrization is required for its function. Real-time analysis of CII activity demonstrates that the effect of CIII is not seen in the absence of either FtsH or HflKC. When CIII is provided ectopically, CII activity increases linearly as a function of the multiplicity of infection, suggesting that CIII enhances CII stability and the lysogenic response. FtsH function is essential for cellular viability as it regulates the balance in the synthesis of phospholipids and lipopolysaccharides. Genetic experiments confirmed that the CIII bacteriostatic effects are due to inhibition of FtsH. Thus, the early presence of CIII following infection stimulates the lysogenic response, while its degradation at later times ensures the reactivation of FtsH allowing the growth of the established lysogenic cell.
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Affiliation(s)
- Oren Kobiler
- Department of Molecular Genetics and Biotechnology, The Hebrew University-Hadassah Medical School, Jerusalem, Israel.
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39
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Mizrahi I, Biran D, Gur E, Ron EZ. Tools for the study of protein quality control systems: use of truncated homoserine trans-succinylase as a model substrate for ATP-dependent proteolysis in Escherichia coli. J Microbiol Methods 2007; 70:82-5. [PMID: 17490766 DOI: 10.1016/j.mimet.2007.03.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2006] [Revised: 03/26/2007] [Accepted: 03/26/2007] [Indexed: 10/23/2022]
Abstract
Protein quality control, mediated by chaperones and ATP-dependent proteases, is essential for maintaining balanced growth and for regulating critical processes. To study these systems it is necessary to have model substrate proteins. However, most cellular proteins are stable and the few unstable proteins are usually regulatory and present in low concentrations, making them unsuitable for studies, especially in vivo. We present HTS(Delta1-6), a truncated homoserine trans-succinylase (HTS) which is unstable, can be expressed at high levels and has an enzymatic, measurable, activity. This protein can serve as a good model substrate for Escherichia coli ATP-dependent proteolysis.
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Affiliation(s)
- Itzhak Mizrahi
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, 69978 Israel
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40
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Srinivasan R, Rajeswari H, Bhatt BN, Indi S, Ajitkumar P. GTP/GDP binding stabilizes bacterial cell division protein FtsZ against degradation by FtsH protease in vitro. Biochem Biophys Res Commun 2007; 357:38-43. [PMID: 17408592 DOI: 10.1016/j.bbrc.2007.03.055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2007] [Accepted: 03/10/2007] [Indexed: 11/18/2022]
Abstract
Factors contributing to the stability of bacterial cell division protein FtsZ remain unknown. In order to identify FtsZ-stabilizing factor(s), we exploited FtsH protease-based in vitro FtsZ degradation assay system. Whole cell lysate from an ftsH-null strain of Escherichia coli inhibited degradation of FtsZ by FtsH in vitro. However, activated charcoal-treated lysate did not inhibit degradation. The loss of ability of the activated charcoal-treated lysate to inhibit degradation of FtsZ was restored when it was replenished with GTP, but not when replenished with other NTPs or dNTPs. The lysate did not protect either FtsZ deletion mutants, which do not bind GTP, or FtsH substrates, sigma(32) and cI-108 proteins, against FtsH. GDP and GTPgammaS also stabilized FtsZ against FtsH. Neither GTP nor GDP inhibited proteolytic activity of FtsH per se. These observations demonstrate that binding of GTP/GDP ligands is responsible for the proteolytic stability of FtsZ against FtsH.
