1
|
Li D, Cai Y, Guo J, Liu Y, Lu F, Li Q, Liu Y, Li Y. Screening signal peptidase based on split-GFP assembly technology to promote the secretion of alkaline protease AprE in Bacillus amyloliquefaciens. Int J Biol Macromol 2024; 269:132166. [PMID: 38723822 DOI: 10.1016/j.ijbiomac.2024.132166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 04/04/2024] [Accepted: 05/05/2024] [Indexed: 05/13/2024]
Abstract
Improving the ability of bacteria to secrete protein is essential for large-scale production of food enzymes. However, due to the lack of effective tracking technology for target proteins, the optimization of the secretory system is facing many problems. In this study, we utilized the split-GFP system to achieve self-assembly into mature GFP in Bacillus amyloliquefaciens and successfully tracked the alkaline protease AprE. The split-GFP system was employed to assess the signal peptidases, a crucial component in the secretory system, and signal peptidase sipA was identified as playing a role in the secretion of AprE. Deletion of sipA resulted in a higher accumulation of the precursor protein of AprE compared to other signal peptidase deletion strains. To explore the mechanism of signal peptidase on signal peptide, molecular docking and calculation of free energy were performed. The action strength of the signal peptidase is determined by its binding affinity with the tripeptides at the C-terminal of the signal peptide. The functions of signal peptides YdbK and NucB rely on sipA, and overexpression of sipA by integrating it into genome of B. amyloliquefaciens increased the activity of extracellular AprE by 19.9 %. These findings provide insights into enhancing the secretion efficiency of chassis strains.
Collapse
Affiliation(s)
- Dengke Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Yian Cai
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Jiejie Guo
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China
| | - Yihan Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Qinggang Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Yexue Liu
- Key Laboratory of Food Nutrition and Safety, Ministry of Education, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| | - Yu Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, PR China.
| |
Collapse
|
2
|
Schäfer AB, Steenhuis M, Jim KK, Neef J, O’Keefe S, Whitehead RC, Swanton E, Wang B, Halbedel S, High S, van Dijl JM, Luirink J, Wenzel M. Dual Action of Eeyarestatin 24 on Sec-Dependent Protein Secretion and Bacterial DNA. ACS Infect Dis 2023; 9:253-269. [PMID: 36637435 PMCID: PMC9926488 DOI: 10.1021/acsinfecdis.2c00404] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Eeyarestatin 24 (ES24) is a promising new antibiotic with broad-spectrum activity. It shares structural similarity with nitrofurantoin (NFT), yet appears to have a distinct and novel mechanism: ES24 was found to inhibit SecYEG-mediated protein transport and membrane insertion in Gram-negative bacteria. However, possible additional targets have not yet been explored. Moreover, its activity was notably better against Gram-positive bacteria, for which its mechanism of action had not yet been investigated. We have used transcriptomic stress response profiling, phenotypic assays, and protein secretion analyses to investigate the mode of action of ES24 in comparison with NFT using the Gram-positive model bacterium Bacillus subtilis and have compared our findings to Gram-negative Escherichia coli. Here, we show the inhibition of Sec-dependent protein secretion in B. subtilis and additionally provide evidence for DNA damage, probably caused by the generation of reactive derivatives of ES24. Interestingly, ES24 caused a gradual dissipation of the membrane potential, which led to delocalization of cytokinetic proteins and subsequent cell elongation in E. coli. However, none of those effects were observed in B. subtilis, thereby suggesting that ES24 displays distinct mechanistic differences with respect to Gram-positive and Gram-negative bacteria. Despite its structural similarity to NFT, ES24 profoundly differed in our phenotypic analysis, which implies that it does not share the NFT mechanism of generalized macromolecule and structural damage. Importantly, ES24 outperformed NFT in vivo in a zebrafish embryo pneumococcal infection model. Our results suggest that ES24 not only inhibits the Sec translocon, but also targets bacterial DNA and, in Gram-negative bacteria, the cell membrane.
Collapse
Affiliation(s)
- Ann-Britt Schäfer
- Division
of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Maurice Steenhuis
- Molecular
Microbiology, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Kin Ki Jim
- Department
of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers - Location Vrije Universiteit
Amsterdam, 1081 HZ Amsterdam, The Netherlands,Amsterdam
Institute for Infection and Immunity, Amsterdam
University Medical Centers, 1081 HZ Amsterdam, The Netherlands
| | - Jolanda Neef
- Department
of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, PO Box 30001, 9700 RB Groningen, The Netherlands
| | - Sarah O’Keefe
- School
of
Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Roger C. Whitehead
- School
of Chemistry, Faculty of Science and Engineering, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Eileithyia Swanton
- School
of
Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Biwen Wang
- Bacterial
Cell Biology and Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Sven Halbedel
- FG11
Division of Enteropathogenic Bacteria and Legionella, Robert Koch Institute, 38855 Wernigerode, Germany,Institute
for Medical Microbiology and Hospital Hygiene, Otto von Guericke University Magdeburg, 39120 Magdeburg, Germany
| | - Stephen High
- School
of
Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Jan Maarten van Dijl
- Department
of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, PO Box 30001, 9700 RB Groningen, The Netherlands
| | - Joen Luirink
- Molecular
Microbiology, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands,
| | - Michaela Wenzel
- Division
of Chemical Biology, Department of Life Sciences, Chalmers University of Technology, 412 96 Gothenburg, Sweden,
| |
Collapse
|
3
|
Naka S, Matsuoka D, Goto K, Misaki T, Nagasawa Y, Ito S, Nomura R, Nakano K, Matsumoto-Nakano M. Cnm of Streptococcus mutans is important for cell surface structure and membrane permeability. Front Cell Infect Microbiol 2022; 12:994014. [PMID: 36176579 PMCID: PMC9513430 DOI: 10.3389/fcimb.2022.994014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/18/2022] [Indexed: 11/18/2022] Open
Abstract
Streptococcus mutans, a Gram-positive facultative anaerobic bacterium, is a major pathogen of dental caries. The protein Cnm of S. mutans is involved in collagen binding, but its other biological functions are unknown. In this study, a Cnm-deficient isogenic mutant and a complementation strain were generated from a Cnm-positive S. mutans strain to help determine the properties of Cnm. Initially, comparison of the cell surface structure was performed by electron microscopy, which demonstrated that Cnm appears to be localized on the cell surface and associated with a protruding cell surface structure. Deep RNA sequencing of the strains revealed that the defect in Cnm caused upregulated expression of many genes related to ABC transporters and cell-surface proteins, while a few genes were downregulated. The amount of biofilm formed by the Cnm-defective strain increased compared with the parental and complemented strains, but the biofilm structure was thinner because of elevated expression of genes encoding glucan synthesis enzymes, leading to increased production of extracellular polysaccharides. Particular antibiotics, including bacitracin and chloramphenicol, had a lower minimum inhibitory concentration for the Cnm-defective strain than particular antibiotics, including bacitracin and chloramphenicol, compared with the parental and complemented strains. Our results suggest that S. mutans Cnm is located on the cell surface, gives rise to the observed protruding cell surface, and is associated with several biological properties related to membrane permeability.
Collapse
Affiliation(s)
- Shuhei Naka
- Department of Pediatric Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Daiki Matsuoka
- Department of Pediatric Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Kana Goto
- Department of Pediatric Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Taro Misaki
- Division of Nephrology, Seirei Hamamatsu General Hospital, Hamamatsu, Japan
- Department of Nursing, Faculty of Nursing, Seirei Christopher University, Hamamatsu, Japan
| | - Yasuyuki Nagasawa
- Department of General Internal Medicine, Hyogo College of Medicine, Nishinomiya, Japan
| | - Seigo Ito
- Department of Internal Medicine, Japan Self-Defense Iruma Hospital, Iruma, Japan
| | - Ryota Nomura
- Department of Pediatric Dentistry, Division of Oral infection and Disease Control, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Kazuhiko Nakano
- Department of Pediatric Dentistry, Division of Oral infection and Disease Control, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Michiyo Matsumoto-Nakano
- Department of Pediatric Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
- *Correspondence: Michiyo Matsumoto-Nakano,
| |
Collapse
|
4
|
Liu S, Xu JZ, Zhang WG. Advances and prospects in metabolic engineering of Escherichia coli for L-tryptophan production. World J Microbiol Biotechnol 2022; 38:22. [PMID: 34989926 DOI: 10.1007/s11274-021-03212-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/15/2021] [Indexed: 10/19/2022]
Abstract
As an important raw material for pharmaceutical, food and feed industry, highly efficient production of L-tryptophan by Escherichia coli has attracted a considerable attention. However, there are complicated and multiple layers of regulation networks in L-tryptophan biosynthetic pathway and thus have difficulty to rewrite the biosynthetic pathway for producing L-tryptophan with high efficiency in E. coli. This review summarizes the biosynthetic pathway of L-tryptophan and highlights the main regulatory mechanisms in E. coli. In addition, we discussed the latest metabolic engineering strategies achieved in E. coli to reconstruct the L-tryptophan biosynthetic pathway. Moreover, we also review a few strategies that can be used in E. coli to improve robustness and streamline of L-tryptophan high-producing strains. Lastly, we also propose the potential strategies to further increase L-tryptophan production by systematic metabolic engineering and synthetic biology techniques.
