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Lauzon D, Vallée-Bélisle A. Functional advantages of building nanosystems using multiple molecular components. Nat Chem 2023; 15:458-467. [PMID: 36759713 DOI: 10.1038/s41557-022-01127-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 12/15/2022] [Indexed: 02/11/2023]
Abstract
Over half of all the natural nanomachines in living organisms are multimeric and likely exploit the self-assembly of their components to provide functional benefits. However, the advantages and disadvantages of building nanosystems using multiple molecular components remain relatively unexplored at the thermodynamic, kinetic and functional levels. In this study we used theory and a simple DNA-based model that forms the same nanostructures with different numbers of components to advance our knowledge in this area. Despite its lower assembly rate, we found that a system built with three components may undergo a more cooperative assembly transition from less preorganized components, which facilitates the emergence of functionalities. Using simple variations of its components, we also found that trimeric nanosystems display a much higher level of programmability than their dimeric counterparts because they can assemble with various levels of cooperativity, self-inhibition and time-dependent properties. We show here how two simple strategies (for example, cutting and adding components) can be employed to efficiently programme the regulatory function of a more complex, artificially selected, RNA-cleaving catalytic nanosystem.
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Affiliation(s)
- D Lauzon
- Laboratoire de Biosenseurs & Nanomachines, Département de Chimie, Université de Montréal, Montréal, Québec, Canada
| | - A Vallée-Bélisle
- Laboratoire de Biosenseurs & Nanomachines, Département de Chimie, Université de Montréal, Montréal, Québec, Canada.
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2
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Skeeters SS, Camp T, Fan H, Zhang K. The expanding role of split protein complementation in opsin-free optogenetics. Curr Opin Pharmacol 2022; 65:102236. [PMID: 35609383 PMCID: PMC9308681 DOI: 10.1016/j.coph.2022.102236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 03/16/2022] [Accepted: 04/08/2022] [Indexed: 11/30/2022]
Abstract
A comprehensive understanding of signaling mechanisms helps interpret fundamental biological processes and restore cell behavior from pathological conditions. Signaling outcome depends not only on the activity of each signaling component but also on their dynamic interaction in time and space, which remains challenging to probe by biochemical and cell-based assays. Opsin-based optogenetics has transformed neural science research with its spatiotemporal modulation of the activity of excitable cells. Motivated by this advantage, opsin-free optogenetics extends the power of light to a larger spectrum of signaling molecules. This review summarizes commonly used opsin-free optogenetic strategies, presents a historical overview of split protein complementation, and highlights the adaptation of split protein recombination as optogenetic sensors and actuators.
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3
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Takase Y, Yamazaki Y, Hayashi Y, Toma-Fukai S, Kamikubo H. Structure elements can be predicted using the contact volume among protein residues. Biophys Physicobiol 2021; 18:50-59. [PMID: 33954082 PMCID: PMC8049775 DOI: 10.2142/biophysico.bppb-v18.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/15/2021] [Indexed: 12/01/2022] Open
Abstract
Previously, the structure elements of dihydrofolate reductase (DHFR) were determined using comprehensive Ala-insertion mutation analysis, which is assumed to be a kind of protein “building blocks.” It is hypothesized that our comprehension of the structure elements could lead to understanding how an amino acid sequence dictates its tertiary structure. However, the comprehensive Ala-insertion mutation analysis is a time- and cost-consuming process and only a set of the DHFR structure elements have been reported so far. Therefore, developing a computational method to predict structure elements is an urgent necessity. We focused on intramolecular residue–residue contacts to predict the structure elements. We introduced a simple and effective parameter: the overlapped contact volume (CV) among the residues and calculated the CV along the DHFR sequence using the crystal structure. Our results indicate that the CV profile can recapitulate its precipitate ratio profile, which was used to define the structure elements in the Ala-insertion mutation analysis. The CV profile allowed us to predict structure elements like the experimentally determined structure elements. The strong correlation between the CV and precipitate ratio profiles indicates the importance of the intramolecular residue–residue contact in maintaining the tertiary structure. Additionally, the CVs between the structure elements are considerably more than those between a structure element and a linker or two linkers, indicating that the structure elements play a fundamental role in increasing the intramolecular adhesion. Thus, we propose that the structure elements can be considered a type of “building blocks” that maintain and dictate the tertiary structures of proteins.
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Affiliation(s)
- Yasumichi Takase
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Yoichi Yamazaki
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Yugo Hayashi
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Sachiko Toma-Fukai
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Hironari Kamikubo
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.,Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
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4
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Abstract
Many proteins can be split into fragments that spontaneously reassemble, without covalent linkage, into a functional protein. For split green fluorescent proteins (GFPs), fragment reassembly leads to a fluorescent readout, which has been widely used to investigate protein-protein interactions. We review the scope and limitations of this approach as well as other diverse applications of split GFPs as versatile sensors, molecular glues, optogenetic tools, and platforms for photophysical studies.
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Affiliation(s)
- Matthew G Romei
- Department of Chemistry, Stanford University, Stanford, California 94305, USA; ,
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA; ,
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5
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Szafranski P. Intercompartmental Piecewise Gene Transfer. Genes (Basel) 2017; 8:genes8100260. [PMID: 28984842 PMCID: PMC5664110 DOI: 10.3390/genes8100260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 09/25/2017] [Accepted: 09/28/2017] [Indexed: 11/16/2022] Open
Abstract
Gene relocation from the residual genomes of organelles to the nuclear genome still continues, although as a scaled down evolutionary phenomenon, limited in occurrence mostly to protists (sensu lato) and land plants. During this process, the structural integrity of transferred genes is usually preserved. However, the relocation of mitochondrial genes that code for respiratory chain and ribosomal proteins is sometimes associated with their fragmentation into two complementary genes. Herein, this review compiles cases of piecewise gene transfer from the mitochondria to the nucleus, and discusses hypothesized mechanistic links between the fission and relocation of those genes.
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Affiliation(s)
- Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
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6
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Szafranski P. Evolutionarily recent, insertional fission of mitochondrial cox2 into complementary genes in bilaterian Metazoa. BMC Genomics 2017; 18:269. [PMID: 28359330 PMCID: PMC5374615 DOI: 10.1186/s12864-017-3626-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 03/14/2017] [Indexed: 11/21/2022] Open
Abstract
Background Mitochondrial genomes (mtDNA) of multicellular animals (Metazoa) with bilateral symmetry (Bilateria) are compact and usually carry 13 protein-coding genes for subunits of three respiratory complexes and ATP synthase. However, occasionally reported exceptions to this typical mtDNA organization prompted speculation that, as in protists and plants, some bilaterian mitogenomes may continue to lose their canonical genes, or may even acquire new genes. To shed more light on this phenomenon, a PCR-based screen was conducted to assess fast-evolving mtDNAs of apocritan Hymenoptera (Arthropoda, Insecta) for genomic rearrangements that might be associated with the modification of mitochondrial gene content. Results Sequencing of segmental inversions, identified in the screen, revealed that the cytochrome oxidase subunit II gene (cox2) of Campsomeris (Dielis) (Scoliidae) was split into two genes coding for COXIIA and COXIIB. The COXII-derived complementary polypeptides apparently form a heterodimer, have reduced hydrophobicity compared with the majority of mitogenome-encoded COX subunits, and one of them, COXIIB, features increased content of Cys residues. Analogous cox2 fragmentation is known only in two clades of protists (chlorophycean algae and alveolates), where it has been associated with piecewise relocation of this gene into the nucleus. In Campsomeris mtDNA, cox2a and cox2b loci are separated by a 3-kb large cluster of several antiparallel overlapping ORFs, one of which, qnu, seems to encode a nuclease that may have played a role in cox2 fission. Conclusions Although discontinuous mitochondrial protein genes encoding fragmented, complementary polypeptides are known in protists and some plants, split cox2 of Campsomeris is the first case of such a gene arrangement found in animals. The reported data also indicate that bilaterian animal mitogenomes may be carrying lineage-specific genes more often than previously thought, and suggest a homing endonuclease-based mechanism for insertional mitochondrial gene fission. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3626-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, ABBR, R851C, Houston, TX, 77030, USA.
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7
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Dai X, Zhu M, Wang YP. Circular permutation of E. coli EPSP synthase: increased inhibitor resistance, improved catalytic activity, and an indicator for protein fragment complementation. Chem Commun (Camb) 2014; 50:1830-2. [PMID: 24402609 DOI: 10.1039/c3cc48722a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We performed the first circular permutation analysis for E. coli 5-enolpyruvylshikimate-3-phosphate synthase, and identified one circular permutant with notably increased resistance to its specific inhibitor and several others with moderately improved catalytic activity. Valid circular permutation sites can be used as effective split sites of protein fragment complementation.
