1
|
Mycobacterium tuberculosis Shikimate Pathway Enzymes as Targets for the Rational Design of Anti-Tuberculosis Drugs. Molecules 2020; 25:molecules25061259. [PMID: 32168746 PMCID: PMC7144000 DOI: 10.3390/molecules25061259] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/06/2020] [Accepted: 02/10/2020] [Indexed: 12/17/2022] Open
Abstract
Roughly a third of the world’s population is estimated to have latent Mycobacterium tuberculosis infection, being at risk of developing active tuberculosis (TB) during their lifetime. Given the inefficacy of prophylactic measures and the increase of drug-resistant M. tuberculosis strains, there is a clear and urgent need for the development of new and more efficient chemotherapeutic agents, with selective toxicity, to be implemented on patient treatment. The component enzymes of the shikimate pathway, which is essential in mycobacteria and absent in humans, stand as attractive and potential targets for the development of new drugs to treat TB. This review gives an update on published work on the enzymes of the shikimate pathway and some insight on what can be potentially explored towards selective drug development.
Collapse
|
2
|
Bou-Nader C, Brégeon D, Pecqueur L, Fontecave M, Hamdane D. Electrostatic Potential in the tRNA Binding Evolution of Dihydrouridine Synthases. Biochemistry 2018; 57:5407-5414. [DOI: 10.1021/acs.biochem.8b00584] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Charles Bou-Nader
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, 11 place Marcelin Berthelot, Paris 75231 Cedex 05, France
| | - Damien Brégeon
- CNRS, IBPS, Biology of Aging and Adaptation, Sorbonne Université, 7 quai Saint Bernard, Paris 7525 Cedex 05, France
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, 11 place Marcelin Berthelot, Paris 75231 Cedex 05, France
| | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, 11 place Marcelin Berthelot, Paris 75231 Cedex 05, France
| | - Djemel Hamdane
- Laboratoire de Chimie des Processus Biologiques, CNRS-UMR 8229, Collège De France, 11 place Marcelin Berthelot, Paris 75231 Cedex 05, France
| |
Collapse
|
3
|
Cordeiro TN, Herranz-Trillo F, Urbanek A, Estaña A, Cortés J, Sibille N, Bernadó P. Structural Characterization of Highly Flexible Proteins by Small-Angle Scattering. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1009:107-129. [DOI: 10.1007/978-981-10-6038-0_7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
4
|
Wang WJ, Cheng W, Luo M, Yan Q, Yu HM, Li Q, Cao DD, Huang S, Xu A, Mariuzza RA, Chen Y, Zhou CZ. Activity Augmentation of Amphioxus Peptidoglycan Recognition Protein BbtPGRP3 via Fusion with a Chitin Binding Domain. PLoS One 2015; 10:e0140953. [PMID: 26479246 PMCID: PMC4610682 DOI: 10.1371/journal.pone.0140953] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Accepted: 10/02/2015] [Indexed: 11/19/2022] Open
Abstract
Peptidoglycan recognition proteins (PGRPs), which have been identified in most animals, are pattern recognition molecules that involve antimicrobial defense. Resulting from extraordinary expansion of innate immune genes, the amphioxus encodes many PGRPs of diverse functions. For instance, three isoforms of PGRP encoded by Branchiostoma belcheri tsingtauense, termed BbtPGRP1~3, are fused with a chitin binding domain (CBD) at the N-terminus. Here we report the 2.7 Å crystal structure of BbtPGRP3, revealing an overall structure of an N-terminal hevein-like CBD followed by a catalytic PGRP domain. Activity assays combined with site-directed mutagenesis indicated that the individual PGRP domain exhibits amidase activity towards both DAP-type and Lys-type peptidoglycans (PGNs), the former of which is favored. The N-terminal CBD not only has the chitin-binding activity, but also enables BbtPGRP3 to gain a five-fold increase of amidase activity towards the Lys-type PGNs, leading to a significantly broadened substrate spectrum. Together, we propose that modular evolution via domain shuffling combined with gene horizontal transfer makes BbtPGRP1~3 novel PGRPs of augmented catalytic activity and broad recognition spectrum.
