1
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Ketterson ED. What Do Ecology, Evolution, and Behavior Have in Common? The Organism in the Middle. Am Nat 2020; 196:103-118. [PMID: 32673095 DOI: 10.1086/709699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Biologists who publish in The American Naturalist are drawn to its unifying mission of covering research in the fields of ecology, evolution, behavior, and integrative biology. Presented here is one scientist's attempt to straddle these fields by focusing on a single organism. It is also an account of how time spent in the field stimulates a naturalist to wonder "why did that animal just do that?" and how research is guided by chance and intention interacting with the scientific literature and the people one meets along the way. With respect to the science, the examples come from bird migration, hormones and their connection to phenotypic integration, sexual and natural selection, and urban ecology. They also come from research on the impact of environmental change on the timing of reproduction and the potential for allochrony in migratory species to influence population divergence.
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2
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Gao L, Wu X, Zhu C, Jin Z, Wang W, Xia X. Metabolic engineering to improve the biomanufacturing efficiency of acetic acid bacteria: advances and prospects. Crit Rev Biotechnol 2020; 40:522-538. [DOI: 10.1080/07388551.2020.1743231] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ling Gao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, PR China
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology Shandong Academy of Sciences, Jinan, PR China
| | - Xiaodan Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education School of Biotechnology, Jiangnan University, Wuxi, PR China
| | - Cailin Zhu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education School of Biotechnology, Jiangnan University, Wuxi, PR China
| | - Zhengyu Jin
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, PR China
| | - Wu Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education School of Biotechnology, Jiangnan University, Wuxi, PR China
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education School of Biotechnology, Jiangnan University, Wuxi, PR China
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3
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Hussey BJ, McMillen DR. Programmable T7-based synthetic transcription factors. Nucleic Acids Res 2019; 46:9842-9854. [PMID: 30169636 PMCID: PMC6182181 DOI: 10.1093/nar/gky785] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/21/2018] [Indexed: 12/31/2022] Open
Abstract
Despite recent progress on synthetic transcription factor generation in eukaryotes, there remains a need for high-activity bacterial versions of these systems. In synthetic biology applications, it is useful for transcription factors to have two key features: they should be orthogonal (influencing only their own targets, with minimal off-target effects), and programmable (able to be directed to a wide range of user-specified transcriptional start sites). The RNA polymerase of the bacteriophage T7 has a number of appealing properties for synthetic biological designs: it can produce high transcription rates; it is a compact, single-subunit polymerase that has been functionally expressed in a variety of organisms; and its viral origin reduces the connection between its activity and that of its host's transcriptional machinery. We have created a system where a T7 RNA polymerase is recruited to transcriptional start sites by DNA binding proteins, either directly or bridged through protein–protein interactions, yielding a modular and programmable system for strong transcriptional activation of multiple orthogonal synthetic transcription factor variants in Escherichia coli. To our knowledge this is the first exogenous, programmable activator system in bacteria.
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Affiliation(s)
- Brendan J Hussey
- Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Cell and Systems Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Impact Centre, University of Toronto, Toronto, Ontario M5S 1A7, Canada
| | - David R McMillen
- Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Cell and Systems Biology, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, Canada.,Impact Centre, University of Toronto, Toronto, Ontario M5S 1A7, Canada
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4
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Fernández‐Cabezón L, Cros A, Nikel PI. Evolutionary Approaches for Engineering Industrially Relevant Phenotypes in Bacterial Cell Factories. Biotechnol J 2019; 14:e1800439. [DOI: 10.1002/biot.201800439] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/08/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Lorena Fernández‐Cabezón
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark 2800 Kongens Lyngby Denmark
| | - Antonin Cros
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark 2800 Kongens Lyngby Denmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark 2800 Kongens Lyngby Denmark
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5
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van Tol N, Flores Andaluz G, Leeggangers HACF, Roushan MR, Hooykaas PJJ, van der Zaal BJ. Zinc Finger Artificial Transcription Factor-Mediated Chloroplast Genome Interrogation in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2019; 60:393-406. [PMID: 30398644 PMCID: PMC6375250 DOI: 10.1093/pcp/pcy216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/01/2018] [Indexed: 06/08/2023]
Abstract
The large majority of core photosynthesis proteins in plants are encoded by nuclear genes, but a small portion have been retained in the plastid genome. These plastid-encoded chloroplast proteins fulfill essential roles in the process of photochemistry. Here, we report the use of nuclear-encoded, chloroplast-targeted zinc finger artificial transcription factors (ZF-ATFs) with effector domains of prokaryotic origin to modulate the expression of chloroplast genes, and to enhance the photochemical activity and growth characteristics of Arabidopsis thaliana plants. This technique was named chloroplast genome interrogation. Using this novel approach, we obtained evidence that ZF-ATFs can indeed be translocated to chloroplasts of Arabidopsis plants, can modulate their growth and operating light use efficiency of PSII, and finally can induce statistically significant changes in the expression levels of several chloroplast genes. Our data suggest that the distortion of chloroplast gene expression might be a feasible approach to manipulate the efficiency of photosynthesis in plants.
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Affiliation(s)
- Niels van Tol
- Institute of Biology Leiden, Faculty of Science, Leiden University, Sylviusweg 72, Leiden, BE, The Netherlands
| | - Gema Flores Andaluz
- Institute of Biology Leiden, Faculty of Science, Leiden University, Sylviusweg 72, Leiden, BE, The Netherlands
| | - Hendrika A C F Leeggangers
- Institute of Biology Leiden, Faculty of Science, Leiden University, Sylviusweg 72, Leiden, BE, The Netherlands
| | - M Reza Roushan
- Institute of Biology Leiden, Faculty of Science, Leiden University, Sylviusweg 72, Leiden, BE, The Netherlands
| | - Paul J J Hooykaas
- Institute of Biology Leiden, Faculty of Science, Leiden University, Sylviusweg 72, Leiden, BE, The Netherlands
| | - Bert J van der Zaal
- Institute of Biology Leiden, Faculty of Science, Leiden University, Sylviusweg 72, Leiden, BE, The Netherlands
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6
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Zhang K, Lu X, Li Y, Jiang X, Liu L, Wang H. New technologies provide more metabolic engineering strategies for bioethanol production in Zymomonas mobilis. Appl Microbiol Biotechnol 2019; 103:2087-2099. [PMID: 30661108 DOI: 10.1007/s00253-019-09620-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/02/2019] [Accepted: 01/03/2019] [Indexed: 02/06/2023]
Abstract
Bioethanol has been considered as a potentially renewable energy source, and metabolic engineering plays an important role in the production of biofuels. As an efficient ethanol-producing bacterium, Zymomonas mobilis has garnered special attention due to its high sugar uptake, ethanol yield, and tolerance. Different metabolic engineering strategies have been used to establish new metabolic pathways for Z. mobilis to broaden its substrate range, remove competing pathways, and enhance its tolerance to ethanol and lignocellulosic hydrolysate inhibitors. Recent advances in omics technology, computational modeling and simulation, system biology, and synthetic biology contribute to the efficient re-design and manipulation of microbes via metabolic engineering at the whole-cell level. In this review, we summarize the progress of some new technologies used for metabolic engineering to improve bioethanol production and tolerance in Z. mobilis. Some successful examples of metabolic engineering used to develop strains for ethanol production are described in detail. Lastly, some important strategies for future metabolic engineering efforts are also highlighted.
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Affiliation(s)
- Kun Zhang
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Xinxin Lu
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Yi Li
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Xiaobing Jiang
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Lei Liu
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China
| | - Hailei Wang
- Henan Province Engineering Laboratory for Bioconversion Technology of Functional Microbes, College of Life Sciences, Henan Normal University, Xinxiang, 453007, Henan, China.
