101
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Angov E, Legler PM, Mease RM. Adjustment of codon usage frequencies by codon harmonization improves protein expression and folding. Methods Mol Biol 2011; 705:1-13. [PMID: 21125377 DOI: 10.1007/978-1-61737-967-3_1] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Over the past two decades, prokaryotic expression systems have been widely exploited for the bioproduction of many therapeutic proteins. Much of the success can be attributed to the implementation of basic principles of prokaryotic protein translation and protein folding to the problems of heterologous expression (e.g. codon usage substitutions, tRNA isoacceptor co-expression, chaperone co-expression); however, expression in a heterologous host still remains an empirical process. To improve heterologous protein expression further we have developed an algorithm termed "codon harmonization" that best approximates codon usage frequencies from the native host and adjusts these for use in the heterologous system. The success of this methodology may be due to improved protein folding during translation. Although so far exclusively applied to Escherichia coli, codon harmonization may provide a general strategy for improving the expression of soluble, functional proteins during heterologous host expression.
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Affiliation(s)
- Evelina Angov
- Division of Malaria Vaccine Development, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
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102
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Abstract
Using the basic principles of molecular biology and laboratory techniques presented in this chapter, researchers should be able to create a wide variety of AAV vectors for both clinical and basic research applications. Basic vector design concepts are covered for both protein coding gene expression and small non-coding RNA gene expression cassettes. AAV plasmid vector backbones (available via AddGene) are described, along with critical sequence details for a variety of modular expression components that can be inserted as needed for specific applications. Protocols are provided for assembling the various DNA components into AAV vector plasmids in Escherichia coli, as well as for transferring these vector sequences into baculovirus genomes for large-scale production of AAV in the insect cell production system.
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Affiliation(s)
- John T Gray
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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103
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Bekesi A, Pukancsik M, Haasz P, Felfoldi L, Leveles I, Muha V, Hunyadi-Gulyas E, Erdei A, Medzihradszky KF, Vertessy BG. Association of RNA with the uracil-DNA-degrading factor has major conformational effects and is potentially involved in protein folding. FEBS J 2010; 278:295-315. [PMID: 21134127 DOI: 10.1111/j.1742-4658.2010.07951.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recently, a novel uracil-DNA-degrading factor protein (UDE) was identified in Drosophila melanogaster, with homologues only in pupating insects. Its unique uracil-DNA-degrading activity and a potential domain organization pattern have been described. UDE seems to be the first representative of a new protein family with unique enzyme activity that has a putative role in insect development. In addition, UDE may also serve as potential tool in molecular biological applications. Owing to lack of homology with other proteins with known structure and/or function, de novo data are required for a detailed characterization of UDE structure and function. Here, experimental evidence is provided that recombinant protein is present in two distinct conformers. One of these contains a significant amount of RNA strongly bound to the protein, influencing its conformation. Detailed biophysical characterization of the two distinct conformational states (termed UDE and RNA-UDE) revealed essential differences. UDE cannot be converted into RNA-UDE by addition of the same RNA, implying putatively joint processes of RNA binding and protein folding in this conformational species. By real-time PCR and sequencing after random cloning, the bound RNA pool was shown to consist of UDE mRNA and the two ribosomal RNAs, also suggesting cotranslational RNA-assisted folding. This finding, on the one hand, might open a way to obtain a conformationally homogeneous UDE preparation, promoting successful crystallization; on the other hand, it might imply a further molecular function of the protein. In fact, RNA-dependent complexation of UDE was also demonstrated in a fruit fly pupal extract, suggesting physiological relevance of RNA binding of this DNA-processing enzyme.
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Affiliation(s)
- Angela Bekesi
- Institute of Enzymology, Biological Research Centre, Hungarian Academy of Sciences, Budapest, Hungary.