Collapse
Affiliation(s)
- Wen-Jie Wang
- Hefei National Laboratory for Physical Sciences at Microscale and the Innovation Center for Cell Signaling Network, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Wang Cheng
- Hefei National Laboratory for Physical Sciences at Microscale and the Innovation Center for Cell Signaling Network, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Ming Luo
- Hefei National Laboratory for Physical Sciences at Microscale and the Innovation Center for Cell Signaling Network, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Qingyu Yan
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Hong-Mei Yu
- Hefei National Laboratory for Physical Sciences at Microscale and the Innovation Center for Cell Signaling Network, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Qiong Li
- Hefei National Laboratory for Physical Sciences at Microscale and the Innovation Center for Cell Signaling Network, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Dong-Dong Cao
- Hefei National Laboratory for Physical Sciences at Microscale and the Innovation Center for Cell Signaling Network, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Shengfeng Huang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Anlong Xu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Pharmaceutical Functional Genes, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Roy A. Mariuzza
- University of Maryland Institute for Bioscience and Biotechnology Research, W. M. Keck Laboratory for Structural Biology, Rockville, Maryland, United States of America
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, United States of America
| | - Yuxing Chen
- Hefei National Laboratory for Physical Sciences at Microscale and the Innovation Center for Cell Signaling Network, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
- * E-mail: (YC); (CZZ)
| | - Cong-Zhao Zhou
- Hefei National Laboratory for Physical Sciences at Microscale and the Innovation Center for Cell Signaling Network, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
- * E-mail: (YC); (CZZ)
| |
Collapse
|
5
|
The highly conserved domain of unknown function 1792 has a distinct glycosyltransferase fold. Nat Commun 2014; 5:4339. [PMID: 25023666 PMCID: PMC4352575 DOI: 10.1038/ncomms5339] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 06/07/2014] [Indexed: 01/23/2023] Open
Abstract
More than 33,000 glycosyltransferases have been identified. Structural studies, however, have only revealed two distinct glycosyltransferase (GT) folds, GT-A and GT-B. Here we report a 1.34-Å resolution X-ray crystallographic structure of a previously uncharacterized 'domain of unknown function' 1792 (DUF1792) and show that the domain adopts a new fold and is required for glycosylation of a family of serine-rich repeat streptococcal adhesins. Biochemical studies reveal that the domain is a glucosyltransferase, and it catalyses the transfer of glucose to the branch point of the hexasaccharide O-linked to the serine-rich repeat of the bacterial adhesin, Fap1 of Streptococcus parasanguinis. DUF1792 homologues from both Gram-positive and Gram-negative bacteria also exhibit the activity. Thus, DUF1792 represents a new family of glycosyltransferases; therefore, we designate it as a GT-D glycosyltransferase fold. As the domain is highly conserved in bacteria and not found in eukaryotes, it can be explored as a new antibacterial target.
Collapse
|
6
|
Göbl C, Madl T, Simon B, Sattler M. NMR approaches for structural analysis of multidomain proteins and complexes in solution. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2014; 80:26-63. [PMID: 24924266 DOI: 10.1016/j.pnmrs.2014.05.003] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/14/2014] [Indexed: 05/22/2023]
Abstract
NMR spectroscopy is a key method for studying the structure and dynamics of (large) multidomain proteins and complexes in solution. It plays a unique role in integrated structural biology approaches as especially information about conformational dynamics can be readily obtained at residue resolution. Here, we review NMR techniques for such studies focusing on state-of-the-art tools and practical aspects. An efficient approach for determining the quaternary structure of multidomain complexes starts from the structures of individual domains or subunits. The arrangement of the domains/subunits within the complex is then defined based on NMR measurements that provide information about the domain interfaces combined with (long-range) distance and orientational restraints. Aspects discussed include sample preparation, specific isotope labeling and spin labeling; determination of binding interfaces and domain/subunit arrangements from chemical shift perturbations (CSP), nuclear Overhauser effects (NOEs), isotope editing/filtering, cross-saturation, and differential line broadening; and based on paramagnetic relaxation enhancements (PRE) using covalent and soluble spin labels. Finally, the utility of complementary methods such as small-angle X-ray or neutron scattering (SAXS, SANS), electron paramagnetic resonance (EPR) or fluorescence spectroscopy techniques is discussed. The applications of NMR techniques are illustrated with studies of challenging (high molecular weight) protein complexes.
Collapse
Affiliation(s)
- Christoph Göbl
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany
| | - Tobias Madl
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany; Institute of Molecular Biology, University of Graz, Graz, Austria.
| | - Bernd Simon
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Michael Sattler
- Biomolecular NMR and Center for Integrated Protein Science Munich at Department Chemie, Technische Universität München, Garching, Germany; Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg, Germany.
| |
Collapse
|
7
|
Sorokina M, Stam M, Médigue C, Lespinet O, Vallenet D. Profiling the orphan enzymes. Biol Direct 2014; 9:10. [PMID: 24906382 PMCID: PMC4084501 DOI: 10.1186/1745-6150-9-10] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 05/29/2014] [Indexed: 11/10/2022] Open
Abstract
The emergence of Next Generation Sequencing generates an incredible amount of sequence and great potential for new enzyme discovery. Despite this huge amount of data and the profusion of bioinformatic methods for function prediction, a large part of known enzyme activities is still lacking an associated protein sequence. These particular activities are called "orphan enzymes". The present review proposes an update of previous surveys on orphan enzymes by mining the current content of public databases. While the percentage of orphan enzyme activities has decreased from 38% to 22% in ten years, there are still more than 1,000 orphans among the 5,000 entries of the Enzyme Commission (EC) classification. Taking into account all the reactions present in metabolic databases, this proportion dramatically increases to reach nearly 50% of orphans and many of them are not associated to a known pathway. We extended our survey to "local orphan enzymes" that are activities which have no representative sequence in a given clade, but have at least one in organisms belonging to other clades. We observe an important bias in Archaea and find that in general more than 30% of the EC activities have incomplete sequence information in at least one superkingdom. To estimate if candidate proteins for local orphans could be retrieved by homology search, we applied a simple strategy based on the PRIAM software and noticed that candidates may be proposed for an important fraction of local orphan enzymes. Finally, by studying relation between protein domains and catalyzed activities, it appears that newly discovered enzymes are mostly associated with already known enzyme domains. Thus, the exploration of the promiscuity and the multifunctional aspect of known enzyme families may solve part of the orphan enzyme issue. We conclude this review with a presentation of recent initiatives in finding proteins for orphan enzymes and in extending the enzyme world by the discovery of new activities.