Collapse
Affiliation(s)
- Shuai Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi, 214122, People's Republic of China
| | - Jian-Zhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi, 214122, People's Republic of China.
| | - Wei-Guo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi, 214122, People's Republic of China.
| |
Collapse
|
5
|
Recombinant protein secretion by Bacillus subtilis and Lactococcus lactis: pathways, applications, and innovation potential. Essays Biochem 2021; 65:187-195. [PMID: 33955475 PMCID: PMC8314018 DOI: 10.1042/ebc20200171] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 01/01/2023]
Abstract
Secreted recombinant proteins are of great significance for industry, healthcare and a sustainable bio-based economy. Consequently, there is an ever-increasing need for efficient production platforms to deliver such proteins in high amounts and high quality. Gram-positive bacteria, particularly bacilli such as Bacillus subtilis, are favored for the production of secreted industrial enzymes. Nevertheless, recombinant protein production in the B. subtilis cell factory can be very challenging due to bottlenecks in the general (Sec) secretion pathway as well as this bacterium’s intrinsic capability to secrete a cocktail of highly potent proteases. This has placed another Gram-positive bacterium, Lactococcus lactis, in the focus of attention as an alternative, non-proteolytic, cell factory for secreted proteins. Here we review our current understanding of the secretion pathways exploited in B. subtilis and L. lactis to deliver proteins from their site of synthesis, the cytoplasm, into the fermentation broth. An advantage of this cell factory comparison is that it identifies opportunities for protein secretion pathway engineering to remove or bypass current production bottlenecks. Noteworthy new developments in cell factory engineering are the mini-Bacillus concept, highlighting potential advantages of massive genome minimization, and the application of thus far untapped ‘non-classical’ protein secretion routes. Altogether, it is foreseen that engineered lactococci will find future applications in the production of high-quality proteins at the relatively small pilot scale, while engineered bacilli will remain a favored choice for protein production in bulk.
Collapse
|
6
|
Questing functions and structures of hypothetical proteins from Campylobacter jejuni: a computer-aided approach. Biosci Rep 2021; 40:225019. [PMID: 32458979 PMCID: PMC7284324 DOI: 10.1042/bsr20193939] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 05/17/2020] [Accepted: 05/26/2020] [Indexed: 12/12/2022] Open
Abstract
Campylobacter jejuni (C. jejuni) is considered to be one of the most frequent causes of bacterial gastroenteritis globally, especially in young children. The genome of C. jejuni contains many proteins with unknown functions termed as hypothetical proteins (HPs). These proteins might have essential biological role to show the full spectrum of this bacterium. Hence, our study aimed to determine the functions of HPs, pertaining to the genome of C. jejuni. An in-silico work flow integrating various tools were performed for functional assignment, three-dimensional structure determination, domain architecture predictors, subcellular localization, physicochemical characterization, and protein-protein interactions (PPIs). Sequences of 267 HPs of C. jejuni were analyzed and successfully attributed the function of 49 HPs with higher confidence. Here, we found proteins with enzymatic activity, transporters, binding and regulatory proteins as well as proteins with biotechnological interest. Assessment of the performance of various tools used in this analysis revealed an accuracy of 95% using receiver operating characteristic (ROC) curve analysis. Functional and structural predictions and the results from ROC analyses provided the validity of in-silico tools used in the present study. The approach used for this analysis leads us to assign the function of unknown proteins and relate them with the functions that have already been described in previous literature.
Collapse
|
7
|
Prajapati B, Bernal-Cabas M, López-Álvarez M, Schaffer M, Bartel J, Rath H, Steil L, Becher D, Völker U, Mäder U, van Dijl JM. Double trouble: Bacillus depends on a functional Tat machinery to avoid severe oxidative stress and starvation upon entry into a NaCl-depleted environment. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118914. [PMID: 33245978 DOI: 10.1016/j.bbamcr.2020.118914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 11/08/2020] [Accepted: 11/20/2020] [Indexed: 11/17/2022]
Abstract
The widely conserved twin-arginine translocases (Tat) allow the transport of fully folded cofactor-containing proteins across biological membranes. In doing so, these translocases serve different biological functions ranging from energy conversion to cell division. In the Gram-positive soil bacterium Bacillus subtilis, the Tat machinery is essential for effective growth in media lacking iron or NaCl. It was previously shown that this phenomenon relates to the Tat-dependent export of the heme-containing peroxidase EfeB, which converts Fe2+ to Fe3+ at the expense of hydrogen peroxide. However, the reasons why the majority of tat mutant bacteria perish upon dilution in NaCl-deprived medium and how, after several hours, a sub-population adapts to this condition was unknown. Here we show that, upon growth in the absence of NaCl, the bacteria face two major problems, namely severe oxidative stress at the membrane and starvation leading to death. The tat mutant cells can overcome these challenges if they are fed with arginine, which implies that severe arginine depletion is a major cause of death and resumed arginine synthesis permits their survival. Altogether, our findings show that the Tat system of B. subtilis is needed to preclude severe oxidative stress and starvation upon sudden drops in the environmental Na+ concentration as caused by flooding or rain.
Collapse
Affiliation(s)
- Bimal Prajapati
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands
| | - Margarita Bernal-Cabas
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands
| | - Marina López-Álvarez
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands
| | - Marc Schaffer
- University Medicine Greifswald, Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, Greifswald, Germany
| | - Jürgen Bartel
- University of Greifswald, Institute of Microbiology, Department of Microbial Proteomics, Greifswald, Germany
| | - Hermann Rath
- University Medicine Greifswald, Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, Greifswald, Germany
| | - Leif Steil
- University Medicine Greifswald, Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, Greifswald, Germany
| | - Dörte Becher
- University of Greifswald, Institute of Microbiology, Department of Microbial Proteomics, Greifswald, Germany
| | - Uwe Völker
- University Medicine Greifswald, Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, Greifswald, Germany
| | - Ulrike Mäder
- University Medicine Greifswald, Interfaculty Institute of Genetics and Functional Genomics, Department of Functional Genomics, Greifswald, Germany.
| | - Jan Maarten van Dijl
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology, Groningen, the Netherlands.
| |
Collapse
|
8
|
Steinberg R, Knüpffer L, Origi A, Asti R, Koch HG. Co-translational protein targeting in bacteria. FEMS Microbiol Lett 2019; 365:4966980. [PMID: 29790984 DOI: 10.1093/femsle/fny095] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/09/2018] [Indexed: 01/16/2023] Open
Abstract
About 30% of all bacterial proteins execute their function outside of the cytosol and have to be transported into or across the cytoplasmic membrane. Bacteria use multiple protein transport systems in parallel, but the majority of proteins engage two distinct targeting systems. One is the co-translational targeting by two universally conserved GTPases, the signal recognition particle (SRP) and its receptor FtsY, which deliver inner membrane proteins to either the SecYEG translocon or the YidC insertase for membrane insertion. The other targeting system depends on the ATPase SecA, which targets secretory proteins, i.e. periplasmic and outer membrane proteins, to SecYEG for their subsequent ATP-dependent translocation. While SRP selects its substrates already very early during their synthesis, the recognition of secretory proteins by SecA is believed to occur primarily after translation termination, i.e. post-translationally. In this review we highlight recent progress on how SRP recognizes its substrates at the ribosome and how the fidelity of the targeting reaction to SecYEG is maintained. We furthermore discuss similarities and differences in the SRP-dependent targeting to either SecYEG or YidC and summarize recent results that suggest that some membrane proteins are co-translationally targeted by SecA.
Collapse
Affiliation(s)
- Ruth Steinberg
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany
| | - Lara Knüpffer
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany
| | - Andrea Origi
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany.,Faculty of Biology, Albert-Ludwigs-University Freiburg, Schänzlestr. 1, Freiburg D-79104, Germany
| | - Rossella Asti
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs University Freiburg, Stefan Meier Str. 17, Freiburg D-79104, Germany
| |
Collapse
|
9
|
Bates A, Power CA. David vs. Goliath: The Structure, Function, and Clinical Prospects of Antibody Fragments. Antibodies (Basel) 2019; 8:E28. [PMID: 31544834 PMCID: PMC6640713 DOI: 10.3390/antib8020028] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/12/2019] [Accepted: 04/02/2019] [Indexed: 02/07/2023] Open
Abstract
Since the licensing of the first monoclonal antibody therapy in 1986, monoclonal antibodies have become the largest class of biopharmaceuticals with over 80 antibodies currently approved for a variety of disease indications. The development of smaller, antigen binding antibody fragments, derived from conventional antibodies or produced recombinantly, has been growing at a fast pace. Antibody fragments can be used on their own or linked to other molecules to generate numerous possibilities for bispecific, multi-specific, multimeric, or multifunctional molecules, and to achieve a variety of biological effects. They offer several advantages over full-length monoclonal antibodies, particularly a lower cost of goods, and because of their small size they can penetrate tissues, access challenging epitopes, and have potentially reduced immunogenicity. In this review, we will discuss the structure, production, and mechanism of action of EMA/FDA-approved fragments and of those in clinical and pre-clinical development. We will also discuss current topics of interest surrounding the potential use of antibody fragments for intracellular targeting and blood-brain barrier (BBB) penetration.
Collapse
Affiliation(s)
- Adam Bates
- Biopharm Molecular Discovery, GlaxoSmithKline, Hertfordshire SG1 2NY, UK.
| | - Christine A Power
- Biopharm Molecular Discovery, GlaxoSmithKline, Hertfordshire SG1 2NY, UK.
| |
Collapse
|
10
|
Streptococcus mutans yidC1
and
yidC2
Impact Cell Envelope Biogenesis, the Biofilm Matrix, and Biofilm Biophysical Properties. J Bacteriol 2019; 201:JB.00396-18. [DOI: 10.1128/jb.00396-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/28/2018] [Indexed: 01/25/2023] Open
Abstract
YidC proteins are membrane-localized chaperone insertases that are universally conserved in all bacteria and are traditionally studied in the context of membrane protein insertion and assembly. Both YidC paralogs of the cariogenic pathogen
Streptococcus mutans
are required for proper envelope biogenesis and full virulence, indicating that these proteins may also contribute to optimal biofilm formation in streptococci. Here, we show that the deletion of either
yidC
results in changes to the structure and physical properties of the EPS matrix produced by
S. mutans
, ultimately impairing optimal biofilm development, diminishing its mechanical stability, and facilitating its removal. Importantly, the universal conservation of bacterial
yidC
orthologs, combined with our findings, provide a rationale for YidC as a possible drug target for antibiofilm therapies.