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Affiliation(s)
- Ramanujam Srinivasan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
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41
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Stirnberg M, Fulda S, Huckauf J, Hagemann M, Krämer R, Marin K. A membrane-bound FtsH protease is involved in osmoregulation in Synechocystis sp. PCC 6803: the compatible solute synthesizing enzyme GgpS is one of the targets for proteolysis. Mol Microbiol 2007; 63:86-102. [PMID: 17116240 DOI: 10.1111/j.1365-2958.2006.05495.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein quality control and proteolysis are involved in cell maintenance and environmental acclimatization in bacteria and eukaryotes. The AAA protease FtsH2 of the cyanobacterium Synechocystis sp. PCC 6803 was identified during a screening for mutants impaired in osmoregulation. The ftsH2(-) mutant was salt sensitive because of a decreased level of the osmoprotectant glucosylglycerol (GG). In spite of wild type-like transcription of the ggpS gene in ftsH2(-) cells the GgpS protein content increased but only low levels of GgpS activity were observed. Consequently, salt tolerance of the ftsH2(-) mutant decreased while addition of external osmolyte complemented the salt sensitivity. The proteolytic degradation of the GgpS protein by FtsH2 was demonstrated by an in vitro assay using inverted membrane vesicles. The GgpS is part of a GG synthesizing complex, because yeast two-hybrid screens identified a close interaction with the GG-phosphate phosphatase. Besides GgpS as the first soluble substrate of a cyanobacterial FtsH protease, several other putative targets were identified by a proteomic approach. We present a novel molecular explanation for the salt-sensitive phenotype of bacterial ftsH(-) mutants as the result of accumulation of inactive enzymes for compatible solute synthesis, in this case GgpS the key enzyme of GG synthesis.
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Affiliation(s)
- Marit Stirnberg
- Universität zu Köln, Institut für Biochemie, Zülpicher Str. 47, 50674 Köln, Germany
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42
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Ferreira S, Hjernø K, Larsen M, Wingsle G, Larsen P, Fey S, Roepstorff P, Salomé Pais M. Proteome profiling of Populus euphratica Oliv. upon heat stress. ANNALS OF BOTANY 2006; 98:361-77. [PMID: 16740589 PMCID: PMC2803470 DOI: 10.1093/aob/mcl106] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Populus euphratica is a light-demanding species ecologically characterized as a pioneer. It grows in shelter belts along riversides, being part of the natural desert forest ecosystems in China and Middle Eastern countries. It is able to survive extreme temperatures, drought and salt stress, marking itself out as an important plant species to study the mechanisms responsible for survival of woody plants under heat stress. METHODS Heat effects were evaluated through electrolyte leakage on leaf discs, and LT(50) was determined to occur above 50 degrees C. Protein accumulation profiles of leaves from young plants submitted to 42/37 degrees C for 3 d in a phytotron were determined through 2D-PAGE, and a total of 45 % of up- and downregulated proteins were detected. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF)/TOF analysis, combined with searches in different databases, enabled the identification of 82 % of the selected spots. KEY RESULTS Short-term upregulated proteins are related to membrane destabilization and cytoskeleton restructuring, sulfur assimilation, thiamine and hydrophobic amino acid biosynthesis, and protein stability. Long-term upregulated proteins are involved in redox homeostasis and photosynthesis. Late downregulated proteins are involved mainly in carbon metabolism. CONCLUSIONS Moderate heat response involves proteins related to lipid biogenesis, cytoskeleton structure, sulfate assimilation, thiamine and hydrophobic amino acid biosynthesis, and nuclear transport. Photostasis is achieved through carbon metabolism adjustment, a decrease of photosystem II (PSII) abundance and an increase of PSI contribution to photosynthetic linear electron flow. Thioredoxin h may have a special role in this process in P. euphratica upon moderate heat exposure.
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Affiliation(s)
- Sílvia Ferreira
- Unit of Molecular Biology and Plant Biotechnology, Institute of Applied Science and Technology, Science Faculty of Lisbon University, Campo Grande, 1749-016 Lisbon, Portugal.
