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Jin H, Ji Y, An J, Ha DH, Lee YR, Kim HJ, Lee CG, Jeong W, Kwon IC, Yang EG, Kim KH, Lee C, Chung HS. Engineering Escherichia coli for constitutive production of monophosphoryl lipid A vaccine adjuvant. Biotechnol Bioeng 2024; 121:1144-1162. [PMID: 38184812 DOI: 10.1002/bit.28638] [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: 10/05/2023] [Revised: 11/14/2023] [Accepted: 12/12/2023] [Indexed: 01/08/2024]
Abstract
During the COVID-19 pandemic, expedient vaccine production has been slowed by the shortage of safe and effective raw materials, such as adjuvants, essential components to enhance the efficacy of vaccines. Monophosphoryl lipid A (MPLA) is a potent and safe adjuvant used in human vaccines, including the Shingles vaccine, Shingrix. 3-O-desacyl-4'-monophosphoryl lipid A (MPL), a representative MPLA adjuvant commercialized by GSK, was prepared via chemical conversion of precursors isolated from Salmonella typhimurium R595. However, the high price of these materials limits their use in premium vaccines. To combat the scarcity and high cost of safe raw materials for vaccines, we need to develop a feasible MPLA production method that is easily scaled up to meet industrial requirements. In this study, we engineered peptidoglycan and outer membrane biosynthetic pathways in Escherichia coli and developed a Escherichia coli strain, KHSC0055, that constitutively produces EcML (E. coli-produced monophosphoryl lipid A) without additives such as antibiotics or overexpression inducers. EcML production was optimized on an industrial scale via high-density fed-batch fermentation, and obtained 2.7 g of EcML (about 135,000 doses of vaccine) from a 30-L-scale fermentation. Using KHSC0055, we simplified the production process and decreased the production costs of MPLA. Then, we applied EcML purified from KHSC0055 as an adjuvant for a COVID-19 vaccine candidate (EuCorVac-19) currently in clinical trial stage III in the Philippines. By probing the efficacy and safety of EcML in humans, we established KHSC0055 as an efficient cell factory for MPLA adjuvant production.
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Affiliation(s)
- Hyunjung Jin
- Chemical and Biological Integrative Research Center, Biomedical Research Division, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Yuhyun Ji
- Chemical and Biological Integrative Research Center, Biomedical Research Division, Korea Institute of Science and Technology, Seoul, Republic of Korea
- Department of Life Sciences, Korea University, Seoul, Republic of Korea
| | - Jinsu An
- Chemical and Biological Integrative Research Center, Biomedical Research Division, Korea Institute of Science and Technology, Seoul, Republic of Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea National University of Science and Technology, Seoul, Republic of Korea
| | - Da Hui Ha
- V Plant 125, Wonmudong-gil, Dongsan-myeon, EuBiologics., Co., Ltd., Chuncheon-si, Gangwon-do, Republic of Korea
| | - Ye-Ram Lee
- V Plant 125, Wonmudong-gil, Dongsan-myeon, EuBiologics., Co., Ltd., Chuncheon-si, Gangwon-do, Republic of Korea
| | - Hye-Ji Kim
- V Plant 125, Wonmudong-gil, Dongsan-myeon, EuBiologics., Co., Ltd., Chuncheon-si, Gangwon-do, Republic of Korea
| | - Choon Geun Lee
- V Plant 125, Wonmudong-gil, Dongsan-myeon, EuBiologics., Co., Ltd., Chuncheon-si, Gangwon-do, Republic of Korea
| | - Wooyeon Jeong
- Doping Control Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Ick Chan Kwon
- Medicinal Materials Research Center, Biomedical Research Division, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Eun Gyeong Yang
- Biomedical Research Division, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Ki Hun Kim
- Doping Control Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Chankyu Lee
- V Plant 125, Wonmudong-gil, Dongsan-myeon, EuBiologics., Co., Ltd., Chuncheon-si, Gangwon-do, Republic of Korea
| | - Hak Suk Chung
- Chemical and Biological Integrative Research Center, Biomedical Research Division, Korea Institute of Science and Technology, Seoul, Republic of Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea National University of Science and Technology, Seoul, Republic of Korea
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2
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Jiang C, Wynne M, Huber D. How Quality Control Systems AID Sec-Dependent Protein Translocation. Front Mol Biosci 2021; 8:669376. [PMID: 33928127 PMCID: PMC8076867 DOI: 10.3389/fmolb.2021.669376] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 03/17/2021] [Indexed: 02/01/2023] Open
Abstract
The evolutionarily conserved Sec machinery is responsible for transporting proteins across the cytoplasmic membrane. Protein substrates of the Sec machinery must be in an unfolded conformation in order to be translocated across (or inserted into) the cytoplasmic membrane. In bacteria, the requirement for unfolded proteins is strict: substrate proteins that fold (or misfold) prematurely in the cytoplasm prior to translocation become irreversibly trapped in the cytoplasm. Partially folded Sec substrate proteins and stalled ribosomes containing nascent Sec substrates can also inhibit translocation by blocking (i.e., “jamming”) the membrane-embedded Sec machinery. To avoid these issues, bacteria have evolved a complex network of quality control systems to ensure that Sec substrate proteins do not fold in the cytoplasm. This quality control network can be broken into three branches, for which we have defined the acronym “AID”: (i) avoidance of cytoplasmic intermediates through cotranslationally channeling newly synthesized Sec substrates to the Sec machinery; (ii) inhibition of folding Sec substrate proteins that transiently reside in the cytoplasm by molecular chaperones and the requirement for posttranslational modifications; (iii) destruction of products that could potentially inhibit translocation. In addition, several stress response pathways help to restore protein-folding homeostasis when environmental conditions that inhibit translocation overcome the AID quality control systems.
