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Huynh DT, Chathuranga WG, Chathuranga K, Lee JS, Kim CJ. Mucosal Administration of Lactobacillus casei Surface-Displayed HA1 Induces Protective Immune Responses against Avian Influenza A Virus in Mice. J Microbiol Biotechnol 2024; 34:735-745. [PMID: 37915251 PMCID: PMC11016770 DOI: 10.4014/jmb.2307.07040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/12/2023] [Accepted: 10/18/2023] [Indexed: 11/03/2023]
Abstract
Avian influenza is a serious threat to both public health and the poultry industry worldwide. This respiratory virus can be combated by eliciting robust immune responses at the site of infection through mucosal immunization. Recombinant probiotics, specifically lactic acid bacteria, are safe and effective carriers for mucosal vaccines. In this study, we engineered recombinant fusion protein by fusing the hemagglutinin 1 (HA1) subunit of the A/Aquatic bird/Korea/W81/2005 (H5N2) with the Bacillus subtilis poly γ-glutamic acid synthetase A (pgsA) at the surface of Lactobacillus casei (pgsA-HA1/L. casei). Using subcellular fractionation and flow cytometry we confirmed the surface localization of this fusion protein. Mucosal administration of pgsA-HA1/L. casei in mice resulted in significant levels of HA1-specific serum IgG, mucosal IgA and neutralizing antibodies against the H5N2 virus. Additionally, pgsA-HA1/L. casei-induced systemic and local cell-mediated immune responses specific to HA1, as evidenced by an increased number of IFN-γ and IL-4 secreting cells in the spleens and higher levels of IL-4 in the local lymphocyte supernatants. Finally, mice inoculated with pgsA-HA1/L. casei were protected against a 10LD50 dose of the homologous mouse-adapted H5N2 virus. These results suggest that mucosal immunization with L. casei displaying HA1 on its surface could be a potential strategy for developing a mucosal vaccine against other H5 subtype viruses.
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Affiliation(s)
- Dung T. Huynh
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - W.A. Gayan Chathuranga
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - Kiramage Chathuranga
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - Jong-Soo Lee
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
| | - Chul-Joong Kim
- College of Veterinary Medicine, Chungnam National University, Daejeon 34314, Republic of Korea
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2
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Hasan NS, Ling JG, Bakar MFA, Seman WMKW, Murad AMA, Bakar FDA, Khalid RM. The Lichen Flavin-Dependent Halogenase, DnHal: Identification, Heterologous Expression and Functional Characterization. Appl Biochem Biotechnol 2023; 195:6708-6736. [PMID: 36913095 DOI: 10.1007/s12010-022-04304-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2022] [Indexed: 03/14/2023]
Abstract
Enzymatic halogenation captures scientific interest considering its feasibility in modifying compounds for chemical diversity. Currently, majority of flavin-dependent halogenases (F-Hals) were reported from bacterial origin, and as far as we know, none from lichenized fungi. Fungi are well-known producers of halogenated compounds, so using available transcriptomic dataset of Dirinaria sp., we mined for putative gene encoding for F-Hal. Phylogenetic-based classification of the F-Hal family suggested a non-tryptophan F-Hals, similar to other fungal F-Hals, which mainly act on aromatic compounds. However, after the putative halogenase gene from Dirinaria sp., dnhal was codon-optimized, cloned, and expressed in Pichia pastoris, the ~63 kDa purified enzyme showed biocatalytic activity towards tryptophan and an aromatic compound methyl haematommate, which gave the tell-tale isotopic pattern of a chlorinated product at m/z 239.0565 and 241.0552; and m/z 243.0074 and 245.0025, respectively. This study is the start of understanding the complexities of lichenized fungal F-hals and its ability to halogenate tryptophan and other aromatic. compounds which can be used as green alternatives for biocatalysis of halogenated compounds.
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Affiliation(s)
- Nurain Shahera Hasan
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Jonathan Guyang Ling
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Mohd Faizal Abu Bakar
- Malaysia Genome & Vaccine Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, 43000, Kajang, Selangor, Malaysia
| | - Wan Mohd Khairulikhsan Wan Seman
- Malaysia Genome & Vaccine Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, 43000, Kajang, Selangor, Malaysia
| | - Abdul Munir Abdul Murad
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Farah Diba Abu Bakar
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Rozida Mohd Khalid
- Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
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3
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Halder S, Jaiswal N, Koley H, Mahata N. Cloning, improved expression and purification of invasion plasmid antigen D (IpaD): an effector protein of enteroinvasive Escherichia coli (EIEC). Biotechnol Genet Eng Rev 2023:1-27. [PMID: 36871167 DOI: 10.1080/02648725.2023.2184027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 02/15/2023] [Indexed: 03/06/2023]
Abstract
The widespread increase in broad-spectrum antimicrobial resistance is making it more difficult to treat gastrointestinal infections. Enteroinvasive Escherichia coli is a prominent etiological agent of bacillary dysentery, invading via the fecal-oral route and exerting virulence on the host via the type III secretion system. IpaD, a surface-exposed protein on the T3SS tip that is conserved among EIEC and Shigella, may serve as a broad immunogen for bacillary dysentery protection. For the first time, we present an effective framework for improving the expression level and yield of IpaD in the soluble fraction for easy recovery, as well as ideal storage conditions, which may aid in the development of new protein therapies for gastrointestinal infections in the future. To achieve this, uncharacterized full length IpaD gene from EIEC was cloned into pHis-TEV vector and induction parameters were optimized for enhanced expression in the soluble fraction. After affinity-chromatography based purification, 61% pure protein with a yield of 0.33 mg per litre of culture was obtained. The purified IpaD was retained its secondary structure with a prominent α-helical structure as well as functional activity during storage, at 4°C, -20°C and -80°C using 5% sucrose as cryoprotectants, which is a critical criterion for protein-based treatments.
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Affiliation(s)
- Sudeshna Halder
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, India
| | - Namita Jaiswal
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, India
| | - Hemanta Koley
- Department Bacteriology, National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Nibedita Mahata
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur, India
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4
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Shendge AA, D’Souza JS. Strategic optimization of conditions for the solubilization of GST-tagged amphipathic helix-containing ciliary proteins overexpressed as inclusion bodies in E. coli. Microb Cell Fact 2022; 21:258. [PMID: 36510188 PMCID: PMC9746132 DOI: 10.1186/s12934-022-01979-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/24/2022] [Indexed: 12/14/2022] Open
Abstract
Expression of affinity-tagged recombinant proteins for crystallography, protein-protein interaction, antibody generation, therapeutic applications, etc. mandates the generation of high-yield soluble proteins. Although recent developments suggest the use of yeast, insect, and mammalian cell lines as protein expression platforms, Escherichia coli is still the most popular, due mainly to its ease of growth, feasibility in genetic manipulation and economy. However, some proteins have a spontaneous tendency to form inclusion bodies (IBs) when over-expressed in bacterial expression systems such as E. coli, thus posing a challenge in purification and yield. At times, small peptides undergo degradation during protein production and hence using suitable tags could circumvent the problem. Although several independent techniques have been used to solubilize IBs, these cannot always be applied in a generic sense. Although tagging a GST moiety is known to enhance the solubility of fusion proteins in E. coli, resulting in yields of 10-50 mg/L of the culture, the inherent nature of the protein sequence at times could lead to the formation of IBs. We have been working on a Myc Binding Protein-1 orthologue, viz. Flagellar Associated Protein 174 (FAP174) from the axoneme of Chlamydomonas reinhardtii that binds to an A-Kinase Anchoring Protein 240 (AKAP240) which has been annotated as Flagellar Associated Protein 65 (FAP65). Using an in-silico approach, we have identified two amphipathic helices on FAP65 (CrFAP65AH1 and CrFAP65AH2) that are predicted to bind to FAP174. To test this prediction, we have cloned the GST-tagged peptides, and overexpressed them in E. coli that have resulted in insoluble IBs. The yields of these over-expressed recombinant proteins dropped considerably due to IB formation, indicating aggregation. An integrated approach has been used to solubilize four highly hydrophobic polypeptides, viz. two amphipathic helices and the respective proline variants of FAP65. For solubilizing these polypeptides, variables such as non-denaturing detergents (IGEPAL CA-630), changing the ionic strength of the cell lysis and solubilization buffer, addition of BugBuster®, diluting the cell lysate and sonication were introduced. Our statistically viable results yielded highly soluble and functional polypeptides, indiscreet secondary structures, and a yield of ~ 20 mg/L of the E. coli culture. Our combinatorial strategy using chemical and physical methods to solubilize IBs could prove useful for hydrophobic peptides and proteins with amphipathic helices.