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7
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Zhang J, Wu C, Wang W, Wang W, Wei D. Construction of enhanced transcriptional activators for improving cellulase production in Trichoderma reesei RUT C30. BIORESOUR BIOPROCESS 2018; 5:40. [PMID: 32288986 PMCID: PMC7101855 DOI: 10.1186/s40643-018-0226-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 08/14/2018] [Indexed: 11/21/2022] Open
Abstract
Enhancing cellulase production in Trichoderma reesei is of great interest for an economical biorefinery. Artificial transcription factors are a potentially powerful molecular strategy for improving cellulase production in T. reesei. In this study, enhanced transcriptional activators XYR1VP, ACE2VP, and ACE1VP were constructed by linking the C terminus of XYR1, ACE2, or ACE1 with an activation domain of herpes simplex virus protein VP16. T. reesei transformants TXYR1VP, TACE2VP, and TACE1VP showed improved cellulase and/or xylanase production. TXYR1VP has a cellulase-free phenotype but with significantly elevated xylanase production. Xylanase I and xylanase II activities [U/(mg biomass)] increased by 51% and 80%, respectively, in TXYR1VP in comparison with parental strain RUT C30. The filter paper activity of TACE2VP in the Avicel-based medium increased by 52% compared to that of RUT C30. In the Avicel-based medium, TACE1VP manifested an 80% increase in FPase activity and a 50% increase in xylanase activity as compared to those of RUT C30. Additionally, when pretreated corn stover was hydrolyzed, crude enzymes produced from TACE1VP yielded a greater glucose release than did the enzymes produced by parental strain RUT C30.![]()
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Affiliation(s)
- Jiajia Zhang
- 1New World Institute of Biotechnology, State Key Lab of Bioreactor Engineering, East China University of Science and Technology, P.O.B. 311, 130 Meilong Road, Shanghai, 200237 China
| | - Chuan Wu
- 1New World Institute of Biotechnology, State Key Lab of Bioreactor Engineering, East China University of Science and Technology, P.O.B. 311, 130 Meilong Road, Shanghai, 200237 China
| | - Wei Wang
- 2State Key Lab of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237 China
| | - Wei Wang
- 1New World Institute of Biotechnology, State Key Lab of Bioreactor Engineering, East China University of Science and Technology, P.O.B. 311, 130 Meilong Road, Shanghai, 200237 China
| | - Dongzhi Wei
- 1New World Institute of Biotechnology, State Key Lab of Bioreactor Engineering, East China University of Science and Technology, P.O.B. 311, 130 Meilong Road, Shanghai, 200237 China
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8
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Peters G, Maertens J, Lammertyn J, De Mey M. Exploring of the feature space of de novo developed post-transcriptional riboregulators. PLoS Comput Biol 2018; 14:e1006170. [PMID: 30118473 PMCID: PMC6114898 DOI: 10.1371/journal.pcbi.1006170] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 08/29/2018] [Accepted: 04/30/2018] [Indexed: 11/23/2022] Open
Abstract
Metabolic engineering increasingly depends upon RNA technology to customly rewire the metabolism to maximize production. To this end, pure riboregulators allow dynamic gene repression without the need of a potentially burdensome coexpressed protein like typical Hfq binding small RNAs and clustered regularly interspaced short palindromic repeats technology. Despite this clear advantage, no clear general design principles are available to de novo develop repressing riboregulators, limiting the availability and the reliable development of these type of riboregulators. Here, to overcome this lack of knowledge on the functionality of repressing riboregulators, translation inhibiting RNAs are developed from scratch. These de novo developed riboregulators explore features related to thermodynamical and structural factors previously attributed to translation initiation modulation. In total, 12 structural and thermodynamic features were defined of which six features were retained after removing correlations from an in silico generated riboregulator library. From this translation inhibiting RNA library, 18 riboregulators were selected using a experimental design and subsequently constructed and co-expressed with two target untranslated regions to link the translation inhibiting RNA features to functionality. The pure riboregulators in the design of experiments showed repression down to 6% of the original protein expression levels, which could only be partially explained by a ordinary least squares regression model. To allow reliable forward engineering, a partial least squares regression model was constructed and validated to link the properties of translation inhibiting RNA riboregulators to gene repression. In this model both structural and thermodynamic features were important for efficient gene repression by pure riboregulators. This approach enables a more reliable de novo forward engineering of effective pure riboregulators, which further expands the RNA toolbox for gene expression modulation. To allow reliable forward engineering of microbial cell factories, various metabolic engineering efforts rely on RNA-based technology. As such, programmable riboregulators allow dynamic control over gene expression. However, no clear design principles exist for de novo developed repressing riboregulators, which limits their applicability. Here, various engineering principles are identified and computationally explored. Subsequently, various design criteria are used in an experimental design, which were explored in an in vivo study. This resulted in a regression model that enables a more reliable computational design of repression small RNAs.
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Affiliation(s)
- Gert Peters
- Centre for Synthetic Biology, Ghent University, Ghent, Belgium
| | - Jo Maertens
- Centre for Synthetic Biology, Ghent University, Ghent, Belgium
| | | | - Marjan De Mey
- Centre for Synthetic Biology, Ghent University, Ghent, Belgium
- * E-mail:
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9
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Zhao P, Wang W, Tian P. Development of cyclic AMP receptor protein-based artificial transcription factor for intensifying gene expression. Appl Microbiol Biotechnol 2018; 102:1673-1685. [DOI: 10.1007/s00253-018-8750-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 12/21/2017] [Accepted: 12/27/2017] [Indexed: 10/18/2022]
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10
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Guo S, Yi X, Zhang W, Wu M, Xin F, Dong W, Zhang M, Ma J, Wu H, Jiang M. Inducing hyperosmotic stress resistance in succinate-producing Escherichia coli by using the response regulator DR1558 from Deinococcus radiodurans. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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11
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Gong Z, Nielsen J, Zhou YJ. Engineering Robustness of Microbial Cell Factories. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201700014] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 08/13/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Zhiwei Gong
- Division of BiotechnologyDalian Institute of Chemical PhysicsCAS457 Zhongshan RoadDalian 116023P.R. China
- College of Chemistry and Chemical EngineeringWuhan University of Science and Technology947 Heping RoadWuhan 430081P.R. China
| | - Jens Nielsen
- Department of Biology and Biological EngineeringChalmers University of TechnologyKemivägen 10 Gothenburg SE‐41296Sweden
| | - Yongjin J. Zhou
- Division of BiotechnologyDalian Institute of Chemical PhysicsCAS457 Zhongshan RoadDalian 116023P.R. China
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12
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van Tol N, Rolloos M, Pinas JE, Henkel CV, Augustijn D, Hooykaas PJJ, van der Zaal BJ. Enhancement of Arabidopsis growth characteristics using genome interrogation with artificial transcription factors. PLoS One 2017; 12:e0174236. [PMID: 28358915 PMCID: PMC5373528 DOI: 10.1371/journal.pone.0174236] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 03/06/2017] [Indexed: 11/18/2022] Open
Abstract
The rapidly growing world population has a greatly increasing demand for plant biomass, thus creating a great interest in the development of methods to enhance the growth and biomass accumulation of crop species. In this study, we used zinc finger artificial transcription factor (ZF-ATF)-mediated genome interrogation to manipulate the growth characteristics and biomass of Arabidopsis plants. We describe the construction of two collections of Arabidopsis lines expressing fusions of three zinc fingers (3F) to the transcriptional repressor motif EAR (3F-EAR) or the transcriptional activator VP16 (3F-VP16), and the characterization of their growth characteristics. In total, six different 3F-ATF lines with a consistent increase in rosette surface area (RSA) of up to 55% were isolated. For two lines we demonstrated that 3F-ATF constructs function as dominant in trans acting causative agents for an increase in RSA and biomass, and for five larger plant lines we have investigated 3F-ATF induced transcriptomic changes. Our results indicate that genome interrogation can be used as a powerful tool for the manipulation of plant growth and biomass and that it might supply novel cues for the discovery of genes and pathways involved in these properties.
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Affiliation(s)
- Niels van Tol
- Institute of Biology Leiden, Faculty of Science, Leiden University, Leiden, The Netherlands
- BioSolar Cells, Wageningen, The Netherlands
| | - Martijn Rolloos
- Institute of Biology Leiden, Faculty of Science, Leiden University, Leiden, The Netherlands
| | - Johan E. Pinas
- Institute of Biology Leiden, Faculty of Science, Leiden University, Leiden, The Netherlands
| | - Christiaan V. Henkel
- Institute of Biology Leiden, Faculty of Science, Leiden University, Leiden, The Netherlands
| | - Dieuwertje Augustijn
- Leiden Institute of Chemistry, Faculty of Science, Leiden University, Leiden, The Netherlands
| | - Paul J. J. Hooykaas
- Institute of Biology Leiden, Faculty of Science, Leiden University, Leiden, The Netherlands
| | - Bert J. van der Zaal
- Institute of Biology Leiden, Faculty of Science, Leiden University, Leiden, The Netherlands
- * E-mail:
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13
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Younger AKD, Dalvie NC, Rottinghaus AG, Leonard JN. Engineering Modular Biosensors to Confer Metabolite-Responsive Regulation of Transcription. ACS Synth Biol 2017; 6:311-325. [PMID: 27744683 DOI: 10.1021/acssynbio.6b00184] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Efforts to engineer microbial factories have benefitted from mining biological diversity and high throughput synthesis of novel enzymatic pathways, yet screening and optimizing metabolic pathways remain rate-limiting steps. Metabolite-responsive biosensors may help to address these persistent challenges by enabling the monitoring of metabolite levels in individual cells and metabolite-responsive feedback control. We are currently limited to naturally evolved biosensors, which are insufficient for monitoring many metabolites of interest. Thus, a method for engineering novel biosensors would be powerful, yet we lack a generalizable approach that enables the construction of a wide range of biosensors. As a step toward this goal, we here explore several strategies for converting a metabolite-binding protein into a metabolite-responsive transcriptional regulator. By pairing a modular protein design approach with a library of synthetic promoters and applying robust statistical analyses, we identified strategies for engineering biosensor-regulated bacterial promoters and for achieving design-driven improvements of biosensor performance. We demonstrated the feasibility of this strategy by fusing a programmable DNA binding motif (zinc finger module) with a model ligand binding protein (maltose binding protein), to generate a novel biosensor conferring maltose-regulated gene expression. This systematic investigation provides insights that may guide the development of additional novel biosensors for diverse synthetic biology applications.
