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Cal AJ, Kibblewhite RE, Sikkema WD, Torres LF, Hart-Cooper WM, Orts WJ, Lee CC. Production of polyhydroxyalkanoate copolymers containing 4-hydroxybutyrate in engineered Bacillus megaterium. Int J Biol Macromol 2020; 168:86-92. [PMID: 33290766 DOI: 10.1016/j.ijbiomac.2020.12.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 11/18/2020] [Accepted: 12/03/2020] [Indexed: 11/15/2022]
Abstract
Despite being used as a common platform for the commercial production of many biochemicals, Bacilli are often overlooked as a source of industrial polyhydroxyalkanoates (PHAs), biodegradable plastic replacements. In addition to having a robust expression system, the lack of lipopolysaccharides and ease of lysis make Bacilli an attractive host for the production of PHAs. In this work, a Bacillus megaterium strain was engineered to generate poly(3-hydroxybutyrate-co-4-hydroxybutryate) (P[3HB-co-4HB]) copolymers, which are among the most useful and industrially-relevant copolymers. These copolymers had lower modulus and increased toughness, thus making the copolymer suitable for a broader range of applications. Due to high metabolic flux through succinate, the engineered B. megaterium strain produced P(3HB-co-4HB) with >10% mol fraction 4HB from glucose, without the use of highly regulated and expensive precursors or potentially damaging truncation of central biochemical pathways.
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Affiliation(s)
- Andrew J Cal
- USDA-ARS-Western Regional Research Center, Bioproducts Research Unit, 800 Buchanan St., Albany, CA 94710, USA
| | - Rena E Kibblewhite
- USDA-ARS-Western Regional Research Center, Bioproducts Research Unit, 800 Buchanan St., Albany, CA 94710, USA
| | - W Dirk Sikkema
- USDA-ARS-Western Regional Research Center, Bioproducts Research Unit, 800 Buchanan St., Albany, CA 94710, USA
| | - Lennard F Torres
- USDA-ARS-Western Regional Research Center, Bioproducts Research Unit, 800 Buchanan St., Albany, CA 94710, USA
| | - William M Hart-Cooper
- USDA-ARS-Western Regional Research Center, Bioproducts Research Unit, 800 Buchanan St., Albany, CA 94710, USA
| | - William J Orts
- USDA-ARS-Western Regional Research Center, Bioproducts Research Unit, 800 Buchanan St., Albany, CA 94710, USA
| | - Charles C Lee
- USDA-ARS-Western Regional Research Center, Bioproducts Research Unit, 800 Buchanan St., Albany, CA 94710, USA.
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Li H, O'Hair J, Thapa S, Bhatti S, Zhou S, Yang Y, Fish T, Thannhauser TW. Proteome profile changes during poly-hydroxybutyrate intracellular mobilization in gram positive Bacillus cereus tsu1. BMC Microbiol 2020; 20:122. [PMID: 32429845 PMCID: PMC7236355 DOI: 10.1186/s12866-020-01815-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 05/07/2020] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Bacillus cereus is a bacterial species which grows efficiently on a wide range of carbon sources and accumulates biopolymer poly-hydroxybutyrate (PHB) up to 80% cell dry weight. PHB is an aliphatic polymer produced and stored intracellularly as a reservoir of carbon and energy, its mobilization is a key biological process for sporulation in Bacillus spp. Previously, B. cereus tsu1 was isolated and cultured on rapeseed cake substrate (RCS), with maximum of PHB accumulation reached within 12 h, and depleted after 48 h. Fore-spore and spore structure were observed after 24 h culture. RESULTS Quantitative proteomic analysis of B. cereus tsu1 identified 2952 quantifiable proteins, and 244 significantly changed proteins (SCPs) in the 24 h:12 h pair of samples, and 325 SCPs in the 48 h:12 h pair of samples. Based on gene ontology classification analysis, biological processes enriched only in the 24 h:12 h SCPs include purine nucleotide metabolism, protein folding, metal ion homeostasis, response to stress, carboxylic acid catabolism, and cellular amino acid catabolism. The 48 h:12 h SCPs were enriched into processes including carbohydrate metabolism, protein metabolism, oxidative phosphorylation, and formation of translation ternary structure. A key enzyme for PHB metabolism, poly(R)-hydroxyalkanoic acid synthase (PhaC, KGT44865) accumulated significantly higher in 12 h-culture. Sporulation related proteins SigF and SpoEII were significantly higher in 24 h-samples. Enzymes for nitrate respiration and fermentation accumulated to the highest abundance level in 48 h-culture. CONCLUSIONS Changes in proteome of B. cereus tsu1 during PHB intracellular mobilization were characterized in this study. The key enzyme PhaC for PHB synthesis increased significantly after 12 h-culture which supports the highest PHB accumulation at this time point. The protein abundance level of SpoIIE and SigF also increased, correlating with sporulation in 24 h-culture. Enzymes for nitrate respiration and fermentation were significantly induced in 48 h-culture which indicates the depletion of oxygen at this stage and carbon flow towards fermentative growth. Results from this study provide insights into proteome profile changes during PHB accumulation and reuse, which can be applied to achieve a higher PHB yield and to improve bacterial growth performance and stress resistance.