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Affiliation(s)
- Xiongfeng Dai
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.
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8
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Tomii K, Sawada Y, Honda S. Convergent evolution in structural elements of proteins investigated using cross profile analysis. BMC Bioinformatics 2012; 13:11. [PMID: 22244085 PMCID: PMC3398312 DOI: 10.1186/1471-2105-13-11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 01/16/2012] [Indexed: 11/10/2022] Open
Abstract
Background Evolutionary relations of similar segments shared by different protein folds remain controversial, even though many examples of such segments have been found. To date, several methods such as those based on the results of structure comparisons, sequence-based classifications, and sequence-based profile-profile comparisons have been applied to identify such protein segments that possess local similarities in both sequence and structure across protein folds. However, to capture more precise sequence-structure relations, no method reported to date combines structure-based profiles, and sequence-based profiles based on evolutionary information. The former are generally regarded as representing the amino acid preferences at each position of a specific conformation of protein segment. They might reflect the nature of ancient short peptide ancestors, using the results of structural classifications of protein segments. Results This report describes the development and use of "Cross Profile Analysis" to compare sequence-based profiles and structure-based profiles based on amino acid occurrences at each position within a protein segment cluster. Using systematic cross profile analysis, we found structural clusters of 9-residue and 15-residue segments showing remarkably strong correlation with particular sequence profiles. These correlations reflect structural similarities among constituent segments of both sequence-based and structure-based profiles. We also report previously undetectable sequence-structure patterns that transcend protein family and fold boundaries, and present results of the conformational analysis of the deduced peptide of a segment cluster. These results suggest the existence of ancient short-peptide ancestors. Conclusions Cross profile analysis reveals the polyphyletic and convergent evolution of β-hairpin-like structures, which were verified both experimentally and computationally. The results presented here give us new insights into the evolution of short protein segments.
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Cadima-Couto I, Saraiva N, Santos ACC, Goncalves J. HIV-1 Vif interaction with APOBEC3 deaminases and its characterization by a new sensitive assay. J Neuroimmune Pharmacol 2011; 6:296-307. [PMID: 21279453 DOI: 10.1007/s11481-011-9258-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2010] [Accepted: 01/12/2011] [Indexed: 02/01/2023]
Abstract
The human APOBEC3 (A3) cytidine deaminases, such as APOBEC3G (A3G) and APOBEC3F (A3F), are potent inhibitors of Vif-deficient human immunodeficiency virus type 1 (HIV-1). HIV-1 Vif (viral infectivity factor) binds A3 proteins and targets these proteins for ubiquitination and proteasomal degradation. As such, the therapeutic blockage of Vif-A3 interaction is predicted to stimulate natural antiviral activity by rescuing APOBEC expression and virion packaging. In this study, we describe a successful application of the Protein Fragment Complementation Assay (PCA) based on the enzyme TEM-1 β-lactamase to study Vif-A3 interactions. PCA is based on the interaction between two protein binding partners (e.g., Vif and A3G), which are fused to the two halves of a dissected marker protein (β-lactamase). Binding of the two partners reassembles β-lactamase and hence reconstitutes its activity. To validate our assay, we studied the effect of well-described Vif (DRMR, YRHHY) and A3G (D128K) mutations on the interaction between the two proteins. Additionally, we studied the interaction of human Vif with other members of the A3 family: A3F and APOBEC3C (A3C). Our results demonstrate the applicability of PCA as a simple and reliable technique for the assessment of Vif-A3 interactions. Furthermore, when compared with co-immunoprecipitation assays, PCA appeared to be a more sensitive technique for the quantitative assessment of Vif-A3 interactions. Thus, with our results, we conclude that PCA could be used to quantitatively study specific domains that may be involved in the interaction between Vif and APOBEC proteins.
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Affiliation(s)
- Iris Cadima-Couto
- URIA-IMM, Faculdade de Farmácia da Universidade Lisboa, Av. Das Forças Armadas, 1649-059 Lisbon, Portugal
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10
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Alternative split sites for fragment complementation, and glyphosate function as extra ligand and stabilizer for the AroA enzyme complexes. CHINESE SCIENCE BULLETIN-CHINESE 2011. [DOI: 10.1007/s11434-010-4323-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Schramm AM, Karr D, Mehra-Chaudhary R, Van Doren SR, Furdui CM, Beamer LJ. Breaking the covalent connection: Chain connectivity and the catalytic reaction of PMM/PGM. Protein Sci 2010; 19:1235-42. [PMID: 20512975 DOI: 10.1002/pro.402] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Fragment complementation has been used to investigate the role of chain connectivity in the catalytic reaction of phosphomannomutase/phosphoglucomutase (PMM/PGM) from Pseudomonas aeruginosa, a human pathogen. A heterodimer of PMM/PGM, created from fragments corresponding to its first three and fourth domains, was constructed and enzyme activity reconstituted. NMR spectra demonstrate that the fragment corresponding to the fourth (C-terminal) domain exists as a highly structured, independent folding domain, consistent with its varied conformation observed in enzyme-substrate complexes. Steady-state kinetics and thermodynamics studies reported here show that complete conformational freedom of Domain 4, because of the break in the polypeptide chain, is deleterious to catalytic efficiency primarily as a consequence of increased entropy. This extends observations from studies of the intact enzyme, which showed that the degree of flexibility of a hinge region is controlled by the precise sequence of amino acids optimized through evolutionary constraints. This work also sheds light on the functional advantage gained by combining separate folding domains into a single polypeptide chain.
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Affiliation(s)
- Andrew M Schramm
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA
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12
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Broome AM, Bhavsar N, Ramamurthy G, Newton G, Basilion JP. Expanding the utility of beta-galactosidase complementation: piece by piece. Mol Pharm 2010; 7:60-74. [PMID: 19899815 PMCID: PMC2835542 DOI: 10.1021/mp900188e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ability to image and quantify multiple biomarkers in disease necessitates the development of split reporter fragment platforms. We have divided the beta-galactosidase enzyme into unique, independent polypeptides that are able to reassemble and complement enzymatic activity in bacteria and in mammalian cells. We created two sets of complementing pairs that individually have no enzymatic activity. However, when brought into close geometric proximity, the complementing pairs associated resulting in detectable enzymatic activity. We then constructed a stable ligand complex composed of reporter fragment, linker, and targeting moiety. The targeting moiety, in this case a ligand, allowed cell surface receptor targeting in vitro. Further, we were able to simultaneously visualize two cell surface receptors implicated in cancer development, epidermal growth factor receptor and transferrin receptor, using complementing pairs of the ligand-reporter fragment complex.
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Affiliation(s)
- Ann-Marie Broome
- Department of Biomedical Engineering, Case Center for Imaging Research and National Foundation for Cancer Research Center for Molecular Imaging, Case Western Reserve University
- Department of Radiology, Case Center for Imaging Research and National Foundation for Cancer Research Center for Molecular Imaging, Case Western Reserve University
- Department of Dermatology, Case Western Reserve University
| | - Nihir Bhavsar
- Department of Biomedical Engineering, Case Center for Imaging Research and National Foundation for Cancer Research Center for Molecular Imaging, Case Western Reserve University
| | - Gopal Ramamurthy
- Department of Radiology, Case Center for Imaging Research and National Foundation for Cancer Research Center for Molecular Imaging, Case Western Reserve University
| | - Gail Newton
- Department of Pathology at Harvard Medical School, Brigham and Women’s Hospital, Boston, Massachusetts
| | - James P. Basilion
- Department of Biomedical Engineering, Case Center for Imaging Research and National Foundation for Cancer Research Center for Molecular Imaging, Case Western Reserve University
- Department of Radiology, Case Center for Imaging Research and National Foundation for Cancer Research Center for Molecular Imaging, Case Western Reserve University
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13
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The appearance of pyrrolysine in tRNAHis guanylyltransferase by neutral evolution. Proc Natl Acad Sci U S A 2009; 106:21103-8. [PMID: 19965368 DOI: 10.1073/pnas.0912072106] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
tRNA(His) guanylyltransferase (Thg1) post-transcriptionally adds a G (position -1) to the 5'-terminus of tRNA(His). The Methanosarcina acetivorans Thg1 (MaThg1) gene contains an in-frame TAG (amber) codon. Although a UAG codon typically directs translation termination, its presence in Methanosarcina mRNA may lead to pyrrolysine (Pyl) incorporation achieved by Pyl-tRNA(Pyl), the product of pyrrolysyl-tRNA synthetase. Sequencing of the MaThg1 gene and transcript confirmed the amber codon. Translation of MaThg1 mRNA led to a full-length, Pyl-containing, active enzyme as determined by immunoblotting, mass spectrometry, and biochemical analysis. The nature of the inserted amino acid at the position specified by UAG is not critical, as Pyl or Trp insertion yields active MaThg1 variants in M. acetivorans and equal amounts of full-length protein. These data suggest that Pyl insertion is akin to natural suppression and unlike the active stop codon reassignment that is required for selenocysteine insertion. Only three Pyl-containing proteins have been characterized previously, a set of methylamine methyltransferases in which Pyl is assumed to have specifically evolved to be a key active-site constituent. In contrast, Pyl in MaThg1 is a dispensable residue that appears to confer no selective advantage. Phylogenetic analysis suggests that Thg1 is becoming dispensable in the archaea, and furthermore supports the hypothesis that Pyl appeared in MaThg1 as the result of neutral evolution. This indicates that even the most unusual amino acid can play an ordinary role in proteins.