Collapse
Affiliation(s)
- Maria Sorokina
- Direction des Sciences du Vivant, Commissariat à l'Energie Atomique (CEA), Institut de Génomique, Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, 2 rue Gaston Crémieux, 91057 Evry, France.
| | | | | | | | | |
Collapse
|
8
|
Zhi XY, Yao JC, Li HW, Huang Y, Li WJ. Genome-wide identification, domain architectures and phylogenetic analysis provide new insights into the early evolution of shikimate pathway in prokaryotes. Mol Phylogenet Evol 2014; 75:154-64. [DOI: 10.1016/j.ympev.2014.02.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 02/14/2014] [Accepted: 02/17/2014] [Indexed: 11/30/2022]
|
9
|
Dibrova DV, Cherepanov DA, Galperin MY, Skulachev VP, Mulkidjanian AY. Evolution of cytochrome bc complexes: from membrane-anchored dehydrogenases of ancient bacteria to triggers of apoptosis in vertebrates. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1827:1407-27. [PMID: 23871937 PMCID: PMC3839093 DOI: 10.1016/j.bbabio.2013.07.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2012] [Revised: 07/02/2013] [Accepted: 07/08/2013] [Indexed: 12/30/2022]
Abstract
This review traces the evolution of the cytochrome bc complexes from their early spread among prokaryotic lineages and up to the mitochondrial cytochrome bc1 complex (complex III) and its role in apoptosis. The results of phylogenomic analysis suggest that the bacterial cytochrome b6f-type complexes with short cytochromes b were the ancient form that preceded in evolution the cytochrome bc1-type complexes with long cytochromes b. The common ancestor of the b6f-type and the bc1-type complexes probably resembled the b6f-type complexes found in Heliobacteriaceae and in some Planctomycetes. Lateral transfers of cytochrome bc operons could account for the several instances of acquisition of different types of bacterial cytochrome bc complexes by archaea. The gradual oxygenation of the atmosphere could be the key evolutionary factor that has driven further divergence and spread of the cytochrome bc complexes. On the one hand, oxygen could be used as a very efficient terminal electron acceptor. On the other hand, auto-oxidation of the components of the bc complex results in the generation of reactive oxygen species (ROS), which necessitated diverse adaptations of the b6f-type and bc1-type complexes, as well as other, functionally coupled proteins. A detailed scenario of the gradual involvement of the cardiolipin-containing mitochondrial cytochrome bc1 complex into the intrinsic apoptotic pathway is proposed, where the functioning of the complex as an apoptotic trigger is viewed as a way to accelerate the elimination of the cells with irreparably damaged, ROS-producing mitochondria. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.
Collapse
Affiliation(s)
- Daria V Dibrova
- School of Physics, University of Osnabrueck, D-49069 Osnabrueck, Germany; School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119992, Russia; Institute of Mitoengineering, Lomonosov Moscow State University, Moscow 119992, Russia
| | | | | | | | | |
Collapse
|
10
|
Abstract
Diflavin reductases are essential proteins capable of splitting the two-electron flux from reduced pyridine nucleotides to a variety of one electron acceptors. The primary sequence of diflavin reductases shows a conserved domain organization harboring two catalytic domains bound to the FAD and FMN flavins sandwiched by one or several non-catalytic domains. The catalytic domains are analogous to existing globular proteins: the FMN domain is analogous to flavodoxins while the FAD domain resembles ferredoxin reductases. The first structural determination of one member of the diflavin reductases family raised some questions about the architecture of the enzyme during catalysis: both FMN and FAD were in perfect position for interflavin transfers but the steric hindrance of the FAD domain rapidly prompted more complex hypotheses on the possible mechanisms for the electron transfer from FMN to external acceptors. Hypotheses of domain reorganization during catalysis in the context of the different members of this family were given by many groups during the past twenty years. This review will address the recent advances in various structural approaches that have highlighted specific dynamic features of diflavin reductases.
