201
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Yang G, Ding Y. Recent advances in biocatalyst discovery, development and applications. Bioorg Med Chem 2014; 22:5604-12. [DOI: 10.1016/j.bmc.2014.06.033] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 06/13/2014] [Accepted: 06/17/2014] [Indexed: 12/25/2022]
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202
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203
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Bornscheuer U, Buchholz K, Seibel J. Enzymatic degradation of (ligno)cellulose. Angew Chem Int Ed Engl 2014; 53:10876-93. [PMID: 25136976 DOI: 10.1002/anie.201309953] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Indexed: 11/06/2022]
Abstract
Glycoside-degrading enzymes play a dominant role in the biochemical conversion of cellulosic biomass into low-price biofuels and high-value-added chemicals. New insight into protein functions and substrate structures, the kinetics of recognition, and degradation events has resulted in a substantial improvement of our understanding of cellulose degradation.
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Affiliation(s)
- Uwe Bornscheuer
- Ernst-Moritz-Arndt-Universität Greifswald, Biotechnologie und Enzymkatalyse, Institut für Biochemie, Felix-Hausdorff-Strasse 4, 17487 Greifswald (Germany)
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204
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Bill A, Rosethorne EM, Kent TC, Fawcett L, Burchell L, van Diepen MT, Marelli A, Batalov S, Miraglia L, Orth AP, Renaud NA, Charlton SJ, Gosling M, Gaither LA, Groot-Kormelink PJ. High throughput mutagenesis for identification of residues regulating human prostacyclin (hIP) receptor expression and function. PLoS One 2014; 9:e97973. [PMID: 24886841 PMCID: PMC4041722 DOI: 10.1371/journal.pone.0097973] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 04/25/2014] [Indexed: 12/12/2022] Open
Abstract
The human prostacyclin receptor (hIP receptor) is a seven-transmembrane G protein-coupled receptor (GPCR) that plays a critical role in vascular smooth muscle relaxation and platelet aggregation. hIP receptor dysfunction has been implicated in numerous cardiovascular abnormalities, including myocardial infarction, hypertension, thrombosis and atherosclerosis. Genomic sequencing has discovered several genetic variations in the PTGIR gene coding for hIP receptor, however, its structure-function relationship has not been sufficiently explored. Here we set out to investigate the applicability of high throughput random mutagenesis to study the structure-function relationship of hIP receptor. While chemical mutagenesis was not suitable to generate a mutagenesis library with sufficient coverage, our data demonstrate error-prone PCR (epPCR) mediated mutagenesis as a valuable method for the unbiased screening of residues regulating hIP receptor function and expression. Here we describe the generation and functional characterization of an epPCR derived mutagenesis library compromising >4000 mutants of the hIP receptor. We introduce next generation sequencing as a useful tool to validate the quality of mutagenesis libraries by providing information about the coverage, mutation rate and mutational bias. We identified 18 mutants of the hIP receptor that were expressed at the cell surface, but demonstrated impaired receptor function. A total of 38 non-synonymous mutations were identified within the coding region of the hIP receptor, mapping to 36 distinct residues, including several mutations previously reported to affect the signaling of the hIP receptor. Thus, our data demonstrates epPCR mediated random mutagenesis as a valuable and practical method to study the structure-function relationship of GPCRs.
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Affiliation(s)
- Anke Bill
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Elizabeth M. Rosethorne
- Respiratory Disease Area, Novartis Institutes for Biomedical Research, Horsham, United Kingdom
| | - Toby C. Kent
- Respiratory Disease Area, Novartis Institutes for Biomedical Research, Horsham, United Kingdom
| | - Lindsay Fawcett
- Respiratory Disease Area, Novartis Institutes for Biomedical Research, Horsham, United Kingdom
| | - Lynn Burchell
- Respiratory Disease Area, Novartis Institutes for Biomedical Research, Horsham, United Kingdom
| | - Michiel T. van Diepen
- Respiratory Disease Area, Novartis Institutes for Biomedical Research, Horsham, United Kingdom
| | - Anthony Marelli
- Infectious Diseases, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Sergey Batalov
- Infectious Diseases, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Loren Miraglia
- Infectious Diseases, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Anthony P. Orth
- Infectious Diseases, Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Nicole A. Renaud
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Steven J. Charlton
- Respiratory Disease Area, Novartis Institutes for Biomedical Research, Horsham, United Kingdom
| | - Martin Gosling
- Respiratory Disease Area, Novartis Institutes for Biomedical Research, Horsham, United Kingdom
| | - L. Alex Gaither
- Developmental and Molecular Pathways, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Paul J. Groot-Kormelink
- Respiratory Disease Area, Novartis Institutes for Biomedical Research, Horsham, United Kingdom
- Musculoskeletal Disease Area, Novartis Institutes for Biomedical Research, Basel, Switzerland
- * E-mail:
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205
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Suzuki Y, Ito S, Otsuka K, Iwasawa E, Nakajima M, Yamaguchi I. Preparation of Functional Single-Chain Antibodies against Bioactive Gibberellins by Utilizing Randomly Mutagenized Phage-Display Libraries. Biosci Biotechnol Biochem 2014; 69:610-9. [PMID: 15784991 DOI: 10.1271/bbb.69.610] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Screening randomly mutagenized proteins displayed on a phage surface by biopanning is a powerful strategy to obtain evolved clones with improved properties such as higher stability and functionality. We utilized this method to overcome the problem that functional single-chain antibodies against active gibberellins, a class of plant hormones, can not be prepared by some of the conventional methods. Single-chain antibody libraries with random mutations were constructed from two independent anti-bioactive gibberellin monoclonal antibody lines in a phagemid vector, so that the mutagenized scFvs were expressed in a phage-displayed form upon helper phage infection. From both libraries, scFv clones with binding activity to GA(4) were successfully obtained by successive rounds of biopanning against BSA-GA(4), the original immunogen. The results are highly suggestive that this approach might be a general solution when a single-chain antibody does not show binding activity. We found further that a ribosomal frameshift to complement a nonsense mutation frequently occurred in an amber suppressor strain of E. coli TG1, resulting in the display of a functional antibody, while such a nonsense mutant failed to produce a soluble antibody in a non-amber suppressor strain. This result explains at least partly why single-chain antibodies are sometimes functional only in a phage-displayed form, not in a soluble form.
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Affiliation(s)
- Yoshihito Suzuki
- Department of Applied Biological Chemistry, The University of Tokyo, Japan.
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206
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Qadota H, Benian GM. An approach for exploring interaction between two proteins in vivo. Front Physiol 2014; 5:162. [PMID: 24808865 PMCID: PMC4010775 DOI: 10.3389/fphys.2014.00162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 04/08/2014] [Indexed: 01/13/2023] Open
Abstract
We describe a strategy for exploring the function of protein-protein interactions in striated muscle in vivo. We describe our experience using this strategy to study the interaction of UNC-112 (kindlin) with PAT-4 (integrin linked kinase). Random mutagenesis is used to generate a collection of mutants that are screened for lack of binding or gain of binding using a yeast 2-hybrid assay. The mutant proteins are then expressed in transgenic C. elegans to determine their ability to localize in the sarcomere. We emphasize two advantages of this strategy: (1) for studying the interaction of protein A with protein B, when protein A can interact with multiple proteins, and (2) it explores the function of an interaction rather than the absence of, or reduced level of, a protein as can be obtained with null mutants or knockdown by RNAi. We propose that this method can be generalized for studying the meaning of a protein-protein interaction in muscle for any system in which transgenic animals can be generated and their muscles can be imaged.