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104
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Zhang G, Ignatova Z. Folding at the birth of the nascent chain: coordinating translation with co-translational folding. Curr Opin Struct Biol 2010; 21:25-31. [PMID: 21111607 DOI: 10.1016/j.sbi.2010.10.008] [Citation(s) in RCA: 147] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 10/27/2010] [Accepted: 10/29/2010] [Indexed: 11/29/2022]
Abstract
In the living cells, the folding of many proteins is largely believed to begin co-translationally, during their biosynthesis at the ribosomes. In the ribosomal tunnel, the nascent peptide may establish local interactions and stabilize α-helical structures. Long-range contacts are more likely outside the ribosomes after release of larger segments of the nascent chain. Examples suggest that domains can attain native-like structure on the ribosome with and without population of folding intermediates. The co-translational folding is limited by the speed of the gradual extrusion of the nascent peptide which imposes conformational restraints on its folding landscape. Recent experimental and in silico modeling studies indicate that translation kinetics fine-tunes co-translational folding by providing a time delay for sequential folding of distinct portions of the nascent chain.
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Affiliation(s)
- Gong Zhang
- Department of Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14467 Potsdam, Germany
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105
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Czech A, Fedyunin I, Zhang G, Ignatova Z. Silent mutations in sight: co-variations in tRNA abundance as a key to unravel consequences of silent mutations. MOLECULAR BIOSYSTEMS 2010; 6:1767-72. [PMID: 20617253 DOI: 10.1039/c004796c] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mutations that alter the amino acid sequence are known to potentially exert deleterious effects on protein function, whereas substitutions of nucleotides without amino acid change are assumed to be neutral for the protein's functionality. However, cumulative evidence suggests that synonymous substitutions might also induce phenotypic variability by affecting splicing accuracy, translation fidelity, and conformation and function of proteins. tRNA isoacceptors mediate the translation of codons to amino acids, and asymmetric tRNA abundance causes variations in the rate of translation of each single triplet. Consequently, the effect of a silent point mutation in the coding region could be significant due to differential abundances of the cognate tRNA(s), emphasizing the importance of precise assessment of tRNA composition. Here, we provide an overview of the methods used to quantitatively determine the concentrations of tRNA species and discuss synonymous mutations in the context of tRNA composition of the cell, thus providing a new twist on the detrimental impact of the silent mutations.
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Affiliation(s)
- Andreas Czech
- Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str 24-25, 14467 Potsdam-Golm, Germany
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106
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Cabrita L, Dobson CM, Christodoulou J. Early Nascent Chain Folding Events on the Ribosome. Isr J Chem 2010. [DOI: 10.1002/ijch.201000015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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107
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Saunders R, Deane CM. Synonymous codon usage influences the local protein structure observed. Nucleic Acids Res 2010; 38:6719-28. [PMID: 20530529 PMCID: PMC2965230 DOI: 10.1093/nar/gkq495] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Translation of mRNA into protein is a unidirectional information flow process. Analysing the input (mRNA) and output (protein) of translation, we find that local protein structure information is encoded in the mRNA nucleotide sequence. The Coding Sequence and Structure (CSandS) database developed in this work provides a detailed mapping between over 4000 solved protein structures and their mRNA. CSandS facilitates a comprehensive analysis of codon usage over many organisms. In assigning translation speed, we find that relative codon usage is less informative than tRNA concentration. For all speed measures, no evidence was found that domain boundaries are enriched with slow codons. In fact, genes seemingly avoid slow codons around structurally defined domain boundaries. Translation speed, however, does decrease at the transition into secondary structure. Codons are identified that have structural preferences significantly different from the amino acid they encode. However, each organism has its own set of ‘significant codons’. Our results support the premise that codons encode more information than merely amino acids and give insight into the role of translation in protein folding.
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Affiliation(s)
- Rhodri Saunders
- Department of Statistics, Oxford University, 1 South Parks Road, Oxford OX1 3TG, UK.
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108
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Cannarozzi G, Cannarrozzi G, Schraudolph NN, Faty M, von Rohr P, Friberg MT, Roth AC, Gonnet P, Gonnet G, Barral Y. A role for codon order in translation dynamics. Cell 2010; 141:355-67. [PMID: 20403329 DOI: 10.1016/j.cell.2010.02.036] [Citation(s) in RCA: 258] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2007] [Revised: 06/05/2009] [Accepted: 02/18/2010] [Indexed: 10/19/2022]
Abstract
The genetic code is degenerate. Each amino acid is encoded by up to six synonymous codons; the choice between these codons influences gene expression. Here, we show that in coding sequences, once a particular codon has been used, subsequent occurrences of the same amino acid do not use codons randomly, but favor codons that use the same tRNA. The effect is pronounced in rapidly induced genes, involves both frequent and rare codons and diminishes only slowly as a function of the distance between subsequent synonymous codons. Furthermore, we found that in S. cerevisiae codon correlation accelerates translation relative to the translation of synonymous yet anticorrelated sequences. The data suggest that tRNA diffusion away from the ribosome is slower than translation, and that some tRNA channeling takes place at the ribosome. They also establish that the dynamics of translation leave a significant signature at the level of the genome.