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Affiliation(s)
- Hui Li
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A. Merritt Blvd, Nashville, TN, 37209, USA
| | - Joshua O'Hair
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A. Merritt Blvd, Nashville, TN, 37209, USA
| | - Santosh Thapa
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A. Merritt Blvd, Nashville, TN, 37209, USA
| | - Sarabjit Bhatti
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A. Merritt Blvd, Nashville, TN, 37209, USA
| | - Suping Zhou
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, 3500 John A. Merritt Blvd, Nashville, TN, 37209, USA.
| | - Yong Yang
- R.W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY, 14853, USA
| | - Tara Fish
- R.W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY, 14853, USA
| | - Theodore W Thannhauser
- R.W. Holley Center for Agriculture and Health, USDA-ARS, Cornell University, Ithaca, NY, 14853, USA
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Guérin A, Dargaignaratz C, Clavel T, Broussolle V, Nguyen-the C. Impact of temperature and oxygen on the fate of Bacillus weihenstephanensis in a food-based medium. Food Microbiol 2019; 83:175-180. [DOI: 10.1016/j.fm.2019.05.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/30/2019] [Accepted: 05/22/2019] [Indexed: 10/26/2022]
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Leiser OP, Blackburn JK, Hadfield TL, Kreuzer HW, Wunschel DS, Bruckner-Lea CJ. Laboratory strains of Bacillus anthracis exhibit pervasive alteration in expression of proteins related to sporulation under laboratory conditions relative to genetically related wild strains. PLoS One 2018; 13:e0209120. [PMID: 30557394 PMCID: PMC6296524 DOI: 10.1371/journal.pone.0209120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/20/2018] [Indexed: 11/25/2022] Open
Abstract
The spore forming pathogen Bacillus anthracis is the etiologic agent of anthrax in humans and animals. It cycles through infected hosts as vegetative cells and is eventually introduced into the environment where it generates an endospore resistant to many harsh conditions. The endospores are subsequently taken up by another host to begin the next cycle. Outbreaks of anthrax occur regularly worldwide in wildlife and livestock, and the potential for human infection exists whenever humans encounter infected animals. It is also possible to encounter intentional releases of anthrax spores, as was the case in October 2001. Consequently, it is important to be able to rapidly establish the provenance of infectious strains of B. anthracis. Here, we compare protein expression in seven low-passage wild isolates and four laboratory strains of B. anthracis grown under identical conditions using LC-MS/MS proteomic analysis. Of the 1,023 total identified proteins, 96 had significant abundance differences between wild and laboratory strains. Of those, 28 proteins directly related to sporulation were upregulated in wild isolates, with expression driven by Spo0A, CodY, and AbrB/ScoC. In addition, we observed evidence of changes in cell division and fatty acid biosynthesis between the two classes of strains, despite being grown under identical experimental conditions. These results suggest wild B. anthracis cells are more highly tuned to sporulate than their laboratory cousins, and this difference should be exploited as a method to differentiate between laboratory and low passage wild strains isolated during an anthrax outbreak. This knowledge should distinguish between intentional releases and exposure to strains in nature, providing a basis for the type of response by public health officials and investigators.