Collapse
|
11
|
Pohlschroder M, Pfeiffer F, Schulze S, Abdul Halim MF. Archaeal cell surface biogenesis. FEMS Microbiol Rev 2018; 42:694-717. [PMID: 29912330 PMCID: PMC6098224 DOI: 10.1093/femsre/fuy027] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/12/2018] [Indexed: 12/13/2022] Open
Abstract
Cell surfaces are critical for diverse functions across all domains of life, from cell-cell communication and nutrient uptake to cell stability and surface attachment. While certain aspects of the mechanisms supporting the biosynthesis of the archaeal cell surface are unique, likely due to important differences in cell surface compositions between domains, others are shared with bacteria or eukaryotes or both. Based on recent studies completed on a phylogenetically diverse array of archaea, from a wide variety of habitats, here we discuss advances in the characterization of mechanisms underpinning archaeal cell surface biogenesis. These include those facilitating co- and post-translational protein targeting to the cell surface, transport into and across the archaeal lipid membrane, and protein anchoring strategies. We also discuss, in some detail, the assembly of specific cell surface structures, such as the archaeal S-layer and the type IV pili. We will highlight the importance of post-translational protein modifications, such as lipid attachment and glycosylation, in the biosynthesis as well as the regulation of the functions of these cell surface structures and present the differences and similarities in the biogenesis of type IV pili across prokaryotic domains.
Collapse
Affiliation(s)
| | - Friedhelm Pfeiffer
- Computational Biology Group, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Stefan Schulze
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | |
Collapse
|
12
|
Schultz LG, Tasic L, Fattori J. Chaperone-Assisted Secretion in Bacteria: Protein and DNA Transport via Cell Membranes. CURR PROTEOMICS 2018. [DOI: 10.2174/1570164615666180820154821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Bacteria use an impressive arsenal of secretion systems (1-7) to infect their host cells by exporting
proteins, DNA and DNA-protein complexes via cell membranes. They use chaperone-usher
pathways for host colonization as well. To be targeted for transportation across one (Gram-positive) or
two membranes (Gram-negative), clients must be selected, guided and unfolded to pass through type 3
(T3SS) or type 4 (T4SS) secretion systems. For these processes, bacteria count on secretory chaperones
that guide macromolecular transport via membranes. Moreover, if we know how these processes
occur, we might be able to stop them and avoid bacterial infections. Thus, structural and functional
characterizations of secretory chaperones become interesting, as these proteins are the perfect targets
for blocking bacteria action. Therefore, this review focuses on a story of known mechanisms of chaperone-
secretion assisted transport with special attention on virulence proteins and DNA transport in
bacteria.
Collapse
Affiliation(s)
- Lilian Goulart Schultz
- Chemical Biology Laboratory, Organic Chemistry Department, Institute of Chemistry, University of Campinas, P.O. Box 6154, Campinas, 13083-970, SP, Brazil
| | - Ljubica Tasic
- Chemical Biology Laboratory, Organic Chemistry Department, Institute of Chemistry, University of Campinas, P.O. Box 6154, Campinas, 13083-970, SP, Brazil
| | - Juliana Fattori
- Chemical Biology Laboratory, Organic Chemistry Department, Institute of Chemistry, University of Campinas, P.O. Box 6154, Campinas, 13083-970, SP, Brazil
| |
Collapse
|
13
|
A comprehensive review of signal peptides: Structure, roles, and applications. Eur J Cell Biol 2018; 97:422-441. [DOI: 10.1016/j.ejcb.2018.06.003] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 06/18/2018] [Accepted: 06/18/2018] [Indexed: 01/06/2023] Open
|
14
|
Neef J, Bongiorni C, Goosens VJ, Schmidt B, van Dijl JM. Intramembrane protease RasP boosts protein production in Bacillus. Microb Cell Fact 2017; 16:57. [PMID: 28376795 PMCID: PMC5381017 DOI: 10.1186/s12934-017-0673-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 03/31/2017] [Indexed: 11/10/2022] Open
Abstract
Background The microbial cell factory Bacillus subtilis is a popular industrial platform for high-level production of secreted technical enzymes. Nonetheless, the effective secretion of particular heterologous enzymes remains challenging. Over the past decades various studies have tackled this problem, and major improvements were achieved by optimizing signal peptides or removing proteases involved in product degradation. On the other hand, serious bottlenecks in the protein export process per se remained enigmatic, especially for protein secretion at commercially significant levels by cells grown to high density. The aim of our present study was to assess the relevance of the intramembrane protease RasP for high-level protein production in B. subtilis. Results Deletion of the rasP gene resulted in reduced precursor processing and extracellular levels of the overproduced α-amylases AmyE from B. subtilis and AmyL from Bacillus licheniformis. Further, secretion of the overproduced serine protease BPN’ from Bacillus amyloliquefaciens was severely impaired in the absence of RasP. Importantly, overexpression of rasP resulted in threefold increased production of a serine protease from Bacillus clausii, and 2.5- to 10-fold increased production of an AmyAc α-amylase from Paenibacillus curdlanolyticus, depending on the culture conditions. Of note, growth defects due to overproduction of the two latter enzymes were suppressed by rasP-overexpression. Conclusion Here we show that an intramembrane protease, RasP, sets a limit to high-level production of two secreted heterologous enzymes that are difficult to produce in the B. subtilis cell factory. This finding was unexpected and suggests that proteolytic membrane sanitation is key to effective enzyme production in Bacillus.
Collapse
Affiliation(s)
- Jolanda Neef
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands
| | - Cristina Bongiorni
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA, 94304, USA
| | - Vivianne J Goosens
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands.,Department of Bioengineering, Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
| | - Brian Schmidt
- DuPont Industrial Biosciences, 925 Page Mill Road, Palo Alto, CA, 94304, USA
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P.O. Box 30001, 9700 RB, Groningen, The Netherlands.
| |
Collapse
|
15
|
Abstract
The insertion and assembly of proteins into the inner membrane of bacteria are crucial for many cellular processes, including cellular respiration, signal transduction, and ion and pH homeostasis. This process requires efficient membrane targeting and insertion of proteins into the lipid bilayer in their correct orientation and proper conformation. Playing center stage in these events are the targeting components, signal recognition particle (SRP) and the SRP receptor FtsY, as well as the insertion components, the Sec translocon and the YidC insertase. Here, we will discuss new insights provided from the recent high-resolution structures of these proteins. In addition, we will review the mechanism by which a variety of proteins with different topologies are inserted into the inner membrane of Gram-negative bacteria. Finally, we report on the energetics of this process and provide information on how membrane insertion occurs in Gram-positive bacteria and Archaea. It should be noted that most of what we know about membrane protein assembly in bacteria is based on studies conducted in Escherichia coli.
Collapse
Affiliation(s)
- Andreas Kuhn
- Institute for Microbiology and Molecular Biology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Hans-Georg Koch
- Institute for Biochemistry and Molecular Biology, Faculty of Medicine, Albert-Ludwigs-University of Freiburg, 79104, Freiburg, Germany
| | - Ross E Dalbey
- Department of Chemistry, The Ohio State University, Columbus, OH 43210
| |
Collapse
|
16
|
Ji S, Li W, Baloch AR, Wang M, Li H, Cao B, Zhang H. Efficient biosynthesis of a Cecropin A-melittin mutant in Bacillus subtilis WB700. Sci Rep 2017; 7:40587. [PMID: 28071737 PMCID: PMC5223193 DOI: 10.1038/srep40587] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 12/09/2016] [Indexed: 11/09/2022] Open
Abstract
The efficient production of antimicrobial peptides (AMPs) for clinical applications has attracted the attention of the scientific community. To develop a novel microbial cell factory for the efficient biosynthesis of a cecropin A-melittin mutant (CAM-W), a recombinant Bacillus subtilis WB700 expression system was genetically modified with a novel vector, including a fusion gene encoding CAM-W, the autoprotease EDDIE and the signal peptide SacB under the control of the maltose-inducible promoter Pglv. A total of 159 mg of CAM-W was obtained from 1 L of fermentation supernatant. The purified CAM-W showed a consistent size with the expected molecular weight of 3.2 kDa. Our findings suggest that this novel expression system can be used as a powerful tool for the efficient production of CAM-W.
Collapse
Affiliation(s)
- Shengyue Ji
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100094, China.,College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Weili Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100094, China.,College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Abdul Rasheed Baloch
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Meng Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hengxin Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100094, China
| | - Binyun Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hongfu Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100094, China
| |
Collapse
|
17
|
Chen M, Zhao Z, Yang J, Peng K, Baker MAB, Bai F, Lo CJ. Length-dependent flagellar growth of Vibrio alginolyticus revealed by real time fluorescent imaging. eLife 2017; 6:e22140. [PMID: 28098557 PMCID: PMC5300704 DOI: 10.7554/elife.22140] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 01/15/2017] [Indexed: 01/27/2023] Open
Abstract
Bacterial flagella are extracellular filaments that drive swimming in bacteria. During motor assembly, flagellins are transported unfolded through the central channel in the flagellum to the growing tip. Here, we applied in vivo fluorescent imaging to monitor in real time the Vibrio alginolyticus polar flagella growth. The flagellar growth rate is found to be highly length-dependent. Initially, the flagellum grows at a constant rate (50 nm/min) when shorter than 1500 nm. The growth rate decays sharply when the flagellum grows longer, which decreases to ~9 nm/min at 7500 nm. We modeled flagellin transport inside the channel as a one-dimensional diffusive process with an injection force at its base. When the flagellum is short, its growth rate is determined by the loading speed at the base. Only when the flagellum grows longer does diffusion of flagellin become the rate-limiting step, dramatically reducing the growth rate. Our results shed new light on the dynamic building process of this complex extracellular structure.
