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Okouakoua FY, Kayath CA, Mokemiabeka SN, Moukala DCR, Kaya-Ongoto MD, Nguimbi E. Involvement of the Bacillus SecYEG Pathway in Biosurfactant Production and Biofilm Formation. Int J Microbiol 2024; 2024:6627190. [PMID: 38725978 PMCID: PMC11081756 DOI: 10.1155/2024/6627190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/02/2024] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
With Bacillus species, about 30% of extracellular proteins are translocated through the cytoplasmic membrane, coordinated by the Sec translocase. This system mainly consists of the cytoplasmic ATPase SecA and the membrane-embedded SecYEG channel. The purpose of this work was to investigate the effects of the SecYEG export system on the production of industrial biomolecules, such as biosurfactants, proteases, amylases, and cellulases. Fifty-two isolates of Bacillus species were obtained from traditional fermented foods and then characterized using molecular microbiology methods. The isolates secreted exoenzymes that included cellulases, amylases, and proteases. We present evidence that a biosurfactant-like molecule requires the SecA ATPase and the SecYEG membrane channel for its secretion. In addition, we showed that biomolecules involved in biofilm formation required the SecYEG pathway. This work presents a novel seven-target fragment multiplex PCR assay capable of identification at the species level of Bacillus through a unique SecDF chromosomal gene. The bacterial membrane protein SecDF allowed the discrimination of Bacillus subtilis, B. licheniformis, B. amyloliquefaciens, and B. sonorensis. SecA was able to interact with AprE, AmyE, and TasA. The Rose Bengal inhibitor of SecA crucially affected the interaction of AprE, AmyE, TapA, and TasA with recombinant Gst-SecA. The Rose Bengal prevented Bacillus species from secreting and producing proteases, cellulases, amylases, and biosurfactant-like molecules. It also inhibited the formation of biofilm cell communities. The data support, for the first time, that the SecYEG translocon mediates the secretion of a biosurfactant-like molecule.
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Affiliation(s)
- Frédéric Yannick Okouakoua
- Laboratoire de Biologie Cellulaire et Moléculaire (BCM), Faculté des Sciences et Techniques, Université Marien N'GOUABI, BP. 69, Brazzaville, Congo
- Institut National de Recherche en Sciences Exactes et Naturelles (IRSEN), Avenue de l'Auberge Gascogne, B.P 2400, Brazzaville, Congo
| | - Christian Aimé Kayath
- Laboratoire de Biologie Cellulaire et Moléculaire (BCM), Faculté des Sciences et Techniques, Université Marien N'GOUABI, BP. 69, Brazzaville, Congo
- Institut National de Recherche en Sciences Exactes et Naturelles (IRSEN), Avenue de l'Auberge Gascogne, B.P 2400, Brazzaville, Congo
| | - Saturnin Nicaise Mokemiabeka
- Laboratoire de Biologie Cellulaire et Moléculaire (BCM), Faculté des Sciences et Techniques, Université Marien N'GOUABI, BP. 69, Brazzaville, Congo
- Institut National de Recherche en Sciences Exactes et Naturelles (IRSEN), Avenue de l'Auberge Gascogne, B.P 2400, Brazzaville, Congo
| | - David Charles Roland Moukala
- Laboratoire de Biologie Cellulaire et Moléculaire (BCM), Faculté des Sciences et Techniques, Université Marien N'GOUABI, BP. 69, Brazzaville, Congo
- Institut National de Recherche en Sciences Exactes et Naturelles (IRSEN), Avenue de l'Auberge Gascogne, B.P 2400, Brazzaville, Congo
| | - Moïse Doria Kaya-Ongoto
- Laboratoire de Biologie Cellulaire et Moléculaire (BCM), Faculté des Sciences et Techniques, Université Marien N'GOUABI, BP. 69, Brazzaville, Congo
- Institut National de Recherche en Sciences Exactes et Naturelles (IRSEN), Avenue de l'Auberge Gascogne, B.P 2400, Brazzaville, Congo
| | - Etienne Nguimbi
- Laboratoire de Biologie Cellulaire et Moléculaire (BCM), Faculté des Sciences et Techniques, Université Marien N'GOUABI, BP. 69, Brazzaville, Congo
- Institut National de Recherche en Sciences Exactes et Naturelles (IRSEN), Avenue de l'Auberge Gascogne, B.P 2400, Brazzaville, Congo
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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: 24] [Impact Index Per Article: 8.0] [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.
