1
|
Peculiarities and biotechnological potential of environmental adaptation by Geobacillus species. Appl Microbiol Biotechnol 2018; 102:10425-10437. [PMID: 30310966 DOI: 10.1007/s00253-018-9422-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/25/2018] [Accepted: 09/26/2018] [Indexed: 12/21/2022]
Abstract
The genus Geobacillus comprises thermophilic bacilli capable of endospore formation. The members of this genus provide thermostable proteins and can be used in whole cell applications at elevated temperatures; therefore, these organisms are of biotechnological importance. While these applications have been described in previous reviews, the present paper highlights the environmental adaptations and genome diversifications of Geobacillus spp. and their applications in evolutionary-protein engineering. Despite their obligate thermophilic properties, Geobacillus spp. are widely distributed in nature. Because several isolates demonstrate remarkable properties for cell reproduction in their respective niches, they seem to exist not only as endospores but also as vegetative cells in diverse environments. This suggests their excellence in environmental adaptation via genome diversification; in fact, evidence suggests that Geobacillus spp. were derived from Bacillus spp. while diversifying their genomes via horizontal gene transfer. Moreover, when subjected to an environmental stressor, Geobacillus spp. diversify their genomes using inductive mutations and transposable elements to produce derivative cells that are adaptive to the stressor. Notably, inductive mutations in Geobacillus spp. occur more rapidly and frequently than the stress-induced mutagenesis observed in other microorganisms. Owing to this, Geobacillus spp. can efficiently generate mutant genes coding for thermostable enzyme variants from the thermolabile enzyme genes under appropriate selection pressures. This phenomenon provides a new approach to generate thermostable enzymes, termed as thermoadaptation-directed enzyme evolution, thereby expanding the biotechnological potentials of Geobacillus spp. In this review, we have discussed this approach using successful examples and major challenges yet to be addressed.
Collapse
|
2
|
Drejer EB, Hakvåg S, Irla M, Brautaset T. Genetic Tools and Techniques for Recombinant Expression in Thermophilic Bacillaceae. Microorganisms 2018; 6:microorganisms6020042. [PMID: 29748477 PMCID: PMC6027425 DOI: 10.3390/microorganisms6020042] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/02/2018] [Accepted: 05/03/2018] [Indexed: 01/17/2023] Open
Abstract
Although Escherichia coli and Bacillus subtilis are the most prominent bacterial hosts for recombinant protein production by far, additional species are being explored as alternatives for production of difficult-to-express proteins. In particular, for thermostable proteins, there is a need for hosts able to properly synthesize, fold, and excrete these in high yields, and thermophilic Bacillaceae represent one potentially interesting group of microorganisms for such purposes. A number of thermophilic Bacillaceae including B.methanolicus, B.coagulans, B.smithii, B.licheniformis, Geobacillus thermoglucosidasius, G. kaustophilus, and G. stearothermophilus are investigated concerning physiology, genomics, genetic tools, and technologies, altogether paving the way for their utilization as hosts for recombinant production of thermostable and other difficult-to-express proteins. Moreover, recent successful deployments of CRISPR/Cas9 in several of these species have accelerated the progress in their metabolic engineering, which should increase their attractiveness for future industrial-scale production of proteins. This review describes the biology of thermophilic Bacillaceae and in particular focuses on genetic tools and methods enabling use of these organisms as hosts for recombinant protein production.
Collapse
Affiliation(s)
- Eivind B Drejer
- Department of Biotechnology and Food Science, NTNU: Norwegian University of Science and Technology, 7491 Trondheim, Norway.
| | - Sigrid Hakvåg
- Department of Biotechnology and Food Science, NTNU: Norwegian University of Science and Technology, 7491 Trondheim, Norway.
| | - Marta Irla
- Department of Biotechnology and Food Science, NTNU: Norwegian University of Science and Technology, 7491 Trondheim, Norway.
| | - Trygve Brautaset
- Department of Biotechnology and Food Science, NTNU: Norwegian University of Science and Technology, 7491 Trondheim, Norway.
| |
Collapse
|
3
|
Pogrebnyakov I, Jendresen CB, Nielsen AT. Genetic toolbox for controlled expression of functional proteins in Geobacillus spp. PLoS One 2017; 12:e0171313. [PMID: 28152017 PMCID: PMC5289569 DOI: 10.1371/journal.pone.0171313] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 01/19/2017] [Indexed: 11/20/2022] Open
Abstract
Species of genus Geobacillus are thermophilic bacteria and play an ever increasing role as hosts for biotechnological applications both in academia and industry. Here we screened a number of Geobacillus strains to determine which industrially relevant carbon sources they can utilize. One of the strains, G. thermoglucosidasius C56-YS93, was then chosen to develop a toolbox for controlled gene expression over a wide range of levels. It includes a library of semi-synthetic constitutive promoters (76-fold difference in expression levels) and an inducible promoter from the xylA gene. A library of synthetic in silico designed ribosome binding sites was also created for further tuning of translation. The PxylA was further used to successfully express native and heterologous xylanases in G. thermoglucosidasius. This toolbox enables fine-tuning of gene expression in Geobacillus species for metabolic engineering approaches in production of biochemicals and heterologous proteins.
Collapse
Affiliation(s)
- Ivan Pogrebnyakov
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Christian Bille Jendresen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Alex Toftgaard Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| |
Collapse
|
4
|
Tominaga Y, Ohshiro T, Suzuki H. Conjugative plasmid transfer from Escherichia coli is a versatile approach for genetic transformation of thermophilic Bacillus and Geobacillus species. Extremophiles 2016; 20:375-81. [DOI: 10.1007/s00792-016-0819-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/14/2016] [Indexed: 10/22/2022]
|
5
|
Wada K, Kobayashi J, Furukawa M, Doi K, Ohshiro T, Suzuki H. A thiostrepton resistance gene and its mutants serve as selectable markers in Geobacillus kaustophilus HTA426. Biosci Biotechnol Biochem 2015; 80:368-75. [PMID: 26333661 DOI: 10.1080/09168451.2015.1079478] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Effective utilization of microbes often requires complex genetic modification using multiple antibiotic resistance markers. Because a few markers have been used in Geobacillus spp., the present study was designed to identify a new marker for these thermophiles. We explored antibiotic resistance genes functional in Geobacillus kaustophilus HTA426 and identified a thiostrepton resistance gene (tsr) effective at 50 °C. The tsr gene was further used to generate the mutant tsr(H258Y) functional at 55 °C. Higher functional temperature of the mutant was attributable to the increase in thermostability of the gene product because recombinant protein produced from tsr(H258Y) was more thermostable than that from tsr. In fact, the tsr(H258Y) gene served as a selectable marker for plasmid transformation of G. kaustophilus. This new marker could facilitate complex genetic modification of G. kaustophilus and potentially other Geobacillus spp.