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Affiliation(s)
- Amruta A. Shendge
- grid.452882.10000 0004 1761 3305School of Biological Sciences, UM-DAE Centre for Excellence in Basic Sciences, Kalina campus, Santacruz (E), Mumbai, 400098 India
| | - Jacinta S. D’Souza
- grid.452882.10000 0004 1761 3305School of Biological Sciences, UM-DAE Centre for Excellence in Basic Sciences, Kalina campus, Santacruz (E), Mumbai, 400098 India
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Franzino T, Boubakri H, Cernava T, Abrouk D, Achouak W, Reverchon S, Nasser W, Haichar FEZ. Implications of carbon catabolite repression for plant-microbe interactions. PLANT COMMUNICATIONS 2022; 3:100272. [PMID: 35529946 PMCID: PMC9073323 DOI: 10.1016/j.xplc.2021.100272] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/17/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Carbon catabolite repression (CCR) plays a key role in many physiological and adaptive responses in a broad range of microorganisms that are commonly associated with eukaryotic hosts. When a mixture of different carbon sources is available, CCR, a global regulatory mechanism, inhibits the expression and activity of cellular processes associated with utilization of secondary carbon sources in the presence of the preferred carbon source. CCR is known to be executed by completely different mechanisms in different bacteria, yeast, and fungi. In addition to regulating catabolic genes, CCR also appears to play a key role in the expression of genes involved in plant-microbe interactions. Here, we present a detailed overview of CCR mechanisms in various bacteria. We highlight the role of CCR in beneficial as well as deleterious plant-microbe interactions based on the available literature. In addition, we explore the global distribution of known regulatory mechanisms within bacterial genomes retrieved from public repositories and within metatranscriptomes obtained from different plant rhizospheres. By integrating the available literature and performing targeted meta-analyses, we argue that CCR-regulated substrate use preferences of microorganisms should be considered an important trait involved in prevailing plant-microbe interactions.
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Affiliation(s)
- Theophile Franzino
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - Hasna Boubakri
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Écologie Microbienne, 69622 Villeurbanne, France
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, Graz 8010, Austria
| | - Danis Abrouk
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Écologie Microbienne, 69622 Villeurbanne, France
| | - Wafa Achouak
- Aix Marseille Université, CEA, CNRS, BIAM, Lab Microbial Ecology of the Rhizosphere (LEMiRE), 13108 Saint-Paul-Lez-Durance, France
| | - Sylvie Reverchon
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - William Nasser
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
| | - Feth el Zahar Haichar
- INSA-Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5240, Microbiologie, Adaptation, Pathogénie, Université Lyon, 10 rue Raphaël Dubois, 69622 Villeurbanne, France
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6
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Wang Y, Luo X, Zhao Y, Ye X, Yang F, Li Z, Huang Y, Fang X, Huan M, Li D, Cui Z. Integrated Strategies for Enhancing the Expression of the AqCoA Chitosanase in Pichia pastoris by Combined Optimization of Molecular Chaperones Combinations and Copy Numbers via a Novel Plasmid pMC-GAP. Appl Biochem Biotechnol 2021; 193:4035-4051. [PMID: 34553325 DOI: 10.1007/s12010-021-03668-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/03/2021] [Indexed: 12/21/2022]
Abstract
In our previous study, the chitosanase AqCoA and the chitooligosaccharides it produced were found to exhibit significant protective effects against fungal diseases. In this study, we enhanced the expression of AqCoA using the novel pMC-GAP that enables stable transformation of Escherichia coli, and built an integrated model based on the gene copy number, molecular chaperones, and protein production of AqCoA. In terms of gene dosage, the highest hydrolase activity was 0.32 U/ml in the strain with four copies, which was 1.78-fold higher than that of the strain with only one copy (0.18 U/ml). In addition, we found the chaperones such as PDI, ERO1, HAC1, YDJ1, SSE1, SSA4, and SSO2 improved protein expression. Furthermore, the PDI/ERO1, SSA4/SSE1, and YDJ1/SSO2 pairs synergistically increased the expression levels by 61%, 31%, and 42%, respectively. Finally, we investigated the combined effects of gene copy numbers and molecular chaperones on protein expression. The highest activity reached 2.32 U/ml in the strain with six integrated molecular chaperone expression cassettes and sixteen copies of the target gene, which was 13-fold higher than that of the control strain with only one copy (GAP-1AqCoA). Combined optimization of gene dosage and molecular chaperone combinations significantly increased the expression level of AqCoA, providing a powerful strategy to improve the expression of other heterologous proteins in P. pastoris.
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Affiliation(s)
- Yanxin Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China
| | - Xue Luo
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China
| | - Yuqiang Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China.,Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, 210014, China
| | - Xianfeng Ye
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China
| | - Fan Yang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China
| | - Zhoukun Li
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China
| | - Yan Huang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China
| | - Xiaodong Fang
- Guangzhou Hanyun Parmaceutical Technology Co. Ltd, Guangzhou, 510000, China
| | - Minghui Huan
- Microbial Research Institute of Liaoning Province, Chaoyang, China
| | - Ding Li
- Institute of Veterinary Immunology &Engineering, Jiangsu Academy of Agricultural Sciences, 210014, Nanjing, People's Republic of China.
| | - Zhongli Cui
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China. .,Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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7
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Chakravarthi BVSK, Singh S, Kamalraj S, Gupta VK, Jayabaskaran C. Evaluation of spore inoculum and confirmation of pathway genetic blueprint of T13αH and DBAT from a Taxol-producing endophytic fungus. Sci Rep 2020; 10:21139. [PMID: 33273486 PMCID: PMC7712836 DOI: 10.1038/s41598-020-77605-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 10/21/2020] [Indexed: 02/06/2023] Open
Abstract
Taxol (paclitaxel), a plant-derived anticancer drug, has been among the most successful anticancer drugs of natural origin. Endophytic fungi have been proposed as a prominent alternative source for Taxol and its intermediate Baccatin III, however the very low yields remain a hinderance to their commercial utilization. Significant research efforts towards this end are underway globally. Here, we report the results on our earlier reported Taxol-producing endophytic fungus, Fusarium solani from the standpoint of spores as seed inoculum and media selection for enhanced Taxol and baccatin III yields. Spores produced on M1D medium with 94.76% viability were used for further media optimization for Taxol and Baccatin III production in five different liquid media under static and shaker condition at different cultivation days. Taxol and Baccatin III when quantified through competitive inhibition enzyme immunoassay (CIEIA), showed maximum production at 136.3 µg L−1 and 128.3 µg L−1, respectively in the modified flask basal broth (MFBB) under shaking condition. Further, two important genes of this pathway, namely taxane 13α-hydroxylase (T13αH) and 10-deacetylbaccatin III-10-β-O-acetyltransferase (DBAT) have been identified in this fungus. These findings are hoped to assist in further manipulation and metabolic engineering of the parent F. solani strain towards the enhanced production of Taxol and baccatin III.
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Affiliation(s)
| | - Satpal Singh
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Subban Kamalraj
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Center, Scotland's Rural College (SRUC), SRUC Barony Campus, Parkgate, Dumfries, DG1 3NE, UK
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8
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Wang S, Cui J, Bilal M, Hu H, Wang W, Zhang X. Pseudomonas spp. as cell factories (MCFs) for value-added products: from rational design to industrial applications. Crit Rev Biotechnol 2020; 40:1232-1249. [PMID: 32907412 DOI: 10.1080/07388551.2020.1809990] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
In recent years, there has been increasing interest in microbial biotechnology for the production of value-added compounds from renewable resources. Pseudomonas species have been proposed as a suitable workhorse for high-value secondary metabolite production because of their unique characteristics for fast growth on sustainable carbon sources, a clear inherited background, versatile intrinsic metabolism with diverse enzymatic capacities, and their robustness in an extreme environment. It has also been demonstrated that metabolically engineered Pseudomonas strains can produce several industrially valuable aromatic chemicals and natural products such as phenazines, polyhydroxyalkanoates, rhamnolipids, and insecticidal proteins from renewable feedstocks with remarkably high yields suitable for commercial application. In this review, we summarize cell factory construction in Pseudomonas for the biosynthesis of native and non-native bioactive compounds in P. putida, P. chlororaphis, P. aeruginosa, as well as pharmaceutical proteins production by P. fluorescens. Additionally, some novel strategies together with metabolic engineering strategies in order to improve the biosynthetic abilities of Pseudomonas as an ideal chassis are discussed. Finally, we proposed emerging opportunities, challenges, and essential strategies to enable the successful development of Pseudomonas as versatile microbial cell factories for the bioproduction of diverse bioactive compounds.
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Affiliation(s)
- Songwei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiajia Cui
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, China
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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9
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Gnaim R, Sheviryov J, Golberg A, Ames G, Oziel M, González CA. Label-Free cDNA Detection Based on Radiofrequency Scattering Parameters: A New Approach for an Inexpensive Gene Sensor. J Med Device 2020. [DOI: 10.1115/1.4045909] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Abstract
A new gene detection technique that is fast, inexpensive, and easy-to-use is urgently needed in hospitals, clinics, and laboratories without access to expensive equipments. The lack of a practical, minimally invasive, and economical method constitutes the main impediment to the promotion of genetic medicine in developing countries. Radiofrequency scattering parameters are an inexpensive gene sensor potentially capable of noninvasively identifying biological materials. They represent a quantitative value for the electromagnetic reflection/transmission characteristics of certain molecular markers in a given frequency domain. The S21 parameter is the difference between the signal received and that transmitted. The aim of this study is to evaluate the S21 transmittance parameters (magnitude and phase) as an indirect impedance measurement for detecting the label-free complementary deoxyribonucleic acid (cDNA) amplification of the 16S ribosomal subunit gene. S21 values showed differences associated with distinct cDNA concentrations. Hence, this technique could possibly facilitate the design of an inexpensive, label-free, and easy-to-use gene sensor.
