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Dhakal D, Kumar Jha A, Pokhrel A, Shrestha A, Sohng JK. Genetic Manipulation of
Nocardia
Species. ACTA ACUST UNITED AC 2016; 40:10F.2.1-10F.2.18. [DOI: 10.1002/9780471729259.mc10f02s40] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Dipesh Dhakal
- Institute of Biomolecule Reconstruction, Department of BT‐Convergent Pharmaceutical Engineering, Sun Moon University, Chungnam Republic of Korea
| | - Amit Kumar Jha
- Institute of Biomolecule Reconstruction, Department of BT‐Convergent Pharmaceutical Engineering, Sun Moon University, Chungnam Republic of Korea
| | - Anaya Pokhrel
- Institute of Biomolecule Reconstruction, Department of BT‐Convergent Pharmaceutical Engineering, Sun Moon University, Chungnam Republic of Korea
| | - Anil Shrestha
- Institute of Biomolecule Reconstruction, Department of BT‐Convergent Pharmaceutical Engineering, Sun Moon University, Chungnam Republic of Korea
| | - Jae Kyung Sohng
- Institute of Biomolecule Reconstruction, Department of BT‐Convergent Pharmaceutical Engineering, Sun Moon University, Chungnam Republic of Korea
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Dai R, Zhang B, Zhao G, Ding X. Site-specific recombination for cloning of large DNA fragments in vitro. Eng Life Sci 2015. [DOI: 10.1002/elsc.201400267] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Ruixue Dai
- State Key Laboratory of Genetic Engineering; Department of Microbiology and Microbial Engineering; School of Life Science; Fudan University; Shanghai P. R. China
| | - Bo Zhang
- State Key Laboratory of Genetic Engineering; Department of Microbiology and Microbial Engineering; School of Life Science; Fudan University; Shanghai P. R. China
| | - Guoping Zhao
- State Key Laboratory of Genetic Engineering; Department of Microbiology and Microbial Engineering; School of Life Science; Fudan University; Shanghai P. R. China
- Laboratory of Synthetic Biology; Institute of Plant Physiology and Ecology; Shanghai Institute for Biological Science, Chinese Academy of Science; Shanghai P. R. China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics; Chinese National Human Genome Centre at Shanghai; Shanghai P. R. China
| | - Xiaoming Ding
- State Key Laboratory of Genetic Engineering; Department of Microbiology and Microbial Engineering; School of Life Science; Fudan University; Shanghai P. R. China
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Luo Q, Hiessl S, Steinbüchel A. Functional diversity of Nocardia in metabolism. Environ Microbiol 2013; 16:29-48. [PMID: 23981049 DOI: 10.1111/1462-2920.12221] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 07/12/2013] [Accepted: 07/19/2013] [Indexed: 11/29/2022]
Abstract
Bacteria affiliated in the genus Nocardia are aerobic and Gram-positive actinomycetes that are widely found in aquatic and terrestrial habitats. As occasional pathogens, several of them cause infection diseases called 'nocardiosis' affecting lungs, central nervous system, cutaneous tissues and others. In addition, members of the genus Nocardia exhibit an enormous metabolic versatility. On one side, many secondary metabolites have been isolated from members of this genus that exhibit various biological activities such as antimicrobial, antitumor, antioxidative and immunosuppressive activities. On the other side, many species are capable of degrading or converting aliphatic and aromatic toxic hydrocarbons, natural or synthetic polymers, and other widespread environmental pollutants. Because of these valuable properties and the application potential, Nocardia species have attracted much interest in academia and industry in recent years. A solid basis of genetic tools including a set of shuttle vectors and an efficient electroporation method for further genetic and metabolic engineering studies has been established to conduct efficient research. Associated with the increasing data of nocardial genome sequences, the functional diversity of Nocardia will be much faster and better understood.
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Affiliation(s)
- Quan Luo
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstraße 3, 48149, Münster, Germany
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Shibayama Y, Dabbs ER, Yazawa K, Mikami Y. Functional analysis of a small cryptic plasmid pYS1 from Nocardia. Plasmid 2011; 66:26-37. [DOI: 10.1016/j.plasmid.2011.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 04/20/2011] [Accepted: 04/22/2011] [Indexed: 11/16/2022]
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Xia HY, Tian YQ, Zhang R, Lin KC, Qin ZJ. Characterization of Nocardia plasmid pXT107. Acta Biochim Biophys Sin (Shanghai) 2006; 38:620-4. [PMID: 16953300 DOI: 10.1111/j.1745-7270.2006.00207.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Nocardia, Rhodococcus and Streptomyces, all members of the actinomycetes family, are Gram-positive eubacteria with high G+C content and able to form mycelium. We report here a newly identified plasmid pXT107 of Nocardia sp. 107, one of the smallest circular plasmids found in Nocardia. The complete nucleotide sequence of pXT107 consisted of 4335 bp with 65% G+C content, and encoded one replication extragenic palindromic (Rep) and six hypothetical proteins. The Rep, double-strand origin and single-strand origin of pXT107 resembled those of typical rolling-circle-replication plasmids, such as pNI100 of Nocardia, pRE8424 of Rhodococcus and pIJ101 of Streptomyces. The Escherichia coli-Nocardia shuttle plasmid pHAQ22, containing the rep gene of pXT107, is able to propagate in Nocardia but not in Streptomyces.
