1
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Paul S, Olymon K, Martinez GS, Sarkar S, Yella VR, Kumar A. MLDSPP: Bacterial Promoter Prediction Tool Using DNA Structural Properties with Machine Learning and Explainable AI. J Chem Inf Model 2024; 64:2705-2719. [PMID: 38258978 DOI: 10.1021/acs.jcim.3c02017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Bacterial promoters play a crucial role in gene expression by serving as docking sites for the transcription initiation machinery. However, accurately identifying promoter regions in bacterial genomes remains a challenge due to their diverse architecture and variations. In this study, we propose MLDSPP (Machine Learning and Duplex Stability based Promoter prediction in Prokaryotes), a machine learning-based promoter prediction tool, to comprehensively screen bacterial promoter regions in 12 diverse genomes. We leveraged biologically relevant and informative DNA structural properties, such as DNA duplex stability and base stacking, and state-of-the-art machine learning (ML) strategies to gain insights into promoter characteristics. We evaluated several machine learning models, including Support Vector Machines, Random Forests, and XGBoost, and assessed their performance using accuracy, precision, recall, specificity, F1 score, and MCC metrics. Our findings reveal that XGBoost outperformed other models and current state-of-the-art promoter prediction tools, namely Sigma70pred and iPromoter2L, achieving F1-scores >95% in most systems. Significantly, the use of one-hot encoding for representing nucleotide sequences complements these structural features, enhancing our XGBoost model's predictive capabilities. To address the challenge of model interpretability, we incorporated explainable AI techniques using Shapley values. This enhancement allows for a better understanding and interpretation of the predictions of our model. In conclusion, our study presents MLDSPP as a novel, generic tool for predicting promoter regions in bacteria, utilizing original downstream sequences as nonpromoter controls. This tool has the potential to significantly advance the field of bacterial genomics and contribute to our understanding of gene regulation in diverse bacterial systems.
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Affiliation(s)
- Subhojit Paul
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Kaushika Olymon
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Gustavo Sganzerla Martinez
- Microbiology and Immunology, Dalhousie University, Halifax, Nova Scotia B3H 4H7, Canada
- Pediatrics, Izaak Walton Killam (IWK) Health Center, Canadian Center for Vaccinology (CCfV), Halifax, Nova Scotia B3H 4H7, Canada
| | - Sharmilee Sarkar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Venkata Rajesh Yella
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Guntur 522302, Andhra Pradesh, India
| | - Aditya Kumar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
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2
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Chen Y, Arlt VM, Stürzenbaum SR. MosSCI-mediated exogenous gene expression is modulated by genomic positioning. Biotechnol J 2023; 18:e2300062. [PMID: 37177911 DOI: 10.1002/biot.202300062] [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: 02/07/2023] [Revised: 05/09/2023] [Accepted: 05/11/2023] [Indexed: 05/15/2023]
Abstract
Although the Mos1-mediated single-copy insertion (MosSCI) technique has been widely used to generate stable transgenic Caenorhabditis elegans strains, the link between stability of expression and integration site still needs to be explored. Here, experimental evidence is provided that transgenes are not able to match the level of transcription of their native counterpart, and that insertions at certain locations can result in an external stress-mediated increase in expression. Insertion site ttTi5605 on chromosome II was shown to be a superior location, at least when introducing reproduction related genes. Thus, this study provides a reference for the selection of an optimal site for MosSCI which provides acceptable expression performance whilst minimizing undesirable secondary effects.
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Affiliation(s)
- Yuzhi Chen
- Department of Analytical, Environmental and Forensic Sciences, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Volker M Arlt
- Toxicology Department, GAB Consulting GmbH, Heidelberg, Germany
| | - Stephen R Stürzenbaum
- Department of Analytical, Environmental and Forensic Sciences, School of Cancer & Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK
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3
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Lei Q, Ma J, Du G, Zhou J, Guan X. Efficient expression of a cytokine combination in Saccharomyces cerevisiae for cultured meat production. Food Res Int 2023; 170:113017. [PMID: 37316083 DOI: 10.1016/j.foodres.2023.113017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 06/16/2023]
Abstract
Cultured meat technology is a novel and promising alternative strategy for meat production, and it provides an efficient, safe, and sustainable way to supply animal protein. Cytokines play an important role in promoting the rapid proliferation of cells, but the high cost and potential food safety concerns of commercial cytokines have hindered their application in large-scale cultured meat production. Herein, Saccharomyces cerevisiae C800 was used as a starting strain in which four cytokines were exogenously expressed simultaneously using the Cre-loxP system, including long-chain human insulin growth factor-1, platelet-derived growth factor-BB, basic fibroblast growth factor, and epidermal growth factor. Through promoter optimization, endogenous protease knockout, genomic co-expression, expression frame gene order optimization, and fermentation optimization, a recombinant strain CPK2B2 co-expressing four cytokines was obtained with a yield of 18.35 mg/L. After cell lysis and filter sterilization, the CPK2B2 lysate was directly added to the culture medium of porcine muscle satellite cells (MuSCs). CPK2B2 lysate promoted the growth of MuSCs and increased the proportion of G2/S cells and EdU+ cells significantly, indicating its efficacy in promoting cell proliferation. This study provides a simple and cost-saving strategy by using S. cerevisiae to produce a recombinant cytokine combination for cultured meat production.
