1
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Yang Y, Braga MV, Dean MD. Insertion-Deletion Events Are Depleted in Protein Regions with Predicted Secondary Structure. Genome Biol Evol 2024; 16:evae093. [PMID: 38735759 PMCID: PMC11102076 DOI: 10.1093/gbe/evae093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/16/2024] [Accepted: 04/21/2024] [Indexed: 05/14/2024] Open
Abstract
A fundamental goal in evolutionary biology and population genetics is to understand how selection shapes the fate of new mutations. Here, we test the null hypothesis that insertion-deletion (indel) events in protein-coding regions occur randomly with respect to secondary structures. We identified indels across 11,444 sequence alignments in mouse, rat, human, chimp, and dog genomes and then quantified their overlap with four different types of secondary structure-alpha helices, beta strands, protein bends, and protein turns-predicted by deep-learning methods of AlphaFold2. Indels overlapped secondary structures 54% as much as expected and were especially underrepresented over beta strands, which tend to form internal, stable regions of proteins. In contrast, indels were enriched by 155% over regions without any predicted secondary structures. These skews were stronger in the rodent lineages compared to the primate lineages, consistent with population genetic theory predicting that natural selection will be more efficient in species with larger effective population sizes. Nonsynonymous substitutions were also less common in regions of protein secondary structure, although not as strongly reduced as in indels. In a complementary analysis of thousands of human genomes, we showed that indels overlapping secondary structure segregated at significantly lower frequency than indels outside of secondary structure. Taken together, our study shows that indels are selected against if they overlap secondary structure, presumably because they disrupt the tertiary structure and function of a protein.
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Affiliation(s)
- Yi Yang
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Matthew V Braga
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Matthew D Dean
- Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
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2
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Miton CM, Tokuriki N. Insertions and Deletions (Indels): A Missing Piece of the Protein Engineering Jigsaw. Biochemistry 2023; 62:148-157. [PMID: 35830609 DOI: 10.1021/acs.biochem.2c00188] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Over the years, protein engineers have studied nature and borrowed its tricks to accelerate protein evolution in the test tube. While there have been considerable advances, our ability to generate new proteins in the laboratory is seemingly limited. One explanation for these shortcomings may be that insertions and deletions (indels), which frequently arise in nature, are largely overlooked during protein engineering campaigns. The profound effect of indels on protein structures, by way of drastic backbone alterations, could be perceived as "saltation" events that bring about significant phenotypic changes in a single mutational step. Should we leverage these effects to accelerate protein engineering and gain access to unexplored regions of adaptive landscapes? In this Perspective, we describe the role played by indels in the functional diversification of proteins in nature and discuss their untapped potential for protein engineering, despite their often-destabilizing nature. We hope to spark a renewed interest in indels, emphasizing that their wider study and use may prove insightful and shape the future of protein engineering by unlocking unique functional changes that substitutions alone could never achieve.
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Affiliation(s)
- Charlotte M Miton
- Michael Smith Laboratories, University of British Columbia, Vancouver, V6T 1Z4 BC, Canada
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, V6T 1Z4 BC, Canada
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3
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Savino S, Desmet T, Franceus J. Insertions and deletions in protein evolution and engineering. Biotechnol Adv 2022; 60:108010. [PMID: 35738511 DOI: 10.1016/j.biotechadv.2022.108010] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 11/17/2022]
Abstract
Protein evolution or engineering studies are traditionally focused on amino acid substitutions and the way these contribute to fitness. Meanwhile, the insertion and deletion of amino acids is often overlooked, despite being one of the most common sources of genetic variation. Recent methodological advances and successful engineering stories have demonstrated that the time is ripe for greater emphasis on these mutations and their understudied effects. This review highlights the evolutionary importance and biotechnological relevance of insertions and deletions (indels). We provide a comprehensive overview of approaches that can be employed to include indels in random, (semi)-rational or computational protein engineering pipelines. Furthermore, we discuss the tolerance to indels at the structural level, address how domain indels can link the function of unrelated proteins, and feature studies that illustrate the surprising and intriguing potential of frameshift mutations.
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Affiliation(s)
- Simone Savino
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Tom Desmet
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Jorick Franceus
- Centre for Synthetic Biology (CSB), Department of Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium..
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4
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Mendoza Rengifo E, Stelmastchuk Benassi Fontolan L, Ribamar Ferreira-Junior J, Bleicher L, Penner-Hahn J, Charles Garratt R. UNEXPECTED PLASTICITY OF THE QUATERNARY STRUCTURE OF IRON-MANGANESE SUPEROXIDE DISMUTASES. J Struct Biol 2022; 214:107855. [PMID: 35390463 DOI: 10.1016/j.jsb.2022.107855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/08/2022] [Accepted: 04/01/2022] [Indexed: 10/18/2022]
Abstract
Protein 3D structure can be remarkably robust to the accumulation of mutations during evolution. On the other hand, sometimes a single amino acid substitution can be sufficient to generate dramatic and completely unpredictable structural consequences. In an attempt to rationally alter the preferences for the metal ion at the active site of a member of the Iron/Manganese superoxide dismutase family, two examples of the latter phenomenon were identified. Site directed mutants of SOD from Trichoderma reesei were generated and studied crystallographically together with the wild type enzyme. Despite being chosen for their potential impact on the redox potential of the metal, two of the mutations (D150G and G73A) in fact resulted in significant alterations to the protein quaternary structure. The D150G mutant presented alternative inter-subunit contacts leading to a loss of symmetry of the wild type tetramer, whereas the G73A mutation transformed the tetramer into an octamer despite not participating directly in any of the inter-subunit interfaces. We conclude that there is considerable intrinsic plasticity in the Fe/MnSOD fold that can be unpredictably affected by single amino acid substitutions. In much the same way as phenotypic defects at the organism level can reveal much about normal function, so too can such mutations teach us much about the subtleties of protein structure.
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Affiliation(s)
- Emerita Mendoza Rengifo
- Laboratory of Structural Biology, Sao Carlos Institute of Physics, University of Sao Paulo, Sao Carlos, Sao Paulo, Brazil
| | | | - Jose Ribamar Ferreira-Junior
- Laboratory of Biotechnology, School of Arts, Sciences and Humanities, University of Sao Paulo, Sao Paulo, Brazil
| | - Lucas Bleicher
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - James Penner-Hahn
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, United States
| | - Richard Charles Garratt
- Laboratory of Structural Biology, Sao Carlos Institute of Physics, University of Sao Paulo, Sao Carlos, Sao Paulo, Brazil.