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Affiliation(s)
- Hai-Yang Xia
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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Ishikawa J, Chiba K, Kurita H, Satoh H. Contribution of rpoB2 RNA polymerase beta subunit gene to rifampin resistance in Nocardia species. Antimicrob Agents Chemother 2006; 50:1342-6. [PMID: 16569850 PMCID: PMC1426977 DOI: 10.1128/aac.50.4.1342-1346.2006] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nocardia species are gram-positive environmental saprophytes, but some cause the infectious disease nocardiosis. The complete genomic sequence of Nocardia farcinica IFM 10152 has been determined, and analyses indicated the presence of two different RNA polymerase beta subunit genes, rpoB and rpoB2, in the genome (J. Ishikawa, A. Yamashita, Y. Mikami, Y. Hoshino, H. Kurita, K. Hotta, T. Shiba, and M. Hattori, Proc. Natl. Acad. Sci. USA 101:14925-14930, 2004). These genes share 88.8% identity at the nucleotide level. Moreover, comparison of their amino acid sequences with those of other bacterial RpoB proteins suggested that the nocardial RpoB protein is likely to be rifampin (RIF) sensitive, whereas RpoB2 protein contains substitutions at the RIF-binding region that are likely to confer RIF resistance. Southern analysis indicated that rpoB duplication is widespread in Nocardia species and is correlated with the RIF-resistant phenotype. The introduction of rpoB2 by using a newly developed Nocardia-Escherichia coli shuttle plasmid vector and transformation system conferred RIF resistance to Nocardia asteroides IFM 0319T, which has neither RIF resistance nor rpoB duplication. Furthermore, unmarked rpoB2 deletion mutants of N. farcinica IFM 10152 showed no significant resistance to RIF. These results indicated the contribution of rpoB2 to RIF resistance in Nocardia species. Since this is the first example of genetic engineering of the Nocardia genome, we believe that this study, as well as our determination of the N. farcinica genome sequence, will be a landmark in Nocardia genetics.
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Affiliation(s)
- Jun Ishikawa
- Department of Bioactive Molecules, National Institute of Infectious Diseases, 1-23-1, Toyama, Shinjuku, Tokyo 162-8640, Japan.
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Dhingra G, Kumari R, Bala S, Majumdar S, Malhotra S, Sharma P, Lal S, Cullum J, Lal R. Development of cloning vectors and transformation methods for Amycolatopsis. J Ind Microbiol Biotechnol 2003; 30:195-204. [PMID: 12687493 DOI: 10.1007/s10295-003-0040-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2002] [Accepted: 01/08/2003] [Indexed: 10/23/2022]
Abstract
The genus Amycolatopsis is of industrial importance, as its species are known to produce commercial antibiotics. It belongs to the family Pseudonocardiaceae and has an eventful taxonomic history. Initially strains were identified as Streptomyces, then later as Nocardia. However, based on biochemical, morphological and molecular features, the genus Amycolatopsis, containing seventeen species, was created. The development of molecular genetic techniques for this group has been slow. The scarcity of molecular genetic tools including stable plasmids, antibiotic resistance markers, transposons, reporter genes, cloning vectors, and high efficiency transformation protocols has made progress slow, but efforts in the past decade have led to the development of cloning vectors and transformation methods for these organisms. Some of the cloning vectors have broad host range (pRL series) whereas others have limited host range (pMEA300 and pMEA100). The cloning vector pMEA300 has been completely sequenced, while only the minimal replicon (pA- rep) has been sequenced from pRL plasmids. Direct transformation of mycelia and electroporation are the most widely applicable methods for transforming species of Amycolatopsis. Conjugational transfer from Escherichia coli has been reported only in the species A. japonicum, and gene disruption and replacements using homologous recombination are now possible in some strains.
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Affiliation(s)
- Gauri Dhingra
- Molecular Biology Laboratory, University of Delhi, Department of Zoology, Delhi 110007, India
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Stegmann E, Pelzer S, Wilken K, Wohlleben W. Development of three different gene cloning systems for genetic investigation of the new species Amycolatopsis japonicum MG417-CF17, the ethylenediaminedisuccinic acid producer. J Biotechnol 2001; 92:195-204. [PMID: 11640989 DOI: 10.1016/s0168-1656(01)00360-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For the first time gene cloning systems have been developed for Amycolatopsis japonicum. Direct transformation, polyethyleneglycol (PEG) induced protoplast transformation and conjugal transfer was established for A. japonicum MG417-CF17, the ethylenediaminedisuccinic acid (EDDS) producer. The direct transformation procedure was modified to introduce DNA. The most important parameter for an efficient DNA uptake was the age of the culture. Using of mycelium from 36-h old cultures resulted in the highest transformation frequencies. Further, conditions for transformation of A. japonicum protoplasts were established. The efficiency of transformation depended mainly on the source of PEG and the components of the regeneration agar. The replicative plasmid pULVK2A carrying pA-rep and the apramycin resistance gene was transferred into the EDDS producer with a frequency of 0.38 colonies microg(-1) DNA by using the direct transformation procedure and with a frequency of 0.56 colonies microg(-1) DNA by using the PEG induced protoplast transformation. The plasmid was genetically stable, and could easily be reisolated from A. japonicum. We also demonstrated that conjugal transfer of the plasmid pSET152 from Escherichia coli ET12567 (pUB307) to Amycolatopsis spores is possible. The plasmid pSET152 integrated in the A. japonicum chromosome. A titre of 2.4 x 10(-4) exconjugants per recipient was obtained.