Collapse
Affiliation(s)
- Meiting Chen
- Department of Physics and Graduate Institute of Biophysics, National Central University, Jhongli, Taiwan
| | - Ziyi Zhao
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Jin Yang
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Kai Peng
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China
| | - Matthew AB Baker
- EMBL Australia Node for Single Molecule Science, University of New South Wales, Sydney, Australia
| | - Fan Bai
- Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, Peking University, Beijing, China, (FB)
| | - Chien-Jung Lo
- Department of Physics and Graduate Institute of Biophysics, National Central University, Jhongli, Taiwan, (C-JL)
| |
Collapse
|
18
|
Hohmann HP, van Dijl JM, Krishnappa L, Prágai Z. Host Organisms:Bacillus subtilis. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Hans-Peter Hohmann
- Nutrition Innovation Center R&D Biotechnology; DSM Nutritional Products Ltd; Wurmisweg 576 CH-4303 Kaiseraugst Switzerland
| | - Jan M. van Dijl
- University of Groningen, University Medical Center Groningen; Department of Medical Microbiology; Hanzeplein 1 9700 RB Groningen The Netherlands
| | - Laxmi Krishnappa
- University of Groningen, University Medical Center Groningen; Department of Medical Microbiology; Hanzeplein 1 9700 RB Groningen The Netherlands
| | - Zoltán Prágai
- Nutrition Innovation Center R&D Biotechnology; DSM Nutritional Products Ltd; Wurmisweg 576 CH-4303 Kaiseraugst Switzerland
| |
Collapse
|
19
|
Pechsrichuang P, Songsiriritthigul C, Haltrich D, Roytrakul S, Namvijtr P, Bonaparte N, Yamabhai M. OmpA signal peptide leads to heterogenous secretion of B. subtilis chitosanase enzyme from E. coli expression system. SPRINGERPLUS 2016; 5:1200. [PMID: 27516938 PMCID: PMC4963352 DOI: 10.1186/s40064-016-2893-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 07/21/2016] [Indexed: 01/24/2023]
Abstract
The production of secreted recombinant proteins from E. coli is pivotal to the biotechnological industry because it reduces the cost of downstream processing. Proteins destined for secretion contain an N-terminal signal peptide that is cleaved by secretion machinery in the plasma membrane. The resulting protein is released in an active mature form. In this study, Bacillus subtilis chitosanase (Csn) was used as a model protein to compare the effect of two signal peptides on the secretion of heterologous recombinant protein. The results showed that the E. coli secretion machinery could recognize both native bacillus and E. coli signal peptides. However, only the native bacillus signal peptide could generate the same N-terminal sequence as in the wild type bacteria. When the recombinant Csn constructs contained the E. coli OmpA signal peptide, the secreted enzymes were heterogeneous, comprising a mixed population of secreted enzymes with different N-terminal sequences. Nevertheless, the E. coli OmpA signal peptide was found to be more efficient for high expression and secretion of bacillus Csn. These findings may be used to help engineer other recombinant proteins for secretory production in E. coli.
Collapse
Affiliation(s)
- Phornsiri Pechsrichuang
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology (SUT), 111 University Avenue, Meung District, Nakhon Ratchasima, 30000 Thailand
| | | | - Dietmar Haltrich
- Food Biotechnology Laboratory, BOKU - University of National Resources and Life Sciences, Vienna, Austria
| | - Sittiruk Roytrakul
- Genome Institute, National Center for Genetic Engineering and Biotechnology, Pathumthani, Thailand
| | - Peenida Namvijtr
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology (SUT), 111 University Avenue, Meung District, Nakhon Ratchasima, 30000 Thailand
| | - Napolean Bonaparte
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology (SUT), 111 University Avenue, Meung District, Nakhon Ratchasima, 30000 Thailand
| | - Montarop Yamabhai
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology (SUT), 111 University Avenue, Meung District, Nakhon Ratchasima, 30000 Thailand
| |
Collapse
|
20
|
Global analysis of the impact of linezolid onto virulence factor production in S. aureus USA300. Int J Med Microbiol 2016; 306:131-40. [PMID: 26996810 DOI: 10.1016/j.ijmm.2016.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/10/2016] [Accepted: 02/15/2016] [Indexed: 12/20/2022] Open
Abstract
The translation inhibitor linezolid is an antibiotic of last resort against Gram-positive pathogens including methicillin resistant strains of the nosocomial pathogen Staphylococcus aureus. Linezolid is reported to inhibit production of extracellular virulence factors, but the molecular cause is unknown. To elucidate the physiological response of S. aureus to linezolid in general and the inhibition of virulence factor synthesis in particular a holistic study was performed. Linezolid was added to exponentially growing S. aureus cells and the linezolid stress response was analyzed with transcriptomics and quantitative proteomics methods. In addition, scanning and transmission electron microscopy experiments as well as fluorescence microscopy analyses of the cellular DNA and membrane were performed. As previously observed in studies on other translation inhibitors, S. aureus adapts its protein biosynthesis machinery to the reduced translation efficiency. For example the synthesis of ribosomal proteins was induced. Also unexpected results like a decline in the amount of extracellular and membrane proteins were obtained. In addition, cell shape and size changed after linezolid stress and cell division was diminished. Finally, the chromosome was condensed after linezolid stress and lost contact to the membrane. These morphological changes cannot be explained by established theories. A new hypothesis is discussed, which suggests that the reduced amount of membrane and extracellular proteins and observed defects in cell division are due to the disintegration of transertion complexes by linezolid.
Collapse
|
21
|
Yan S, Wu G. Evolutionary evidence on suitability of SecD as a target for development of antibacterial agents against Staphylococcus aureus. Ecol Evol 2016; 6:1393-410. [PMID: 27087922 PMCID: PMC4775529 DOI: 10.1002/ece3.1951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 12/15/2015] [Accepted: 12/16/2015] [Indexed: 11/22/2022] Open
Abstract
Staphylococcus aureus causes many infections and its drug resistance is a worrying challenge for medical care. The SecD subunit of Sec secretion system in methicillin‐resistant S. aureus is an attractive target because SecD dysfunction leads to the death of bacteria and SecD as a target is more efficient than SecA and SecF. Evolution could have made SecD to become insensitive to antibacterial agents although the drugs directly against SecD have yet to develop. So far, no detailed information on SecD evolution has been available, thus 2686 SecD sequences with full taxonomic information from kingdom to species were analyzed. First, the variance of pairwise p‐distance was evaluated for each taxonomic group. Second, the variance was further partitioned into intergroup and intragroup variances for quantification of horizontal and vertical gene transfer. Third, phylogenetic tree was built to trace the evolutionary pathway. The results showed that overall evolution of SecDs appears to have undergone horizontal and vertical gene transfer. Only 0.5% horizontal transfers were found between any two SecDs in S. aureus, 6.8% and 8.8% horizontal transfers were found between any two Staphylococcus SecDs from different and the same species, and only one SecD from S. aureus was located far away from its sister cluster. Thus, statistic and evolutionary analyses demonstrate that the SecDs from staphylococcus species have a small chance of mutating, and provide taxonomic evidence to use the SecD as a potential target for new generation of antibacterial agents against S. aureus.
Collapse
Affiliation(s)
- Shaomin Yan
- Guangxi Bioscience and Biotechnology Research Center Guangxi Academy of Sciences 98 Daling Road Nanning Guangxi 530007 China
| | - Guang Wu
- Guangxi Bioscience and Biotechnology Research Center Guangxi Academy of Sciences 98 Daling Road Nanning Guangxi 530007 China
| |
Collapse
|
22
|
Crowley PJ, Brady LJ. Evaluation of the effects of Streptococcus mutans chaperones and protein secretion machinery components on cell surface protein biogenesis, competence, and mutacin production. Mol Oral Microbiol 2015; 31:59-77. [PMID: 26386361 DOI: 10.1111/omi.12130] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2015] [Indexed: 11/29/2022]
Abstract
The respective contributions of components of the protein translocation/maturation machinery to cell surface biogenesis in Streptococcus mutans are not fully understood. Here we used a genetic approach to characterize the effects of deletion of genes encoding the ribosome-associated chaperone RopA (Trigger Factor), the surface-localized foldase PrsA, and the membrane-localized chaperone insertases YidC1 and YidC2, both singly and in combination, on bacterial growth, chain length, self-aggregation, cell surface hydrophobicity, autolysis, and antigenicity of surface proteins P1 (AgI/II, PAc), WapA, GbpC, and GtfD. The single and double deletion mutants, as well as additional mutant strains lacking components of the signal recognition particle pathway, were also evaluated for their effects on mutacin production and genetic competence.
Collapse
Affiliation(s)
- P J Crowley
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| | - L J Brady
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA
| |
Collapse
|
23
|
Xanthomonas campestris pv. vesicatoria Secretes Proteases and Xylanases via the Xps Type II Secretion System and Outer Membrane Vesicles. J Bacteriol 2015; 197:2879-93. [PMID: 26124239 DOI: 10.1128/jb.00322-15] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 06/19/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Many plant-pathogenic bacteria utilize type II secretion (T2S) systems to secrete degradative enzymes into the extracellular milieu. T2S substrates presumably mediate the degradation of plant cell wall components during the host-pathogen interaction and thus promote bacterial virulence. Previously, the Xps-T2S system from Xanthomonas campestris pv. vesicatoria was shown to contribute to extracellular protease activity and the secretion of a virulence-associated xylanase. The identities and functions of additional T2S substrates from X. campestris pv. vesicatoria, however, are still unknown. In the present study, the analysis of 25 candidate proteins from X. campestris pv. vesicatoria led to the identification of two type II secreted predicted xylanases, a putative protease and a lipase which was previously identified as a virulence factor of X. campestris pv. vesicatoria. Studies with mutant strains revealed that the identified xylanases and the protease contribute to virulence and in planta growth of X. campestris pv. vesicatoria. When analyzed in the related pathogen X. campestris pv. campestris, several T2S substrates from X. campestris pv. vesicatoria were secreted independently of the T2S systems, presumably because of differences in the T2S substrate specificities of the two pathogens. Furthermore, in X. campestris pv. vesicatoria T2S mutants, secretion of T2S substrates was not completely absent, suggesting the contribution of additional transport systems to protein secretion. In line with this hypothesis, T2S substrates were detected in outer membrane vesicles, which were frequently observed for X. campestris pv. vesicatoria. We, therefore, propose that extracellular virulence-associated enzymes from X. campestris pv. vesicatoria are targeted to the Xps-T2S system and to outer membrane vesicles. IMPORTANCE The virulence of plant-pathogenic bacteria often depends on TS2 systems, which secrete degradative enzymes into the extracellular milieu. T2S substrates are being studied in several plant-pathogenic bacteria, including Xanthomonas campestris pv. vesicatoria, which causes bacterial spot disease in tomato and pepper. Here, we show that the T2S system from X. campestris pv. vesicatoria secretes virulence-associated xylanases, a predicted protease, and a lipase. Secretion assays with the related pathogen X. campestris pv. campestris revealed important differences in the T2S substrate specificities of the two pathogens. Furthermore, electron microscopy showed that T2S substrates from X. campestris pv. vesicatoria are targeted to outer membrane vesicles (OMVs). Our results, therefore, suggest that OMVs provide an alternative transport route for type II secreted extracellular enzymes.