Collapse
Affiliation(s)
- Louise Aigrain
- Gene Machines Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK; E-Mail:
| | - Fataneh Fatemi
- Institut de Chimie des Substances Naturelles, CNRS, UPR 2301, Centre de Recherche de Gif, 1 Av. de la Terrasse, 91198 Gif-sur-Yvette Cedex, France; E-Mails: (F.F.); (O.F.); (E.L.)
| | - Oriane Frances
- Institut de Chimie des Substances Naturelles, CNRS, UPR 2301, Centre de Recherche de Gif, 1 Av. de la Terrasse, 91198 Gif-sur-Yvette Cedex, France; E-Mails: (F.F.); (O.F.); (E.L.)
| | - Ewen Lescop
- Institut de Chimie des Substances Naturelles, CNRS, UPR 2301, Centre de Recherche de Gif, 1 Av. de la Terrasse, 91198 Gif-sur-Yvette Cedex, France; E-Mails: (F.F.); (O.F.); (E.L.)
| | - Gilles Truan
- Université de Toulouse; INSA, UPS, INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France
- INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France
- CNRS, UMR5504, F-31400 Toulouse, France
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +33-567048813; Fax: +33-567048814
| |
Collapse
|
11
|
Baker P, Hillis C, Carere J, Seah SYK. Protein-protein interactions and substrate channeling in orthologous and chimeric aldolase-dehydrogenase complexes. Biochemistry 2012; 51:1942-52. [PMID: 22316175 DOI: 10.1021/bi201832a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial aldolase-dehydrogenase complexes catalyze the last steps in the meta cleavage pathway of aromatic hydrocarbon degradation. The aldolase (TTHB246) and dehydrogenase (TTHB247) from Thermus thermophilus were separately expressed and purified from recombinant Escherichia coli. The aldolase forms a dimer, while the dehydrogenase is a monomer; these enzymes can form a stable tetrameric complex in vitro, consisting of two aldolase and two dehydrogenase subunits. Upon complex formation, the K(m) value of 4-hydroxy-2-oxopentanoate, the substrate of TTHB246, is decreased 4-fold while the K(m) of acetaldehyde, the substrate of TTHB247, is increased 3-fold. The k(cat) values of each enzyme were reduced by ~2-fold when they were in a complex. The half-life of TTHB247 at 50 °C increased by ~4-fold when it was in a complex with TTHB246. The acetaldehyde product from TTHB246 could be efficiently channelled directly to TTHB247, but the channeling efficiency for the larger propionaldehyde was ~40% lower. A single A324G substitution in TTHB246 increased the channeling efficiency of propionaldehyde to a value comparable to that of acetaldehyde. Stable and catalytically competent chimeric complexes could be formed between the T. thermophilus enzymes and the orthologous aldolase (BphI) and dehydrogenase (BphJ) from the biphenyl degradation pathway of Burkholderia xenovorans LB400. However, channeling efficiencies for acetaldehyde in these chimeric complexes were ~10%. Structural and sequence analysis suggests that interacting residues in the interface of the aldolase-dehydrogenase complex are highly conserved among homologues, but coevolution of partner enzymes is required to fine-tune this interaction to allow for efficient substrate channeling.
Collapse
Affiliation(s)
- Perrin Baker
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | | | | | | |
Collapse
|
12
|
Role of the interface between the FMN and FAD domains in the control of redox potential and electronic transfer of NADPH-cytochrome P450 reductase. Biochem J 2011; 435:197-206. [PMID: 21265736 DOI: 10.1042/bj20101984] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
CPR (NADPH-cytochrome P450 reductase) is a multidomain protein containing two flavin-containing domains joined by a connecting domain thought to control the necessary movements of the catalytic domains during electronic cycles. We present a detailed biochemical analysis of two chimaeric CPRs composed of the association of human or yeast FMN with the alternative connecting/FAD domains. Despite the assembly of domains having a relatively large evolutionary distance between them, our data support the idea that the integrity of the catalytic cycle is conserved in our chimaeric enzymes, whereas the recognition, interactions and positioning of both catalytic domains are probably modified. The main consequences of the chimaerogenesis are a decrease in the internal electron-transfer rate between both flavins correlated with changes in the geometry of chimaeric CPRs in solution. Results of the present study highlight the role of the linker and connecting domain in the recognition at the interfaces between the catalytic domains and the impact of interdomain interactions on the redox potentials of the flavins, the internal electron-transfer efficiency and the global conformation and dynamic equilibrium of the CPRs.
Collapse
|
13
|
Valleriani A, Zhang G, Nagar A, Ignatova Z, Lipowsky R. Length-dependent translation of messenger RNA by ribosomes. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:042903. [PMID: 21599226 DOI: 10.1103/physreve.83.042903] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2010] [Indexed: 05/30/2023]
Abstract
A simple measure for the efficiency of protein synthesis by ribosomes is provided by the steady state amount of protein per messenger RNA (mRNA), the so-called translational ratio, which is proportional to the translation rate. Taking the degradation of mRNA into account, we show theoretically that both the translation rate and the translational ratio decrease with increasing mRNA length, in agreement with available experimental data for the prokaryote Escherichia coli. We also show that, compared to prokaryotes, mRNA degradation in eukaryotes leads to a less rapid decrease of the translational ratio. This finding is consistent with the fact that, compared to prokaryotes, eukaryotes tend to have longer proteins.