Collapse
Affiliation(s)
- Keisuke Wada
- a Faculty of Agriculture, Applied Molecular Microbiology and Biomass Chemistry, Bioscience and Biotechnology , Kyushu University , Fukuoka , Japan
| | - Jyumpei Kobayashi
- b Faculty of Agriculture, Functional Genomics of Extremophiles , Graduate School, Kyushu University , Fukuoka , Japan.,c Department of Chemistry and Biotechnology , Graduate School of Engineering, Tottori University , Tottori , Japan
| | - Megumi Furukawa
- b Faculty of Agriculture, Functional Genomics of Extremophiles , Graduate School, Kyushu University , Fukuoka , Japan
| | - Katsumi Doi
- d Faculty of Agriculture, Microbial Genetics Division, Institute of Genetic Resources , Graduate School, Kyushu University , Fukuoka , Japan
| | - Takashi Ohshiro
- c Department of Chemistry and Biotechnology , Graduate School of Engineering, Tottori University , Tottori , Japan
| | - Hirokazu Suzuki
- b Faculty of Agriculture, Functional Genomics of Extremophiles , Graduate School, Kyushu University , Fukuoka , Japan.,c Department of Chemistry and Biotechnology , Graduate School of Engineering, Tottori University , Tottori , Japan
| |
Collapse
|
6
|
Unique plasmids generated via pUC replicon mutagenesis in an error-prone thermophile derived from Geobacillus kaustophilus HTA426. Appl Environ Microbiol 2015; 81:7625-32. [PMID: 26319877 DOI: 10.1128/aem.01574-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 08/17/2015] [Indexed: 01/10/2023] Open
Abstract
The plasmid pGKE75-catA138T, which comprises pUC18 and the catA138T gene encoding thermostable chloramphenicol acetyltransferase with an A138T amino acid replacement (CATA138T), serves as an Escherichia coli-Geobacillus kaustophilus shuttle plasmid that confers moderate chloramphenicol resistance on G. kaustophilus HTA426. The present study examined the thermoadaptation-directed mutagenesis of pGKE75-catA138T in an error-prone thermophile, generating the mutant plasmid pGKE75(αβ)-catA138T responsible for substantial chloramphenicol resistance at 65°C. pGKE75(αβ)-catA138T contained no mutation in the catA138T gene but had two mutations in the pUC replicon, even though the replicon has no apparent role in G. kaustophilus. Biochemical characterization suggested that the efficient chloramphenicol resistance conferred by pGKE75(αβ)-catA138T is attributable to increases in intracellular CATA138T and acetyl-coenzyme A following a decrease in incomplete forms of pGKE75(αβ)-catA138T. The decrease in incomplete plasmids may be due to optimization of plasmid replication by RNA species transcribed from the mutant pUC replicon, which were actually produced in G. kaustophilus. It is noteworthy that G. kaustophilus was transformed with pGKE75(αβ)-catA138T using chloramphenicol selection at 60°C. In addition, a pUC18 derivative with the two mutations propagated in E. coli at a high copy number independently of the culture temperature and high plasmid stability. Since these properties have not been observed in known plasmids, the outcomes extend the genetic toolboxes for G. kaustophilus and E. coli.
Collapse
|
7
|
Abstract
The genus Geobacillus comprises a group of Gram-positive thermophilic bacteria, including obligate aerobes, denitrifiers, and facultative anaerobes that can grow over a range of 45-75°C. Originally classified as group five Bacillus spp., strains of Bacillus stearothermophilus came to prominence as contaminants of canned food and soon became the organism of choice for comparative studies of metabolism and enzymology between mesophiles and thermophiles. More recently, their catabolic versatility, particularly in the degradation of hemicellulose and starch, and rapid growth rates have raised their profile as organisms with potential for second-generation (lignocellulosic) biorefineries for biofuel or chemical production. The continued development of genetic tools to facilitate both fundamental investigation and metabolic engineering is now helping to realize this potential, for both metabolite production and optimized catabolism. In addition, this catabolic versatility provides a range of useful thermostable enzymes for industrial application. A number of genome-sequencing projects have been completed or are underway allowing comparative studies. These reveal a significant amount of genome rearrangement within the genus, the presence of large genomic islands encompassing all the hemicellulose utilization genes and a genomic island incorporating a set of long chain alkane monooxygenase genes. With G+C contents of 45-55%, thermostability appears to derive in part from the ability to synthesize protamine and spermine, which can condense DNA and raise its Tm.
Collapse
|
8
|
Kananavičiūtė R, Čitavičius D. Genetic engineering of Geobacillus spp. J Microbiol Methods 2015; 111:31-9. [DOI: 10.1016/j.mimet.2015.02.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 02/02/2015] [Accepted: 02/02/2015] [Indexed: 11/15/2022]
|
9
|
Kobayashi J, Furukawa M, Ohshiro T, Suzuki H. Thermoadaptation-directed evolution of chloramphenicol acetyltransferase in an error-prone thermophile using improved procedures. Appl Microbiol Biotechnol 2015; 99:5563-72. [PMID: 25783628 DOI: 10.1007/s00253-015-6522-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 02/26/2015] [Accepted: 03/04/2015] [Indexed: 10/23/2022]
Abstract
Enhancing the thermostability of thermolabile enzymes extends their practical utility. We previously demonstrated that an error-prone thermophile derived from Geobacillus kaustophilus HTA426 can generate mutant genes encoding enzyme variants that are more thermostable than the parent enzyme. Here, we used this approach, termed as thermoadaptation-directed enzyme evolution, to increase the thermostability of the chloramphenicol acetyltransferase (CAT) of Staphylococcus aureus and successfully generated a CAT variant with an A138T replacement (CAT(A138T)). This variant was heterologously produced, and its enzymatic properties were compared with those of the wild type. We found that CAT(A138T) had substantially higher thermostability than CAT but had comparable activities, showing that the A138T replacement enhanced protein thermostability without affecting the catalytic activity. Because variants CAT(A138S) and CAT(A138V), which were generated via in vitro site-directed mutagenesis, were more thermostable than CAT, the thermostability enhancement resulting from the A138T replacement can be attributed to both the presence of a hydroxyl group and the bulk of the threonine side chain. CAT(A138T) conferred chloramphenicol resistance to G. kaustophilus cells at high temperature more efficiently than CAT. Therefore, the gene encoding CAT(A138T) may be useful as a genetic marker in Geobacillus spp. Notably, CAT(A138T) generation was achieved only by implementing improved procedures (plasmid-based mutations on solid media); previous procedures (chromosome-based mutations in liquid media) were unsuccessful. This result suggests that this improved procedure is crucial for successful thermoadaptation-directed evolution in certain cases and increases the opportunities for generating thermostable enzymes.
Collapse
Affiliation(s)
- Jyumpei Kobayashi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, 680-8552, Japan
| | | | | | | |
Collapse
|
10
|
Affiliation(s)
- David J Studholme
- Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK
| |
Collapse
|
11
|
Permanasari ED, Angkawidjaja C, Koga Y, Kanaya S. Role of N-terminal extension of Bacillus stearothermophilus RNase H2 and C-terminal extension of Thermotoga maritima RNase H2. FEBS J 2013; 280:5065-79. [PMID: 23937561 DOI: 10.1111/febs.12479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Revised: 08/01/2013] [Accepted: 08/07/2013] [Indexed: 11/28/2022]
Abstract
Bacillus stearothermophilus RNase H2 (BstRNH2) and Thermotoga maritima RNase H2 (TmaRNH2) have N-terminal and C-terminal extensions, respectively, as compared with Aquifex aeolicus RNase H2 (AaeRNH2). To analyze the role of these extensions, BstRNH2 and TmaRNH2 without these extensions were constructed, and their biochemical properties were compared with those of their intact partners and AaeRNH2. The far-UV CD spectra of all proteins were similar, suggesting that the protein structure is not significantly altered by removal of these extensions. However, both the junction ribonuclease and RNase H activities of BstRNH2 and TmaRNH2, as well as their substrate-binding affinities, were considerably decreased by removal of these extensions. The stability of BstRNH2 and TmaRNH2 was also decreased by removal of these extensions. The activity, substrate binding affinity and stability of TmaRNH2 without the C-terminal 46 residues were partly restored by the attachment of the N-terminal extension of BstRNH2. These results suggest that the N-terminal extension of BstRNH2 functions as a substrate-binding domain and stabilizes the RNase H domain. Because the C-terminal extension of TmaRNH2 assumes a helix hairpin structure and does not make direct contact with the substrate, this extension is probably required to make the conformation of the substrate-binding site functional. AaeRNH2 showed comparable junction ribonuclease activity to those of BstRNH2 and TmaRNH2, and was more stable than these proteins, indicating that bacterial RNases H2 do not always require an N-terminal or C-terminal extension to increase activity, substrate-binding affinity, and/or stability.