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Affiliation(s)
- Andrew K. D. Younger
- Interdisciplinary
Biological Sciences Graduate Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil C. Dalvie
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Austin G. Rottinghaus
- Department
of Chemical and Biological Engineering, University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Joshua N. Leonard
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry
of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Member, Robert
H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois 60208, United States
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14
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Roointan A, Morowvat MH. Road to the future of systems biotechnology: CRISPR-Cas-mediated metabolic engineering for recombinant protein production. Biotechnol Genet Eng Rev 2017; 32:74-91. [PMID: 28052722 DOI: 10.1080/02648725.2016.1270095] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The rising potential for CRISPR-Cas-mediated genome editing has revolutionized our strategies in basic and practical bioengineering research. It provides a predictable and precise method for genome modification in a robust and reproducible fashion. Emergence of systems biotechnology and synthetic biology approaches coupled with CRISPR-Cas technology could change the future of cell factories to possess some new features which have not been found naturally. We have discussed the possibility and versatile potentials of CRISPR-Cas technology for metabolic engineering of a recombinant host for heterologous protein production. We describe the mechanisms involved in this metabolic engineering approach and present the diverse features of its application in biotechnology and protein production.
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Affiliation(s)
- Amir Roointan
- a Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies , Shiraz , Iran.,c Department of Medical Biotechnology, School of Medicine , Fasa University of Medical Sciences , Fasa , Iran
| | - Mohammad Hossein Morowvat
- a Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies , Shiraz , Iran.,b Pharmaceutical Sciences Research Center, School of Pharmacy , Shiraz University of Medical Sciences , Shiraz , Iran
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15
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Guo Y, Dong Y, Hong X, Pang X, Chen D, Chen X. Directed Evolution of Dunaliella salina Ds-26-16 and Salt-Tolerant Response in Escherichia coli. Int J Mol Sci 2016; 17:ijms17111813. [PMID: 27801872 PMCID: PMC5133814 DOI: 10.3390/ijms17111813] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 10/17/2016] [Accepted: 10/25/2016] [Indexed: 12/02/2022] Open
Abstract
Identification and evolution of salt tolerant genes are crucial steps in developing salt tolerant crops or microorganisms using biotechnology. Ds-26-16, a salt tolerant gene that was isolated from Dunaliella salina, encodes a transcription factor that can confer salt tolerance to a number of organisms including Escherichia coli (E. coli), Haematococcus pluvialis and tobacco. To further improve its salt tolerance, a random mutagenesis library was constructed using deoxyinosine triphosphate-mediated error-prone PCR technology, and then screened using an E. coli expression system that is based on its broad-spectrum salt tolerance. Seven variants with enhanced salt tolerance were obtained. Variant EP-5 that contained mutation S32P showed the most improvement with the E. coli transformant enduring salt concentrations up to 1.54 M, in comparison with 1.03 M for the wild type gene. Besides, Ds-26-16 and EP-5 also conferred E. coli transformant tolerance to freezing, cold, heat, Cu2+ and alkaline. Homology modeling revealed that mutation S32P in EP-5 caused the conformational change of N- and C-terminal α-helixes. Expression of Ds-26-16 and EP-5 maintained normal cellular morphology, increased the intracellular antioxidant enzymatic activity, reduced malondialdehyde content, and stimulated Nitric Oxide synthesis, thus enhancing salt tolerance to E. coli transformants.
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Affiliation(s)
- Yuan Guo
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, No. 94 Weijin Rd., Tianjin 300071, China.
| | - Yanping Dong
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, No. 94 Weijin Rd., Tianjin 300071, China.
| | - Xiao Hong
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, No. 94 Weijin Rd., Tianjin 300071, China.
| | - Xiaonan Pang
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, No. 94 Weijin Rd., Tianjin 300071, China.
| | - Defu Chen
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, No. 94 Weijin Rd., Tianjin 300071, China.
| | - Xiwen Chen
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, No. 94 Weijin Rd., Tianjin 300071, China.
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16
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Tools and Principles for Microbial Gene Circuit Engineering. J Mol Biol 2016; 428:862-88. [DOI: 10.1016/j.jmb.2015.10.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 10/05/2015] [Accepted: 10/06/2015] [Indexed: 12/26/2022]
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17
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Tan F, Wu B, Dai L, Qin H, Shui Z, Wang J, Zhu Q, Hu G, He M. Using global transcription machinery engineering (gTME) to improve ethanol tolerance of Zymomonas mobilis. Microb Cell Fact 2016; 15:4. [PMID: 26758018 PMCID: PMC4711062 DOI: 10.1186/s12934-015-0398-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 12/15/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND With the increasing global crude oil crisis and resulting environmental concerns, the production of biofuels from renewable resources has become increasingly important. One of the major challenges faced during the process of biofuel production is the low tolerance of the microbial host towards increasing biofuel concentrations. RESULTS Here, we demonstrate that the ethanol tolerance of Zymomonas mobilis can be greatly enhanced through the random mutagenesis of global transcription factor RpoD protein, (σ(70)). Using an enrichment screening, four mutants with elevated ethanol tolerance were isolated from error-prone PCR libraries. All mutants showed significant growth improvement in the presence of ethanol stress when compared to the control strain. After an ethanol (9 %) stress exposure lasting 22 h, the rate of glucose consumption was approximately 1.77, 1.78 and 1.39 g L(-1) h(-1) in the best ethanol-tolerant strain ZM4-mrpoD4, its rebuilt mutant strain ZM4-imrpoD and the control strain, respectively. Our results indicated that both ZM4-mrpoD4 and ZM4-imrpoD consumed glucose at a faster rate after the initial 9 % (v/v) ethanol stress, as nearly 0.64 % of the initial glucose remained after 54 h incubation versus approximately 5.43 % for the control strain. At 9 % ethanol stress, the net ethanol productions by ZM4-mrpoD4 and ZM4-imrpoD during the 30-54 h were 13.0-14.1 g/l versus only 6.6-7.7 g/l for the control strain. The pyruvate decarboxylase activity of ZM4-mrpoD4 was 62.23 and 68.42 U/g at 24 and 48 h, respectively, which were 2.6 and 1.6 times higher than the control strain. After 24 and 48 h of 9 % ethanol stress, the alcohol dehydrogenase activities of ZM4-mrpoD4 were also augmented, showing an approximate 1.4 and 1.3 times increase, respectively, when compared to the control strain. Subsequent quantitative real-time PCR analysis under these stress conditions revealed that the relative expression of pdc in cultured (6 and 24 h) ZM4-mrpoD4 increased by 9.0- and 12.7-fold when compared to control strain. CONCLUSIONS Collectively, these results demonstrate that the RpoD mutation can enhance ethanol tolerance in Z. mobilis. Our results also suggested that RpoD may play an important role in resisting high ethanol concentration in Z. mobilis and manipulating RpoD via global transcription machinery engineering (gTME) can provide an alternative and useful approach for strain improvement for complex phenotypes.
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Affiliation(s)
- Furong Tan
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renmin Nanlu, Chengdu, 610041, China.
| | - Bo Wu
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renmin Nanlu, Chengdu, 610041, China.
| | - Lichun Dai
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renmin Nanlu, Chengdu, 610041, China.
| | - Han Qin
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renmin Nanlu, Chengdu, 610041, China.
| | - Zongxia Shui
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renmin Nanlu, Chengdu, 610041, China.
| | - Jingli Wang
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renmin Nanlu, Chengdu, 610041, China.
| | - Qili Zhu
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renmin Nanlu, Chengdu, 610041, China.
| | - Guoquan Hu
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renmin Nanlu, Chengdu, 610041, China.
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture, Chengdu, 610041, China.
| | - Mingxiong He
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renmin Nanlu, Chengdu, 610041, China.
- Key Laboratory of Development and Application of Rural Renewable Energy, Ministry of Agriculture, Chengdu, 610041, China.
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Luan G, Bao G, Lin Z, Li Y, Chen Z, Li Y, Cai Z. Comparative genome analysis of a thermotolerant Escherichia coli obtained by Genome Replication Engineering Assisted Continuous Evolution (GREACE) and its parent strain provides new understanding of microbial heat tolerance. N Biotechnol 2015; 32:732-8. [DOI: 10.1016/j.nbt.2015.01.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 01/27/2015] [Accepted: 01/30/2015] [Indexed: 11/15/2022]
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Peters G, Coussement P, Maertens J, Lammertyn J, De Mey M. Putting RNA to work: Translating RNA fundamentals into biotechnological engineering practice. Biotechnol Adv 2015; 33:1829-44. [PMID: 26514597 DOI: 10.1016/j.biotechadv.2015.10.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 10/13/2015] [Accepted: 10/22/2015] [Indexed: 11/19/2022]
Abstract
Synthetic biology, in close concert with systems biology, is revolutionizing the field of metabolic engineering by providing novel tools and technologies to rationally, in a standardized way, reroute metabolism with a view to optimally converting renewable resources into a broad range of bio-products, bio-materials and bio-energy. Increasingly, these novel synthetic biology tools are exploiting the extensive programmable nature of RNA, vis-à-vis DNA- and protein-based devices, to rationally design standardized, composable, and orthogonal parts, which can be scaled and tuned promptly and at will. This review gives an extensive overview of the recently developed parts and tools for i) modulating gene expression ii) building genetic circuits iii) detecting molecules, iv) reporting cellular processes and v) building RNA nanostructures. These parts and tools are becoming necessary armamentarium for contemporary metabolic engineering. Furthermore, the design criteria, technological challenges, and recent metabolic engineering success stories of the use of RNA devices are highlighted. Finally, the future trends in transforming metabolism through RNA engineering are critically evaluated and summarized.