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5
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Shams A, Higgins SA, Fellmann C, Laughlin TG, Oakes BL, Lew R, Kim S, Lukarska M, Arnold M, Staahl BT, Doudna JA, Savage DF. Comprehensive deletion landscape of CRISPR-Cas9 identifies minimal RNA-guided DNA-binding modules. Nat Commun 2021; 12:5664. [PMID: 34580310 PMCID: PMC8476515 DOI: 10.1038/s41467-021-25992-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 09/10/2021] [Indexed: 11/28/2022] Open
Abstract
Proteins evolve through the modular rearrangement of elements known as domains. Extant, multidomain proteins are hypothesized to be the result of domain accretion, but there has been limited experimental validation of this idea. Here, we introduce a technique for genetic minimization by iterative size-exclusion and recombination (MISER) for comprehensively making all possible deletions of a protein. Using MISER, we generate a deletion landscape for the CRISPR protein Cas9. We find that the catalytically-dead Streptococcus pyogenes Cas9 can tolerate large single deletions in the REC2, REC3, HNH, and RuvC domains, while still functioning in vitro and in vivo, and that these deletions can be stacked together to engineer minimal, DNA-binding effector proteins. In total, our results demonstrate that extant proteins retain significant modularity from the accretion process and, as genetic size is a major limitation for viral delivery systems, establish a general technique to improve genome editing and gene therapy-based therapeutics.
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Affiliation(s)
- Arik Shams
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Sean A Higgins
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
- Scribe Therapeutics, Alameda, CA, 94501, USA
| | - Christof Fellmann
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Gladstone Institutes, San Francisco, CA, 94158, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Thomas G Laughlin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Division of Biological Sciences, University of California, San Diego, San Diego, CA, 92093, USA
| | - Benjamin L Oakes
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
- Scribe Therapeutics, Alameda, CA, 94501, USA
| | - Rachel Lew
- Gladstone Institutes, San Francisco, CA, 94158, USA
| | - Shin Kim
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Maria Lukarska
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Madeline Arnold
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Brett T Staahl
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
- Scribe Therapeutics, Alameda, CA, 94501, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
- Gladstone Institutes, San Francisco, CA, 94158, USA
- Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - David F Savage
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, 94720, USA.
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6
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Emond S, Petek M, Kay EJ, Heames B, Devenish SRA, Tokuriki N, Hollfelder F. Accessing unexplored regions of sequence space in directed enzyme evolution via insertion/deletion mutagenesis. Nat Commun 2020; 11:3469. [PMID: 32651386 PMCID: PMC7351745 DOI: 10.1038/s41467-020-17061-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 06/01/2020] [Indexed: 11/22/2022] Open
Abstract
Insertions and deletions (InDels) are frequently observed in natural protein evolution, yet their potential remains untapped in laboratory evolution. Here we introduce a transposon-based mutagenesis approach (TRIAD) to generate libraries of random variants with short in-frame InDels, and screen TRIAD libraries to evolve a promiscuous arylesterase activity in a phosphotriesterase. The evolution exhibits features that differ from previous point mutagenesis campaigns: while the average activity of TRIAD variants is more compromised, a larger proportion has successfully adapted for the activity. Different functional profiles emerge: (i) both strong and weak trade-off between activities are observed; (ii) trade-off is more severe (20- to 35-fold increased kcat/KM in arylesterase with 60-400-fold decreases in phosphotriesterase activity) and (iii) improvements are present in kcat rather than just in KM, suggesting adaptive solutions. These distinct features make TRIAD an alternative to widely used point mutagenesis, accessing functional innovations and traversing unexplored fitness landscape regions.
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Affiliation(s)
- Stephane Emond
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
- Evonetix Ltd, Coldhams Business Park, Norman Way, Cambridge, CB1 3LH, UK.
| | - Maya Petek
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Emily J Kay
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
| | - Brennen Heames
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- Institute for Evolution and Biodiversity, Westfälische Wilhelms-Universität, Hüfferstrasse 1, 48149, Münster, Germany
| | - Sean R A Devenish
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- Fluidic Analytics, The Paddocks Business Centre, Cherry Hinton Road, Cambridge, CB1 8DH, UK
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
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7
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Brown CA, Del Corsso C, Zoidl C, Donaldson LW, Spray DC, Zoidl G. Tubulin-Dependent Transport of Connexin-36 Potentiates the Size and Strength of Electrical Synapses. Cells 2019; 8:E1146. [PMID: 31557934 PMCID: PMC6829524 DOI: 10.3390/cells8101146] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/17/2019] [Accepted: 09/20/2019] [Indexed: 12/12/2022] Open
Abstract
Connexin-36 (Cx36) electrical synapses strengthen transmission in a calcium/calmodulin (CaM)/calmodulin-dependent kinase II (CaMKII)-dependent manner similar to a mechanism whereby the N-methyl-D-aspartate (NMDA) receptor subunit NR2B facilitates chemical transmission. Since NR2B-microtubule interactions recruit receptors to the cell membrane during plasticity, we hypothesized an analogous modality for Cx36. We determined that Cx36 binding to tubulin at the carboxy-terminal domain was distinct from Cx43 and NR2B by binding a motif overlapping with the CaM and CaMKII binding motifs. Dual patch-clamp recordings demonstrated that pharmacological interference of the cytoskeleton and deleting the binding motif at the Cx36 carboxyl-terminal (CT) reversibly abolished Cx36 plasticity. Mechanistic details of trafficking to the gap-junction plaque (GJP) were probed pharmacologically and through mutational analysis, all of which affected GJP size and formation between cell pairs. Lys279, Ile280, and Lys281 positions were particularly critical. This study demonstrates that tubulin-dependent transport of Cx36 potentiates synaptic strength by delivering channels to GJPs, reinforcing the role of protein transport at chemical and electrical synapses to fine-tune communication between neurons.