Collapse
Affiliation(s)
- Angelo Valleriani
- Max Planck Institute of Colloids and Interfaces, Department of Theory and Bio-Systems, D-14424 Potsdam, Germany.
| | | | | | | | | |
Collapse
|
14
|
Strickland KC, Holmes RS, Oleinik NV, Krupenko NI, Krupenko SA. Phylogeny and evolution of aldehyde dehydrogenase-homologous folate enzymes. Chem Biol Interact 2011; 191:122-8. [PMID: 21215736 DOI: 10.1016/j.cbi.2010.12.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Revised: 12/22/2010] [Accepted: 12/24/2010] [Indexed: 10/18/2022]
Abstract
Folate coenzymes function as one-carbon group carriers in intracellular metabolic pathways. Folate-dependent reactions are compartmentalized within the cell and are catalyzed by two distinct groups of enzymes, cytosolic and mitochondrial. Some folate enzymes are present in both compartments and are likely the products of gene duplications. A well-characterized cytosolic folate enzyme, FDH (10-formyltetrahydro-folate dehydrogenase, ALDH1L1), contains a domain with significant sequence similarity to aldehyde dehydrogenases. This domain enables FDH to catalyze the NADP(+)-dependent conversion of short-chain aldehydes to corresponding acids in vitro. The aldehyde dehydrogenase-like reaction is the final step in the overall FDH mechanism, by which a tetrahydrofolate-bound formyl group is oxidized to CO(2) in an NADP(+)-dependent fashion. We have recently cloned and characterized another folate enzyme containing an ALDH domain, a mitochondrial FDH. Here the biological roles of the two enzymes, a comparison of the respective genes, and some potential evolutionary implications are discussed. The phylogenic analysis suggests that the vertebrate ALDH1L2 gene arose from a duplication event of the ALDH1L1 gene prior to the emergence of osseous fish >500 millions years ago.
Collapse
Affiliation(s)
- Kyle C Strickland
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | | | | | | | | |
Collapse
|
15
|
Wang W, Baker P, Seah SYK. Comparison of two metal-dependent pyruvate aldolases related by convergent evolution: substrate specificity, kinetic mechanism, and substrate channeling. Biochemistry 2010; 49:3774-82. [PMID: 20364820 DOI: 10.1021/bi100251u] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
HpaI and BphI are two pyruvate class II aldolases found in aromatic meta-cleavage degradation pathways that catalyze similar reactions but are not related in sequence. Steady-state kinetic analysis of the aldol addition reactions and product inhibition assays showed that HpaI exhibits a rapid equilibrium random order mechanism while BphI exhibits a compulsory order mechanism, with pyruvate binding first. Both aldolases are able to utilize aldehyde acceptors two to five carbons in length; however, HpaI showed broader specificity and had a preference for aldehydes containing longer linear alkyl chains or C2-OH substitutions. Both enzymes were able to bind 2-keto acids larger than pyruvate, but only HpaI was able to utilize both pyruvate and 2-ketobutanoate as carbonyl donors in the aldol addition reaction. HpaI lacks stereospecific control producing racemic mixtures of 4-hydroxy-2-oxopentanoate (HOPA) from pyruvate and acetaldehyde while BphI synthesizes only (4S)-HOPA. BphI is also able to utilize acetaldehyde produced by the reduction of acetyl-CoA catalyzed by the associated aldehyde dehydrogenase, BphJ. This aldehyde was directly channeled from the dehydrogenase to the aldolase active sites, with an efficiency of 84%. Furthermore, the BphJ reductive deacylation reaction increased 4-fold when BphI was catalyzing the aldol addition reaction. Therefore, the BphI-BphJ enzyme complex exhibits unique bidirectionality in substrate channeling and allosteric activation.
Collapse
Affiliation(s)
- Weijun Wang
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | | | | |
Collapse
|
16
|
He HW, Zhang J, Zhou HM, Yan YB. Conformational change in the C-terminal domain is responsible for the initiation of creatine kinase thermal aggregation. Biophys J 2005; 89:2650-8. [PMID: 16006628 PMCID: PMC1366765 DOI: 10.1529/biophysj.105.066142] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2005] [Accepted: 06/29/2005] [Indexed: 11/18/2022] Open
Abstract
Protein conformational changes may be associated with particular properties such as its function, transportation, assembly, tendency to aggregate, and potential cytotoxicity. In this research, the conformational change that is responsible for the fast destabilization and aggregation of rabbit muscle creatine kinase (EC 2.7.3.2) induced by heat was studied by intrinsic fluorescence and infrared spectroscopy. A pretransitional change of the tryptophan microenvironments was found from the intrinsic fluorescence spectra. A further analysis of the infrared spectra using quantitative second-derivative and two-dimensional correlation analysis indicated that the changes of the beta-sheet structures in the C-terminal domain and the loops occurred before the formation of intermolecular cross-beta-sheet structures and the unfolding of alpha-helices. These results suggested that the pretransitional conformational changes in the active site and the C-terminal domain might result in the modification of the domain-domain interactions and the formation of an inactive dimeric form that was prone to aggregate. Our results highlighted the fact that some minor conformational changes, which were usually negligible or undetectable by normal methods, might play a crucial role in protein stability and aggregation. Our results also suggested that the changes in domain-domain interactions, but not the dissociation of the dimer, might play a crucial role in the thermal denaturation and aggregation of this dimeric two-domain protein.