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Affiliation(s)
- Gert Peters
- Centre of Expertise Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Pieter Coussement
- Centre of Expertise Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Jo Maertens
- Centre of Expertise Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - Jeroen Lammertyn
- BIOSYST-MeBioS, KU Leuven, Willem de Croylaan 42, 3001 Louvain, Belgium
| | - Marjan De Mey
- Centre of Expertise Industrial Biotechnology and Biocatalysis, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium.
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Transcriptomic Analysis of 3-Hydroxypropanoic Acid Stress in Escherichia coli. Appl Biochem Biotechnol 2015; 178:527-43. [PMID: 26472673 DOI: 10.1007/s12010-015-1892-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 10/08/2015] [Indexed: 10/22/2022]
Abstract
The stress response of Escherichia coli to 3-hydroxypropanoic acid (3-HP) was elucidated through global transcriptomic analysis. Around 375 genes showed difference of more than 2-fold in 3-HP-treated samples. Further analysis revealed that the toxicity effect of 3-HP was due to the cation and anion components of this acid and some effects-specific to 3-HP. Genes related to the oxidative stress, DNA protection, and repair were upregulated in treated cells due to the lowered cytoplasmic pH caused by accumulated cations. 3-HP-treated E. coli used the arginine acid tolerance mechanism to increase the cytoplasmic pH. Additionally, the anion effects were manifested as imbalance in the osmotic pressure. Analysis of top ten highly upregulated genes suggests the formation of 3-hydroxypropionaldehyde under 3-HP stress. The transcriptomic analysis shed light on the global genetic reprogramming due to 3-HP stress and suggests strategies for increasing the tolerance of E. coli toward 3-HP.
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Tan FR, Dai LC, Wu B, Qin H, Shui ZX, Wang JL, Zhu QL, Hu QC, Ruan ZY, He MX. Improving furfural tolerance of Zymomonas mobilis by rewiring a sigma factor RpoD protein. Appl Microbiol Biotechnol 2015; 99:5363-71. [PMID: 25895089 DOI: 10.1007/s00253-015-6577-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Revised: 03/23/2015] [Accepted: 03/25/2015] [Indexed: 01/21/2023]
Abstract
Furfural from lignocellulosic hydrolysates is the key inhibitor for bio-ethanol fermentation. In this study, we report a strategy of improving the furfural tolerance in Zymomonas mobilis on the transcriptional level by engineering its global transcription sigma factor (σ(70), RpoD) protein. Three furfural tolerance RpoD mutants (ZM4-MF1, ZM4-MF2, and ZM4-MF3) were identified from error-prone PCR libraries. The best furfural-tolerance strain ZM4-MF2 reached to the maximal cell density (OD600) about 2.0 after approximately 30 h, while control strain ZM4-rpoD reached its highest cell density of about 1.3 under the same conditions. ZM4-MF2 also consumed glucose faster and yield higher ethanol; expression levels and key Entner-Doudoroff (ED) pathway enzymatic activities were also compared to control strain under furfural stress condition. Our results suggest that global transcription machinery engineering could potentially be used to improve stress tolerance and ethanol production in Z. mobilis.
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Affiliation(s)
- Fu-Rong Tan
- Biogas Institute of Ministry of Agriculture, Biomass Energy Technology Research Centre, Section 4-13, Renming Nanlu, Chengdu, 610041, People's Republic of China
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Liu W, Jiang R. Combinatorial and high-throughput screening approaches for strain engineering. Appl Microbiol Biotechnol 2015; 99:2093-104. [DOI: 10.1007/s00253-015-6400-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 01/09/2015] [Accepted: 01/10/2015] [Indexed: 12/31/2022]
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van Tol N, van der Zaal BJ. Artificial transcription factor-mediated regulation of gene expression. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 225:58-67. [PMID: 25017160 DOI: 10.1016/j.plantsci.2014.05.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 05/22/2014] [Accepted: 05/23/2014] [Indexed: 06/03/2023]
Abstract
The transcriptional regulation of endogenous genes with artificial transcription factors (TFs) can offer new tools for plant biotechnology. Three systems are available for mediating site-specific DNA recognition of artificial TFs: those based on zinc fingers, TALEs, and on the CRISPR/Cas9 technology. Artificial TFs require an effector domain that controls the frequency of transcription initiation at endogenous target genes. These effector domains can be transcriptional activators or repressors, but can also have enzymatic activities involved in chromatin remodeling or epigenetic regulation. Artificial TFs are able to regulate gene expression in trans, thus allowing them to evoke dominant mutant phenotypes. Large scale changes in transcriptional activity are induced when the DNA binding domain is deliberately designed to have lower binding specificity. This technique, known as genome interrogation, is a powerful tool for generating novel mutant phenotypes. Genome interrogation has clear mechanistic and practical advantages over activation tagging, which is the technique most closely resembling it. Most notably, genome interrogation can lead to the discovery of mutant phenotypes that are unlikely to be found when using more conventional single gene-based approaches.
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Affiliation(s)
- Niels van Tol
- Department of Molecular and Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Bert J van der Zaal
- Department of Molecular and Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE Leiden, The Netherlands.
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Wang H, Yang L, Wu K, Li G. Rational selection and engineering of exogenous principal sigma factor (σ(HrdB)) to increase teicoplanin production in an industrial strain of Actinoplanes teichomyceticus. Microb Cell Fact 2014; 13:10. [PMID: 24428890 PMCID: PMC3897980 DOI: 10.1186/1475-2859-13-10] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Accepted: 01/09/2014] [Indexed: 11/13/2022] Open
Abstract
Background Transcriptional engineering has presented a strong ability of phenotypic improvement in microorganisms. However, it could not be directly applied to Actinoplanes teichomyceticus L-27 because of the paucity of endogenous transcription factors in the strain. In this study, exogenous transcription factors were rationally selected and transcriptional engineering was carried out to increase the productivity of teicoplanin in L-27. Results It was illuminated that the σHrdB molecules shared strong similarity of amino acid sequences among some genera of actinomycetes. Combining this advantage with the ability of transcriptional engineering, exogenous sigma factor σHrdB molecules were rationally selected and engineered to improve L-27. hrdB genes from Actinoplanes missouriensis 431, Micromonospora aurantiaca ATCC 27029 and Salinispora arenicola CNS-205 were selected based on molecular evolutionary analysis. Random mutagenesis, DNA shuffling and point mutation were subsequently performed to generate diversified mutants. A recombinant was identified through screening program, yielding 5.3 mg/ml of teicoplanin, over 2-fold compared to that of L-27. More significantly, the engineered strain presented a good performance in 500-l pilot scale fermentation, which meant its valuable potential application in industry. Conclusions Through rational selection and engineering of exogenous transcriptional factor, we have extended the application of transcriptional engineering. To our knowledge, it is the first time to focus on the related issue. In addition, possessing the advantage of efficient metabolic perturbation in transcription level, this strategy could be useful in analyzing metabolic and physiological mechanisms of strains, especially those with the only information on taxonomy.
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Affiliation(s)
| | - Liu Yang
- School of Food and Bioengineering, Qilu University of Technology, Jinan 250353, PR China.
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25
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Advances in genetic circuit design: novel biochemistries, deep part mining, and precision gene expression. Curr Opin Chem Biol 2013; 17:878-92. [DOI: 10.1016/j.cbpa.2013.10.003] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 10/03/2013] [Indexed: 01/14/2023]
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26
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Lee SW, Kim E, Kim JS, Oh MK. Artificial transcription regulator as a tool for improvement of cellular property in Saccharomyces cerevisiae. Chem Eng Sci 2013. [DOI: 10.1016/j.ces.2012.09.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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27
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Engineering of transcriptional regulators enhances microbial stress tolerance. Biotechnol Adv 2013; 31:986-91. [DOI: 10.1016/j.biotechadv.2013.02.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 01/17/2013] [Accepted: 02/25/2013] [Indexed: 11/20/2022]
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28
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Lee H, Park SJ, Han MJ, Eom GT, Choi MJ, Kim SH, Oh YH, Song BK, Lee SH. Expression of a lipase on the cell-surface of Escherichia coli using the OmpW anchoring motif and its application to enantioselective reactions. Biotechnol Lett 2013; 35:1677-83. [PMID: 23881313 DOI: 10.1007/s10529-013-1260-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 05/29/2013] [Indexed: 12/11/2022]
Abstract
Microbial-surface display is the expression of proteins or peptides on the surface of cells by fusing an appropriate protein as an anchoring motif. Here, the outer membrane protein W (OmpW) was selected as a fusion partner for functional expression of Pseudomonas fluorescence SIK W1 lipase (TliA) on the cell-surface of Escherichia coli. Localization of the truncated OmpW-TliA fusion protein on the cell-surface was confirmed by immunoblotting and functional assay of lipase activity. Enantioselective hydrolysis of rac-phenylethyl butanoate by the displayed lipase resulted in optically active (R)-phenyl ethanol with 96% enantiomeric excess and 44% of conversion in 5 days. Thus, a small outer membrane protein OmpW, is a useful anchoring motif for displaying an active enzyme of ~50 kDa on the cell-surface and the surface-displayed lipase can be employed as an enantioselective biocatalyst in organic synthesis.