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Affiliation(s)
- Chen Jiang
- School of Biosciences and the Institute for Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Max Wynne
- School of Biosciences and the Institute for Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Damon Huber
- School of Biosciences and the Institute for Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
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3
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Abstract
Bacterial endoribonuclease toxins belong to a protein family that inhibits bacterial growth by degrading mRNA or rRNA sequences. The toxin genes are organized in pairs with its cognate antitoxins in the chromosome and thus the activities of the toxins are antagonized by antitoxin proteins or RNAs during active translation. In response to a variety of cellular stresses, the endoribonuclease toxins appear to be released from antitoxin molecules via proteolytic cleavage of antitoxin proteins or preferential degradation of antitoxin RNAs and cleave a diverse range of mRNA or rRNA sequences in a sequence-specific or codon-specific manner, resulting in various biological phenomena such as antibiotic tolerance and persister cell formation. Given that substrate specificity of each endoribonuclease toxin is determined by its structure and the composition of active site residues, we summarize the biology, structure, and substrate specificity of the updated bacterial endoribonuclease toxins.
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Affiliation(s)
- Yoontak Han
- Department of Life Sciences, Korea University, Seoul 02481, Korea
| | - Eun-Jin Lee
- Department of Life Sciences, Korea University, Seoul 02481, Korea
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4
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Masuda H, Inouye M. Toxins of Prokaryotic Toxin-Antitoxin Systems with Sequence-Specific Endoribonuclease Activity. Toxins (Basel) 2017; 9:toxins9040140. [PMID: 28420090 PMCID: PMC5408214 DOI: 10.3390/toxins9040140] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 04/09/2017] [Accepted: 04/10/2017] [Indexed: 01/21/2023] Open
Abstract
Protein translation is the most common target of toxin-antitoxin system (TA) toxins. Sequence-specific endoribonucleases digest RNA in a sequence-specific manner, thereby blocking translation. While past studies mainly focused on the digestion of mRNA, recent analysis revealed that toxins can also digest tRNA, rRNA and tmRNA. Purified toxins can digest single-stranded portions of RNA containing recognition sequences in the absence of ribosome in vitro. However, increasing evidence suggests that in vivo digestion may occur in association with ribosomes. Despite the prevalence of recognition sequences in many mRNA, preferential digestion seems to occur at specific positions within mRNA and also in certain reading frames. In this review, a variety of tools utilized to study the nuclease activities of toxins over the past 15 years will be reviewed. A recent adaptation of an RNA-seq-based technique to analyze entire sets of cellular RNA will be introduced with an emphasis on its strength in identifying novel targets and redefining recognition sequences. The differences in biochemical properties and postulated physiological roles will also be discussed.
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Affiliation(s)
- Hisako Masuda
- School of Sciences, Indiana University Kokomo, Kokomo, IN 46902, USA.
| | - Masayori Inouye
- Department of Biochemistry, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08854, USA.