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Engineering Bacillus subtilis Cells as Factories: Enzyme Secretion and Value-added Chemical Production. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-020-0104-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Zhang K, Su L, Wu J. Recent Advances in Recombinant Protein Production byBacillus subtilis. Annu Rev Food Sci Technol 2020; 11:295-318. [DOI: 10.1146/annurev-food-032519-051750] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bacillus subtilis has become a widely used microbial cell factory for the production of recombinant proteins, especially those associated with foods and food processing. Recent advances in genetic manipulation and proteomic analysis have been used to greatly improve protein production in B. subtilis. This review begins with a discussion of genome-editing technologies and application of the CRISPR–Cas9 system to B. subtilis. A summary of the characteristics of crucial legacy strains is followed by suggestions regarding the choice of origin strain for genetic manipulation. Finally, the review analyzes the genes and operons of B. subtilis that are important for the production of secretory proteins and provides suggestions and examples of how they can be altered to improve protein production. This review is intended to promote the engineering of this valuable microbial cell factory for better recombinant protein production.
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Affiliation(s)
- Kang Zhang
- State Key Laboratory of Food Science and Technology, School of Biotechnology, Key Laboratory of Industrial Biotechnology, Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Lingqia Su
- State Key Laboratory of Food Science and Technology, School of Biotechnology, Key Laboratory of Industrial Biotechnology, Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, School of Biotechnology, Key Laboratory of Industrial Biotechnology, Ministry of Education, and International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
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Engineering Biology to Construct Microbial Chassis for the Production of Difficult-to-Express Proteins. Int J Mol Sci 2020; 21:ijms21030990. [PMID: 32024292 PMCID: PMC7037952 DOI: 10.3390/ijms21030990] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/28/2020] [Accepted: 01/31/2020] [Indexed: 12/12/2022] Open
Abstract
A large proportion of the recombinant proteins manufactured today rely on microbe-based expression systems owing to their relatively simple and cost-effective production schemes. However, several issues in microbial protein expression, including formation of insoluble aggregates, low protein yield, and cell death are still highly recursive and tricky to optimize. These obstacles are usually rooted in the metabolic capacity of the expression host, limitation of cellular translational machineries, or genetic instability. To this end, several microbial strains having precisely designed genomes have been suggested as a way around the recurrent problems in recombinant protein expression. Already, a growing number of prokaryotic chassis strains have been genome-streamlined to attain superior cellular fitness, recombinant protein yield, and stability of the exogenous expression pathways. In this review, we outline challenges associated with heterologous protein expression, some examples of microbial chassis engineered for the production of recombinant proteins, and emerging tools to optimize the expression of heterologous proteins. In particular, we discuss the synthetic biology approaches to design and build and test genome-reduced microbial chassis that carry desirable characteristics for heterologous protein expression.