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Affiliation(s)
- E Stegmann
- Eberhard-Karls-Universität Tübingen, Mikrobiologie/Biotechnologie, Auf der Morgenstelle 28, D-72076 Tübingen, Germany
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Fernandes PJ, Powell JAC, Archer JAC. Construction of Rhodococcus random mutagenesis libraries using Tn5 transposition complexes. MICROBIOLOGY (READING, ENGLAND) 2001; 147:2529-2536. [PMID: 11535792 DOI: 10.1099/00221287-147-9-2529] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The ability to generate tagged mutants of Rhodococcus spp. will facilitate a deeper understanding of this medically and commercially important genus. The absence of efficient transposon systems in these organisms has here been overcome by the use of Tn5-based DNA-protein transposition complexes which can transpose at high efficiency. To achieve this, electroporation efficiencies and antibiotic selection were optimized. A Rhodococcus rhodochrous CW25 Tn5 insertion library of 1500 mutants was created. Southern blotting of 23 representative mutants demonstrated random insertion. A number of auxotrophic mutants were isolated and the disrupted regions involved were identified by inverse PCR and subsequent sequencing. Transposition of Tn5 was confirmed by the presence of 9 bp direct repeats of Rhodococcus DNA flanking the transposon insertion site. To further test this system, a Tn5 insertion library was constructed in a wild-type soil isolate of Rhodococcus spp. This is the first viable transposon knockout system reported for Rhodococcus.
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Affiliation(s)
- Paula J Fernandes
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK1
| | - Justin A C Powell
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK1
| | - John A C Archer
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK1
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Valentin HE, Dennis D. Application of an optimized electroporation procedure for replacement of the polyhydroxyalkanoate synthase I gene in Nocardia corallina. Can J Microbiol 1996; 42:715-9. [PMID: 8764686 DOI: 10.1139/m96-098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
To develop a system for gene replacement in Nocardia corallina, a protocol for electroporation was optimized by systematic alterations of growth conditions, field strength, time constant and the electroporation buffer. Transformation efficiencies of 0.5 x 10(6) - 3 x 10(6) transformants/microgram plasmid DNA were obtained routinely. The gene encoding the polyhydroxyalkanoate (PHA) synthase I of N. corallina was cloned and interrupted by insertion of a kanamycin-resistance gene. The resulting plasmid was introduced into N. corallina by electroporation to inactivate the wild-type gene by homologous recombination. Kanamycin-resistant clones were screened by Southern hybridization for the absence of the wild-type gene and analyzed for PHA accumulation.
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Affiliation(s)
- H E Valentin
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA
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Valentin HF, Dennis D. Metabolic pathway for poly(3-hydroxybutyrate-co-3-hydroxyvalerate) formation in Nocardia corallina: inactivation of mutB by chromosomal integration of a kanamycin resistance gene. Appl Environ Microbiol 1996; 62:372-9. [PMID: 8593043 PMCID: PMC167808 DOI: 10.1128/aem.62.2.372-379.1996] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The gene encoding the large subunit of the methylmalonyl-coenzyme A (CoA) mutase in Nocardia corallina (mutBNc) was cloned. A 4.3-kbp BamHI fragment containing almost the entire mutBNc was identified by Southern hybridization experiments employing a digoxigenin-labeled probe deduced from mutB of Streptomyces cinnamonensis, mutBNc was interrupted by insertion of a kanamycin resistance gene block (mutB::kan or mutB::neo) and introduced into N. corallina to obtain mutB-negative strains by homologous recombination. Four of sixteen kanamycin-resistant clones occurred via double-crossover events and harbored only the interrupted mutBNc. These exhibited no growth on odd-chain fatty acids in the presence of kanamycin but exhibited wild-type growth on even-chain fatty acids, glucose, and succinate. Whereas the wild type of N. corallina accumulates a copolyester of 3-hydroxybutyrate (3HB) and 3-hydroxyvalerate (3HV) containing more than 60 mol% 3HV from most carbon sources, mutB-negative strains accumulated poly(3HB-co-3HV) containing only 2 to 6 mol% 3HV. Methylmalonyl-CoA mutase activity was not found in these clones. Therefore, this study provides strong evidence that the majority of 3HV units in poly(3HB-co-3HV) accumulated by N. corallina are synthesized via the methylmalonyl-CoA pathway.
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Affiliation(s)
- H F Valentin
- Department of Biology, James Madison University, Harrisonburg, Virginia 22807, USA.
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