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14
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Zhou XL, Yao P, Ruan LL, Zhu B, Luo J, Qu LH, Wang ED. A unique insertion in the CP1 domain of Giardia lamblia leucyl-tRNA synthetase. Biochemistry 2009; 48:1340-7. [PMID: 19170608 DOI: 10.1021/bi801832j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Leucyl-tRNA synthetase (LeuRS) catalyzes the esterification of the tRNA(Leu) isoacceptor with leucine. It contains a large insertion domain, connective peptide 1 (CP1), for amino acid editing. Here, we cloned the gene encoding LeuRS from Giardia lamblia (GlLeuRS), one of the most ancient eukaryotes. GlLeuRS was purified from an Escherichia coli overproduction strain, and its properties were investigated. The isolated CP1 domain of GlLeuRS (GlLeuRS-CP1) was an active protein for editing mischarged G. lamblia tRNA(Leu)(AAG) (GltRNA(Leu)). Insertion of 49 amino acid residues within the CP1 domain (the so-called 49-amino acid motif) was important for the optimal aminoacylation activity of GlLeuRS and was crucial for the editing capacity of GlLeuRS-CP1. Additionally, the motif can confer editing activity on the editing-defective isolated CP1 domain from E. coli LeuRS (EcLeuRS-CP1). We also found that GlLeuRS could not rescue a Saccharomyces cerevisiae leuS null strain, suggesting different recognition modes for these two LeuRSs with respect to tRNA(Leu).
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Affiliation(s)
- Xiao-Long Zhou
- State Key Laboratory of Molecular Biology, Graduate School of the Chinese Academy of Sciences, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, People's Republic of China
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15
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Dutta S, Koide A, Koide S. High-throughput analysis of the protein sequence-stability landscape using a quantitative yeast surface two-hybrid system and fragment reconstitution. J Mol Biol 2008; 382:721-33. [PMID: 18674545 DOI: 10.1016/j.jmb.2008.07.036] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2008] [Revised: 07/07/2008] [Accepted: 07/12/2008] [Indexed: 12/11/2022]
Abstract
Stability evaluation of many mutants can lead to a better understanding of the sequence determinants of a structural motif and of factors governing protein stability and protein evolution. The traditional biophysical analysis of protein stability is low throughput, limiting our ability to widely explore sequence space in a quantitative manner. In this study, we have developed a high-throughput library screening method for quantifying stability changes, which is based on protein fragment reconstitution and yeast surface display. Our method exploits the thermodynamic linkage between protein stability and fragment reconstitution and the ability of the yeast surface display technique to quantitatively evaluate protein-protein interactions. The method was applied to a fibronectin type III (FN3) domain. Characterization of fragment reconstitution was facilitated by the co-expression of two FN3 fragments, thus establishing a yeast surface two-hybrid method. Importantly, our method does not rely on competition between clones and thus eliminates a common limitation of high-throughput selection methods in which the most stable variants are recovered predominantly. Thus, it allows for the isolation of sequences that exhibit a desired level of stability. We identified more than 100 unique sequences for a beta-bulge motif, which was significantly more informative than natural sequences of the FN3 family in revealing the sequence determinants for the beta-bulge. Our method provides a powerful means for the rapid assessment of the stability of many variants, for the systematic assessment of the contribution of different factors to protein stability, and for enhancement of the protein stability.
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Affiliation(s)
- Sanjib Dutta
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
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16
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Dun BQ, Wang XJ, Lu W, Zhao ZL, Hou SN, Zhang BM, Li GY, Evans TC, Xu MQ, Lin M. Reconstitution of glyphosate resistance from a split 5-enolpyruvyl shikimate-3-phosphate synthase gene in Escherichia coli and transgenic tobacco. Appl Environ Microbiol 2007; 73:7997-8000. [PMID: 17951442 PMCID: PMC2168149 DOI: 10.1128/aem.00956-07] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2007] [Accepted: 10/10/2007] [Indexed: 11/20/2022] Open
Abstract
A highly N-phosphonomethylglycine (glyphosate)-resistant Pseudomonas fluorescens G2 5-enolpyruvyl shikimate-3-phosphate synthase (EPSPS) was mapped to identify potential split sites using a transposon-based linker-scanning procedure. Intein-mediated protein complementation was used to reconstitute glyphosate resistance from the genetically divided G2 EPSPS gene in Escherichia coli strain ER2799 and transgenic tobacco.
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Affiliation(s)
- Bao-Qing Dun
- Biotechnology Research Institute, Chinese Academy of Agriculture Sciences, Beijing 100081, China.
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17
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Pastor JJ, Granados G, Carulla N, Rabanal F, Giralt E. Redesign of Protein Domains Using One-Bead-One-Compound Combinatorial Chemistry. J Am Chem Soc 2007; 129:14922-32. [DOI: 10.1021/ja073969x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jose J. Pastor
- Contribution from the Institute for Biomedical Research, Barcelona Science Park, 08028 Barcelona, Spain, and Department of Organic Chemistry, University of Barcelona, 08028 Barcelona Spain
| | - Giovanna Granados
- Contribution from the Institute for Biomedical Research, Barcelona Science Park, 08028 Barcelona, Spain, and Department of Organic Chemistry, University of Barcelona, 08028 Barcelona Spain
| | - Natàlia Carulla
- Contribution from the Institute for Biomedical Research, Barcelona Science Park, 08028 Barcelona, Spain, and Department of Organic Chemistry, University of Barcelona, 08028 Barcelona Spain
| | - Francesc Rabanal
- Contribution from the Institute for Biomedical Research, Barcelona Science Park, 08028 Barcelona, Spain, and Department of Organic Chemistry, University of Barcelona, 08028 Barcelona Spain
| | - Ernest Giralt
- Contribution from the Institute for Biomedical Research, Barcelona Science Park, 08028 Barcelona, Spain, and Department of Organic Chemistry, University of Barcelona, 08028 Barcelona Spain
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18
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Carey J, Lindman S, Bauer M, Linse S. Protein reconstitution and three-dimensional domain swapping: benefits and constraints of covalency. Protein Sci 2007; 16:2317-33. [PMID: 17962398 PMCID: PMC2211703 DOI: 10.1110/ps.072985007] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2007] [Revised: 07/30/2007] [Accepted: 08/01/2007] [Indexed: 10/22/2022]
Abstract
The phenomena of protein reconstitution and three-dimensional domain swapping reveal that highly similar structures can be obtained whether a protein is comprised of one or more polypeptide chains. In this review, we use protein reconstitution as a lens through which to examine the range of protein tolerance to chain interruptions and the roles of the primary structure in related features of protein structure and folding, including circular permutation, natively unfolded proteins, allostery, and amyloid fibril formation. The results imply that noncovalent interactions in a protein are sufficient to specify its structure under the constraints imposed by the covalent backbone.
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Affiliation(s)
- Jannette Carey
- Chemistry Department, Princeton University, NJ 08544-1009, USA.
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Xu Y, Xu G, Liu B, Gu G. Cre reconstitution allows for DNA recombination selectively in dual-marker-expressing cells in transgenic mice. Nucleic Acids Res 2007; 35:e126. [PMID: 17893102 PMCID: PMC2095822 DOI: 10.1093/nar/gkm559] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Cre/LoxP-based DNA recombination has been used to introduce desired DNA rearrangements in various organisms, having for example, greatly assisted genetic analyses in mice. For most applications, single gene promoters are used to drive Cre production for conditional gene activation/inactivation or lineage-tracing experiments. Such a manipulation introduces Cre in all cells in which the utilized promoter is active. To overcome the limited selectivity of single promoters for cell-type-specific recombination, we have explored the ‘dual promoter combinatorial control’ of Cre activity, so that Cre activity could be restricted to cells that express dual protein markers. We efficiently reconstituted Cre activity from two modified, inactive Cre fragments. Cre re-association was greatly enhanced by fusing the Cre fragments separately to peptides that can form a tight antiparallel leucine zipper. The co-expressed Cre fusion fragments showed substantial activity in cultured cells. As proof of principle of the utility of this technique in vivo for manipulating genes specifically in dual-marker-positive cells, we expressed each inactive Cre fragments in transgenic mice via individual promoters. Result showed the effective reconstitution of Cre activates LoxP recombination in the co-expressing cells.