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Affiliation(s)
- Rima Gnaim
- Porter School of Environment and Earth Sciences, Tel Aviv University, Tel Aviv 69978, Israel; The Triangle Regional Research and Development Center, Kfar Qari' 30075, Israel; Porter School, Tel Aviv University, Room 214, Ramat Aviv 69978, Israel
| | - Julia Sheviryov
- Porter School of Environment and Earth Sciences, Tel Aviv University, Tel Aviv 69978, Israel; Porter School, Room 214, Ramat Aviv 69978, Israel
| | - Alexander Golberg
- Porter School of Environment and Earth Sciences, Tel Aviv University, Tel Aviv 69978, Israel; Porter School, Room 215, Ramat Aviv 69978, Israel
| | - Gerardo Ames
- Centro de Investigación en Instrumentación e Imagenología Médica (Ci3M), Universidad Autónoma Metropolitana—Iztapalapa, CDMX 09340, Mexico; Centro de Investigación en Instrumentación e Imagenología Médica (Ci3M), Avenue San Rafael Atlixco 186, Leyes de Reforma 1ra Secc 09340, México
| | - Moshe Oziel
- Department of Physiology and Pharmacology, Faculty of Medicine, Tel Aviv University, Ramat Aviv 69978, Israel
| | - César A. González
- Instituto Politécnico Nacional-Escuela Superior de Medicina, CDMX 11340, México; Plan de San Luis esq. Díaz Mirón, Col. Casco de Santo Tomas, CDMX 11300, México
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10
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Iyyappan J, Baskar G, Bharathiraja B, Saravanathamizhan R. Malic acid production from biodiesel derived crude glycerol using morphologically controlled Aspergillus niger in batch fermentation. BIORESOURCE TECHNOLOGY 2018; 269:393-399. [PMID: 30205264 DOI: 10.1016/j.biortech.2018.09.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/30/2018] [Accepted: 09/01/2018] [Indexed: 06/08/2023]
Abstract
In the present investigation, the effects of crude glycerol concentration, spore inoculum concentration, yeast extract concentration and shaking frequency on seed morphology of Aspergillus niger PJR1 on malic acid production were investigated and dispersed fungal mycelium with higher biomass (20.25 ± 0.91 g/L) was obtained when A. niger PJR1 grow on crude glycerol. Dry cell weight under dispersed fermentation was 21.28% higher than usual pellet fermentation. The optimal crude glycerol, nitrogen source and nitrogen source concentration were found to be 160 g/L, yeast extract and 1.5 g/L, respectively. Batch fermentation in a shake flask culture containing 160 g/L crude glycerol resulted in the yield of malic acid 83.23 ± 1.86 g/L, after 192 h at 25 °C. Results revealed that morphological control of A. niger is an efficient method for increased malic acid production when crude glycerol derived from biodiesel production is used as feedstock.
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Affiliation(s)
- J Iyyappan
- Vel Tech High Tech Dr. Rangarajan Dr. Sakunthala Engineering College, Chennai 600062, India
| | - G Baskar
- Department of Biotechnology, St. Joseph's College of Engineering, Chennai 600119, India.
| | - B Bharathiraja
- Vel Tech High Tech Dr. Rangarajan Dr. Sakunthala Engineering College, Chennai 600062, India
| | - R Saravanathamizhan
- Department of Chemical Engineering, A. C. Tech Campus, Anna University, Chennai 600025, India
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11
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Ranasinghe C, Guo Q, Sapienza PJ, Lee AL, Quinn DM, Cheatum CM, Kohen A. Protein Mass Effects on Formate Dehydrogenase. J Am Chem Soc 2017; 139:17405-17413. [PMID: 29083897 PMCID: PMC5800309 DOI: 10.1021/jacs.7b08359] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Isotopically labeled enzymes (denoted as "heavy" or "Born-Oppenheimer" enzymes) have been used to test the role of protein dynamics in catalysis. The original idea was that the protein's higher mass would reduce the frequency of its normal-modes without altering its electrostatics. Heavy enzymes have been used to test if the vibrations in the native enzyme are coupled to the chemistry it catalyzes, and different studies have resulted in ambiguous findings. Here the temperature-dependence of intrinsic kinetic isotope effects of the enzyme formate dehydrogenase is used to examine the distribution of H-donor to H-acceptor distance as a function of the protein's mass. The protein dynamics are altered in the heavy enzyme to diminish motions that determine the transition state sampling in the native enzyme, in accordance with a Born-Oppenheimer-like effect on bond activation. Findings of this work suggest components related to fast frequencies that can be explained by Born-Oppenheimer enzyme hypothesis (vibrational) and also slower time scale events that are non-Born-Oppenheimer in nature (electrostatic), based on evaluations of protein mass dependence of donor-acceptor distance and forward commitment to catalysis along with steady state and single turnover measurements. Together, the findings suggest that the mass modulation affected both local, fast, protein vibrations associated with the catalyzed chemistry and the protein's macromolecular electrostatics at slower time scales; that is, both Born-Oppenheimer and non-Born-Oppenheimer effects are observed. Comparison to previous studies leads to the conclusion that isotopic labeling of the protein may have different effects on different systems, however, making heavy enzyme studies a very exciting technique for exploring the dynamics link to catalysis in proteins.
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Affiliation(s)
- Chethya Ranasinghe
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1727, USA
| | - Qi Guo
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1727, USA
| | - Paul J. Sapienza
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Andrew L. Lee
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Daniel M. Quinn
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1727, USA
| | | | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, IA 52242-1727, USA
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12
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Safety evaluation and antimicrobial properties of Lactobacillus pentosus 22C isolated from traditional yogurt. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2017. [DOI: 10.1007/s11694-017-9471-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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13
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Chakravarty I, Kundu S. Improved production of Daptomycin in an airlift bioreactor by morphologically modified and immobilized cells of Streptomyces roseosporus. AMB Express 2016; 6:101. [PMID: 27771916 PMCID: PMC5075331 DOI: 10.1186/s13568-016-0274-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 10/17/2016] [Indexed: 11/27/2022] Open
Abstract
The increased threat of drug resistance has challenged the existence of several conventional and non-conventional antibiotics in the recent times. Daptomycin is a novel cyclic-lipopeptide antibiotic produced by Streptomyces roseosporus that has progressed as a significant anti-MRSA (methicillin-resistant Staphylococcus aureus) antibiotic. But, the economic practicality of this highly valued secondary metabolite is deterred by its poor production and tedious processing methodology. The present study aims at strategic improvement of Daptomycin production through morphological variations of S. roseosporus cells. Free cells, pelletized cells and immobilized cells on ultra porous refractory brick and silk sachets were investigated for the production of Daptomycin in a lab-scale 2.0 l air-lift bioreactor. The effect(s) of nitrogen source, inoculum size and oxygen stress were analyzed for pellet formation of S. roseosporus. Interestingly, free cells produced 750 mg/l of Daptomycin in a single batch. But, the three phase broth viscosity increased due to vigorous growth of free cells which hampered the oxygen transfer rate. The cell degeneration over the time deterred pellet reusability. 1430 mg/l Daptomycin was produced using pellets for 2 batches. On the contrary, mechanical stability, buoyancy and reusability of refractory bricks and silk sachets were beneficial. Daptomycin production was recorded for 6–8 batches. Immobilized cells on refractory bricks and silk sachets led to 4895 mg/l and 3623 mg/l Daptomycin production respectively. Cell immobilization improved the three phase broth rheology and hence, the hydrodynamics within the reactor. Therefore, whole-cell immobilization could contribute to the ameliorated production of this life-saving drug.
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Expression, purification and kinetic characterization of recombinant benzoate dioxygenase from Rhodococcus ruber UKMP-5M. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2016; 5:133-142. [PMID: 28097167 PMCID: PMC5219908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In this study, benzoate dioxygenase from Rhodococcus ruber UKMP-5M was catalyzed by oxidating the benzene ring to catechol and other derivatives. The benzoate dioxygenase (benA gene) from Rhodococcus ruber UKMP-5M was then expressed, purified, characterized, The benA gene was amplified (642 bp), and the product was cloned into a pGEM-T vector. The recombinant plasmid pGEMT-benA was digested by double restriction enzymes BamHI and HindIII to construct plasmid pET28b-benA and was then ligated into Escherichia coli BL21 (DE3). The recombinant E. coli was induced with 0.5 mM isopropyl β-D-thiogalactoside (IPTG) at 22˚C to produce benzoate dioxygenase. The enzyme was then purified by ion exchange chromatography after 8 purification folds. The resulting product was 25 kDa, determined by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) and western blotting. Benzoate dioxygenase activity was found to be 6.54 U/mL and the optimal pH and temperature were 8.5 and 25°C, respectively. Maximum velocity (Vmax) and Michaelis constant (Km) were 7.36 U/mL and 5.58 µM, respectively. The end metabolite from the benzoate dioxygenase reaction was cyclohexane dione, which was determined by gas chromatography mass spectrometry (GC-MS).