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Affiliation(s)
- Owen P. Leiser
- Chemical and Biological Signature Science, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Jason K. Blackburn
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Spatial Epidemiology & Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, Florida, United States of America
| | - Ted L. Hadfield
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Spatial Epidemiology & Ecology Research Laboratory, Department of Geography, University of Florida, Gainesville, Florida, United States of America
| | - Helen W. Kreuzer
- Chemical and Biological Signature Science, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - David S. Wunschel
- Chemical and Biological Signature Science, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Cindy J. Bruckner-Lea
- Chemical and Biological Signature Science, Pacific Northwest National Laboratory, Richland, Washington, United States of America
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Sadykov MR, Ahn JS, Widhelm TJ, Eckrich VM, Endres JL, Driks A, Rutkowski GE, Wingerd KL, Bayles KW. Poly(3-hydroxybutyrate) fuels the tricarboxylic acid cycle andde novolipid biosynthesis duringBacillus anthracissporulation. Mol Microbiol 2017; 104:793-803. [DOI: 10.1111/mmi.13665] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2017] [Indexed: 11/27/2022]
Affiliation(s)
- Marat R. Sadykov
- Department of Pathology and Microbiology; University of Nebraska Medical Center; Omaha NE 68198 USA
| | - Jong-Sam Ahn
- Department of Pathology and Microbiology; University of Nebraska Medical Center; Omaha NE 68198 USA
| | - Todd J. Widhelm
- Department of Pathology and Microbiology; University of Nebraska Medical Center; Omaha NE 68198 USA
| | - Valerie M. Eckrich
- Department of Pathology and Microbiology; University of Nebraska Medical Center; Omaha NE 68198 USA
| | - Jennifer L. Endres
- Department of Pathology and Microbiology; University of Nebraska Medical Center; Omaha NE 68198 USA
| | - Adam Driks
- Department of Microbiology and Immunology; Loyola University Chicago, Stritch School of Medicine; Maywood IL 60153 USA
| | | | | | - Kenneth W. Bayles
- Department of Pathology and Microbiology; University of Nebraska Medical Center; Omaha NE 68198 USA
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Simultaneous Biosynthesis of Polyhydroxyalkanoates and Extracellular Polymeric Substance (EPS) from Crude Glycerol from Biodiesel Production by Different Bacterial Strains. Appl Biochem Biotechnol 2016; 180:1110-1127. [DOI: 10.1007/s12010-016-2155-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/01/2016] [Indexed: 02/04/2023]
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Tsuge T, Hyakutake M, Mizuno K. Class IV polyhydroxyalkanoate (PHA) synthases and PHA-producing Bacillus. Appl Microbiol Biotechnol 2015; 99:6231-40. [PMID: 26135986 DOI: 10.1007/s00253-015-6777-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Revised: 06/11/2015] [Accepted: 06/17/2015] [Indexed: 12/28/2022]
Abstract
This review highlights the recent investigations of class IV polyhydroxyalkanoate (PHA) synthases, the newest classification of PHA synthases. Class IV synthases are prevalent in organisms of the Bacillus genus and are composed of a catalytic subunit PhaC (approximately 40 kDa), which has a PhaC box sequence ([GS]-X-C-X-[GA]-G) at the active site, and a second subunit PhaR (approximately 20 kDa). The representative PHA-producing Bacillus strains are Bacillus megaterium and Bacillus cereus; the nucleotide sequence of phaC and the genetic organization of the PHA biosynthesis gene locus are somewhat different between these two strains. It is generally considered that class IV synthases favor short-chain-length monomers such as 3-hydroxybutyrate (C4) and 3-hydroxyvalerate (C5) for polymerization, but can polymerize some unusual monomers as minor components. In Escherichia coli expressing PhaRC from B. cereus YB-4, the biosynthesized PHA undergoes synthase-catalyzed alcoholytic cleavage using endogenous and exogenous alcohols. This alcoholysis is thought to be shared among class IV synthases, and this reaction is useful not only for the regulation of PHA molecular weight but also for the modification of the PHA carboxy terminus. The novel properties of class IV synthases will open up the possibility for the design of new PHA materials.