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Affiliation(s)
- Cherie A Brown
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada.
| | - Cristiane Del Corsso
- Department of Biophysics and Physiology, Federal University of Rio de Janeiro-RJ, Rio de Janeiro 21941-901, Brazil.
| | - Christiane Zoidl
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada.
| | - Logan W Donaldson
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada.
| | - David C Spray
- Department of Neuroscience, Albert Einstein College, Bronx, NY 10461, USA.
- Department of Medicine, Albert Einstein College, Bronx, NY 10461, USA.
| | - Georg Zoidl
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada.
- Department of Psychology, York University, Toronto, ON M3J 1P3, Canada.
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8
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Pavlenko OS, Gra OA, Mustafaev ON, Kabarbaeva KV, Sadovskaya NS, Tyurin AA, Fadeev VS, Goldenkova-Pavlova IV. Thermostable Lichenase from Clostridium thermocellum as a Host Protein in the Domain Insertion Approach. BIOCHEMISTRY. BIOKHIMIIA 2019; 84:931-940. [PMID: 31522675 DOI: 10.1134/s0006297919080091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 12/17/2023]
Abstract
Clostridium thermocellum lichenase (endo-β-1,3;1,4-glucan-D-glycosyl hydrolase, EC 3.2.1.73 (P29716)) has been tested for the insertion of two model fluorescent proteins (EGFP and TagRFP) into two regions of this enzyme. Functional folding of the resulting proteins was confirmed by retention of lichenase activity and EGFP and TagRFP fluorescence. These results convincingly demonstrate that (i) the two experimentally selected lichenase loop regions may serve as the areas for domain insertion without disturbing enzyme folding in vivo; (ii) lichenase permits not only single but also tandem insertions of large protein domains. High specific activity, outstanding thermostability, and efficient in vitro refolding of thermostable lichenase make it an attractive new host protein for the insertional fusion of domains in the engineering of multifunctional proteins.
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Affiliation(s)
- O S Pavlenko
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia.
| | - O A Gra
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia
| | - O N Mustafaev
- Baku State University, Department of Biophysics and Molecular Biology, Baku, AZ1106, Azerbaijan.
| | - K V Kabarbaeva
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia
| | - N S Sadovskaya
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia
| | - A A Tyurin
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia
| | - V S Fadeev
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia
| | - I V Goldenkova-Pavlova
- Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Moscow, 127276, Russia.
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9
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Wang F, Shen L, Zhou H, Wang S, Wang X, Tao P. Machine Learning Classification Model for Functional Binding Modes of TEM-1 β-Lactamase. Front Mol Biosci 2019; 6:47. [PMID: 31355207 PMCID: PMC6629954 DOI: 10.3389/fmolb.2019.00047] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 06/11/2019] [Indexed: 11/13/2022] Open
Abstract
TEM family of enzymes is one of the most commonly encountered β-lactamases groups with different catalytic capabilities against various antibiotics. Despite the studies investigating the catalytic mechanism of TEM β-lactamases, the binding modes of these enzymes against ligands in different functional catalytic states have been largely overlooked. But the binding modes may play a critical role in the function and even the evolution of these proteins. In this work, a newly developed machine learning analysis approach to the recognition of protein dynamics states was applied to compare the binding modes of TEM-1 β-lactamase with regard to penicillin in different catalytic states. While conventional analysis methods, including principal components analysis (PCA), could not differentiate TEM-1 in different binding modes, the application of a machine learning method led to excellent classification models differentiating these states. It was also revealed that both reactant/product states and apo/product states are more differentiable than the apo/reactant states. The feature importance generated by the training procedure of the machine learning model was utilized to evaluate the contribution from residues at active sites and in different secondary structures. Key active site residues, Ser70 and Ser130, play a critical role in differentiating reactant/product states, while other active site residues are more important for differentiating apo/product states. Overall, this study provides new insights into the different dynamical function states of TEM-1 and may open a new venue for β-lactamases functional and evolutional studies in general.
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Affiliation(s)
- Feng Wang
- Department of Chemistry, Center for Scientific Computation, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, TX, United States
| | - Li Shen
- Department of Chemistry, Center for Scientific Computation, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, TX, United States
| | - Hongyu Zhou
- Department of Chemistry, Center for Scientific Computation, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, TX, United States
| | - Shouyi Wang
- Department of Industrial, Manufacturing, and Systems Engineering, University of Texas at Arlington, Arlington, TX, United States
| | - Xinlei Wang
- Department of Statistical Science, Southern Methodist University, Dallas, TX, United States
| | - Peng Tao
- Department of Chemistry, Center for Scientific Computation, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, TX, United States
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10
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Halliwell LM, Jathoul AP, Bate JP, Worthy HL, Anderson JC, Jones DD, Murray JAH. ΔFlucs: Brighter Photinus pyralis firefly luciferases identified by surveying consecutive single amino acid deletion mutations in a thermostable variant. Biotechnol Bioeng 2017; 115:50-59. [PMID: 28921549 DOI: 10.1002/bit.26451] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 11/05/2022]
Abstract
The bright bioluminescence catalyzed by Photinus pyralis firefly luciferase (Fluc) enables a vast array of life science research such as bio imaging in live animals and sensitive in vitro diagnostics. The effectiveness of such applications is improved using engineered enzymes that to date have been constructed using amino acid substitutions. We describe ΔFlucs: consecutive single amino acid deletion mutants within six loop structures of the bright and thermostable ×11 Fluc. Deletion mutations are a promising avenue to explore new sequence and functional space and isolate novel mutant phenotypes. However, this method is often overlooked and to date there have been no surveys of the effects of consecutive single amino acid deletions in Fluc. We constructed a large semi-rational ΔFluc library and isolated significantly brighter enzymes after finding ×11 Fluc activity was largely tolerant to deletions. Targeting an "omega-loop" motif (T352-G360) significantly enhanced activity, altered kinetics, reduced Km for D-luciferin, altered emission colors, and altered substrate specificity for redshifted analog DL-infraluciferin. Experimental and in silico analyses suggested remodeling of the Ω-loop impacts on active site hydrophobicity to increase light yields. This work demonstrates the further potential of deletion mutations, which can generate useful Fluc mutants and broaden the palette of the biomedical and biotechnological bioluminescence enzyme toolbox.
