401
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Min D, Arbing MA, Jefferson RE, Bowie JU. A simple DNA handle attachment method for single molecule mechanical manipulation experiments. Protein Sci 2016; 25:1535-44. [PMID: 27222403 PMCID: PMC4972209 DOI: 10.1002/pro.2952] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 05/23/2016] [Indexed: 12/16/2022]
Abstract
Manipulating single molecules and systems of molecules with mechanical force is a powerful technique to examine their physical properties. Applying force requires attachment of the target molecule to larger objects using some sort of molecular tether, such as a strand of DNA. DNA handle attachment often requires difficult manipulations of the target molecule, which can preclude attachment to unstable, hard to obtain, and/or large, complex targets. Here we describe a method for covalent DNA handle attachment to proteins that simply requires the addition of a preprepared reagent to the protein and a short incubation. The handle attachment method developed here provides a facile approach for studying the biomechanics of biological systems.
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Affiliation(s)
- Duyoung Min
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, Los Angeles, California
| | - Mark A Arbing
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, Los Angeles, California
| | - Robert E Jefferson
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, Los Angeles, California
| | - James U Bowie
- Department of Chemistry and Biochemistry, UCLA-DOE Institute, Molecular Biology Institute, Los Angeles, California
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402
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Bhagi-Damodaran A, Hosseinzadeh P, Mirts E, Reed J, Petrik ID, Lu Y. Design of Heteronuclear Metalloenzymes. Methods Enzymol 2016; 580:501-37. [PMID: 27586347 PMCID: PMC5156654 DOI: 10.1016/bs.mie.2016.05.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Heteronuclear metalloenzymes catalyze some of the most fundamentally interesting and practically useful reactions in nature. However, the presence of two or more metal ions in close proximity in these enzymes makes them more difficult to prepare and study than homonuclear metalloenzymes. To meet these challenges, heteronuclear metal centers have been designed into small and stable proteins with rigid scaffolds to understand how these heteronuclear centers are constructed and the mechanism of their function. This chapter describes methods for designing heterobinuclear metal centers in a protein scaffold by giving specific examples of a few heme-nonheme bimetallic centers engineered in myoglobin and cytochrome c peroxidase. We provide step-by-step procedures on how to choose the protein scaffold, design a heterobinuclear metal center in the protein scaffold computationally, incorporate metal ions into the protein, and characterize the resulting metalloproteins, both structurally and functionally. Finally, we discuss how an initial design can be further improved by rationally tuning its secondary coordination sphere, electron/proton transfer rates, and the substrate affinity.
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Affiliation(s)
- A Bhagi-Damodaran
- University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - P Hosseinzadeh
- University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - E Mirts
- University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - J Reed
- University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - I D Petrik
- University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Y Lu
- University of Illinois at Urbana-Champaign, Urbana, IL, United States.
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403
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Rodrigues CDA, Ramírez-Guadiana FH, Meeske AJ, Wang X, Rudner DZ. GerM is required to assemble the basal platform of the SpoIIIA-SpoIIQ transenvelope complex during sporulation in Bacillus subtilis. Mol Microbiol 2016; 102:260-273. [PMID: 27381174 DOI: 10.1111/mmi.13457] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2016] [Indexed: 11/29/2022]
Abstract
Sporulating Bacillus subtilis cells assemble a multimeric membrane complex connecting the mother cell and developing spore that is required to maintain forespore differentiation. An early step in the assembly of this transenvelope complex (called the A-Q complex) is an interaction between the extracellular domains of the forespore membrane protein SpoIIQ and the mother cell membrane protein SpoIIIAH. This interaction provides a platform onto which the remaining components of the complex assemble and also functions as an anchor for cell-cell signalling and morphogenetic proteins involved in spore development. SpoIIQ is required to recruit SpoIIIAH to the sporulation septum on the mother cell side; however, the mechanism by which SpoIIQ specifically localizes to the septal membranes on the forespore side has remained enigmatic. Here, we identify GerM, a lipoprotein previously implicated in spore germination, as the missing factor required for SpoIIQ localization. Our data indicate that GerM and SpoIIIAH, derived from the mother cell, and SpoIIQ, from the forespore, have reciprocal localization dependencies suggesting they constitute a tripartite platform for the assembly of the A-Q complex and a hub for the localization of mother cell and forespore proteins.
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Affiliation(s)
- Christopher D A Rodrigues
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Fernando H Ramírez-Guadiana
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Alexander J Meeske
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - Xindan Wang
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA
| | - David Z Rudner
- Department of Microbiology and Immunobiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA, 02115, USA.
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404
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Aparicio T, Jensen SI, Nielsen AT, de Lorenzo V, Martínez-García E. The Ssr protein (T1E_1405) from Pseudomonas putida DOT-T1E enables oligonucleotide-based recombineering in platform strain P. putida EM42. Biotechnol J 2016; 11:1309-1319. [PMID: 27367544 DOI: 10.1002/biot.201600317] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 06/16/2016] [Accepted: 06/20/2016] [Indexed: 11/10/2022]
Abstract
Some strains of the soil bacterium Pseudomonas putida have become in recent years platforms of choice for hosting biotransformations of industrial interest. Despite availability of many genetic tools for this microorganism, genomic editing of the cell factory P. putida EM42 (a derivative of reference strain KT2440) is still a time-consuming endeavor. In this work we have investigated the in vivo activity of the Ssr protein encoded by the open reading frame T1E_1405 from Pseudomonas putida DOT-T1E, a plausible functional homologue of the β protein of the Red recombination system of λ phage of Escherichia coli. A test based on the phenotypes of pyrF mutants of P. putida (the yeast's URA3 ortholog) was developed for quantifying the ability of Ssr to promote invasion of the genomic DNA replication fork by synthetic oligonucleotides. The efficiency of the process was measured by monitoring the inheritance of the changes entered into pyrF by oligonucleotides bearing mutated sequences. Ssr fostered short and long genomic deletions/insertions at considerable frequencies as well as single-base swaps not affected by mismatch repair. These results not only demonstrate the feasibility of recombineering in P. putida, but they also enable a suite of multiplexed genomic manipulations in this biotechnologically important bacterium.
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Affiliation(s)
- Tomás Aparicio
- Systems Biology Program, National Center of Biotechnology CSIC, Madrid, Spain
| | - Sheila I Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Alex T Nielsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Victor de Lorenzo
- Systems Biology Program, National Center of Biotechnology CSIC, Madrid, Spain.
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405
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Gimpel JA, Nour-Eldin HH, Scranton MA, Li D, Mayfield SP. Refactoring the Six-Gene Photosystem II Core in the Chloroplast of the Green Algae Chlamydomonas reinhardtii. ACS Synth Biol 2016. [PMID: 26214707 DOI: 10.1021/acssynbio.5b00076] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Oxygenic photosynthesis provides the energy to produce all food and most of the fuel on this planet. Photosystem II (PSII) is an essential and rate-limiting component of this process. Understanding and modifying PSII function could provide an opportunity for optimizing photosynthetic biomass production, particularly under specific environmental conditions. PSII is a complex multisubunit enzyme with strong interdependence among its components. In this work, we have deleted the six core genes of PSII in the eukaryotic alga Chlamydomonas reinhardtii and refactored them in a single DNA construct. Complementation of the knockout strain with the core PSII synthetic module from three different green algae resulted in reconstitution of photosynthetic activity to 85, 55, and 53% of that of the wild-type, demonstrating that the PSII core can be exchanged between algae species and retain function. The strains, synthetic cassettes, and refactoring strategy developed for this study demonstrate the potential of synthetic biology approaches for tailoring oxygenic photosynthesis and provide a powerful tool for unraveling PSII structure-function relationships.
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Affiliation(s)
- Javier A. Gimpel
- California Center for Algae
Biotechnology Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0368, United States
| | - Hussam H. Nour-Eldin
- California Center for Algae
Biotechnology Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0368, United States
| | - Melissa A. Scranton
- California Center for Algae
Biotechnology Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0368, United States
| | - Daphne Li
- California Center for Algae
Biotechnology Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0368, United States
| | - Stephen P. Mayfield
- California Center for Algae
Biotechnology Division of Biological Sciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0368, United States
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406
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Finnigan GC, Thorner J. mCAL: A New Approach for Versatile Multiplex Action of Cas9 Using One sgRNA and Loci Flanked by a Programmed Target Sequence. G3 (BETHESDA, MD.) 2016; 6:2147-56. [PMID: 27185399 PMCID: PMC4938667 DOI: 10.1534/g3.116.029801] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/10/2016] [Indexed: 02/06/2023]
Abstract
Genome editing exploiting CRISPR/Cas9 has been adopted widely in academia and in the biotechnology industry to manipulate DNA sequences in diverse organisms. Molecular engineering of Cas9 itself and its guide RNA, and the strategies for using them, have increased efficiency, optimized specificity, reduced inappropriate off-target effects, and introduced modifications for performing other functions (transcriptional regulation, high-resolution imaging, protein recruitment, and high-throughput screening). Moreover, Cas9 has the ability to multiplex, i.e., to act at different genomic targets within the same nucleus. Currently, however, introducing concurrent changes at multiple loci involves: (i) identification of appropriate genomic sites, especially the availability of suitable PAM sequences; (ii) the design, construction, and expression of multiple sgRNA directed against those sites; (iii) potential difficulties in altering essential genes; and (iv) lingering concerns about "off-target" effects. We have devised a new approach that circumvents these drawbacks, as we demonstrate here using the yeast Saccharomyces cerevisiae First, any gene(s) of interest are flanked upstream and downstream with a single unique target sequence that does not normally exist in the genome. Thereafter, expression of one sgRNA and cotransformation with appropriate PCR fragments permits concomitant Cas9-mediated alteration of multiple genes (both essential and nonessential). The system we developed also allows for maintenance of the integrated, inducible Cas9-expression cassette or its simultaneous scarless excision. Our scheme-dubbed mCAL for " M: ultiplexing of C: as9 at A: rtificial L: oci"-can be applied to any organism in which the CRISPR/Cas9 methodology is currently being utilized. In principle, it can be applied to install synthetic sequences into the genome, to generate genomic libraries, and to program strains or cell lines so that they can be conveniently (and repeatedly) manipulated at multiple loci with extremely high efficiency.