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Advances and prospects of Bacillus subtilis cellular factories: From rational design to industrial applications. Metab Eng 2018; 50:109-121. [DOI: 10.1016/j.ymben.2018.05.006] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 05/02/2018] [Accepted: 05/10/2018] [Indexed: 01/29/2023]
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Protein Secretion in Gram-Positive Bacteria: From Multiple Pathways to Biotechnology. Curr Top Microbiol Immunol 2017; 404:267-308. [PMID: 27885530 DOI: 10.1007/82_2016_49] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A number of Gram-positive bacteria are important players in industry as producers of a diverse array of economically interesting metabolites and proteins. As discussed in this overview, several Gram-positive bacteria are valuable hosts for the production of heterologous proteins. In contrast to Gram-negative bacteria, proteins secreted by Gram-positive bacteria are released into the culture medium where conditions for correct folding are more appropriate, thus facilitating the isolation and purification of active proteins. Although seven different protein secretion pathways have been identified in Gram-positive bacteria, the majority of heterologous proteins are produced via the general secretion or Sec pathway. Not all proteins are equally well secreted, because heterologous protein production often faces bottlenecks including hampered secretion, susceptibility to proteases, secretion stress, and metabolic burden. These bottlenecks are associated with reduced yields leading to non-marketable products. In this chapter, besides a general overview of the different protein secretion pathways, possible hurdles that may hinder efficient protein secretion are described and attempts to improve yield are discussed including modification of components of the Sec pathway. Attention is also paid to omics-based approaches that may offer a more rational approach to optimize production of heterologous proteins.
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Yan S, Wu G. Bottleneck in secretion of α-amylase in Bacillus subtilis. Microb Cell Fact 2017; 16:124. [PMID: 28724440 PMCID: PMC5518135 DOI: 10.1186/s12934-017-0738-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 07/10/2017] [Indexed: 11/10/2022] Open
Abstract
Amylase plays an important role in biotechnology industries, and Gram-positive bacterium Bacillus subtilis is a major host to produce heterogeneous α-amylases. However, the secretion stress limits the high yield of α-amylase in B. subtilis although huge efforts have been made to address this secretion bottleneck. In this question-oriented review, every effort is made to answer the following questions, which look simple but are long-standing, through reviewing of literature: (1) Does α-amylase need a specific and dedicated chaperone? (2) What signal sequence does CsaA recognize? (3) Does CsaA require ATP for its operation? (4) Does an unfolded α-amylase is less soluble than a folded one? (5) Does α-amylase aggregate before transporting through Sec secretion system? (6) Is α-amylase sufficient stable to prevent itself from misfolding? (7) Does α-amylase need more disulfide bonds to be stabilized? (8) Which secretion system does PrsA pass through? (9) Is PrsA ATP-dependent? (10) Is PrsA reused after folding of α-amylase? (11) What is the fate of PrsA? (12) Is trigger factor (TF) ATP-dependent? The literature review suggests that not only the most of those questions are still open to answers but also it is necessary to calculate ATP budget in order to better understand how B. subtilis uses its energy for production and secretion.
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Affiliation(s)
- Shaomin Yan
- National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, Guangxi, China
| | - Guang Wu
- National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, Guangxi, China.
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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
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Chen J, Zhao L, Fu G, Zhou W, Sun Y, Zheng P, Sun J, Zhang D. A novel strategy for protein production using non-classical secretion pathway in Bacillus subtilis. Microb Cell Fact 2016; 15:69. [PMID: 27125780 PMCID: PMC4850722 DOI: 10.1186/s12934-016-0469-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/21/2016] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The Gram-positive bacterium Bacillus subtilis has been widely used as a cell factory for the production of proteins due to its generally regarded as safe (GRAS) nature and secretion capability. Of the known secretory pathways in B. subtilis, the majority of proteins are exported from the cytoplasm by Sec pathway, Tat pathway and ABC transporters, etc. However, the production of heterologous proteins by B. subtilis is unfortunately not that straight forward because of the bottlenecks in classical secretion pathways. The aim of this work is to explore a new method for protein production based on non-classical secretion pathway. RESULTS One D-psicose 3-epimerase (RDPE) which converts D-fructose into D-psicose from Ruminococcus sp. 5_1_39BFAA was successfully and substantially secreted into the extracellular milieu without the direction of signal peptide. Subsequently, we demonstrated that RDPE contained no native signal peptide, and the secretion of RDPE was not dependent on Sec or Tat pathway or due to cell lysis, which indicated that RDPE is a non-classically secreted protein. Then, we attempted to evaluate the possibility of using RDPE as a signal to export eighteen reporter proteins into the culture medium. Five of eleven homologous proteins, two of five heterologous proteins from other bacterium and two heterologous proteins of eukaryotic source were successfully secreted into the extracellular milieu at different secretion levels when they were fused to RDPE mediated by a flexible 21-bp linker to keep a distance between two single proteins. Furthermore, the secretion rates of two fusion proteins (RDPE-DnaK and RDPE-RFP) reached more than 50 %. In addition, most of the fusion proteins retained enzyme or biological activity of their corresponding target proteins, and all of the fusions still had the activity of RDPE. CONCLUSIONS We found and identified a heterologous non-classically secreted protein RDPE, and showed that RDPE could direct proteins of various types into the culture medium, and thus non-classical protein secretion pathway can be used as a novel secretion pathway for recombinant proteins. This novel strategy for recombinant protein production is helpful to make B. subtilis as a more ideal cell factory for protein production.