Collapse
Affiliation(s)
- Hua-Wei He
- Department of Biological Sciences and Biotechnology, and State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing, China
| | | | | | | |
Collapse
|
17
|
Maher AD, Kuchel PW, Ortega F, de Atauri P, Centelles J, Cascante M. Mathematical modelling of the urea cycle. A numerical investigation into substrate channelling. ACTA ACUST UNITED AC 2003; 270:3953-61. [PMID: 14511377 DOI: 10.1046/j.1432-1033.2003.03783.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Metabolite channelling, the process in which consecutive enzymes have confined substrate transfer in metabolic pathways, has been proposed as a biochemical mechanism that has evolved because it enhances catalytic rates and protects unstable intermediates. Results from experiments on the synthesis of radioactive urea [Cheung, C., Cohen, N.S. & Raijman, L (1989) J. Biol. Chem.264, 4038-4044] have been interpreted as implying channelling of arginine between argininosuccinate lyase and arginase in permeabilized hepatocytes. To investigate this interpretation further, a mathematical model of the urea cycle was written, using Mathematica it simulates time courses of the reactions. The model includes all relevant intermediates, peripheral metabolites, and subcellular compartmentalization. Analysis of the output from the simulations supports the argument for a high degree of, but not absolute, channelling and offers insights for future experiments that could shed more light on the quantitative aspects of this phenomenon in the urea cycle and other pathways.
Collapse
Affiliation(s)
- Anthony D Maher
- School of Molecular and Microbial Biosciences, University of Sydney, Australia.
| | | | | | | | | | | |
Collapse
|
18
|
Ostermeier M, Benkovic SJ. Evolution of protein function by domain swapping. ADVANCES IN PROTEIN CHEMISTRY 2001; 55:29-77. [PMID: 11050932 DOI: 10.1016/s0065-3233(01)55002-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- M Ostermeier
- Department of Chemical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | | |
Collapse
|
19
|
Nicholas HB, Arst HN, Caddick MX. Evaluating low level sequence identities. Are Aspergillus QUTA and AROM homologous? EUROPEAN JOURNAL OF BIOCHEMISTRY 2001; 268:414-9. [PMID: 11168377 DOI: 10.1046/j.1432-1033.2001.01893.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A review published several years ago [Hawkins, A.R. & Lamb, H.K. (1995) Eur. J. Biochem. 232, 7-18] proposed that genetic, biochemical and physiological data can override sequence comparison in the determination of homology in instances where structural information is unavailable. Their lead example was the hypothesis that the transcriptional activator protein for quinate catabolism in Aspergillus nidulans, QUTA, is derived from the pentafunctional AROM protein by a gene duplication followed by cleavage [Hawkins, A.R., Lamb, H.K., Moore, J.D. & Roberts, C.F. (1993) Gene 136, 49-54]. We tested this hypothesis by a sensitive combination of position-specific log-odds scoring matrix methods. The position-specific log-odds scoring matrices were derived from a large number of 3-dehydroquinate synthase and 5-enolpyruvylshikimate-3-phosphate synthase domains that were proposed to be the domains from the AROM protein that gave rise to the transcriptional activator protein for quinate metabolism. We show that the degree and pattern of similarity between these position-specific log-odds scoring matrices and the transcriptional activator protein for quinate catabolism in A. nidulans is that expected for random sequences of the same composition. This level of similarity provides no support for the suggested gene duplication and cleavage. The lack of any trace of evidence for homology following a comprehensive sequence analysis indicates that the homology hypothesis is without foundation, underlining the necessity to accept only similarity of sequence and/or structure as evidence of evolutionary relatedness. Further, QUTA is homologous throughout its entire length to an extended family of fungal transcriptional regulatory proteins, rendering the hypothesized QUTA-AROM homology even more problematic.
Collapse
Affiliation(s)
- H B Nicholas
- Pittsburgh Supercomputing Center, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA.
| | | | | |
Collapse
|
20
|
Abstract
The recent growth in structural data, and ensuing analyses, have revealed the structural and functional versatility of protein families. With respect to enzymes, local active-site mutations, variations in surface loops and recruitment of additional domains accommodate the diverse substrate specificities and catalytic activities observed within several superfamilies. Conversely, some functions have more than one structural solution, having evolved independently several times during evolution. Combined with the existence of multi-functional genes, which have arisen by gene recruitment, these phenomena must be considered in the process of genome annotation.