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Affiliation(s)
- Yanwen Xu
- Program in Developmental Biology and Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA, Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong and Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, TN 37208, USA
| | - Gang Xu
- Program in Developmental Biology and Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA, Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong and Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, TN 37208, USA
| | - Bindong Liu
- Program in Developmental Biology and Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA, Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong and Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, TN 37208, USA
| | - Guoqiang Gu
- Program in Developmental Biology and Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA, Department of Medicine and Therapeutics, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong and Center for AIDS Health Disparities Research, Meharry Medical College, Nashville, TN 37208, USA
- *To whom correspondence should be addressed. +1 615 936 3634+1 615 936 5673
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20
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Sun YC, Li Y, Zhang H, Yan HQ, Dowling DN, Wang YP. Reconstitution of the enzyme AroA and its glyphosate tolerance by fragment complementation. FEBS Lett 2006; 580:1521-7. [PMID: 16469313 DOI: 10.1016/j.febslet.2006.01.075] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2005] [Revised: 01/07/2006] [Accepted: 01/10/2006] [Indexed: 11/27/2022]
Abstract
5-Enolpyruvylshikimate-3-phosphate (EPSP) synthase (AroA) is a key enzyme in the aromatic amino acid biosynthetic pathway in microorganisms and plants, and is the target of the herbicide glyphosate. Glyphosate tolerance activity of the enzyme could be obtained by natural occurrence or by site-directed mutagenesis. A functional Pseudomonas putida AroA was obtained by co-expression of two protein fragments AroA(P. putida)-N210 and AroA(P. putida)-C212 in Escherichia coli aroA mutant strain AB2829. From sequence analysis, the equivalent split site on E. coli AroA was chosen for further study. The result indicated that functional E. coli AroA could also be reconstituted from two protein fragments AroA(E. coli)-N218 and AroA(E. coli)-C219, under both in vivo and in vitro conditions. This result suggested that the fragment complementation property of this family of enzyme may be general. Additional experiments indicated that the glyphosate tolerance property of AroA could also be reconstituted in parallel with its enzyme activity. The implication of this finding is discussed.
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Affiliation(s)
- Yi-Cheng Sun
- National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, PR China
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21
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Mock ML, Michon T, van Hest JCM, Tirrell DA. Stereoselective Incorporation of an Unsaturated Isoleucine Analogue into a Protein Expressed in E. coli. Chembiochem 2006; 7:83-7. [PMID: 16397872 DOI: 10.1002/cbic.200500201] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The unsaturated amino acid 2-amino-3-methyl-4-pentenoic acid (E-Ile) was prepared in the form of its (2S,3S),(2R,3R) and (2S,3R),(2R,3S) stereoisomeric pairs. The translational activities of SS-E-Ile and SR-E-Ile were assessed in an E. coli strain rendered auxotrophic for isoleucine. SS-E-Ile was incorporated into the test protein mouse dihydrofolate reductase (mDHFR) in place of isoleucine at a rate of up to 72 %; SR-E-Ile yielded no conclusive evidence for incorporation. ATP/PPi exchange assays indicated that SS-E-Ile was activated by the isoleucyl-tRNA synthetase at a rate comparable to that characteristic of isoleucine; SR-E-Ile was activated approximately 100-times more slowly than SS-E-Ile.
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Affiliation(s)
- Marissa L Mock
- Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 210-41, Pasadena, California 91125, USA
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22
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Nicolás E, Ferrer C, Taboada L, Giralt E. Coupe du Roi Bisection of Proteins. Spontaneous Tetramerization of Two Peptides That Span the Sequence of the Rabbit Uteroglobin Monomer. J Am Chem Soc 2005; 127:17719-33. [PMID: 16351101 DOI: 10.1021/ja0539793] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The study of dividing objects into isometric segments has yielded novel approaches to the synthesis of high-symmetry organic compounds. Reported herein is the first application of this concept to a protein, rabbit uteroglobin (UG). Bisection of UG into two identical homochiral segments led to the design of the heterodimeric 70mer peptide alpha(1,2)-S-S-alpha(3,4) that spans the sequence of the native UG monomer. The ability of this compound to form a globular 140mer tetramer consisting of two noncovalently bound heterodimers was assessed by ultracentrifugation at sedimentation equilibrium and by fluorescent spectroscopy. On the other hand, the monomeric peptides alpha(1,2)-SH and alpha(3,4)-SH were shown to selectively form the alpha(1,2)-S-S-alpha(3,4) heterodimer via spontaneous air oxidation in phosphate buffer at neutral pH.
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Affiliation(s)
- Ernesto Nicolás
- Department of Organic Chemistry, Martí i Franquès 1, Universitat de Barcelona, Barcelona 08028, Spain.
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23
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Dutta S, Batori V, Koide A, Koide S. High-affinity fragment complementation of a fibronectin type III domain and its application to stability enhancement. Protein Sci 2005; 14:2838-48. [PMID: 16199661 PMCID: PMC2253215 DOI: 10.1110/ps.051603005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The tenth fibronectin type III (FN3) domain of human fibronectin (FNfn10), a prototype of the ubiquitous FN3 domain, is a small, monomeric beta-sandwich protein. In this study, we have bisected FNfn10 in each loop to generate a total of six fragment pairs. We found that fragment pairs bisected at multiple loops of FNfn10 show complementation in vivo as tested with a yeast two-hybrid system. The dissociation constant of these fragment pairs determined in vitro were as low as 3 nM, resulting in one of the tightest fragment complementation systems reported so far. Furthermore, we show that the affinity of fragment complementation is correlated with the stability of the uncut parent protein. Exploring this correlation, we screened a yeast two-hybrid library of one fragment and identified mutations that suppress the effect of a destabilizing mutation in the other fragment. One of the identified mutations significantly increased the stability of the uncut wild-type protein, proving that fragment complementation can be used as a novel strategy for the selection of proteins with enhanced stability.
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Affiliation(s)
- Sanjib Dutta
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA
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24
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Zhao MW, Zhu B, Hao R, Xu MG, Eriani G, Wang ED. Leucyl-tRNA synthetase from the ancestral bacterium Aquifex aeolicus contains relics of synthetase evolution. EMBO J 2005; 24:1430-9. [PMID: 15775966 PMCID: PMC1142543 DOI: 10.1038/sj.emboj.7600618] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2004] [Accepted: 02/15/2005] [Indexed: 11/10/2022] Open
Abstract
The editing reactions catalyzed by aminoacyl-tRNA synthetases are critical for the faithful protein synthesis by correcting misactivated amino acids and misaminoacylated tRNAs. We report that the isolated editing domain of leucyl-tRNA synthetase from the deep-rooted bacterium Aquifex aeolicus (alphabeta-LeuRS) catalyzes the hydrolytic editing of both mischarged tRNA(Leu) and minihelix(Leu). Within the domain, we have identified a crucial 20-amino-acid peptide that confers editing capacity when transplanted into the inactive Escherichia coli LeuRS editing domain. Likewise, fusion of the beta-subunit of alphabeta-LeuRS to the E. coli editing domain activates its editing function. These results suggest that alphabeta-LeuRS still carries the basic features from a primitive synthetase molecule. It has a remarkable capacity to transfer autonomous active modules, which is consistent with the idea that modern synthetases arose after exchange of small idiosyncratic domains. It also has a unique alphabeta-heterodimeric structure with separated catalytic and tRNA-binding sites. Such an organization supports the tRNA/synthetase coevolution theory that predicts sequential addition of tRNA and synthetase domains.