Collapse
|
24
|
Schrempf H, Merling P. Extracellular Streptomyces lividans vesicles: composition, biogenesis and antimicrobial activity. Microb Biotechnol 2015; 8:644-58. [PMID: 25851532 PMCID: PMC4476819 DOI: 10.1111/1751-7915.12274] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 02/09/2015] [Accepted: 02/09/2015] [Indexed: 11/27/2022] Open
Abstract
We selected Streptomyces lividans to elucidate firstly the biogenesis and antimicrobial activities of extracellular vesicles that a filamentous and highly differentiated Gram-positive bacterium produces. Vesicle types range in diameter from 110 to 230 nm and 20 to 60 nm, respectively; they assemble to clusters, and contain lipids and phospholipids allowing their in situ imaging by specific fluorescent dyes. The presence of the identified secondary metabolite undecylprodigiosin provokes red fluorescence of a portion of the heterogeneous vesicle populations facilitating in vivo monitoring. Protuberances containing vesicles generate at tips, and alongside of substrate hyphae, and enumerate during late vegetative growth to droplet-like exudates. Owing to in situ imaging in the presence and absence of a green fluorescent vancomycin derivative, we conclude that protuberances comprising vesicles arise at sites with enhanced levels of peptidoglycan subunits [pentapeptide of lipid II (C55)-linked disaccharides], and reduced levels of polymerized and cross-linked peptidoglycan within hyphae. These sites correlate with enhanced levels of anionic phospholipids and lipids. Vesicles provoke pronounced damages of Aspergillus proliferans, Verticillium dahliae and induced clumping and distortion of Escherichia coli. These harmful effects are likely attributable to the action of the identified vesicular compounds including different enzyme types, components of signal transduction cascades and undecylprodigiosin. Based on our pioneering findings, we highlight novel clues with environmental implications and application potential.
Collapse
Affiliation(s)
- Hildgund Schrempf
- FB Biology/Chemistry, Applied Genetics of Microorganisms, University Osnabrück, Barbarastr. 13, D-49069, Osnabrück, Germany
| | - Philipp Merling
- FB Biology/Chemistry, Applied Genetics of Microorganisms, University Osnabrück, Barbarastr. 13, D-49069, Osnabrück, Germany
| |
Collapse
|
25
|
Yan S, Wu G. Large-scale evolutionary analyses on SecB subunits of bacterial sec system. PLoS One 2015; 10:e0120417. [PMID: 25775430 PMCID: PMC4361572 DOI: 10.1371/journal.pone.0120417] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 01/21/2015] [Indexed: 01/10/2023] Open
Abstract
Protein secretion systems are extremely important in bacteria because they are involved in many fundamental cellular processes. Of the various secretion systems, the Sec system is composed of seven different subunits in bacteria, and subunit SecB brings secreted preproteins to subunit SecA, which with SecYEG and SecDF forms a complex for the translocation of secreted preproteins through the inner membrane. Because of the wide existence of Sec system across bacteria, eukaryota, and archaea, each subunit of the Sec system has a complicated evolutionary relationship. Until very recently, 5,162 SecB sequences have been documented in UniProtKB, however no phylogenetic study has been conducted on a large sampling of SecBs from bacterial Sec secretion system, and no statistical study has been conducted on such size of SecBs in order to exhaustively investigate their variances of pairwise p-distance along taxonomic lineage from kingdom to phylum, to class, to order, to family, to genus and to organism. To fill in these knowledge gaps, 3,813 bacterial SecB sequences with full taxonomic lineage from kingdom to organism covering 4 phyla, 11 classes, 41 orders, 82 families, 269 genera, and 3,744 organisms were studied. Phylogenetic analysis revealed how the SecBs evolved without compromising their function with examples of 3-D structure comparison of two SecBs from Proteobacteria, and possible factors that affected the SecB evolution were considered. The average pairwise p-distances showed that the variance varied greatly in each taxonomic group. Finally, the variance was further partitioned into inter- and intra-clan variances, which could correspond to vertical and horizontal gene transfers, with relevance for Achromobacter, Brevundimonas, Ochrobactrum, and Pseudoxanthomonas.
Collapse
Affiliation(s)
- Shaomin Yan
- State Key Laboratory of Non-food Biomass Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Biomass Industrialization Engineering Institute, Guangxi Key Laboratory of Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
| | - Guang Wu
- State Key Laboratory of Non-food Biomass Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Biomass Industrialization Engineering Institute, Guangxi Key Laboratory of Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi, 530007, China
- * E-mail:
| |
Collapse
|
26
|
Bundalovic-Torma C, Parkinson J. Comparative Genomics and Evolutionary Modularity of Prokaryotes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 883:77-96. [PMID: 26621462 DOI: 10.1007/978-3-319-23603-2_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The soaring number of high-quality genomic sequences has ushered in the era of post-genomic research where our understanding of organisms has dramatically shifted towards defining the function of genes within their larger biological contexts. As a result, novel high-throughput experimental technologies are being increasingly employed to uncover physical and functional associations of genes and proteins in complex biological processes. Through the construction and analysis of physical, genetic and metabolic networks generated for the model organisms, such as Escherichia coli, organizational principles of the genome have been deduced, such as modularity, which has important implications toward understanding prokaryotic evolution and adaptation to novel lifestyles.
Collapse
Affiliation(s)
- Cedoljub Bundalovic-Torma
- Department of Molecular Structure and Function, The Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, 686 Bay St. Rm 21-9830, Toronto, ON, Canada, M5G 0A4.
| | - John Parkinson
- Department of Molecular Structure and Function, The Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, 686 Bay St. Rm 20-9709, Toronto, ON, Canada, M5G 0A4.
| |
Collapse
|
27
|
Hooper SL, Burstein HJ. Minimization of extracellular space as a driving force in prokaryote association and the origin of eukaryotes. Biol Direct 2014; 9:24. [PMID: 25406691 PMCID: PMC4289276 DOI: 10.1186/1745-6150-9-24] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 11/03/2014] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Internalization-based hypotheses of eukaryotic origin require close physical association of host and symbiont. Prior hypotheses of how these associations arose include chance, specific metabolic couplings between partners, and prey-predator/parasite interactions. Since these hypotheses were proposed, it has become apparent that mixed-species, close-association assemblages (biofilms) are widespread and predominant components of prokaryotic ecology. Which forces drove prokaryotes to evolve the ability to form these assemblages are uncertain. Bacteria and archaea have also been found to form membrane-lined interconnections (nanotubes) through which proteins and RNA pass. These observations, combined with the structure of the nuclear envelope and an energetic benefit of close association (see below), lead us to propose a novel hypothesis of the driving force underlying prokaryotic close association and the origin of eukaryotes. RESULTS Respiratory proton transport does not alter external pH when external volume is effectively infinite. Close physical association decreases external volume. For small external volumes, proton transport decreases external pH, resulting in each transported proton increasing proton motor force to a greater extent. We calculate here that in biofilms this effect could substantially decrease how many protons need to be transported to achieve a given proton motor force. Based as it is solely on geometry, this energetic benefit would occur for all prokaryotes using proton-based respiration. CONCLUSIONS This benefit may be a driving force in biofilm formation. Under this hypothesis a very wide range of prokaryotic species combinations could serve as eukaryotic progenitors. We use this observation and the discovery of prokaryotic nanotubes to propose that eukaryotes arose from physically distinct, functionally specialized (energy factory, protein factory, DNA repository/RNA factory), obligatorily symbiotic prokaryotes in which the protein factory and DNA repository/RNA factory cells were coupled by nanotubes and the protein factory ultimately internalized the other two. This hypothesis naturally explains many aspects of eukaryotic physiology, including the nuclear envelope being a folded single membrane repeatedly pierced by membrane-bound tubules (the nuclear pores), suggests that species analogous or homologous to eukaryotic progenitors are likely unculturable as monocultures, and makes a large number of testable predictions. REVIEWERS This article was reviewed by Purificación López-García and Toni Gabaldón.
Collapse
Affiliation(s)
- Scott L Hooper
- Department of Biological Sciences, Ohio University, Athens, OH 45701 USA
| | - Helaine J Burstein
- Department of Biological Sciences, Ohio University, Athens, OH 45701 USA
| |
Collapse
|
28
|
Molecular engineering of secretory machinery components for high-level secretion of proteins in Bacillus species. ACTA ACUST UNITED AC 2014; 41:1599-607. [DOI: 10.1007/s10295-014-1506-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Accepted: 08/27/2014] [Indexed: 12/19/2022]
Abstract
Abstract
Secretory expression of valuable enzymes by Bacillus subtilis and its related species has attracted intensive work over the past three decades. Although many proteins have been expressed and secreted, the titers of some recombinant enzymes are still low to meet the needs of practical applications. Signal peptides that located at the N-terminal of nascent peptide chains play crucial roles in the secretion process. In this mini-review, we summarize recent progress in secretory expression of recombinant proteins in Bacillus species. In particular, we highlighted and discussed the advances in molecular engineering of secretory machinery components, construction of signal sequence libraries and identification of functional signal peptides with high-throughput screening strategy. The prospects of future research are also proposed.