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Affiliation(s)
- Gina Cannarozzi
- Institute of Computational Science, ETH Zurich, 8092 Zurich, Switzerland
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109
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Zhou T, Gu W, Wilke CO. Detecting positive and purifying selection at synonymous sites in yeast and worm. Mol Biol Evol 2010; 27:1912-22. [PMID: 20231333 DOI: 10.1093/molbev/msq077] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We present a new computational method to identify positive and purifying selection at synonymous sites in yeast and worm. We define synonymous substitutions that change codons from preferred to unpreferred or vice versa as nonconservative synonymous substitutions and all other substitutions as conservative. Using a maximum-likelihood framework, we then test whether conservative and nonconservative synonymous substitutions occur at equal rates. Our approach replaces the standard rate of synonymous substitutions per synonymous site, dS, with two new rates, the conservative synonymous substitution rate (dS(C)) and the nonconservative synonymous substitution rate (dS(N)). Based on the ratio dS(N)/dS(C), we find that 0.05% of all yeast genes and none of worm genes show evidence of positive selection at synonymous sites (dS(N)/dS(C) > 1). On the other hand, 9.44% of all yeast genes and 5.12% of all worm genes show evidence of significant purifying selection on synonymous sites (dS(N)/dS(C) < 1). We also find that dS(N) correlates strongly with gene expression level, whereas the correlation between expression level and dS(C) is very weak. Thus, dS(N) captures most of the signal of selection for translational accuracy and speed, whereas dS(C) is not strongly influenced by this selection pressure. We suggest that the ratio dN/dS(C) may be more appropriate than the ratio dN/dS to identify positive or purifying selection on amino acids.
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Affiliation(s)
- Tong Zhou
- Center for Computational Biology and Bioinformatics, University of Texas at Austin, TX, USA
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110
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Increased incidence of rare codon clusters at 5' and 3' gene termini: implications for function. BMC Genomics 2010; 11:118. [PMID: 20167116 PMCID: PMC2833160 DOI: 10.1186/1471-2164-11-118] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Accepted: 02/18/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The process of translation can be affected by the use of rare versus common codons within the mRNA transcript. RESULTS Here, we show that rare codons are enriched at the 5' and 3' termini of genes from E. coli and other prokaryotes. Genes predicted to be secreted show significant enrichment in 5' rare codon clusters, but not 3' rare codon clusters. Surprisingly, no correlation between 5' mRNA structure and rare codon usage was observed. CONCLUSIONS Potential functional roles for the enrichment of rare codons at terminal positions are explored.