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Affiliation(s)
- Ming-Wei Zhao
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, Shanghai, PR China
| | - Bin Zhu
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, Shanghai, PR China
| | - Rui Hao
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, Shanghai, PR China
| | - Min-Gang Xu
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, Shanghai, PR China
| | - Gilbert Eriani
- UPR9002, IBMC du CNRS and Université Louis Pasteur, Strasbourg, France
| | - En-Duo Wang
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, Shanghai, PR China
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, 320 Yeu Yang Road, Shanghai 200031, China. Tel.: +86 21 549 21241; Fax: +86 21 549 21011; E-mail:
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25
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Paschon DE, Ostermeier M. Construction of protein fragment complementation libraries using incremental truncation. Methods Enzymol 2004; 388:103-16. [PMID: 15289065 DOI: 10.1016/s0076-6879(04)88010-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Affiliation(s)
- David E Paschon
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
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26
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Pezo V, Metzgar D, Hendrickson TL, Waas WF, Hazebrouck S, Döring V, Marlière P, Schimmel P, De Crécy-Lagard V. Artificially ambiguous genetic code confers growth yield advantage. Proc Natl Acad Sci U S A 2004; 101:8593-7. [PMID: 15163798 PMCID: PMC423239 DOI: 10.1073/pnas.0402893101] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A primitive genetic code is thought to have encoded statistical, ambiguous proteins in which more than one amino acid was inserted at a given codon. The relative vitality of organisms bearing ambiguous proteins and the kinds of pressures that forced development of the highly specific modern genetic code are unknown. Previous work demonstrated that, in the absence of selective pressure, enforced ambiguity in cells leads to death or to sequence reversion to eliminate the ambiguous phenotype. Here, we report the creation of a nonreverting strain of bacteria that produced statistical proteins. Ablating the editing activity of isoleucyl-tRNA synthetase resulted in an ambiguous code in which, through supplementation of a limited supply of isoleucine with an alternative amino acid that was noncoding, the mutant generating statistical proteins was favored over the wild-type isogenic strain. Such organisms harboring statistical proteins could have had an enhanced adaptive capacity and could have played an important role in the early development of living systems.
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Affiliation(s)
- V Pezo
- Evologic SA, 93 Rue Henri Rochefort, 91000 Evry, France
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27
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28
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Hiraga K, Yamagishi A, Oshima T. Mapping of unit boundaries of a protein: exhaustive search for permissive sites for duplication by complementation analysis of random fragment libraries of tryptophan synthase alpha subunit. J Mol Biol 2004; 335:1093-104. [PMID: 14698302 DOI: 10.1016/j.jmb.2003.11.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
To identify peptide units that make up a single-domain protein, we searched for possible combinations of N and C-fragments that exhibit functional complementation, and attempted an exhaustive evaluation of peptide unit boundaries. The tryptophan synthase alpha subunit was used as a model enzyme, which has a single TIM (beta8/alpha8) barrel domain. Libraries comprising randomly digested N and C-fragments were constructed, and clones expressing enzymatic activity were selected by the ability to confer growth of the Escherichia coli trpA mutant on a medium lacking tryptophan. More than 50 clones were obtained, and two cleavable positions were found on the loops after extra-helix 2' and helix 5. Half of the clones harbored N and C-fragments having an overlap between two fragments. The remaining clones harbored one fragment made by the fusion of N and C-fragments with insertional sequence duplication. Mapping the frequency of occurrence of fragment overlap and insertional duplication showed significant peaks at two loops, which coincide with the cleavable sites. These results suggest that the boundaries of unit fragments are located at these positions, and that bisection, fragment overlap and insertion are all possible at the unit boundaries.
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Affiliation(s)
- Kaori Hiraga
- Department of Molecular Biology, Tokyo University of Pharmacy and Life Science, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan
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29
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Du X, Wang ED. E292 is important for the aminoacylation activity of Escherichia coli leucyl-tRNA synthetase. JOURNAL OF PROTEIN CHEMISTRY 2003; 22:71-6. [PMID: 12739900 DOI: 10.1023/a:1023071928587] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Escherichia coli leucyl-tRNA synthetase (LeuRS) has a large connecting polypeptide (CP1) inserted into its active site. It was demonstrated that the peptide bond between E292-A293 was crucial for the aminoacylation activity of E. coli LeuRS. To investigate the effect of E292 on the function of Escherichia coli LeuRS, E292 was mutated to K, F, S, D, Q and A. These mutations at 292 did not change the specific activity of the amino acid activation reaction. Though the conformational change of these mutants was not detected in CD, their aminoacylation activities were impaired to varying extents. The mutation of E to K decreased the aminoacylation activity to the largest extent. Analysis of the Km values of these mutants for the three substrates showed that the E292 was not involved in the binding of leucine and that all mutants had stronger binding with ATP.
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Affiliation(s)
- Xing Du
- State Key Laboratory of Molecular Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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30
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Xu MG, Chen JF, Martin F, Zhao MW, Eriani G, Wang ED. Leucyl-tRNA synthetase consisting of two subunits from hyperthermophilic bacteria Aquifex aeolicus. J Biol Chem 2002; 277:41590-6. [PMID: 12196521 DOI: 10.1074/jbc.m205126200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In a hyperthermophilic bacterium, Aquifex aeolicus, leucyl-tRNA synthetase (LeuRS) consists of two non-identical polypeptide subunits (alpha and beta), different from the canonical LeuRS, which has a single polypeptide chain. By PCR, using genome DNA of A. aeolicus as a template, genes encoding the alpha and beta subunits were amplified and cloned in Escherichia coli. The alpha subunit could not be expressed stably in vivo, whereas the beta subunit was overproduced and purified by a simple procedure. The beta subunit was inactive in catalysis but was able to bind tRNA(Leu). Interestingly, the heterodimer alphabeta-LeuRS could be overproduced in E. coli cells containing both genes and was purified to 95% homogeneity as a hybrid dimer. The kinetics of A. aeolicus LeuRS in pre-steady and steady states and cross-recognition of LeuRS and tRNA(Leu) from A. aeolicus and E. coli were studied. Magnesium concentration, pH value, and temperature aminoacylation optima were determined to be 12 mm, 7.8, and 70 degrees C, respectively. Under optimal conditions, A. aeolicus alphabeta-LeuRS is stable up to 65 degrees C.
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Affiliation(s)
- Min-Gang Xu
- State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, China
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31
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Garg RP, Ma Y, Hoyt JC, Parry RJ. Molecular characterization and analysis of the biosynthetic gene cluster for the azoxy antibiotic valanimycin. Mol Microbiol 2002; 46:505-17. [PMID: 12406225 DOI: 10.1046/j.1365-2958.2002.03169.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Streptomyces viridifaciens MG456-hF10 produces the antibiotic valanimycin, a naturally occurring azoxy compound. Valanimycin is known to be derived from valine and serine with the intermediacy of isobutylamine and isobutylhydroxylamine, but little is known about the stages in the pathway leading to the formation of the azoxy group. In previous studies, a cosmid containing S. viridifaciens DNA was isolated that conferred valanimycin production upon Strepto-myces lividans TK24. Subcloning of DNA from the valanimycin-producing cosmid has led to the identi-fication of a 22 kb segment of DNA sufficient to allow valanimycin production in S. lividans TK24. Sequencing of this DNA segment and the surrounding DNA revealed the presence of 20 genes. Gene disruption experiments defined the boundaries of the valanimycin gene cluster, which appears to contain 14 genes. The cluster includes an amino acid decar-boxylase gene (vlmD), a valanimycin resistance gene (vlmF ), at least two regulatory genes (vlmE, vlmI ), two genes encoding a flavin monooxygenase (vlmH, vlmR), a seryl tRNA synthetase gene (vlmL ) and seven genes of unknown function. Overproduction and characterization of VlmD demonstrated that it catalyses the decarboxylation of l-valine. An unusual feature of the valanimycin gene cluster is that four genes involved in branched amino acid biosynthesis are located near its 5' end.
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Affiliation(s)
- Ram P Garg
- Department of Chemistry, Rice University, St Houston, TX 77005, USA
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32
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Abstract
Protein folding is a topic of fundamental interest since it concerns the mechanisms by which the genetic message is translated into the three-dimensional and functional structure of proteins. In these post-genomic times, the knowledge of the fundamental principles are required in the exploitation of the information contained in the increasing number of sequenced genomes. Protein folding also has practical applications in the understanding of different pathologies and the development of novel therapeutics to prevent diseases associated with protein misfolding and aggregation. Significant advances have been made ranging from the Anfinsen postulate to the "new view" which describes the folding process in terms of an energy landscape. These new insights arise from both theoretical and experimental studies. The problem of folding in the cellular environment is briefly discussed. The modern view of misfolding and aggregation processes that are involved in several pathologies such as prion and Alzheimer diseases. Several approaches of structure prediction, which is a very active field of research, are described.
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Affiliation(s)
- Jeannine M Yon
- Institut de Biochimie Biophysique Moléculaire et Cellulaire, UMR Centre National de la Recherche Scientifique, Université de Paris-Sud, Orsay, France.