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Tikh IB, Samuelson JC. Leveraging modern DNA assembly techniques for rapid, markerless genome modification. Biol Methods Protoc 2016; 1:bpw004. [PMID: 32368618 PMCID: PMC7189271 DOI: 10.1093/biomethods/bpw004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 09/06/2016] [Accepted: 09/26/2016] [Indexed: 11/14/2022] Open
Abstract
The ability to alter the genomic material of a prokaryotic cell is necessary for experiments designed to define the biology of the organism. In addition, the production of biomolecules may be significantly improved by application of engineered prokaryotic host cells. Furthermore, in the age of synthetic biology, speed and efficiency are key factors when choosing a method for genome alteration. To address these needs, we have developed a method for modification of the Escherichia coli genome named FAST-GE for Fast Assembly-mediated Scarless Targeted Genome Editing. Traditional cloning steps such as plasmid transformation, propagation and isolation were eliminated. Instead, we developed a DNA assembly-based approach for generating scarless strain modifications, which may include point mutations, deletions and gene replacements, within 48 h after the receipt of polymerase chain reaction primers. The protocol uses established, but optimized, genome modification components such as I-SceI endonuclease to improve recombination efficiency and SacB as a counter-selection mechanism. All DNA-encoded components are assembled into a single allele-exchange vector named pDEL. We were able to rapidly modify the genomes of both E. coli B and K-12 strains with high efficiency. In principle, the method may be applied to other prokaryotic organisms capable of circular dsDNA uptake and homologous recombination.
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Affiliation(s)
- Ilya B Tikh
- Protein Expression and Modification Division, New England BioLabs, Inc., Ipswich, MA, 01938-2723, USA
| | - James C Samuelson
- Protein Expression and Modification Division, New England BioLabs, Inc., Ipswich, MA, 01938-2723, USA
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Toxin-Antitoxin Modules Are Pliable Switches Activated by Multiple Protease Pathways. Toxins (Basel) 2016; 8:toxins8070214. [PMID: 27409636 PMCID: PMC4963847 DOI: 10.3390/toxins8070214] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 06/24/2016] [Accepted: 06/27/2016] [Indexed: 02/06/2023] Open
Abstract
Toxin-antitoxin (TA) modules are bacterial regulatory switches that facilitate conflicting outcomes for cells by promoting a pro-survival phenotypic adaptation and/or by directly mediating cell death, all through the toxin activity upon degradation of antitoxin. Intensive study has revealed specific details of TA module functions, but significant gaps remain about the molecular details of activation via antitoxin degradation used by different bacteria and in different environments. This review summarizes the current state of knowledge about the interaction of antitoxins with cellular proteases Lon and ClpP to mediate TA module activation. An understanding of these processes can answer long-standing questions regarding stochastic versus specific activation of TA modules and provide insight into the potential for manipulation of TA modules to alter bacterial growth.
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7
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Sala A, Bordes P, Genevaux P. Multitasking SecB chaperones in bacteria. Front Microbiol 2014; 5:666. [PMID: 25538690 PMCID: PMC4257090 DOI: 10.3389/fmicb.2014.00666] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/17/2014] [Indexed: 12/17/2022] Open
Abstract
Protein export in bacteria is facilitated by the canonical SecB chaperone, which binds to unfolded precursor proteins, maintains them in a translocation competent state and specifically cooperates with the translocase motor SecA to ensure their proper targeting to the Sec translocon at the cytoplasmic membrane. Besides its key contribution to the Sec pathway, SecB chaperone tasking is critical for the secretion of the Sec-independent heme-binding protein HasA and actively contributes to the cellular network of chaperones that control general proteostasis in Escherichia coli, as judged by the significant interplay found between SecB and the trigger factor, DnaK and GroEL chaperones. Although SecB is mainly a proteobacterial chaperone associated with the presence of an outer membrane and outer membrane proteins, secB-like genes are also found in Gram-positive bacteria as well as in certain phages and plasmids, thus suggesting alternative functions. In addition, a SecB-like protein is also present in the major human pathogen Mycobacterium tuberculosis where it specifically controls a stress-responsive toxin–antitoxin system. This review focuses on such very diverse chaperone functions of SecB, both in E. coli and in other unrelated bacteria.