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Okuno T, Yamanaka K, Ogura T. An AAA protease FtsH can initiate proteolysis from internal sites of a model substrate, apo-flavodoxin. Genes Cells 2006; 11:261-8. [PMID: 16483314 DOI: 10.1111/j.1365-2443.2006.00940.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Escherichia coli FtsH, which belongs to the AAA (ATPases associated with diverse cellular activities) family, is an ATP-dependent and membrane-bound protease. FtsH degrades misassembled membrane proteins and a subset of cytoplasmic regulatory proteins. It has been proposed that ATP-dependent proteases unfold substrate proteins and initiate a processive proteolysis from either terminus of the substrate polypeptide. We have found that FtsH degrades E. coli apo-flavodoxin (apo-Fld) but not holo-Fld containing non-covalently bound flavin mononucleotide (FMN). A mutant Fld carrying a substitution of Tyr94 to Asp (Fld(YD)) with a lower affinity for FMN was efficiently degraded by FtsH. To elucidate the directionality of Fld(YD) degradation by FtsH, we constructed several Fld(YD) fusion proteins with glutathione S-transferase (GST), green fluorescent protein (GFP), or both GST and GFP. It was found that FtsH was able to initiate degradation of the Fld(YD) moiety even when it was sandwiched by GST and GFP. Evidence indicated that FtsH can initiate proteolysis of GST-Fld(YD)-GFP from the Fld(YD) moiety by translocating an internal loop to the protease chamber in an ATP-dependent manner and that, at least, the proteolysis in the C to N direction proceeds processively.
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Affiliation(s)
- Takashi Okuno
- Division of Molecular Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
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44
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Führer F, Langklotz S, Narberhaus F. The C-terminal end of LpxC is required for degradation by the FtsH protease. Mol Microbiol 2006; 59:1025-36. [PMID: 16420369 DOI: 10.1111/j.1365-2958.2005.04994.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lipopolysaccharide (LPS) biosynthesis is essential in Gram negative bacteria. LpxC, the key enzyme in LPS formation, catalyses the limiting reaction and controls the ratio between LPS and phospholipids. As overproduction of LPS is toxic, the cellular amount of LpxC must be regulated carefully. The membrane-bound protease FtsH controls the level of LpxC via proteolysis making FtsH the only essential protease of Escherichia coli. We found that the chaperones DnaK and DnaJ co-purified with LpxC. However, degradation of LpxC was DnaK/J-independent in contrast to turnover of the heat shock sigma factor sigma32 (RpoH). The stability of LpxC in a bacterial one-hybrid system suggested that a terminus of LpxC might be important for degradation. Different LpxC truncations and extensions were constructed. Removal of at least five amino acids from the C-terminus abolished degradation by FtsH in vivo. While addition of two aspartic acids to LpxC did not alter its half-life, the exchange of the last two residues against aspartic acids resulted in stabilization. All stable LpxC enzymes were active in vivo as assayed by their high toxicity. Our data demonstrate that the C-terminus of LpxC contains a signal sequence necessary for FtsH-dependent degradation.
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Affiliation(s)
- Frank Führer
- Lehrstuhl für Biologie der Mikroorganismen, Ruhr-Universität Bochum, Bochum, Germany
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45
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Abstract
Temperature is an important parameter that free-living cells monitor constantly. The expression of heat-shock, cold-shock and some virulence genes is coordinated in response to temperature changes. Apart from protein-mediated transcriptional control mechanisms, translational control by RNA thermometers is a widely used regulatory strategy. RNA thermometers are complex RNA structures that change their conformation in response to temperature. Most, but not all, RNA thermometers are located in the 5'-untranslated region and mask ribosome-binding sites by base pairing at low temperatures. Melting of the structure at increasing temperature permits ribosome access and translation initiation. Different cis-acting RNA thermometers and a trans-acting thermometer will be presented.
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Affiliation(s)
- Franz Narberhaus
- Lehrstuhl für Biologie der Mikroorganismen, Ruhr-Universität Bochum, Bochum, Germany.
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46
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Okuno T, Yamanaka K, Ogura T. Characterization of mutants of the Escherichia coli AAA protease, FtsH, carrying a mutation in the central pore region. J Struct Biol 2006; 156:109-14. [PMID: 16563799 DOI: 10.1016/j.jsb.2006.02.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2005] [Revised: 02/02/2006] [Accepted: 02/09/2006] [Indexed: 10/24/2022]
Abstract
Escherichia coli FtsH is an ATP-dependent and membrane-bound protease, which belongs to the ATPases associated with diverse cellular activities family. FtsH degrades a subset of cytoplasmic regulatory proteins and misassembled membrane proteins. It has been proposed that ATP-dependent proteases unfold and translocate substrate proteins into the protease chamber. Previously, we reported that Phe228 and Gly230 in the conserved motif, @XG (where @ is an aromatic residue and X is any residue), in the central pore of the FtsH ATPase ring have important roles in proteolysis and its coupling to ATP hydrolysis. In this paper, we constructed and characterized additional pore mutants. Results indicated that certain acidic residues located in the pore region are also important for the activity of FtsH. Proteolytic activities of most mutants are correlated with their ATPase activities. Evidence also indicated that Val229, the 2nd residue of the @XG motif, may have a substrate-specific role.