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Affiliation(s)
- Qingzi Lei
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jun Ma
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Guocheng Du
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
| | - Xin Guan
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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4
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Olaitan AO, Dureja C, Youngblom MA, Topf MA, Shen WJ, Gonzales-Luna AJ, Deshpande A, Hevener KE, Freeman J, Wilcox MH, Palmer KL, Garey KW, Pepperell CS, Hurdle JG. Decoding a cryptic mechanism of metronidazole resistance among globally disseminated fluoroquinolone-resistant Clostridioides difficile. Nat Commun 2023; 14:4130. [PMID: 37438331 DOI: 10.1038/s41467-023-39429-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 06/13/2023] [Indexed: 07/14/2023] Open
Abstract
Severe outbreaks and deaths have been linked to the emergence and global spread of fluoroquinolone-resistant Clostridioides difficile over the past two decades. At the same time, metronidazole, a nitro-containing antibiotic, has shown decreasing clinical efficacy in treating C. difficile infection (CDI). Most metronidazole-resistant C. difficile exhibit an unusual resistance phenotype that can only be detected in susceptibility tests using molecularly intact heme. Here, we describe the mechanism underlying this trait. We find that most metronidazole-resistant C. difficile strains carry a T-to-G mutation (which we term PnimBG) in the promoter of gene nimB, resulting in constitutive transcription. Silencing or deleting nimB eliminates metronidazole resistance. NimB is related to Nim proteins that are known to confer resistance to nitroimidazoles. We show that NimB is a heme-dependent flavin enzyme that degrades nitroimidazoles to amines lacking antimicrobial activity. Furthermore, occurrence of the PnimBG mutation is associated with a Thr82Ile substitution in DNA gyrase that confers fluoroquinolone resistance in epidemic strains. Our findings suggest that the pandemic of fluoroquinolone-resistant C. difficile occurring over the past few decades has also been characterized by widespread resistance to metronidazole.
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Affiliation(s)
- Abiola O Olaitan
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Chetna Dureja
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
| | - Madison A Youngblom
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Madeline A Topf
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Wan-Jou Shen
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
| | - Anne J Gonzales-Luna
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Aditi Deshpande
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
| | - Kirk E Hevener
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jane Freeman
- Department of Microbiology, Leeds Teaching Hospitals Trust, Leeds, UK
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK
| | - Mark H Wilcox
- Department of Microbiology, Leeds Teaching Hospitals Trust, Leeds, UK
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK
| | - Kelli L Palmer
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX, USA
| | - Kevin W Garey
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Caitlin S Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin-Madison, Madison, WI, USA.
| | - Julian G Hurdle
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA.
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5
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Johnson KC, Sabel JL, Cole J, Pruett CL, Plymale R, Reyna NS. From genetics to biotechnology: Synthetic biology as a flexible course-embedded research experience. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 50:580-591. [PMID: 36053869 PMCID: PMC9826443 DOI: 10.1002/bmb.21662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 06/15/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
The need for changing how science is taught and the expansion of undergraduate research experiences is essential to foster critical thinking in the Natural Sciences. Most faculty research programs only involve a small number of upper-level undergraduate students each semester. The course-based undergraduate research experience (CURE) model enables more students to take ownership over an independent project and experience authentic research. Further, by creating projects that fit into a curriculum's learning goals and student-oriented outcomes, departments help strengthen critical thinking skills in the classroom. Here, we report on the incorporation of a synthetic biology CURE into a mid-level cellular biology course and two advanced level genetics/molecular biology courses. Synthetic biology involves systematic engineering of novel organisms, such as bacteria and plants, to work as functional devices to solve problems in medicine, agriculture, and manufacturing. The value of synthetic biology and its ultimate utility as a teaching tool relies on reusable, standard genetic parts that can be interchanged using common genetic engineering principles. This Synthetic biology CURE effectively achieves five essential goals: (1) a sense of project ownership; (2) self-efficacy: mastery of a manageable number of techniques; (3) increased tolerance for obstacles through challenging research; (4) increased communication skills; and (5) a sense of belonging in a larger scientific community. Based upon our student assessment data, we demonstrate that this course-based synthetic biology laboratory engages students directly in an authentic research experience and models important elements of collaboration, discovery, iteration, and critical thinking.