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Affiliation(s)
- Ambre Sala
- Laboratoire de Microbiologie et Génétique Moléculaire, Centre National de la Recherche Scientifique, Université Paul Sabatier, Toulouse, France
| | - Patricia Bordes
- Laboratoire de Microbiologie et Génétique Moléculaire, Centre National de la Recherche Scientifique, Université Paul Sabatier, Toulouse, France
| | - Pierre Genevaux
- Laboratoire de Microbiologie et Génétique Moléculaire, Centre National de la Recherche Scientifique, Université Paul Sabatier, Toulouse, France
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8
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Sakr S, Cirinesi AM, Ullers RS, Schwager F, Georgopoulos C, Genevaux P. Lon protease quality control of presecretory proteins in Escherichia coli and its dependence on the SecB and DnaJ (Hsp40) chaperones. J Biol Chem 2010; 285:23506-14. [PMID: 20504766 DOI: 10.1074/jbc.m110.133058] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Various environmental insults result in irreversible damage to proteins and protein complexes. To cope, cells have evolved dedicated protein quality control mechanisms involving molecular chaperones and proteases. Here, we provide both genetic and biochemical evidence that the Lon protease and the SecB and DnaJ/Hsp40 chaperones are involved in the quality control of presecretory proteins in Escherichia coli. We showed that mutations in the lon gene alleviate the cold-sensitive phenotype of a secB mutant. Such suppression was not observed with either clpP or clpQ protease mutants. In comparison to the respective single mutants, the double secB lon mutant strongly accumulates aggregates of SecB substrates at physiological temperatures, suggesting that the chaperone and the protease share substrates. These observations were extended in vitro by showing that the main substrates identified in secB lon aggregates, namely proOmpF and proOmpC, are highly sensitive to specific degradation by Lon. In contrast, both substrates are significantly protected from Lon degradation by SecB. Interestingly, the chaperone DnaJ by itself protects substrates better from Lon degradation than SecB or the complete DnaK/DnaJ/GrpE chaperone machinery. In agreement with this finding, a DnaJ mutant protein that does not functionally interact in vivo with DnaK efficiently suppresses the SecB cold-sensitive phenotype, highlighting the role of DnaJ in assisting presecretory proteins. Taken together, our data suggest that when the Sec secretion pathway is compromised, a pool of presecretory proteins is transiently maintained in a translocation-competent state and, thus, protected from Lon degradation by either the SecB or DnaJ chaperones.
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Affiliation(s)
- Samer Sakr
- Laboratoire de Microbiologie et Génétique Moléculaire, CNRS and the Université Paul Sabatier, 31062 Toulouse Cedex 9, France
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9
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Abstract
The Rcs phosphorelay, consisting of a hybrid sensor kinase, a phosphotransferase, and a response regulator, regulates a large number of bacterial functions. These include capsule production, the target originally defined for these regulators, a small regulatory RNA, and a growing list of additional genes, many of unknown function. At the core of this phosphorelay is the response regulator RcsB that activates the expression of the target genes. In addition to RcsB, some but not all of these targets require a co-regulator. One such co-regulator is RcsA, which has not been described as working except with RcsB; RcsA is itself regulated at both the transcriptional and post-transcriptional levels. Signaling to the system is also complex, and numerous plasmids, mutations, and environmental conditions have been described as activating this system. Activation of the system on cell surfaces and the nature of some of the regulated functions suggest a role for this phosphorelay in biofilm formation. Here, we describe reporters and mutants that allow the genetic dissection of the system from two directions. In cases where a condition activates the system, for instance, causing an increase in capsule synthesis (a phenotype easily observed in colonies), specific tests can identify at what stage the signal feeds into the system. In cases where a target of the phosphorelay is identified, specific tests can define the genetic requirements for regulation of the target. Finally, in cases where overproduction of capsule interferes with other studies, mutants allow the study of cells in the absence of capsule formation.
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Affiliation(s)
- Nadim Majdalani
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD, USA
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10
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Schmidt O, Schuenemann VJ, Hand NJ, Silhavy TJ, Martin J, Lupas AN, Djuranovic S. prlF and yhaV encode a new toxin-antitoxin system in Escherichia coli. J Mol Biol 2007; 372:894-905. [PMID: 17706670 PMCID: PMC2699681 DOI: 10.1016/j.jmb.2007.07.016] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2007] [Revised: 07/10/2007] [Accepted: 07/12/2007] [Indexed: 10/23/2022]
Abstract
Toxin-antitoxin systems consist of a stable toxin, frequently with endonuclease activity, and a small, labile antitoxin, which sequesters the toxin into an inactive complex. Under unfavorable conditions, the antitoxin is degraded, leading to activation of the toxin and resulting in growth arrest, possibly also in bacterial programmed cell death. Correspondingly, these systems are generally viewed as agents of the stress response in prokaryotes. Here we show that prlF and yhaV encode a novel toxin-antitoxin system in Escherichia coli. YhaV, a ribonuclease of the RelE superfamily, causes reversible bacteriostasis that is counteracted by PrlF, a swapped-hairpin transcription factor homologous to MazE. The two proteins form a tight, hexameric complex, which binds with high specificity to a conserved sequence in the promoter region of the prlF-yhaV operon. As homologs of MazE and RelE, respectively, PrlF and YhaV provide an evolutionary connection between the two best-characterized toxin-antitoxin systems in E. coli, mazEF and relEB.