Collapse
Affiliation(s)
- A E Todd
- Biomolecular Structure and Modelling Unit Department of Biochemistry and Molecular Biology, University College London, Gower Street, London,WC1E 6BT, UK
| | | | | |
Collapse
|
21
|
Löster K, Josić D. Analysis of protein aggregates by combination of cross-linking reactions and chromatographic separations. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 1997; 699:439-61. [PMID: 9392387 DOI: 10.1016/s0378-4347(97)00215-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Chemical cross-linking provides a method that covalently bridges near-neighbour associations within proteins and protein aggregates. Combined with chromatographic separations and protein-chemical methods, it may be used to localize and to investigate three-dimensional relations as present under natural conditions. This paper reviews the chemistry and application of cross-linking reagents and the development of combination experimental approaches in view of chromatographic separations and cross-linking reactions. Investigations of homooligomeric and heterooligomeric protein associations as well as conformational analysis are presented.
Collapse
Affiliation(s)
- K Löster
- Institut für Molekularbiologie und Biochemie, Freie Universität Berlin, Berlin-Dahlem, Germany
| | | |
Collapse
|
22
|
Jost B, Duluc I, Richardson M, Lathe R, Freund JN. Functional diversity and interactions between the repeat domains of rat intestinal lactase. Biochem J 1997; 327 ( Pt 1):95-103. [PMID: 9355740 PMCID: PMC1218768 DOI: 10.1042/bj3270095] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Lactase-phlorizin hydrolase (LPH), a major digestive enzyme in the small intestine of newborns, is synthesized as a high-molecular-mass precursor comprising four tandemly repeated domains. Proteolytic cleavage of the precursor liberates the pro segment (LPHalpha) corresponding to domains I and II and devoid of known enzymic function. The mature enzyme (LPHbeta) comprises domains III and IV and is anchored in the brush border membrane via a C-terminal hydrophobic segment. To analyse the roles of the different domains of LPHalpha and LPHbeta, and the interactions between them, we have engineered a series of modified derivatives of the rat LPH precursor. These were expressed in cultured cells under the control of a cytomegalovirus promoter. The results show that recombinant LPHbeta harbouring both domains III and IV produces lactase activity. Neither domain III nor IV is alone sufficient to generate active enzyme, although the corresponding proteins are transport-competent. Tandem duplication of domains III or IV did not restore lactase activity, demonstrating the separate roles of both domains within LPHbeta. Further, the development of lactase activity did not require LPHalpha; however, LPHalpha potentiated the production of active LPHbeta but the individual LPHalpha subdomains I and II were unable to do so. Lactase activity and targeting required the C-terminal transmembrane anchor of LPH; this requirement was terminal transmembrane anchor or LPH; this requirement was not satisfied by the signal/anchor region of another digestive enzyme: sucrase-isomaltase. On the basis of this study we suggest that multiple levels of intramolecular interactions occur within the LPH precursor to produce the mature enzyme, and that the repeat domains of the precursor have distinct and specific functions in protein processing, substrate recognition and catalysis. We propose a functional model of LPHbeta in which substrate is channelled from an entry point located within domain II to the active site located in domain IV.
Collapse
Affiliation(s)
- B Jost
- Institut National de la Santé et de la Recherche Médicale, Unité 381, 3 avenue Molière, 67200 Strasbourg, France
| | | | | | | | | |
Collapse
|
23
|
Netzer WJ, Hartl FU. Recombination of protein domains facilitated by co-translational folding in eukaryotes. Nature 1997; 388:343-9. [PMID: 9237751 DOI: 10.1038/41024] [Citation(s) in RCA: 317] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The evolution of complex genomes requires that new combinations of pre-existing protein domains successfully fold into modular polypeptides. During eukaryotic translation model two-domain polypeptides fold efficiently by sequential and co-translational folding of their domains. In contrast, folding of the same proteins in Escherichia coli is posttranslational, and leads to intramolecular misfolding of concurrently folding domains. Sequential domain folding in eukaryotes may have been critical in the evolution of modular polypeptides, by increasing the probability that random gene-fusion events resulted in immediately foldable protein structures.
Collapse
Affiliation(s)
- W J Netzer
- Cellular Biochemistry & Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
| | | |
Collapse
|
24
|
Lamb HK, Newton GH, Levett LJ, Cairns E, Roberts CF, Hawkins AR. The QUTA activator and QUTR repressor proteins of Aspergillus nidulans interact to regulate transcription of the quinate utilization pathway genese. MICROBIOLOGY (READING, ENGLAND) 1996; 142 ( Pt 6):1477-1490. [PMID: 8704987 DOI: 10.1099/13500872-142-6-1477] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Genetic evidence suggests that the activity of the native QUTA transcription activator protein is negated by the action of the QUTR transcription repressor protein. When Aspergillus nidulans was transformed with plasmids containing the wild-type qutA gene, transformants that constitutively expressed the quinate pathway enzymes were isolated. The constitutive phenotype of these transformants was associated with an increased copy number of the transforming qutA gene and elevated qutA mRNA levels. Conversely, when A. nidulans was transformed with plasmids containing the qutR gene under the control of the constitutive pgk promoter, transformants with a super-repressed phenotype (unable to utilize quinate as a carbon source) were isolated. The super-repressed phenotype of these transformants was associated with an increased copy number of the transforming qutR gene and elevated qutR mRNA levels. These copy-number-dependent phenotypes argue that the levels of the QUTA and QUTR proteins were elevated in the high-copy-number transformants. When diploid strains were formed by combining haploid strains that contained high copy numbers of either the qutA gene (constitutive phenotype) or the qutR gene (super-repressing; non-inducible phenotype), the resulting diploid phenotype was one of quinate-inducible production of the quinate pathway enzymes, in a manner similar to wild-type. The simplest interpretation of these observations is that the QUTR repressor protein mediates its repressing activity through a direct interaction with the QUTA activator protein. Other possible interpretations are discussed in the text. Experiments in which truncated versions of the QUTA protein were produced in the presence of a wild-type QUTA protein indicate that the QUTR repressor protein recognizes and binds to the C-terminal half of the QUTA activator protein.