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Affiliation(s)
- Gregory C Finnigan
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202
| | - Jeremy Thorner
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202
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407
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Mus F, Crook MB, Garcia K, Garcia Costas A, Geddes BA, Kouri ED, Paramasivan P, Ryu MH, Oldroyd GED, Poole PS, Udvardi MK, Voigt CA, Ané JM, Peters JW. Symbiotic Nitrogen Fixation and the Challenges to Its Extension to Nonlegumes. Appl Environ Microbiol 2016. [PMID: 27084023 DOI: 10.1128/aem.01055-01016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023] Open
Abstract
Access to fixed or available forms of nitrogen limits the productivity of crop plants and thus food production. Nitrogenous fertilizer production currently represents a significant expense for the efficient growth of various crops in the developed world. There are significant potential gains to be had from reducing dependence on nitrogenous fertilizers in agriculture in the developed world and in developing countries, and there is significant interest in research on biological nitrogen fixation and prospects for increasing its importance in an agricultural setting. Biological nitrogen fixation is the conversion of atmospheric N2 to NH3, a form that can be used by plants. However, the process is restricted to bacteria and archaea and does not occur in eukaryotes. Symbiotic nitrogen fixation is part of a mutualistic relationship in which plants provide a niche and fixed carbon to bacteria in exchange for fixed nitrogen. This process is restricted mainly to legumes in agricultural systems, and there is considerable interest in exploring whether similar symbioses can be developed in nonlegumes, which produce the bulk of human food. We are at a juncture at which the fundamental understanding of biological nitrogen fixation has matured to a level that we can think about engineering symbiotic relationships using synthetic biology approaches. This minireview highlights the fundamental advances in our understanding of biological nitrogen fixation in the context of a blueprint for expanding symbiotic nitrogen fixation to a greater diversity of crop plants through synthetic biology.
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Affiliation(s)
- Florence Mus
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Matthew B Crook
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kevin Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amaya Garcia Costas
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Barney A Geddes
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Evangelia D Kouri
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | | | - Min-Hyung Ryu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Michael K Udvardi
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
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408
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Mus F, Crook MB, Garcia K, Garcia Costas A, Geddes BA, Kouri ED, Paramasivan P, Ryu MH, Oldroyd GED, Poole PS, Udvardi MK, Voigt CA, Ané JM, Peters JW. Symbiotic Nitrogen Fixation and the Challenges to Its Extension to Nonlegumes. Appl Environ Microbiol 2016; 82:3698-3710. [PMID: 27084023 PMCID: PMC4907175 DOI: 10.1128/aem.01055-16] [Citation(s) in RCA: 218] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Access to fixed or available forms of nitrogen limits the productivity of crop plants and thus food production. Nitrogenous fertilizer production currently represents a significant expense for the efficient growth of various crops in the developed world. There are significant potential gains to be had from reducing dependence on nitrogenous fertilizers in agriculture in the developed world and in developing countries, and there is significant interest in research on biological nitrogen fixation and prospects for increasing its importance in an agricultural setting. Biological nitrogen fixation is the conversion of atmospheric N2 to NH3, a form that can be used by plants. However, the process is restricted to bacteria and archaea and does not occur in eukaryotes. Symbiotic nitrogen fixation is part of a mutualistic relationship in which plants provide a niche and fixed carbon to bacteria in exchange for fixed nitrogen. This process is restricted mainly to legumes in agricultural systems, and there is considerable interest in exploring whether similar symbioses can be developed in nonlegumes, which produce the bulk of human food. We are at a juncture at which the fundamental understanding of biological nitrogen fixation has matured to a level that we can think about engineering symbiotic relationships using synthetic biology approaches. This minireview highlights the fundamental advances in our understanding of biological nitrogen fixation in the context of a blueprint for expanding symbiotic nitrogen fixation to a greater diversity of crop plants through synthetic biology.
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Affiliation(s)
- Florence Mus
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Matthew B Crook
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Kevin Garcia
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Amaya Garcia Costas
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
| | - Barney A Geddes
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Evangelia D Kouri
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | | | - Min-Hyung Ryu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Philip S Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Michael K Udvardi
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jean-Michel Ané
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - John W Peters
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, Montana, USA
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409
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A Highly Thermostable Kanamycin Resistance Marker Expands the Tool Kit for Genetic Manipulation of Caldicellulosiruptor bescii. Appl Environ Microbiol 2016; 82:4421-4428. [PMID: 27208106 DOI: 10.1128/aem.00570-16] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 05/10/2016] [Indexed: 01/17/2023] Open
Abstract
UNLABELLED Caldicellulosiruptor bescii, an anaerobic Gram-positive bacterium with an optimal growth temperature of 78°C, is the most thermophilic cellulose degrader known. It is of great biotechnological interest, as it efficiently deconstructs nonpretreated lignocellulosic plant biomass. Currently, its genetic manipulation relies on a mutant uracil auxotrophic background strain that contains a random deletion in the pyrF genome region. The pyrF gene serves as a genetic marker to select for uracil prototrophy, and it can also be counterselected for loss via resistance to the compound 5-fluoroorotic acid (5-FOA). To expand the C. bescii genetic tool kit, kanamycin resistance was developed as a selection for genetic manipulation. A codon-optimized version of the highly thermostable kanamycin resistance gene (named Cbhtk) allowed the use of kanamycin selection to obtain transformants of either replicating or integrating vector constructs in C. bescii These strains showed resistance to kanamycin at concentrations >50 μg · ml(-1), whereas wild-type C. bescii was sensitive to kanamycin at 10 μg · ml(-1) In addition, placement of the Cbhtk marker between homologous recombination regions in an integrating vector allowed direct selection of a chromosomal mutation using both kanamycin and 5-FOA. Furthermore, the use of kanamycin selection enabled the targeted deletion of the pyrE gene in wild-type C. bescii, generating a uracil auxotrophic genetic background strain resistant to 5-FOA. The pyrE gene functioned as a counterselectable marker, like pyrF, and was used together with Cbhtk in the ΔpyrE background strain to delete genes encoding lactate dehydrogenase and the CbeI restriction enzyme. IMPORTANCE Caldicellulosiruptor bescii is a thermophilic anaerobic bacterium with an optimal growth temperature of 78°C, and it has the ability to efficiently deconstruct nonpretreated lignocellulosic plant biomass. It is, therefore, of biotechnological interest for genetic engineering applications geared toward biofuel production. The current genetic system used with C. bescii is based upon only a single selection strategy, and this uses the gene involved in a primary biosynthetic pathway. There are many advantages with an additional genetic selection using an antibiotic. This presents a challenge for thermophilic microorganisms, as only a limited number of antibiotics are stable above 50°C, and a thermostable version of the enzyme conferring antibiotic resistance must be obtained. In this work, we have developed a selection system for C. bescii using the antibiotic kanamycin and have shown that, in combination with the biosynthetic gene marker, it can be used to efficiently delete genes in this organism.
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410
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Engineering Corynebacterium glutamicum for fast production of l-lysine and l-pipecolic acid. Appl Microbiol Biotechnol 2016; 100:8075-90. [DOI: 10.1007/s00253-016-7682-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/07/2016] [Accepted: 06/13/2016] [Indexed: 11/25/2022]
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411
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Chen W, Zeng D, Shen R, Ma X, Zhang Q, Chen L, Liu YG, Zhu Q. Rapid in vitro splicing of coding sequences from genomic DNA by isothermal recombination reaction-based PCR. BIOTECHNOL BIOTEC EQ 2016. [DOI: 10.1080/13102818.2016.1191374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Wenxuan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou, China
- Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, Guangzhou, China
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Dongchang Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou, China
- Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, Guangzhou, China
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Rongxin Shen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou, China
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Xingliang Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou, China
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Qunyu Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou, China
- Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, Guangzhou, China
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou, China
- Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, Guangzhou, China
- College of Life Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, Guangzhou, China
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou, China
- Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, Guangzhou, China
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Qinlong Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangzhou, China
- Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, Guangzhou, China
- College of Life Sciences, South China Agricultural University, Guangzhou, China
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412
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Vasta JD, Raines RT. Human Collagen Prolyl 4-Hydroxylase Is Activated by Ligands for Its Iron Center. Biochemistry 2016; 55:3224-33. [PMID: 27183028 DOI: 10.1021/acs.biochem.6b00251] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Collagen is the most abundant protein in animals. The posttranslational hydroxylation of proline residues in collagen contributes greatly to its conformational stability. Deficient hydroxylation is associated with a variety of disease states, including scurvy. The hydroxylation of proline residues in collagen is catalyzed by an Fe(II)- and α-ketoglutarate-dependent dioxygenase, collagen prolyl 4-hydroxylase (CP4H). CP4H has long been known to suffer oxidative inactivation during catalysis, and the cofactor ascorbate (vitamin C) is required to reactivate the enzyme by reducing its iron center from Fe(III) to Fe(II). Herein, we report on the discovery of the first synthetic activators of CP4H. Specifically, we find that 2,2'-bipyridine-4-carboxylate and 2,2'-bipyridine-5-carboxylate serve as ligands for the iron center in human CP4H that enhance the rate of ascorbate-dependent reactivation. This new mode of CP4H activation is available to other biheteroaryl compounds but does not necessarily extend to other prolyl 4-hydroxylases. As collagen is weakened in many indications, analogous activators of CP4H could have therapeutic benefits.
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Affiliation(s)
- James D Vasta
- Department of Biochemistry and ‡Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Ronald T Raines
- Department of Biochemistry and ‡Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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413
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Abstract
Several groups have generated programmable transcription factors based on the versatile Cas9 protein, yet their relative potency and effectiveness across various cell types and species remain unexplored. Here, we compare Cas9 activator systems and examine their ability to induce robust gene expression in several human, mouse, and fly cell lines. We also explore the potential for improved activation through the combination of the most potent activator systems and assess the role of cooperativity in maximizing gene expression.