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Affiliation(s)
| | - Amit P Jathoul
- School of Biosciences, University of Cardiff, Cardiff, UK
| | - Jack P Bate
- School of Biosciences, University of Cardiff, Cardiff, UK
| | | | | | - D Dafydd Jones
- School of Biosciences, University of Cardiff, Cardiff, UK
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11
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Morelli A, Cabezas Y, Mills LJ, Seelig B. Extensive libraries of gene truncation variants generated by in vitro transposition. Nucleic Acids Res 2017; 45:e78. [PMID: 28130425 PMCID: PMC5449547 DOI: 10.1093/nar/gkx030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/20/2017] [Indexed: 11/14/2022] Open
Abstract
The detailed analysis of the impact of deletions on proteins or nucleic acids can reveal important functional regions and lead to variants with improved macromolecular properties. We present a method to generate large libraries of mutants with deletions of varying length that are randomly distributed throughout a given gene. This technique facilitates the identification of crucial sequence regions in nucleic acids or proteins. The approach utilizes in vitro transposition to generate 5΄ and 3΄ fragment sub-libraries of a given gene, which are then randomly recombined to yield a final library comprising both terminal and internal deletions. The method is easy to implement and can generate libraries in three to four days. We used this approach to produce a library of >9000 random deletion mutants of an artificial RNA ligase enzyme representing 32% of all possible deletions. The quality of the library was assessed by next-generation sequencing and detailed bioinformatics analysis. Finally, we subjected this library to in vitro selection and obtained fully functional variants with deletions of up to 18 amino acids of the parental enzyme that had been 95 amino acids in length.
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Affiliation(s)
- Aleardo Morelli
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.,BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA
| | - Yari Cabezas
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.,BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA
| | - Lauren J Mills
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Burckhard Seelig
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA.,BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA
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12
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Jackson EL, Spielman SJ, Wilke CO. Computational prediction of the tolerance to amino-acid deletion in green-fluorescent protein. PLoS One 2017; 12:e0164905. [PMID: 28369116 PMCID: PMC5378326 DOI: 10.1371/journal.pone.0164905] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 03/21/2017] [Indexed: 01/29/2023] Open
Abstract
Proteins evolve through two primary mechanisms: substitution, where mutations alter a protein's amino-acid sequence, and insertions and deletions (indels), where amino acids are either added to or removed from the sequence. Protein structure has been shown to influence the rate at which substitutions accumulate across sites in proteins, but whether structure similarly constrains the occurrence of indels has not been rigorously studied. Here, we investigate the extent to which structural properties known to covary with protein evolutionary rates might also predict protein tolerance to indels. Specifically, we analyze a publicly available dataset of single-amino-acid deletion mutations in enhanced green fluorescent protein (eGFP) to assess how well the functional effect of deletions can be predicted from protein structure. We find that weighted contact number (WCN), which measures how densely packed a residue is within the protein's three-dimensional structure, provides the best single predictor for whether eGFP will tolerate a given deletion. We additionally find that using protein design to explicitly model deletions results in improved predictions of functional status when combined with other structural predictors. Our work suggests that structure plays fundamental role in constraining deletions at sites in proteins, and further that similar biophysical constraints influence both substitutions and deletions. This study therefore provides a solid foundation for future work to examine how protein structure influences tolerance of more complex indel events, such as insertions or large deletions.
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Affiliation(s)
- Eleisha L. Jackson
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas, United States of America
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Stephanie J. Spielman
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Claus O. Wilke
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas, United States of America
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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13
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Liu SS, Wei X, Ji Q, Xin X, Jiang B, Liu J. A facile and efficient transposon mutagenesis method for generation of multi-codon deletions in protein sequences. J Biotechnol 2016; 227:27-34. [DOI: 10.1016/j.jbiotec.2016.03.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 03/17/2016] [Accepted: 03/21/2016] [Indexed: 12/17/2022]
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14
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Liu SS, Wei X, Dong X, Xu L, Liu J, Jiang B. Structural plasticity of green fluorescent protein to amino acid deletions and fluorescence rescue by folding-enhancing mutations. BMC BIOCHEMISTRY 2015. [PMID: 26206151 PMCID: PMC4513630 DOI: 10.1186/s12858-015-0046-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BACKGROUND Green fluorescent protein (GFP) and its derivative fluorescent proteins (FPs) are among the most commonly used reporter systems for studying gene expression and protein interaction in biomedical research. Most commercially available FPs have been optimized for their oligomerization state to prevent potential structural constraints that may interfere with the native function of fused proteins. Other approach to reducing structural constraints may include minimizing the structure of GFPs. Previous studies in an enhanced GFP variant (EGFP) identified a series of deletions that can retain GFP fluorescence. In this study, we interrogated the structural plasticity of a UV-optimized GFP variant (GFP(UV)) to amino acid deletions, characterized the effects of deletions and explored the feasibility of rescuing the fluorescence of deletion mutants using folding-enhancing mutations. METHODS Transposon mutagenesis was used to screen amino acid deletions in GFP that led to fluorescent and nonfluorescent phenotypes. The fluorescent GFP mutants were characterized for their whole-cell fluorescence and fraction soluble. Fluorescent GFP mutants with internal deletions were purified and characterized for their spectral and folding properties. Folding-ehancing mutations were introduced to deletion mutants to rescue their compromised fluorescence. RESULTS We identified twelve amino acid deletions that can retain the fluorescence of GFP(UV). Seven of these deletions are either at the N- or C- terminus, while the other five are located at internal helices or strands. Further analysis suggested that the five internal deletions diminished the efficiency of protein folding and chromophore maturation. Protein expression under hypothermic condition or incorporation of folding-enhancing mutations could rescue the compromised fluorescence of deletion mutants. In addition, we generated dual deletion mutants that can retain GFP fluorescence. CONCLUSION Our results suggested that a "size-minimized" GFP may be developed by iterative incorporation of amino acid deletions, followed by fluorescence rescue with folding-enhancing mutations.
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Affiliation(s)
- Shu-su Liu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China.
| | - Xuan Wei
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China.
| | - Xue Dong
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China.
| | - Liang Xu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China.
| | - Jia Liu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China. .,Department of Chemistry and Biochemistry, University of Maryland, College Park, USA.
| | - Biao Jiang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China.
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15
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Abstract
In this issue of Structure, Arpino and colleagues describe in atomic detail how a protein stomachs a deletion within a helix, an event that rarely occurs in nature or in the lab. Can insertions and deletions (InDels) trigger dramatic structural transitions?