Collapse
Affiliation(s)
- Etin-Diah Permanasari
- Department of Material and Life Science, Graduate School of Engineering, Osaka University, Japan
| | | | | | | |
Collapse
|
12
|
Construction of a stable replicating shuttle vector for Caldicellulosiruptor species: use for extending genetic methodologies to other members of this genus. PLoS One 2013; 8:e62881. [PMID: 23658781 PMCID: PMC3643907 DOI: 10.1371/journal.pone.0062881] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 03/26/2013] [Indexed: 01/27/2023] Open
Abstract
The recalcitrance of plant biomass is the most important barrier to its economic conversion by microbes to products of interest. Thermophiles have special advantages for biomass conversion and members of the genus Caldicellulosiruptor are the most thermophilic cellulolytic microbes known. In this study, we report the construction of a replicating shuttle vector for Caldicellulosiruptor species based on pBAS2, the smaller of two native C. bescii plasmids. The entire plasmid was cloned into an E. coli cloning vector containing a pSC101 origin of replication and an apramycin resistance cassette for selection in E. coli. The wild-type C. bescii pyrF locus was cloned under the transcriptional control of the regulatory region of the ribosomal protein S30EA (Cbes2105), and the resulting vector was transformed into a new spontaneous deletion mutant in the pyrFA locus of C. bescii that allowed complementation with the pyrF gene alone. Plasmid DNA was methylated in vitro with a recently described cognate methyltransferase, M.CbeI, and transformants were selected for uracil prototrophy. The plasmid was stably maintained in low copy with selection but rapidly lost without selection. There was no evidence of DNA rearrangement during transformation and replication in C. bescii. A similar approach was used to screen for transformability of other members of this genus using M.CbeI to overcome restriction as a barrier and was successful for transformation of C. hydrothermalis, an attractive species for many applications. Plasmids containing a carbohydrate binding domain (CBM) and linker region from the C. bescii celA gene were maintained with selection and were structurally stable through transformation and replication in C. bescii and E. coli.
Collapse
|
13
|
Gao C, Xue Y, Ma Y. Protoplast transformation of recalcitrant alkaliphilic Bacillus sp. with methylated plasmid DNA and a developed hard agar regeneration medium. PLoS One 2011; 6:e28148. [PMID: 22132233 PMCID: PMC3223237 DOI: 10.1371/journal.pone.0028148] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Accepted: 11/02/2011] [Indexed: 11/19/2022] Open
Abstract
Among the diverse alkaliphilic Bacillus strains, only a little have been reported to be genetically transformed. In this study, an efficient protoplast transformation procedure was developed for recalcitrant alkaliphilic Bacillus sp. N16-5. The procedure involved polyethylene glycol-induced DNA uptake by the protoplasts and subsequent protoplast regeneration with a developed hard agar regeneration medium. An in vivo methylation strategy was introduced to methylate the exogenous plasmid DNA for improving the transformation efficiency. The transformation efficiency reached to 1.1×105 transformants per µg plasmid DNA with methylated plasmid pHCMC04 and the developed hard agar regeneration medium. This procedure might also be applicable to the genetic transformation of other Bacillus strains.
Collapse
Affiliation(s)
- Chenghua Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Graduate School of the Chinese Academy of Sciences, Beijing, China
| | - Yanfen Xue
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yanhe Ma
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- * E-mail:
| |
Collapse
|
14
|
Maehara T, Itaya M, Ogura M, Tanaka T. Effect of Bacillus subtilis BsuM restriction-modification on plasmid transfer by polyethylene glycol-induced protoplast fusion. FEMS Microbiol Lett 2011; 325:49-55. [DOI: 10.1111/j.1574-6968.2011.02410.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Revised: 08/16/2011] [Accepted: 09/02/2011] [Indexed: 11/29/2022] Open
Affiliation(s)
- Tomoko Maehara
- Institute of Oceanic Research and Development; Tokai University; Shimizu; Shizuoka; Japan
| | - Mitsuhiro Itaya
- Institute for Advanced Biosciences; Keio University; Tsuruoka; Yamagata; Japan
| | - Mitsuo Ogura
- Institute of Oceanic Research and Development; Tokai University; Shimizu; Shizuoka; Japan
| | - Teruo Tanaka
- Institute of Oceanic Research and Development; Tokai University; Shimizu; Shizuoka; Japan
| |
Collapse
|
15
|
Zhang XZ, Zhang YHP. One-step production of biocommodities from lignocellulosic biomass by recombinant cellulolytic Bacillus subtilis: Opportunities and challenges. Eng Life Sci 2010. [DOI: 10.1002/elsc.201000011] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
16
|
Zhang M, Nakai H, Imanaka T. Useful Host-Vector Systems in Bacillus stearothermophilus. Appl Environ Microbiol 2010; 54:3162-4. [PMID: 16347805 PMCID: PMC204443 DOI: 10.1128/aem.54.12.3162-3164.1988] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We isolated a highly transformable thermophile, Bacillus stearothermophilus SIC1, which exhibited the following features. The growth temperature ranged from 45 to 65 degrees C in L broth. The maximum cell concentration in 2L broth (2% tryptone, 1% yeast extract, 0.5% NaCl, pH 7.2) was determined as an optical density at 660 nm of 7.8, and the generation time was 11 min at 60 degrees C. Strain SIC1 was a prototroph and was transformed by the protoplast procedure not only with repB plasmids (high-copy-number plasmids such as pTB913 and pUB110) but also with repA plasmids (low-copy-number plasmids such as pTB53). Transformation efficiencies with repB and repA plasmids were about 2 x 10 to 5 x 10 and 5 x 10 transformants per mug of DNA, respectively. The transformant carrying plasmid pTB913Y/K could grow at 63 degrees C in the presence of kanamycin. The regeneration frequency of protoplasts was 60%, and only 1 day was needed for regeneration at 55 degrees C.