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111
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Gu W, Zhou T, Wilke CO. A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes. PLoS Comput Biol 2010; 6:e1000664. [PMID: 20140241 PMCID: PMC2816680 DOI: 10.1371/journal.pcbi.1000664] [Citation(s) in RCA: 232] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Accepted: 12/30/2009] [Indexed: 12/05/2022] Open
Abstract
Recent studies have suggested that the thermodynamic stability of mRNA secondary structure near the start codon can regulate translation efficiency in Escherichia coli, and that translation is more efficient the less stable the secondary structure. We survey the complete genomes of 340 species for signals of reduced mRNA secondary structure near the start codon. Our analysis includes bacteria, archaea, fungi, plants, insects, fishes, birds, and mammals. We find that nearly all species show evidence for reduced mRNA stability near the start codon. The reduction in stability generally increases with increasing genomic GC content. In prokaryotes, the reduction also increases with decreasing optimal growth temperature. Within genomes, there is variation in the stability among genes, and this variation correlates with gene GC content, codon bias, and gene expression level. For birds and mammals, however, we do not find a genome-wide trend of reduced mRNA stability near the start codon. Yet the most GC rich genes in these organisms do show such a signal. We conclude that reduced stability of the mRNA secondary structure near the start codon is a universal feature of all cellular life. We suggest that the origin of this reduction is selection for efficient recognition of the start codon by initiator-tRNA. Synonymous mutations are mutations that change the nucleotide sequence of a gene without changing the amino-acid sequence. Because these mutations don't alter the expressed protein, they are frequently also called silent mutations. Yet increasing evidence demonstrates that synonymous mutations are not that silent. In particular, experimental work in Escherichia coli has shown that the choice of synonymous codons near the start codon can greatly influence protein production. Codons that allow the mRNA to fold into a stable secondary structure seem to inhibit efficient translation initiation. This observation suggests that selection should prefer reduced mRNA stability near the start codon in many organisms. Here, we show that this prediction generally holds true in most organisms, including bacteria, archaea, fungi, plants, insects, and fishes. In birds and mammals it doesn't hold true genome-wide, but it does hold true in the most GC-rich genes. In all organisms, the extent to which mRNA stability is reduced increases with increasing GC content. In prokaryotes, it also increases with decreasing optimal growing temperature. Thus, it seems that all organisms have to optimize their synonymous sites near the start codon to guarantee efficient protein translation.
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Affiliation(s)
- Wanjun Gu
- Key Laboratory of Child Development and Learning Science of Ministry of Education of China, Southeast University, Nanjing, Jiangsu, China
| | - Tong Zhou
- Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas, United States of America
- Section of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Claus O. Wilke
- Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, Texas, United States of America
- Section of Integrative Biology, The University of Texas at Austin, Austin, Texas, United States of America
- Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
- * E-mail:
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112
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Warnecke T, Hurst LD. GroEL dependency affects codon usage--support for a critical role of misfolding in gene evolution. Mol Syst Biol 2010; 6:340. [PMID: 20087338 PMCID: PMC2824523 DOI: 10.1038/msb.2009.94] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Accepted: 11/09/2009] [Indexed: 11/12/2022] Open
Abstract
Integrating genome-scale sequence, expression, structural and protein interaction data from E. coli we establish an interaction between chaperone (GroEL) dependency and optimal codon usage. Highly expressed sporadic substrates of GroEL employ more optimal codons than expected, show enrichment for optimal codons at structurally sensitive sites and greater conservation of codon optimality under conditions of relaxed purifying selection. We suggest that highly expressed genes cannot routinely utilize GroEL for error control so that codon usage has evolved to provide complementary error limitation, whereas obligate GroEL substrates experience relaxed selection on codon usage. Our results support a critical role of misfolding prevention in gene evolution.
Errors during gene expression are relatively commonplace, which has prompted speculations that many features of gene and genome anatomy and organization have evolved to reduce or mitigate such errors. One type of error that can be particularly costly occurs when the polypeptide chain that emerges from the ribosome fails to fold into its native structure. Some aberrantly folded proteins, exposing hydrophobic residues that would normally be buried, may begin to promiscuously interact with other proteins, become toxic to the cell and thus pose a substantial fitness concern (Gregersen et al, 2006). In trans, molecular chaperones have long been recognized to play crucial roles in misfolding prevention and remedy. In cis, it has recently been suggested that the use of optimal codons limits mistranslation-induced protein misfolding (Drummond and Wilke, 2008). Evidence for the latter is centred on the argument that synonymous codons differ in their propensity to cause