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414
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Shi Z, Vickers CE. Molecular Cloning Designer Simulator (MCDS): All-in-one molecular cloning and genetic engineering design, simulation and management software for complex synthetic biology and metabolic engineering projects. Metab Eng Commun 2016; 3:173-186. [PMID: 29468123 PMCID: PMC5779711 DOI: 10.1016/j.meteno.2016.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 03/30/2016] [Accepted: 05/10/2016] [Indexed: 01/15/2023] Open
Abstract
Molecular Cloning Designer Simulator (MCDS) is a powerful new all-in-one cloning and genetic engineering design, simulation and management software platform developed for complex synthetic biology and metabolic engineering projects. In addition to standard functions, it has a number of features that are either unique, or are not found in combination in any one software package: (1) it has a novel interactive flow-chart user interface for complex multi-step processes, allowing an integrated overview of the whole project; (2) it can perform a user-defined workflow of cloning steps in a single execution of the software; (3) it can handle multiple types of genetic recombineering, a technique that is rapidly replacing classical cloning for many applications; (4) it includes experimental information to conveniently guide wet lab work; and (5) it can store results and comments to allow the tracking and management of the whole project in one platform. MCDS is freely available from https://mcds.codeplex.com. MCDS is an all-in-one in silico design, simulation and management platform. MCDS supports the design, simulation management of most cloning and recombineering technologies. MCDS has a novel interactive flowchart that allows simpler and more precise transactions. MCDS enables complete information integrity and consistency by keeping all details in one file.
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Affiliation(s)
- Zhenyu Shi
- Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Claudia E Vickers
- Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
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415
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Hammerling MJ, Gollihar J, Mortensen C, Alnahhas RN, Ellington AD, Barrick JE. Expanded Genetic Codes Create New Mutational Routes to Rifampicin Resistance inEscherichia coli. Mol Biol Evol 2016; 33:2054-63. [DOI: 10.1093/molbev/msw094] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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416
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Tang H, Wang S, Wang J, Song M, Xu M, Zhang M, Shen Y, Hou J, Bao X. N-hypermannose glycosylation disruption enhances recombinant protein production by regulating secretory pathway and cell wall integrity in Saccharomyces cerevisiae. Sci Rep 2016; 6:25654. [PMID: 27156860 PMCID: PMC4860636 DOI: 10.1038/srep25654] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/14/2016] [Indexed: 12/30/2022] Open
Abstract
Saccharomyces cerevisiae is a robust host for heterologous protein expression. The efficient expression of cellulases in S. cerevisiae is important for the consolidated bioprocess that directly converts lignocellulose into valuable products. However, heterologous proteins are often N-hyperglycosylated in S. cerevisiae, which may affect protein activity. In this study, the expression of three heterologous proteins, β-glucosidase, endoglucanase and cellobiohydrolase, was found to be N-hyperglycosylated in S. cerevisiae. To block the formation of hypermannose glycan, these proteins were expressed in strains with deletions in key Golgi mannosyltransferases (Och1p, Mnn9p and Mnn1p), respectively. Their extracellular activities improved markedly in the OCH1 and MNN9 deletion strains. Interestingly, truncation of the N-hypermannose glycan did not increase the specific activity of these proteins, but improved the secretion yield. Further analysis showed OCH1 and MNN9 deletion up-regulated genes in the secretory pathway, such as protein folding and vesicular trafficking, but did not induce the unfolded protein response. The cell wall integrity was also affected by OCH1 and MNN9 deletion, which contributed to the release of secretory protein extracellularly. This study demonstrated that mannosyltransferases disruption improved protein secretion through up-regulating secretory pathway and affecting cell wall integrity and provided new insights into glycosylation engineering for protein secretion.
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Affiliation(s)
- Hongting Tang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China
| | - Shenghuan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China
| | - Jiajing Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China
| | - Meihui Song
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China
| | - Mengyang Xu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China
| | - Mengying Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China
| | - Yu Shen
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China
| | - Xiaoming Bao
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China
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417
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Bromann K, Toivari M, Viljanen K, Ruohonen L, Nakari-Setälä T. Engineering Aspergillus nidulans for heterologous ent-kaurene and gamma-terpinene production. Appl Microbiol Biotechnol 2016; 100:6345-6359. [PMID: 27098256 DOI: 10.1007/s00253-016-7517-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 02/29/2016] [Accepted: 03/31/2016] [Indexed: 12/14/2022]
Abstract
Terpenes are a large and varied group of natural products with a wide array of bioactivities and applications. The chemical production of industrially relevant terpenes can be expensive and time-consuming due to the structural complexity of these compounds. Here, we studied Aspergillus nidulans as a heterologous host for monoterpene and diterpene production. Previously, we identified a novel diterpene gene cluster in A. nidulans and showed that overexpression of the cluster-specific transcription factor (pbcR) led to ent-pimara-8(14),15-diene (PD) production. We report further characterization of the A. nidulans PD synthase gene (pbcA). In A. nidulans, overexpression of pbcA resulted in PD production, while deletion of pbcA abolished PD production. Overexpression of Fusarium fujikuroi ent-kaurene synthase (cps/ks) and Citrus unshiu gamma-terpinene synthase resulted in ent-kaurene and gamma-terpinene production, respectively. A. nidulans is a fungal model organism and a close relative to other industrially relevant Aspergillus species. A. nidulans is a known producer of many secondary metabolites, but its ability to produce heterologous monoterpene and diterpene compounds has not been characterized. Here, we show that A. nidulans is capable of heterologous terpene production and thus has potential as a production host for industrially relevant compounds. The genetic engineering principles reported here could also be applied to other Aspergilli.
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Affiliation(s)
- Kirsi Bromann
- VTT Technical Research Centre of Finland Ltd., 02044 VTT, Espoo, Finland.
| | - Mervi Toivari
- VTT Technical Research Centre of Finland Ltd., 02044 VTT, Espoo, Finland
| | - Kaarina Viljanen
- Orion Pharma, Orion Corporation, Orionintie 1, 02200, Espoo, Finland
| | - Laura Ruohonen
- VTT Technical Research Centre of Finland Ltd., 02044 VTT, Espoo, Finland
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418
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A New Strategy for Production of 5-Aminolevulinic Acid in Recombinant Corynebacterium glutamicum with High Yield. Appl Environ Microbiol 2016; 82:2709-2717. [PMID: 26921424 DOI: 10.1128/aem.00224-16] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 02/20/2016] [Indexed: 12/15/2022] Open
Abstract
UNLABELLED 5-Aminolevulinic acid (ALA), a nonprotein amino acid involved in tetrapyrrole synthesis, has been widely applied in agriculture, medicine, and food production. Many engineered metabolic pathways have been constructed; however, the production yields are still low. In this study, several 5-aminolevulinic acid synthases (ALASs) from different sources were evaluated and compared with respect to their ALA production capacities in an engineered Corynebacterium glutamicum CgS1 strain that can accumulate succinyl-coenzyme A (CoA). A codon-optimized ALAS from Rhodobacter capsulatus SB1003 displayed the best potential. Recombinant strain CgS1/pEC-SB produced 7.6 g/liter ALA using a mineral salt medium in a fed-batch fermentation mode. Employing two-stage fermentation, 12.46 g/liter ALA was produced within 17 h, with a productivity of 0.73 g/liter/h, in recombinant C. glutamicum Through overexpression of the heterologous nonspecific ALA exporter RhtA from Escherichia coli, the titer was further increased to 14.7 g/liter. This indicated that strain CgS1/pEC-SB-rhtA holds attractive industrial application potential for the future. IMPORTANCE In this study, a two-stage fermentation strategy was used for production of the value-added nonprotein amino acid 5-aminolevulinic acid from glucose and glycine in a generally recognized as safe (GRAS) host,Corynebacterium glutamicum The ALA titer represented the highest in the literature, to our knowledge. This high production capacity, combined with the potential easy downstream processes, made the recombinant strain an attractive candidate for industrial use in the future.
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419
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Heller J, Zhao J, Rosenfield G, Kowbel DJ, Gladieux P, Glass NL. Characterization of Greenbeard Genes Involved in Long-Distance Kind Discrimination in a Microbial Eukaryote. PLoS Biol 2016; 14:e1002431. [PMID: 27077707 PMCID: PMC4831770 DOI: 10.1371/journal.pbio.1002431] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 03/11/2016] [Indexed: 01/09/2023] Open
Abstract
Microorganisms are capable of communication and cooperation to perform social activities. Cooperation can be enforced using kind discrimination mechanisms in which individuals preferentially help or punish others, depending on genetic relatedness only at certain loci. In the filamentous fungus Neurospora crassa, genetically identical asexual spores (germlings) communicate and fuse in a highly regulated process, which is associated with fitness benefits during colony establishment. Recognition and chemotropic interactions between isogenic germlings requires oscillation of the mitogen-activated protein kinase (MAPK) signal transduction protein complex (NRC-1, MEK-2, MAK-2, and the scaffold protein HAM-5) to specialized cell fusion structures termed conidial anastomosis tubes. Using a population of 110 wild N. crassa isolates, we investigated germling fusion between genetically unrelated individuals and discovered that chemotropic interactions are regulated by kind discrimination. Distinct communication groups were identified, in which germlings within one communication group interacted at high frequency, while germlings from different communication groups avoided each other. Bulk segregant analysis followed by whole genome resequencing identified three linked genes (doc-1, doc-2, and doc-3), which were associated with communication group phenotype. Alleles at doc-1, doc-2, and doc-3 fell into five haplotypes that showed transspecies polymorphism. Swapping doc-1 and doc-2 alleles from different communication group strains was necessary and sufficient to confer communication group affiliation. During chemotropic interactions, DOC-1 oscillated with MAK-2 to the tips of conidial anastomosis tubes, while DOC-2 was statically localized to the plasma membrane. Our data indicate that doc-1, doc-2, and doc-3 function as "greenbeard" genes, involved in mediating long-distance kind recognition that involves actively searching for one's own type, resulting in cooperation between non-genealogical relatives. Our findings serve as a basis for investigations into the mechanisms associated with attraction, fusion, and kind recognition in other eukaryotic species.