Collapse
Affiliation(s)
- M Zhang
- Department of Fermentation Technology, Faculty of Engineering, Osaka University, Yamadaoka, Suita-shi, Osaka 565, Japan
| | | | | |
Collapse
|
17
|
Construction of a gene knockout system for application in Paenibacillus alvei CCM 2051T, exemplified by the S-layer glycan biosynthesis initiation enzyme WsfP. Appl Environ Microbiol 2009; 75:3077-85. [PMID: 19304819 DOI: 10.1128/aem.00087-09] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The gram-positive bacterium Paenibacillus alvei CCM 2051T is covered by an oblique surface layer (S-layer) composed of glycoprotein subunits. The S-layer O-glycan is a polymer of [-->3)-beta-D-Galp-(1[alpha-D-Glcp-(1-->6)]-->4)-beta-D-ManpNAc-(1-->] repeating units that is linked by an adaptor of -[GroA-2-->OPO2-->4-beta-D-ManpNAc-(1-->4)]-->3)-alpha-L-Rhap-(1-->3)-alpha-L-Rhap-(1-->3)-alpha-L-Rhap-(1-->3)-beta-D-Galp-(1--> to specific tyrosine residues of the S-layer protein. For elucidation of the mechanism governing S-layer glycan biosynthesis, a gene knockout system using bacterial mobile group II intron-mediated gene disruption was developed. The system is further based on the sgsE S-layer gene promoter of Geobacillus stearothermophilus NRS 2004/3a and on the Geobacillus-Bacillus-Escherichia coli shuttle vector pNW33N. As a target gene, wsfP, encoding a putative UDP-Gal:phosphoryl-polyprenol Gal-1-phosphate transferase, representing the predicted initiation enzyme of S-layer glycan biosynthesis, was disrupted. S-layer protein glycosylation was completely abolished in the insertional P. alvei CCM 2051T wsfP mutant, according to sodium dodecyl sulfate-polyacrylamide gel electrophoresis evidence and carbohydrate analysis. Glycosylation was fully restored by plasmid-based expression of wsfP in the glycan-deficient P. alvei mutant, confirming that WsfP initiates S-layer protein glycosylation. This is the first report on the successful genetic manipulation of bacterial S-layer protein glycosylation in vivo, including transformation of and heterologous gene expression and gene disruption in the model organism P. alvei CCM 2051T.
Collapse
|
18
|
Workman WE, McLinden JH, Dean DH, Copeland JC. Genetic Engineering Applications to Biotechnology in the GenusBacillus. Crit Rev Biotechnol 2008. [DOI: 10.3109/07388558509150784] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
19
|
Wiegel J, Ljungdahl LG, Demain AL. The Importance of Thermophilic Bacteria in Biotechnology. Crit Rev Biotechnol 2008. [DOI: 10.3109/07388558509150780] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
20
|
Complete nucleotide sequence of pGS18, a 62.8-kb plasmid from Geobacillus stearothermophilus strain 18. Extremophiles 2008; 12:415-29. [DOI: 10.1007/s00792-008-0145-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Accepted: 01/22/2008] [Indexed: 11/26/2022]
|
21
|
Identification andin silico characterisation of putative conjugative transfer genes onGeobacillus stearothermophilus plasmids. ANN MICROBIOL 2007. [DOI: 10.1007/bf03175081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
|
22
|
AIBA SHUICHI, KOIZUMI JUNICHI, RU JIASHI. ENHANCED PRODUCTION OF α-AMYLASE AND PLASMID STABILITY IN BATCH AND/OR CONTINUOUS CULTURES OF BACILLUS STEAROTHERMOPHILUS (pAT9). CHEM ENG COMMUN 2007. [DOI: 10.1080/00986448608911386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- SHUICHI AIBA
- a Department of Fermentation Technology, Faculty of Engineering , Osaka University , Yamada-Oka, Suita-shi, Osaka, 565, Japan
| | - JUN-ICHI KOIZUMI
- a Department of Fermentation Technology, Faculty of Engineering , Osaka University , Yamada-Oka, Suita-shi, Osaka, 565, Japan
| | - JIA SHI RU
- a Department of Fermentation Technology, Faculty of Engineering , Osaka University , Yamada-Oka, Suita-shi, Osaka, 565, Japan
| |
Collapse
|
23
|
Wu CY, Chen CL, Lee YH, Cheng YC, Wu YC, Shu HY, Götz F, Liu ST. Nonribosomal Synthesis of Fengycin on an Enzyme Complex Formed by Fengycin Synthetases. J Biol Chem 2007; 282:5608-16. [PMID: 17182617 DOI: 10.1074/jbc.m609726200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Fengycin, a lipopeptidic antibiotic, is synthesized nonribosomally by five fengycin synthetases (FenC, FenD, FenE, FenA, and FenB) in Bacillus subtilis F29-3. This work demonstrates that these fengycin synthetases interlock to form a chain, which coils into a 14.5-nm structure. In this chain, fengycin synthetases are linked in the order FenC-FenD-FenE-FenA-FenB by interactions between the C-terminal region of an upstream enzyme and the N-terminal region of its downstream partner enzyme, with their amino acid activation modules arranged colinearly with the amino acids in fengycin. This work also reveals that fengycin is synthesized on this fengycin synthetase chain, explaining how fengycin is synthesized efficiently and accurately. The results from this investigation demonstrate that forming a peptide synthetase complex is crucial to nonribosomal peptide synthesis.
Collapse
Affiliation(s)
- Cheng-Yeu Wu
- Molecular Genetics Laboratory, Department of Microbiology and Immunology, Chang-Gung University, 259 Wen-Hwa 1st Road, Kwei-Shan, Taoyuan 333, Taiwan
| | | | | | | | | | | | | | | |
Collapse
|
24
|
Imanaka T. Application of recombinant DNA technology to the production of useful biomaterials. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2005; 33:1-27. [PMID: 2944355 DOI: 10.1007/bfb0002451] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
25
|
Lin TP, Chen CL, Fu HC, Wu CY, Lin GH, Huang SH, Chang LK, Liu ST. Functional analysis of fengycin synthetase FenD. ACTA ACUST UNITED AC 2005; 1730:159-64. [PMID: 16102594 DOI: 10.1016/j.bbaexp.2005.02.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2004] [Revised: 11/27/2004] [Accepted: 02/15/2005] [Indexed: 10/25/2022]
Abstract
Fengycin is a cyclic lipopeptidic antibiotic produced nonribosomally by Bacillus subtilis. A fengycin synthetase mutant of B. subtilis F29-3 was generated with Tn917lux, which contains a transposon inserted in a 7716-bp gene, fenD. The mutation can be genetically complemented by transforming a plasmid carrying a wild-type fenD, confirming the participation of the gene in fengycin synthesis. Sequencing and biochemical analysis reveal that this gene encodes an enzyme that includes two amino acid-activating modules, FenD1 and FenD2, which activate l-Tyr and l-Thr, the third and the fourth amino acids in fengycin, respectively.
Collapse
Affiliation(s)
- Tsuey-Pin Lin
- Department of Health and Nutrition, Chia Nan University of Pharmacy and Science, Tainan 701, Taiwan
| | | | | | | | | | | | | | | |
Collapse
|
26
|
Couñago R, Shamoo Y. Gene replacement of adenylate kinase in the gram-positive thermophile Geobacillus stearothermophilus disrupts adenine nucleotide homeostasis and reduces cell viability. Extremophiles 2005; 9:135-44. [PMID: 15647886 DOI: 10.1007/s00792-004-0428-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2004] [Accepted: 10/25/2004] [Indexed: 11/28/2022]
Abstract
Thermophilic bacteria are of great value for industry and research communities. Unfortunately, the cellular processes and mechanisms of these organisms remain largely understudied. In the present study, we investigate how the inactivation of adenylate kinase (AK) affects the adenine nucleotide homeostasis of a gram-positive moderate thermophile, Geobacillus stearothermophilus strain NUB3621-R. AK plays a major role in the adenine nucleotide homeostasis of living cells and has been shown to be essential for the gram-negative mesophile Escherichia coli. To study the role of AK in the maintenance of adenylate energy charge (EC) and cell viability of G. stearothermophilus, we generated a recombinant strain of this organism in which its endogenous gene coding for the essential protein adenylate kinase (AK) has been replaced with the adk gene from the mesophile Bacillus subtilis. PCR, DNA sequencing and Southern analysis were performed to confirm proper gene replacement and preservation of neighboring genes. The highest growing temperature for recombinant cells was almost 20 degrees C lower than for wild-type cells (56 vs. 75 degrees C). This temperature-sensitive phenotype was secondary to heat inactivation of B. subtilis AK, as evidenced by enzyme activity assays and EC measurements. At higher temperatures (65 degrees C), recombinant cells also had lower EC values (0.09) compared to wild-type cells (0.45), which reflects a disruption of adenine nucleotide homeostasis following AK inactivation.