Collapse
Affiliation(s)
- Heather K Lamb
- Department of Biochemistry and Genetics, Medical School, Framlington Place, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK
| | - Giles H Newton
- Department of Biochemistry and Genetics, Medical School, Framlington Place, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK
| | - Lisa J Levett
- Department of Biochemistry and Genetics, Medical School, Framlington Place, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK
| | - Elaine Cairns
- Department of Biochemistry and Genetics, Medical School, Framlington Place, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK
| | - Clive F Roberts
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Alastair R Hawkins
- Department of Biochemistry and Genetics, Medical School, Framlington Place, University of Newcastle, Newcastle upon Tyne NE2 4HH, UK
| |
Collapse
|
25
|
Levesley I, Newton GH, Lamb HK, van Schothorst E, Dalgleish RWM, Samson ACR, Roberts CF, Hawkins AR. Domain structure and function within the QUTA protein of Aspergillus nidulans: implications for the control of transcription. MICROBIOLOGY (READING, ENGLAND) 1996; 142 ( Pt 1):87-98. [PMID: 8581174 DOI: 10.1099/13500872-142-1-87] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
QUTA is a positively acting regulatory protein that regulates the expression of the eight genes comprising the quinic acid utilization gene (qut) gene cluster in Aspergillus nidulans. It has been proposed that the QUTA protein is composed of two domains that are related to the N-terminal two domains-dehydroquinate (DHQ) synthase and 5-enolpyruvyl shikimate-3-phosphate (EPSP) synthase-of the pentadomain AROM protein. The AROM protein is an enzyme catalysing five consecutive steps in the shikimate pathway, two of which are common to the qut pathway. A genetic and molecular analysis of non-inducible qutA mutants showed that all 23 mutations analysed map within the N-terminal half of the encoded QUTA protein. One dominant mutation (qutA382) introduces a stop codon at the boundary between the two domains that were identified on the basis of amino acid sequence alignments between the QUTA protein and the N-terminal two domains of the pentafunctional AROM protein. The truncated protein encoded by mutant qutA382 has DNA-binding ability but no transcription activation function. A second dominant mutation (in strain qutA214) is missense, changing 457E-->K in a region of localized high negative charge and potentially identifies a transcription activation domain in the N-terminus of the EPSP-synthase-like domain of the QUTA protein. A series of qualitative and quantitative Northern blot experiments with mRNA derived from wild-type and mutant qutA strains supported the view that the QUTA protein regulates the expression of the qut gene cluster, including the qutA gene which encodes it. A series of Western blot and zinc-binding experiments demonstrated that a putative zinc binuclear cluster motif located within the N-terminus of the QUTA protein is able to bind zinc in vitro.
Collapse
Affiliation(s)
- Ian Levesley
- Department of Genetics, Adrian Building, University of Leicester, Leicester LE1 7RH, UK
| | - Giles H Newton
- Department of Biochemistry and Genetics, Catherine Cookson Building, New Medical School, University of Newcastle upon Tyne NE2 4HH, UK
| | - Heather K Lamb
- Department of Biochemistry and Genetics, Catherine Cookson Building, New Medical School, University of Newcastle upon Tyne NE2 4HH, UK
| | - Evert van Schothorst
- Department of Genetics, Adrian Building, University of Leicester, Leicester LE1 7RH, UK
| | - Raymond W M Dalgleish
- Department of Genetics, Adrian Building, University of Leicester, Leicester LE1 7RH, UK
| | - Anthony C R Samson
- Department of Biochemistry and Genetics, Catherine Cookson Building, New Medical School, University of Newcastle upon Tyne NE2 4HH, UK
| | - Clive F Roberts
- Department of Genetics, Adrian Building, University of Leicester, Leicester LE1 7RH, UK
| | - Alastair R Hawkins
- Department of Biochemistry and Genetics, Catherine Cookson Building, New Medical School, University of Newcastle upon Tyne NE2 4HH, UK
| |
Collapse
|
26
|
Amino acid activation and polymerization at modular multienzymes in nonribosomal peptide biosynthesis. Amino Acids 1996; 10:201-27. [DOI: 10.1007/bf00807324] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/1995] [Accepted: 11/20/1995] [Indexed: 10/26/2022]
|