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Affiliation(s)
- Hiroshi Qadota
- Department of Pathology, Emory University Atlanta, GA, USA
| | - Guy M Benian
- Department of Pathology, Emory University Atlanta, GA, USA
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207
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Soo VWC, Cheng HY, Kwan BW, Wood TK. de novo synthesis of a bacterial toxin/antitoxin system. Sci Rep 2014; 4:4807. [PMID: 24797297 PMCID: PMC4010927 DOI: 10.1038/srep04807] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 04/10/2014] [Indexed: 12/14/2022] Open
Abstract
The prevalence of toxin/antitoxin (TA) systems in almost all genomes suggests they evolve rapidly. Here we show that an antitoxin from a type V system (GhoS, an endoribonuclease specific for the mRNA of the toxin GhoT) can be converted into a novel toxin (ArT) simply by adding two mutations. In contrast to GhoS, which increases growth, the new toxin ArT decreases growth dramatically in Escherichia coli. Transmission electron microscopy analysis revealed that the nucleoid in ArT-producing cells is concentrated and appears hollow. Whole-transcriptome profiling revealed ArT cleaves 50 additional transcripts, which shows that the endoribonuclease activity of GhoS has been broadened as it was converted to ArT. Furthermore, we evolved an antitoxin for the new toxin ArT from two unrelated antitoxin templates, the protein-based antitoxin MqsA and RNA-based antitoxin ToxI, and showed that the evolved MqsA and ToxI variants are able to counteract the toxicity of ArT. In addition, the de novo TA system was found to increase persistence, a phenotype commonly associated with TA systems. Therefore, toxins and antitoxins from disparate systems can be interconverted.
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Affiliation(s)
- Valerie W. C. Soo
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Hsin-Yao Cheng
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Brian W. Kwan
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Thomas K. Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
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208
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Kim JN, Kwon YM. Phenotypic characterization of Salmonella RyhB-1 mutations that modulate target regulation. Curr Microbiol 2014; 69:212-7. [PMID: 24691548 DOI: 10.1007/s00284-014-0572-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 02/08/2014] [Indexed: 01/30/2023]
Abstract
Recently, we reported the global regulatory roles of the two small RNAs in Salmonella typhimurium, ryhB-1 and ryhB-2. However, the genetic basis of the sRNA-target interactions remains unknown. To identify the nucleotides of RyhB-1 that are functionally important for its regulatory actions, we introduced random single-point mutations into ryhB-1 gene on the chromosome of Salmonella typhimurium carrying a sodB-lacZ translational fusion by an error-prone PCR method. We reasoned that mutants expressing variant RyhB-1 with weakened interaction with sodB transcript would produce a higher level of SodB when compared to wild type, leading to darker blue colonies on X-gal agar plates. Five mutants displaying a significant increase in β-galactosidase activity under the condition inducing RyhB-1 expression were isolated. Quantitative real-time PCR analysis showed that the expression levels of eight target mRNAs in these five mutants were significantly changed when compared to the parent strain. Interestingly, two mutations affected growth and cell survival under H2O2-stressed conditions. The results suggest that there are strong selective constraints against mutational changes in ryhB-1 gene sequence, leading to high levels of nucleotide conservation in ryhB-1 gene sequences among the genus of Salmonella.
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Affiliation(s)
- Jeong Nam Kim
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, 72701, USA,
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209
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Sommer B, Waege I, Pöllmann D, Seitz T, Thomm M, Sterner R, Hausner W. Activation of a chimeric Rpb5/RpoH subunit using library selection. PLoS One 2014; 9:e87485. [PMID: 24489922 PMCID: PMC3906176 DOI: 10.1371/journal.pone.0087485] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 12/29/2013] [Indexed: 11/19/2022] Open
Abstract
Rpb5 is a general subunit of all eukaryotic RNA polymerases which consists of a N-terminal and a C-terminal domain. The corresponding archaeal subunit RpoH contains only the conserved C-terminal domain without any N-terminal extensions. A chimeric construct, termed rp5H, which encodes the N-terminal yeast domain and the C-terminal domain from Pyrococcus furiosus is unable to complement the lethal phenotype of a yeast rpb5 deletion strain (Δrpb5). By applying a random mutagenesis approach we found that the amino acid exchange E197K in the C-terminal domain of the chimeric Rp5H, either alone or with additional exchanges in the N-terminal domain, leads to heterospecific complementation of the growth deficiency of Δrpb5. Moreover, using a recently described genetic system for Pyrococcus we could demonstrate that the corresponding exchange E62K in the archaeal RpoH subunit alone without the eukaryotic N-terminal extension was stable, and growth experiments indicated no obvious impairment in vivo. In vitro transcription experiments with purified RNA polymerases showed an identical activity of the wild type and the mutant Pyrococcus RNA polymerase. A multiple alignment of RpoH sequences demonstrated that E62 is present in only a few archaeal species, whereas the great majority of sequences within archaea and eukarya contain a positively charged amino acid at this position. The crystal structures of the Sulfolobus and yeast RNA polymerases show that the positively charged arginine residues in subunits RpoH and Rpb5 most likely form salt bridges with negatively charged residues from subunit RpoK and Rpb1, respectively. A similar salt bridge might stabilize the interaction of Rp5H-E197K with a neighboring subunit of yeast RNA polymerase and thus lead to complementation of Δrpb5.
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Affiliation(s)
- Bettina Sommer
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Ingrid Waege
- Institute of Microbiology and Archaea Center, University of Regensburg, Regensburg, Germany
| | - David Pöllmann
- Institute of Microbiology and Archaea Center, University of Regensburg, Regensburg, Germany
| | - Tobias Seitz
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
| | - Michael Thomm
- Institute of Microbiology and Archaea Center, University of Regensburg, Regensburg, Germany
| | - Reinhard Sterner
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, Regensburg, Germany
- * E-mail: (RS); (WH)
| | - Winfried Hausner
- Institute of Microbiology and Archaea Center, University of Regensburg, Regensburg, Germany
- * E-mail: (RS); (WH)
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210
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Olson KE, Dolan GF, Müller UF. In vivo evolution of a catalytic RNA couples trans-splicing to translation. PLoS One 2014; 9:e86473. [PMID: 24466112 PMCID: PMC3900562 DOI: 10.1371/journal.pone.0086473] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 12/09/2013] [Indexed: 12/17/2022] Open
Abstract
How does a non-coding RNA evolve in cells? To address this question experimentally we evolved a trans-splicing variant of the group I intron ribozyme from Tetrahymena over 21 cycles of evolution in E.coli cells. Sequence variation was introduced during the evolution by mutagenic and recombinative PCR, and increasingly active ribozymes were selected by their repair of an mRNA mediating antibiotic resistance. The most efficient ribozyme contained four clustered mutations that were necessary and sufficient for maximum activity in cells. Surprisingly, these mutations did not increase the trans-splicing activity of the ribozyme. Instead, they appear to have recruited a cellular protein, the transcription termination factor Rho, and facilitated more efficient translation of the ribozyme’s trans-splicing product. In addition, these mutations affected the expression of several other, unrelated genes. These results suggest that during RNA evolution in cells, four mutations can be sufficient to evolve new protein interactions, and four mutations in an RNA molecule can generate a large effect on gene regulation in the cell.
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Affiliation(s)
- Karen E. Olson
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Gregory F. Dolan
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
| | - Ulrich F. Müller
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
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211
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Abstract
The RNA world hypothesis describes a stage in the early evolution of life in which RNA served as genome and as the only genome-encoded catalyst. To test whether RNA world organisms could have used cyclic trimetaphosphate as an energy source, we developed an in vitro selection strategy for isolating ribozymes that catalyze the triphosphorylation of RNA 5′-hydroxyl groups with trimetaphosphate. Several active sequences were isolated, and one ribozyme was analyzed in more detail. The ribozyme was truncated to 96 nt, while retaining full activity. It was converted to a trans-format and reacted with rates of 0.16 min−1 under optimal conditions. The secondary structure appears to contain a four-helical junction motif. This study showed that ribozymes can use trimetaphosphate to triphosphorylate RNA 5′-hydroxyl groups and suggested that RNA world organisms could have used trimetaphosphate as their energy source.