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Affiliation(s)
- Jingqi Chen
- />Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- />Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
| | - Liuqun Zhao
- />Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- />Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
| | - Gang Fu
- />Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- />National Engineering Laboratory for Industrial Enzymes, Tianjin, 300308 People’s Republic of China
| | - Wenjuan Zhou
- />Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- />Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
| | - Yuanxia Sun
- />Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- />National Engineering Laboratory for Industrial Enzymes, Tianjin, 300308 People’s Republic of China
| | - Ping Zheng
- />Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- />Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
| | - Jibin Sun
- />Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- />Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
| | - Dawei Zhang
- />Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- />Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 People’s Republic of China
- />National Engineering Laboratory for Industrial Enzymes, Tianjin, 300308 People’s Republic of China
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Tools to cope with difficult-to-express proteins. Appl Microbiol Biotechnol 2016; 100:4347-55. [DOI: 10.1007/s00253-016-7514-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 03/28/2016] [Accepted: 03/30/2016] [Indexed: 12/26/2022]
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Optimization of the secretion pathway for heterologous proteins in Bacillus subtilis. BIOTECHNOL BIOPROC E 2015. [DOI: 10.1007/s12257-014-0843-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Chen J, Fu G, Gai Y, Zheng P, Zhang D, Wen J. Combinatorial Sec pathway analysis for improved heterologous protein secretion in Bacillus subtilis: identification of bottlenecks by systematic gene overexpression. Microb Cell Fact 2015; 14:92. [PMID: 26112883 PMCID: PMC4482152 DOI: 10.1186/s12934-015-0282-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/11/2015] [Indexed: 11/10/2022] Open
Abstract
Background Secretory expression of valuable proteins by B. subtilis and its related species has attracted intensive work over the past three decades. Although very high yields can be achieved with homologous proteins, production of heterologous proteins by B. subtilis is unfortunately not the straight forward. The Sec pathway is the major route for protein secretion in B. subtilis. Therefore, the aim of this work was to identify the bottlenecks of the Sec pathway and improve the secretion of heterologous proteins by molecular genetic techniques. Results Two α-amylases (AmyL and AmyS) both under the control of the PHpaII promoter and equipped with their native signal peptides SPamyl and SPamyS were successfully secreted with significantly different expression levels. To improve the secretion efficiency, 23 main genes or gene operons involved in or closely related to the Sec pathway were overexpressed singly by increasing an additional copy on the chromosome, and the overexpression of prsA enhanced the production of α-amylases (AmyL and AmyS) by 3.2- and 5.5-fold, respectively. With the induction by xylose of different concentrations, prsA overexpression level was optimized and the secretion efficiency of α-amylase was further improved. Moreover, combinatorial overexpression of prsA and nine screened genes or gene operons, respectively, was performed, and the overexpression of prsA combined with partial dnaK operon improved the α-amylase activity of AmyL and AmyS by 160 and 173%, respectively, compared with the overexpression of prsA singly. Finally, the performance of the recombinant B. subtilis 1A237 was evaluated with the fed-batch fermentation in 7.5 L fermentor, and the level of secreted AmyL and AmyS reached 1,352 and 2,300 U/mL with the productivity of 16.1 U/mL h and 27.4 U/mL h, respectively. Conclusions Our systematic gene overexpression approach was designed to investigate the bottleneck of Sec pathway in B. subtilis. The deficiency of PrsA lipoprotein and chaperones of DnaK series was main rate-limiting factors for heterologous proteins secretion. Systematic and deep insight into how components of Sec pathway interact with each other may be the key to improving the yield of heterologous proteins thoroughly. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0282-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jingqi Chen
- Department of Biological Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China. .,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.