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Affiliation(s)
- Hyuk Lee
- Division of Drug Discovery Research, Korea Research Institute of Chemical Technology, P.O. Box 107, 141 Gajeong-ro, Yuseong-gu, Daejeon, 305-600, Republic of Korea,
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29
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Smith RP, Riesenfeld SJ, Holloway AK, Li Q, Murphy KK, Feliciano NM, Orecchia L, Oksenberg N, Pollard KS, Ahituv N. A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design. Genome Biol 2013; 14:R72. [PMID: 23867016 PMCID: PMC4054837 DOI: 10.1186/gb-2013-14-7-r72] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 03/08/2013] [Accepted: 07/18/2013] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Large-scale annotation efforts have improved our ability to coarsely predict regulatory elements throughout vertebrate genomes. However, it is unclear how complex spatiotemporal patterns of gene expression driven by these elements emerge from the activity of short, transcription factor binding sequences. RESULTS We describe a comprehensive promoter extension assay in which the regulatory potential of all 6 base-pair (bp) sequences was tested in the context of a minimal promoter. To enable this large-scale screen, we developed algorithms that use a reverse-complement aware decomposition of the de Bruijn graph to design a library of DNA oligomers incorporating every 6-bp sequence exactly once. Our library multiplexes all 4,096 unique 6-mers into 184 double-stranded 15-bp oligomers, which is sufficiently compact for in vivo testing. We injected each multiplexed construct into zebrafish embryos and scored GFP expression in 15 tissues at two developmental time points. Twenty-seven constructs produced consistent expression patterns, with the majority doing so in only one tissue. Functional sequences are enriched near biologically relevant genes, match motifs for developmental transcription factors, and are required for enhancer activity. By concatenating tissue-specific functional sequences, we generated completely synthetic enhancers for the notochord, epidermis, spinal cord, forebrain and otic lateral line, and show that short regulatory sequences do not always function modularly. CONCLUSIONS This work introduces a unique in vivo catalog of short, functional regulatory sequences and demonstrates several important principles of regulatory element organization. Furthermore, we provide resources for designing compact, reverse-complement aware k-mer libraries.
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Affiliation(s)
- Robin P Smith
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA
| | - Samantha J Riesenfeld
- Gladstone Institutes, University of California San Francisco, 1650 Owens St, San Francisco, CA 94158, USA
| | - Alisha K Holloway
- Gladstone Institutes, University of California San Francisco, 1650 Owens St, San Francisco, CA 94158, USA
| | - Qiang Li
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA
- Current address: Institute for Pediatrics, Translational Research Center for Development and Disease, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Karl K Murphy
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA
| | - Natalie M Feliciano
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA
| | - Lorenzo Orecchia
- Division of Biostatistics, University of California San Francisco, 1650 Owens St, CA 94158, USA
| | - Nir Oksenberg
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA
| | - Katherine S Pollard
- Institute for Human Genetics, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA
- Gladstone Institutes, University of California San Francisco, 1650 Owens St, San Francisco, CA 94158, USA
- Department of Mathematics, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California San Francisco, 1550 4th St, San Francisco, CA 94158, USA
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Sarachana T, Hu VW. Genome-wide identification of transcriptional targets of RORA reveals direct regulation of multiple genes associated with autism spectrum disorder. Mol Autism 2013; 4:14. [PMID: 23697635 PMCID: PMC3665583 DOI: 10.1186/2040-2392-4-14] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 04/24/2013] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND We have recently identified the nuclear hormone receptor RORA (retinoic acid-related orphan receptor-alpha) as a novel candidate gene for autism spectrum disorder (ASD). Our independent cohort studies have consistently demonstrated the reduction of RORA transcript and/or protein levels in blood-derived lymphoblasts as well as in the postmortem prefrontal cortex and cerebellum of individuals with ASD. Moreover, we have also shown that RORA has the potential to be under negative and positive regulation by androgen and estrogen, respectively, suggesting the possibility that RORA may contribute to the male bias of ASD. However, little is known about transcriptional targets of this nuclear receptor, particularly in humans. METHODS Here we identify transcriptional targets of RORA in human neuronal cells on a genome-wide level using chromatin immunoprecipitation (ChIP) with an anti-RORA antibody followed by whole-genome promoter array (chip) analysis. Selected potential targets of RORA were then validated by an independent ChIP followed by quantitative PCR analysis. To further demonstrate that reduced RORA expression results in reduced transcription of RORA targets, we determined the expression levels of the selected transcriptional targets in RORA-deficient human neuronal cells, as well as in postmortem brain tissues from individuals with ASD who exhibit reduced RORA expression. RESULTS The ChIP-on-chip analysis reveals that RORA1, a major isoform of RORA protein in human brain, can be recruited to as many as 2,764 genomic locations corresponding to promoter regions of 2,544 genes across the human genome. Gene ontology analysis of this dataset of genes that are potentially directly regulated by RORA1 reveals statistically significant enrichment in biological functions negatively impacted in individuals with ASD, including neuronal differentiation, adhesion and survival, synaptogenesis, synaptic transmission and plasticity, and axonogenesis, as well as higher level functions such as development of the cortex and cerebellum, cognition, memory, and spatial learning. Independent ChIP-quantitative PCR analyses confirm binding of RORA1 to promoter regions of selected ASD-associated genes, including A2BP1, CYP19A1, ITPR1, NLGN1, and NTRK2, whose expression levels (in addition to HSD17B10) are also decreased in RORA1-repressed human neuronal cells and in prefrontal cortex tissues from individuals with ASD. CONCLUSIONS Findings from this study indicate that RORA transcriptionally regulates A2BP1, CYP19A1, HSD17B10, ITPR1, NLGN1, and NTRK2, and strongly suggest that reduction of this sex hormone-sensitive nuclear receptor in the brain causes dysregulated expression of these ASD-relevant genes as well as their associated pathways and functions which, in turn, may contribute to the underlying pathobiology of ASD.
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Affiliation(s)
- Tewarit Sarachana
- Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Sciences, 2300 I Street NW, Washington, DC, 20037, USA.
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Kim HJ, Turner TL, Jin YS. Combinatorial genetic perturbation to refine metabolic circuits for producing biofuels and biochemicals. Biotechnol Adv 2013; 31:976-85. [PMID: 23562845 DOI: 10.1016/j.biotechadv.2013.03.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 03/18/2013] [Accepted: 03/28/2013] [Indexed: 12/25/2022]
Abstract
Recent advances in metabolic engineering have enabled microbial factories to compete with conventional processes for producing fuels and chemicals. Both rational and combinatorial approaches coupled with synthetic and systematic tools play central roles in metabolic engineering to create and improve a selected microbial phenotype. Compared to knowledge-based rational approaches, combinatorial approaches exploiting biological diversity and high-throughput screening have been demonstrated as more effective tools for improving various phenotypes of interest. In particular, identification of unprecedented targets to rewire metabolic circuits for maximizing yield and productivity of a target chemical has been made possible. This review highlights general principles and the features of the combinatorial approaches using various libraries to implement desired phenotypes for strain improvement. In addition, recent applications that harnessed the combinatorial approaches to produce biofuels and biochemicals will be discussed.
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Affiliation(s)
- Hyo Jin Kim
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, 1206 West Gregory Dr., Urbana, IL 61801, USA
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Skretas G, Kolisis FN. Combinatorial approaches for inverse metabolic engineering applications. Comput Struct Biotechnol J 2013; 3:e201210021. [PMID: 24688681 PMCID: PMC3962077 DOI: 10.5936/csbj.201210021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 02/11/2013] [Accepted: 02/17/2013] [Indexed: 11/22/2022] Open
Abstract
Traditional metabolic engineering analyzes biosynthetic and physiological pathways, identifies bottlenecks, and makes targeted genetic modifications with the ultimate goal of increasing the production of high-value products in living cells. Such efforts have led to the development of a variety of organisms with industrially relevant properties. However, there are a number of cellular phenotypes important for research and the industry for which the rational selection of cellular targets for modification is not easy or possible. In these cases, strain engineering can be alternatively carried out using “inverse metabolic engineering”, an approach that first generates genetic diversity by subjecting a population of cells to a particular mutagenic process, and then utilizes genetic screens or selections to identify the clones exhibiting the desired phenotype. Given the availability of an appropriate screen for a particular property, the success of inverse metabolic engineering efforts usually depends on the level and quality of genetic diversity which can be generated. Here, we review classic and recently developed combinatorial approaches for creating such genetic diversity and discuss the use of these methodologies in inverse metabolic engineering applications.