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Affiliation(s)
- Janina E Moretti
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
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212
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Steemson JD, Baake M, Rakonjac J, Arcus VL, Liddament MT. Tracking molecular recognition at the atomic level with a new protein scaffold based on the OB-fold. PLoS One 2014; 9:e86050. [PMID: 24465865 PMCID: PMC3896448 DOI: 10.1371/journal.pone.0086050] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 12/05/2013] [Indexed: 11/19/2022] Open
Abstract
The OB-fold is a small, versatile single-domain protein binding module that occurs in all forms of life, where it binds protein, carbohydrate, nucleic acid and small-molecule ligands. We have exploited this natural plasticity to engineer a new class of non-immunoglobulin alternatives to antibodies with unique structural and biophysical characteristics. We present here the engineering of the OB-fold anticodon recognition domain from aspartyl tRNA synthetase taken from the thermophile Pyrobaculum aerophilum. For this single-domain scaffold we have coined the term OBody. Starting from a naïve combinatorial library, we engineered an OBody with 3 nM affinity for hen egg-white lysozyme, by optimising the affinity of a naïve OBody 11,700-fold over several affinity maturation steps, using phage display. At each maturation step a crystal structure of the engineered OBody in complex with hen egg-white lysozyme was determined, showing binding elements in atomic detail. These structures have given us an unprecedented insight into the directed evolution of affinity for a single antigen on the molecular scale. The engineered OBodies retain the high thermal stability of the parental OB-fold despite mutation of up to 22% of their residues. They can be expressed in soluble form and also purified from bacteria at high yields. They also lack disulfide bonds. These data demonstrate the potential of OBodies as a new scaffold for the engineering of specific binding reagents and provide a platform for further development of future OBody-based applications.
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Affiliation(s)
- John D. Steemson
- Department of Biological Sciences, University of Waikato, Hamilton, New Zealand
| | - Matthias Baake
- Department of Biological Sciences, University of Waikato, Hamilton, New Zealand
| | - Jasna Rakonjac
- Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand
| | - Vickery L. Arcus
- Department of Biological Sciences, University of Waikato, Hamilton, New Zealand
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213
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Improved activity and pH stability of E. coli ATCC 11105 penicillin acylase by error-prone PCR. Appl Microbiol Biotechnol 2014; 98:4467-77. [DOI: 10.1007/s00253-013-5476-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 12/13/2013] [Accepted: 12/15/2013] [Indexed: 11/27/2022]
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214
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Alemán F, Caballero F, Ródenas R, Rivero RM, Martínez V, Rubio F. The F130S point mutation in the Arabidopsis high-affinity K(+) transporter AtHAK5 increases K(+) over Na(+) and Cs(+) selectivity and confers Na(+) and Cs(+) tolerance to yeast under heterologous expression. FRONTIERS IN PLANT SCIENCE 2014; 5:430. [PMID: 25228905 PMCID: PMC4151339 DOI: 10.3389/fpls.2014.00430] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 08/13/2014] [Indexed: 05/20/2023]
Abstract
Potassium (K(+)) is an essential macronutrient required for plant growth, development and high yield production of crops. Members of group I of the KT/HAK/KUP family of transporters, such as HAK5, are key components for K(+) acquisition by plant roots at low external K(+) concentrations. Certain abiotic stress conditions such as salinity or Cs(+)-polluted soils may jeopardize plant K(+) nutrition because HAK5-mediated K(+) transport is inhibited by Na(+) and Cs(+). Here, by screening in yeast a randomly-mutated collection of AtHAK5 transporters, a new mutation in AtHAK5 sequence is identified that greatly increases Na(+) tolerance. The single point mutation F130S, affecting an amino acid residue conserved in HAK5 transporters from several species, confers high salt tolerance, as well as Cs(+) tolerance. This mutation increases more than 100-fold the affinity of AtHAK5 for K(+) and reduces the K i values for Na(+) and Cs(+), suggesting that the F130 residue may contribute to the structure of the pore region involved in K(+) binding. In addition, this mutation increases the V max for K(+). All this changes occur without increasing the amount of the AtHAK5 protein in yeast and support the idea that this residue is contributing to shape the selectivity filter of the AtHAK5 transporter.
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Affiliation(s)
| | | | | | | | | | - Francisco Rubio
- *Correspondence: Francisco Rubio, Centro de Edafología y Biología Aplicada del Segura-CSIC, Campus de Espinardo, 30100 Murcia, Spain e-mail:
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215
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Copp JN, Hanson-Manful P, Ackerley DF, Patrick WM. Error-prone PCR and effective generation of gene variant libraries for directed evolution. Methods Mol Biol 2014; 1179:3-22. [PMID: 25055767 DOI: 10.1007/978-1-4939-1053-3_1] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Any single-enzyme directed evolution strategy has two fundamental requirements: the need to efficiently introduce variation into a gene of interest and the need to create an effective library from those variants. Generation of a maximally diverse gene library is particularly important when employing nontargeted mutagenesis strategies such as error-prone PCR (epPCR), which seek to explore very large areas of sequence space. Here we present comprehensive protocols and tips for using epPCR to generate gene variants that exhibit a relatively balanced spectrum of mutations and for capturing as much diversity as possible through effective cloning of those variants. The detailed library preparation methods that we describe are generally applicable to any directed evolution strategy that uses restriction enzymes to clone gene variants into an expression plasmid.
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Affiliation(s)
- Janine N Copp
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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216
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Riaño-Umbarila L, Olamendi-Portugal T, Morelos-Juárez C, Gurrola GB, Possani LD, Becerril B. A novel human recombinant antibody fragment capable of neutralizing Mexican scorpion toxins. Toxicon 2013; 76:370-6. [DOI: 10.1016/j.toxicon.2013.09.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 08/08/2013] [Accepted: 09/12/2013] [Indexed: 11/24/2022]
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217
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Carlson HJ, Campbell RE. Circular permutated red fluorescent proteins and calcium ion indicators based on mCherry. Protein Eng Des Sel 2013; 26:763-72. [PMID: 24151339 DOI: 10.1093/protein/gzt052] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2023] Open
Abstract
Red fluorescent indicators for calcium ion (Ca(2+)) are preferable, relative to blue-shifted alternatives, for biological imaging applications due to the lower phototoxicity, lower autofluorescent background and deeper tissue penetration associated with longer wavelength light. Accordingly, we undertook the development of a genetically encoded Ca(2+) indicator based on the popular and widely utilized Discosoma-derived red fluorescent protein, mCherry. Starting from a promising but dimly fluorescent circular permutated variant of mCherry, we first engineered a 13-fold brighter variant (cp196V1.2) through directed evolution. This bright cp196V1.2 was then used as the scaffold for creation of eight distinct libraries of potential Ca(2+) indicators via permutation at different sites within the 7th and 10th β-strands, and fusion of calmodulin and M13 to the new termini. Screening of these libraries led to the conclusion that, consistent with previous investigations of homologous fluorescent proteins, the 146-145 site in β-strand 7 is the most promising permutation site for construction of useful Ca(2+) indicators. Further rounds of directed evolution ultimately led to an indicator that exhibits a 250% change in intrinsic brightness in response to Ca(2+) and an exceptionally high affinity (Kd = 6 nM) for Ca(2+).
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Affiliation(s)
- Haley J Carlson
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
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218
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Zhan T, Zhang K, Chen Y, Lin Y, Wu G, Zhang L, Yao P, Shao Z, Liu Z. Improving glyphosate oxidation activity of glycine oxidase from Bacillus cereus by directed evolution. PLoS One 2013; 8:e79175. [PMID: 24223901 PMCID: PMC3818420 DOI: 10.1371/journal.pone.0079175] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 09/20/2013] [Indexed: 11/18/2022] Open
Abstract
Glyphosate, a broad spectrum herbicide widely used in agriculture all over the world, inhibits 5-enolpyruvylshikimate-3-phosphate synthase in the shikimate pathway, and glycine oxidase (GO) has been reported to be able to catalyze the oxidative deamination of various amines and cleave the C-N bond in glyphosate. Here, in an effort to improve the catalytic activity of the glycine oxidase that was cloned from a glyphosate-degrading marine strain of Bacillus cereus (BceGO), we used a bacteriophage T7 lysis-based method for high-throughput screening of oxidase activity and engineered the gene encoding BceGO by directed evolution. Six mutants exhibiting enhanced activity toward glyphosate were screened from two rounds of error-prone PCR combined with site directed mutagenesis, and the beneficial mutations of the six evolved variants were recombined by DNA shuffling. Four recombinants were generated and, when compared with the wild-type BceGO, the most active mutant B3S1 showed the highest activity, exhibiting a 160-fold increase in substrate affinity, a 326-fold enhancement in catalytic efficiency against glyphosate, with little difference between their pH and temperature stabilities. The role of these mutations was explored through structure modeling and molecular docking, revealing that the Arg(51) mutation is near the active site and could be an important residue contributing to the stabilization of glyphosate binding, while the role of the remaining mutations is unclear. These results provide insight into the application of directed evolution in optimizing glycine oxidase function and have laid a foundation for the development of glyphosate-tolerant crops.