Collapse
|
29
|
Handtke S, Volland S, Methling K, Albrecht D, Becher D, Nehls J, Bongaerts J, Maurer KH, Lalk M, Liesegang H, Voigt B, Daniel R, Hecker M. Cell physiology of the biotechnological relevant bacterium Bacillus pumilus-an omics-based approach. J Biotechnol 2014; 192 Pt A:204-14. [PMID: 25281541 DOI: 10.1016/j.jbiotec.2014.08.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/15/2014] [Accepted: 08/22/2014] [Indexed: 12/18/2022]
Abstract
Members of the species Bacillus pumilus get more and more in focus of the biotechnological industry as potential new production strains. Based on exoproteome analysis, B. pumilus strain Jo2, possessing a high secretion capability, was chosen for an omics-based investigation. The proteome and metabolome of B. pumilus cells growing either in minimal or complex medium was analyzed. In total, 1542 proteins were identified in growing B. pumilus cells, among them 1182 cytosolic proteins, 297 membrane and lipoproteins and 63 secreted proteins. This accounts for about 43% of the 3616 proteins encoded in the B. pumilus Jo2 genome sequence. By using GC-MS, IP-LC/MS and H NMR methods numerous metabolites were analyzed and assigned to reconstructed metabolic pathways. In the genome sequence a functional secretion system including the components of the Sec- and Tat-secretion machinery was found. Analysis of the exoproteome revealed secretion of about 70 proteins with predicted secretion signals. In addition, selected production-relevant genome features such as restriction modification systems and NRPS clusters of B. pumilus Jo2 are discussed.
Collapse
Affiliation(s)
- Stefan Handtke
- Institute for Microbiology, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Sonja Volland
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany.
| | - Karen Methling
- Institute of Biochemistry, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Dirk Albrecht
- Institute for Microbiology, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Dörte Becher
- Institute for Microbiology, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Jenny Nehls
- Institute of Biochemistry, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Johannes Bongaerts
- Department of Chemistry and Biotechnology, Aachen University of Applied Sciences, Heinrich-Mußmannstr. 1, 52428 Jülich, Germany.
| | | | - Michael Lalk
- Institute of Biochemistry, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Heiko Liesegang
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany.
| | - Birgit Voigt
- Institute for Microbiology, Ernst-Moritz-Arndt University, Greifswald, Germany.
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University Göttingen, Göttingen, Germany.
| | - Michael Hecker
- Institute for Microbiology, Ernst-Moritz-Arndt University, Greifswald, Germany.
| |
Collapse
|
30
|
Laouami S, Clair G, Armengaud J, Duport C. Proteomic evidences for rex regulation of metabolism in toxin-producing Bacillus cereus ATCC 14579. PLoS One 2014; 9:e107354. [PMID: 25216269 PMCID: PMC4162614 DOI: 10.1371/journal.pone.0107354] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 08/14/2014] [Indexed: 01/07/2023] Open
Abstract
The facultative anaerobe, Bacillus cereus, causes diarrheal diseases in humans. Its ability to deal with oxygen availability is recognized to be critical for pathogenesis. The B. cereus genome comprises a gene encoding a protein with high similarities to the redox regulator, Rex, which is a central regulator of anaerobic metabolism in Bacillus subtilis and other Gram-positive bacteria. Here, we showed that B. cereus rex is monocistronic and down-regulated in the absence of oxygen. The protein encoded by rex is an authentic Rex transcriptional factor since its DNA binding activity depends on the NADH/NAD+ ratio. Rex deletion compromised the ability of B. cereus to cope with external oxidative stress under anaerobiosis while increasing B. cereus resistance against such stress under aerobiosis. The deletion of rex affects anaerobic fermentative and aerobic respiratory metabolism of B. cereus by decreasing and increasing, respectively, the carbon flux through the NADH-recycling lactate pathway. We compared both the cellular proteome and exoproteome of the wild-type and Δrex cells using a high throughput shotgun label-free quantitation approach and identified proteins that are under control of Rex-mediated regulation. Proteomics data have been deposited to the ProteomeXchange with identifier PXD000886. The data suggest that Rex regulates both the cross-talk between metabolic pathways that produce NADH and NADPH and toxinogenesis, especially in oxic conditions.
Collapse
Affiliation(s)
- Sabrina Laouami
- Avignon Université/INRA, SQPOV UMR408, Avignon, France
- INRA, SQPOV UMR408, Avignon, France
| | - Géremy Clair
- Avignon Université/INRA, SQPOV UMR408, Avignon, France
- INRA, SQPOV UMR408, Avignon, France
- Laboratoire de Biochimie des Systèmes Perturbés, CEA Marcoule, DSV-iBEB-SBTN-LBSP, Bagnols-sur-Cèze, France
| | - Jean Armengaud
- Laboratoire de Biochimie des Systèmes Perturbés, CEA Marcoule, DSV-iBEB-SBTN-LBSP, Bagnols-sur-Cèze, France
| | - Catherine Duport
- Avignon Université/INRA, SQPOV UMR408, Avignon, France
- INRA, SQPOV UMR408, Avignon, France
| |
Collapse
|
31
|
Denks K, Vogt A, Sachelaru I, Petriman NA, Kudva R, Koch HG. The Sec translocon mediated protein transport in prokaryotes and eukaryotes. Mol Membr Biol 2014; 31:58-84. [DOI: 10.3109/09687688.2014.907455] [Citation(s) in RCA: 123] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
|
32
|
Degradation of extracytoplasmic catalysts for protein folding in Bacillus subtilis. Appl Environ Microbiol 2013; 80:1463-8. [PMID: 24362423 DOI: 10.1128/aem.02799-13] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The general protein secretion pathway of Bacillus subtilis has a high capacity for protein export from the cytoplasm, which is exploited in the biotechnological production of a wide range of enzymes. These exported proteins pass the membrane in an unfolded state, and accordingly, they have to fold into their active and protease-resistant conformations once membrane passage is completed. The lipoprotein PrsA and the membrane proteins HtrA and HtrB facilitate the extracytoplasmic folding and quality control of exported proteins. Among the native exported proteins of B. subtilis are at least 10 proteases that have previously been implicated in the degradation of heterologous secreted proteins. Recently, we have shown that these proteases also degrade many native membrane proteins, lipoproteins, and secreted proteins. The present studies were therefore aimed at assessing to what extent these proteases also degrade extracytoplasmic catalysts for protein folding. To this end, we employed a collection of markerless protease mutant strains that lack up to 10 different extracytoplasmic proteases. The results show that PrsA, HtrA, and HtrB are indeed substrates of multiple extracytoplasmic proteases. Thus, improved protein secretion by multiple-protease-mutant strains may be related to both reduced proteolysis and improved posttranslocational protein folding and quality control.
Collapse
|
33
|
Microbials for the production of monoclonal antibodies and antibody fragments. Trends Biotechnol 2013; 32:54-60. [PMID: 24183828 PMCID: PMC3906537 DOI: 10.1016/j.tibtech.2013.10.002] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 10/03/2013] [Accepted: 10/04/2013] [Indexed: 01/31/2023]
Abstract
Glycosylated full length antibodies are currently produced in mammalian cells. Antibody fragments can be produced in microbial organisms. Strain engineering allows production of full length antibodies in microbials. Microbials provide several advantages over mammalian cells.
Monoclonal antibodies (mAbs) and antibody fragments represent the most important biopharmaceutical products today. Because full length antibodies are glycosylated, mammalian cells, which allow human-like N-glycosylation, are currently used for their production. However, mammalian cells have several drawbacks when it comes to bioprocessing and scale-up, resulting in long processing times and elevated costs. By contrast, antibody fragments, that are not glycosylated but still exhibit antigen binding properties, can be produced in microbial organisms, which are easy to manipulate and cultivate. In this review, we summarize recent advances in the expression systems, strain engineering, and production processes for the three main microbials used in antibody and antibody fragment production, namely Saccharomyces cerevisiae, Pichia pastoris, and Escherichia coli.
Collapse
|
34
|
Xia Y, Peng L. Photoactivatable Lipid Probes for Studying Biomembranes by Photoaffinity Labeling. Chem Rev 2013; 113:7880-929. [DOI: 10.1021/cr300419p] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yi Xia
- Aix-Marseille Université, Centre Interdisciplinaire de Nanoscience de Marseille, CNRS UMR 7325, Campus de Luminy, 13288 Marseille, France
| | - Ling Peng
- Aix-Marseille Université, Centre Interdisciplinaire de Nanoscience de Marseille, CNRS UMR 7325, Campus de Luminy, 13288 Marseille, France
| |
Collapse
|
35
|
Albiniak AM, Matos CFRO, Branston SD, Freedman RB, Keshavarz-Moore E, Robinson C. High-level secretion of a recombinant protein to the culture medium with a Bacillus subtilis twin-arginine translocation system in Escherichia coli. FEBS J 2013; 280:3810-21. [PMID: 23745597 DOI: 10.1111/febs.12376] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Revised: 05/10/2013] [Accepted: 05/15/2013] [Indexed: 11/29/2022]
Abstract
The twin-arginine translocation (Tat) system transports folded proteins across the plasma membrane in bacteria, and heterologous proteins can be exported by this pathway if a Tat-type signal peptide is present at the N-terminus. The system thus has potential for biopharmaceutical production in Escherichia coli, where export to the periplasm is often a favoured approach. Previous studies have shown that E. coli cells can export high levels of protein by the Tat pathway, and the protein product accummulates almost exclusively in the periplasm. In this study, we analysed E. coli cells that express the Bacillus subtilis TatAdCd system in place of the native TatABC system. We show that a heterologous model protein, comprising the TorA signal peptide linked to green fluorescent protein (TorA-GFP), is efficiently exported by the TatAdCd system. However, whereas the GFP is exported initially to the periplasm during batch fermentation, the mature protein is increasingly found in the extracellular culture medium. By the end of a 16-h fermentation, ~ 90% of exported GFP is present in the medium as active mature protein. The total protein profiles of the medium and periplasm are essentially identical, confirming that the outer membrane becomes leaky during the fermentation process. The cells are otherwise intact, and there is no large-scale release of cytoplasmic contents. Export levels are relatively high, with ~ 0.35 g GFP·L⁻¹ culture present in the medium. This system thus offers a means of producing recombinant protein in E. coli and harvesting directly from the medium, with potential advantages in terms of ease of purification and downstream processing.