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Affiliation(s)
- Georgios Skretas
- Institute of Biology, Medicinal Chemistry and Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N Kolisis
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens - Zografou Campus, Athens, Greece
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Lo TM, Teo WS, Ling H, Chen B, Kang A, Chang MW. Microbial engineering strategies to improve cell viability for biochemical production. Biotechnol Adv 2013; 31:903-14. [PMID: 23403071 DOI: 10.1016/j.biotechadv.2013.02.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 02/05/2013] [Accepted: 02/05/2013] [Indexed: 11/16/2022]
Abstract
Efficient production of biochemicals using engineered microbes as whole-cell biocatalysts requires robust cell viability. Robust viability leads to high productivity and improved bioprocesses by allowing repeated cell recycling. However, cell viability is negatively affected by a plethora of stresses, namely chemical toxicity and metabolic imbalances, primarily resulting from bio-synthesis pathways. Chemical toxicity is caused by substrates, intermediates, products, and/or by-products, and these compounds often interfere with important metabolic processes and damage cellular infrastructures such as cell membrane, leading to poor cell viability. Further, stresses on engineered cells are accentuated by metabolic imbalances, which are generated by heavy metabolic resource consumption due to enzyme overexpression, redistribution of metabolic fluxes, and impaired intracellular redox state by co-factor imbalance. To address these challenges, herein, we discuss a range of key microbial engineering strategies, substantiated by recent advances, to improve cell viability for commercially sustainable production of biochemicals from renewable resources.
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Affiliation(s)
- Tat-Ming Lo
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459, Singapore
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Kang K, Robinson GW, Hennighausen L. Comprehensive meta-analysis of Signal Transducers and Activators of Transcription (STAT) genomic binding patterns discerns cell-specific cis-regulatory modules. BMC Genomics 2013; 14:4. [PMID: 23324445 PMCID: PMC3564941 DOI: 10.1186/1471-2164-14-4] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 01/01/2013] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Cytokine-activated transcription factors from the STAT (Signal Transducers and Activators of Transcription) family control common and context-specific genetic programs. It is not clear to what extent cell-specific features determine the binding capacity of seven STAT members and to what degree they share genetic targets. Molecular insight into the biology of STATs was gained from a meta-analysis of 29 available ChIP-seq data sets covering genome-wide occupancy of STATs 1, 3, 4, 5A, 5B and 6 in several cell types. RESULTS We determined that the genomic binding capacity of STATs is primarily defined by the cell type and to a lesser extent by individual family members. For example, the overlap of shared binding sites between STATs 3 and 5 in T cells is greater than that between STAT5 in T cells and non-T cells. Even for the top 1,000 highly enriched STAT binding sites, ~15% of STAT5 binding sites in mouse female liver are shared by other STATs in different cell types while in T cells ~90% of STAT5 binding sites are co-occupied by STAT3, STAT4 and STAT6. In addition, we identified 116 cis-regulatory modules (CRM), which are recognized by all STAT members across cell types defining a common JAK-STAT signature. Lastly, in liver STAT5 binding significantly coincides with binding of the cell-specific transcription factors HNF4A, FOXA1 and FOXA2 and is associated with cell-type specific gene transcription. CONCLUSIONS Our results suggest that genomic binding of STATs is primarily determined by the cell type and further specificity is achieved in part by juxtaposed binding of cell-specific transcription factors.
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Affiliation(s)
- Keunsoo Kang
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Drive, Bethesda, MD, 20892-0822, USA
| | - Gertraud W Robinson
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Drive, Bethesda, MD, 20892-0822, USA
| | - Lothar Hennighausen
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 8 Center Drive, Bethesda, MD, 20892-0822, USA
- National Department of Nanobiomedical Science and WCU Research Center of Nanobiomedical Science, Dankook University, Cheonan, Chungnam, 330-714, Republic of Korea
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Taher L, Smith RP, Kim MJ, Ahituv N, Ovcharenko I. Sequence signatures extracted from proximal promoters can be used to predict distal enhancers. Genome Biol 2013; 14:R117. [PMID: 24156763 PMCID: PMC3983659 DOI: 10.1186/gb-2013-14-10-r117] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 10/24/2013] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Gene expression is controlled by proximal promoters and distal regulatory elements such as enhancers. While the activity of some promoters can be invariant across tissues, enhancers tend to be highly tissue-specific. RESULTS We compiled sets of tissue-specific promoters based on gene expression profiles of 79 human tissues and cell types. Putative transcription factor binding sites within each set of sequences were used to train a support vector machine classifier capable of distinguishing tissue-specific promoters from control sequences. We obtained reliable classifiers for 92% of the tissues, with an area under the receiver operating characteristic curve between 60% (for subthalamic nucleus promoters) and 98% (for heart promoters). We next used these classifiers to identify tissue-specific enhancers, scanning distal non-coding sequences in the loci of the 200 most highly and lowly expressed genes. Thirty percent of reliable classifiers produced consistent enhancer predictions, with significantly higher densities in the loci of the most highly expressed compared to lowly expressed genes. Liver enhancer predictions were assessed in vivo using the hydrodynamic tail vein injection assay. Fifty-eight percent of the predictions yielded significant enhancer activity in the mouse liver, whereas a control set of five sequences was completely negative. CONCLUSIONS We conclude that promoters of tissue-specific genes often contain unambiguous tissue-specific signatures that can be learned and used for the de novo prediction of enhancers.
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Affiliation(s)
- Leila Taher
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, Rostock, 18057, Germany
| | - Robin P Smith
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Mee J Kim
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, 94158, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Ivan Ovcharenko
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
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Basak S, Jiang R. Enhancing E. coli tolerance towards oxidative stress via engineering its global regulator cAMP receptor protein (CRP). PLoS One 2012; 7:e51179. [PMID: 23251448 PMCID: PMC3522674 DOI: 10.1371/journal.pone.0051179] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 10/30/2012] [Indexed: 12/11/2022] Open
Abstract
Oxidative damage to microbial hosts often occurs under stressful conditions during bioprocessing. Classical strain engineering approaches are usually both time-consuming and labor intensive. Here, we aim to improve E. coli performance under oxidative stress via engineering its global regulator cAMP receptor protein (CRP), which can directly or indirectly regulate redox-sensing regulators SoxR and OxyR, and other ~400 genes in E. coli. Error-prone PCR technique was employed to introduce modifications to CRP, and three mutants (OM1~OM3) were identified with improved tolerance via H(2)O(2) enrichment selection. The best mutant OM3 could grow in 12 mM H(2)O(2) with the growth rate of 0.6 h(-1), whereas the growth of wild type was completely inhibited at this H(2)O(2) concentration. OM3 also elicited enhanced thermotolerance at 48°C as well as resistance against cumene hydroperoxide. The investigation about intracellular reactive oxygen species (ROS), which determines cell viability, indicated that the accumulation of ROS in OM3 was always lower than in WT with or without H(2)O(2) treatment. Genome-wide DNA microarray analysis has shown not only CRP-regulated genes have demonstrated great transcriptional level changes (up to 8.9-fold), but also RpoS- and OxyR-regulated genes (up to 7.7-fold). qRT-PCR data and enzyme activity assay suggested that catalase (katE) could be a major antioxidant enzyme in OM3 instead of alkyl hydroperoxide reductase or superoxide dismutase. To our knowledge, this is the first work on improving E. coli oxidative stress resistance by reframing its transcription machinery through its native global regulator. The positive outcome of this approach may suggest that engineering CRP can be successfully implemented as an efficient strain engineering alternative for E. coli.
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Affiliation(s)
- Souvik Basak
- School of Chemical & Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
| | - Rongrong Jiang
- School of Chemical & Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
- * E-mail:
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37
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Vandenbon A, Kumagai Y, Akira S, Standley DM. A novel unbiased measure for motif co-occurrence predicts combinatorial regulation of transcription. BMC Genomics 2012; 13 Suppl 7:S11. [PMID: 23282148 PMCID: PMC3521209 DOI: 10.1186/1471-2164-13-s7-s11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Background Multiple transcription factors (TFs) are involved in the generation of gene expression patterns, such as tissue-specific gene expression and pleiotropic immune responses. However, how combinations of TFs orchestrate diverse gene expression patterns is poorly understood. Here we propose a new measure for regulatory motif co-occurrence and a new methodology to systematically identify TF pairs significantly co-occurring in a set of promoter sequences. Results Initial analyses suggest that non-CpG promoters have a higher potential for combinatorial regulation than CpG island-associated promoters, and that co-occurrences are strongly influenced by motif similarity. We applied our method to large-scale gene expression data from various tissues, and showed how our measure for motif co-occurrence is not biased by motif over-representation. Our method identified, amongst others, the binding motifs of HNF1 and FOXP1 to be significantly co-occurring in promoters of liver/kidney specific genes. Binding sites tend to be positioned proximally to each other, suggesting interactions exist between this pair of transcription factors. Moreover, the binding sites of several TFs were found to co-occur with NF-κB and IRF sites in sets of genes with similar expression patterns in dendritic cells after Toll-like receptor stimulation. Of these, we experimentally verified that CCAAT enhancer binding protein alpha positively regulates its target promoters synergistically with NF-κB. Conclusions Both computational and experimental results indicate that the proposed method can clarify TF interactions that could not be observed by currently available prediction methods.