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Affiliation(s)
- Jens Heller
- The Plant and Microbial Biology Department, The University of California, Berkeley, California, United States of America
| | - Jiuhai Zhao
- The Plant and Microbial Biology Department, The University of California, Berkeley, California, United States of America
| | - Gabriel Rosenfield
- The Plant and Microbial Biology Department, The University of California, Berkeley, California, United States of America
| | - David J. Kowbel
- The Plant and Microbial Biology Department, The University of California, Berkeley, California, United States of America
| | | | - N. Louise Glass
- The Plant and Microbial Biology Department, The University of California, Berkeley, California, United States of America
- * E-mail:
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420
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Hutchison CA, Chuang RY, Noskov VN, Assad-Garcia N, Deerinck TJ, Ellisman MH, Gill J, Kannan K, Karas BJ, Ma L, Pelletier JF, Qi ZQ, Richter RA, Strychalski EA, Sun L, Suzuki Y, Tsvetanova B, Wise KS, Smith HO, Glass JI, Merryman C, Gibson DG, Venter JC. Design and synthesis of a minimal bacterial genome. Science 2016; 351:aad6253. [DOI: 10.1126/science.aad6253] [Citation(s) in RCA: 838] [Impact Index Per Article: 104.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 02/05/2016] [Indexed: 12/17/2022]
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421
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Wagner JM, Chan S, Evans TJ, Kahng S, Kim J, Arbing MA, Eisenberg D, Korotkov KV. Structures of EccB1 and EccD1 from the core complex of the mycobacterial ESX-1 type VII secretion system. BMC STRUCTURAL BIOLOGY 2016; 16:5. [PMID: 26922638 PMCID: PMC4769845 DOI: 10.1186/s12900-016-0056-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 02/23/2016] [Indexed: 11/24/2022]
Abstract
Background The ESX-1 type VII secretion system is an important determinant of virulence in pathogenic mycobacteria, including Mycobacterium tuberculosis. This complicated molecular machine secretes folded proteins through the mycobacterial cell envelope to subvert the host immune response. Despite its important role in disease very little is known about the molecular architecture of the ESX-1 secretion system. Results This study characterizes the structures of the soluble domains of two conserved core ESX-1 components – EccB1 and EccD1. The periplasmic domain of EccB1 consists of 4 repeat domains and a central domain, which together form a quasi 2-fold symmetrical structure. The repeat domains of EccB1 are structurally similar to a known peptidoglycan binding protein suggesting a role in anchoring the ESX-1 system within the periplasmic space. The cytoplasmic domain of EccD1has a ubiquitin-like fold and forms a dimer with a negatively charged groove. Conclusions These structures represent a major step towards resolving the molecular architecture of the entire ESX-1 assembly and may contribute to ESX-1 targeted tuberculosis intervention strategies. Electronic supplementary material The online version of this article (doi:10.1186/s12900-016-0056-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jonathan M Wagner
- Department of Molecular & Cellular Biochemistry and Center for Structural Biology, University of Kentucky, 741 South Limestone, Lexington, KY, 40536, USA. .,Present address: Department of Molecular Physiology and Biological Physics and The Myles H. Thaler Center for AIDS and Human Retrovirus Research, University of Virginia, Charlottesville, VA, USA.
| | - Sum Chan
- UCLA-DOE Institute, University of California Los Angeles, Los Angeles, CA, 90095-1570, USA.
| | - Timothy J Evans
- Department of Molecular & Cellular Biochemistry and Center for Structural Biology, University of Kentucky, 741 South Limestone, Lexington, KY, 40536, USA. .,Present address: Division of Regulatory Services, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA.
| | - Sara Kahng
- UCLA-DOE Institute, University of California Los Angeles, Los Angeles, CA, 90095-1570, USA.
| | - Jennifer Kim
- UCLA-DOE Institute, University of California Los Angeles, Los Angeles, CA, 90095-1570, USA.
| | - Mark A Arbing
- UCLA-DOE Institute, University of California Los Angeles, Los Angeles, CA, 90095-1570, USA.
| | - David Eisenberg
- UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry & Biochemistry, and Howard Hughes Medical Institute, University of California Los Angeles, Los Angeles, CA, 90095-1570, USA.
| | - Konstantin V Korotkov
- Department of Molecular & Cellular Biochemistry and Center for Structural Biology, University of Kentucky, 741 South Limestone, Lexington, KY, 40536, USA.
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422
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Jones ML, Das S, Belda H, Collins CR, Blackman MJ, Treeck M. A versatile strategy for rapid conditional genome engineering using loxP sites in a small synthetic intron in Plasmodium falciparum. Sci Rep 2016; 6:21800. [PMID: 26892670 PMCID: PMC4759600 DOI: 10.1038/srep21800] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 02/01/2016] [Indexed: 11/09/2022] Open
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423
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Digital detection of endonuclease mediated gene disruption in the HIV provirus. Sci Rep 2016; 6:20064. [PMID: 26829887 PMCID: PMC4735761 DOI: 10.1038/srep20064] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 12/18/2015] [Indexed: 12/11/2022] Open
Abstract
Genome editing by designer nucleases is a rapidly evolving technology utilized in a highly diverse set of research fields. Among all fields, the T7 endonuclease mismatch cleavage assay, or Surveyor assay, is the most commonly used tool to assess genomic editing by designer nucleases. This assay, while relatively easy to perform, provides only a semi-quantitative measure of mutation efficiency that lacks sensitivity and accuracy. We demonstrate a simple droplet digital PCR assay that quickly quantitates a range of indel mutations with detection as low as 0.02% mutant in a wild type background and precision (≤6%CV) and accuracy superior to either mismatch cleavage assay or clonal sequencing when compared to next-generation sequencing. The precision and simplicity of this assay will facilitate comparison of gene editing approaches and their optimization, accelerating progress in this rapidly-moving field.
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424
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Integrated in vivo and in vitro nascent chain profiling reveals widespread translational pausing. Proc Natl Acad Sci U S A 2016; 113:E829-38. [PMID: 26831095 DOI: 10.1073/pnas.1520560113] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although the importance of the nonuniform progression of elongation in translation is well recognized, there have been few attempts to explore this process by directly profiling nascent polypeptides, the relevant intermediates of translation. Such approaches will be essential to complement other approaches, including ribosome profiling, which is extremely powerful but indirect with respect to the actual translation processes. Here, we use the nascent polypeptide's chemical trait of having a covalently attached tRNA moiety to detect translation intermediates. In a case study, Escherichia coli SecA was shown to undergo nascent polypeptide-dependent translational pauses. We then carried out integrated in vivo and in vitro nascent chain profiling (iNP) to characterize 1,038 proteome members of E. coli that were encoded by the first quarter of the chromosome with respect to their propensities to accumulate polypeptidyl-tRNA intermediates. A majority of them indeed undergo single or multiple pauses, some occurring only in vitro, some occurring only in vivo, and some occurring both in vivo and in vitro. Thus, translational pausing can be intrinsically robust, subject to in vivo alleviation, or require in vivo reinforcement. Cytosolic and membrane proteins tend to experience different classes of pauses; membrane proteins often pause multiple times in vivo. We also note that the solubility of cytosolic proteins correlates with certain categories of pausing. Translational pausing is widespread and diverse in nature.
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425
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Conway JM, Pierce WS, Le JH, Harper GW, Wright JH, Tucker AL, Zurawski JV, Lee LL, Blumer-Schuette SE, Kelly RM. Multidomain, Surface Layer-associated Glycoside Hydrolases Contribute to Plant Polysaccharide Degradation by Caldicellulosiruptor Species. J Biol Chem 2016; 291:6732-47. [PMID: 26814128 DOI: 10.1074/jbc.m115.707810] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Indexed: 01/08/2023] Open
Abstract
The genome of the extremely thermophilic bacterium Caldicellulosiruptor kronotskyensisencodes 19 surface layer (S-layer) homology (SLH) domain-containing proteins, the most in any Caldicellulosiruptorspecies genome sequenced to date. These SLH proteins include five glycoside hydrolases (GHs) and one polysaccharide lyase, the genes for which were transcribed at high levels during growth on plant biomass. The largest GH identified so far in this genus, Calkro_0111 (2,435 amino acids), is completely unique toC. kronotskyensisand contains SLH domains. Calkro_0111 was produced recombinantly inEscherichia colias two pieces, containing the GH16 and GH55 domains, respectively, as well as putative binding and spacer domains. These displayed endo- and exoglucanase activity on the β-1,3-1,6-glucan laminarin. A series of additional truncation mutants of Calkro_0111 revealed the essential architectural features required for catalytic function. Calkro_0402, another of the SLH domain GHs inC. kronotskyensis, when produced inE. coli, was active on a variety of xylans and β-glucans. Unlike Calkro_0111, Calkro_0402 is highly conserved in the genus Caldicellulosiruptorand among other biomass-degrading Firmicutes but missing from Caldicellulosiruptor bescii As such, the gene encoding Calkro_0402 was inserted into the C. besciigenome, creating a mutant strain with its S-layer extensively decorated with Calkro_0402. This strain consequently degraded xylans more extensively than wild-typeC. bescii The results here provide new insights into the architecture and role of SLH domain GHs and demonstrate that hemicellulose degradation can be enhanced through non-native SLH domain GHs engineered into the genomes of Caldicellulosiruptorspecies.