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Affiliation(s)
- Tao Zhan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Kai Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Yangyan Chen
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Yongjun Lin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Gaobing Wu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Lili Zhang
- Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, College of Life Science, Tarim University, Alar, Xinjiang, P. R. China
| | - Pei Yao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, the Third Institute of Oceanography, State Oceanic Administration, Xiamen, Fujian, P. R. China
| | - Ziduo Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
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219
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Amini ZN, Müller UF. Low selection pressure aids the evolution of cooperative ribozyme mutations in cells. J Biol Chem 2013; 288:33096-106. [PMID: 24089519 DOI: 10.1074/jbc.m113.511469] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Understanding the evolution of functional RNA molecules is important for our molecular understanding of biology. Here we tested experimentally how two evolutionary parameters, selection pressure and recombination, influenced the evolution of an evolving RNA population. This was done using four parallel evolution experiments that employed low or gradually increasing selection pressure, and recombination events either at the end or dispersed throughout the evolution. As model system, a trans-splicing group I intron ribozyme was evolved in Escherichia coli cells over 12 rounds of selection and amplification, including mutagenesis and recombination. The low selection pressure resulted in higher efficiency of the evolved ribozyme populations, whereas differences in recombination did not have a strong effect. Five mutations were responsible for the highest efficiency. The first mutation swept quickly through all four evolving populations, whereas the remaining four mutations accumulated later and more efficiently under low selection pressure. To determine why low selection pressure aided this evolution, all evolutionary intermediates between the wild type and the 5-mutation variant were constructed, and their activities at three different selection pressures were determined. The resulting fitness profiles showed a high cooperativity among the four late mutations, which can explain why high selection pressure led to inefficient evolution. These results show experimentally how low selection pressure can benefit the evolution of cooperative mutations in functional RNAs.
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Affiliation(s)
- Zhaleh N Amini
- From the Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093
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220
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Xie J, Zhao Y, Zhang H, Liu Z, Lu Z. Improving methyl parathion hydrolase to enhance its chlorpyrifos-hydrolysing efficiency. Lett Appl Microbiol 2013; 58:53-9. [PMID: 24010722 DOI: 10.1111/lam.12155] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 08/29/2013] [Accepted: 09/03/2013] [Indexed: 12/07/2022]
Abstract
UNLABELLED Methyl parathion hydrolase (MPH) can degrade a wide range of organophosphorus compounds, but its efficiency in hydrolysing chlorpyrifos, one of the most popular pesticides applied for crop protection, is much lower than that in hydrolysing the preferred substrate methyl parathion. In this study, random mutagenesis was adopted to improve MPH to enhance its efficiency in hydrolysing the poorly hydrolysed substrate chlorpyrifos. Rapid screening of the improved MPH variants was carried out using Bacillus subtilis WB800 secretory expression system to investigate the distribution of improved MPH variants based on the size of clear haloes as a result of chlorpyrifos hydrolysis. Four improved MPH variants were isolated, and one variant K3, in particular, showed a 5-fold increase in kcat value for chlorpyrifos hydrolysis. Furthermore, most of the MPH variants obtained in this study possessed enhanced thermostability and pH stability. The approaches adopted in this study could be extended to create other MPH variants with increased activity for hydrolysing other poorly hydrolysed substrates. SIGNIFICANCE AND IMPACT OF THE STUDY Chlorpyrifos is one of the toxic organophosphorus compounds (OP compounds) widely used for insecticides control. Water, soil and foodstuff have been contaminated seriously by chlorpyrifos in some areas. It is urgent to find effective methods to remove its contamination. This work contributes to improve methyl parathion hydrolase (MPH) to enhance its efficiency in hydrolysing the poorly hydrolysed substrate chlorpyrifos. Our study brings new insights for enzymatic strategy for the decontamination of toxic OP compounds.
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Affiliation(s)
- J Xie
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China; University of Chinese Academy of Sciences, Beijing, China
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221
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A C-terminal acidic domain regulates degradation of the transcriptional coactivator Bob1. Mol Cell Biol 2013; 33:4628-40. [PMID: 24061476 DOI: 10.1128/mcb.01590-12] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Bob1 (Obf-1 or OCA-B) is a 34-kDa transcriptional coactivator encoded by the Pou2af1 gene that is essential for normal B-cell development and immune responses in mice. During lymphocyte activation, Bob1 protein levels dramatically increase independently of mRNA levels, suggesting that the stability of Bob1 is regulated. We used a fluorescent protein-based reporter system to analyze protein stability in response to genetic and physiological perturbations and show that, while Bob1 degradation is proteasome mediated, it does not require ubiquitination of Bob1. Furthermore, degradation of Bob1 in B cells appears to be largely independent of the E3 ubiquitin ligase Siah. We propose a novel mechanism of Bob1 turnover in B cells, whereby an acidic region in the C terminus of Bob1 regulates the activity of degron signals elsewhere in the protein. Changes that make the C terminus more acidic, including tyrosine phosphorylation-mimetic mutations, stabilize the instable murine Bob1 protein, indicating that B cells may regulate Bob1 stability and activity via signaling pathways. Finally, we show that expressing a stable Bob1 mutant in B cells suppresses cell proliferation and induces changes in surface marker expression commonly seen during B-cell differentiation.
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222
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Gaj T, Sirk SJ, Barbas CF. Expanding the scope of site-specific recombinases for genetic and metabolic engineering. Biotechnol Bioeng 2013; 111:1-15. [PMID: 23982993 DOI: 10.1002/bit.25096] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 08/12/2013] [Accepted: 08/13/2013] [Indexed: 12/20/2022]
Abstract
Site-specific recombinases are tremendously valuable tools for basic research and genetic engineering. By promoting high-fidelity DNA modifications, site-specific recombination systems have empowered researchers with unprecedented control over diverse biological functions, enabling countless insights into cellular structure and function. The rigid target specificities of many sites-specific recombinases, however, have limited their adoption in fields that require highly flexible recognition abilities. As a result, intense effort has been directed toward altering the properties of site-specific recombination systems by protein engineering. Here, we review key developments in the rational design and directed molecular evolution of site-specific recombinases, highlighting the numerous applications of these enzymes across diverse fields of study.
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Affiliation(s)
- Thomas Gaj
- The Skaggs Institute for Chemical Biology and the Departments of Chemistry and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California, 92037
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223
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Abstract
Random PCR mutagenesis enables the rapid and inexpensive construction of a library of mutant genetic elements.
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Affiliation(s)
- Jessica S Dymond
- The High Throughput Biology Center and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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224
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Monzel C, Degreif-Dünnwald P, Gröpper C, Griesinger C, Unden G. The cytoplasmic PASC domain of the sensor kinase DcuS of Escherichia coli: role in signal transduction, dimer formation, and DctA interaction. Microbiologyopen 2013; 2:912-27. [PMID: 24039243 PMCID: PMC3892338 DOI: 10.1002/mbo3.127] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 07/31/2013] [Indexed: 01/05/2023] Open
Abstract
The cytoplasmic PASC domain of the fumarate responsive sensor kinase DcuS of Escherichia coli links the transmembrane to the kinase domain. PASC is also required for interaction with the transporter DctA serving as a cosensor of DcuS. Earlier studies suggested that PASC functions as a hinge and transmits the signal to the kinase. Reorganizing the PASC dimer interaction and, independently, removal of DctA, converts DcuS to the constitutive ON state (active without fumarate stimulation). ON mutants were categorized with respect to these two biophysical interactions and the functional state of DcuS: type I-ON mutations grossly reorganize the homodimer, and decrease interaction with DctA. Type IIA-ON mutations create the ON state without grossly reorganizing the homodimer, whereas interaction with DctA is decreased. The type IIB-ON mutations were neither in PASC/PASC, nor in DctA/DcuS interaction affected, similar to fumarate activated wild-typic DcuS. OFF mutations never affected dimer stability. The ON mutations provide novel mechanistic insight: PASC dimerization is essential to silence the kinase. Reorganizing the homodimer and its interaction with DctA activate the kinase. The study suggests a novel ON homo-dimer conformation (type IIB) and an OFF conformation for PASC. Type IIB-ON corresponds to the fumarate induced wild-type conformation, representing an interesting target for structural biology.