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Affiliation(s)
- Kristen C. Johnson
- Department of Life SciencesUniversity of New HampshireManchesterNew HampshireUSA
| | - Jaime L. Sabel
- Department of Biological SciencesUniversity of MemphisMemphisTennesseeUSA
| | - Judith Cole
- Department of Biological SciencesUniversity of MemphisMemphisTennesseeUSA
| | | | - Ruth Plymale
- Department of BiologyOuachita Baptist UniversityArkadelphiaArkansasUSA
| | - Nathan S. Reyna
- Department of BiologyOuachita Baptist UniversityArkadelphiaArkansasUSA
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6
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Drysdale V, Cmielewski P, Donnelley M, Reyne N, Parsons D, McCarron A. Comparison of physical perturbation devices for enhancing lentiviral vector-mediated gene transfer to the airway epithelium. Hum Gene Ther 2022; 33:1062-1072. [PMID: 35920214 DOI: 10.1089/hum.2022.086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Natural airway defences currently impede the efficacy of viral vector-mediated airway gene therapy. Conditioning airways prior to vector delivery can disrupt these barriers, improving viral vector access to target receptors and airway stem cells. This study aimed to assess and quantify the in vivo histological and gene transfer effects of physical perturbation devices to identify effective conditioning approaches. A range of flexible wire baskets with varying configurations, a Brush, biopsy forceps, and a balloon catheter were examined. We first evaluated the histological effects of physical perturbation devices in rat tracheas that were excised 10 minutes after conditioning. Based on the histological findings, a selection of devices were used to condition rat tracheas in vivo before delivering a lentiviral vector containing the LacZ reporter gene. After 7 days, excised tracheas were X-gal processed and examined en face to quantify the area of LacZ staining. Histological observations 10 minutes after conditioning found that physical perturbation dislodged cells from the basement membrane to varying degrees, with some producing significant levels of epithelial cell removal. When a subset of devices were assessed for their ability to enhance gene transfer, only the NGage® wire basket (Cook Medical) produced a significant increase in the proportion of X-gal-stained area when compared to unconditioned tracheas (8-fold, p = 0.00025). These results suggest that a range of factors contribute to perturbation-enhanced gene transfer. Overall, this study supports existing evidence that physical perturbation can assist airway gene transfer, and will help to identify the characteristics of an effective device for airway gene therapy.
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Affiliation(s)
- Victoria Drysdale
- The University of Adelaide, Adelaide Medical School , Adelaide, South Australia, Australia.,The University of Adelaide, Robinson Research Institute , Adelaide, South Australia, Australia.,Women's and Children's Hospital Adelaide, North Adelaide, South Australia, Australia;
| | - Patricia Cmielewski
- The University of Adelaide, Adelaide Medical School , Adelaide, South Australia, Australia.,The University of Adelaide, Robinson Research Institute , Adelaide, South Australia, Australia.,Women's and Children's Hospital Adelaide, North Adelaide, South Australia, Australia;
| | - Martin Donnelley
- The University of Adelaide, Adelaide Medical School , Adelaide, South Australia, Australia.,The University of Adelaide, Robinson Research Institute , Adelaide, South Australia, Australia.,Women's and Children's Hospital Adelaide, Respiratory and Sleep Medicine , North Adelaide, South Australia, Australia;
| | - Nicole Reyne
- The University of Adelaide, Adelaide Medical School , Adelaide, South Australia, Australia.,The University of Adelaide, Robinson Research Institute , Adelaide, South Australia, Australia.,Women's and Children's Hospital Adelaide, North Adelaide, South Australia, Australia;
| | - David Parsons
- The University of Adelaide, Adelaide Medical School , Adelaide, South Australia, Australia.,The University of Adelaide, Robinson Research Institute, Adelaide, South Australia, Australia.,Women's and Children's Hospital Adelaide, Respiratory and Sleep Medicine, North Adelaide, South Australia, Australia;
| | - Alexandra McCarron
- The University of Adelaide, Adelaide Medical School , Adelaide, South Australia, Australia.,The University of Adelaide, Robinson Research Institute , Adelaide, South Australia, Australia.,Women's and Children's Hospital Adelaide, Respiratory and Sleep Medicine , North Adelaide, South Australia, Australia;
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7
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Jia T, Ge Q, Zhang S, Zhang Z, Liu A, Fan S, Jiang X, Feng Y, Zhang L, Niu D, Huang S, Gong W, Yuan Y, Shang H. UDP-Glucose Dehydrogenases: Identification, Expression, and Function Analyses in Upland Cotton ( Gossypium hirsutum). Front Genet 2021; 11:597890. [PMID: 33505427 PMCID: PMC7831515 DOI: 10.3389/fgene.2020.597890] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 11/27/2020] [Indexed: 11/17/2022] Open
Abstract
UDP-glucose dehydrogenase (UGD; EC1.1.1.22) is a NAD+-dependent enzyme that catalyzes the two-fold oxidation of UDP-glucose (UDP-Glc) to produce UDP-glucuronic acid and plays an important role in plant cell wall synthesis. A total of 42 UGD genes from four Gossypium genomes including G. hirsutum, G. arboretum, G. barbadense, and G. raimondii were identified and found that the UGD gene family has conservative evolution patterns in gene structure and protein domain. The growth of fibers can be effectively promoted after adding the UDP-Glc to the medium, and the GhUGD gene expression enhanced. In addition, the transgenic Arabidopsis lines over-expressing GH_D12G1806 had longer root lengths and higher gene expression level than the wild-type plants of Columbia-0. These results indicated that UGD may play important roles in cotton fiber development and has a guiding significance for dissecting fiber development mechanism.