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33
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Nordin BE, Schimmel P. Plasticity of recognition of the 3'-end of mischarged tRNA by class I aminoacyl-tRNA synthetases. J Biol Chem 2002; 277:20510-7. [PMID: 11923317 DOI: 10.1074/jbc.m202023200] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Certain aminoacyl-tRNA synthetases prevent potential errors in protein synthesis through deacylation of mischarged tRNAs. For example, the close homologs isoleucyl-tRNA synthetase (IleRS) and valyl-tRNA synthetase (ValRS) deacylate Val-tRNA(Ile) and Thr-tRNA(Val), respectively. Here we examined the chemical requirements at the 3'-end of the tRNA for these hydrolysis reactions. Single atom substitutions at the 2'- and 3'-hydroxyls of a variety of mischarged RNAs revealed that, while acylation is at the 2'-OH for both enzymes, IleRS catalyzes deacylation specifically from the 3'-OH and not from the 2'-OH. In contrast, ValRS can deacylate non-cognate amino acids from the 2'-OH. Moreover, for IleRS the specificity for a 3'-O location of the scissile ester bond could be forced to the 2'-position by introduction of a 3'-O-methyl moiety. Cumulatively, these and other results suggest that the editing sites of these class I aminoacyl-tRNA synthetases have a degree of inherent plasticity for substrate recognition. The ability to adapt to subtle differences in mischarged RNAs may be important for the high accuracy of aminoacylation.
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Affiliation(s)
- Brian E Nordin
- Skaggs Institute for Chemical Biology and the Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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34
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Hendrickson TL, Nomanbhoy TK, de Crécy-Lagard V, Fukai S, Nureki O, Yokoyama S, Schimmel P. Mutational separation of two pathways for editing by a class I tRNA synthetase. Mol Cell 2002; 9:353-62. [PMID: 11864608 DOI: 10.1016/s1097-2765(02)00449-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Aminoacyl tRNA synthetases (aaRSs) catalyze the first step in protein biosynthesis, establishing a connection between codons and amino acids. To maintain accuracy, aaRSs have evolved a second active site that eliminates noncognate amino acids. Isoleucyl tRNA synthetase edits valine by two tRNA(Ile)-dependent pathways: hydrolysis of valyl adenylate (Val-AMP, pretransfer editing) and hydrolysis of mischarged Val-tRNA(Ile) (posttransfer editing). Not understood is how a single editing site processes two distinct substrates--an adenylate and an aminoacyl tRNA ester. We report here distinct mutations within the center for editing that alter adenylate but not aminoacyl ester hydrolysis, and vice versa. These results are consistent with a molecular model that shows that the single editing active site contains two valyl binding pockets, one specific for each substrate.
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Affiliation(s)
- Tamara L Hendrickson
- The Scripps Research Institute and, The Skaggs Institute for Chemical Biology, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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35
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Stathopoulos C, Kim W, Li T, Anderson I, Deutsch B, Palioura S, Whitman W, Söll D. Cysteinyl-tRNA synthetase is not essential for viability of the archaeon Methanococcus maripaludis. Proc Natl Acad Sci U S A 2001; 98:14292-7. [PMID: 11717392 PMCID: PMC64675 DOI: 10.1073/pnas.201540498] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The methanogenic archaea Methanocaldococcus jannaschii and Methanothermobacter thermautotrophicus contain a dual-specificity prolyl-tRNA synthetase (ProCysRS) that accurately forms both prolyl-tRNA (Pro-tRNA) and cysteinyl-tRNA (Cys-tRNA) suitable for in vivo translation. This intriguing enzyme may even perform its dual role in organisms that possess a canonical single-specificity cysteinyl-tRNA synthetase (CysRS), raising the question as to whether this latter aminoacyl-tRNA synthetase is indeed required for cell viability. To test the postulate that all synthetase genes are essential, we disrupted the cysS gene (encoding CysRS) of Methanococcus maripaludis. The knockout strain was viable under normal growth conditions. Biochemical analysis showed that the pure M. maripaludis ProCysRS was capable of forming Cys-tRNA, implying that the dual-specificity enzyme compensates in vivo for the loss of CysRS. The canonical CysRS has a higher affinity for cysteine than ProCysRS, a reason why M. maripaludis may have acquired cysS by a late lateral gene transfer. These data challenge the notion that all twenty aminoacyl-tRNA synthetases are essential for the viability of a cell.
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Affiliation(s)
- C Stathopoulos
- Department of Molecular Biophysics, Yale University, New Haven, CT 06520-8114, USA
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36
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Dubail I, Autret N, Beretti JL, Kayal S, Berche P, Charbit A. Functional assembly of two membrane-binding domains in listeriolysin O, the cytolysin of Listeria monocytogenes. MICROBIOLOGY (READING, ENGLAND) 2001; 147:2679-2688. [PMID: 11577147 DOI: 10.1099/00221287-147-10-2679] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Listeriolysin O (LLO) is a major virulence factor secreted by the pathogenic Listeria monocytogenes and acts as pore-forming cytolysin. Based on sequence similarities between LLO and perfringolysin (PFO), the cytolysin from Clostridium perfringens of known crystallographic structure, two truncated LLO proteins were produced: LLO-d123, comprising the first three predicted domains, and LLO-d4, the last C-terminal domain. The two proteins were efficiently secreted into the culture supernatant of L. monocytogenes and were able to bind to cell membranes. Strikingly, when expressed simultaneously, the two secreted domains LLO-d123 and LLO-d4 reassembled into a haemolytically active form. Two in-frame linker insertions were generated in the hinge region between the d123 and d4 domains. In both cases, the insertion created a major cleavage site for proteolytic degradation and abolished cytolytic activity, which might suggest that the region connecting d123 and d4 participates in the interaction between the two portions of the monomer.
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Affiliation(s)
- Iharilalao Dubail
- Laboratoire de Microbiologie, INSERM U-411, Faculté de Médecine Necker-Enfants Malades, 156 rue de Vaugirard, 75730 Paris Cedex 15, France1
| | - Nicolas Autret
- Laboratoire de Microbiologie, INSERM U-411, Faculté de Médecine Necker-Enfants Malades, 156 rue de Vaugirard, 75730 Paris Cedex 15, France1
| | - Jean-Luc Beretti
- Laboratoire de Microbiologie, INSERM U-411, Faculté de Médecine Necker-Enfants Malades, 156 rue de Vaugirard, 75730 Paris Cedex 15, France1
| | - Samer Kayal
- Laboratoire de Microbiologie, INSERM U-411, Faculté de Médecine Necker-Enfants Malades, 156 rue de Vaugirard, 75730 Paris Cedex 15, France1
| | - Patrick Berche
- Laboratoire de Microbiologie, INSERM U-411, Faculté de Médecine Necker-Enfants Malades, 156 rue de Vaugirard, 75730 Paris Cedex 15, France1
| | - Alain Charbit
- Laboratoire de Microbiologie, INSERM U-411, Faculté de Médecine Necker-Enfants Malades, 156 rue de Vaugirard, 75730 Paris Cedex 15, France1
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Nomanbhoy TK, Schimmel P. Active site of an aminoacyl-tRNA synthetase dissected by energy-transfer-dependent fluorescence. Bioorg Med Chem Lett 2001; 11:1485-91. [PMID: 11412966 DOI: 10.1016/s0960-894x(01)00127-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Aminoacyl-tRNA synthetases establish the rules of the genetic code by catalyzing attachment of amino acids to specific transfer RNAs (tRNAs) that bear the anticodon triplets of the code. Each of the 20 amino acids has its own distinct aminoacyl-tRNA synthetase. Here we use energy-transfer-dependent fluorescence from the nucleotide probe N-methylanthraniloyl dATP (mdATP) to investigate the active site of a specific aminoacyl-tRNA synthetase. Interaction of the enzyme with the cognate amino acid and formation of the aminoacyl adenylate intermediate were detected. In addition to providing a convenient tool to characterize enzymatic parameters, the probe allowed investigation of the role of conserved residues within the active site. Specifically, a residue that is critical for binding could be distinguished from one that is important for the transition state of adenylate formation. Amino acid binding and adenylate synthesis by two other aminoacyl-tRNA synthetases was also investigated with mdATP. Thus, a key step in the synthesis of aminoacyl-tRNA can in general be dissected with this probe.
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Affiliation(s)
- T K Nomanbhoy
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, Beckman Center, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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38
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Ni X, Schachman HK. In vivo assembly of aspartate transcarbamoylase from fragmented and circularly permuted catalytic polypeptide chains. Protein Sci 2001; 10:519-27. [PMID: 11344320 PMCID: PMC2374128 DOI: 10.1110/ps.38901] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Previous studies on Escherichia coli aspartate transcarbamoylase (ATCase) demonstrated that active, stable enzyme was formed in vivo from complementing polypeptides of the catalytic (c) chain encoded by gene fragments derived from the pyrBI operon. However, the enzyme lacked the allosteric properties characteristic of wild-type ATCase. In order to determine whether the loss of homotropic and heterotropic properties was attributable to the location of the interruption in the polypeptide chain rather than to the lack of continuity, we constructed a series of fragmented genes so that the breaks in the polypeptide chains would be dispersed in different domains and diverse regions of the structure. Also, analogous molecules containing circularly permuted c chains with altered termini were constructed for comparison with the ATCase molecules containing fragmented c chains. Studies were performed on four sets of ATCase molecules containing cleaved c chains at positions between residues 98 and 99, 121 and 122, 180 and 181, and 221 and 222; the corresponding circularly permuted chains had N termini at positions 99, 122, 181, and 222. All of the ATCase molecules containing fragmented or circularly permuted c chains exhibited the homotropic and heterotropic properties characteristic of the wild-type enzyme. Hill coefficients (n(H:)) and changes in them upon the addition of ATP and CTP were similar to those observed with wild-type ATCase. In addition, the conformational changes revealed by the decrease in sedimentation coefficient upon the addition of a bisubstrate analog were virtually identical to that for the wild-type enzyme. Differential scanning calorimetry showed that neither the breakage of the polypeptide chains nor the newly formed covalent bond between the termini in the wild-type enzyme had a significant impact on the thermal stability of the assembled dodecamers. The studies demonstrate that continuity of the polypeptide chain within structural domains is not essential for the assembly, activity, and allosteric properties of ATCase.