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Affiliation(s)
- Christian Monzel
- Institute for Microbiology and Wine Research, Johannes Gutenberg-University, Mainz, Germany
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225
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Gaytán P, Roldán-Salgado A. Elimination of redundant and stop codons during the chemical synthesis of degenerate oligonucleotides. Combinatorial testing on the chromophore region of the red fluorescent protein mKate. ACS Synth Biol 2013; 2:453-62. [PMID: 23654278 DOI: 10.1021/sb3001326] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although some strategies have been reported for the elimination of stop and redundant codons during the chemical synthesis of degenerate oligonucleotides, incorporating an expensive cocktail of 20 trimer-phosphoramidites is currently a commonly employed and straightforward approach. As an alternative option, we describe here a cheaper strategy based on standard monomer-phosphoramidites and a simplified resin-splitting procedure. The accurate division of the resin, containing the growing oligonucleotide, into four columns represents the key step in this approach. The synthesis of the degenerate codon NDT in column 1, loaded with 60% of the resin, produces 12 codons, while a degenerate codon VMA in column 2, loaded with 30% of the resin, produces 6 codons. Codons ATG and TGG, independently synthesized in columns 3 and 4, respectively, and loaded with 5% each, completes the 20 different codons. The experimental frequency of each mutant codon in the library was assessed by randomizing 12 contiguous codons that encode for amino acids located in the chromophore region of the enhanced red fluorescent protein mKate-S158A. Furthermore, randomization of three contiguous codons that encode for the amino acids Phe62, Met63, and Tyr64, which are equivalent to Phe64, Ser65, and Tyr66 in GFP, gave rise to some red and golden yellow fluorescent mutants displaying interesting phenotypes and spectroscopic properties. The absorption and emission spectra of two of these mutants also suggested that the complete maturation of the red and golden yellow chromophores in mKate proceeds via the formation of a green-type chromophore and a cyan-type chromophore, respectively.
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Affiliation(s)
- Paul Gaytán
- Instituto de Biotecnología-Universidad Nacional Autónoma de México, Ap. Postal 510-3 Cuernavaca, Morelos 62250, México.
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226
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Structural and functional studies on the interaction of adenovirus fiber knobs and desmoglein 2. J Virol 2013; 87:11346-62. [PMID: 23946456 DOI: 10.1128/jvi.01825-13] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Human adenovirus (Ad) serotypes Ad3, Ad7, Ad11, and Ad14, as well as a recently emerged strain of Ad14 (Ad14p1), use the epithelial junction protein desmoglein 2 (DSG2) as a receptor for infection. Unlike Ad interaction with CAR and CD46, structural details for Ad binding to DSG2 are still elusive. Using an approach based on Escherichia coli expression libraries of random Ad3 and Ad14p1 fiber knob mutants, we identified amino acid residues that, when mutated individually, ablated or reduced Ad knob binding to DSG2. These residues formed three clusters inside one groove at the extreme distal end of the fiber knob. The Ad3 fiber knob mutant library was also used to identify variants with increased affinity to DSG2. We found a number of mutations within or near the EF loop of the Ad3 knob that resulted in affinities to DSG2 that were several orders of magnitude higher than those to the wild-type Ad3 knob. Crystal structure analysis of one of the mutants showed that the introduced mutations make the EF loop more flexible, which might facilitate the interaction with DSG2. Our findings have practical relevance for cancer therapy. We have recently reported that an Ad3 fiber knob-containing recombinant protein (JO-1) is able to trigger opening of junctions between epithelial cancer cells which, in turn, greatly improved the intratumoral penetration and efficacy of therapeutic agents (I. Beyer, et al., Clin. Cancer Res. 18:3340-3351, 2012; I. Beyer, et al., Cancer Res. 71:7080-7090, 2011). Here, we show that affinity-enhanced versions of JO-1 are therapeutically more potent than the parental protein in a series of cancer models.
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227
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Nov Y, Fulton A, Jaeger KE. Optimal scanning of all single-point mutants of a protein. J Comput Biol 2013; 20:990-7. [PMID: 23859465 DOI: 10.1089/cmb.2013.0026] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In protein engineering, useful information may be gained from systematically generating and screening all single-point mutants of a given protein. We model and analyze an iterative two-stage procedure to generate all these mutants. At each position, L variants are generated in the first stage via saturation mutagenesis and are sequenced. In the second stage, the missing variants (out of the 19 possible single-point substitutions) are produced via site-directed mutagenesis. We study the economic tradeoff associated with varying L, and derive its optimal value given the experimental parameters.
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Affiliation(s)
- Yuval Nov
- 1 Department of Statistics, University of Haifa , Haifa, Israel
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228
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Gloeckner C, Kranaster R, Marx A. Directed evolution of DNA polymerases: construction and screening of DNA polymerase mutant libraries. ACTA ACUST UNITED AC 2013; 2:89-109. [PMID: 23836552 DOI: 10.1002/9780470559277.ch090183] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The protocols in this article describe the construction of a mutant DNA polymerase library using error-prone PCR (epPCR) as a method for gene randomization, followed by screening of the library using two different approaches. The examples described use an N-terminally truncated form of the thermostable DNA polymerase I of Thermus aquaticus (Taq DNA polymerase), namely Klentaq (KTQ), and protocols are included for the identification of variants with (1) increased DNA lesion-bypass ability and (2) enhanced selectivity for DNA match/mismatch recognition. The screening assays are based on double-stranded DNA detection (using SYBR Green I) which can be carried out using standard laboratory equipment. The described assays are designed for use in a 384-well plate format to increase screening throughput and reduce material costs. For improved accuracy and ease of liquid handling, the use of an automated liquid handling device is recommended. Curr. Protoc. Chem Biol. 2:89-109. © 2010 by John Wiley & Sons, Inc.
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229
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Gu H, Furukawa K, Weinberg Z, Berenson DF, Breaker RR. Small, highly active DNAs that hydrolyze DNA. J Am Chem Soc 2013; 135:9121-9. [PMID: 23679108 PMCID: PMC3763483 DOI: 10.1021/ja403585e] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
DNA phosphoester bonds are exceedingly resistant to hydrolysis in the absence of chemical or enzymatic catalysts. This property is particularly important for organisms with large genomes, as resistance to hydrolytic degradation permits the long-term storage of genetic information. Here we report the creation and analysis of two classes of engineered deoxyribozymes that selectively and rapidly hydrolyze DNA. Members of class I deoxyribozymes carry a catalytic core composed of only 15 conserved nucleotides and attain an observed rate constant (k(obs)) of ~1 min(-1) when incubated near neutral pH in the presence of Zn(2+). Natural DNA sequences conforming to the class I consensus sequence and structure were found that undergo hydrolysis under selection conditions (2 mM Zn(2+), pH 7), which demonstrates that the inherent structure of certain DNA regions might promote catalytic reactions, leading to genomic instability.