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Affiliation(s)
- Oliver Schmidt
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Verena J Schuenemann
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Nicholas J Hand
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Thomas J Silhavy
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Jörg Martin
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Andrei N Lupas
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, 72076 Tübingen, Germany.
| | - Sergej Djuranovic
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, 72076 Tübingen, Germany
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11
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Coles M, Djuranovic S, Söding J, Frickey T, Koretke K, Truffault V, Martin J, Lupas AN. AbrB-like Transcription Factors Assume a Swapped Hairpin Fold that Is Evolutionarily Related to Double-Psi β Barrels. Structure 2005; 13:919-28. [PMID: 15939023 DOI: 10.1016/j.str.2005.03.017] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2005] [Revised: 03/29/2005] [Accepted: 03/29/2005] [Indexed: 11/24/2022]
Abstract
AbrB is a key transition-state regulator of Bacillus subtilis. Based on the conservation of a betaalphabeta structural unit, we proposed a beta barrel fold for its DNA binding domain, similar to, but topologically distinct from, double-psi beta barrels. However, the NMR structure revealed a novel fold, the "looped-hinge helix." To understand this discrepancy, we undertook a bioinformatics study of AbrB and its homologs; these form a large superfamily, which includes SpoVT, PrlF, MraZ, addiction module antidotes (PemI, MazE), plasmid maintenance proteins (VagC, VapB), and archaeal PhoU homologs. MazE and MraZ form swapped-hairpin beta barrels. We therefore reexamined the fold of AbrB by NMR spectroscopy and found that it also forms a swapped-hairpin barrel. The conservation of the core betaalphabeta element supports a common evolutionary origin for swapped-hairpin and double-psi barrels, which we group into a higher-order class, the cradle-loop barrels, based on the peculiar shape of their ligand binding site.
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Affiliation(s)
- Murray Coles
- Department of Protein Evolution, Max-Planck-Institute for Developmental Biology, 72076 Tübingen, Germany
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12
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Hand NJ, Silhavy TJ. Null mutations in a Nudix gene, ygdP, implicate an alarmone response in a novel suppression of hybrid jamming. J Bacteriol 2003; 185:6530-9. [PMID: 14594825 PMCID: PMC262091 DOI: 10.1128/jb.185.22.6530-6539.2003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2003] [Accepted: 08/18/2003] [Indexed: 11/20/2022] Open
Abstract
Induction of the toxic LamB-LacZ protein fusion, Hyb42-1, leads to a lethal generalized protein export defect. The prlF1 suppressor causes hyperactivation of the cytoplasmic Lon protease and relieves the inducer sensitivity of Hyb42-1. Since prlF1 does not cause a detectable change in the stability or level of the hybrid protein, we conducted a suppressor screen, seeking factors genetically downstream of lon with prlF1-like phenotypes. Two independent insertions in the ygdP open reading frame relieve the toxicity of the fusion protein and share two additional properties with prlF1: cold sensitivity and the ability to suppress the temperature sensitivity of a degP null mutation. Despite these similarities, ygdP does not appear to act in the same genetic pathway as prlF1 and lon, suggesting a fundamental link between the phenotypes. We speculate that the common properties of the suppressors relate to secretion defects. The ygdP gene (also known as nudH) has been shown to encode a Nudix protein that acts as a dinucleotide oligophosphate (alarmone) hydrolase. Our results suggest that loss of ygdP function leads to the induction of an alarmone-mediated response that affects secretion. Using an epitope-tagged ygdP construct, we present evidence that this response is sensitive to secretion-related stress and is regulated by differential proteolysis of YgdP in a self-limiting manner.
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Affiliation(s)
- Nicholas J Hand
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
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13
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Gibson KE, Silhavy TJ. SprE levels are growth phase regulated in a sigma(S)-dependent manner at the level of translation. J Bacteriol 2000; 182:4117-20. [PMID: 10869095 PMCID: PMC94602 DOI: 10.1128/jb.182.14.4117-4120.2000] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
SprE regulates sigma(S) levels in response to nutrient availability by promoting ClpXP-mediated degradation. Paradoxically, we observe that SprE is similarly regulated, accumulating preferentially upon starvation. This regulation of SprE levels is sigma(S) dependent, altering SprE synthesis at the level of translation. Thus, we demonstrate that SprE and sigma(S) function within a regulatory feedback loop.