Collapse
Affiliation(s)
- Rafael Couñago
- Biochemistry and Cell Biology Department, Rice University, 6100 Main st. MS 140, Houston, TX 77251-1892, USA
| | | |
Collapse
|
27
|
Muroya A, Nakano R, Ohtani N, Haruki M, Morikawa M, Kanaya S. Importance of an N-terminal extension in ribonuclease HII from Bacillus stearothermophilus for substrate binding. J Biosci Bioeng 2002. [DOI: 10.1016/s1389-1723(02)80010-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
28
|
Lin TP, Chen CL, Chang LK, Tschen JS, Liu ST. Functional and transcriptional analyses of a fengycin synthetase gene, fenC, from Bacillus subtilis. J Bacteriol 1999; 181:5060-7. [PMID: 10438779 PMCID: PMC93996 DOI: 10.1128/jb.181.16.5060-5067.1999] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A 37-kb DNA fragment containing five fengycin synthetase genes, including fenC, fenD, fenE, fenA, and fenB, was cloned and sequenced. Among these genes, fenC encodes a fengycin synthetase 2,560 amino acids long with an estimated molecular mass of 287 kDa. This protein contains two amino acid activation modules, FenC1 and FenC2, which activate L-glutamic acid and L-ornithine, respectively. Primer extension, using mRNA isolated from the log-phase cells, identified a transcription start site located 86 nucleotides upstream from the initiation codon of fenC, implying that a promoter is located upstream from the start site. Primer extension using total RNA isolated from stationary-phase cells also identified a transcription start site located 61 nucleotides upstream from the initiation codon of fenC. Gene fusion studies demonstrated that in nHA medium, the cells transcribe the fengycin synthetase genes at two different stages of cell growth. The promoter is active during the log phase, and the activity reaches the highest level during the late log phase. The activity decreases sharply but is maintained at a low level for approximately 24 h after cells enter the early stationary phase. The results of this investigation also suggest that the transcription of fenC is positively regulated during the late log phase. Results presented herein provide further insight into fengycin synthesis by B. subtilis F29-3.
Collapse
Affiliation(s)
- T P Lin
- Graduate Institute of Microbiology and Immunology, National Yang-Ming University, Shih-Pai, Taipei 112, Taiwan
| | | | | | | | | |
Collapse
|
29
|
Studholme DJ, Jackson RA, Leak DJ. Phylogenetic analysis of transformable strains of thermophilic Bacillus species. FEMS Microbiol Lett 1999; 172:85-90. [PMID: 10079532 DOI: 10.1111/j.1574-6968.1999.tb13454.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Few strains of thermophilic Bacillus spp are readily transformable with plasmid DNA. Given the considerable phylogenetic and phenotypic diversity amongst thermophilic bacilli, we have examined whether transformability is a trait associated with a particular phylogenetic group, by sequencing the 16S ribosomal RNA genes from transformable strains NUB3621, K1041, and NRRL1174. Although all of these strains were described in the literature as B. stearothermophilus, only NRRL1174 is closely related to the type strain of this species. Based on its 16S rDNA sequence and physiological data K1041 appeared to belong to the species B. thermodenitrificans, while NUB3621 showed a slightly closer relationship to B. thermoglucosidasius than to B. stearothermophilus. Therefore we conclude that the trait of transformability, though possibly strain-specific, is not limited to a single species of thermophilic Bacillus.
Collapse
Affiliation(s)
- D J Studholme
- Department of Biochemistry, Imperial College of Science, Technology and Medicine, London, UK
| | | | | |
Collapse
|
30
|
Takagi M, Nishioka M, Kakihara H, Kitabayashi M, Inoue H, Kawakami B, Oka M, Imanaka T. Characterization of DNA polymerase from Pyrococcus sp. strain KOD1 and its application to PCR. Appl Environ Microbiol 1997; 63:4504-10. [PMID: 9361436 PMCID: PMC168769 DOI: 10.1128/aem.63.11.4504-4510.1997] [Citation(s) in RCA: 192] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The DNA polymerase gene from the archaeon Pyrococcus sp. strain KOD1 (KOD DNA polymerase) contains a long open reading frame of 5,013 bases that encodes 1,671 amino acid residues (GenBank accession no. D29671). Similarity analysis revealed that the DNA polymerase contained a putative 3'-5' exonuclease activity and two in-frame intervening sequences of 1,080 bp (360 amino acids; KOD pol intein-1) and 1,611 bp (537 amino acids; KOD pol intein-2), which are located in the middle of regions conserved among eukaryotic and archaeal alpha-like DNA polymerases. The mature form of the DNA polymerase gene was expressed in Escherichia coli, and the recombinant enzyme was purified and characterized. 3'-5' exonuclease activity was confirmed, and although KOD DNA polymerase's optimum temperature (75 degrees C) and mutation frequency (3.5 x 10(-3)) were similar to those of a DNA polymerase from Pyrococcus furiosus (Pfu DNA polymerase), the KOD DNA polymerase exhibited an extension rate (100 to 130 nucleotides/s) 5 times higher and a processivity (persistence of sequential nucleotide polymerization) 10 to 15 times higher than those of Pfu DNA polymerase. These characteristics enabled the KOD DNA polymerase to perform a more accurate PCR in a shorter reaction time.
Collapse
Affiliation(s)
- M Takagi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Japan
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Yang H, Park SM, Nolan WG, Lu CD, Abdelal AT. Cloning and characterization of the arginine-specific carbamoyl-phosphate synthetase from Bacillus stearothermophilus. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 249:443-9. [PMID: 9370352 DOI: 10.1111/j.1432-1033.1997.00443.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Bacillus stearothermophilus contains two carbamoyl-phosphate synthetases (CPS), one specific for pyrimidine biosynthesis and the other for arginine biosynthesis. The pyrimidine-specific CPS is repressed by exogenous pyrimidines, and its activity is inhibited by UMP and activated by 5-phospho-alpha-D-ribosyl diphosphate. The arginine-specific CPS is similarly repressed by exogenous arginine but its activity is not sensitive to these or other potential effectors. Each of the two enzymes consist of two unequal subunits, as is the case for other microbial CPS; however, the large subunit for the arginine-specific CPS is smaller than that for the pyrimidine-specific enzyme. Comparison of the derived amino acid sequence for the cloned large subunit of the arginine-specific CPS with those for subunits from pyrimidine-sensitive CPS showed significant similarity throughout the polypeptides except at the carboxy terminus, which was identified by other laboratories to contain the binding site for the pyrimidine effector. Unlike the results previously reported for CPS from an enteric mesophile, the kinetic properties of the arginine-specific CPS were not affected by growth of B. stearothermophilus at temperatures near the minimal growth temperature. Furthermore, calorimetric studies showed that the thermal stability of cloned CPS was identical regardless of the growth temperature of B. stearothermophilus between 42 degrees C and 63 degrees C. The thermal stability of cloned CPS was not affected by expression at 37 C in Bacillus subtilis or Escherichia coli. In contrast, the thermal stabilities for CPS and other proteins were higher in extracts of cells grown at higher temperatures. These results indicate that cellular factors, probably chaperonins, are necessary for thermal stability of proteins at and below the optimal temperature for this thermophile.