Collapse
Affiliation(s)
- Anna M Albiniak
- School of Life Sciences, University of Warwick, Coventry, UK
| | | | | | | | | | | |
Collapse
|
36
|
Ren C, Patel R, Robinson C. Exclusively membrane-inserted state of an uncleavable Tat precursor protein suggests lateral transfer into the bilayer from the translocon. FEBS J 2013; 280:3354-64. [PMID: 23647663 DOI: 10.1111/febs.12327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Revised: 02/28/2013] [Accepted: 04/04/2013] [Indexed: 11/26/2022]
Abstract
In bacteria, the export of proteins by the twin-arginine translocase (Tat) pathway is directed by cleavable N-terminal signal peptides. We studied the relationship between transport and maturation using a substrate, YedY, that contains an Ala > Leu substitution at the -1 position of the signal peptide. This blocks maturation and leads to the accumulation of a membrane-bound precursor form with the mature domain exposed to the periplasm. Its accumulation does not block transport of other Tat substrates, indicating that exit from the translocation channel has taken place, and the precursor protein is fir mLy integrated into the membrane bilayer. The membrane-integrated nature of the precursor, and complete absence of precursor protein in the periplasm, strongly suggest that the precursor has undergone lateral transfer into the bilayer during translocation. We propose that subsequent proteolytic processing releases the mature protein into the periplasm. A delay in processing results in an inhibition of cell growth, emphasizing a requirement for efficient maturation of Tat substrates.
Collapse
Affiliation(s)
- Chao Ren
- School of Life Sciences, University of Warwick, Coventry, UK
| | | | | |
Collapse
|
37
|
Freudl R. Leaving home ain't easy: protein export systems in Gram-positive bacteria. Res Microbiol 2013; 164:664-74. [PMID: 23541477 DOI: 10.1016/j.resmic.2013.03.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 02/05/2013] [Indexed: 10/27/2022]
Abstract
Transport of proteins into or across biological membranes is catalyzed by membrane-bound transport machineries. In Gram-positive bacteria, the vast majority of proteins are exported out of the cytosol by the conserved general secretion (Sec) system or, alternatively, by the twin-arginine translocation (Tat) system, that closely resemble their well-studied counterparts in Gram-negative bacteria. Besides these common major export routes, additional unique protein export systems (such as accessory Sec2 systems and/or type VII/WXG100 secretion systems) exist in some Gram-positive bacteria that are specifically involved in the secretion of limited subsets of proteins.
Collapse
Affiliation(s)
- Roland Freudl
- Institut für Bio- und Geowissenschaften 1, Biotechnologie, Forschungszentrum Jülich GmbH, D-52425 Jülich, Germany.
| |
Collapse
|
38
|
Benz M, Soll J, Ankele E. Arabidopsis thaliana Oxa proteins locate to mitochondria and fulfill essential roles during embryo development. PLANTA 2013; 237:573-88. [PMID: 23179441 DOI: 10.1007/s00425-012-1793-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 10/19/2012] [Indexed: 05/12/2023]
Abstract
Members of the Alb3/Oxa1/YidC protein family function as insertases in chloroplasts, mitochondria, and bacteria. Due to independent gene duplications, all organisms possess two isoforms, Oxa1 and Oxa2 except gram-negative bacteria, which encode only for one YidC-like protein. The genome of Arabidopsis thaliana however, encodes for eight different isoforms. The localization of three of these isoforms has been identified earlier: Alb3 and Alb4 located in thylakoid membranes of chloroplasts while AtOxa1 was found in the inner membrane of mitochondria. Here, we show that the second Oxa1 protein, Oxa1b as well as two Oxa2 proteins are also localized in mitochondria. The last two isoforms most likely encode truncated versions of Oxa-like proteins, which might be inoperable pseudogenes. Homozygous mutant lines were only obtained for Oxa1b, which did not reveal any significant phenotypes, while T-DNA insertion lines of Oxa1a, Oxa2a and Oxa2b resulted only in heterozygous plants indicating that these genes are indispensable for plant development. Phenotyping heterozygous lines showed that embryos are either retarded in growth, display an albino phenotype or embryo formation was entirely abolished suggesting that Oxa1a and both Oxa2 proteins function in embryo formation although at different developmental stages as indicated by the various phenotypes observed.
Collapse
Affiliation(s)
- Monique Benz
- Energy Biosciences Institute, University of California, 2151 Berkeley Way, Berkeley, CA 94720-5230, USA.
| | | | | |
Collapse
|
39
|
Zhang L, Selão TT, Pisareva T, Qian J, Sze SK, Carlberg I, Norling B. Deletion of Synechocystis sp. PCC 6803 leader peptidase LepB1 affects photosynthetic complexes and respiration. Mol Cell Proteomics 2013; 12:1192-203. [PMID: 23358502 DOI: 10.1074/mcp.m112.022145] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The cyanobacterium Synechocystis sp. PCC 6803 possesses two leader peptidases, LepB1 (Sll0716) and LepB2 (Slr1377), responsible for the processing of signal peptide-containing proteins. Deletion of the gene for LepB1 results in an inability to grow photoautotrophically and an extreme light sensitivity. Here we show, using a combination of Blue Native/SDS-PAGE, Western blotting and iTRAQ analysis, that lack of LepB1 strongly affects the cell's ability to accumulate wild-type levels of both photosystem I (PSI) and cytochrome (Cyt) b6f complexes. The impaired assembly of PSI and Cyt b6f is considered to be caused by the no or slow processing of the integral subunits PsaF and Cyt f respectively. In particular, PsaF, one of the PSI subunits, was found incorporated into PSI in its unprocessed form, which could influence the assembly and/or stability of PSI. In contrast to these results, we found the amount of assembled photosystem II (PSII) unchanged, despite a slower processing of PsbO. Thus, imbalance in the ratios of PSI and Cyt b6f to photosystem II leads to an imbalanced photosynthetic electron flow up- and down-stream of the plastoquinone pool, resulting in the observed light sensitivity of the mutant. We conclude that LepB1 is the natural leader peptidase for PsaF, PsbO, and Cyt f. The maturation of PsbO and Cyt f can be partially performed by LepB2, whereas PsaF processing is completely dependent on LepB1. iTRAQ analysis also revealed a number of indirect effects accompanying the mutation, primarily a strong induction of the CydAB oxidase as well as a significant decrease in phycobiliproteins and chlorophyll/heme biosynthesis enzymes.
Collapse
Affiliation(s)
- Lifang Zhang
- Nanyang Technological University, School of Biological Sciences, 637551 Singapore
| | | | | | | | | | | | | |
Collapse
|
40
|
Monteferrante CG, MacKichan C, Marchadier E, Prejean MV, Carballido-López R, van Dijl JM. Mapping the twin-arginine protein translocation network of Bacillus subtilis. Proteomics 2013. [PMID: 23180473 DOI: 10.1002/pmic.201200416] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Bacteria employ twin-arginine translocation (Tat) pathways for the transport of folded proteins to extracytoplasmic destinations. In recent years, most studies on bacterial Tat pathways addressed the membrane-bound TatA(B)C subunits of the Tat translocase, and the specific interactions between this translocase and its substrate proteins. In contrast, relatively few studies investigated possible coactors in the TatA(B)C-dependent protein translocation process. The present studies were aimed at identifying interaction partners of the Tat pathway of Bacillus subtilis, which is a paradigm for studies on protein secretion by Gram-positive bacteria. Specifically, 36 interaction partners of the TatA and TatC subunits were identified by rigorous application of the yeast two-hybrid (Y2H) approach. Our Y2H analyses revealed that the three TatA isoforms of B. subtilis can form homo- and heterodimers. Subsequently, the secretion of the Tat substrates YwbN and PhoD was tested in mutant strains lacking genes for the TatAC interaction partners identified in our genome-wide Y2H screens. Our results show that the cell wall-bound protease WprA is important for YwbN secretion, and that the HemAT and CsbC proteins are required for PhoD secretion under phosphate starvation conditions. Taken together, our findings imply that the Bacillus Tat pathway is embedded in an intricate protein-protein interaction network.
Collapse
Affiliation(s)
- Carmine G Monteferrante
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | | | | | | | | |
Collapse
|
41
|
Kartal B, de Almeida NM, Maalcke WJ, Op den Camp HJM, Jetten MSM, Keltjens JT. How to make a living from anaerobic ammonium oxidation. FEMS Microbiol Rev 2013; 37:428-61. [PMID: 23210799 DOI: 10.1111/1574-6976.12014] [Citation(s) in RCA: 295] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 10/25/2012] [Accepted: 11/21/2012] [Indexed: 11/28/2022] Open
Abstract
Anaerobic ammonium-oxidizing (anammox) bacteria primarily grow by the oxidation of ammonium coupled to nitrite reduction, using CO2 as the sole carbon source. Although they were neglected for a long time, anammox bacteria are encountered in an enormous species (micro)diversity in virtually any anoxic environment that contains fixed nitrogen. It has even been estimated that about 50% of all nitrogen gas released into the atmosphere is made by these 'impossible' bacteria. Anammox catabolism most likely resides in a special cell organelle, the anammoxosome, which is surrounded by highly unusual ladder-like (ladderane) lipids. Ammonium oxidation and nitrite reduction proceed in a cyclic electron flow through two intermediates, hydrazine and nitric oxide, resulting in the generation of proton-motive force for ATP synthesis. Reduction reactions associated with CO2 fixation drain electrons from this cycle, and they are replenished by the oxidation of nitrite to nitrate. Besides ammonium or nitrite, anammox bacteria use a broad range of organic and inorganic compounds as electron donors. An analysis of the metabolic opportunities even suggests alternative chemolithotrophic lifestyles that are independent of these compounds. We note that current concepts are still largely hypothetical and put forward the most intriguing questions that need experimental answers.