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Affiliation(s)
- K E Gibson
- Department of Molecular Biology, Princeton University, NJ 08544, USA
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14
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Golbik R, Lupas AN, Koretke KK, Baumeister W, Peters J. The Janus face of the archaeal Cdc48/p97 homologue VAT: protein folding versus unfolding. Biol Chem 1999; 380:1049-62. [PMID: 10543442 DOI: 10.1515/bc.1999.131] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Members of the AAA family of ATPases have been implicated in chaperone-like activities. We used the archaeal Cdc48/p97 homologue VAT as a model system to investigate the effect of an AAA protein on the folding and unfolding of two well-studied, heterologous substrates, cyclophilin and penicillinase. We found that, depending on the Mg2+ concentration, VAT assumes two states with maximum rates of ATP hydrolysis that differ by an order of magnitude. In the low-activity state, VAT accelerated the refolding of penicillinase, whereas in the high-activity state, it accelerated its unfolding. Both reactions were ATP-dependent. In its interaction with cyclophilin, VAT was ATP-independent and only promoted refolding. The N-terminal domain of VAT, which lacks ATPase activity, also accelerated the refolding of cyclophilin but showed no effect on penicillinase. VAT appears to be structurally equivalent over its entire length to Sec18/NSF, suggesting that these results apply more broadly to group II AAA proteins.
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Affiliation(s)
- R Golbik
- Department of Biochemistry, Martin-Luther-University, Halle-Wittenberg, Halle, Germany
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15
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Abstract
This map is an update of the edition 9 map by Berlyn et al. (M. K. B. Berlyn, K. B. Low, and K. E. Rudd, p. 1715-1902, in F. C. Neidhardt et al., ed., Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). It uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. The latter are included as synonyms. An alphabetical list of genes showing map location, synonyms, the protein or RNA product of the gene, phenotypes of mutants, and reference citations is provided. In addition to genes known to correspond to gene sequences, other genes, often older, that are described by phenotype and older mapping techniques and that have not been correlated with sequences are included.
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Affiliation(s)
- M K Berlyn
- Department of Biology and School of Forestry and Environmental Studies, Yale University, New Haven, Connecticut 06520-8104, USA.
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16
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Cosma CL, Crotwell MD, Burrows SY, Silhavy TJ. Folding-based suppression of extracytoplasmic toxicity conferred by processing-defective LamB. J Bacteriol 1998; 180:3120-30. [PMID: 9620961 PMCID: PMC107812 DOI: 10.1128/jb.180.12.3120-3130.1998] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/1997] [Accepted: 04/14/1998] [Indexed: 02/07/2023] Open
Abstract
We have utilized processing-defective derivatives of the outer membrane maltoporin, LamB, to study protein trafficking functions in the cell envelope of Escherichia coli. Our model proteins contain amino acid substitutions in the consensus site for cleavage by signal peptidase. As a result, the signal sequence is cleaved with reduced efficiency, effectively tethering the precursor protein to the inner membrane. These mutant porins are toxic when secreted to the cell envelope. Furthermore, strains producing these proteins exhibit altered outer membrane permeability, suggesting that the toxicity stems from some perturbation of the cell envelope (J. H. Carlson and T. J. Silhavy, J. Bacteriol. 175:3327-3334, 1993). We have characterized a multicopy suppressor of the processing-defective porins that appears to act by a novel mechanism. Using fractionation experiments and conformation-specific antibodies, we found that the presence of this multicopy suppressor allowed the processing-defective LamB precursors to be folded and localized to the outer membrane. Analysis of the suppressor plasmid revealed that these effects are mediated by the presence of a truncated derivative of the polytopic inner membrane protein, TetA. The suppression mediated by TetA' is independent of the CpxA/CpxR regulon and the sigma E regulon, both of which are involved in regulating protein trafficking functions in the cell envelope.
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Affiliation(s)
- C L Cosma
- Department of Molecular Biology, Princeton University, New Jersey 08544, USA
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17
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Jones CH, Danese PN, Pinkner JS, Silhavy TJ, Hultgren SJ. The chaperone-assisted membrane release and folding pathway is sensed by two signal transduction systems. EMBO J 1997; 16:6394-406. [PMID: 9351822 PMCID: PMC1170246 DOI: 10.1093/emboj/16.21.6394] [Citation(s) in RCA: 205] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The assembly of interactive protein subunits into extracellular structures, such as pilus fibers in the Enterobacteriaceae, is dependent on the activity of PapD-like periplasmic chaperones. The ability of PapD to undergo a beta zippering interaction with the hydrophobic C-terminus of pilus subunits facilitates their folding and release from the cytoplasmic membrane into the periplasm. In the absence of the chaperone, subunits remained tethered to the membrane and were driven off-pathway via non-productive interactions. These off-pathway reactions were detrimental to cell growth; wild-type growth was restored by co-expression of PapD. Subunit misfolding in the absence of PapD was sensed by two parallel pathways: the Cpx two-component signaling system and the sigma E modulatory pathway.