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Affiliation(s)
- Hongzhou Gu
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, 06520 United States
- Howard Hughes Medical Institute, New Haven, Connecticut, 06520 United States
| | - Kazuhiro Furukawa
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, 06520 United States
| | - Zasha Weinberg
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, 06520 United States
- Howard Hughes Medical Institute, New Haven, Connecticut, 06520 United States
| | - Daniel F. Berenson
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520 United States
| | - Ronald R. Breaker
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, 06520 United States
- Howard Hughes Medical Institute, New Haven, Connecticut, 06520 United States
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520 United States
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230
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Arab-Jaziri F, Bissaro B, Dion M, Saurel O, Harrison D, Ferreira F, Milon A, Tellier C, Fauré R, O’Donohue MJ. Engineering transglycosidase activity into a GH51 α-l-arabinofuranosidase. N Biotechnol 2013; 30:536-44. [DOI: 10.1016/j.nbt.2013.04.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 04/12/2013] [Accepted: 04/13/2013] [Indexed: 11/17/2022]
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231
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Wang Z, Wang HY, Feng H. A simple and reproducible method for directed evolution: combination of random mutation with dITP and DNA fragmentation with endonuclease V. Mol Biotechnol 2013; 53:49-54. [PMID: 22351430 DOI: 10.1007/s12033-012-9516-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
An alternative method to combine mutagenesis PCR with dITP and fragmentation by endonuclease V for directed evolution was developed. In comparison to the routine protocol for directed evolution, dITP was used as mutation reagent in the mutagenesis PCR. Subsequently, the incorporated dITP in the PCR products could represent as being the target of endonuclease V. Finally, the mutated dsDNA was fragmented by endonuclease V and then shuffled via assembly and reamplification as is usually done. In this study, the gene encoding kanamycin resistance has been used as reporter to verify the novel method for directed evolution. However, the mutation frequency could be easily adjusted by the amount of dITP used in the mutagenesis PCR reaction. Besides, this protocol yielded the mutation types with an obvious bias to transition substitutions as the normal error-prone PCR did. Conclusively, this novel method for directed evolution has been demonstrated to be efficient, reproducible, and easy to handle in actual practice. Using this protocol, we have successfully constructed a random mutation library for the gene encoding a serine alkaline protease.
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Affiliation(s)
- Zun Wang
- The Key Laboratory for Bio-resources and Eco-Environment of Ministry of Education, The Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, 29, Wangjiang Rd, Chengdu, 610064 Sichuan, People's Republic of China
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232
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Le Y, Chen H, Zagursky R, Wu JHD, Shao W. Thermostable DNA ligase-mediated PCR production of circular plasmid (PPCP) and its application in directed evolution via in situ error-prone PCR. DNA Res 2013; 20:375-82. [PMID: 23633530 PMCID: PMC3738163 DOI: 10.1093/dnares/dst016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Polymerase chain reaction (PCR) is a powerful method to produce linear DNA fragments. Here we describe the Tma thermostable DNA ligase-mediated PCR production of circular plasmid (PPCP) and its application in directed evolution via in situ error-prone PCR. In this thermostable DNA ligase-mediated whole-plasmid amplification method, the resultant DNA nick between the 5′ end of the PCR primer and the extended newly synthesized DNA 3′ end of each PCR cycle is ligated by Tma DNA ligase, resulting in circular plasmid DNA product that can be directly transformed. The template plasmid DNA is eliminated by ‘selection marker swapping’ upon transformation. When performed under an error-prone condition with Taq DNA polymerase, PPCP allows one-step construction of mutagenesis libraries based on in situ error-prone PCR so that random mutations are introduced into the target gene without altering the expression vector plasmid. A significant difference between PPCP and previously published methods is that PPCP allows exponential amplification of circular DNA. We used this method to create random mutagenesis libraries of a xylanase gene and two cellulase genes. Screening of these libraries resulted in mutant proteins with desired properties, demonstrating the usefulness of in situ error-prone PPCP for creating random mutagenesis libraries for directed evolution.
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Affiliation(s)
- Yilin Le
- Biofuels Institute, School of Environment, Jiangsu University, Zhenjiang, Jiangsu 212013, PR China
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233
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Holmqvist E, Reimegård J, Wagner EGH. Massive functional mapping of a 5'-UTR by saturation mutagenesis, phenotypic sorting and deep sequencing. Nucleic Acids Res 2013; 41:e122. [PMID: 23609548 PMCID: PMC3695526 DOI: 10.1093/nar/gkt267] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We present here a method that enables functional screening of large number of mutations in a single experiment through the combination of random mutagenesis, phenotypic cell sorting and high-throughput sequencing. As a test case, we studied post-transcriptional gene regulation of the bacterial csgD messenger RNA, which is regulated by a small RNA (sRNA). A 109 bp sequence within the csgD 5′-UTR, containing all elements for expression and sRNA-dependent control, was mutagenized close to saturation. We monitored expression from a translational gfp fusion and collected fractions of cells with distinct expression levels by fluorescence-activated cell sorting. Deep sequencing of mutant plasmids from cells in different activity-sorted fractions identified functionally important positions in the messenger RNA that impact on intrinsic (translational activity per se) and extrinsic (sRNA-based) gene regulation. The results obtained corroborate previously published data. In addition to pinpointing nucleotide positions that change expression levels, our approach also reveals mutations that are silent in terms of gene expression and/or regulation. This method provides a simple and informative tool for studies of regulatory sequences in RNA, in particular addressing RNA structure–function relationships (e.g. sRNA-mediated control, riboswitch elements). However, slight protocol modifications also permit mapping of functional DNA elements and functionally important regions in proteins.
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Affiliation(s)
- Erik Holmqvist
- Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, SciLifeLab Uppsala, Box 596, S-75124 Uppsala, Sweden
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234
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Dibenedetto S, Cluet D, Stebe PN, Baumle V, Léault J, Terreux R, Bickle M, Chassey BDE, Mikaelian I, Colas P, Spichty M, Zoli M, Rudkin BB. Calcineurin A versus NS5A-TP2/HD domain containing 2: a case study of site-directed low-frequency random mutagenesis for dissecting target specificity of peptide aptamers. Mol Cell Proteomics 2013; 12:1939-52. [PMID: 23579184 PMCID: PMC3708177 DOI: 10.1074/mcp.m112.024612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We previously identified a peptide aptamer (named R5G42) via functional selection for its capacity to slow cell proliferation. A yeast two-hybrid screen of human cDNA libraries, using R5G42 as “bait,” allowed the identification of two binding proteins with very different functions: calcineurin A (CnA) (PP2B/PPP3CA), a protein phosphatase well characterized for its role in the immune response, and NS5A-TP2/HD domain containing 2, a much less studied protein induced subsequent to hepatitis C virus non-structural protein 5A expression in HepG2 hepatocellular carcinoma cells, with no known activity. Our objective in the present study was to dissect the dual target specificity of R5G42 in order to have tools with which to better characterize the actions of the peptide aptamers toward their individual targets. This was achieved through the selection of random mutants of the variable loop, derived from R5G42, evaluating their specificity toward CnA and NS5A-TP2 and analyzing their sequence. An interdisciplinary approach involving biomolecular computer simulations with integration of the sequence data and yeast two-hybrid binding phenotypes of these mutants yielded two structurally distinct conformers affording the potential molecular basis of the binding diversity of R5G42. Evaluation of the biological impact of CnA- versus NS5A-TP2-specific peptide aptamers indicated that although both contributed to the anti-proliferative effect of R5G42, CnA-binding was essential to stimulate the nuclear translocation of nuclear factor of activated T cells, indicative of the activation of endogenous CnA. By dissecting the target specificity of R5G42, we have generated novel tools with which to study each target individually. Apta-C8 is capable of directly activating CnA independent of binding to NS5A-TP2 and will be an important tool in studying the role of CnA activation in the regulation of different signaling pathways, whereas Apta-E1 will allow dissection of the function of NS5A-TP2, serving as an example of the usefulness of peptide aptamer technology for investigating signaling pathways.