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15
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Wang B, Chen J, Li H, Sun F, Li Y, Shi G. Pellet-dispersion strategy to simplify the seed cultivation of Aspergillus niger and optimize citric acid production. Bioprocess Biosyst Eng 2016; 40:45-53. [PMID: 27573803 DOI: 10.1007/s00449-016-1673-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/17/2016] [Indexed: 11/25/2022]
Abstract
Citric acid (CA) as an extremely important platform compound has attracted intense attention due to wide applications and huge markets. Here, we proposed a novel method, using pellet inoculation to replace spores, and constructed the seed recycling cultivation process, effectively avoided the longtime (spore preparation 30 days) of seed culture (including spores germination 12 h) in the traditional batch-fermentation. On this basis, using pellet-dispersion strategy, the bottleneck caused by the mycelium structure was overcome, with the seed restoring high cell-viability with CA titer (11.0 g/L) even in the eighth batch compared to that in the control (4.6 g/L). The optimum morphology of these recycling cultured seeds for CA production was dispersed pattern rather than pellets. And the CA production was 130.5 g/L on average in 5 L five-conjoined-fermenters recycling eight batches, especially increasing 3.1 g/L compared with the control. To our knowledge, this is the first that reported the application of these strategies in effective production of CA. Our fermentation strategies not only significantly enhanced CA productivity, but also severed as a promising stepping-stone for other fermentations dominated with the filamentous fungi.
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Affiliation(s)
- Baoshi Wang
- National Engineering Laboratory for Cereal Fermentation Technology, Wuxi, 214122, China
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Jiangsu Guoxin Union Energy Co., Ltd., Wuxi, 214203, China
| | - Jian Chen
- National Engineering Laboratory for Cereal Fermentation Technology, Wuxi, 214122, China
| | - Hua Li
- National Engineering Laboratory for Cereal Fermentation Technology, Wuxi, 214122, China
| | - Fuxin Sun
- Jiangsu Guoxin Union Energy Co., Ltd., Wuxi, 214203, China
| | - Youran Li
- National Engineering Laboratory for Cereal Fermentation Technology, Wuxi, 214122, China
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Guiyang Shi
- National Engineering Laboratory for Cereal Fermentation Technology, Wuxi, 214122, China.
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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16
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Baek SH, Kwon EY, Kim YH, Hahn JS. Metabolic engineering and adaptive evolution for efficient production of D-lactic acid in Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2015; 100:2737-48. [PMID: 26596574 DOI: 10.1007/s00253-015-7174-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 10/23/2015] [Accepted: 11/10/2015] [Indexed: 12/01/2022]
Abstract
There is an increasing demand for microbial production of lactic acid (LA) as a monomer of biodegradable poly lactic acid (PLA). Both optical isomers, D-LA and L-LA, are required to produce stereocomplex PLA with improved properties. In this study, we developed Saccharomyces cerevisiae strains for efficient production of D-LA. D-LA production was achieved by expressing highly stereospecific D-lactate dehydrogenase gene (ldhA, LEUM_1756) from Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 in S. cerevisiae lacking natural LA production activity. D-LA consumption after glucose depletion was inhibited by deleting DLD1 encoding D-lactate dehydrogenase and JEN1 encoding monocarboxylate transporter. In addition, ethanol production was reduced by deleting PDC1 and ADH1 genes encoding major pyruvate decarboxylase and alcohol dehydrogenase, respectively, and glycerol production was eliminated by deleting GPD1 and GPD2 genes encoding glycerol-3-phosphate dehydrogenase. LA tolerance of the engineered D-LA-producing strain was enhanced by adaptive evolution and overexpression of HAA1 encoding a transcriptional activator involved in weak acid stress response, resulting in effective D-LA production up to 48.9 g/L without neutralization. In a flask fed-batch fermentation under neutralizing condition, our evolved strain produced 112.0 g/L D-LA with a yield of 0.80 g/g glucose and a productivity of 2.2 g/(L · h).
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Affiliation(s)
- Seung-Ho Baek
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Eunice Y Kwon
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Yong Hwan Kim
- Department of Chemical Engineering, Kwangwoon University, 20 Gwangun-ro, Nowon-gu, Seoul, 01897, Republic of Korea
| | - Ji-Sook Hahn
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
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Husain AR, Hadad Y, Zainal Alam MNH. Development of Low-Cost Microcontroller-Based Interface for Data Acquisition and Control of Microbioreactor Operation. ACTA ACUST UNITED AC 2015; 21:660-70. [PMID: 26185253 DOI: 10.1177/2211068215594770] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Indexed: 12/27/2022]
Abstract
This article presents the development of a low-cost microcontroller-based interface for a microbioreactor operation. An Arduino MEGA 2560 board with 54 digital input/outputs, including 15 pulse-width-modulation outputs, has been chosen to perform the acquisition and control of the microbioreactor. The microbioreactor (volume = 800 µL) was made of poly(dimethylsiloxane) and poly(methylmethacrylate) polymers. The reactor was built to be equipped with sensors and actuators for the control of reactor temperature and the mixing speed. The article discusses the circuit of the microcontroller-based platform, describes the signal conditioning steps, and evaluates the capacity of the proposed low-cost microcontroller-based interface in terms of control accuracy and system responses. It is demonstrated that the proposed microcontroller-based platform is able to operate parallel microbioreactor operation with satisfactory performances. Control accuracy at a deviation less than 5% of the set-point values and responses in the range of few seconds have been recorded.
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Affiliation(s)
- Abdul Rashid Husain
- Department of Control and Mechatronic Engineering, Faculty of Electrical Engineering, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| | - Yaser Hadad
- Department of Control and Mechatronic Engineering, Faculty of Electrical Engineering, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
| | - Muhd Nazrul Hisham Zainal Alam
- Process Systems Engineering Centre, Faculty of Chemical Engineering, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
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18
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Artificial neural network associated to UV/Vis spectroscopy for monitoring bioreactions in biopharmaceutical processes. Bioprocess Biosyst Eng 2015; 38:1045-54. [DOI: 10.1007/s00449-014-1346-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 12/19/2014] [Indexed: 12/13/2022]
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19
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Saeb AT, David SK, Al-Brahim H. In silico detection of virulence gene homologues in the human pathogen sphingomonas spp. Evol Bioinform Online 2014; 10:229-38. [PMID: 25574122 PMCID: PMC4266192 DOI: 10.4137/ebo.s20710] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/09/2014] [Accepted: 11/11/2014] [Indexed: 11/05/2022] Open
Abstract
There is an ongoing debate about the clinical significance of Sphingomonas paucimobilis as a virulent bacterial pathogen. In the present study, we investigated the presence of different virulence factors and genes in Sphingomonas bacteria. We utilized phylogenetic, comparative genomics and bioinformatics analysis to investigate the potentiality of Sphingomonas bacteria as virulent pathogenic bacteria. The 16S ribosomal RNA gene (16S rDNA) phylogenetic tree showed that the closest bacterial taxon to Sphingomonas is Brucella with a bootstrap value of 87 followed by Helicobacter, Campylobacter, Pseudomonas, and then Legionella. Sphingomonas shared no virulence factors with Helicobacter or Campylobacter, despite their close phylogenic relationship. In spite of the phylogenetic divergence between Sphingomonas and Pseudomonas, they shared many major virulence factors, such as adherence, antiphagocytosis, iron uptake, proteases, and quorum sensing. In conclusion, Sphingomonas spp. contains several major virulence factors resembling Pseudomonas sp., Legionella sp., Brucella sp., and Bordetella sp. virulence factors. Similarity of virulence factors did not match phylogenetic relationships. These findings suggest horizontal gene transfer of virulence factors rather than sharing a common pathogenic ancestor. Sphingomonas spp. is potential virulent bacterial pathogen.