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Affiliation(s)
- Tingting Jia
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shuya Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhen Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Aiying Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Senmiao Fan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiao Jiang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yulong Feng
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Lipeng Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Doudou Niu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shen Huang
- Zhengzhou University of Light Industry College of Food and Bioengineering, Zhengzhou, China
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
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8
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Zhu G, Zhang C, Wang Y, Wang Y, Li D, Yu X, Zhu W, Fu C, Lou S, Fan L, Ma L, Wang L, Pan Y. Variants in miRNA regulome and their association with the risk of nonsyndromic orofacial clefts. Epigenomics 2020; 12:1109-1121. [PMID: 32408759 DOI: 10.2217/epi-2020-0124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Aim: To investigate the associations between single nucleotide polymorphisms (SNPs) in miRNA regulome and nonsyndromic orofacial clefts. Materials & methods: The associations were evaluated by logistic regression model in stage I (504 cases and 455 controls) and stage II (1500 cases and 1386 controls). Functional experiments including luciferase activity assay, cell apoptosis and proliferation, serum miRNA expression, and mouse embryo RNA sequencing were performed. Results: Rs3830766 in the enhancer of hsa-miR-4260 was associated with cleft lip only (CLO) and enhancer activity. Hsa-miR-4260 expression decreased in the serum of CLO. Overexpression of miR-4260 inhibited cell proliferation and promoted cell apoptosis. UBB was the target gene of hsa-miR-4260. Conclusion: Rs3830766 in the hsa-miR-4260 enhancer that can interact with UBB was relevant to CLO.
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Affiliation(s)
- Guirong Zhu
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Chi Zhang
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Yuting Wang
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Yuli Wang
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Dandan Li
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Xin Yu
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Weihao Zhu
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Chengyi Fu
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Shu Lou
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Liwen Fan
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Lan Ma
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China
| | - Lin Wang
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Yongchu Pan
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
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9
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Corts AD, Thomason LC, Gill RT, Gralnick JA. Efficient and Precise Genome Editing in Shewanella with Recombineering and CRISPR/Cas9-Mediated Counter-Selection. ACS Synth Biol 2019; 8:1877-1889. [PMID: 31277550 DOI: 10.1021/acssynbio.9b00188] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Dissimilatory metal-reducing bacteria, particularly those from the genus Shewanella, are of importance for bioremediation of metal contaminated sites and sustainable energy production. However, studies on this species have suffered from a lack of effective genetic tools for precise and high throughput genome manipulation. Here we report the development of a highly efficient system based on single-stranded DNA oligonucleotide recombineering coupled with CRISPR/Cas9-mediated counter-selection. Our system uses two plasmids: a sgRNA targeting vector and an editing vector, the latter harboring both Cas9 and the phage recombinase W3 Beta. Following the experimental analysis of Cas9 activity, we demonstrate the ability of this system to efficiently and precisely engineer different Shewanella strains with an average efficiency of >90% among total transformed cells, compared to ≃5% by recombineering alone, and regardless of the gene modified. We also show that different genetic changes can be introduced: mismatches, deletions, and small insertions. Surprisingly, we found that use of CRISPR/Cas9 alone allows selection of recombinase-independent S. oneidensis mutations, albeit at lower efficiency and frequency. With synthesized single-stranded DNA as substrates for homologous recombination and Cas9 as a counter-selectable marker, this new system provides a rapid, scalable, versatile, and scarless tool that will accelerate progress in Shewanella genomic engineering.
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Affiliation(s)
- Anna D. Corts
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota−Twin Cities, St. Paul, Minnesota 55108, United States
| | - Lynn C. Thomason
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Ryan T. Gill
- DTU BIOSUSTAIN, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Jeffrey A. Gralnick
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota−Twin Cities, St. Paul, Minnesota 55108, United States
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10
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Gilman J, Singleton C, Tennant RK, James P, Howard TP, Lux T, Parker DA, Love J. Rapid, Heuristic Discovery and Design of Promoter Collections in Non-Model Microbes for Industrial Applications. ACS Synth Biol 2019; 8:1175-1186. [PMID: 30995831 DOI: 10.1021/acssynbio.9b00061] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Well-characterized promoter collections for synthetic biology applications are not always available in industrially relevant hosts. We developed a broadly applicable method for promoter identification in atypical microbial hosts that requires no a priori understanding of cis-regulatory element structure. This novel approach combines bioinformatic filtering with rapid empirical characterization to expand the promoter toolkit and uses machine learning to improve the understanding of the relationship between DNA sequence and function. Here, we apply the method in Geobacillus thermoglucosidasius, a thermophilic organism with high potential as a synthetic biology chassis for industrial applications. Bioinformatic screening of G. kaustophilus, G. stearothermophilus, G. thermodenitrificans, and G. thermoglucosidasius resulted in the identification of 636 100 bp putative promoters, encompassing the genome-wide design space and lacking known transcription factor binding sites. Eighty of these sequences were characterized in vivo, and activities covered a 2-log range of predictable expression levels. Seven sequences were shown to function consistently regardless of the downstream coding sequence. Partition modeling identified sequence positions upstream of the canonical -35 and -10 consensus motifs that were predicted to strongly influence regulatory activity in Geobacillus, and artificial neural network and partial least squares regression models were derived to assess if there were a simple, forward, quantitative method for in silico prediction of promoter function. However, the models were insufficiently general to predict pre hoc promoter activity in vivo, most probably as a result of the relatively small size of the training data set compared to the size of the modeled design space.