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Affiliation(s)
- Takeharu Tsuge
- Department of Innovative and Engineered Materials, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8502, Japan,
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Wu D, Yuan Y, Liu P, Wu Y, Gao M. Cellular responses in Bacillus thuringiensis CS33 during bacteriophage BtCS33 infection. J Proteomics 2014; 101:192-204. [PMID: 24565692 DOI: 10.1016/j.jprot.2014.02.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 12/09/2013] [Accepted: 02/16/2014] [Indexed: 11/26/2022]
Abstract
UNLABELLED Bacillus thuringiensis (Bt) has been widely used for 50years as a biopesticide for controlling insect pests. However, bacteriophage infection can cause failures in 50%-80% of the batches during Bt fermentation, resulting in severe losses. In the present work, the physiological and biochemical impacts of Bt strain CS33 have been studied during bacteriophage infection. This study adopted a gel-based proteomics approach to probe the sequential changed proteins in phage-infected Bt cells. To phage, it depressed the host energy metabolism by suppressing the respiration chain, the TCA cycle, and the utilization of PHB on one hand; on the other hand, it hijacked the host translational machine for its own macromolecular synthesis. To host, superinfection exclusion might be triggered by the changes of S-layer protein and flagella related proteins, which were located on the cell surface and might play as the candidates for the phage recognition. More importantly, the growth rate, cell mass, and ICPs yield were significantly decreased. The low yield of ICPs was mainly due to the suppressed utilization of PHB granules. Further functional study on these altered proteins may lead to a better understanding of the pathogenic mechanisms and the identification of new targets for phage control. BIOLOGICAL SIGNIFICANCE B. thuringiensis (Bt) has been widely used for 50years as a safe biopesticide for controlling agricultural and sanitary insect pests. However, bacteriophage infection can cause severe losses during B. thuringiensis fermentation. The processes and consequences of interactions between bacteriophage and Bt were still poorly understood, and the molecular mechanisms involved were more unknown. This study adopted a gel-based proteomics approach to probe the physiological and biochemical impacts of Bt strain CS33 after phage-infection. The interactions between phage BtCS33 and its host Bt strain CS33 occurred mainly on four aspects. First, phage synthesized its nucleic acids through metabolic regulation by increasing the amount of NDK. Second, it is reasonable to infer that a phage resistance or superinfection exclusion was triggered by several increased or decreased proteins (SLP, FliD, FlaB), which were located on the cell surface and might play as candidates for the phage recognition. Third, combining the decreased flavoproteins (SdhA and EtfB) and the down regulated Fe-S cluster biosynthesis pathway together, it can be suggested that the respiration chain was weakened after phage infection. Additionally, three key enzymes (AcnB, FumC and AdhA) involved in the TCA cycle were all decreased, indicating the TCA cycle was seriously inhibited after infection. Fourth, the growth rate, cell mass and ICPs yield of the host were significantly decreased. To the best of our knowledge, this work represents the first systematic study on the interactions of an insecticidal bacterium with its phage, and has contributed novel information to understand the molecular events in the important biological pesticide producer, B. thuringiensis, in response to phage challenge.
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Affiliation(s)
- Dandan Wu
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Yihui Yuan
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Pengming Liu
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Yan Wu
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Meiying Gao
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, People's Republic of China.
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Rosenbusch KE, Bakker D, Kuijper EJ, Smits WK. C. difficile 630Δerm Spo0A regulates sporulation, but does not contribute to toxin production, by direct high-affinity binding to target DNA. PLoS One 2012; 7:e48608. [PMID: 23119071 PMCID: PMC3485338 DOI: 10.1371/journal.pone.0048608] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 09/26/2012] [Indexed: 12/19/2022] Open
Abstract
Clostridium difficile is a Gram positive, anaerobic bacterium that can form highly resistant endospores. The bacterium is the causative agent of C. difficile infection (CDI), for which the symptoms can range from a mild diarrhea to potentially fatal pseudomembranous colitis and toxic megacolon. Endospore formation in Firmicutes, including C. difficile, is governed by the key regulator for sporulation, Spo0A. In Bacillus subtilis, this transcription factor is also directly or indirectly involved in various other cellular processes. Here, we report that C. difficile Spo0A shows a high degree of similarity to the well characterized B. subtilis protein and recognizes a similar binding sequence. We find that the laboratory strain C. difficile 630Δerm contains an 18bp-duplication near the DNA-binding domain compared to its ancestral strain 630. In vitro binding assays using purified C-terminal DNA binding domain of the C. difficile Spo0A protein demonstrate direct binding to DNA upstream of spo0A and sigH, early sporulation genes and several other putative targets. In vitro binding assays suggest that the gene encoding the major clostridial toxin TcdB may be a direct target of Spo0A, but supernatant derived from a spo0A negative strain was no less toxic towards Vero cells than that obtained from a wild type strain, in contrast to previous reports. These results identify for the first time direct (putative) targets of the Spo0A protein in C. difficile and make a positive effect of Spo0A on production of the large clostridial toxins unlikely.
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Affiliation(s)
- Katharina E. Rosenbusch
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Dennis Bakker
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ed J. Kuijper
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Wiep Klaas Smits
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
- * E-mail:
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Wu D, He J, Gong Y, Chen D, Zhu X, Qiu N, Sun M, Li M, Yu Z. Proteomic analysis reveals the strategies of Bacillus thuringiensis
YBT-1520 for survival under long-term heat stress. Proteomics 2011; 11:2580-91. [DOI: 10.1002/pmic.201000392] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 03/04/2011] [Accepted: 03/14/2011] [Indexed: 11/05/2022]
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