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Affiliation(s)
- C H Jones
- Department of Molecular Microbiology, Washington University Medical School, St Louis, MO 63110, USA
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18
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Goldman BS, Beckman DL, Bali A, Monika EM, Gabbert KK, Kranz RG. Molecular and immunological analysis of an ABC transporter complex required for cytochrome c biogenesis. J Mol Biol 1997; 268:724-38. [PMID: 9175857 DOI: 10.1006/jmbi.1997.0992] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The helABC genes are predicted to encode an ATP-binding cassette (ABC) transporter necessary for heme export for ligation in bacterial cytochrome c biogenesis. The recent discoveries of homologs of the helB and helC genes in plant mitochondrial genomes suggest this is a highly conserved transporter in prokaryotes and some eukaryotes with the HelB and HelC proteins comprising the transmembrane components. Molecular genetic analysis in the Gram-negative bacterium Rhodobacter capsulatus was used to show that the helABC and helDX genes are part of an operon linked to the secDF genes. To facilitate analysis of this transporter, strains with non-polar deletions in each gene, epitope and reporter-tagged HelABCD proteins, and antisera specific to the HelA and HelX proteins were generated. We directly demonstrate that this transporter is present in the cytoplasmic membrane as an HelABCD complex. The HelB and HelC but not HelD proteins are necessary for the binding and stability of the HelA protein, the cytoplasmic subunit containing the ATP-binding region. In addition we show that the HelA protein co-immunoprecipitates with either the HelC or HelD proteins. Thus, the HelABCD heme export complex is distinguished by the presence of four membrane-associated subunits and represents a unique subfamily of ABC transporters.
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Affiliation(s)
- B S Goldman
- Department of Biology, Washington University, St. Louis, MO 63130, USA
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19
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Abstract
Proteolysis in Escherichia coli serves to rid the cell of abnormal and misfolded proteins and to limit the time and amounts of availability of critical regulatory proteins. Most intracellular proteolysis is initiated by energy-dependent proteases, including Lon, ClpXP, and HflB; HflB is the only essential E. coli protease. The ATPase domains of these proteases mediate substrate recognition. Recognition elements in target are not well defined, but are probably not specific amino acid sequences. Naturally unstable protein substrates include the regulatory sigma factors for heat shock and stationary phase gene expression, sigma 32 and RpoS. Other cellular proteins serve as environmental sensors that modulate the availability of the unstable proteins to the proteases, resulting in rapid changes in sigma factor levels and therefore in gene transcription. Many of the specific proteases found in E. coli are well-conserved in both prokaryotes and eukaryotes, and serve critical functions in developmental systems.
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Affiliation(s)
- S Gottesman
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, Maryland 20892-4255, USA.
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20
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Abstract
Progress in our understanding of several biological processes promises to broaden the usefulness of Escherichia coli as a tool for gene expression. There is an expanding choice of tightly regulated prokaryotic promoters suitable for achieving high-level gene expression. New host strains facilitate the formation of disulfide bonds in the reducing environment of the cytoplasm and offer higher protein yields by minimizing proteolytic degradation. Insights into the process of protein translocation across the bacterial membranes may eventually make it possible to achieve robust secretion of specific proteins into the culture medium. Studies involving molecular chaperones have shown that in specific cases, chaperones can be very effective for improved protein folding, solubility, and membrane transport. Negative results derived from such studies are also instructive in formulating different strategies. The remarkable increase in the availability of fusion partners offers a wide range of tools for improved protein folding, solubility, protection from proteases, yield, and secretion into the culture medium, as well as for detection and purification of recombinant proteins. Codon usage is known to present a potential impediment to high-level gene expression in E. coli. Although we still do not understand all the rules governing this phenomenon, it is apparent that "rare" codons, depending on their frequency and context, can have an adverse effect on protein levels. Usually, this problem can be alleviated by modification of the relevant codons or by coexpression of the cognate tRNA genes. Finally, the elucidation of specific determinants of protein degradation, a plethora of protease-deficient host strains, and methods to stabilize proteins afford new strategies to minimize proteolytic susceptibility of recombinant proteins in E. coli.
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Affiliation(s)
- S C Makrides
- Department of Molecular Biology, T Cell Sciences, Inc., Needham, Massachusetts 02194, USA
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21
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Pratt LA, Silhavy TJ. The response regulator SprE controls the stability of RpoS. Proc Natl Acad Sci U S A 1996; 93:2488-92. [PMID: 8637901 PMCID: PMC39824 DOI: 10.1073/pnas.93.6.2488] [Citation(s) in RCA: 187] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
In Escherichia coli, the sigma factor, RpoS, is a central regulator in stationary-phase cells. We have identified a gene, sprE (stationary-phase regulator), as essential for the negative regulation of rpoS expression. SprE negatively regulates the rpoS gene product at the level of protein stability, perhaps in response to nutrient availability. The ability of SprE to destabilize RpoS is dependent on the ClpX/ClpP protease. Based on homology, SprE is a member of the response regulator family of proteins. SprE is the first response regulator identified that is implicated in the control of protein stability. Moreover, SprE is the first reported protein that appears to regulate rpoS in response to a specific environmental parameter.