mistranslation. Translationally optimal codons, typically represented by more abundant cognate tRNAs (Duret, 2000), are thought less likely to cause ribosomal stalling and/or incorporation of the wrong amino acid. Here, we suggest that the role, if any, of error limitation in cis can be revealed by studying its interaction with well-established error management systems in trans (chaperones). If codon usage does indeed play a tangible role in misfolding prevention, we would expect selection on codon identity to vary with the degree to which a protein can rely on other error control mechanisms, namely chaperones. We use the E. coli chaperonin GroEL as a model system to explore whether there is any interaction between optimal codon usage and chaperone dependency. Kerner et al (2005) had previously determined GroEL substrates on a genome-wide scale. Based on enrichment in GroEL complexes the authors assigned ∼250 proteins to three classes reflecting GroEL dependency: class-I proteins, only a small fraction of which (<1%) associates with GroEL and which spontaneously regain some activity; class-II proteins, which only exhibit spontaneous refolding at more permissive temperatures and class-III proteins, which are obligate substrates of GroEL and largely fail to refold even under more benign conditions. Notably, although on average less abundant than class-I/II proteins (‘sporadic clients'), class-III proteins (‘obligate clients') occupy ∼80% of GroEL's capacity in vivo. Consequently, a higher proportion (∼100% versus ∼20% for class-II and ∼1% for class-I) of these proteins is routinely processed by the GroEL system. We demonstrate that sporadic but not obligate clients of GroEL exhibit enhanced codon adaptation, carefully controlling for possible confounding factors, notably expression level and protein length (Figure 1). We also point out that genes that recently entered the E. coli genome via horizontal gene transfer will distort equilibrium analyses of codon usage in bacteria and should thus be routinely eliminated from analysis. Building on earlier work by Zhou et al (2009), we further show that sporadic substrates are conspicuously enriched for optimal codons at structurally sensitive sites, consistent with more severe fitness implications of codon choice for these proteins. Lastly, we reveal that codon optimality in sporadic clients is more highly conserved in S. dysenteriae. S. dysenteriae is an E. coli clone that has diverged relatively recently from the E. coli K12 strain and has adopted an intracellular lifestyle (Balbi et al, 2009). Concomitant with that lifestyle, Shigella has experienced a lower effective population size and therefore reduced efficiency of purifying selection. This has generated conditions where, overall, codon optimality has started to decay. However, when we followed the fate of ancestrally optimal codons at buried sites in the S. dysenteriae and E. coli K12 genomes, we found that a lower fraction of buried sites has lost codon optimality in sporadic substrates (Figure 4), again consistent with greater structural importance of codon choice in these substrates. Based on the these findings, we suggest the following explanation: As mentioned above, class-III substrates are defined not only by GroEL being critical for proper folding, but also by occupying most of GroEL's capacity (∼80%). With a high proportion of class-III protein passaged through the GroEL system, mistranslation errors in these proteins weigh less severely as GroEL can remedy at least some misfolding that ensues. In contrast, class-I and II genes are more highly expressed and cannot routinely rely on GroEL to rectify folding errors. Yet class-I/II proteins are clearly liable to misfold as testified by their sporadic association with GroEL. We argue that augmenting GroEL's capacity to address the misfolding propensity of these genes would be prohibitively costly to the organism and that, as an alternative strategy, these genes employ optimal codons to reduce the rate of misfolding error. Our findings (a) reveal a cis–trans interaction between codon usage and chaperones in providing an integrated error management system, (b) provide independent evidence for a role of misfolding in shaping gene evolution and (c) suggest that the burden of deleterious mutations in long-term bottlenecking populations like that of the insect endosymbiont Buchnera not only comprises unfavourable amino-acid (Moran, 1996) but also synonymous substitutions. It has recently been suggested that the use of optimal codons limits mistranslation-induced protein misfolding, yet evidence for this remains largely circumstantial. In contrast, molecular chaperones have long been recognized to play crucial roles in misfolding prevention and remedy. We propose that putative error limitation in cis can be elucidated by examining the interaction between codon usage and chaperoning processes. Using Escherichia coli as a model system, we find that codon optimality covaries with dependency on the chaperonin GroEL. Sporadic but not obligate substrates of GroEL exhibit higher average codon adaptation and are conspicuously enriched for optimal codons at structurally sensitive sites. Further, codon optimality of sporadic clients is more conserved in the E. coli clone Shigella dysenteriae. We suggest that highly expressed genes cannot routinely use GroEL for error control so that codon usage has evolved to provide complementary error limitation. These findings provide independent evidence for a role of misfolding in shaping gene evolution and highlight the need to co-characterize adaptations in cis and trans to unravel the workings of integrated molecular systems.
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Affiliation(s)
- Tobias Warnecke
- Department of Biology and Biochemistry, University of Bath, Bath, UK.