| | - Gang Fu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China. .,National Engineering Laboratory for Industrial Enzymes, Tianjin, 300308, People's Republic of China.
| | - Yuanming Gai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China. .,National Engineering Laboratory for Industrial Enzymes, Tianjin, 300308, People's Republic of China.
| | - Ping Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China. .,National Engineering Laboratory for Industrial Enzymes, Tianjin, 300308, People's Republic of China.
| | - Jianping Wen
- Department of Biological Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.
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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.
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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:
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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.
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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.
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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.
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Anné J, Vrancken K, Van Mellaert L, Van Impe J, Bernaerts K. Protein secretion biotechnology in Gram-positive bacteria with special emphasis on Streptomyces lividans. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1750-61. [PMID: 24412306 DOI: 10.1016/j.bbamcr.2013.12.023] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 12/26/2013] [Accepted: 12/31/2013] [Indexed: 02/07/2023]
Abstract
Proteins secreted by Gram-positive bacteria are released into the culture medium with the obvious benefit that they usually retain their native conformation. This property makes these host cells potentially interesting for the production of recombinant proteins, as one can take full profit of established protocols for the purification of active proteins. Several state-of-the-art strategies to increase the yield of the secreted proteins will be discussed, using Streptomyces lividans as an example and compared with approaches used in some other host cells. It will be shown that approaches such as increasing expression and translation levels, choice of secretion pathway and modulation of proteins thereof, avoiding stress responses by changing expression levels of specific (stress) proteins, can be helpful to boost production yield. In addition, the potential of multi-omics approaches as a tool to understand the genetic background and metabolic fluxes in the host cell and to seek for new targets for strain and protein secretion improvement is discussed. It will be shown that S. lividans, along with other Gram-positive host cells, certainly plays a role as a production host for recombinant proteins in an economically viable way. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.
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Affiliation(s)
- Jozef Anné
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Laboratory of Molecular Bacteriology, Herestraat 49, box 1037, B-3000 Leuven, Belgium.
| | - Kristof Vrancken
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Laboratory of Molecular Bacteriology, Herestraat 49, box 1037, B-3000 Leuven, Belgium.
| | - Lieve Van Mellaert
- Rega Institute for Medical Research, Katholieke Universiteit Leuven, Laboratory of Molecular Bacteriology, Herestraat 49, box 1037, B-3000 Leuven, Belgium.
| | - Jan Van Impe
- Chemical and Biochemical Process Technology and Control Section (BioTeC), Department of Chemical Engineering, KU Leuven, Willem de Croylaan 46 box 2423, B-3001 Leuven, Belgium.
| | - Kristel Bernaerts
- Chemical and Biochemical Process Technology and Control Section (BioTeC), Department of Chemical Engineering, KU Leuven, Willem de Croylaan 46 box 2423, B-3001 Leuven, Belgium.