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Affiliation(s)
- Amr Tm Saeb
- Biotechnology Department, Strategic Center for Diabetes Research, King Saud University, Riyadh, Saudi Arabia
| | - Satish Kumar David
- Information Technology Department, Strategic Center for Diabetes Research, King Saud University, Riyadh, Saudi Arabia
| | - Hissa Al-Brahim
- Biotechnology Department, Strategic Center for Diabetes Research, King Saud University, Riyadh, Saudi Arabia
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20
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Rajendran K, Mahadevan S, Rajendhran J, Paramasamy G, Mandal AB. Investigations to Enhance Production of Penicillin G Acylase from RecombinantBacillus badius pacExpressed inEscherichia coliDH5α. CHEM ENG COMMUN 2014. [DOI: 10.1080/00986445.2013.845750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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21
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Zhou Y, Nie K, Zhang X, Liu S, Wang M, Deng L, Wang F, Tan T. Production of fumaric acid from biodiesel-derived crude glycerol by Rhizopus arrhizus. BIORESOURCE TECHNOLOGY 2014; 163:48-53. [PMID: 24787316 DOI: 10.1016/j.biortech.2014.04.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 04/06/2014] [Accepted: 04/07/2014] [Indexed: 05/28/2023]
Abstract
This work investigated the capability of Rhizopus arrhizus to assimilate biodiesel-derived crude glycerol and convert it into fumaric acid. After optimizing the initial glycerol concentration, spore inoculum and yeast extract concentration, smaller pellets (0.7 mm) and higher biomass (3.11 g/L) were obtained when R. arrhizus grew on crude glycerol. It was found that crude glycerol was more suitable than glucose for smaller R. arrhizus pellet forming. When 80 g/L crude glycerol was used as carbon source, the fumaric acid production of 4.37 g/L was obtained at 192 h. With a highest concentration of 22.81 g/L achieved in the co-fermentation of crude glycerol (40 g/L) and glucose (40 g/L) at 144 h, the fumaric acid production was enhanced by 553.6%, compared to the fermentation using glycerol (80 g/L) as sole carbon source. Moreover, the production cost of fumaric acid in co-fermentation was reduced by approximately 14% compared to glucose fermentation.
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Affiliation(s)
- Yuqing Zhou
- Beijing Bioprocess Key Laboratory, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Kaili Nie
- Beijing Bioprocess Key Laboratory, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China; Amoy - BUCT Industrial Bio-technovation Institute, Amoy 361022, PR China
| | - Xin Zhang
- Beijing Bioprocess Key Laboratory, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Shihong Liu
- Beijing Bioprocess Key Laboratory, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Meng Wang
- Beijing Bioprocess Key Laboratory, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Li Deng
- Beijing Bioprocess Key Laboratory, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China; Amoy - BUCT Industrial Bio-technovation Institute, Amoy 361022, PR China.
| | - Fang Wang
- Beijing Bioprocess Key Laboratory, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China; State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Tianwei Tan
- Beijing Bioprocess Key Laboratory, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
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Hagström ÅK, Wang HL, Liénard MA, Lassance JM, Johansson T, Löfstedt C. A moth pheromone brewery: production of (Z)-11-hexadecenol by heterologous co-expression of two biosynthetic genes from a noctuid moth in a yeast cell factory. Microb Cell Fact 2013; 12:125. [PMID: 24330839 PMCID: PMC4126085 DOI: 10.1186/1475-2859-12-125] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 12/09/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Moths (Lepidoptera) are highly dependent on chemical communication to find a mate. Compared to conventional unselective insecticides, synthetic pheromones have successfully served to lure male moths as a specific and environmentally friendly way to control important pest species. However, the chemical synthesis and purification of the sex pheromone components in large amounts is a difficult and costly task. The repertoire of enzymes involved in moth pheromone biosynthesis in insecta can be seen as a library of specific catalysts that can be used to facilitate the synthesis of a particular chemical component. In this study, we present a novel approach to effectively aid in the preparation of semi-synthetic pheromone components using an engineered vector co-expressing two key biosynthetic enzymes in a simple yeast cell factory. RESULTS We first identified and functionally characterized a ∆11 Fatty-Acyl Desaturase and a Fatty-Acyl Reductase from the Turnip moth, Agrotis segetum. The ∆11-desaturase produced predominantly Z11-16:acyl, a common pheromone component precursor, from the abundant yeast palmitic acid and the FAR transformed a series of saturated and unsaturated fatty acids into their corresponding alcohols which may serve as pheromone components in many moth species. Secondly, when we co-expressed the genes in the Brewer's yeast Saccharomyces cerevisiae, a set of long-chain fatty acids and alcohols that are not naturally occurring in yeast were produced from inherent yeast fatty acids, and the presence of (Z)-11-hexadecenol (Z11-16:OH), demonstrated that both heterologous enzymes were active in concert. A 100 ml batch yeast culture produced on average 19.5 μg Z11-16:OH. Finally, we demonstrated that oxidized extracts from the yeast cells containing (Z)-11-hexadecenal and other aldehyde pheromone compounds elicited specific electrophysiological activity from male antennae of the Tobacco budworm, Heliothis virescens, supporting the idea that genes from different species can be used as a molecular toolbox to produce pheromone components or pheromone component precursors of potential use for control of a variety of moths. CONCLUSIONS This study is a first proof-of-principle that it is possible to "brew" biologically active moth pheromone components through in vitro co-expression of pheromone biosynthetic enzymes, without having to provide supplementary precursors. Substrates present in the yeast alone appear to be sufficient.
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Affiliation(s)
- Åsa K Hagström
- Pheromone Group, Department of Biology, Lund University, Lund, Sweden.
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23
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Ercan D, Demirci A. Current and future trends for biofilm reactors for fermentation processes. Crit Rev Biotechnol 2013; 35:1-14. [PMID: 23919241 DOI: 10.3109/07388551.2013.793170] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Biofilms in the environment can both cause detrimental and beneficial effects. However, their use in bioreactors provides many advantages including lesser tendencies to develop membrane fouling and lower required capital costs, their higher biomass density and operation stability, contribution to resistance of microorganisms, etc. Biofilm formation occurs naturally by the attachment of microbial cells to the support without use of any chemicals agent in biofilm reactors. Biofilm reactors have been studied and commercially used for waste water treatment and bench and pilot-scale production of value-added products in the past decades. It is important to understand the fundamentals of biofilm formation, physical and chemical properties of a biofilm matrix to run the biofilm reactor at optimum conditions. This review includes the principles of biofilm formation; properties of a biofilm matrix and their roles in the biofilm formation; factors that improve the biofilm formation, such as support materials; advantages and disadvantages of biofilm reactors; and industrial applications of biofilm reactors.
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Affiliation(s)
- Duygu Ercan
- Department of Agricultural and Biological Engineering, The Pennsylvania State University, University Park , Pennsylvania , USA and
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24
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Kim D, Yoo M, Kim E, Hong SG. Anthranilate degradation by a cold-adaptedPseudomonassp. J Basic Microbiol 2013; 55:354-62. [DOI: 10.1002/jobm.201300079] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 04/13/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Dockyu Kim
- Division of Life Sciences; Korea Polar Research Institute; Incheon Korea
| | - Miyoun Yoo
- Department of Systems Biology; Yonsei University; Seoul Korea
- Yonsei/Paris-Sud Project; Yonsei International Campus; Incheon Korea
| | - Eungbin Kim
- Department of Systems Biology; Yonsei University; Seoul Korea
- Yonsei/Paris-Sud Project; Yonsei International Campus; Incheon Korea
| | - Soon Gyu Hong
- Division of Life Sciences; Korea Polar Research Institute; Incheon Korea
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25
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Yegin S, Fernandez-Lahore M. A Thermolabile Aspartic Proteinase from Mucor mucedo DSM 809: Gene Identification, Cloning, and Functional Expression in Pichia pastoris. Mol Biotechnol 2012; 54:661-72. [DOI: 10.1007/s12033-012-9608-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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26
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Retallack DM, Jin H, Chew L. Reliable protein production in a Pseudomonas fluorescens expression system. Protein Expr Purif 2012; 81:157-65. [DOI: 10.1016/j.pep.2011.09.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 09/20/2011] [Accepted: 09/20/2011] [Indexed: 10/17/2022]
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27
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Shrestha KL, Liu SW, Huang CP, Wu HM, Wang WC, Li YK. Characterization and identification of essential residues of the glycoside hydrolase family 64 laminaripentaose-producing- -1, 3-glucanase. Protein Eng Des Sel 2011; 24:617-25. [DOI: 10.1093/protein/gzr031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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28
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Jin H, Cantin GT, Maki S, Chew LC, Resnick SM, Ngai J, Retallack DM. Soluble periplasmic production of human granulocyte colony-stimulating factor (G-CSF) in Pseudomonas fluorescens. Protein Expr Purif 2011; 78:69-77. [PMID: 21396452 DOI: 10.1016/j.pep.2011.03.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 03/02/2011] [Accepted: 03/02/2011] [Indexed: 11/28/2022]
Abstract
Cost-effective production of soluble recombinant protein in a bacterial system remains problematic with respect to expression levels and quality of the expressed target protein. These constraints have particular meaning today as "biosimilar" versions of innovator protein drugs are entering the clinic and the marketplace. A high throughput, parallel processing approach to expression strain engineering was used to evaluate soluble expression of human granulocyte colony-stimulating factor (G-CSF) in Pseudomonas fluorescens. The human g-csf gene was optimized for expression in P. fluorescens and cloned into a set of periplasmic expression vectors. These plasmids were transformed into a variety of P. fluorescens host strains each having a unique phenotype, to evaluate soluble expression in a 96-well growth and protein expression format. To identify a strain producing high levels of intact, soluble Met-G-CSF product, more than 150 protease defective host strains from the Pfēnex Expression Technology™ toolbox were screened in parallel using biolayer interferometry (BLI) to quantify active G-CSF binding to its receptor. A subset of these strains was screened by LC-MS analysis to assess the quality of the expressed G-CSF protein. A single strain with an antibiotic resistance marker insertion in the pfaI gene was identified that produced>99% Met-GCSF. A host with a complete deletion of the autotransporter-coding gene pfaI from the genome was constructed, and expression of soluble, active Met-GSCF in this strain was observed to be 350mg/L at the 1 liter fermentation scale.