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Affiliation(s)
- Agnes Tóth-Petróczy
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dan S Tawfik
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.
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16
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Hartley AM, Zaki AJ, McGarrity AR, Robert-Ansart C, Moskalenko AV, Jones GF, Craciun MF, Russo S, Elliott M, Macdonald JE, Jones DD. Functional modulation and directed assembly of an enzyme through designed non-natural post-translation modification. Chem Sci 2015; 6:3712-3717. [PMID: 28706718 PMCID: PMC5496188 DOI: 10.1039/c4sc03900a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/31/2015] [Indexed: 11/21/2022] Open
Abstract
Designed phenyl azide incorporation combined with bioorthogonal Click chemistry to regulate enzyme activity, or promote its stable assembly on graphene.
Post-translational modification (PTM) modulates and supplements protein functionality. In nature this high precision event requires specific motifs and/or associated modification machinery. To overcome the inherent complexity that hinders PTM's wider use, we have utilized a non-native biocompatible Click chemistry approach to site-specifically modify TEM β-lactamase that adds new functionality. In silico modelling was used to design TEM β-lactamase variants with the non-natural amino acid p-azido-l-phenylalanine (azF) placed at functionally strategic positions permitting residue-specific modification with alkyne adducts by exploiting strain-promoted azide–alkyne cycloaddition. Three designs were implemented so that the modification would: (i) inhibit TEM activity (Y105azF); (ii) restore activity compromised by the initial mutation (P174azF); (iii) facilitate assembly on pristine graphene (W165azF). A dibenzylcyclooctyne (DBCO) with amine functionality was enough to modulate enzymatic activity. Modification of TEMW165azF with a DBCO–pyrene adduct had little effect on activity despite the modification site being close to a key catalytic residue but allowed directed assembly of the enzyme on graphene, potentially facilitating the construction of protein-gated carbon transistor systems.
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Affiliation(s)
| | - Athraa J Zaki
- School of Physics and Astronomy , Cardiff University , Cardiff , Wales , UK
| | | | | | | | - Gareth F Jones
- Centre for Graphene Science , University of Exeter , Exeter , Devon , UK
| | - Monica F Craciun
- Centre for Graphene Science , University of Exeter , Exeter , Devon , UK
| | - Saverio Russo
- Centre for Graphene Science , University of Exeter , Exeter , Devon , UK
| | - Martin Elliott
- School of Physics and Astronomy , Cardiff University , Cardiff , Wales , UK
| | - J Emyr Macdonald
- School of Physics and Astronomy , Cardiff University , Cardiff , Wales , UK
| | - D Dafydd Jones
- School of Biosciences , Cardiff University , Cardiff , UK .
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17
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Kiljunen S, Pajunen MI, Dilks K, Storf S, Pohlschroder M, Savilahti H. Generation of comprehensive transposon insertion mutant library for the model archaeon, Haloferax volcanii, and its use for gene discovery. BMC Biol 2014; 12:103. [PMID: 25488358 PMCID: PMC4300041 DOI: 10.1186/s12915-014-0103-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 11/26/2014] [Indexed: 12/04/2022] Open
Abstract
Background Archaea share fundamental properties with bacteria and eukaryotes. Yet, they also possess unique attributes, which largely remain poorly characterized. Haloferax volcanii is an aerobic, moderately halophilic archaeon that can be grown in defined media. It serves as an excellent archaeal model organism to study the molecular mechanisms of biological processes and cellular responses to changes in the environment. Studies on haloarchaea have been impeded by the lack of efficient genetic screens that would facilitate the identification of protein functions and respective metabolic pathways. Results Here, we devised an insertion mutagenesis strategy that combined Mu in vitro DNA transposition and homologous-recombination-based gene targeting in H. volcanii. We generated an insertion mutant library, in which the clones contained a single genomic insertion. From the library, we isolated pigmentation-defective and auxotrophic mutants, and the respective insertions pinpointed a number of genes previously known to be involved in carotenoid and amino acid biosynthesis pathways, thus validating the performance of the methodologies used. We also identified mutants that had a transposon insertion in a gene encoding a protein of unknown or putative function, demonstrating that novel roles for non-annotated genes could be assigned. Conclusions We have generated, for the first time, a random genomic insertion mutant library for a halophilic archaeon and used it for efficient gene discovery. The library will facilitate the identification of non-essential genes behind any specific biochemical pathway. It represents a significant step towards achieving a more complete understanding of the unique characteristics of halophilic archaea. Electronic supplementary material The online version of this article (doi:10.1186/s12915-014-0103-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Saija Kiljunen
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland.
| | - Maria I Pajunen
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland. .,Current address: Department of Biosciences, Division of Biochemistry and Biotechnology, University of Helsinki, Helsinki, Finland.
| | - Kieran Dilks
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Stefanie Storf
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
| | | | - Harri Savilahti
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland.
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18
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Arpino JAJ, Rizkallah PJ, Jones DD. Structural and dynamic changes associated with beneficial engineered single-amino-acid deletion mutations in enhanced green fluorescent protein. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2152-62. [PMID: 25084334 PMCID: PMC4118826 DOI: 10.1107/s139900471401267x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 05/31/2014] [Indexed: 01/23/2023]
Abstract
Single-amino-acid deletions are a common part of the natural evolutionary landscape but are rarely sampled during protein engineering owing to limited and prejudiced molecular understanding of mutations that shorten the protein backbone. Single-amino-acid deletion variants of enhanced green fluorescent protein (EGFP) have been identified by directed evolution with the beneficial effect of imparting increased cellular fluorescence. Biophysical characterization revealed that increased functional protein production and not changes to the fluorescence parameters was the mechanism that was likely to be responsible. The structure EGFP(D190Δ) containing a deletion within a loop revealed propagated changes only after the deleted residue. The structure of EGFP(A227Δ) revealed that a `flipping' mechanism was used to adjust for residue deletion at the end of a β-strand, with amino acids C-terminal to the deletion site repositioning to take the place of the deleted amino acid. In both variants new networks of short-range and long-range interactions are generated while maintaining the integrity of the hydrophobic core. Both deletion variants also displayed significant local and long-range changes in dynamics, as evident by changes in B factors compared with EGFP. Rather than being detrimental, deletion mutations can introduce beneficial structural effects through altering core protein properties, folding and dynamics, as well as function.