Collapse
Affiliation(s)
- H Yang
- Department of Biology, Georgia State University, Atlanta, USA
| | | | | | | | | |
Collapse
|
32
|
Effect of culture temperature and dissolved oxygen concentration on expression of α-amylase gene in batch culture of spore-forming host, Bacillus subtilis 1A289. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s0922-338x(97)82786-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
33
|
Liang Q, Fulco AJ. Transcriptional regulation of the genes encoding cytochromes P450BM-1 and P450BM-3 in Bacillus megaterium by the binding of Bm3R1 repressor to Barbie box elements and operator sites. J Biol Chem 1995; 270:18606-14. [PMID: 7629191 DOI: 10.1074/jbc.270.31.18606] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
We previously reported (Liang, Q., He, J.-S., and Fulco, A.J. (1995) J. Biol. Chem. 270, 4438-4450) that Bm3R1, a repressor regulating the expression of P450BM-3 in Bacillus megaterium, could bind to Barbie box sequences in the 5'-flanking regions of barbiturate-inducible genes. We've now shown that pentobarbital does not inhibit in vitro binding of Bm3R1 to the P450BM-3 and P450BM-1 Barbie boxes (BB3 and BB1), although the palindromic operator sequence (OIII) of P450BM-3 did have a strong competitive effect on such binding. G39E-Bm3R1, a mutant of Bm3R1, did not bind to either Barbie box. In the presence of Bm3R1, portions of the regulatory regions of P450BM-3 and P450BM-1 were protected from DNase I digestion. These included 11 of the 15 base pairs of BB3 plus 7 base pairs 3' to BB3, BB1 plus 16 base pairs 3' to BB1, and, in the 5'-flanking region of P450BM-1, segments covering most of two palindromic sequences (OII and OIII) of 24 and 52 base pairs. These DNase I-protected regions (including OIII) showed considerable sequence identity, especially in a conserved poly(A) motif. Barbiturates did not inhibit binding of Bm3R1 to OI. OII in vitro while G39E-Bm3R1 did not bind. The regulatory effects of Bm3R1 on P450BM-1 and P450BM-3 were also evaluated in vivo using heterologous chloramphenicol acetyltransferase constructs and Western blotting. In the G39E mutant strain, both P450BM-1 and P450BM-3 were constitutively expressed, and the regulatory proteins Bm1P1 and Bm3P1, although still pentobarbital-inducible, had significantly higher basal levels of synthesis. In toto, our results show that Bm3R1 represses both P450BM-1 and P450BM-3 expression and that it may effect this by coordinate binding to operator and Barbie box sequences to produce looping of the P450BM-1 and P450BM-3 regulatory regions through protein-protein interaction.
Collapse
Affiliation(s)
- Q Liang
- Department of Biological Chemistry, School of Medicine, University of California, Los Angeles 90024-1737, USA
| | | |
Collapse
|
34
|
Chen CL, Chang LK, Chang YS, Liu ST, Tschen JS. Transposon mutagenesis and cloning of the genes encoding the enzymes of fengycin biosynthesis in Bacillus subtilis. MOLECULAR & GENERAL GENETICS : MGG 1995; 248:121-5. [PMID: 7651334 DOI: 10.1007/bf02190792] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A total of 20 Bacillus subtilis F29-3 mutants defective in fengycin biosynthesis was obtained by Tn917 mutagenesis. Cloning and mapping results showed that the transposon in these mutants was inserted in eleven different locations on the chromosome. We were able to use the chromosomal sequence adjacent to the transposon as a probe to screen for cosmid clones containing the fengycin biosynthesis genes. One of the clones obtained, pFC660, was 46 kb long. Eight transposon insertion sites were mapped within this plasmid. Among the eleven different mutants analyzed, four mutants had Tn917 inserted in regions which encoded peptide sequences similar to part of gramicidin S synthetase, surfactin synthetase, and tyrocidine synthetase. Our results suggest that fengycin is synthesized nonribosomally by the multienzyme thiotemplate mechanism.
Collapse
Affiliation(s)
- C L Chen
- Institute of Botany, National Chung-Hsing University, Taichung, Taiwan
| | | | | | | | | |
Collapse
|
35
|
Wahlund TM, Madigan MT. Genetic transfer by conjugation in the thermophilic green sulfur bacterium Chlorobium tepidum. J Bacteriol 1995; 177:2583-8. [PMID: 7730296 PMCID: PMC176923 DOI: 10.1128/jb.177.9.2583-2588.1995] [Citation(s) in RCA: 68] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The broad-host-range IncQ group plasmids pDSK519 and pGSS33 were transferred by conjugation from Escherichia coli into the thermophilic green sulfur bacterium Chlorobium tepidum. C. tepidum exconjugants expressed the kanamycin and ampicillin-chloramphenicol resistances encoded by pDSK519 and pGSS33, respectively. Ampicillin resistance was a particularly good marker for selection in C. tepidum. Both pDSK519 and pGSS33 were stably maintained in C. tepidum at temperatures below 42 degrees C and could be transferred between C. tepidum and E. coli without modifications. Conjugation frequencies ranged from 10(-1) to 10(-4) exconjugants per donor cell, and frequencies of 10(-2) to 10(-3) were consistently obtained when ampicillin resistance was used as a selectable marker. Methods for growth of C. tepidum on agar, isolation of plating strains and antibiotic-resistant mutants of wild-type C. tepidum cells, and optimum conditions for conjugation were also investigated.
Collapse
Affiliation(s)
- T M Wahlund
- Department of Microbiology, Southern Illinois University, Carbondale 62901-6508, USA
| | | |
Collapse
|
36
|
Chang LK, Chen CL, Chang YS, Tschen JS, Chen YM, Liu ST. Construction of Tn917ac1, a transposon useful for mutagenesis and cloning of Bacillus subtilis genes. Gene 1994; 150:129-34. [PMID: 7959038 DOI: 10.1016/0378-1119(94)90871-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A Tn917 derivative was constructed for the purposes of mutagenesis and cloning of Bacillus subtilis genes. This transposon, Tn917ac1 (4.6 kb), consisted of terminal inverted repeats of Tn917, the res sequence, a ColE1 origin of replication (ori) and two drug-resistance genes. The plasmid carrying this transposon, named pD917, contained the erm-tnpR-tnpA gene cluster of Tn917 and a temperature-sensitive ori of pE194. For the purpose of mutagenesis, transposition of Tn917ac1 was induced by culturing strains harboring pD917 in a medium containing a low concentration of erythromycin. Cells with a Tn917ac1 insertion in the chromosome were selected on agar containing chloramphenicol after heat treatment to eliminate the plasmidic form of pD917. DNA fragments adjacent to Tn917ac1 could be cloned by restriction digestion of the chromosomal DNA and by transforming the self-ligated restriction fragments into Escherichia coli. Sequence analysis revealed that Tn917ac1 was integrated into the chromosome of B. subtilis by transposition in a recE strain and by transposition or integration of pD917 in a wild-type strain. Tn917ac1 has been demonstrated to be useful for mutating and cloning of the genes involved in the biosynthesis of fengycin in B. subtilis F29-3.