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18
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Yan S, Wu G. Secretory pathway of cellulase: a mini-review. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:177. [PMID: 24295495 PMCID: PMC4177124 DOI: 10.1186/1754-6834-6-177] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 11/19/2013] [Indexed: 05/07/2023]
Abstract
Cellulase plays an important role in modern industry and holds great potential in biofuel production. Many different types of organisms produce cellulase, which go through secretory pathways to reach the extracellular space, where enzymatic reactions take place. Secretory pathways in various cells have been the focus of many research fields; however, there are few studies on secretory pathways of cellulases in the literature. It is therefore necessary and important to review the current knowledge on the secretory pathways of cellulases. In this mini-review, we address the subcellular locations of cellulases in different organisms, discuss the secretory pathways of cellulases in different organisms, and examine the secretory mechanisms of cellulases. These sections start with a description of general secreted proteins, advance to the situation of cellulases, and end with the knowledge of cellulases, as documented in UniProt Knowledgebase (UniProtKB). Finally, gaps in existing knowledge are highlighted, which may shed light on future studies for biofuel engineering.
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Affiliation(s)
- Shaomin Yan
- State Key Laboratory of Non-food Biomass Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, 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 Key Laboratory of Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi 530007, China
- DreamSciTech, Apt 207, Zhencaili 26, Zhujiang Road, Hexi District, Tianjin, 300222, China
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19
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Miyazaki T, Noda S, Tanaka T, Kondo A. Hyper secretion of Thermobifida fusca β-glucosidase via a Tat-dependent signal peptide using Streptomyces lividans. Microb Cell Fact 2013; 12:88. [PMID: 24083334 PMCID: PMC3850917 DOI: 10.1186/1475-2859-12-88] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 09/28/2013] [Indexed: 12/02/2022] Open
Abstract
Background Protein production as secretory-form is a powerful tool in industrial enzyme production due to the simple purification procedure. Streptomyces lividans is a versatile host for secretory production of useful proteins. In order to expand the amount of secreted protein, signal peptide sequences, which encourage protein secretion from inside cell to extracellular environment, are one of the most significant factors. In this study, we focused on Streptomyces lividans as a host strain to secrete useful proteins, and screened for signal peptides from the biomass-degradation enzymes derived from Thermobifida fusca YX and S. lividans. Results Three candidate signal peptides were isolated and evaluated for their protein secretion ability using β-glucosidase derived from T. fusca YX, which is a non-secreted protein, as a model protein. Using S. lividans xylanase C signal peptide, the amount of produced the β-glucosidase reached 10 times as much as that when using Streptomyces cinnamoneus phospholipase D signal peptide, which was identified as a versatile signal peptide in our previous report. In addition, the introduction of the β-glucosidase fused to xylanase C signal peptide using two kinds of plasmid, pUC702 and pTYM18, led to further protein secretion, and the maximal level of produced the β-glucosidase increased up to 17 times (1.1 g/l) compared to using only pUC702 carrying the β-glucosidase fused to S. cinnamoneus phospholipase D signal peptide. Conclusion In the present study, we focused on signal peptide sequences derived from biomass degradation enzymes, which are usually secreted into the culture supernatant, and screened for signal peptides leading to effective protein secretion. Using the signal peptides, the hyper-protein secretion system was successfully demonstrated for the cytoplasmic β-glucosidase.
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Affiliation(s)
- Takaya Miyazaki
- Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan.
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Liu L, Liu Y, Shin HD, Chen RR, Wang NS, Li J, Du G, Chen J. Developing Bacillus spp. as a cell factory for production of microbial enzymes and industrially important biochemicals in the context of systems and synthetic biology. Appl Microbiol Biotechnol 2013; 97:6113-27. [DOI: 10.1007/s00253-013-4960-4] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 04/25/2013] [Accepted: 04/27/2013] [Indexed: 01/29/2023]
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21
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Mulder KC, Bandola J, Schumann W. Construction of an artificial secYEG operon allowing high level secretion of α-amylase. Protein Expr Purif 2013; 89:92-6. [DOI: 10.1016/j.pep.2013.02.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 02/04/2013] [Accepted: 02/06/2013] [Indexed: 10/27/2022]
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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: 216] [Impact Index Per Article: 19.6] [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.
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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.
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