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Affiliation(s)
- L A Pratt
- Department of Molecular Biology, Princeton University, New Jersey 08544, USA
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22
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Wall JG, Plückthun A. Effects of overexpressing folding modulators on the in vivo folding of heterologous proteins in Escherichia coli. Curr Opin Biotechnol 1995; 6:507-16. [PMID: 7579662 DOI: 10.1016/0958-1669(95)80084-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Interest continues to increase in the use of folding modulators to overcome problems with heterologous protein folding in Escherichia coli. Currently, this approach, though highly successful with a number of individual proteins, remains a somewhat hit-and-miss affair. Ongoing research directed at unraveling the precise role and specificity of these folding modulators should generate a clearer understanding of the potential and limitations of overexpressing folding catalysts in vivo. This will facilitate the development, in the not too distant future, of a more structured and rational approach to improving the folding of heterologous gene products in E. coli.
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Affiliation(s)
- J G Wall
- University of Zürich, Switzerland
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23
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Snyder WB, Silhavy TJ. Beta-galactosidase is inactivated by intermolecular disulfide bonds and is toxic when secreted to the periplasm of Escherichia coli. J Bacteriol 1995; 177:953-63. [PMID: 7860606 PMCID: PMC176689 DOI: 10.1128/jb.177.4.953-963.1995] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The wild-type LamB-LacZ hybrid protein inhibits the export machinery upon induction when assayed by biochemical and genetic techniques, a phenotype referred to as hybrid protein jamming. This hybrid protein also renders cells sensitive to growth in the presence of the inducer maltose, presumably because of the jamming. We constructed a new version of this fusion by adding alkaline phosphatase, encoded by phoA, to the C terminus of the LamB-LacZ hybrid protein. This tripartite protein, LamB-LacZ-PhoA, is as toxic to cells as the hybrid LamB-LacZ; however, it does not jam at temperatures greater than 33 degrees C. Extreme C-terminal sequences of LacZ function as a critical folding domain and are therefore responsible for stabilizing the LacZ structure. To determine if this region of LacZ is important for jamming, we recombined a late nonsense mutation (X90) onto the hybrid construct. We found the toxicity of this new hybrid, LamB-LacZX90, to be nearly identical to that of the full-length protein, but it also does not jam the secretion machinery. This suggests that jamming is caused by LacZ folding. We found no inhibition of secretion in the tripartite and X90 fusion strains at 37 degrees C, suggesting that the toxicity of the new fusions is novel. Under these conditions, the tripartite and X90 fusion proteins form disulfide-bonded aggregates with high molecular weights in the periplasm. Accordingly, we believe that LacZ disrupts some essential function(s) in the periplasm.
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Affiliation(s)
- W B Snyder
- Department of Molecular Biology, Princeton University, New Jersey 08544
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Flower AM, Doebele RC, Silhavy TJ. PrlA and PrlG suppressors reduce the requirement for signal sequence recognition. J Bacteriol 1994; 176:5607-14. [PMID: 8083155 PMCID: PMC196762 DOI: 10.1128/jb.176.18.5607-5614.1994] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Selection for suppressors of defects in the signal sequence of secretory proteins has led most commonly to identification of prlA alleles and less often to identification of prlG alleles. These genes, secY/prlA and secE/prlG, encode integral membrane components of the protein translocation system of Escherichia coli. We demonstrate that an outer membrane protein, LamB, that lacks a signal sequence can be exported with reasonable efficiency in both prlA and prlG suppressor strains. Although the signal sequence is not absolutely required for export of LamB, the level of export in the absence of prl suppressor alleles is exceedingly low. Such strains are phenotypically LamB-, and functional LamB can be detected only by using sensitive infectious-center assays. Suppression of the LamB signal sequence deletion is dependent on normal components of the export pathway, indicating that suppression is not occurring through a bypass mechanism. Our results indicate that the majority of the known prlA suppressors function by an identical mechanism and, further, that the prlG suppressors work in a similar fashion. We propose that both PrlA and PrlG suppressors lack a proofreading activity that normally rejects defective precursors from the export pathway.
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Affiliation(s)
- A M Flower
- Department of Molecular Biology, Princeton University, New Jersey 08544
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25
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Jacq A, Holland B. The components of the Escherichia coli protein-transport apparatus. Curr Opin Struct Biol 1993. [DOI: 10.1016/0959-440x(93)90080-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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