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Affiliation(s)
- Jonathan M Conway
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - William S Pierce
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - Jaycee H Le
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - George W Harper
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - John H Wright
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - Allyson L Tucker
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - Jeffrey V Zurawski
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - Laura L Lee
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - Sara E Blumer-Schuette
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
| | - Robert M Kelly
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695
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426
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SutA is a bacterial transcription factor expressed during slow growth in Pseudomonas aeruginosa. Proc Natl Acad Sci U S A 2016; 113:E597-605. [PMID: 26787849 DOI: 10.1073/pnas.1514412113] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Microbial quiescence and slow growth are ubiquitous physiological states, but their study is complicated by low levels of metabolic activity. To address this issue, we used a time-selective proteome-labeling method [bioorthogonal noncanonical amino acid tagging (BONCAT)] to identify proteins synthesized preferentially, but at extremely low rates, under anaerobic survival conditions by the opportunistic pathogen Pseudomonas aeruginosa. One of these proteins is a transcriptional regulator that has no homology to any characterized protein domains and is posttranscriptionally up-regulated during survival and slow growth. This small, acidic protein associates with RNA polymerase, and chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing suggests that the protein associates with genomic DNA through this interaction. ChIP signal is found both in promoter regions and throughout the coding sequences of many genes and is particularly enriched at ribosomal protein genes and in the promoter regions of rRNA genes. Deletion of the gene encoding this protein affects expression of these and many other genes and impacts biofilm formation, secondary metabolite production, and fitness in fluctuating conditions. On the basis of these observations, we have designated the protein SutA (survival under transitions A).
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427
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PGL germ granule assembly protein is a base-specific, single-stranded RNase. Proc Natl Acad Sci U S A 2016; 113:1279-84. [PMID: 26787882 DOI: 10.1073/pnas.1524400113] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cellular RNA-protein (RNP) granules are ubiquitous and have fundamental roles in biology and RNA metabolism, but the molecular basis of their structure, assembly, and function is poorly understood. Using nematode "P-granules" as a paradigm, we focus on the PGL granule scaffold protein to gain molecular insights into RNP granule structure and assembly. We first identify a PGL dimerization domain (DD) and determine its crystal structure. PGL-1 DD has a novel 13 α-helix fold that creates a positively charged channel as a homodimer. We investigate its capacity to bind RNA and discover unexpectedly that PGL-1 DD is a guanosine-specific, single-stranded endonuclease. Discovery of the PGL homodimer, together with previous results, suggests a model in which the PGL DD dimer forms a fundamental building block for P-granule assembly. Discovery of the PGL RNase activity expands the role of RNP granule assembly proteins to include enzymatic activity in addition to their job as structural scaffolds.
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428
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Clostridium thermocellum releases coumaric acid during degradation of untreated grasses by the action of an unknown enzyme. Appl Microbiol Biotechnol 2016; 100:2907-15. [PMID: 26762388 DOI: 10.1007/s00253-016-7294-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/20/2015] [Accepted: 12/26/2015] [Indexed: 12/17/2022]
Abstract
Clostridium thermocellum is an anaerobic thermophile with the ability to digest lignocellulosic biomass that has not been pretreated with high temperatures. Thermophilic anaerobes have previously been shown to more readily degrade grasses than wood. Part of the explanation for this may be the presence of relatively large amounts of coumaric acid in grasses, with linkages to both hemicellulose and lignin. We found that C. thermocellum and cell-free cellulase preparations both release coumaric acid from bagasse and switchgrass. Cellulase preparations from a mutant strain lacking the scaffoldin cipA still showed activity, though diminished. Deletion of all three proteins in C. thermocellum with ferulic acid esterase domains, either singly or in combination, did not eliminate the activity. Further work will be needed to identify the novel enzyme(s) responsible for the release of coumaric acid from grasses and to determine whether these enzymes are important factors of microbial biomass degradation.
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429
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Yang Y, Chi Y, Tang X, Ertl HCJ, Zhou D. Rapid, Efficient, and Modular Generation of Adenoviral Vectors via Isothermal Assembly. ACTA ACUST UNITED AC 2016; 113:16.26.1-16.26.18. [PMID: 31773916 DOI: 10.1002/0471142727.mb1626s113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Adenoviral vectors have yielded promising results as carriers for gene transfer and vaccines in basic research and clinical applications. However, most common procedures to construct adenoviral vectors and manipulate adenovirus (Ad) genomes are complex and labor-intensive. An easy and detailed protocol for the rapid, efficient, and modular generation of chimpanzee Ad serotype 68 (AdC68) as a molecular clone via isothermal assembly, which directionally assembles multiple DNA fragments in a single isothermal reaction without restriction enzymes or ligases, is presented. Any serotype of adenovirus with the sequence of genome known can be constructed as a molecular clone by this method. Recombinant adenoviral vectors can be created via one-step isothermal assembly in <3 days, and recombinant Ads can be rescued within 8 days. This protocol is practical for manipulations of Ad genomes, because an entire Ad genome can be divided into specific fragments within modular plasmids. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Yong Yang
- Vaccine Research Center of Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Yudan Chi
- Vaccine Research Center of Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Xinying Tang
- Vaccine Research Center of Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | | | - Dongming Zhou
- Vaccine Research Center of Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
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430
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Cahn JKB, Brinkmann-Chen S, Buller AR, Arnold FH. Artificial domain duplication replicates evolutionary history of ketol-acid reductoisomerases. Protein Sci 2015; 25:1241-8. [PMID: 26644020 DOI: 10.1002/pro.2852] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 12/01/2015] [Indexed: 11/11/2022]
Abstract
The duplication of protein structural domains has been proposed as a common mechanism for the generation of new protein folds. A particularly interesting case is the class II ketol-acid reductoisomerase (KARI), which putatively arose from an ancestral class I KARI by duplication of the C-terminal domain and corresponding loss of obligate dimerization. As a result, the class II enzymes acquired a deeply embedded figure-of-eight knot. To test this evolutionary hypothesis we constructed a novel class II KARI by duplicating the C-terminal domain of a hyperthermostable class I KARI. The new protein is monomeric, as confirmed by gel filtration and X-ray crystallography, and has the deeply knotted class II KARI fold. Surprisingly, its catalytic activity is nearly unchanged from the parent KARI. This provides strong evidence in support of domain duplication as the mechanism for the evolution of the class II KARI fold and demonstrates the ability of domain duplication to generate topological novelty in a function-neutral manner.
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Affiliation(s)
- Jackson K B Cahn
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125
| | - Sabine Brinkmann-Chen
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125
| | - Andrew R Buller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125
| | - Frances H Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125
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431
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Ma T, Zhou Y, Li X, Zhu F, Cheng Y, Liu Y, Deng Z, Liu T. Genome mining of astaxanthin biosynthetic genes from Sphingomonas sp. ATCC 55669 for heterologous overproduction in Escherichia coli. Biotechnol J 2015; 11:228-37. [PMID: 26580858 PMCID: PMC5064606 DOI: 10.1002/biot.201400827] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 08/07/2015] [Accepted: 10/19/2015] [Indexed: 02/01/2023]
Abstract
As a highly valued keto-carotenoid, astaxanthin is widely used in nutritional supplements and pharmaceuticals. Therefore, the demand for biosynthetic astaxanthin and improved efficiency of astaxanthin biosynthesis has driven the investigation of metabolic engineering of native astaxanthin producers and heterologous hosts. However, microbial resources for astaxanthin are limited. In this study, we found that the α-Proteobacterium Sphingomonas sp. ATCC 55669 could produce astaxanthin naturally. We used whole-genome sequencing to identify the astaxanthin biosynthetic pathway using a combined PacBio-Illumina approach. The putative astaxanthin biosynthetic pathway in Sphingomonas sp. ATCC 55669 was predicted. For further confirmation, a high-efficiency targeted engineering carotenoid synthesis platform was constructed in E. coli for identifying the functional roles of candidate genes. All genes involved in astaxanthin biosynthesis showed discrete distributions on the chromosome. Moreover, the overexpression of exogenous E. coli idi in Sphingomonas sp. ATCC 55669 increased astaxanthin production by 5.4-fold. This study described a new astaxanthin producer and provided more biosynthesis components for bioengineering of astaxanthin in the future.
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Affiliation(s)
- Tian Ma
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, China
| | - Yuanjie Zhou
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, China
| | - Xiaowei Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, China
| | - Fayin Zhu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, China
| | - Yongbo Cheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, China
| | - Yi Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Wuhan, China. .,Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan, China. .,Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Wuhan, China.
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432
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Koskela EV, Frey AD. Homologous recombinatorial cloning without the creation of single-stranded ends: exonuclease and ligation-independent cloning (ELIC). Mol Biotechnol 2015; 57:233-40. [PMID: 25370826 DOI: 10.1007/s12033-014-9817-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
We describe a new type of molecular cloning that complements the available strategies for homologous recombinatorial cloning. Purified, linear double-stranded DNA molecules with homologous ends are simply mixed in water and they transform readily into E. coli. Insert and linear vector need as few as ten base pairs of homologous sequence at their ends and essentially no incubation or enzyme treatments are needed for creating recombinants from linear fragments. Our method outcompetes most existing cloning methods in simplicity and affordability and is well-suited for high-throughput applications.
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Affiliation(s)
- Essi V Koskela
- Department of Chemical Technology and Biotechnology, Aalto University, 00076, Aalto, Finland
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433
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Lanier MH, Kim T, Cooper JA. CARMIL2 is a novel molecular connection between vimentin and actin essential for cell migration and invadopodia formation. Mol Biol Cell 2015; 26:4577-88. [PMID: 26466680 PMCID: PMC4678016 DOI: 10.1091/mbc.e15-08-0552] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 10/07/2015] [Indexed: 12/12/2022] Open
Abstract
CARMIL2 is a novel and direct molecular connection between vimentin filaments and actin assembly during cell migration and invadopodia formation. Through two distinct domains, CARMIL2 localizes to vimentin filaments and regulates actin assembly. The biochemical activities of both domains are necessary for cell migration and invasion. Cancer cell migration requires the regulation of actin networks at protrusions associated with invadopodia and other leading edges. Carcinomas become invasive after undergoing an epithelial–mesenchymal transition characterized by the appearance of vimentin filaments. While vimentin expression correlates with cell migration, the molecular connections between vimentin- and actin-based membrane protrusions are not understood. We report here that CARMIL2 (capping protein, Arp2/3, myosin-I linker 2) provides such a molecular link. CARMIL2 localizes to vimentin, regulates actin capping protein (CP), and binds to membranes. CARMIL2 is necessary for invadopodia formation, as well as cell polarity, lamellipodial assembly, membrane ruffling, macropinocytosis, and collective cell migration. Using point mutants and chimeras with defined biochemical and cellular properties, we discovered that localization to vimentin and CP binding are both essential for the function of CARMIL2 in cells. On the basis of these results, we propose a model in which dynamic vimentin filaments target CARMIL2 to critical membrane-associated locations, where CARMIL2 regulates CP, and thus actin assembly, to create cell protrusions.