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Affiliation(s)
- James Gilman
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
| | - Chloe Singleton
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
| | - Richard K. Tennant
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
| | - Paul James
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
| | - Thomas P. Howard
- School of Natural and Environmental Sciences, Newcastle University, Devonshire Building, Newcastle-upon-Tyne NE1 7RU, U.K
| | - Thomas Lux
- Plant Genome and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Munich 85764, Germany
| | - David A. Parker
- Biodomain, Shell Technology Center Houston, 3333 Highway 6 South, Houston, Texas 77082-3101, United States
| | - John Love
- The BioEconomy Centre, Biosciences, College of Life and Environmental Sciences, Stocker Road, University of Exeter, Exeter EX4 4QD, U.K
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11
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Teh MY, Ooi KH, Danny Teo SX, Bin Mansoor ME, Shaun Lim WZ, Tan MH. An Expanded Synthetic Biology Toolkit for Gene Expression Control in Acetobacteraceae. ACS Synth Biol 2019; 8:708-723. [PMID: 30865830 DOI: 10.1021/acssynbio.8b00168] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The availability of different host chassis will greatly expand the range of applications in synthetic biology. Members of the Acetobacteraceae family of Gram-negative bacteria form an attractive class of nonmodel microorganisms that can be exploited to produce industrial chemicals, food and beverage, and biomaterials. One such biomaterial is bacterial cellulose, which is a strong and ultrapure natural polymer used in tissue engineering scaffolds, wound dressings, electronics, food additives, and other products. However, despite the potential of Acetobacteraceae in biotechnology, there has been considerably little effort to fundamentally reprogram the bacteria for enhanced performance. One limiting factor is the lack of a well-characterized, comprehensive toolkit to control expression of genes in biosynthetic pathways and regulatory networks to optimize production and cell viability. Here, we address this shortcoming by building an expanded genetic toolkit for synthetic biology applications in Acetobacteraceae. We characterized the performance of multiple natural and synthetic promoters, ribosome binding sites, terminators, and degradation tags in three different strains, namely, Gluconacetobacter xylinus ATCC 700178, Gluconacetobacter hansenii ATCC 53582, and Komagataeibacter rhaeticus iGEM. Our quantitative data revealed strain-specific and common design rules for the precise control of gene expression in these industrially relevant bacterial species. We further applied our tools to synthesize a biodegradable cellulose-chitin copolymer, adjust the structure of the cellulose film produced, and implement CRISPR interference for ready down-regulation of gene expression. Collectively, our genetic parts will enable the efficient engineering of Acetobacteraceae bacteria for the biomanufacturing of cellulose-based materials and other commercially valuable products.
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Affiliation(s)
- Min Yan Teh
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 637459 Singapore
| | - Kean Hean Ooi
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 637459 Singapore
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Shun Xiang Danny Teo
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 637459 Singapore
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, 138672 Singapore
| | | | - Wen Zheng Shaun Lim
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 637459 Singapore
| | - Meng How Tan
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 637459 Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, 138672 Singapore
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12
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Uluşeker C, Torres-Bacete J, García JL, Hanczyc MM, Nogales J, Kahramanoğulları O. Quantifying dynamic mechanisms of auto-regulation in Escherichia coli with synthetic promoter in response to varying external phosphate levels. Sci Rep 2019; 9:2076. [PMID: 30765722 PMCID: PMC6376016 DOI: 10.1038/s41598-018-38223-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 12/13/2018] [Indexed: 12/16/2022] Open
Abstract
Escherichia coli have developed one of the most efficient regulatory response mechanisms to phosphate starvation. The machinery involves a cascade with a two-component system (TCS) that relays the external signal to the genetic circuit, resulting in a feedback response. Achieving a quantitative understanding of this system has implications in synthetic biology and biotechnology, for example, in applications for wastewater treatment. To this aim, we present a computational model and experimental results with a detailed description of the TCS, consisting of PhoR and PhoB, together with the mechanisms of gene expression. The model is parameterised within the feasible range, and fitted to the dynamic response of our experimental data on PhoB as well as PhoA, the product of this network that is used in alkaline phosphatase production. Deterministic and stochastic simulations with our model predict the regulation dynamics in higher external phosphate concentrations while reproducing the experimental observations. In a cycle of simulations and experimental verification, our model predicts and explores phenotypes with various synthetic promoter designs that can optimise the inorganic phosphate intake in E. coli. Sensitivity analysis demonstrates that the Pho-controlled genes have a significant influence over the phosphate response. Together with experimental findings, our model should thus provide insights for the investigations on engineering new sensors and regulators for living technologies.