Collapse
Affiliation(s)
- L K Chang
- Institute of Botany, National Taiwan University, Taipei
| | | | | | | | | | | |
Collapse
|
37
|
De Rossi E, Brigidi P, Welker NE, Riccardi G, Matteuzzi D. New shuttle vector for cloning in Bacillus stearothermophilus. Res Microbiol 1994; 145:579-83. [PMID: 7871236 DOI: 10.1016/0923-2508(94)90074-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cloning vector plasmid pRP9 was constructed on the basis of the broad host-range plasmid pLM6. pRP9 was a small plasmid (2.9 kb), possessed a convenient polyrestriction site sequence and efficiently transformed Bacillus subtilis, Bacillus stearothermophilus and Escherichia coli. Furthermore, pRP9 presented a very high segregational stability in Bacillus hosts. Also, the structural stability in Bacillus strains, grown under selective pressure, of pRP9 carrying a 3-kb fragment, was high. No single-stranded and high-molecular weight pRP9 DNA was found in B. stearothermophilus. The host/vector systems described possessed all the properties required for efficient gene cloning.
Collapse
Affiliation(s)
- E De Rossi
- Department of Genetics and Microbiology A. Buzzati Traverso, University of Pavia, Italy
| | | | | | | | | |
Collapse
|
38
|
Lee SP, Morikawa M, Takagi M, Imanaka T. Cloning of the aapT gene and characterization of its product, alpha-amylase-pullulanase (AapT), from thermophilic and alkaliphilic Bacillus sp. strain XAL601. Appl Environ Microbiol 1994; 60:3764-73. [PMID: 7986049 PMCID: PMC201885 DOI: 10.1128/aem.60.10.3764-3773.1994] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
A thermophilic and alkaliphilic Bacillus sp. strain, XAL601, was isolated from soil. It produces a thermostable and alkaline-stable enzyme with both alpha-amylase and pullulanase activities. The alpha-amylase-pullulanase gene (aapT) from this Bacillus strain was cloned, and its nucleotide sequence was determined (GenBank accession number D28467). A very large open reading frame composed of 6,096 bases, which encodes 2,032 amino acid residues with an M(r) of 224,992, was found. The deduced amino acid sequence revealed that the four highly conserved regions that are common among amylolytic enzymes were well conserved. These include an active center and common substrate-binding sites of various amylases. In the C-terminal region, a six-amino-acid sequence (Gly-Ser-Gly-Thr-Thr-Pro) is repeated 12 times. The aapT gene was then subcloned in Escherichia coli and overexpressed under the control of the lac promoter. Purification of AapT from this recombinant E. coli was performed, and it was shown that the aapT gene product exhibits both alpha-amylase and pullulanase activities with one active site. The optimum temperature and pH for enzyme activity were found to be 70 degrees C and pH 9, respectively. Furthermore, AapT was found to strongly adsorb to crystalline cellulose (Avicel) and raw corn starch. Final hydrolyzed products from soluble starch range from maltose (G2) to maltotetraose (G4). Only maltotriose (G3) was produced from pullulan. The enzyme also hydrolyzes raw starch under a broad range of conditions (60 to 70 degrees C and pH 8 to 9).
Collapse
Affiliation(s)
- S P Lee
- Department of Biotechnology, Faculty of Engineering, Osaka University, Japan
| | | | | | | |
Collapse
|
39
|
Takata H, Takaha T, Kuriki T, Okada S, Takagi M, Imanaka T. Properties and active center of the thermostable branching enzyme from Bacillus stearothermophilus. Appl Environ Microbiol 1994; 60:3096-104. [PMID: 7944355 PMCID: PMC201776 DOI: 10.1128/aem.60.9.3096-3104.1994] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Although the branching enzyme (EC 2.4.1.18) is a member of the alpha-amylase family, the characteristics are not understood. The thermostable branching enzyme gene from Bacillus stearothermophilus TRBE14 was cloned and expressed in Escherichia coli. The branching enzyme was purified to homogeneity, and various enzymatic properties were analyzed by our improved assay method. About 80% of activity was retained when the enzyme was heated at 60 degrees C for 30 min, and the optimum temperature for activity was around 50 degrees C. The enzyme was stable in the range of pH 7.5 to 9.5, and the optimum pH was 7.5. The nucleotide sequence of the gene was determined, and the active center of the enzyme was analyzed by means of site-directed mutagenesis. The catalytic residues were tentatively identified as two Asp residues and a Glu residue by comparison of the amino acid sequences of various branching enzymes from different sources and enzymes of the alpha-amylase family. When the Asp residues and Glu were replaced by Asn and Gln, respectively, the branching enzyme activities disappeared. The results suggested that these three residues are the catalytic residues and that the catalytic mechanism of the branching enzyme is basically identical to that of alpha-amylase. On the basis of these results, four conserved regions including catalytic residues and most of the substrate-binding residues of various branching enzymes are proposed.
Collapse
Affiliation(s)
- H Takata
- Biochemical Research Laboratories, Ezaki Glico Co., Ltd., Osaka, Japan
| | | | | | | | | | | |
Collapse
|
40
|
Rosado A, Duarte GF, Seldin L. Optimization of electroporation procedure to transform B. polymyxa SCE2 and other nitrogen-fixing Bacillus. J Microbiol Methods 1994. [DOI: 10.1016/0167-7012(94)90020-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
41
|
Wang GF, Kuriki T, Roy KL, Kaneda T. The primary structure of branched-chain alpha-oxo acid dehydrogenase from Bacillus subtilis and its similarity to other alpha-oxo acid dehydrogenases. EUROPEAN JOURNAL OF BIOCHEMISTRY 1993; 213:1091-9. [PMID: 8504804 DOI: 10.1111/j.1432-1033.1993.tb17858.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The bfmB mutant of Bacillus subtilis requires branched short-chain carboxylic acids for growth because the organism is known to be defective in branched-chain alpha-oxo acid dehydrogenase. The DNA in the region of bfmB has now been cloned and sequenced, and the gene has been analyzed. The results show that there are three open reading frames in the area, each of which is preceded by a putative ribosome binding site, and the last of which is followed by a putative transcription termination site with inverted repeats. The amino acid sequences deduced by analysis of the reading frames are highly similar (with 32-49% identity) to the E1 alpha, El beta and E2 components of pyruvate, 2-oxoglutarate and branched-chain alpha-oxo acid dehydrogenases from different sources. The thiamin diphosphate binding, putative subunit interaction and phosphorylation sites of the E1 alpha of four reported branched-chain alpha-oxo acid dehydrogenases from different sources are very similar to those of the first open reading frame (E1 alpha) of bfmB. A similar result is also obtained with the lipoyl-binding site (lysine) and its domain of the E2 component of alpha-oxo acid dehydrogenases from different sources. The present data, along with the reported biochemical data, lead to the conclusion that bfmB encodes a branched-chain alpha-oxo acid dehydrogenase, which is composed of E1 alpha, E1 beta and E2 genes. This organization is identical to that of the 2-oxoglutarate dehydrogenase in B. subtilis.
Collapse
Affiliation(s)
- G F Wang
- Alberta Research Council, Edmonton, Canada
| | | | | | | |
Collapse
|
42
|
Kuriki T, Yanase M, Takata H, Takesada Y, Imanaka T, Okada S. A New Way of Producing Isomalto-Oligosaccharide Syrup by Using the Transglycosylation Reaction of Neopullulanase. Appl Environ Microbiol 1993; 59:953-9. [PMID: 16348919 PMCID: PMC202222 DOI: 10.1128/aem.59.4.953-959.1993] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A new way of producing isomalto-oligosaccharide syrup from starch was developed. Isomalto-oligosaccharides contain one or more α-(1→6)-glucosidic linkages with or without α-(1→4)-glucosidic linkages. The isomalto-oligosaccharide syrups are receiving increased attention as food additives because it is thought that they help prevent dental caries and improve human intestinal microflora, acting as a growth factor for bifidobacteria. The new system for production of isomalto-oligosaccharide syrup is based on the strong α-(1→6)-transglycosylation reaction of neopullulanase.