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Affiliation(s)
- M Hunter Lanier
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO 63110
| | - Taekyung Kim
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO 63110
| | - John A Cooper
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO 63110
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434
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Beilharz K, van Raaphorst R, Kjos M, Veening JW. Red Fluorescent Proteins for Gene Expression and Protein Localization Studies in Streptococcus pneumoniae and Efficient Transformation with DNA Assembled via the Gibson Assembly Method. Appl Environ Microbiol 2015; 81:7244-52. [PMID: 26253684 PMCID: PMC4579452 DOI: 10.1128/aem.02033-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 07/31/2015] [Indexed: 11/20/2022] Open
Abstract
During the last decades, a wide range of fluorescent proteins (FPs) have been developed and improved. This has had a great impact on the possibilities in biological imaging and the investigation of cellular processes at the single-cell level. Recently, we have benchmarked a set of green fluorescent proteins (GFPs) and generated a codon-optimized superfolder GFP for efficient use in the important human pathogen Streptococcus pneumoniae and other low-GC Gram-positive bacteria. In the present work, we constructed and compared four red fluorescent proteins (RFPs) in S. pneumoniae. Two orange-red variants, mOrange2 and TagRFP, and two far-red FPs, mKate2 and mCherry, were codon optimized and examined by fluorescence microscopy and plate reader assays. Notably, protein fusions of the RFPs to FtsZ were constructed by direct transformation of linear Gibson assembly (isothermal assembly) products, a method that speeds up the strain construction process significantly. Our data show that mCherry is the fastest-maturing RFP in S. pneumoniae and is best suited for studying gene expression, while mKate2 and TagRFP are more stable and are the preferred choices for protein localization studies. The RFPs described here will be useful for cell biology studies that require multicolor labeling in S. pneumoniae and related organisms.
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Affiliation(s)
- Katrin Beilharz
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Groningen, The Netherlands
| | - Renske van Raaphorst
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Groningen, The Netherlands
| | - Morten Kjos
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Groningen, The Netherlands
| | - Jan-Willem Veening
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, Centre for Synthetic Biology, University of Groningen, Groningen, The Netherlands
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435
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Lin S, Ewen-Campen B, Ni X, Housden BE, Perrimon N. In Vivo Transcriptional Activation Using CRISPR/Cas9 in Drosophila. Genetics 2015; 201:433-42. [PMID: 26245833 PMCID: PMC4596659 DOI: 10.1534/genetics.115.181065] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 08/04/2015] [Indexed: 12/30/2022] Open
Abstract
A number of approaches for Cas9-mediated transcriptional activation have recently been developed, allowing target genes to be overexpressed from their endogenous genomic loci. However, these approaches have thus far been limited to cell culture, and this technique has not been demonstrated in vivo in any animal. The technique involving the fewest separate components, and therefore the most amenable to in vivo applications, is the dCas9-VPR system, where a nuclease-dead Cas9 is fused to a highly active chimeric activator domain. In this study, we characterize the dCas9-VPR system in Drosophila cells and in vivo. We show that this system can be used in cell culture to upregulate a range of target genes, singly and in multiplex, and that a single guide RNA upstream of the transcription start site can activate high levels of target transcription. We observe marked heterogeneity in guide RNA efficacy for any given gene, and we confirm that transcription is inhibited by guide RNAs binding downstream of the transcription start site. To demonstrate one application of this technique in cells, we used dCas9-VPR to identify target genes for Twist and Snail, two highly conserved transcription factors that cooperate during Drosophila mesoderm development. In addition, we simultaneously activated both Twist and Snail to identify synergistic responses to this physiologically relevant combination. Finally, we show that dCas9-VPR can activate target genes and cause dominant phenotypes in vivo, providing the first demonstration of dCas9 activation in a multicellular animal. Transcriptional activation using dCas9-VPR thus offers a simple and broadly applicable technique for a variety of overexpression studies.
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Affiliation(s)
- Shuailiang Lin
- Tsinghua-Peking-National Institute of Biological Sciences Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China Department of Genetics
| | | | | | | | - Norbert Perrimon
- Department of Genetics Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115
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436
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Walck-Shannon E, Reiner D, Hardin J. Polarized Rac-dependent protrusions drive epithelial intercalation in the embryonic epidermis of C. elegans. Development 2015; 142:3549-60. [PMID: 26395474 DOI: 10.1242/dev.127597] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 08/26/2015] [Indexed: 12/24/2022]
Abstract
Cell intercalation is a fundamental, coordinated cell rearrangement process that shapes tissues throughout animal development. Studies of intercalation within epithelia have focused almost exclusively on the localized constriction of specific apical junctions. Another widely deployed yet poorly understood alternative mechanism of epithelial intercalation relies on basolateral protrusive activity. Using the dorsal embryonic epidermis of Caenorhabditis elegans, we have investigated this alternative mechanism using high-resolution live cell microscopy and genetic analysis. We find that as dorsal epidermal cells migrate past one another they produce F-actin-rich protrusions polarized at their extending (medial) edges. These protrusions are controlled by the C. elegans Rac and RhoG orthologs CED-10 and MIG-2, which function redundantly to polarize actin polymerization upstream of the WAVE complex and WASP, respectively. We also identify UNC-73, the C. elegans ortholog of Trio, as a guanine nucleotide exchange factor (GEF) upstream of both CED-10 and MIG-2. Further, we identify a novel polarizing cue, CRML-1, which is the ortholog of human capping Arp2/3 myosin I linker (CARMIL), that localizes to the nonprotrusive lateral edges of dorsal cells. CRML-1 genetically suppresses UNC-73 function and, indirectly, actin polymerization. This network identifies a novel, molecularly conserved cassette that regulates epithelial intercalation via basolateral protrusive activity.
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Affiliation(s)
- Elise Walck-Shannon
- Graduate Program in Genetics, University of Wisconsin-Madison, 1117 W. Johnson Street, Madison, WI 53706, USA
| | - David Reiner
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, 101 Manning Drive, Chapel Hill, NC 27514, USA Center for Translational Cancer Research, Institute of Biosciences and Technology and Department of Medical Physiology, Texas A&M Health Science Center, 2121 W. Holcombe Boulevard, Houston, TX 77030, USA
| | - Jeff Hardin
- Graduate Program in Genetics, University of Wisconsin-Madison, 1117 W. Johnson Street, Madison, WI 53706, USA Department of Zoology, University of Wisconsin-Madison, 1117 W. Johnson Street, Madison, WI 53706, USA
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437
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Jajesniak P, Wong TS. QuickStep-Cloning: a sequence-independent, ligation-free method for rapid construction of recombinant plasmids. J Biol Eng 2015; 9:15. [PMID: 26388935 PMCID: PMC4574722 DOI: 10.1186/s13036-015-0010-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 07/21/2015] [Indexed: 11/16/2022] Open
Abstract
Background Molecular cloning is an essential step in biological engineering. Methods involving megaprimer-based PCR of a whole plasmid are promising alternatives to the traditional restriction-ligation-based molecular cloning. Their widespread use, however, is hampered by some of their inherent characteristics, e.g., linear amplification, use of self-annealing megaprimers and difficulty with performing point insertion of DNA. These limitations result in low product yield and reduced flexibility in the design of a genetic construct. Result Here, we present a novel technique of directional cloning, which overcomes these problems yet retaining the simplicity of whole-plasmid amplification. QuickStep-Cloning utilizes asymmetric PCRs to create a megaprimer pair with 3′-overhangs, and hence, facilitates the subsequent exponential whole-plasmid amplification. QuickStep-Cloning generates nicked-circular plasmids, thereby permitting direct bacterial transformation without DNA ligation. It allows DNA fragment integration into any plasmid at any position, in an efficient, time- and cost-effective manner, without tedious intermediate DNA gel purification, modified oligonucleotides, specialty enzymes and ultra-competent cells. The method is compatible with competent E. coli cells prepared using the conventional calcium chloride method. Conclusion QuickStep-Cloning expands the versatility of megaprimer-based cloning. It is an excellent addition to the cloning toolbox, for the benefit of protein engineers, metabolic engineers and synthetic biologists. Electronic supplementary material The online version of this article (doi:10.1186/s13036-015-0010-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pawel Jajesniak
- ChELSI Institute and Advanced Biomanufacturing Centre, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD UK
| | - Tuck Seng Wong
- ChELSI Institute and Advanced Biomanufacturing Centre, Department of Chemical and Biological Engineering, University of Sheffield, Mappin Street, Sheffield, S1 3JD UK
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438
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Molza AE, Mangat K, Le Rumeur E, Hubert JF, Menhart N, Delalande O. Structural Basis of Neuronal Nitric-oxide Synthase Interaction with Dystrophin Repeats 16 and 17. J Biol Chem 2015; 290:29531-41. [PMID: 26378238 DOI: 10.1074/jbc.m115.680660] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Indexed: 01/08/2023] Open
Abstract
Duchenne muscular dystrophy is a lethal genetic defect that is associated with the absence of dystrophin protein. Lack of dystrophin protein completely abolishes muscular nitric-oxide synthase (NOS) function as a regulator of blood flow during muscle contraction. In normal muscles, nNOS function is ensured by its localization at the sarcolemma through an interaction of its PDZ domain with dystrophin spectrin-like repeats R16 and R17. Early studies suggested that repeat R17 is the primary site of interaction but ignored the involved nNOS residues, and the R17 binding site has not been described at an atomic level. In this study, we characterized the specific amino acids involved in the binding site of nNOS-PDZ with dystrophin R16-17 using combined experimental biochemical and structural in silico approaches. First, 32 alanine-scanning mutagenesis variants of dystrophin R16-17 indicated the regions where mutagenesis modified the affinity of the dystrophin interaction with the nNOS-PDZ. Second, using small angle x-ray scattering-based models of dystrophin R16-17 and molecular docking methods, we generated atomic models of the dystrophin R16-17·nNOS-PDZ complex that correlated well with the alanine scanning identified regions of dystrophin. The structural regions constituting the dystrophin interaction surface involve the A/B loop and the N-terminal end of helix B of repeat R16 and the N-terminal end of helix A' and a small fraction of helix B' and a large part of the helix C' of repeat R17. The interaction surface of nNOS-PDZ involves its main β-sheet and its specific C-terminal β-finger.