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Affiliation(s)
- Hongfan Jin
- Pfenex Inc., 10790 Roselle street, San Diego, CA 92121, USA.
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Braga ARC, Gomes PA, Kalil SJ. Formulation of Culture Medium with Agroindustrial Waste for β-Galactosidase Production from Kluyveromyces marxianus ATCC 16045. FOOD BIOPROCESS TECH 2011. [DOI: 10.1007/s11947-011-0511-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Simões C, Alakomi H, Maukonen J, Saarela M. Expression of clpL1 and clpL2 genes in Lactobacillus rhamnosus VTT E-97800 after exposure to acid and heat stress treatments or to freeze-drying. Benef Microbes 2010; 1:253-7. [DOI: 10.3920/bm2010.0021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The aim of the study was to evaluate the potential of utilising the information on expression levels of selected stress genes in assessing the quality of probiotic products. For this purpose RT-qPCR methods were developed to study the expression of clpL1 and clpL2 stress genes in Lactobacillus rhamnosus VTT E-97800 (E800) cells after exposure to processing-related stress conditions or to freeze-drying. Heat treatments in laboratory scale were performed with E800 cells incubated at 47 °C or 50 °C for 60 min. Acid treatments were performed both at laboratory and fermenter scale. At laboratory scale E800 cells were inoculated into General Edible Medium (GEM) adjusted to pH 4.0 and pH 3.5 and incubated at 37 °C for 180 min, whereas fermenter-grown cells were exposed to pH 4.0 for 60 min at the end of the fermentation. RNA from fresh cells and freeze-dried powders was reverse transcribed after isolation, quantification and standardisation. clpL1 and clpL2 transcripts were analysed by RT-qPCR with SYBR Green I. clpL1 was induced in L. rhamnosus E800 cells exposed to 50 °C and to a much lesser extent to 47 °C. No induction was observed for clpL2 in E800 cells during either acid or heat treatment, in any of the conditions applied. RNA isolation from freeze-dried powders was unsuccessful although several attempts were made with high quality products. In conclusion, our results suggest that developing quality indicators for probiotic products based on differences in the expression of stress genes is a challenging task for several reasons: at least with some genes (like in the present study with clpL) quite harsh conditions are needed to detect differences in the gene expression; mRNA isolation from freeze-dried powders was unsuccessful which hampers the quality analysis of large proportion of probiotic products; and furthermore RT-qPCR proved to be a too laborious procedure for routine use.
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Affiliation(s)
- C. Simões
- Department of Biotechnology, VTT Technical Research Centre of Finland, P.O. box 1000, 02044 VTT Espoo, Finland
| | - H. Alakomi
- Department of Biotechnology, VTT Technical Research Centre of Finland, P.O. box 1000, 02044 VTT Espoo, Finland
| | - J. Maukonen
- Department of Biotechnology, VTT Technical Research Centre of Finland, P.O. box 1000, 02044 VTT Espoo, Finland
| | - M. Saarela
- Department of Biotechnology, VTT Technical Research Centre of Finland, P.O. box 1000, 02044 VTT Espoo, Finland
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Li D, Yan Y, Ping S, Chen M, Zhang W, Li L, Lin W, Geng L, Liu W, Lu W, Lin M. Genome-wide investigation and functional characterization of the beta-ketoadipate pathway in the nitrogen-fixing and root-associated bacterium Pseudomonas stutzeri A1501. BMC Microbiol 2010; 10:36. [PMID: 20137101 PMCID: PMC2907835 DOI: 10.1186/1471-2180-10-36] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Accepted: 02/08/2010] [Indexed: 11/20/2022] Open
Abstract
Background Soil microorganisms are mainly responsible for the complete mineralization of aromatic compounds that usually originate from plant products or environmental pollutants. In many cases, structurally diverse aromatic compounds can be converted to a small number of structurally simpler intermediates, which are metabolized to tricarboxylic acid intermediates via the β-ketoadipate pathway. This strategy provides great metabolic flexibility and contributes to increased adaptation of bacteria to their environment. However, little is known about the evolution and regulation of the β-ketoadipate pathway in root-associated diazotrophs. Results In this report, we performed a genome-wide analysis of the benzoate and 4-hydroxybenzoate catabolic pathways of Pseudomonas stutzeri A1501, with a focus on the functional characterization of the β-ketoadipate pathway. The P. stutzeri A1501 genome contains sets of catabolic genes involved in the peripheral pathways for catabolism of benzoate (ben) and 4-hydroxybenzoate (pob), and in the catechol (cat) and protocatechuate (pca) branches of the β-ketoadipate pathway. A particular feature of the catabolic gene organization in A1501 is the absence of the catR and pcaK genes encoding a LysR family regulator and 4-hydroxybenzoate permease, respectively. Furthermore, the BenR protein functions as a transcriptional activator of the ben operon, while transcription from the catBC promoter can be activated in response to benzoate. Benzoate degradation is subject to carbon catabolite repression induced by glucose and acetate in A1501. The HPLC analysis of intracellular metabolites indicated that low concentrations of 4-hydroxybenzoate significantly enhance the ability of A1501 to degrade benzoate. Conclusions The expression of genes encoding proteins involved in the β-ketoadipate pathway is tightly modulated by both pathway-specific and catabolite repression controls in A1501. This strain provides an ideal model system for further study of the evolution and regulation of aromatic catabolic pathways.
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Affiliation(s)
- Danhua Li
- College of Biological Sciences, China Agricultural University, Beijing 100094, China
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KANDASAMY K, MARIMUTHU M, SUNG GY, AHN CG, KIM S. Complementary Metal-Oxide Semiconductor (CMOS) Image Sensor: An Insight as a Point-of-Care Label-Free Immunosensor. ANAL SCI 2010; 26:1215-7. [DOI: 10.2116/analsci.26.1215] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
| | | | - Gun Yong SUNG
- BT Convergence Technology Research Department, Electronics and Telecommunications Research Institute (ETRI)
| | - Chang Geun AHN
- BT Convergence Technology Research Department, Electronics and Telecommunications Research Institute (ETRI)
| | - Sanghyo KIM
- College of Bionanotechnology, Kyungwon University
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Krull R, Cordes C, Horn H, Kampen I, Kwade A, Neu TR, Nörtemann B. Morphology of filamentous fungi: linking cellular biology to process engineering using Aspergillus niger. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2010; 121:1-21. [PMID: 20490972 DOI: 10.1007/10_2009_60] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
In various biotechnological processes, filamentous fungi, e.g. Aspergillus niger, are widely applied for the production of high value-added products due to their secretion efficiency. There is, however, a tangled relationship between the morphology of these microorganisms, the transport phenomena and the related productivity. The morphological characteristics vary between freely dispersed mycelia and distinct pellets of aggregated biomass. Hence, advantages and disadvantages for mycel or pellet cultivation have to be balanced out carefully. Due to this inadequate understanding of morphogenesis of filamentous microorganisms, fungal morphology, along with reproducibility of inocula of the same quality, is often a bottleneck of productivity in industrial production. To obtain an optimisation of the production process it is of great importance to gain a better understanding of the molecular and cell biology of these microorganisms as well as the approaches in biochemical engineering and particle technique, in particular to characterise the interactions between the growth conditions, cell morphology, spore-hyphae-interactions and product formation. Advances in particle and image analysis techniques as well as micromechanical devices and their applications to fungal cultivations have made available quantitative morphological data on filamentous cells. This chapter provides the ambitious aspects of this line of action, focussing on the control and characterisation of the morphology, the transport gradients and the approaches to understand the metabolism of filamentous fungi. Based on these data, bottlenecks in the morphogenesis of A. niger within the complex production pathways from gene to product should be identified and this may improve the production yield.