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Affiliation(s)
- X Ni
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
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39
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Wigley WC, Stidham RD, Smith NM, Hunt JF, Thomas PJ. Protein solubility and folding monitored in vivo by structural complementation of a genetic marker protein. Nat Biotechnol 2001; 19:131-6. [PMID: 11175726 DOI: 10.1038/84389] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Protein misfolding is the basis of a number of human diseases and presents an obstacle to the production of soluble recombinant proteins. We present a general method to assess the solubility and folding of proteins in vivo. The basis of this assay is structural complementation between the alpha- and omega- fragments of beta-galactosidase (beta-gal). Fusions of the alpha-fragment to the C terminus of target proteins with widely varying in vivo folding yield and/or solubility levels, including the Alzheimer's amyloid beta (A beta) peptide and a non-amyloidogenic mutant thereof, reveal an unambiguous correlation between beta-gal activity and the solubility/folding of the target. Thus, structural complementation provides a means of monitoring protein solubility/misfolding in vivo, and should find utility in the screening for compounds that influence the pathological consequences of these processes.
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Affiliation(s)
- W C Wigley
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas TX 75235, USA
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40
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Stacey MG, Kopp OR, Kim TH, von Arnim AG. Modular domain structure of Arabidopsis COP1. Reconstitution of activity by fragment complementation and mutational analysis of a nuclear localization signal in planta. PLANT PHYSIOLOGY 2000; 124:979-90. [PMID: 11080276 PMCID: PMC59198 DOI: 10.1104/pp.124.3.979] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2000] [Accepted: 06/08/2000] [Indexed: 05/21/2023]
Abstract
The Arabidopsis COP1 protein functions as a developmental regulator, in part by repressing photomorphogenesis in darkness. Using complementation of a cop1 loss-of-function allele with transgenes expressing fusions of cop1 mutant proteins and beta-glucuronidase, it was confirmed that COP1 consists of two modules, an amino terminal module conferring a basal function during development and a carboxyl terminal module conferring repression of photomorphogenesis. The amino-terminal zinc-binding domain of COP1 was indispensable for COP1 function. In contrast, the debilitating effects of site-directed mutations in the single nuclear localization signal of COP1 were partially compensated by high-level transgene expression. The carboxyl-terminal module of COP1, though unable to substantially ameliorate a cop1 loss-of-function allele on its own, was sufficient for conferring a light-quality-dependent hyperetiolation phenotype in the presence of wild-type COP1. Moreover, partial COP1 activity could be reconstituted in vivo from two non-covalently linked, complementary polypeptides that represent the two functional modules of COP1. Evidence is presented for efficient association of the two sub-fragments of the split COP1 protein in Arabidopsis and in a yeast two-hybrid assay.
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Affiliation(s)
- M G Stacey
- Department of Botany, The University of Tennessee, Knoxville, Tennessee 37996-1100, USA
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41
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42
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Chan KW, Csanády L, Seto-Young D, Nairn AC, Gadsby DC. Severed molecules functionally define the boundaries of the cystic fibrosis transmembrane conductance regulator's NH(2)-terminal nucleotide binding domain. J Gen Physiol 2000; 116:163-80. [PMID: 10919864 PMCID: PMC2229491 DOI: 10.1085/jgp.116.2.163] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The cystic fibrosis transmembrane conductance regulator is a Cl(-) channel that belongs to the family of ATP-binding cassette proteins. The CFTR polypeptide comprises two transmembrane domains, two nucleotide binding domains (NBD1 and NBD2), and a regulatory (R) domain. Gating of the channel is controlled by kinase-mediated phosphorylation of the R domain and by ATP binding, and, likely, hydrolysis at the NBDs. Exon 13 of the CFTR gene encodes amino acids (aa's) 590-830, which were originally ascribed to the R domain. In this study, CFTR channels were severed near likely NH(2)- or COOH-terminal boundaries of NBD1. CFTR channel activity, assayed using two-microelectrode voltage clamp and excised patch recordings, provided a sensitive measure of successful assembly of each pair of channel segments as the sever point was systematically shifted along the primary sequence. Substantial channel activity was taken as an indication that NBD1 was functionally intact. This approach revealed that the COOH terminus of NBD1 extends beyond aa 590 and lies between aa's 622 and 634, while the NH(2) terminus of NBD1 lies between aa's 432 and 449. To facilitate biochemical studies of the expressed proteins, a Flag epitope was added to the NH(2) termini of full length CFTR, and of CFTR segments truncated before the normal COOH terminus (aa 1480). The functionally identified NBD1 boundaries are supported by Western blotting, coimmunoprecipitation, and deglycosylation studies, which showed that an NH(2)-terminal segment representing aa's 3-622 (Flag3-622) or 3-633 (Flag3-633) could physically associate with a COOH-terminal fragment representing aa's 634-1480 (634-1480); however, the latter fragment was glycosylated to the mature form only in the presence of Flag3-633. Similarly, 433-1480 could physically associate with Flag3-432 and was glycosylated to the mature form; however, 449-1480 protein seemed unstable and could hardly be detected even when expressed with Flag3-432. In excised-patch recordings, all functional severed CFTR channels displayed the hallmark characteristics of CFTR, including the requirement of phosphorylation and exposure to MgATP for gating, ability to be locked open by pyrophosphate or AMP-PNP, small single channel conductances, and high apparent affinity of channel opening by MgATP. Our definitions of the boundaries of the NBD1 domain in CFTR are supported by comparison with the solved NBD structures of HisP and RbsA.
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Affiliation(s)
- Kim W. Chan
- Laboratory of Cardiac/Membrane Physiology, The Rockefeller University, New York, New York 10021
| | - László Csanády
- Laboratory of Cardiac/Membrane Physiology, The Rockefeller University, New York, New York 10021
| | - Donna Seto-Young
- Laboratory of Cardiac/Membrane Physiology, The Rockefeller University, New York, New York 10021
| | - Angus C. Nairn
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, New York 10021
| | - David C. Gadsby
- Laboratory of Cardiac/Membrane Physiology, The Rockefeller University, New York, New York 10021
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43
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Ghosh I, Hamilton AD, Regan L. Antiparallel Leucine Zipper-Directed Protein Reassembly: Application to the Green Fluorescent Protein. J Am Chem Soc 2000. [DOI: 10.1021/ja994421w] [Citation(s) in RCA: 394] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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44
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Sugiura I, Nureki O, Ugaji-Yoshikawa Y, Kuwabara S, Shimada A, Tateno M, Lorber B, Giegé R, Moras D, Yokoyama S, Konno M. The 2.0 A crystal structure of Thermus thermophilus methionyl-tRNA synthetase reveals two RNA-binding modules. Structure 2000; 8:197-208. [PMID: 10673435 DOI: 10.1016/s0969-2126(00)00095-2] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
BACKGROUND The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. The 10 class I synthetases are considered to have in common the catalytic domain structure based on the Rossmann fold, which is totally different from the class II catalytic domain structure. The class I synthetases are further divided into three subclasses, a, b and c, according to sequence homology. No conserved structural features for tRNA recognition by class I synthetases have been established. RESULTS We determined the crystal structure of the class Ia methionyl-tRNA synthetase (MetRS) at 2.0 A resolution, using MetRS from an extreme thermophile, Thermus thermophilus HB8. The T. thermophilus MetRS structure is in full agreement with the biochemical and genetic data from Escherichia coli MetRS. The conserved 'anticodon-binding' residues are spatially clustered on an alpha-helix-bundle domain. The Rossmann-fold and anticodon-binding domains are connected by a beta-alpha-alpha-beta-alpha topology ('SC fold') domain that contains the class I specific KMSKS motif. CONCLUSIONS The alpha-helix-bundle domain identified in the MetRS structure is the signature of the class Ia enzymes, as it was also identified in the class Ia structures of the isoleucyl- and arginyl-tRNA synthetases. The beta-alpha-alpha-beta-alpha topology domain, which can now be identified in all known structures of the class Ia and Ib synthetases, is likely to dock with the inner side of the L-shaped tRNA, thereby positioning the anticodon stem.