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113
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Frugier M, Bour T, Ayach M, Santos MAS, Rudinger-Thirion J, Théobald-Dietrich A, Pizzi E. Low Complexity Regions behave as tRNA sponges to help co-translational folding of plasmodial proteins. FEBS Lett 2009; 584:448-54. [PMID: 19900443 DOI: 10.1016/j.febslet.2009.11.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 11/02/2009] [Accepted: 11/03/2009] [Indexed: 10/20/2022]
Abstract
In most organisms, the information necessary to specify the native 3D-structures of proteins is encoded in the corresponding mRNA sequences. Translational accuracy and efficiency are coupled and sequences that are slowly translated play an essential role in the concomitant folding of protein domains. Here, we suggest that the well-known mechanisms for the regulation of translational efficiency, which involves mRNA structure and/or asymmetric tRNA abundance, do not apply to all organisms. We propose that Plasmodium, the parasite responsible for malaria, uses an alternative strategy to slow down ribosomal speed and avoid multidomain protein misfolding during translation. In our model, the abundant Low Complexity Regions present in Plasmodium proteins replace the codon preferences, which influence the assembly of protein secondary structures.
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Affiliation(s)
- Magali Frugier
- Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, 67084 Strasbourg Cedex, France.
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114
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In silico analysis of chimeric espA, eae and tir fragments of Escherichia coli O157:H7 for oral immunogenic applications. Theor Biol Med Model 2009; 6:28. [PMID: 19995413 PMCID: PMC3224939 DOI: 10.1186/1742-4682-6-28] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2009] [Accepted: 12/08/2009] [Indexed: 01/23/2023] Open
Abstract
Background In silico techniques are highly suited for both the discovery of new and development of existing vaccines. Enterohemorrhagic Escherichia coli O157:H7 (EHEC) exhibits a pattern of localized adherence to host cells, with the formation of microcolonies, and induces a specific histopathological lesion (attaching/effacing). The genes encoding the products responsible for this phenotype are clustered on a 35-kb pathogenicity island. Among these proteins, Intimin, Tir, and EspA, which are expressed by attaching-effacing genes, are responsible for the attachment to epithelial cell that leads to lesions. Results We designed synthetic genes encoding the carboxy-terminal fragment of Intimin, the middle region of Tir and the carboxy-terminal part of EspA. These multi genes were synthesized with codon optimization for a plant host and were fused together by the application of four repeats of five hydrophobic amino acids as linkers. The structure of the synthetic construct gene, its mRNA and deduced protein and their stabilities were analyzed by bioinformatic software. Furthermore, the immunogenicity of this multimeric recombinant protein consisting of three different domains was predicted. Conclusion a structural model for a chimeric gene from LEE antigenic determinants of EHEC is presented. It may define accessibility, solubility and immunogenecity.
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115
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Abstract
Operons (clusters of co-regulated genes with related functions) are common features of bacterial genomes. More recently, functional gene clustering has been reported in eukaryotes, from yeasts to filamentous fungi, plants, and animals. Gene clusters can consist of paralogous genes that have most likely arisen by gene duplication. However, there are now many examples of eukaryotic gene clusters that contain functionally related but non-homologous genes and that represent functional gene organizations with operon-like features (physical clustering and co-regulation). These include gene clusters for use of different carbon and nitrogen sources in yeasts, for production of antibiotics, toxins, and virulence determinants in filamentous fungi, for production of defense compounds in plants, and for innate and adaptive immunity in animals (the major histocompatibility locus). The aim of this article is to review features of functional gene clusters in prokaryotes and eukaryotes and the significance of clustering for effective function.
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Affiliation(s)
- Anne E Osbourn
- Department of Metabolic Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK.