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Affiliation(s)
- Rainer Krull
- Institute of Biochemical Engineering, Technische Universität Braunschweig, Gaussstrasse 17, 38106, Braunschweig, Germany,
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Cloning and nucleotide sequences of carbazole degradation genes from marine bacterium Neptuniibacter sp. strain CAR-SF. Curr Microbiol 2009; 61:50-6. [PMID: 20039169 DOI: 10.1007/s00284-009-9575-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2009] [Accepted: 12/15/2009] [Indexed: 10/20/2022]
Abstract
The marine bacterium Neptuniibacter sp. strain CAR-SF utilizes carbazole as its sole carbon and nitrogen sources. Two sets of clustered genes related to carbazole degradation, the upper and lower pathways, were obtained. The marine bacterium genes responsible for the upper carbazole degradation pathway, carAa, carBa, carBb, and carC, encode the terminal oxygenase component of carbazole 1,9a-dioxygenase, the small and large subunits of the meta-cleavage enzyme, and the meta-cleavage compound hydrolase, respectively. The genes involved in the lower degradation pathway encode the anthranilate dioxygenase large and small subunit AntA and AntB, anthranilate dioxygenase reductase AntC, 4-oxalocrotonate tautomerase, and catechol 2,3-dioxygenase. Reverse transcription-polymerase chain reaction confirmed the involvement of the isolated genes in carbazole degradation. Escherichia coli cells transformed with the CarAa of strain CAR-SF required ferredoxin and ferredoxin reductase for biotransformation of carbazole. Although carAc, which encodes the ferredoxin component of carbazole 1,9a-dioxygenase, was not found immediately downstream of carAaBaBbC, the carAc-like gene may be located elsewhere based on Southern hybridization. This is the first report of genes involved in carbazole degradation isolated from a marine bacterium.
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Takahashi Y, Shintani M, Li L, Yamane H, Nojiri H. Carbazole-degradative IncP-7 plasmid pCAR1.2 is structurally unstable in Pseudomonas fluorescens Pf0-1, which accumulates catechol, the intermediate of the carbazole degradation pathway. Appl Environ Microbiol 2009; 75:3920-9. [PMID: 19376894 PMCID: PMC2698365 DOI: 10.1128/aem.02373-08] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2008] [Accepted: 04/09/2009] [Indexed: 11/20/2022] Open
Abstract
We determined the effect of the host on the function and structure of the nearly identical IncP-7 carbazole-degradative plasmids pCAR1.1 and pCAR1.2. We constructed Pseudomonas aeruginosa PAO1(pCAR1.2) and P. fluorescens Pf0-1Km(pCAR1.2) and compared their growth on carbazole- and succinate-containing media with that of P. putida KT2440(pCAR1.1). We also assessed the stability of the genetic structures of the plasmids in each of the three hosts. Pf0-1Km(pCAR1.2) showed dramatically delayed growth when carbazole was supplied as the sole carbon source, while the three strains grew at nearly the same rate on succinate. Among the carbazole-grown Pf0-1Km(pCAR1.2) cells, two types of deficient strains appeared and dominated the population; such dominance was not observed in the other two strains or for succinate-grown Pf0-1Km(pCAR1.2). Genetic analysis showed that the two deficient strains possessed pCAR1.2 derivatives in which the carbazole-degradative car operon was deleted or its regulatory gene, antR, was deleted by homologous recombination between insertion sequences. From genomic information and quantitative reverse transcription-PCR analyses of the genes involved in carbazole mineralization by Pf0-1Km(pCAR1.2), we found that the cat genes on the chromosome of Pf0-1Km, which are necessary for the degradation of catechol (a toxic intermediate in the carbazole catabolic pathway), were not induced in the presence of carbazole. The resulting accumulation of catechol may have enabled the strain that lost its carbazole-degrading ability to have overall higher fitness than the wild-type strain. These results suggest that the functions of the chromosomal genes contributed to the selection of plasmid derivatives with altered structures.
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Affiliation(s)
- Yurika Takahashi
- Biotechnology Research Center, The University of Tokyo, Yayoi, Bunkyo-ku, Japan
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36
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Dielectrophoresis assisted concentration of micro-particles and their rapid quantitation based on optical means. Biomed Microdevices 2009; 11:987-95. [DOI: 10.1007/s10544-009-9316-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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37
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Morimoto S, Fujii T. A new approach to retrieve full lengths of functional genes from soil by PCR-DGGE and metagenome walking. Appl Microbiol Biotechnol 2009; 83:389-96. [PMID: 19370345 DOI: 10.1007/s00253-009-1992-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2009] [Revised: 03/26/2009] [Accepted: 03/27/2009] [Indexed: 10/20/2022]
Abstract
Metagenomes are a vast genetic resource, and various approaches have been developed to explore them. Here, we present a new approach to retrieve full lengths of functional genes from soil DNA using PCR-denaturing gradient gel electrophoresis (DGGE) followed by metagenome walking. Partial fragments of benzoate 1,2-dioxygenase alpha subunit gene (benA) were detected from a 3-chlorobenzoate (3CB)-dosed soil by PCR-DGGE, and one DGGE band induced by 3CB was used as a target fragment for metagenome walking. The walking retrieved the flanking regions of the target fragment from the soil DNA, resulting in recovery of the full length of benA and also downstream gene (benB). The same strategy retrieved another gene, tfdC, and a complete tfdC and two downstream genes were obtained from the same soil. PCR-DGGE allows screening for target genes based on their potential for degrading contaminants in the environment. This feature provides an advantage over other existing metagenomic approaches.
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Affiliation(s)
- Sho Morimoto
- National Institute for Agro-Environmental Sciences, 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604, Japan.
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38
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Zhang AL, Zhang TY, Luo JX, Fu CY, Qu Z, Yi GH, Su DX, Tu FZ, Pan YW. Inducible expression of human angiostatin by AOXI promoter in P. pastoris using high-density cell culture. Mol Biol Rep 2009; 36:2265-70. [DOI: 10.1007/s11033-008-9443-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2008] [Accepted: 12/19/2008] [Indexed: 10/21/2022]
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Development of stable isotope and selenomethionine labeling methods for proteins expressed in Pseudomonas fluorescens. Protein Expr Purif 2008; 65:57-65. [PMID: 19166940 DOI: 10.1016/j.pep.2008.12.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Revised: 12/16/2008] [Accepted: 12/22/2008] [Indexed: 11/22/2022]
Abstract
Pseudomonas fluorescens is a robust protein expression system that is very well suited for high throughput protein expression for structural genomics studies. Since NMR spectroscopy and X-ray crystallography are both used by various investigators in structure elucidation studies, the availability of target proteins labeled with stable isotopes or selenomethionine is essential for the determination of protein structures. A completely defined medium for the expression and stable isotope labeling of proteins in P. fluorescens has been developed. The expression level of Bacillus thuringiensis Cry34 in the modified medium is comparable to that obtained in the original medium. In addition, more than 95% incorporation of 15N was obtained in Cry34 using 15N ammonium sulfate and the quality of the protein, as assessed by NMR analysis, is comparable to that made using commercial medium. High levels of selenomethionine (SeMet) incorporation in the Xenorhabdus nematophilus insecticidal protein XptA2 were also obtained in P. fluorescens using the defined medium, allowing development of a method for obtaining highly purified XptA2. The following observations were made when inhibitors of endogenous methionine biosynthesis were used in P. fluorescens culture when SeMet was substituted in XptA2: (I) there is little inhibition of cell growth or recombinant XptA2 expression in the presence of SeMet concentrations up to 300 mg/L in cell culture, (II) there was greater than 95% SeMet incorporation ratio in recombinant SeMet-labeled XptA2 (SeMet-XptA2) and the incorporation ratio is consistent and reproducible and (III) finally, purified SeMet-XptA2 possesses similar protein structure and insecticidal activity relative to the unlabeled counterpart XptA2 as shown by bioassay and differential scanning calorimetric analysis. The high SeMet incorporation should provide high accuracy and resolution in XptA2 phase determination by multiwavelength anomalous diffraction (MAD), indicating that P. fluorescens is an excellent expression host to produce SeMet-labeled proteins for structural study.
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40
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Zhan Y, Yu H, Yan Y, Chen M, Lu W, Li S, Peng Z, Zhang W, Ping S, Wang J, Lin M. Genes involved in the benzoate catabolic pathway in Acinetobacter calcoaceticus PHEA-2. Curr Microbiol 2008; 57:609-14. [PMID: 18781356 DOI: 10.1007/s00284-008-9251-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Accepted: 08/13/2008] [Indexed: 11/29/2022]
Abstract
A putative benM gene encoding a LysR-type regulator located upstream from the benA gene was found in Acinetobacter calcoaceticus PHEA-2. Disruption of benM or benA destroyed the ability of PHEA-2 to utilize benzoate. The benM mutant was used to construct a genomic library for isolation of the complete gene cluster responsible for benzoate degradation. Sequence analysis showed that the cluster has three putative operons: benM, benABCDE, and benKP. Unlike many well-characterized benzoate-degrading bacteria, muconate is unable to induce in vivo transcription of the PHEA-2 ben cluster. Reverse transcriptase-polymerase chain reaction (RT-PCR) results showed that the benABCDE operon is activated by the BenM protein in the presence of benzoate. Moreover, a gel-retardation assay demonstrated that BenM binds to the promotor region of the benA gene. The activities of catechol 1,2-dioxygenase (C12O) and catechol 2,3-dioxygenase (C23O) showed that PHEA-2 converted benzoate to catechol for further degradation, possibly via an ortho-cleavage pathway.