Bacillus subtilis
saccharifying α-amylase was simultaneously used with neopullulanase to improve the yield of isomalto-oligosaccharides. The yield of isomalto-oligosaccharides was increased to more than 60%, compared with a yield of 45.0% obtained by the conventional system. To reduce the costs, the use of immobilized neopullulanase was investigated. Almost the same yield of isomalto-oligosaccharides was obtained by using immobilized neopullulanase.
Collapse
Affiliation(s)
- T Kuriki
- Biochemical Research Laboratories, Ezaki Glico Co., Ltd., Nishiyodogawa-ku, Osaka 555, Japan
| | | | | | | | | | | |
Collapse
|
43
|
Kiel JA, Boels JM, Ten Berge AM, Venema G. Two putative insertion sequences flank a truncated glycogen branching enzyme gene in the thermophile Bacillus stearothermophilus CU21. DNA SEQUENCE : THE JOURNAL OF DNA SEQUENCING AND MAPPING 1993; 4:1-9. [PMID: 8312600 DOI: 10.3109/10425179309015616] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We have isolated a region from the Bacillus stearothermophilus CU21 chromosome hybridizing strongly to a fragment of the B. caldolyticus glycogen operon. Sequence analysis of this region revealed the presence of a truncated glgB gene encoding the N-terminus of branching enzyme. A region highly similar to an internal fragment of B. caldolyticus glgC encoding ADP-glucose pyrophosphorylase was located approximately 1kb downstream from the incomplete glgB gene. The two truncated genes appeared to flank a sequence with characteristics of bacterial Insertion Sequences, which was designated RSBst-alpha. The presence of RSBst-alpha at this position indicates that integration of (an) IS-like element(s) may have been involved in deletion formation in the putative glycogen operon. Upstream of glgB an additional incomplete ORF was found with significant similarity to putative transposases from bacterial Insertion Sequences. This region was designated RSBst-beta. Both RSBst-alpha and RSBst-beta appeared to be present in multiple copies in the B. stearothermophilus CU21 chromosome.
Collapse
Affiliation(s)
- J A Kiel
- Department of Genetics, Centre of Biological Sciences, Haren, The Netherlands
| | | | | | | |
Collapse
|
44
|
Cloning, nucleotide sequence, and efficient expression of the gene coding for thermostable aldehyde dehydrogenase from Bacillus stearothermophilus, and characterization of the enzyme. ACTA ACUST UNITED AC 1993. [DOI: 10.1016/0922-338x(93)90001-o] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
45
|
Fujiwara S, Kakihara H, Woo KB, Lejeune A, Kanemoto M, Sakaguchi K, Imanaka T. Cyclization characteristics of cyclodextrin glucanotransferase are conferred by the NH2-terminal region of the enzyme. Appl Environ Microbiol 1992; 58:4016-25. [PMID: 1476442 PMCID: PMC183219 DOI: 10.1128/aem.58.12.4016-4025.1992] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Cyclodextrin glucanotransferase (CGTase; EC 2.4.1.19) is produced mainly by Bacillus strains. CGTase from Bacillus macerans IFO3490 produces alpha-cyclodextrin as the major hydrolysis product from starch, whereas thermostable CGTase from Bacillus stearothermophilus NO2 produces alpha- and beta-cyclodextrins. To analyze the cyclization characteristics of CGTase, we cloned different types of CGTase genes and constructed chimeric genes. CGTase genes from these two strains were cloned in Bacillus subtilis NA-1 by using pTB523 as a vector plasmid, and their nucleotide sequences were determined. Three CGTase genes (cgt-1, cgt-5, and cgt-232) were isolated from B. stearothermophilus NO2. Nucleotide sequence analysis revealed that the three CGTase genes have different nucleotide sequences encoding the same amino acid sequence. Base substitutions were found at the third letter of five codons among the three genes. Each open reading frame was composed of 2,133 bases, encoding 711 amino acids containing 31 amino acids as a signal sequence. The molecular weight of the mature enzyme was estimated to be 75,374. The CGTase gene (cgtM) of B. macerans IFO3490 was composed of 2,142 bases, encoding 714 amino acids containing 27 residues as a signal sequence. The molecular weight of the mature enzyme was estimated to be 74,008. The sequence determined in this work was quite different from that reported previously by other workers. From data on the three-dimensional structure of a CGTase, seven kinds of chimeric CGTase genes were constructed by using cgt-1 from B. stearothermophilus NO2 and cgtM from B. macerans IFO3490. We examined the characteristics of these chimeric enzymes on cyclodextrin production and thermostability. It was found that the cyclization reaction was conferred by the NH2-terminal region of CGTase and that the thermostability of some chimeric enzymes was lower than that of the parental CGTases.
Collapse
Affiliation(s)
- S Fujiwara
- Department of Biotechnology, Faculty of Engineering, Osaka University, Japan
| | | | | | | | | | | | | |
Collapse
|
46
|
A novel oligonucleotide cassette for the overproduction ofEscherichia coli aspartate transcarbamylase inBacillus stearothermophilus. Biotechnol Lett 1992. [DOI: 10.1007/bf01029134] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
47
|
|
48
|
Oskam L, Venema G, Bron S. Plasmid maintenance inBacillus stearothermophilusis strain-dependent. FEMS Microbiol Lett 1992. [DOI: 10.1111/j.1574-6968.1992.tb05098.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|
49
|
Barbiturate-mediated regulation of expression of the cytochrome P450BM-3 gene of Bacillus megaterium by Bm3R1 protein. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)42797-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
|
50
|
Sakoda H, Imanaka T. Cloning and sequencing of the gene coding for alcohol dehydrogenase of Bacillus stearothermophilus and rational shift of the optimum pH. J Bacteriol 1992; 174:1397-402. [PMID: 1735726 PMCID: PMC206437 DOI: 10.1128/jb.174.4.1397-1402.1992] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Using Bacillus subtilis as a host and pTB524 as a vector plasmid, we cloned the thermostable alcohol dehydrogenase (ADH-T) gene (adhT) from Bacillus stearothermophilus NCA1503 and determined its nucleotide sequence. The deduced amino acid sequence (337 amino acids) was compared with the sequences of ADHs from four different origins. The amino acid residues responsible for the catalytic activity of horse liver ADH had been clarified on the basis of three-dimensional structure. Since those catalytic amino acid residues were fairly conserved in ADH-T and other ADHs, ADH-T was inferred to have basically the same proton release system as horse liver ADH. The putative proton release system of ADH-T was elucidated by introducing point mutations at the catalytic amino acid residues, Cys-38 (cysteine at position 38), Thr-40, and His-43, with site-directed mutagenesis. The mutant enzyme Thr-40-Ser (Thr-40 was replaced by serine) showed a little lower level of activity than wild-type ADH-T did. The result indicates that the OH group of serine instead of threonine can also be used for the catalytic activity. To change the pKa value of the putative system, His-43 was replaced by the more basic amino acid arginine. As a result, the optimum pH of the mutant enzyme His-43-Arg was shifted from 7.8 (wild-type enzyme) to 9.0. His-43-Arg exhibited a higher level of activity than wild-type enzyme at the optimum pH.
Collapse
Affiliation(s)
- H Sakoda
- Department of Biotechnology, Faculty of Engineering, Osaka University, Japan
| | | |
Collapse
|