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Affiliation(s)
- James A. J. Arpino
- School of Biosciences, Cardiff University, Park Place, Cardiff CF10 3AT, Wales
| | | | - D. Dafydd Jones
- School of Biosciences, Cardiff University, Park Place, Cardiff CF10 3AT, Wales
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19
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Deletion mutations conferring substrate spectrum extension in the class A β-lactamase. Antimicrob Agents Chemother 2014; 58:6265-9. [PMID: 25049254 DOI: 10.1128/aac.02648-14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe four new deletion mutations in a class A β-lactamase PenA in Burkholderia thailandensis, each conferring an extended substrate spectrum. Single-amino-acid deletions T171del, I173del, and P174del and a two-amino-acid deletion, R165_T167delinsP, occurred in the omega loop, increasing the flexibility of the binding cavity. This rare collection of mutations has significance, allowing exploration of the diverse evolutionary trajectories of β-lactamases and as potential future mutations conferring high-level ceftazidime resistance on isolates from clinical settings, compared with amino acid substitution mutations.
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20
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Arpino JAJ, Reddington SC, Halliwell LM, Rizkallah PJ, Jones DD. Random single amino acid deletion sampling unveils structural tolerance and the benefits of helical registry shift on GFP folding and structure. Structure 2014; 22:889-98. [PMID: 24856363 PMCID: PMC4058518 DOI: 10.1016/j.str.2014.03.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 03/08/2014] [Accepted: 03/10/2014] [Indexed: 12/01/2022]
Abstract
Altering a protein’s backbone through amino acid deletion is a common evolutionary mutational mechanism, but is generally ignored during protein engineering primarily because its effect on the folding-structure-function relationship is difficult to predict. Using directed evolution, enhanced green fluorescent protein (EGFP) was observed to tolerate residue deletion across the breadth of the protein, particularly within short and long loops, helical elements, and at the termini of strands. A variant with G4 removed from a helix (EGFPG4Δ) conferred significantly higher cellular fluorescence. Folding analysis revealed that EGFPG4Δ retained more structure upon unfolding and refolded with almost 100% efficiency but at the expense of thermodynamic stability. The EGFPG4Δ structure revealed that G4 deletion caused a beneficial helical registry shift resulting in a new polar interaction network, which potentially stabilizes a cis proline peptide bond and links secondary structure elements. Thus, deletion mutations and registry shifts can enhance proteins through structural rearrangements not possible by substitution mutations alone. Using directed evolution, the impact of amino acid deletion on EGFP is explored Loops, helices, and strand termini are especially tolerant to amino acid deletion A deletion mutant that enhances cellular production and fluorescence is identified Structure reveals that a helical registry shift creates a new polar network
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Affiliation(s)
- James A J Arpino
- School of Biosciences, Main Building, Park Place, Cardiff University, Cardiff CF10 3AT, UK
| | - Samuel C Reddington
- School of Biosciences, Main Building, Park Place, Cardiff University, Cardiff CF10 3AT, UK
| | - Lisa M Halliwell
- School of Biosciences, Main Building, Park Place, Cardiff University, Cardiff CF10 3AT, UK
| | - Pierre J Rizkallah
- School of Medicine, Cardiff University, WHRI, Main Building, Heath Park, Cardiff CF14 4XN, UK
| | - D Dafydd Jones
- School of Biosciences, Main Building, Park Place, Cardiff University, Cardiff CF10 3AT, UK.
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21
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Salahuddin P, Khan AU. Studies on structure-based sequence alignment and phylogenies of beta-lactamases. Bioinformation 2014; 10:308-13. [PMID: 24966539 PMCID: PMC4070041 DOI: 10.6026/97320630010308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 05/21/2014] [Indexed: 11/23/2022] Open
Abstract
The β-lactamases enzymes cleave the amide bond in β-lactam ring, rendering β-lactam antibiotics harmless to bacteria. In this communication we have studied structure-function relationship and phylogenies of class A, B and D beta-lactamases using structure-based sequence alignment and phylip programs respectively. The data of structure-based sequence alignment suggests that in different isolates of TEM-1, mutations did not occur at or near sequence motifs. Since deletions are reported to be lethal to structure and function of enzyme. Therefore, in these variants antibiotic hydrolysis profile and specificity will be affected. The alignment data of class A enzyme SHV-1, CTX-M-15, class D enzyme, OXA-10, and class B enzyme VIM-2 and SIM-1 show sequence motifs along with other part of polypeptide are essentially conserved. These results imply that conformations of betalactamases are close to native state and possess normal hydrolytic activities towards beta-lactam antibiotics. However, class B enzyme such as IMP-1 and NDM-1 are less conserved than other class A and D studied here because mutation and deletions occurred at critically important region such as active site. Therefore, the structure of these beta-lactamases will be altered and antibiotic hydrolysis profile will be affected. Phylogenetic studies suggest that class A and D beta-lactamases including TOHO-1 and OXA-10 respectively evolved by horizontal gene transfer (HGT) whereas other member of class A such as TEM-1 evolved by gene duplication mechanism. Taken together, these studies justify structure-function relationship of beta-lactamases and phylogenetic studies suggest these enzymes evolved by different mechanisms.
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Affiliation(s)
- Parveen Salahuddin
- Distributed Information Sub-Centre, Interdisciplinary Biotechnology Unit, A. M. U. Aligarh, 202002, India
| | - Asad U Khan
- Distributed Information Sub-Centre, Interdisciplinary Biotechnology Unit, A. M. U. Aligarh, 202002, India
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22
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Jones DD, Arpino JAJ, Baldwin AJ, Edmundson MC. Transposon-based approaches for generating novel molecular diversity during directed evolution. Methods Mol Biol 2014; 1179:159-172. [PMID: 25055777 DOI: 10.1007/978-1-4939-1053-3_11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This chapter introduces a set of transposon-based methods that were developed to sample trinucleotide deletion, trinucleotide replacement, and domain insertion. Each approach has a common initial step that utilizes an engineered version of the Mu transposon called MuDel. The inherent low sequence specificity of MuDel results in its random insertion into target DNA during in vitro transposition. Removal of the transposon using a type IIS restriction endonuclease generates blunt-end random breaks at a frequency of one per target gene and the concomitant loss of 3 bp. Self-ligation or insertion of another DNA cassette results in the sampling of trinucleotide deletion or trinucleotide substitution/domain insertion, respectively.