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Affiliation(s)
- Cansu Uluşeker
- University of Trento, Centre for Integrative Biology, Trento, 38123, Italy.,The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Rovereto, 38068, Italy
| | - Jesús Torres-Bacete
- Centro Nacional de Biotecnología (CNB-CSIC), Systems Biology Department, Madrid, 28049, Spain
| | - José L García
- Centro de Investigaciones Biológicas (CIB-CSIC), Microbial and Plant Biotechnology Department, Madrid, 28040, Spain.,Institute for Integrative Systems Biology (I2Sysbio-CSIC-UV), Applied Systems Biology and Synthetic Biology Department, Paterna, 46980, Spain
| | - Martin M Hanczyc
- University of Trento, Centre for Integrative Biology, Trento, 38123, Italy.,Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Juan Nogales
- Centro Nacional de Biotecnología (CNB-CSIC), Systems Biology Department, Madrid, 28049, Spain
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13
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Bharanikumar R, Premkumar KAR, Palaniappan A. PromoterPredict: sequence-based modelling of Escherichia coli σ 70 promoter strength yields logarithmic dependence between promoter strength and sequence. PeerJ 2018; 6:e5862. [PMID: 30425888 PMCID: PMC6228582 DOI: 10.7717/peerj.5862] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 10/03/2018] [Indexed: 11/20/2022] Open
Abstract
We present PromoterPredict, a dynamic multiple regression approach to predict the strength of Escherichia coli promoters binding the σ70 factor of RNA polymerase. σ70 promoters are ubiquitously used in recombinant DNA technology, but characterizing their strength is demanding in terms of both time and money. We parsed a comprehensive database of bacterial promoters for the -35 and -10 hexamer regions of σ70-binding promoters and used these sequences to construct the respective position weight matrices (PWM). Next we used a well-characterized set of promoters to train a multivariate linear regression model and learn the mapping between PWM scores of the -35 and -10 hexamers and the promoter strength. We found that the log of the promoter strength is significantly linearly associated with a weighted sum of the -10 and -35 sequence profile scores. We applied our model to 100 sets of 100 randomly generated promoter sequences to generate a sampling distribution of mean strengths of random promoter sequences and obtained a mean of 6E-4 ± 1E-7. Our model was further validated by cross-validation and on independent datasets of characterized promoters. PromoterPredict accepts -10 and -35 hexamer sequences and returns the predicted promoter strength. It is capable of dynamic learning from user-supplied data to refine the model construction and yield more robust estimates of promoter strength. PromoterPredict is available as both a web service (https://promoterpredict.com) and standalone tool (https://github.com/PromoterPredict). Our work presents an intuitive generalization applicable to modelling the strength of other promoter classes.
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Affiliation(s)
- Ramit Bharanikumar
- Biotechnology, Sri Venkateswara College of Engineering (Autonomous), Sriperumbudur, Tamil Nadu, India
| | - Keshav Aditya R Premkumar
- Computer Science and Engineering, Sri Venkateswara College of Engineering (Autonomous), Sriperumbudur, Tamil Nadu, India
| | - Ashok Palaniappan
- Bioinformatics, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, Tamil Nadu, India
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14
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Barnett SC, Perry BAL, Dalrymple-Alford JC, Parr-Brownlie LC. Optogenetic stimulation: Understanding memory and treating deficits. Hippocampus 2018; 28:457-470. [DOI: 10.1002/hipo.22960] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 04/24/2018] [Accepted: 05/02/2018] [Indexed: 01/01/2023]
Affiliation(s)
- S. C. Barnett
- Department of Psychology; University of Canterbury; Christchurch 8041 New Zealand
- Brain Research New Zealand; New Zealand
| | - B. A. L. Perry
- Department of Psychology; University of Canterbury; Christchurch 8041 New Zealand
- Brain Research New Zealand; New Zealand
| | - J. C. Dalrymple-Alford
- Department of Psychology; University of Canterbury; Christchurch 8041 New Zealand
- Brain Research New Zealand; New Zealand
- New Zealand Brain Research Institute; Christchurch New Zealand
| | - L. C. Parr-Brownlie
- Brain Research New Zealand; New Zealand
- Department of Anatomy, School of Biomedical Science; Brain Health Research Centre, University of Otago; Dunedin New Zealand
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15
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Abstract
Antibiotics have saved millions of lives over the past decades. However, the accumulation of so many antibiotic resistance genes by some clinically relevant pathogens has begun to lead to untreatable infections worldwide. The current antibiotic resistance crisis will require greater efforts by governments and the scientific community to increase the research and development of new antibacterial drugs with new mechanisms of action. A major challenge is the identification of novel microbial targets, essential for in vivo growth or pathogenicity, whose inhibitors can overcome the currently circulating resistome of human pathogens. In this article, we focus on the potential high value of bacterial transcriptional regulators as targets for the development of new antibiotics, discussing in depth the molecular role of these regulatory proteins in bacterial physiology and pathogenesis. Recent advances in the search for novel compounds that inhibit the biological activity of relevant transcriptional regulators in pathogenic bacteria are reviewed.