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Affiliation(s)
- Yuhua Zhan
- College of Biological Sciences, China Agricultural University, Beijing 100094, People's Republic of China
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41
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Goto T, Ohkuri T, Shioi S, Abe Y, Imoto T, Ueda T. Crystal structures of K33 mutant hen lysozymes with enhanced activities. J Biochem 2008; 144:619-23. [PMID: 18776207 DOI: 10.1093/jb/mvn108] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using random mutagenesis, we previously obtained K33N mutant lysozyme that showed a large lytic halo on the plate coating Micrococcus luteus. In order to examine the effects of mutation of K33N on enzyme activity, we prepared K33N and K33A mutant lysozymes from yeast. It was found that the activities of both the mutant lysozymes were higher than those of the wild-type lysozyme based on the results of the activity measurements against M. luteus (lytic activity) and glycol chitin. Moreover, 3D structures of K33N and K33A mutant lysozyme were solved by X-ray crystallographic analyses. The side chain of K33 in the wild-type lysozyme hydrogen bonded with N37 involved in the substrate-binding region, and the orientation of the side chain of N37 in K33 mutant lysozymes were different in the wild-type lysozyme. These results suggest that the enhancement of activity in K33N mutant lysozyme was due to an alteration in the orientation of the side chain of N37. On the other hand, K33N lysozyme was less stable than the wild-type lysozyme. Lysozyme may sacrifice its enzyme activity to acquire the conformational stability at position 33.
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Affiliation(s)
- Takashi Goto
- Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka 812-8582, Japan
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Bhattacharya S, Salamat S, Morisette D, Banada P, Akin D, Liu YS, Bhunia AK, Ladisch M, Bashir R. PCR-based detection in a micro-fabricated platform. LAB ON A CHIP 2008; 8:1130-1136. [PMID: 18584089 DOI: 10.1039/b802227e] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We present a novel, on-chip system for the electrokinetic capture of bacterial cells and their identification using the polymerase chain reaction (PCR). The system comprises a glass-silicon platform with a set of micro-channels, -chambers, and -electrodes. A platinum thin film resistor, placed in the proximity of the chambers, is used for temperature monitoring. The whole chip assembly is mounted on a Printed Circuit Board (PCB) and wire-bonded to it. The PCB has an embedded heater that is utilized for PCR thermal cycle and is controlled by a Lab-View program. Similar to our previous work, one set of electrodes on the chip inside the bigger chamber (0.6 microl volume) is used for diverting bacterial cells from a flowing stream into to a smaller chamber (0.4 nl volume). A second set of interdigitated electrodes (in smaller chamber) is used to actively trap and concentrate the bacterial cells using dielectrophoresis (DEP). In the presence of the DEP force, with the cells still entrapped in the micro-chamber, PCR mix is injected into the chamber. Subsequently, PCR amplification with SYBR Green detection is used for genetic identification of Listeria monocytogenes V7 cells. The increase in fluorescence is recorded with a photomultiplier tube module mounted over an epifluorescence microscope. This integrated micro-system is capable of genetic amplification and identification of as few as 60 cells of L. monocytogenes V7 in less than 90 min, in 600 nl volume collected from a sample of 10(4) cfu ml(-1). Specificity trials using various concentrations of L. monocytogenes V7, Listeria innocua F4248, and Escherichia coli O157:H7 were carried out successfully using two different primer sets specific for a regulatory gene of L. monocytogenes, prfA and 16S rRNA primer specific for the Listeria spp., and no cross-reactivity was observed.
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Miyakoshi M, Shintani M, Terabayashi T, Kai S, Yamane H, Nojiri H. Transcriptome analysis of Pseudomonas putida KT2440 harboring the completely sequenced IncP-7 plasmid pCAR1. J Bacteriol 2007; 189:6849-60. [PMID: 17675379 PMCID: PMC2045235 DOI: 10.1128/jb.00684-07] [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] [Received: 05/01/2007] [Accepted: 07/19/2007] [Indexed: 11/20/2022] Open
Abstract
The IncP-7 plasmid pCAR1 of Pseudomonas resinovorans CA10 confers the ability to degrade carbazole upon transfer to the recipient strain P. putida KT2440. We designed a customized whole-genome oligonucleotide microarray to study the coordinated expression of pCAR1 and the chromosome in the transconjugant strain KT2440(pCAR1). First, the transcriptome of KT2440(pCAR1) during growth with carbazole as the sole carbon source was compared to that during growth with succinate. The carbazole catabolic car and ant operons were induced, along with the chromosomal cat and pca genes involved in the catechol branch of the beta-ketoadipate pathway. Additionally, the regulatory gene antR encoding the AraC/XylS family transcriptional activator specific for car and ant operons was upregulated. The characterization of the antR promoter revealed that antR is transcribed from an RpoN-dependent promoter, suggesting that the successful expression of the carbazole catabolic operons depends on whether the chromosome contains the specific RpoN-dependent activator. Next, to analyze whether the horizontal transfer of a plasmid alters the transcription network of its host chromosome, we compared the chromosomal transcriptomes of KT2440(pCAR1) and KT2440 under the same growth conditions. Only subtle changes were caused by the transfer of pCAR1, except for the significant induction of the hypothetical gene PP3700, designated parI, which encodes a putative ParA-like ATPase with an N-terminal Xre-type DNA-binding motif. Further transcriptional analyses showed that the parI promoter was positively regulated by ParI itself and the pCAR1-encoded protein ParA.
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Affiliation(s)
- Masatoshi Miyakoshi
- Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
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Glenn SA, Gurich N, Feeney MA, González JE. The ExpR/Sin quorum-sensing system controls succinoglycan production in Sinorhizobium meliloti. J Bacteriol 2007; 189:7077-88. [PMID: 17644606 PMCID: PMC2045190 DOI: 10.1128/jb.00906-07] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Sinorhizobium meliloti is a gram-negative soil bacterium capable of forming a symbiotic nitrogen-fixing relationship with its plant host, Medicago sativa. Various bacterially produced factors are essential for successful nodulation. For example, at least one of two exopolysaccharides produced by S. meliloti (succinoglycan or EPS II) is required for nodule invasion. Both of these polymers are produced in high- and low-molecular-weight (HMW and LMW, respectively) fractions; however, only the LMW forms of either succinoglycan or EPS II are active in nodule invasion. The production of LMW succinoglycan can be generated by direct synthesis or through the depolymerization of HMW products by the action of two specific endoglycanases, ExsH and ExoK. Here, we show that the ExpR/Sin quorum-sensing system in S. meliloti is involved in the regulation of genes responsible for succinoglycan biosynthesis as well as in the production of LMW succinoglycan. Therefore, quorum sensing, which has been shown to regulate the production of EPS II, also plays an important role in succinoglycan biosynthesis.
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Affiliation(s)
- Sarah A Glenn
- Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75083-0688, USA
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45
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Retallack DM, Schneider JC, Mitchell J, Chew L, Liu H. Transport of heterologous proteins to the periplasmic space of Pseudomonas fluorescens using a variety of native signal sequences. Biotechnol Lett 2007; 29:1483-91. [PMID: 17541504 DOI: 10.1007/s10529-007-9415-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2007] [Accepted: 05/02/2007] [Indexed: 10/23/2022]
Abstract
Bacterial expression of recombinant proteins containing disulfide bonds is facilitated by transport of the proteins to the periplasmic space. Several Pseudomonas fluorescens signal sequences have been identified that efficiently direct proteins to the periplasm and provide solubility and yield advantages over the production of proteins fused to the PelB signal sequence in E. coli. For a single chain antibody fragment, the final yield varied from about 1 g/l to 10 g/l when expression in P. fluorescens involved fusion to various P. fluorescens signal sequences.
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Affiliation(s)
- Diane M Retallack
- The Dow Chemical Company, Core Biotechnology Research and Development, 5501 Oberlin Dr, San Diego, CA 92121, USA.
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46
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Madduri KM, Snodderley EM. Expression of phosphinothricin N-acetyltransferase in Escherichia coli and Pseudomonas fluorescens: influence of mRNA secondary structure, host, and other physiological conditions. Protein Expr Purif 2007; 55:352-60. [PMID: 17574436 DOI: 10.1016/j.pep.2007.04.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Revised: 04/17/2007] [Accepted: 04/18/2007] [Indexed: 11/23/2022]
Abstract
Expression of a plant codon optimized pat gene encoding phosphinothricin acetyltransferase (PAT) in bacterial expression systems required modification of the 5' end of the pat ORF. Modifications necessary for improving the expression were identified by a coupled in vitro transcription and translation process. The dramatic improvement in the expression of PAT was due to the removal of a potential secondary structure that could have resulted in the inhibition of translational initiation. Therefore, in vitro transcription and translation is a versatile tool to optimize gene sequence for protein overexpression. Additionally, this method was shown to be successful in both Escherichia coli and Pseudomonas fluorescens. Gene sequence optimization and choice of host along with cultivation conditions also had major impact on PAT expression. P. fluorescens was a better host than E. coli resulting in 30-fold more expression of PAT. We were able to recover approximately 95mg of purified PAT from P. fluorescens using a three step chromatographic process.
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Affiliation(s)
- Krishna M Madduri
- Dow AgroSciences LLC, 9330 Zionsville Road, Indianapolis, IN 46268, USA.
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