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Affiliation(s)
- Alexis Vandenbon
- Laboratory of Systems Immunology, Immunology Frontier Research Center, Osaka University, 3-1 Yamada-oka, Suita, Osaka 565-0871, Japan.
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Improved production of L-threonine in Escherichia coli by use of a DNA scaffold system. Appl Environ Microbiol 2012; 79:774-82. [PMID: 23160128 DOI: 10.1128/aem.02578-12] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite numerous approaches for the development of l-threonine-producing strains, strain development is still hampered by the intrinsic inefficiency of metabolic reactions caused by simple diffusion and random collisions of enzymes and metabolites. A scaffold system, which can promote the proximity of metabolic enzymes and increase the local concentration of intermediates, was reported to be one of the most promising solutions. Here, we report an improvement in l-threonine production in Escherichia coli using a DNA scaffold system, in which a zinc finger protein serves as an adapter for the site-specific binding of each enzyme involved in l-threonine production to a precisely ordered location on a DNA double helix to increase the proximity of enzymes and the local concentration of metabolites to maximize production. The optimized DNA scaffold system for l-threonine production significantly increased the efficiency of the threonine biosynthetic pathway in E. coli, substantially reducing the production time for l-threonine (by over 50%). In addition, this DNA scaffold system enhanced the growth rate of the host strain by reducing the intracellular concentration of toxic intermediates, such as homoserine. Our DNA scaffold system can be used as a platform technology for the construction and optimization of artificial metabolic pathways as well as for the production of many useful biomaterials.
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Expanding the synthetic biology toolbox: engineering orthogonal regulators of gene expression. Curr Opin Biotechnol 2012; 23:689-94. [DOI: 10.1016/j.copbio.2011.12.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 12/14/2011] [Accepted: 12/15/2011] [Indexed: 01/06/2023]
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The mouse DXZ4 homolog retains Ctcf binding and proximity to Pls3 despite substantial organizational differences compared to the primate macrosatellite. Genome Biol 2012; 13:R70. [PMID: 22906166 PMCID: PMC3491370 DOI: 10.1186/gb-2012-13-8-r70] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 08/20/2012] [Indexed: 12/20/2022] Open
Abstract
Background The X-linked macrosatellite DXZ4 is a large homogenous tandem repeat that in females adopts an alternative chromatin organization on the primate X chromosome in response to X-chromosome inactivation. It is packaged into heterochromatin on the active X chromosome but into euchromatin and bound by the epigenetic organizer protein CTCF on the inactive X chromosome. Because its DNA sequence diverges rapidly beyond the New World monkeys, the existence of DXZ4 outside the primate lineage is unknown. Results Here we extend our comparative genome analysis and report the identification and characterization of the mouse homolog of the macrosatellite. Furthermore, we provide evidence of DXZ4 in a conserved location downstream of the PLS3 gene in a diverse group of mammals, and reveal that DNA sequence conservation is restricted to the CTCF binding motif, supporting a central role for this protein at this locus. However, many features that characterize primate DXZ4 differ in mouse, including the overall size of the array, the mode of transcription, the chromatin organization and conservation between adjacent repeat units of DNA sequence and length. Ctcf binds Dxz4 but is not exclusive to the inactive X chromosome, as evidenced by association in some males and equal binding to both X chromosomes in trophoblast stem cells. Conclusions Characterization of Dxz4 reveals substantial differences in the organization of DNA sequence, chromatin packaging, and the mode of transcription, so the potential roles performed by this sequence in mouse have probably diverged from those on the primate X chromosome.
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41
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Lo K, Raftery AE, Dombek KM, Zhu J, Schadt EE, Bumgarner RE, Yeung KY. Integrating external biological knowledge in the construction of regulatory networks from time-series expression data. BMC SYSTEMS BIOLOGY 2012; 6:101. [PMID: 22898396 PMCID: PMC3465231 DOI: 10.1186/1752-0509-6-101] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Accepted: 07/24/2012] [Indexed: 01/27/2023]
Abstract
BACKGROUND Inference about regulatory networks from high-throughput genomics data is of great interest in systems biology. We present a Bayesian approach to infer gene regulatory networks from time series expression data by integrating various types of biological knowledge. RESULTS We formulate network construction as a series of variable selection problems and use linear regression to model the data. Our method summarizes additional data sources with an informative prior probability distribution over candidate regression models. We extend the Bayesian model averaging (BMA) variable selection method to select regulators in the regression framework. We summarize the external biological knowledge by an informative prior probability distribution over the candidate regression models. CONCLUSIONS We demonstrate our method on simulated data and a set of time-series microarray experiments measuring the effect of a drug perturbation on gene expression levels, and show that it outperforms leading regression-based methods in the literature.
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Affiliation(s)
- Kenneth Lo
- Department of Microbiology, University of Washington, Box 358070, Seattle, WA, 98195, USA
| | - Adrian E Raftery
- Department of Statistics, University of Washington, Box 354320, Seattle, WA, 98195, USA
| | - Kenneth M Dombek
- Department of Biochemistry, University of Washington, Box 357350, Seattle, WA, 98195, USA
| | - Jun Zhu
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY, 10029, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY, 10029, USA
| | - Roger E Bumgarner
- Department of Microbiology, University of Washington, Box 358070, Seattle, WA, 98195, USA
| | - Ka Yee Yeung
- Department of Microbiology, University of Washington, Box 358070, Seattle, WA, 98195, USA
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42
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Chen T, Wang J, Zeng L, Li R, Li J, Chen Y, Lin Z. Significant rewiring of the transcriptome and proteome of an Escherichia coli strain harboring a tailored exogenous global regulator IrrE. PLoS One 2012; 7:e37126. [PMID: 22792156 PMCID: PMC3390347 DOI: 10.1371/journal.pone.0037126] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Accepted: 04/17/2012] [Indexed: 12/25/2022] Open
Abstract
Cell reprogramming for microorganisms via engineered or artificial transcription factors and RNA polymerase mutants has presented a powerful tool for eliciting complex traits that are practically useful particularly for industrial strains, and for understanding at the global level the regulatory network of gene transcription. We previously further showed that an exogenous global regulator IrrE (derived from the extreme radiation-resistant bacterium Deinococcus radiodurans) can be tailored to confer Escherichia coli (E. coli) with significantly enhanced tolerances to different stresses. In this work, based on comparative transcriptomic and proteomic analyses of the representative strains E1 and E0, harboring the ethanol-tolerant IrrE mutant E1 and the ethanol-intolerant wild type IrrE, respectively, we found that the transcriptome and proteome of E. coli were extensively rewired by the tailored IrrE protein. Overall, 1196 genes (or approximately 27% of E. coli genes) were significantly altered at the transcriptomic level, including notably genes in the nitrate-nitrite-nitric oxide (NO) pathway, and genes for non-coding RNAs. The proteomic profile revealed significant up- or downregulation of several proteins associated with syntheses of the cell membrane and cell wall. Analyses of the intracellular NO level and cell growth under reduced temperature supported a close correlation between NO and ethanol tolerance, and also suggests a role for membrane fluidity. The significantly different omic profiles of strain E1 indicate that IrrE functions as a global regulator in E. coli, and that IrrE may be evolved for other cellular tolerances. In this sense, it will provide synthetic biology with a practical and evolvable regulatory “part” that operates at a higher level of complexity than local regulators. This work also suggests a possibility of introducing and engineering other exogenous global regulators to rewire the genomes of microorganism cells.
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Affiliation(s)
- Tingjian Chen
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Jianqing Wang
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Lingli Zeng
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Rizong Li
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Jicong Li
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Yilu Chen
- College of Biotechnology and Pharmaceutical Engineering, Nanjing University of Technology, Nanjing, China
| | - Zhanglin Lin
- Department of Chemical Engineering, Tsinghua University, Beijing, China
- * E-mail:
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43
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Wang J, Zhang Y, Chen Y, Lin M, Lin Z. Global regulator engineering significantly improvedEscherichia colitolerances toward inhibitors of lignocellulosic hydrolysates. Biotechnol Bioeng 2012; 109:3133-42. [DOI: 10.1002/bit.24574] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Revised: 04/06/2012] [Accepted: 05/30/2012] [Indexed: 01/09/2023]
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Abstract
The biological production of fuels from renewable sources has been regarded as a feasible solution to the energy and environmental problems in the foreseeable future. Recently, the biofuel product spectrum has expanded from ethanol and fatty acid methyl esters (biodiesel) to other molecules, such as higher alcohols and alkanes, with more desirable fuel properties. In general, biosynthesis of these fuel molecules can be divided into two phases: carbon chain elongation and functional modification. In addition to natural fatty acid and isoprenoid chain elongation pathways, keto acid-based chain elongation followed by decarboxylation and reduction has been explored for higher alcohol production. Other issues such as metabolic balance, strain robustness, and industrial production process efficiency have also been addressed. These successes may provide both scientific insights into and practical applications toward the ultimate goal of sustainable fuel production.