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16
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Shali A, Rigi G, Pornour M, Ahmadian G. Expression and Secretion of Cyan Fluorescent Protein (CFP) in B. subtilis using the Chitinase Promoter from Bacillus pumilus SG2. IRANIAN BIOMEDICAL JOURNAL 2017; 21:240-8. [PMID: 28088132 PMCID: PMC5459939 DOI: 10.18869/acadpub.ibj.21.4.240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Background: Improved cyan fluorescent protein (ICFP) is a monochromic, green fluorescent protein (GFP) derivative produced by Aequorea macrodactyla in a process similar to GFP. This protein has strong absorption spectra at wavelengths 426-446 nm. ICFP can be used in cell, organelle or intracellular protein labeling, investigating the protein-protein interactions as well as assessing the promoter activities. Methods: In our previous study, the promoters of two chitinases (ChiS and ChiL) from Bacillus pumilus SG2 were assessed in B. subtilis and their regulatory elements were characterized. In the present study, icfp was cloned downstream of several truncated promoters obtained in the former study, and ICFP expression was evaluated in B. subtilis. Results: Extracellular expression and secretion of ICFP were analyzed under the control of different truncated versions of ChiSL promoters grown on different media. Results from SDS-PAGE and fluorimetric analyses showed that there were different expression rates of CFP; however, the UPChi-ICFP3 construct exhibited a higher level of expression and secretion in the culture medium. Conclusion: Our presented results revealed that inserting this truncated form of Chi promoter upstream of the ICFP, as a reporter gene, in B. subtilis led to an approximately ten fold increase in ICFP expression.
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Affiliation(s)
- Abbas Shali
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB) , P.O. Box 14155-6343 , Tehran, Iran
| | - Garshasb Rigi
- Department of Biology, Faculty of Science, Behbahan Khatam Alanbia University of Technology, Behbahan, Khuzestan, Iran
| | - Majid Pornour
- Medical Laser Research Center, Academic Center for Education, Culture and Research (ACECR), Tehran, Iran
| | - Gholamreza Ahmadian
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB) , P.O. Box 14155-6343 , Tehran, Iran
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17
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Arthur LL, Chung JJ, Jankirama P, Keefer KM, Kolotilin I, Pavlovic-Djuranovic S, Chalker DL, Grbic V, Green R, Menassa R, True HL, Skeath JB, Djuranovic S. Rapid generation of hypomorphic mutations. Nat Commun 2017; 8:14112. [PMID: 28106166 PMCID: PMC5263891 DOI: 10.1038/ncomms14112] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 11/30/2016] [Indexed: 01/05/2023] Open
Abstract
Hypomorphic mutations are a valuable tool for both genetic analysis of gene function and for synthetic biology applications. However, current methods to generate hypomorphic mutations are limited to a specific organism, change gene expression unpredictably, or depend on changes in spatial-temporal expression of the targeted gene. Here we present a simple and predictable method to generate hypomorphic mutations in model organisms by targeting translation elongation. Adding consecutive adenosine nucleotides, so-called polyA tracks, to the gene coding sequence of interest will decrease translation elongation efficiency, and in all tested cell cultures and model organisms, this decreases mRNA stability and protein expression. We show that protein expression is adjustable independent of promoter strength and can be further modulated by changing sequence features of the polyA tracks. These characteristics make this method highly predictable and tractable for generation of programmable allelic series with a range of expression levels.
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Affiliation(s)
- Laura L. Arthur
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Joyce J. Chung
- Department of Biology, Washington University, St Louis, Missouri 63105, USA
| | - Preetam Jankirama
- Department of Biology, The University of Western Ontario, 1151 Richmond Street, London, Ontario, Canada N6A5B7
- Science and Technology Branch, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario, Canada N5V4T3
| | - Kathryn M. Keefer
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Igor Kolotilin
- Scattered Gold Biotechnology Inc. 14 Denali Terrace, London, Ontario, Canada N5X 3W2
| | - Slavica Pavlovic-Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Douglas L. Chalker
- Department of Biology, Washington University, St Louis, Missouri 63105, USA
| | - Vojislava Grbic
- Department of Biology, The University of Western Ontario, 1151 Richmond Street, London, Ontario, Canada N6A5B7
| | - Rachel Green
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205, USA
| | - Rima Menassa
- Science and Technology Branch, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario, Canada N5V4T3
| | - Heather L. True
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri 63110, USA
- The Hope Center for Neurological Diseases, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - James B. Skeath
- Department of Genetics, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Sergej Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, St Louis, Missouri 63110, USA
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18
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Matos IMN, Coelho MM, Schartl M. Gene copy silencing and DNA methylation in natural and artificially produced allopolyploid fish. ACTA ACUST UNITED AC 2016; 219:3072-3081. [PMID: 27445349 DOI: 10.1242/jeb.140418] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 07/19/2016] [Indexed: 12/28/2022]
Abstract
Allelic silencing is an important mechanism for coping with gene dosage changes in polyploid organisms that is well known in allopolyploid plants. Only recently, it was shown in the allotriploid fish Squalius alburnoides that this process also occurs in vertebrates. However, it is still unknown whether this silencing mechanism is common to other allopolyploid fish, and which mechanisms might be responsible for allelic silencing. We addressed these questions in a comparative study between Squalius alburnoides and another allopolyploid complex, the Amazon molly (Poecilia formosa). We examined the allelic expression patterns for three target genes in four somatic tissues of natural allo-anorthoploids and laboratory-produced tri-genomic hybrids of S. alburnoides and P. formosa. Also, for both complexes, we evaluated the correlation between total DNA methylation level and the ploidy status and genomic composition of the individuals. We found that allelic silencing also occurs in other allopolyploid organisms besides the single one that was previously known. We found and discuss disparities within and between the two considered complexes concerning the pattern of allele-specific expression and DNA methylation levels. Disparities might be due to intrinsic characteristics of each genome involved in the hybridization process. Our findings also support the idea that long-term evolutionary processes have an effect on the allele expression patterns and possibly also on DNA methylation levels.