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Affiliation(s)
- Anne-Elisabeth Molza
- From the Université de Rennes1, Campus Santé, 35043 Rennes, France, the Institut de Génétique et Développement de Rennes, IGDR, UMR CNRS 6290, Rennes, France, and
| | | | - Elisabeth Le Rumeur
- From the Université de Rennes1, Campus Santé, 35043 Rennes, France, the Institut de Génétique et Développement de Rennes, IGDR, UMR CNRS 6290, Rennes, France, and
| | - Jean-François Hubert
- From the Université de Rennes1, Campus Santé, 35043 Rennes, France, the Institut de Génétique et Développement de Rennes, IGDR, UMR CNRS 6290, Rennes, France, and
| | - Nick Menhart
- the Illinois Institute of Technology, Chicago, Illinois 60616
| | - Olivier Delalande
- From the Université de Rennes1, Campus Santé, 35043 Rennes, France, the Institut de Génétique et Développement de Rennes, IGDR, UMR CNRS 6290, Rennes, France, and
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439
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Afroz T, Luo ML, Beisel CL. Impact of Residual Inducer on Titratable Expression Systems. PLoS One 2015; 10:e0137421. [PMID: 26348036 PMCID: PMC4562711 DOI: 10.1371/journal.pone.0137421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 08/17/2015] [Indexed: 11/19/2022] Open
Abstract
Inducible expression systems are widely employed for the titratable control of gene expression, yet molecules inadvertently present in the growth medium or synthesized by the host cells can alter the response profile of some of these systems. Here, we explored the quantitative impact of these residual inducers on the apparent response properties of inducible systems. Using a simple mathematical model, we found that the presence of residual inducer shrinks the apparent dynamic range and causes the apparent Hill coefficient to converge to one. We also found that activating systems were more sensitive than repressing systems to the presence of residual inducer and the response parameters were most heavily dependent on the original Hill coefficient. Experimental interrogation of common titratable systems based on an L-arabinose inducible promoter or a thiamine pyrophosphate-repressing riboswitch in Escherichia coli confirmed the predicted trends. We finally found that residual inducer had a distinct effect on "all-or-none" systems, which exhibited increased sensitivity to the added inducer until becoming fully induced. Our findings indicate that residual inducer or repressor alters the quantitative response properties of titratable systems, impacting their utility for scientific discovery and pathway engineering.
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Affiliation(s)
- Taliman Afroz
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Michelle L Luo
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Chase L Beisel
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, United States of America
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440
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Abstract
The functionality of cellular membranes relies on the molecular order imparted by lipids. In eukaryotes, sterols such as cholesterol modulate membrane order, yet they are not typically found in prokaryotes. The structurally similar bacterial hopanoids exhibit similar ordering properties as sterols in vitro, but their exact physiological role in living bacteria is relatively uncharted. We present evidence that hopanoids interact with glycolipids in bacterial outer membranes to form a highly ordered bilayer in a manner analogous to the interaction of sterols with sphingolipids in eukaryotic plasma membranes. Furthermore, multidrug transport is impaired in a hopanoid-deficient mutant of the gram-negative Methylobacterium extorquens, which introduces a link between membrane order and an energy-dependent, membrane-associated function in prokaryotes. Thus, we reveal a convergence in the architecture of bacterial and eukaryotic membranes and implicate the biosynthetic pathways of hopanoids and other order-modulating lipids as potential targets to fight pathogenic multidrug resistance.
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441
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Kostylev M, Otwell AE, Richardson RE, Suzuki Y. Cloning Should Be Simple: Escherichia coli DH5α-Mediated Assembly of Multiple DNA Fragments with Short End Homologies. PLoS One 2015; 10:e0137466. [PMID: 26348330 PMCID: PMC4562628 DOI: 10.1371/journal.pone.0137466] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 08/17/2015] [Indexed: 11/18/2022] Open
Abstract
Numerous DNA assembly technologies exist for generating plasmids for biological studies. Many procedures require complex in vitro or in vivo assembly reactions followed by plasmid propagation in recombination-impaired Escherichia coli strains such as DH5α, which are optimal for stable amplification of the DNA materials. Here we show that despite its utility as a cloning strain, DH5α retains sufficient recombinase activity to assemble up to six double-stranded DNA fragments ranging in size from 150 bp to at least 7 kb into plasmids in vivo. This process also requires surprisingly small amounts of DNA, potentially obviating the need for upstream assembly processes associated with most common applications of DNA assembly. We demonstrate the application of this process in cloning of various DNA fragments including synthetic genes, preparation of knockout constructs, and incorporation of guide RNA sequences in constructs for clustered regularly interspaced short palindromic repeats (CRISPR) genome editing. This consolidated process for assembly and amplification in a widely available strain of E. coli may enable productivity gain across disciplines involving recombinant DNA work.
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Affiliation(s)
- Maxim Kostylev
- Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, La Jolla, California, United States of America
- * E-mail: (YS), (MK)
| | - Anne E. Otwell
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
| | - Ruth E. Richardson
- School of Civil and Environmental Engineering, Cornell University, Ithaca, New York, United States of America
| | - Yo Suzuki
- Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, La Jolla, California, United States of America
- * E-mail: (YS), (MK)
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442
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Growth-Phase-Specific Modulation of Cell Morphology and Gene Expression by an Archaeal Histone Protein. mBio 2015; 6:e00649-15. [PMID: 26350964 PMCID: PMC4600100 DOI: 10.1128/mbio.00649-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
In all three domains of life, organisms use nonspecific DNA-binding proteins to compact and organize the genome as well as to regulate transcription on a global scale. Histone is the primary eukaryotic nucleoprotein, and its evolutionary roots can be traced to the archaea. However, not all archaea use this protein as the primary DNA-packaging component, raising questions regarding the role of histones in archaeal chromatin function. Here, quantitative phenotyping, transcriptomic, and proteomic assays were performed on deletion and overexpression mutants of the sole histone protein of the hypersaline-adapted haloarchaeal model organism Halobacterium salinarum. This protein is highly conserved among all sequenced haloarchaeal species and maintains hallmark residues required for eukaryotic histone functions. Surprisingly, despite this conservation at the sequence level, unlike in other archaea or eukaryotes, H. salinarum histone is required to regulate cell shape but is not necessary for survival. Genome-wide expression changes in histone deletion strains were global, significant but subtle in terms of fold change, bidirectional, and growth phase dependent. Mass spectrometric proteomic identification of proteins from chromatin enrichments yielded levels of histone and putative nucleoid-associated proteins similar to those of transcription factors, consistent with an open and transcriptionally active genome. Taken together, these data suggest that histone in H. salinarum plays a minor role in DNA compaction but important roles in growth-phase-dependent gene expression and regulation of cell shape. Histone function in haloarchaea more closely resembles a regulator of gene expression than a chromatin-organizing protein like canonical eukaryotic histone. Histones comprise the major protein component of eukaryotic chromatin and are required for both genome packaging and global regulation of expression. The current paradigm maintains that archaea whose genes encode histone also use these proteins to package DNA. In contrast, here we demonstrate that the sole histone encoded in the genome of the salt-adapted archaeon Halobacterium salinarum is both unessential and unlikely to be involved in DNA compaction despite conservation of residues important for eukaryotic histones. Rather, H. salinarum histone is required for global regulation of gene expression and cell shape. These data are consistent with the hypothesis that H. salinarum histone, strongly conserved across all other known salt-adapted archaea, serves a novel role in gene regulation and cell shape maintenance. Given that archaea possess the ancestral form of eukaryotic histone, this study has important implications for understanding the evolution of histone function.
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443
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Affiliation(s)
- Kristin Hagen
- EA European Academy of Technology and Innovation Assessment GmbH, Bad Neuenahr-Ahrweiler, Germany
| | - Margret Engelhard
- EA European Academy of Technology and Innovation Assessment GmbH, Bad Neuenahr-Ahrweiler, Germany
| | - Georg Toepfer
- Center for Literary and Cultural Research Berlin, Berlin, Germany
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444
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Regulation of Telomere Length Requires a Conserved N-Terminal Domain of Rif2 in Saccharomyces cerevisiae. Genetics 2015; 201:573-86. [PMID: 26294668 PMCID: PMC4596670 DOI: 10.1534/genetics.115.177899] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 08/19/2015] [Indexed: 12/26/2022] Open
Abstract
The regulation of telomere length equilibrium is essential for cell growth and survival since critically short telomeres signal DNA damage and cell cycle arrest. While the broad principles of length regulation are well established, the molecular mechanism of how these steps occur is not fully understood. We mutagenized the RIF2 gene in Saccharomyces cerevisiae to understand how this protein blocks excess telomere elongation. We identified an N-terminal domain in Rif2 that is essential for length regulation, which we have termed BAT domain for Blocks Addition of Telomeres. Tethering this BAT domain to Rap1 blocked telomere elongation not only in rif2Δ mutants but also in rif1Δ and rap1C-terminal deletion mutants. Mutation of a single amino acid in the BAT domain, phenylalanine at position 8 to alanine, recapitulated the rif2Δ mutant phenotype. Substitution of F8 with tryptophan mimicked the wild-type phenylalanine, suggesting the aromatic amino acid represents a protein interaction site that is essential for telomere length regulation.