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Affiliation(s)
- Silvia Dibenedetto
- Differentiation & Cell Cycle Group, Laboratoire de Biologie Moléculaire de la Cellule, UMR5239, Centre National pour la Recherche Scientifique (CNRS), Ecole Normale Supérieure de Lyon, Université Lyon 1, Lyon, France
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235
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Burak E, Yogev O, Sheffer S, Schueler-Furman O, Pines O. Evolving dual targeting of a prokaryotic protein in yeast. Mol Biol Evol 2013; 30:1563-73. [PMID: 23462316 DOI: 10.1093/molbev/mst039] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Dual targeting is an important and abundant phenomenon. Indeed, we estimate that more than a third of the yeast mitochondrial proteome is dual localized. The enzyme fumarase is a highly conserved protein in all organisms with respect to its sequence, structure, and enzymatic activity. In eukaryotes, it is dual localized to the cytosol and mitochondria. In Saccharomyces cerevisiae, the dual localization of fumarase is achieved by the reverse translocation mechanism; all fumarase molecules harbor a mitochondrial targeting sequence (MTS), are targeted to mitochondria, begin their translocation, and are processed by mitochondrial processing peptidase in the matrix. A subset of these processed fumarase molecules in transit is then fully imported into the matrix, whereas the majority moves back into the cytosol by reverse translocation. The proposed driving force for fumarase distribution is protein folding during import. Here, we asked how reverse translocation could have evolved on a prokaryotic protein that had already acquired expression from the nuclear genome and a targeting sequence. To address this question, we used, as a model, the Escherichia coli FumC Class II fumarase, which is homologous to eukaryotic fumarases (∼58% identity and ∼74% similarity to the yeast Fum1). Starting with an exclusively mitochondrial targeted FumC (attached to a strong MTS), we show that two randomly acquired mutations within the prokaryotic FumC sequence are sufficient to cause substantial dual targeting by reverse translocation. In fact, the unmutated MTS-FumC also has some ability to be dual targeted but only at low temperatures. Our results suggest that in this case, evolution of dual targeting by reverse translocation is based on naturally occurring and fortuitously conserved features of fumarase folding.
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Affiliation(s)
- Efrat Burak
- Department of Microbiology Molecular Genetics, IMRIC, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
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236
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Bouquier N, Fromont S, Debant A, Schmidt S. Random mutagenesis of peptide aptamers as an optimization strategy for inhibitor screening. Methods Mol Biol 2013; 928:97-118. [PMID: 22956136 DOI: 10.1007/978-1-62703-008-3_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
Accumulating work over the past decade has shown that peptide aptamer screening represents a valid strategy for inhibitor identification that can be applied to a variety of different targets. Because of the screening method in cells and the highly combinatorial libraries available, this approach yields rapidly highly specific candidate inhibitors. Once a hit peptide has been identified, its interaction strength and affinity towards its target protein can be optimized even more, in order to increase its inhibition efficiency when subsequently applied in vivo. A condition to a successful optimization is that gain of inhibition strength should not result in loss of specificity. Here we present a simple method for peptide aptamer optimization, which can be achieved by PCR-based random mutagenesis combined with a selection screen in yeast using a strong selective drug. The rationale of this approach, which has proven valid and efficient, is that stronger interaction in yeast will also lead to stronger inhibition. Our optimization method is effective, without loss of specificity, which is of a great importance for the discovery of inhibitors that target specific protein-protein interactions.
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Affiliation(s)
- Nathalie Bouquier
- Centre de Recherche de Biochimie Macromoléculaire, CNRS-UMR 5237, Universités Montpellier I et II, Montpellier Cedex, France
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237
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Construction and analysis of randomized protein-encoding libraries using error-prone PCR. Methods Mol Biol 2013; 996:251-67. [PMID: 23504429 DOI: 10.1007/978-1-62703-354-1_15] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In contrast to site-directed mutagenesis and rational design, directed evolution harnesses Darwinian principles to identify proteins with new or improved properties. The critical first steps in a directed evolution experiment are as follows: (a) to introduce random diversity into the gene of interest and (b) to capture that diversity by cloning the resulting population of molecules into a suitable expression vector, en bloc. Error-prone PCR (epPCR) is a common method for introducing random mutations into a gene. In this chapter, we describe detailed protocols for epPCR and for the construction of large, maximally diverse libraries of cloned variants. We also describe the utility of an online program, PEDEL-AA, for analyzing the compositions of epPCR libraries. The methods described here were used to construct several libraries in our laboratory. A side-by-side comparison of the results is used to show that, ultimately, epPCR is a highly stochastic process.
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238
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Protein Engineering as a Tool for the Development of Novel Bioproduction Systems. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 137:25-40. [DOI: 10.1007/10_2013_199] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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239
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Li M, Gan Z, Cui Y, Shi C, Shi X. Structure and function characterization of the phytoene desaturase related to the lutein biosynthesis in Chlorella protothecoides CS-41. Mol Biol Rep 2012; 40:3351-61. [PMID: 23271125 DOI: 10.1007/s11033-012-2410-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Accepted: 12/18/2012] [Indexed: 10/27/2022]
Abstract
Phytoene desaturase is the key enzyme involved in the biosynthesis pathway of lutein. The unicellular microalga, Chlorella protothecoides CS-41, had been selected for the heterotrophic production of high concentrations of lutein. In this study, a cDNA copy of the pds gene from C. protothecoides was obtained using the rapid amplification of cDNA ends (RACE) technique. Phylogenetic analysis of the deduced amino acid sequence revealed that the phytoene desaturases derived from the algal family. Expression of the pds gene in Escherichia coli produced a single protein of 61 kDa. The PDS activity of the expressed protein was confirmed by the production of ζ-carotene as the result from the action of the enzyme's desaturation activity, which was identified by high-performance liquid chromatography and heterologous complementation analysis. Using random and site-directed mutagenesis, a single amino acid mutation (N144D) was identified and confirmed. This mutant encodes an inactive enzyme, which implies that amino acid 144 is crutial to the activity of the PDS enzyme. Therefore, by gene cloning and expression in prokaryotic cells, the gene for ζ-carotene production or as part of the biosynthetic pathway of lutein had been characterized from Chlorella protothecoides CS-41.
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Affiliation(s)
- Meiya Li
- Department of Food Science & Technology, MOST-USDA Joint Research Center for Food Safety and Bor Luh Food Safety Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, People's Republic of China
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240
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Ruff AJ, Marienhagen J, Verma R, Roccatano D, Genieser HG, Niemann P, Shivange AV, Schwaneberg U. dRTP and dPTP a complementary nucleotide couple for the Sequence Saturation Mutagenesis (SeSaM) method. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.molcatb.2012.04.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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241
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Rodríguez-Rodríguez ER, Ledezma-Candanoza LM, Contreras-Ferrat LG, Olamendi-Portugal T, Possani LD, Becerril B, Riaño-Umbarila L. A Single Mutation in Framework 2 of the Heavy Variable Domain Improves the Properties of a Diabody and a Related Single-Chain Antibody. J Mol Biol 2012; 423:337-50. [DOI: 10.1016/j.jmb.2012.07.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 07/02/2012] [Accepted: 07/06/2012] [Indexed: 10/28/2022]
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242
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Hayden EJ, Weikert C, Wagner A. Directional selection causes decanalization in a group I ribozyme. PLoS One 2012; 7:e45351. [PMID: 23028955 PMCID: PMC3445466 DOI: 10.1371/journal.pone.0045351] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 08/14/2012] [Indexed: 11/19/2022] Open
Abstract
A canalized genotype is robust to environmental or genetic perturbations. Canalization is expected to result from stabilizing selection on a well-adapted phenotype. Decanalization, the loss of robustness, might follow periods of directional selection toward a new optimum. The evolutionary forces causing decanalization are still unknown, in part because it is difficult to determine the fitness effects of mutations in populations of organisms with complex genotypes and phenotypes. Here, we report direct experimental measurements of robustness in a system with a simple genotype and phenotype, the catalytic activity of an RNA enzyme. We find that the robustness of a population of RNA enzymes decreases during a period of directional selection in the laboratory. The decrease in robustness is primarily caused by the selective sweep of a genotype that is decanalized relative to the wild-type, both in terms of mutational robustness and environmental robustness (thermodynamic stability). Our results experimentally demonstrate that directional selection can cause decanalization on short time scales, and demonstrate co-evolution of mutational and environmental robustness.
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Affiliation(s)
- Eric J Hayden
- Department of Bioengineering, Stanford University, Stanford, California, United States of America.