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Affiliation(s)
- I Sugiura
- Department of Chemistry, Faculty of Science, Ochanomizu University, Otsuka, Bunkyo-Ku, 112-8610, Japan
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45
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Nomanbhoy TK, Hendrickson TL, Schimmel P. Transfer RNA-dependent translocation of misactivated amino acids to prevent errors in protein synthesis. Mol Cell 1999; 4:519-28. [PMID: 10549284 DOI: 10.1016/s1097-2765(00)80203-8] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Misactivation of amino acids by aminoacyl-tRNA synthetases can lead to significant errors in protein synthesis that are prevented by editing reactions. As an example, discrete sites in isoleucyl-tRNA synthetase for amino acid activation and editing are about 25 A apart. The details of how misactivated valine is translocated from one site to the other are unknown. Here, we present a kinetic study in which a fluorescent probe is used to monitor translocation of misactivated valine from the active site to the editing site. Isoleucine-specific tRNA, and not other tRNAs, is essential for translocation of misactivated valine. Misactivation and translocation occur on the same enzyme molecule, with translocation being rate limiting for editing. These results illustrate a remarkable capacity for a specific tRNA to enhance amino acid fine structure recognition by triggering a unimolecular translocation event.
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Affiliation(s)
- T K Nomanbhoy
- Skaggs Institute for Chemical Biology, Scripps Research Institute, Beckman Center, La Jolla, California 92037, USA
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46
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Michaels JE, Shiba K, Miller WT. Autonomous folding of a C-terminal inhibitory fragment of Escherichia coli isoleucine-tRNA synthetase. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1433:103-9. [PMID: 10446363 DOI: 10.1016/s0167-4838(99)00153-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
We previously reported that C-terminal fragments of Escherichia coli Ile-tRNA synthetase, a monomeric enzyme of 939 amino acids, act as dominant negative inhibitors of the wild-type enzyme in vivo and in vitro. Our experiments suggested that it is possible to block the functional assembly of a monomeric protein by interfering with the folding pathway. We postulated that the inhibitory C-terminal fragments fold autonomously, and in the presence of full-length Ile-tRNA synthetase, trap the N-terminal portion of polypeptide in an unproductive complex. Here, we report the results of experiments aimed at understanding the mechanism of dominant negative inhibition. We have carried out biophysical experiments on fragment 585-939 of Ile-tRNA synthetase, which we previously determined to be the minimal inhibitory unit. Circular dichroism and fluorescence spectroscopy indicate that this fragment forms a compact and stable structure in solution. The secondary structure of this fragment is predominantly alpha-helical, consistent with the crystal structure of Ile-tRNA synthetase from another organism. The C-terminal fragment is capable of forming native-like secondary and tertiary structure after refolding from guanidine HCl. Taken together, the results are consistent with the hypothesis that the inhibitory fragment of Ile-tRNA synthetase forms an independent folding unit.
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Affiliation(s)
- J E Michaels
- Department of Physiology and Biophysics, School of Medicine, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
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47
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Beligere GS, Dawson PE. Conformationally Assisted Protein Ligation Using C-Terminal Thioester Peptides. J Am Chem Soc 1999. [DOI: 10.1021/ja9907919] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gangamani S. Beligere
- Departments of Cell Biology and Chemistry The Skaggs Institute for Chemical Biology The Scripps Research Institute La Jolla, California 92037
| | - Philip E. Dawson
- Departments of Cell Biology and Chemistry The Skaggs Institute for Chemical Biology The Scripps Research Institute La Jolla, California 92037
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48
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Ye D, Willhite DC, Blanke SR. Identification of the minimal intracellular vacuolating domain of the Helicobacter pylori vacuolating toxin. J Biol Chem 1999; 274:9277-82. [PMID: 10092603 DOI: 10.1074/jbc.274.14.9277] [Citation(s) in RCA: 92] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Helicobacter pylori secretes a cytotoxin (VacA) that induces the formation of large vacuoles originating from late endocytic vesicles in sensitive mammalian cells. Although evidence is accumulating that VacA is an A-B toxin, distinct A and B fragments have not been identified. To localize the putative catalytic A-fragment, we transfected HeLa cells with plasmids encoding truncated forms of VacA fused to green fluorescence protein. By analyzing truncated VacA fragments for intracellular vacuolating activity, we reduced the minimal functional domain to the amino-terminal 422 residues of VacA, which is less than one-half of the full-length protein (953 amino acids). VacA is frequently isolated as a proteolytically nicked protein of two fragments that remain noncovalently associated and retain vacuolating activity. Neither the amino-terminal 311 residue fragment (p33) nor the carboxyl-terminal 642 residue fragment (p70) of proteolytically nicked VacA are able to induce cellular vacuolation by themselves. However, co-transfection of HeLa cells with separate plasmids expressing both p33 and p70 resulted in vacuolated cells. Further analysis revealed that a minimal fragment comprising just residues 312-478 functionally complemented p33. Collectively, our results suggest a novel molecular architecture for VacA, with cytosolic localization of both fragments of nicked toxin required to mediate intracellular vacuolating activity.
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Affiliation(s)
- D Ye
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5513, USA
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49
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Ostermeier M, Nixon AE, Shim JH, Benkovic SJ. Combinatorial protein engineering by incremental truncation. Proc Natl Acad Sci U S A 1999; 96:3562-7. [PMID: 10097076 PMCID: PMC22333 DOI: 10.1073/pnas.96.7.3562] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have developed a combinatorial approach, using incremental truncation libraries of overlapping N- and C-terminal gene fragments, that examines all possible bisection points within a given region of an enzyme that will allow the conversion of a monomeric enzyme into its functional heterodimer. This general method for enzyme bisection will have broad applications in the engineering of new catalytic functions through domain swapping and chemical synthesis of modified peptide fragments and in the study of enzyme evolution and protein folding. We have tested this methodology on Escherichia coli glycinamide ribonucleotide formyltransferase (PurN) and, by genetic selection, identified PurN heterodimers capable of glycinamide ribonucleotide transformylation. Two were chosen for physical characterization and were found to be comparable to the wild-type PurN monomer in terms of stability to denaturation, activity, and binding of substrate and cofactor. Sequence analysis of 18 randomly chosen, active PurN heterodimers revealed that the breakpoints primarily clustered in loops near the surface of the enzyme, that the breaks could result in the deletion of highly conserved residues and, most surprisingly, that the active site could be bisected.
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Affiliation(s)
- M Ostermeier
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802-6300, USA
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50
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Nordin BE, Schimmel P. RNA determinants for translational editing. Mischarging a minihelix substrate by a tRNA synthetase. J Biol Chem 1999; 274:6835-8. [PMID: 10066735 DOI: 10.1074/jbc.274.11.6835] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The fidelity of protein synthesis requires efficient discrimination of amino acid substrates by aminoacyl-tRNA synthetases. Accurate discrimination of the structurally similar amino acids, valine and isoleucine, by isoleucyl-tRNA synthetase (IleRS) results, in part, from a hydrolytic editing reaction, which prevents misactivated valine from being stably joined to tRNAIle. The editing reaction is dependent on the presence of tRNAIle, which contains discrete D-loop nucleotides that are necessary to promote editing of misactivated valine. RNA minihelices comprised of just the acceptor-TPsiC helix of tRNAIle are substrates for specific aminoacylation by IleRS. These substrates lack the aforementioned D-loop nucleotides. Because minihelices contain determinants for aminoacylation, we thought that they might also play a role in editing that has not previously been recognized. Here we show that, in contrast to tRNAIle, minihelixIle is unable to trigger the hydrolysis of misactivated valine and, in fact, is mischarged with valine. In addition, mutations in minihelixIle that enhance or suppress charging with isoleucine do the same with valine. Thus, minihelixIle contains signals for charging (by IleRS) that are independent of the amino acid and, by itself, minihelixIle provides no determinants for editing. An RNA hairpin that mimics the D-stem/loop of tRNAIle is also unable to induce the hydrolysis of misactivated valine, both by itself and in combination with minihelixIle. Thus, the native tertiary fold of tRNAIle is required to promote efficient editing. Considering that the minihelix is thought to be the more ancestral part of the tRNA structure, these results are consistent with the idea that, during the development of the genetic code, RNA determinants for editing were added after the establishment of an aminoacylation system.
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Affiliation(s)
- B E Nordin
- Skaggs Institute for Chemical Biology and Departments of Molecular Biology and Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA
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