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Affiliation(s)
- D Dafydd Jones
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff, CF10 3AT, UK,
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23
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Substrate spectrum extension of PenA in Burkholderia thailandensis with a single amino acid deletion, Glu168del. Antimicrob Agents Chemother 2012; 56:4005-8. [PMID: 22564834 DOI: 10.1128/aac.00598-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe a deletion mutation in a class A β-lactamase, PenA, of Burkholderia thailandensis that extended the substrate spectrum of the enzyme to include ceftazidime. Glu168del was located in a functional domain called the omega loop causing expansion of the space in the loop, which in turn increased flexibility at the active site. This deletion mutation represents a rare but significant alternative mechanical path to substrate spectrum extension in PenA besides more common substitution mutations.
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Jones DD. Recombining low homology, functionally rich regions of bacterial subtilisins by combinatorial fragment exchange. PLoS One 2011; 6:e24319. [PMID: 21915310 PMCID: PMC3168465 DOI: 10.1371/journal.pone.0024319] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 08/08/2011] [Indexed: 11/19/2022] Open
Abstract
Combinatorial fragment exchange was utilised to recombine key structural and functional low homology regions of bacilli subtilisins to generate new active hybrid proteases with altered substrate profiles. Up to six different regions comprising mostly of loop residues from the commercially important subtilisin Savinase were exchanged with the structurally equivalent regions of six other subtilisins. The six additional subtilisins derive from diverse origins and included thermophilic and intracellular subtilisins as well as other academically and commercially relevant subtilisins. Savinase was largely tolerant to fragment exchange; rational replacement of all six regions with 5 of 6 donating subtilisin sequences preserved activity, albeit reduced compared to Savinase. A combinatorial approach was used to generate hybrid Savinase variants in which the sequences derived from all seven subtilisins at each region were recombined to generate new region combinations. Variants with different substrate profiles and with greater apparent activity compared to Savinase and the rational fragment exchange variants were generated with the substrate profile exhibited by variants dependent on the sequence combination at each region.
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Affiliation(s)
- D Dafydd Jones
- School of Biosciences, Cardiff University, Cardiff, United Kingdom.
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25
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Berrondo M, Gray JJ. Computed structures of point deletion mutants and their enzymatic activities. Proteins 2011; 79:2844-60. [PMID: 21905110 DOI: 10.1002/prot.23109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 04/08/2011] [Accepted: 05/13/2011] [Indexed: 11/11/2022]
Abstract
Point deletions in enzymes can vary in effect from negligible to complete loss of activity; however, these effects are not generally predictable. Deletions are widely observed in nature and often result in diseases such as cancer, cystic fibrosis, or osteogenesis imperfecta. Here, we have developed an algorithm to model the perturbed structures of deletion mutants with the ultimate goal of predicting their activities. The algorithm works by deleting the specified residue from the wild-type structure, creating a gap that is closed using a combination of local and global moves that change the backbone torsion angles of the protein structure. On a set of five proteins for which both wild-type and deletion mutant x-ray crystal structures are available, the algorithm produces deep, narrow energy funnels within 1.5 Å of the crystal structure for the deletion mutants. To assess the ability of our algorithm to predict activity from the predicted structures, we tested the correlation of experimental activity with several measures of the predicted structure ensemble using a set of 45 point deletions from ricin. Estimates incorporating likely prevalence of active and inactive deletion sites suggest that activity can be predicted correctly over 60% of the time from the active site root-mean squared deviation of the lowest energy predicted structures. The predictions are stronger than simple sequence organization measures, but more fundamental work is required in structure prediction and enzyme activity determination to allow consistent prediction of activity.
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Affiliation(s)
- Monica Berrondo
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
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26
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Salverda MLM, De Visser JAGM, Barlow M. Natural evolution of TEM-1 β-lactamase: experimental reconstruction and clinical relevance. FEMS Microbiol Rev 2011; 34:1015-36. [PMID: 20412308 DOI: 10.1111/j.1574-6976.2010.00222.x] [Citation(s) in RCA: 193] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
TEM-1 β-lactamase is one of the most well-known antibiotic resistance determinants around. It confers resistance to penicillins and early cephalosporins and has shown an astonishing functional plasticity in response to the introduction of novel drugs derived from these antibiotics. Since its discovery in the 1960s, over 170 variants of TEM-1 - with different amino acid sequences and often resistance phenotypes - have been isolated in hospitals and clinics worldwide. Next to this well-documented 'natural' evolution, the in vitro evolution of TEM-1 has been the focus of attention of many experimental studies. In this review, we compare the natural and laboratory evolution of TEM-1 in order to address the question to what extent the evolution of antibiotic resistance can be repeated, and hence might have been predicted, under laboratory conditions. We also use the comparison to gain an insight into the adaptive relevance of hitherto uncharacterized substitutions present in clinical isolates and to predict substitutions not yet observed in nature. Based on new structural insights, we review what is known about substitutions in TEM-1 that contribute to the extension of its resistance phenotype. Finally, we address the clinical relevance of TEM alleles during the past decade, which has been dominated by the emergence of another β-lactamase, CTX-M.