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Affiliation(s)
- Han Li
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA.
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45
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Zhang H, Chong H, Ching CB, Jiang R. Random mutagenesis of global transcription factor cAMP receptor protein for improved osmotolerance. Biotechnol Bioeng 2011; 109:1165-72. [DOI: 10.1002/bit.24411] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 11/07/2011] [Accepted: 12/08/2011] [Indexed: 11/08/2022]
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46
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Shen T, Aneas I, Sakabe N, Dirschinger RJ, Wang G, Smemo S, Westlund JM, Cheng H, Dalton N, Gu Y, Boogerd CJ, Cai CL, Peterson K, Chen J, Nobrega MA, Evans SM. Tbx20 regulates a genetic program essential to adult mouse cardiomyocyte function. J Clin Invest 2011; 121:4640-54. [PMID: 22080862 DOI: 10.1172/jci59472] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2011] [Accepted: 10/05/2011] [Indexed: 12/19/2022] Open
Abstract
Human mutations in or variants of TBX20 are associated with congenital heart disease, cardiomyopathy, and arrhythmias. To investigate whether cardiac disease in patients with these conditions results from an embryonic or ongoing requirement for Tbx20 in myocardium, we ablated Tbx20 specifically in adult cardiomyocytes in mice. This ablation resulted in the onset of severe cardiomyopathy accompanied by arrhythmias, with death ensuing within 1 to 2 weeks of Tbx20 ablation. Accounting for this dramatic phenotype, we identified molecular signatures that posit Tbx20 as a central integrator of a genetic program that maintains cardiomyocyte function in the adult heart. Expression of a number of genes encoding critical transcription factors, ion channels, and cytoskeletal/myofibrillar proteins was downregulated consequent to loss of Tbx20. Genome-wide ChIP analysis of Tbx20-binding regions in the adult heart revealed that many of these genes were direct downstream targets of Tbx20 and uncovered a previously undescribed DNA-binding site for Tbx20. Bioinformatics and in vivo functional analyses revealed a cohort of transcription factors that, working with Tbx20, integrated multiple environmental signals to maintain ion channel gene expression in the adult heart. Our data provide insight into the mechanisms by which mutations in TBX20 cause adult heart disease in humans.
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Affiliation(s)
- Tao Shen
- Skaggs School of Pharmacy, UCSD, La Jolla, California 92093, USA
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Makino T, Skretas G, Georgiou G. Strain engineering for improved expression of recombinant proteins in bacteria. Microb Cell Fact 2011; 10:32. [PMID: 21569582 PMCID: PMC3120638 DOI: 10.1186/1475-2859-10-32] [Citation(s) in RCA: 139] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 05/14/2011] [Indexed: 01/17/2023] Open
Abstract
Protein expression in Escherichia coli represents the most facile approach for the preparation of non-glycosylated proteins for analytical and preparative purposes. So far, the optimization of recombinant expression has largely remained a matter of trial and error and has relied upon varying parameters, such as expression vector, media composition, growth temperature and chaperone co-expression. Recently several new approaches for the genome-scale engineering of E. coli to enhance recombinant protein expression have been developed. These methodologies now enable the generation of optimized E. coli expression strains in a manner analogous to metabolic engineering for the synthesis of low-molecular-weight compounds. In this review, we provide an overview of strain engineering approaches useful for enhancing the expression of hard-to-produce proteins, including heterologous membrane proteins.
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Affiliation(s)
- Tomohiro Makino
- Department of Chemical Engineering, The University of Texas at Austin, 78712, USA
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48
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Purcell O, di Bernardo M, Grierson CS, Savery NJ. A multi-functional synthetic gene network: a frequency multiplier, oscillator and switch. PLoS One 2011; 6:e16140. [PMID: 21359152 PMCID: PMC3040778 DOI: 10.1371/journal.pone.0016140] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Accepted: 12/13/2010] [Indexed: 01/15/2023] Open
Abstract
We present the design and analysis of a synthetic gene network that performs frequency multiplication. It takes oscillatory transcription factor concentrations, such as those produced from the currently available genetic oscillators, as an input, and produces oscillations with half the input frequency as an output. Analysis of the bifurcation structure also reveals novel, programmable multi-functionality; in addition to functioning as a frequency multiplier, the network is able to function as a switch or an oscillator, depending on the temporal nature of the input. Multi-functionality is often observed in neuronal networks, where it is suggested to allow for the efficient coordination of different responses. This network represents a significant theoretical addition that extends the capabilities of synthetic gene networks.
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Affiliation(s)
- Oliver Purcell
- Department of Engineering Mathematics, Bristol Centre for Complexity Sciences, University of Bristol, Bristol, United Kingdom.
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Chen T, Wang J, Yang R, Li J, Lin M, Lin Z. Laboratory-evolved mutants of an exogenous global regulator, IrrE from Deinococcus radiodurans, enhance stress tolerances of Escherichia coli. PLoS One 2011; 6:e16228. [PMID: 21267412 PMCID: PMC3022760 DOI: 10.1371/journal.pone.0016228] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 12/09/2010] [Indexed: 01/28/2023] Open
Abstract
Background The tolerance of cells toward different stresses is very important for industrial strains of microbes, but difficult to improve by the manipulation of single genes. Traditional methods for enhancing cellular tolerances are inefficient and time-consuming. Recently, approaches employing global transcriptional or translational engineering methods have been increasingly explored. We found that an exogenous global regulator, irrE from an extremely radiation-resistant bacterium, Deinococcus radiodurans, has the potential to act as a global regulator in Escherichia coli, and that laboratory-evolution might be applied to alter this regulator to elicit different phenotypes for E. coli. Methodology/Principal Findings To extend the methodology for strain improvement and to obtain higher tolerances toward different stresses, we here describe an approach of engineering irrE gene in E. coli. An irrE library was constructed by randomly mutating the gene, and this library was then selected for tolerance to ethanol, butanol and acetate stresses. Several mutants showing significant tolerances were obtained and characterized. The tolerances of E. coli cells containing these mutants were enhanced 2 to 50-fold, based on cell growth tests using different concentrations of alcohols or acetate, and enhanced 10 to 100-fold based on ethanol or butanol shock experiments. Intracellular reactive oxygen species (ROS) assays showed that intracellular ROS levels were sharply reduced for cells containing the irrE mutants. Sequence analysis of the mutants revealed that the mutations distribute cross all three domains of the protein. Conclusions To our knowledge, this is the first time that an exogenous global regulator has been artificially evolved to suit its new host. The successes suggest the possibility of improving tolerances of industrial strains by introducing and engineering exogenous global regulators, such as those from extremophiles. This new approach can be applied alone or in combination with other global methods, such as global transcriptional machinery engineering (gTME) for strain improvements.
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Affiliation(s)
- Tingjian Chen
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Jianqing Wang
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Rong Yang
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Jicong Li
- Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Min Lin
- Key Laboratory of Crop Biotechnology, Ministry of Agriculture, Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- * E-mail: (ZL); (ML)
| | - Zhanglin Lin
- Department of Chemical Engineering, Tsinghua University, Beijing, China
- * E-mail: (ZL); (ML)
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Chern CG, Fan MJ, Huang SC, Yu SM, Wei FJ, Wu CC, Trisiriroj A, Lai MH, Chen S, Hsing YIC. Methods for rice phenomics studies. Methods Mol Biol 2011; 678:129-138. [PMID: 20931377 DOI: 10.1007/978-1-60761-682-5_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
With the completion of the rice genome sequencing project, the next major challenge is the large-scale determination of gene function. A systematic phenotypic profiling of mutant collections will provide major insights into gene functions important for crop growth or production. Thus, detailed phenomics analysis is the key to functional genomics. Currently, the two major types of rice mutant collections are insertional mutants and chemical or irradiation-induced mutants. Here we describe how to manipulate a rice mutant population, including conducting phenomics studies and the subsequent propagation and seed storage. We list the phenotypes screened and also describe how to collect data systematically for a database of the qualitative and quantitative phenotypic traits. Thus, data on mutant lines, phenotypes, and segregation rate for all kinds of mutant populations, as well as integration sites for insertional mutant populations, would be searchable, and the collection would be a good resource for rice functional genomics study.
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Affiliation(s)
- Chyr-Guan Chern
- Taiwan Agricultural Research Institute, Wufeng, Taichung, Taiwan
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