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243
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Kumar A, Singh S. Directed evolution: tailoring biocatalysts for industrial applications. Crit Rev Biotechnol 2012; 33:365-78. [DOI: 10.3109/07388551.2012.716810] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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244
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Qadota H, Moerman DG, Benian GM. A molecular mechanism for the requirement of PAT-4 (integrin-linked kinase (ILK)) for the localization of UNC-112 (Kindlin) to integrin adhesion sites. J Biol Chem 2012; 287:28537-51. [PMID: 22761445 PMCID: PMC3436513 DOI: 10.1074/jbc.m112.354852] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 06/11/2012] [Indexed: 11/06/2022] Open
Abstract
Caenorhabditis elegans muscle cells attach to basement membrane through adhesion plaques. PAT-3 (β-integrin), UNC-112 (kindlin), and PAT-4 (integrin-linked kinase) are associated with these structures. Genetic analysis indicated that PAT-4 is required for UNC-112 to be properly localized. We investigated the molecular basis of this requirement. We show that the cytoplasmic tail of PAT-3 binds to full-length UNC-112 and that the N- and C-terminal halves of UNC-112 bind to each other. We demonstrate competition between the UNC-112 C-terminal half and PAT-4 for binding to the UNC-112 N-terminal half. The D382V mutation results in lack of binding to PAT-4 and lack of localization to adhesion structures. T346A or E349K mutations, which abolish interaction of the N- and C-terminal halves, permit D382V UNC-112 to localize to adhesion structures. The following model is proposed. UNC-112 exists in closed inactive and open active conformations, and upon binding of PAT-4 to the UNC-112 N-terminal half, UNC-112 is converted into the open state, able to bind to PAT-3.
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Affiliation(s)
- Hiroshi Qadota
- From the Department of Pathology, Emory University, Atlanta, Georgia 30322 and
- the Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Donald G. Moerman
- the Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Guy M. Benian
- From the Department of Pathology, Emory University, Atlanta, Georgia 30322 and
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245
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Kierny MR, Cunningham TD, Kay BK. Detection of biomarkers using recombinant antibodies coupled to nanostructured platforms. NANO REVIEWS 2012; 3:NANO-3-17240. [PMID: 22833780 PMCID: PMC3404449 DOI: 10.3402/nano.v3i0.17240] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 05/30/2012] [Accepted: 06/09/2012] [Indexed: 12/14/2022]
Abstract
The utility of biomarker detection in tomorrow's personalized health care field will mean early and accurate diagnosis of many types of human physiological conditions and diseases. In the search for biomarkers, recombinant affinity reagents can be generated to candidate proteins or post-translational modifications that differ qualitatively or quantitatively between normal and diseased tissues. The use of display technologies, such as phage-display, allows for manageable selection and optimization of affinity reagents for use in biomarker detection. Here we review the use of recombinant antibody fragments, such as scFvs and Fabs, which can be affinity-selected from phage-display libraries, to bind with both high specificity and affinity to biomarkers of cancer, such as Human Epidermal growth factor Receptor 2 (HER2) and Carcinoembryonic antigen (CEA). We discuss how these recombinant antibodies can be fabricated into nanostructures, such as carbon nanotubes, nanowires, and quantum dots, for the purpose of enhancing detection of biomarkers at low concentrations (pg/mL) within complex mixtures such as serum or tissue extracts. Other sensing technologies, which take advantage of 'Surface Enhanced Raman Scattering' (gold nanoshells), frequency changes in piezoelectric crystals (quartz crystal microbalance), or electrical current generation and sensing during electrochemical reactions (electrochemical detection), can effectively provide multiplexed platforms for detection of cancer and injury biomarkers. Such devices may soon replace the traditional time consuming ELISAs and Western blots, and deliver rapid, point-of-care diagnostics to market.
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Affiliation(s)
- Michael R Kierny
- Department of Biological Sciences, University of Illinois at Chicago (UIC), Chicago, IL, USA
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246
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Machado HB, Dekishima Y, Luo H, Lan EI, Liao JC. A selection platform for carbon chain elongation using the CoA-dependent pathway to produce linear higher alcohols. Metab Eng 2012; 14:504-11. [PMID: 22819734 DOI: 10.1016/j.ymben.2012.07.002] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 06/01/2012] [Accepted: 07/09/2012] [Indexed: 01/16/2023]
Abstract
Production of green chemicals and fuels using metabolically engineered organisms has been a promising alternative to petroleum-based production. Higher chain alcohols (C4-C8) are of interest because they can be used as chemical feedstock as well as fuels. Recently, the feasibility of n-hexanol synthesis using Escherichia coli has been demonstrated by extending the modified Clostridium CoA-dependent n-butanol synthesis pathway, thereby elongating carbon chain length via reactions in reversed β-oxidation, (or β-reduction). Here, we developed an anaerobic growth selection platform that allows selection or enrichment of enzymes for increased synthesis of C6 and C8 linear alcohols. Using this selection, we were able to improve the carbon flux towards the synthesis of C6 and C8 acyl-CoA intermediates. Replacement of the original enzyme Clostridium acetobutylicum Hbd with Ralstonia eutropha homologue PaaH1 increased production of n-hexanol by 10-fold. Further directed evolution by random mutagenesis of PaaH1 improved n-hexanol and n-octanol production. This anaerobic growth selection platform may be useful for selecting enzymes for production of long-chain alcohols and acids using this CoA-dependent pathway.
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Affiliation(s)
- Hidevaldo B Machado
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, 5531 Boelter Hall, Los Angeles, California 90095-1570, USA
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247
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Kipnis Y, Dellus-Gur E, Tawfik DS. TRINS: a method for gene modification by randomized tandem repeat insertions. Protein Eng Des Sel 2012; 25:437-44. [DOI: 10.1093/protein/gzs023] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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248
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Gröger H, Asano Y, Bornscheuer UT, Ogawa J. Development of biocatalytic processes in Japan and Germany: from research synergies to industrial applications. Chem Asian J 2012; 7:1138-53. [PMID: 22550022 DOI: 10.1002/asia.201200105] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Indexed: 11/09/2022]
Affiliation(s)
- Harald Gröger
- Faculty of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany.
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249
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One- plus two-hybrid system for the efficient selection of missense mutant alleles defective in protein-protein interactions. Methods Mol Biol 2012. [PMID: 22218862 DOI: 10.1007/978-1-61779-455-1_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2025]
Abstract
In an effort to develop a method for the high-throughput analysis of protein interaction interfaces, we devised a novel yeast genetic screening method, termed the "one- plus two-hybrid system," which efficiently selects specific missense mutations that disrupt known protein-protein interactions. This system modifies the standard yeast two-hybrid system to allow the operation of dual reporter systems within the same cell. The one-hybrid screening system is used first to positively select intact prey proteins, harboring informative missense mutations, from a large library of randomly generated mutant alleles. Next, among the isolated missense mutants of the prey proteins, interaction-defective mutants for a given protein (bait) are selected using the two-hybrid screening system. As a validation of the feasibility of this method, we utilized this technique to rapidly characterize the molecular determinants of the interactions between vitamin D receptor and its transcriptional coactivator protein, thyroid hormone receptor-associated protein 220. This efficient and rapid method should prove useful in the systematic analysis of large numbers of interaction interfaces.
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250
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Redesigning the NEDD8 pathway with a bacterial genetic screen for ubiquitin-like molecule transfer. J Mol Biol 2012; 418:161-6. [PMID: 22391419 DOI: 10.1016/j.jmb.2012.02.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 02/22/2012] [Accepted: 02/24/2012] [Indexed: 11/20/2022]
Abstract
Pathways of ubiquitin-like (UBL) molecule transfer regulate a myriad of cellular cascades. Here, we report a high-throughput assay that correlates catalytic human NEDD8 transfer to bacterial survival. The assay was utilized to screen mutant NEDD8 and NAE (NEDD8-activating enzyme) libraries to engineer a more stable NEDD8 and redesign the NEDD8-NAE interface. This approach will be useful in understanding the specificities underlying UBL pathways.
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