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445
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Alcohol Selectivity in a Synthetic Thermophilic n-Butanol Pathway Is Driven by Biocatalytic and Thermostability Characteristics of Constituent Enzymes. Appl Environ Microbiol 2015; 81:7187-200. [PMID: 26253677 DOI: 10.1128/aem.02028-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 07/29/2015] [Indexed: 02/06/2023] Open
Abstract
n-Butanol is generated as a natural product of metabolism by several microorganisms, but almost all grow at mesophilic temperatures. A synthetic pathway for n-butanol production from acetyl coenzyme A (acetyl-CoA) that functioned at 70°C was assembled in vitro from enzymes recruited from thermophilic bacteria to inform efforts for engineering butanol production into thermophilic hosts. Recombinant versions of eight thermophilic enzymes (β-ketothiolase [Thl], 3-hydroxybutyryl-CoA dehydrogenase [Hbd], and 3-hydroxybutyryl-CoA dehydratase [Crt] from Caldanaerobacter subterraneus subsp. tengcongensis; trans-2-enoyl-CoA reductase [Ter] from Spirochaeta thermophila; bifunctional acetaldehyde dehydrogenase/alcohol dehydrogenase [AdhE] from Clostridium thermocellum; and AdhE, aldehyde dehydrogenase [Bad], and butanol dehydrogenase [Bdh] from Thermoanaerobacter sp. strain X514) were utilized to examine three possible pathways for n-butanol. These pathways differed in the two steps required to convert butyryl-CoA to n-butanol: Thl-Hbd-Crt-Ter-AdhE (C. thermocellum), Thl-Hbd-Crt-Ter-AdhE (Thermoanaerobacter X514), and Thl-Hbd-Crt-Ter-Bad-Bdh. n-Butanol was produced at 70°C, but with different amounts of ethanol as a coproduct, because of the broad substrate specificities of AdhE, Bad, and Bdh. A reaction kinetics model, validated via comparison to in vitro experiments, was used to determine relative enzyme ratios needed to maximize n-butanol production. By using large relative amounts of Thl and Hbd and small amounts of Bad and Bdh, >70% conversion to n-butanol was observed in vitro, but with a 60% decrease in the predicted pathway flux. With more-selective hypothetical versions of Bad and Bdh, >70% conversion to n-butanol is predicted, with a 19% increase in pathway flux. Thus, more-selective thermophilic versions of Bad, Bdh, and AdhE are needed to fully exploit biocatalytic n-butanol production at elevated temperatures.
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446
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Meyer AJ, Garry DJ, Hall B, Byrom MM, McDonald HG, Yang X, Yin YW, Ellington AD. Transcription yield of fully 2'-modified RNA can be increased by the addition of thermostabilizing mutations to T7 RNA polymerase mutants. Nucleic Acids Res 2015. [PMID: 26209133 PMCID: PMC4551944 DOI: 10.1093/nar/gkv734] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
On average, mutations are deleterious to proteins. Mutations conferring new function to a protein often come at the expense of protein folding or stability, reducing overall activity. Over the years, a panel of T7 RNA polymerases have been designed or evolved to accept nucleotides with modified ribose moieties. These modified RNAs have proven useful, especially in vivo, but the transcriptional yields tend to be quite low. Here we show that mutations previously shown to increase the thermal tolerance of T7 RNA polymerase can increase the activity of mutants with expanded substrate range. The resulting polymerase mutants can be used to generate 2'-O-methyl modified RNA with yields much higher than enzymes currently employed.
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Affiliation(s)
- Adam J Meyer
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Daniel J Garry
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Bradley Hall
- Altermune Technologies, LLC, Irvine, CA 92606, USA
| | - Michelle M Byrom
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Hannah G McDonald
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Xu Yang
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Y Whitney Yin
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Andrew D Ellington
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA Center for Systems & Synthetic Biology, University of Texas at Austin, Austin, TX 78712, USA
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447
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Kushwaha M, Salis HM. A portable expression resource for engineering cross-species genetic circuits and pathways. Nat Commun 2015; 6:7832. [PMID: 26184393 PMCID: PMC4518296 DOI: 10.1038/ncomms8832] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 06/16/2015] [Indexed: 12/24/2022] Open
Abstract
Genetic circuits and metabolic pathways can be reengineered to allow organisms to process signals and manufacture useful chemicals. However, their functions currently rely on organism-specific regulatory parts, fragmenting synthetic biology and metabolic engineering into host-specific domains. To unify efforts, here we have engineered a cross-species expression resource that enables circuits and pathways to reuse the same genetic parts, while functioning similarly across diverse organisms. Our engineered system combines mixed feedback control loops and cross-species translation signals to autonomously self-regulate expression of an orthogonal polymerase without host-specific promoters, achieving nontoxic and tuneable gene expression in diverse Gram-positive and Gram-negative bacteria. Combining 50 characterized system variants with mechanistic modelling, we show how the cross-species expression resource's dynamics, capacity and toxicity are controlled by the control loops' architecture and feedback strengths. We also demonstrate one application of the resource by reusing the same genetic parts to express a biosynthesis pathway in both model and non-model hosts. Organism-specific genetic parts are often used to express circuits and pathways, limiting their portability. Here the authors engineer a cross-species expression resource, without using host-specific parts, to control protein and pathway expression in non-model bacteria.
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Affiliation(s)
- Manish Kushwaha
- Department of Biological Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Howard M Salis
- 1] Department of Biological Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA [2] Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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448
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Finnigan GC, Thorner J. Complex in vivo Ligation Using Homologous Recombination and High-efficiency Plasmid Rescue from Saccharomyces cerevisiae. Bio Protoc 2015; 5:e1521. [PMID: 26523287 DOI: 10.21769/bioprotoc.1521] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
The protocols presented here allow for the facile generation of a wide variety of complex multipart DNA constructs (tagged gene products, gene fusions, chimeric proteins, and other variants) using homologous recombination and in vivo ligation in budding yeast (Saccharomyces cerevisiae). This method is straightforward, efficient and cost-effective, and can be used both for vector creation and for subsequent one-step, high frequency integration into a chromosomal locus in yeast. The procedure utilizes PCR with extended oligonucleotide "tails" of homology between multiple fragments to allow for reassembly in yeast in a single transformation followed by a method for highly efficient plasmid extraction from yeast (for transformation into bacteria). The latter is an improvement on existing methods of yeast plasmid extraction, which, historically, has been a limiting step in recovery of desired constructs. We describe the utility and convenience of our techniques, and provide several examples.
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Affiliation(s)
- Gregory C Finnigan
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, USA
| | - Jeremy Thorner
- Division of Biochemistry, Biophysics and Structural Biology, Department of Molecular and Cell Biology, University of California, Berkeley, USA
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449
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Tangen U, Minero GAS, Sharma A, Wagler PF, Cohen R, Raz O, Marx T, Ben-Yehezkel T, McCaskill JS. DNA-library assembly programmed by on-demand nano-liter droplets from a custom microfluidic chip. BIOMICROFLUIDICS 2015. [PMID: 26221198 PMCID: PMC4499045 DOI: 10.1063/1.4926616] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Nanoscale synthetic biology can benefit from programmable nanoliter-scale processing of DNA in microfluidic chips if they are interfaced effectively to biochemical arrays such as microwell plates. Whereas active microvalve chips require complex fabrication and operation, we show here how a passive and readily fabricated microchip can be employed for customizable nanoliter scale pipetting and reaction control involving DNA. This recently developed passive microfluidic device, supporting nanoliter scale combinatorial droplet generation and mixing, is here used to generate a DNA test library with one member per droplet exported to addressed locations on microwell plates. Standard DNA assembly techniques, such as Gibson assembly, compatible with isothermal on-chip operation, are employed and checked using off-chip PCR and assembly PCR. The control of output droplet sequences and mixing performance was verified using dyes and fluorescently labeled DNA solutions, both on-chip and in external capillary channels. Gel electrophoresis of products and DNA sequencing were employed to further verify controlled combination and functional enzymatic assembly. The scalability of the results to larger DNA libraries is also addressed by combinatorial input expansion using sequential injection plugs from a multiwell plate. Hence, the paper establishes a proof of principle of the production of functional combinatorial mixtures at the nanoliter scale for one sequence per well DNA libraries.
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Affiliation(s)
- Uwe Tangen
- Faculty of Chemistry and Biochemistry, Microsystems Chemistry and BioIT (BioMIP), Ruhr-University Bochum , 44780 Bochum, Germany
| | - Gabriel Antonio S Minero
- Faculty of Chemistry and Biochemistry, Microsystems Chemistry and BioIT (BioMIP), Ruhr-University Bochum , 44780 Bochum, Germany
| | - Abhishek Sharma
- Faculty of Chemistry and Biochemistry, Microsystems Chemistry and BioIT (BioMIP), Ruhr-University Bochum , 44780 Bochum, Germany
| | - Patrick F Wagler
- Faculty of Chemistry and Biochemistry, Microsystems Chemistry and BioIT (BioMIP), Ruhr-University Bochum , 44780 Bochum, Germany
| | - Rafael Cohen
- Department of Biological Chemistry, Weizmann Institute of Science , Rehovot, Israel
| | - Ofir Raz
- Department of Biological Chemistry, Weizmann Institute of Science , Rehovot, Israel
| | - Tzipy Marx
- Department of Biological Chemistry, Weizmann Institute of Science , Rehovot, Israel
| | - Tuval Ben-Yehezkel
- Department of Biological Chemistry, Weizmann Institute of Science , Rehovot, Israel
| | - John S McCaskill
- Faculty of Chemistry and Biochemistry, Microsystems Chemistry and BioIT (BioMIP), Ruhr-University Bochum , 44780 Bochum, Germany
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450
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Tang H, Bao X, Shen Y, Song M, Wang S, Wang C, Hou J. Engineering protein folding and translocation improves heterologous protein secretion inSaccharomyces cerevisiae. Biotechnol Bioeng 2015; 112:1872-82. [DOI: 10.1002/bit.25596] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 03/11/2015] [Accepted: 03/16/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Hongting Tang
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
| | - Xiaoming Bao
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
| | - Yu Shen
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
| | - Meihui Song
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
| | - Shenghuan Wang
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
| | - Chengqiang Wang
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
| | - Jin Hou
- State Key Laboratory of Microbial Technology; Shandong University; Jinan 250100 China
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