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27
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Edwards WR, Williams AJ, Morris JL, Baldwin AJ, Allemann RK, Jones DD. Regulation of β-Lactamase Activity by Remote Binding of Heme: Functional Coupling of Unrelated Proteins through Domain Insertion. Biochemistry 2010; 49:6541-9. [DOI: 10.1021/bi100793y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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28
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Wang Z, Martin J, Abubucker S, Yin Y, Gasser RB, Mitreva M. Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance. BMC Evol Biol 2009; 9:23. [PMID: 19175938 PMCID: PMC2644674 DOI: 10.1186/1471-2148-9-23] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Accepted: 01/28/2009] [Indexed: 11/25/2022] Open
Abstract
Background Amino acid insertions and deletions in proteins are considered relatively rare events, and their associations with the evolution and adaptation of organisms are not yet understood. In this study, we undertook a systematic analysis of over 214,000 polypeptides from 32 nematode species and identified insertions and deletions unique to nematode proteins in more than 1000 families and provided indirect evidence that these alterations are linked to the evolution and adaptation of nematodes. Results Amino acid alterations in sequences of nematodes were identified by comparison with homologous sequences from a wide range of eukaryotic (metzoan) organisms. This comparison revealed that the proteins inferred from transcriptomic datasets for nematodes contained more deletions than insertions, and that the deletions tended to be larger in length than insertions, indicating a decreased size of the transcriptome of nematodes compared with other organisms. The present findings showed that this reduction is more pronounced in parasitic nematodes compared with the free-living nematodes of the genus Caenorhabditis. Consistent with a requirement for conservation in proteins involved in the processing of genetic information, fewer insertions and deletions were detected in such proteins. On the other hand, more insertions and deletions were recorded for proteins inferred to be involved in the endocrine and immune systems, suggesting a link with adaptation. Similarly, proteins involved in multiple cellular pathways tended to display more deletions and insertions than those involved in a single pathway. The number of insertions and deletions shared by a range of plant parasitic nematodes were higher for proteins involved in lipid metabolism and electron transport compared with other nematodes, suggesting an association between metabolic adaptation and parasitism in plant hosts. We also identified three sizable deletions from proteins found to be specific to and shared by parasitic nematodes, which, given their uniqueness, might serve as target candidates for drug design. Conclusion This study illustrates the significance of using comparative genomics approaches to identify molecular elements unique to parasitic nematodes, which have adapted to a particular host organism and mode of existence during evolution. While the focus of this study was on nematodes, the approach has applicability to a wide range of other groups of organisms.
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Affiliation(s)
- Zhengyuan Wang
- The Genome Center, Department of Genetics, Washington University School of Medicine, St Louis, MO 63110, USA.
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29
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Baldwin AJ, Arpino JAJ, Edwards WR, Tippmann EM, Jones DD. Expanded chemical diversity sampling through whole protein evolution. MOLECULAR BIOSYSTEMS 2009; 5:764-6. [DOI: 10.1039/b904031e] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Edwards WR, Busse K, Allemann RK, Jones DD. Linking the functions of unrelated proteins using a novel directed evolution domain insertion method. Nucleic Acids Res 2008; 36:e78. [PMID: 18559359 PMCID: PMC2490766 DOI: 10.1093/nar/gkn363] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
We have successfully developed a new directed evolution method for generating integral protein fusions comprising of one domain inserted within another. Creating two connections between the insert and accepting parent domain can result in the inter-dependence of the separate protein activities, thus providing a general strategy for constructing molecular switches. Using an engineered transposon termed MuDel, contiguous trinucleotide sequences were removed at random positions from the bla gene encoding TEM-1 β-lactamase. The deleted trinucleotide sequence was then replaced by a DNA cassette encoding cytochrome b562 with differing linking sequences at each terminus and sampling all three reading frames. The result was a variety of chimeric genes encoding novel integral fusion proteins that retained TEM-1 activity. While most of the tolerated insertions were observed in loops, several also occurred close to the termini of α-helices and β-strands. Several variants conferred a switching phenotype on Escherichia coli, with bacterial tolerance to ampicillin being dependent on the presence of haem in the growth medium. The magnitude of the switching phenotype ranged from 4- to 128-fold depending on the insertion position within TEM-1 and the linker sequences that join the two domains.
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Affiliation(s)
- Wayne R Edwards
- School of Biosciences and School of Chemistry, Cardiff University, Cardiff, UK
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Baldwin AJ, Busse K, Simm AM, Jones DD. Expanded molecular diversity generation during directed evolution by trinucleotide exchange (TriNEx). Nucleic Acids Res 2008; 36:e77. [PMID: 18559360 PMCID: PMC2490759 DOI: 10.1093/nar/gkn358] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Trinucleotide exchange (TriNEx) is a method for generating novel molecular diversity during directed evolution by random substitution of one contiguous trinucleotide sequence for another. Single trinucleotide sequences were deleted at random positions in a target gene using the engineered transposon MuDel that were subsequently replaced with a randomized trinucleotide sequence donated by the DNA cassette termed SubSeq(NNN). The bla gene encoding TEM-1 beta-lactamase was used as a model to demonstrate the effectiveness of TriNEx. Sequence analysis revealed that the mutations were distributed throughout bla, with variants containing single, double and triple nucleotide changes. Many of the resulting amino acid substitutions had significant effects on the in vivo activity of TEM-1, including up to a 64-fold increased activity toward ceftazidime and up to an 8-fold increased resistance to the inhibitor clavulanate. Many of the observed amino acid substitutions were only accessible by exchanging at least two nucleotides per codon, including charge-switch (R164D) and aromatic substitution (W165Y) mutations. TriNEx can therefore generate a diverse range of protein variants with altered properties by combining the power of site-directed saturation mutagenesis with the capacity of whole-gene mutagenesis to randomly introduce mutations throughout a gene.
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Bershtein S, Tawfik DS. Advances in laboratory evolution of enzymes. Curr Opin Chem Biol 2008; 12:151-8. [PMID: 18284924 DOI: 10.1016/j.cbpa.2008.01.027] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2007] [Revised: 01/17/2008] [Accepted: 01/24/2008] [Indexed: 11/19/2022]
Abstract
We address recent developments in the area of laboratory, or directed evolution, with a focus on enzymes and on new methodologies of generic potential. We survey three main areas: (i) library making techniques, including the application of computational and rational methods for library design; (ii) screening and selection techniques, including recent applications of enzyme screening by FACS (fluorescence activated cell sorter); (iii) new approaches for performing directed evolution, and in particular, the application of 'neutral drifts' (libraries generated by rounds of mutation and selection for the enzyme's original function) and of consensus mutations to generate highly evolvable starting points for directed evolution.
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Affiliation(s)
- Shimon Bershtein
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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Emond S, Mondon P, Pizzut-Serin S, Douchy L, Crozet F, Bouayadi K, Kharrat H, Potocki-Véronèse G, Monsan P, Remaud-Simeon M. A novel random mutagenesis approach using human mutagenic DNA polymerases to generate enzyme variant libraries. Protein Eng Des Sel 2008; 21:267-74. [DOI: 10.1093/protein/gzn004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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