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Affiliation(s)
- Takashi Okuno
- Division of Molecular Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
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47
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Abstract
The lysis-lysogeny decision of bacteriophage lambda (lambda) is a paradigm for developmental genetic networks. There are three key features, which characterize the network. First, after infection of the host bacterium, a decision between lytic or lysogenic development is made that is dependent upon environmental signals and the number of infecting phages per cell. Second, the lysogenic prophage state is very stable. Third, the prophage enters lytic development in response to DNA-damaging agents. The CI and Cro regulators define the lysogenic and lytic states, respectively, as a bistable genetic switch. Whereas CI maintains a stable lysogenic state, recent studies indicate that Cro sets the lytic course not by directly blocking CI expression but indirectly by lowering levels of CII which activates cI transcription. We discuss how a relatively simple phage like lambda employs a complex genetic network in decision-making processes, providing a challenge for theoretical modeling.
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Affiliation(s)
- Amos B Oppenheim
- Department of Molecular Genetics and Biotechnology, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel.
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48
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Abstract
FtsH is a cytoplasmic membrane protein that has N-terminally located transmembrane segments and a main cytosolic region consisting of AAA-ATPase and Zn2+-metalloprotease domains. It forms a homo-hexamer, which is further complexed with an oligomer of the membrane-bound modulating factor HflKC. FtsH degrades a set of short-lived proteins, enabling cellular regulation at the level of protein stability. FtsH also degrades some misassembled membrane proteins, contributing to their quality maintenance. It is an energy-utilizing and processive endopeptidase with a special ability to dislocate membrane protein substrates out of the membrane, for which its own membrane-embedded nature is essential. We discuss structure-function relationships of this intriguing enzyme, including the way it recognizes the soluble and membrane-integrated substrates differentially, on the basis of the solved structure of the ATPase domain as well as extensive biochemical and genetic information accumulated in the past decade on this enzyme.
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Affiliation(s)
- Koreaki Ito
- Institute for Virus Research, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan.
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49
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Wegrzyn G, Wegrzyn A. Genetic switches during bacteriophage lambda development. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2005; 79:1-48. [PMID: 16096026 DOI: 10.1016/s0079-6603(04)79001-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- Grzegorz Wegrzyn
- Department of Molecular Biology, University of Gdańsk, 80-822 Gdańsk, Poland
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50
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Kobiler O, Oppenheim AB, Herman C. Recruitment of host ATP-dependent proteases by bacteriophage lambda. J Struct Biol 2004; 146:72-8. [PMID: 15037238 DOI: 10.1016/j.jsb.2003.10.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2003] [Revised: 10/21/2003] [Indexed: 11/29/2022]
Abstract
Upon infection of a bacterial cell, the temperate bacteriophage lambda executes a regulated temporal program with two possible outcomes: (1) Cell lysis and virion production or (2) establishment of a dormant state, lysogeny, in which the phage genome (prophage) is integrated into the host chromosome. The prophage is replicated passively as part of the host chromosome until it is induced to resume the lytic cycle. In this review, we summarize the evidence that implicates every known ATP-dependent protease in the regulation of specific steps in the phage life cycle. The proteolysis of specific regulatory proteins appears to fine-tune phage gene expression. The bacteriophage utilizes multiple proteases to irreversibly inactivate specific regulators resulting in a temporally regulated program of gene expression. Evolutionary forces may have favored the utilization of overlapping protease specificities for differential proteolysis of phage regulators according to different phage life styles.
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Affiliation(s)
- Oren Kobiler
- Department of Molecular Genetics and Biotechnology, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel
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