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Affiliation(s)
- Isa M N Matos
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal Department of Physiological Chemistry, Biocenter, University of Würzburg, Würzburg 97078, Germany
| | - Maria M Coelho
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa 1749-016, Portugal
| | - Manfred Schartl
- Department of Physiological Chemistry, Biocenter, University of Würzburg, Würzburg 97078, Germany Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg 97078, Germany Texas Institute for Advanced Study and Department of Biology, Texas A&M University, College Station, TX 77843, USA
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19
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Bradshaw JC, Gongola AB, Reyna NS. Rapid Verification of Terminators Using the pGR-Blue Plasmid and Golden Gate Assembly. J Vis Exp 2016:54064. [PMID: 27167700 PMCID: PMC4941997 DOI: 10.3791/54064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The goal of this protocol is to allow for the rapid verification of bioinformatically identified terminators. Further, the plasmid (pGR-Blue) is designed specifically for this protocol and allows for the quantification of terminator efficiency. As a proof of concept, six terminators were bioinformatically identified in the mycobacteriophage Bernal13. Once identified, terminators were then made as oligonucleotides with the appropriate sticky ends and annealed together. Using Golden Gate Assembly (GGA), terminators were then cloned into pGR-Blue. Under visible light, false positive colonies appear blue and positively transformed colonies are white/yellow. After induction of an arabinose inducible promoter (pBad) with arabinose, colony strength can be determined by measuring the ratio of green fluorescent protein (GFP) produced to red fluorescent protein (RFP) produced. With pGR-Blue, the protocol can be completed in as little as three days and is ideal in an educational setting. Additionally, results show that this protocol is useful as a means for understanding in silico predictions of terminator efficiency related to the regulation of transcription.
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20
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Li J, Zhang Y. Theoretical analysis of transcription process with polymerase stalling. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:052713. [PMID: 26066205 DOI: 10.1103/physreve.91.052713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Indexed: 06/04/2023]
Abstract
Experimental evidence shows that in gene transcription RNA polymerase has the possibility to be stalled at a certain position of the transcription template. This may be due to the template damage or protein barriers. Once stalled, polymerase may backtrack along the template to the previous nucleotide to wait for the repair of the damaged site, simply bypass the barrier or damaged site and consequently synthesize an incorrect messenger RNA, or degrade and detach from the template. Thus, the effective transcription rate (the rate to synthesize correct product mRNA) and the transcription effectiveness (the ratio of the effective transcription rate to the effective transcription initiation rate) are both influenced by polymerase stalling events. So far, no theoretical model has been given to discuss the gene transcription process including polymerase stalling. In this study, based on the totally asymmetric simple exclusion process, the transcription process including polymerase stalling is analyzed theoretically. The dependence of the effective transcription rate, effective transcription initiation rate, and transcription effectiveness on the transcription initiation rate, termination rate, as well as the backtracking rate, bypass rate, and detachment (degradation) rate when stalling, are discussed in detail. The results showed that backtracking restart after polymerase stalling is an ideal mechanism to increase both the effective transcription rate and the transcription effectiveness. Without backtracking, detachment of stalled polymerase can also help to increase the effective transcription rate and transcription effectiveness. Generally, the increase of the bypass rate of the stalled polymerase will lead to the decrease of the effective transcription rate and transcription effectiveness. However, when both detachment rate and backtracking rate of the stalled polymerase vanish, the effective transcription rate may also be increased by the bypass mechanism.
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Affiliation(s)
- Jingwei Li
- Laboratory of Mathematics for Nonlinear Science, Shanghai Key Laboratory for Contemporary Applied Mathematics, Centre for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanghai 200433, China
| | - Yunxin Zhang
- Laboratory of Mathematics for Nonlinear Science, Shanghai Key Laboratory for Contemporary Applied Mathematics, Centre for Computational Systems Biology, School of Mathematical Sciences, Fudan University, Shanghai 200433, China
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