Collapse
Affiliation(s)
- Boran Kartal
- Department of Microbiology, Faculty of Science, Institute of Wetland and Water Research, Radboud University of Nijmegen, Nijmegen, The Netherlands
| | | | | | | | | | | |
Collapse
|
42
|
van Dijl JM, Hecker M. Bacillus subtilis: from soil bacterium to super-secreting cell factory. Microb Cell Fact 2013; 12:3. [PMID: 23311580 PMCID: PMC3564730 DOI: 10.1186/1475-2859-12-3] [Citation(s) in RCA: 215] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 01/11/2013] [Indexed: 12/17/2022] Open
Abstract
The biotechnology industry has become a key element in modern societies. Within this industry, the production of recombinant enzymes and biopharmaceutical proteins is of major importance. The global markets for such recombinant proteins are growing rapidly and, accordingly, there is a continuous need for new production platforms that can deliver protein products in greater yields, with higher quality and at lower costs. This calls for the development of next-generation super-secreting cell factories. One of the microbial cell factories that can meet these challenges is the Gram-positive bacterium Bacillus subtilis, an inhabitant of the upper layers of the soil that has the capacity to secrete proteins in the gram per litre range. The engineering of B. subtilis into a next-generation super-secreting cell factory requires combined Systems and Synthetic Biology approaches. In this way, the bacterial protein secretion machinery can be optimized from the single molecule to the network level while, at the same time, taking into account the balanced use of cellular resources. Although highly ambitious, this is an achievable objective due to recent advances in functional genomics and Systems- and Synthetic Biological analyses of B. subtilis cells.
Collapse
Affiliation(s)
- Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, P,O, box 30001, Groningen, 9700 RB, the Netherlands.
| | | |
Collapse
|
43
|
Vertès AA. Protein Secretion Systems of Corynebacterium glutamicum. CORYNEBACTERIUM GLUTAMICUM 2013. [DOI: 10.1007/978-3-642-29857-8_13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
44
|
Scheele S, Oertel D, Bongaerts J, Evers S, Hellmuth H, Maurer KH, Bott M, Freudl R. Secretory production of an FAD cofactor-containing cytosolic enzyme (sorbitol-xylitol oxidase from Streptomyces coelicolor) using the twin-arginine translocation (Tat) pathway of Corynebacterium glutamicum. Microb Biotechnol 2012; 6:202-6. [PMID: 23163932 PMCID: PMC3917463 DOI: 10.1111/1751-7915.12005] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 10/08/2012] [Accepted: 10/13/2012] [Indexed: 12/02/2022] Open
Abstract
Carbohydrate oxidases are biotechnologically interesting enzymes that require a tightly or covalently bound cofactor for activity. Using the industrial workhorse Corynebacterium glutamicum as the expression host, successful secretion of a normally cytosolic FAD cofactor-containing sorbitol–xylitol oxidase from Streptomyces coelicolor was achieved by using the twin-arginine translocation (Tat) protein export machinery for protein translocation across the cytoplasmic membrane. Our results demonstrate for the first time that, also for cofactor-containing proteins, a secretory production strategy is a feasible and promising alternative to conventional intracellular expression strategies.
Collapse
Affiliation(s)
- Sandra Scheele
- Institut für Bio- und Geowissenschaften 1, Biotechnologie, Forschungszentrum Jülich GmbH, Jülich, Germany
| | | | | | | | | | | | | | | |
Collapse
|
45
|
Degradation of the twin-arginine translocation substrate YwbN by extracytoplasmic proteases of Bacillus subtilis. Appl Environ Microbiol 2012; 78:7801-4. [PMID: 22923395 DOI: 10.1128/aem.02023-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial twin-arginine translocases can export fully folded proteins from the cytoplasm. Such proteins are usually resistant to proteolysis. Here we show that multiple extracellular proteases degrade the B. subtilis Tat substrate YwbN. This suggests either that secreted YwbN is not fully folded or that folded YwbN exposes protease cleavage sites.
Collapse
|
46
|
High-salinity growth conditions promote Tat-independent secretion of Tat substrates in Bacillus subtilis. Appl Environ Microbiol 2012; 78:7733-44. [PMID: 22923407 DOI: 10.1128/aem.02093-12] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Gram-positive bacterium Bacillus subtilis contains two Tat translocases, which can facilitate transport of folded proteins across the plasma membrane. Previous research has shown that Tat-dependent protein secretion in B. subtilis is a highly selective process and that heterologous proteins, such as the green fluorescent protein (GFP), are poor Tat substrates in this organism. Nevertheless, when expressed in Escherichia coli, both B. subtilis Tat translocases facilitated exclusively Tat-dependent export of folded GFP when the twin-arginine (RR) signal peptides of the E. coli AmiA, DmsA, or MdoD proteins were attached. Therefore, the present studies were aimed at determining whether the same RR signal peptide-GFP precursors would also be exported Tat dependently in B. subtilis. In addition, we investigated the secretion of GFP fused to the full-length YwbN protein, a strict Tat substrate in B. subtilis. Several investigated GFP fusion proteins were indeed secreted in B. subtilis, but this secretion was shown to be completely Tat independent. At high-salinity growth conditions, the Tat-independent secretion of GFP as directed by the RR signal peptides from the E. coli AmiA, DmsA, or MdoD proteins was significantly enhanced, and this effect was strongest in strains lacking the TatAy-TatCy translocase. This implies that high environmental salinity has a negative influence on the avoidance of Tat-independent secretion of AmiA-GFP, DmsA-GFP, and MdoD-GFP. We conclude that as-yet-unidentified control mechanisms reject the investigated GFP fusion proteins for translocation by the B. subtilis Tat machinery and, at the same time, set limits to their Tat-independent secretion, presumably via the Sec pathway.
Collapse
|
47
|
Szabo Z, Pohlschroder M. Diversity and subcellular distribution of archaeal secreted proteins. Front Microbiol 2012; 3:207. [PMID: 22783239 PMCID: PMC3387779 DOI: 10.3389/fmicb.2012.00207] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 05/21/2012] [Indexed: 12/12/2022] Open
Abstract
Secreted proteins make up a significant percentage of a prokaryotic proteome and play critical roles in important cellular processes such as polymer degradation, nutrient uptake, signal transduction, cell wall biosynthesis, and motility. The majority of archaeal proteins are believed to be secreted either in an unfolded conformation via the universally conserved Sec pathway or in a folded conformation via the Twin arginine transport (Tat) pathway. Extensive in vivo and in silico analyses of N-terminal signal peptides that target proteins to these pathways have led to the development of computational tools that not only predict Sec and Tat substrates with high accuracy but also provide information about signal peptide processing and targeting. Predictions therefore include indications as to whether a substrate is a soluble secreted protein, a membrane or cell wall anchored protein, or a surface structure subunit, and whether it is targeted for post-translational modification such as glycosylation or the addition of a lipid. The use of these in silico tools, in combination with biochemical and genetic analyses of transport pathways and their substrates, has resulted in improved predictions of the subcellular localization of archaeal secreted proteins, allowing for a more accurate annotation of archaeal proteomes, and has led to the identification of potential adaptations to extreme environments, as well as phyla-specific pathways among the archaea. A more comprehensive understanding of the transport pathways used and post-translational modifications of secreted archaeal proteins will also facilitate the identification and heterologous expression of commercially valuable archaeal enzymes.
Collapse
|
48
|
Nevo-Dinur K, Govindarajan S, Amster-Choder O. Subcellular localization of RNA and proteins in prokaryotes. Trends Genet 2012; 28:314-22. [DOI: 10.1016/j.tig.2012.03.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 03/15/2012] [Accepted: 03/19/2012] [Indexed: 10/28/2022]
|
49
|
TatAc, the third TatA subunit of Bacillus subtilis, can form active twin-arginine translocases with the TatCd and TatCy subunits. Appl Environ Microbiol 2012; 78:4999-5001. [PMID: 22544248 DOI: 10.1128/aem.01108-12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two independent twin-arginine translocases (Tat) for protein secretion were previously identified in the Gram-positive bacterium Bacillus subtilis. These consist of the TatAd-TatCd and TatAy-TatCy subunits. The function of a third TatA subunit named TatAc was unknown. Here, we show that TatAc can form active protein translocases with TatCd and TatCy.
Collapse
|
50
|
Nam SE, Kim AC, Paetzel M. Crystal structure of Bacillus subtilis signal peptide peptidase A. J Mol Biol 2012; 419:347-58. [PMID: 22472423 DOI: 10.1016/j.jmb.2012.03.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 03/16/2012] [Accepted: 03/26/2012] [Indexed: 11/28/2022]
Abstract
Signal peptide peptidase A (SppA) is a membrane-bound self-compartmentalized serine protease that functions to cleave the remnant signal peptides left behind after protein secretion and cleavage by signal peptidases. SppA is found in plants, archaea and bacteria. Here, we report the first crystal structure of a Gram-positive bacterial SppA. The 2.4-Å-resolution structure of Bacillus subtilis SppA (SppA(BS)) catalytic domain reveals eight SppA(BS) molecules in the asymmetric unit, forming a dome-shaped octameric complex. The octameric state of SppA(BS) is supported by analytical size-exclusion chromatography and multi-angle light scattering analysis. Our sequence analysis, mutagenesis and activity assays are consistent with Ser147 serving as the nucleophile and Lys199 serving as the general base; however, they are located in different region of the protein, more than 29 Å apart. Only upon assembling the octamer do the serine and lysine come within close proximity, with neighboring protomers each providing one-half of the catalytic dyad, thus producing eight separate active sites within the complex, twice the number seen within Escherichia coli SppA (SppA(EC)). The SppA(BS) S1 substrate specificity pocket is deep, narrow and hydrophobic, but with a polar bottom. The S3 pocket, which is constructed from two neighboring proteins, is shallower, wider and more polar than the S1 pocket. A comparison of these pockets to those seen in SppA(EC) reveals a significant difference in the size and shape of the S1 pocket, which we show is reflected in the repertoire of peptides the enzymes are capable of cleaving.
Collapse
Affiliation(s)
- Sung-Eun Nam
- Department of Molecular Biology and Biochemistry, Simon Fraser University, South Science Building 8888 University Drive, Burnaby, British Columbia, Canada V5A 1S6
| | | | | |
Collapse
|