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116
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Tanner DR, Cariello DA, Woolstenhulme CJ, Broadbent MA, Buskirk AR. Genetic identification of nascent peptides that induce ribosome stalling. J Biol Chem 2009; 284:34809-18. [PMID: 19840930 DOI: 10.1074/jbc.m109.039040] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Several nascent peptides stall ribosomes during their own translation in both prokaryotes and eukaryotes. Leader peptides that induce stalling can regulate downstream gene expression. Interestingly, stalling peptides show little sequence similarity and interact with the ribosome through distinct mechanisms. To explore the scope of regulation by stalling peptides and to better understand the mechanism of stalling, we identified and characterized new examples from random libraries. We created a genetic selection that ties the life of Escherichia coli cells to stalling at a specific site. This selection relies on the natural bacterial system that rescues arrested ribosomes. We altered transfer-messenger RNA, a key component of this rescue system, to direct the completion of a necessary protein if and only if stalling occurs. We identified three classes of stalling peptides: C-terminal Pro residues, SecM-like peptides, and the novel stalling sequence FXXYXIWPP. Like the leader peptides SecM and TnaC, the FXXYXIWPP peptide induces stalling efficiently by inhibiting peptidyl transfer. The nascent peptide exit tunnel and peptidyltransferase center are implicated in this stalling event, although mutations in the ribosome affect stalling on SecM and FXXYXIWPP differently. We conclude that ribosome stalling can be caused by numerous sequences and is more common than previously believed.
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Affiliation(s)
- Douglas R Tanner
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA
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117
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Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation. PLoS Genet 2009; 5:e1000548. [PMID: 19578405 PMCID: PMC2697378 DOI: 10.1371/journal.pgen.1000548] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Accepted: 06/03/2009] [Indexed: 12/31/2022] Open
Abstract
In species with large effective population sizes, highly expressed genes tend to be encoded by codons with highly abundant cognate tRNAs to maximize translation rate. However, there has been little evidence for a similar bias of synonymous codons in highly expressed human genes. Here, we ask instead whether there is evidence for the selection for codons associated with low abundance tRNAs. Rather than averaging the codon usage of complete genes, we scan the genes for windows with deviating codon usage. We show that there is a significant over representation of human genes that contain clusters of codons with low abundance cognate tRNAs. We name these regions, which on average have a 50% reduction in the amount of cognate tRNA available compared to the remainder of the gene, RTS (rare tRNA score) clusters. We observed a significant reduction in the substitution rate between the human RTS clusters and their orthologous chimp sequence, when compared to non-RTS cluster sequences. Overall, the genes with an RTS cluster have higher tissue specificity than the non-RTS cluster genes. Furthermore, these genes are functionally enriched for transcription regulation. As genes that regulate transcription in lower eukaryotes are known to be involved in translation on demand, this suggests that the mechanism of translation level expression regulation also exists within the human genome.
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118
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Sharma AK, Sharma MK. Plants as bioreactors: Recent developments and emerging opportunities. Biotechnol Adv 2009; 27:811-832. [PMID: 19576278 PMCID: PMC7125752 DOI: 10.1016/j.biotechadv.2009.06.004] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Revised: 06/15/2009] [Accepted: 06/16/2009] [Indexed: 12/18/2022]
Abstract
In recent years, the use of plants as bioreactors has emerged as an exciting area of research and significant advances have created new opportunities. The driving forces behind the rapid growth of plant bioreactors include low production cost, product safety and easy scale up. As the yield and concentration of a product is crucial for commercial viability, several strategies have been developed to boost up protein expression in transgenic plants. Augmenting tissue-specific transcription, elevating transcript stability, tissue-specific targeting, translation optimization and sub-cellular accumulation are some of the strategies employed. Various kinds of products that are currently being produced in plants include vaccine antigens, medical diagnostics proteins, industrial and pharmaceutical proteins, nutritional supplements like minerals, vitamins, carbohydrates and biopolymers. A large number of plant-derived recombinant proteins have reached advanced clinical trials. A few of these products have already been introduced in the market.
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Affiliation(s)
- Arun K Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India.
| | - Manoj K Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
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119
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Zhou T, Weems M, Wilke CO. Translationally optimal codons associate with structurally sensitive sites in proteins. Mol Biol Evol 2009; 26:1571-80. [PMID: 19349643 DOI: 10.1093/molbev/msp070] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The mistranslation-induced protein misfolding hypothesis predicts that selection should prefer high-fidelity codons at sites at which translation errors are structurally disruptive and lead to protein misfolding and aggregation. To test this hypothesis, we analyzed the relationship between codon usage bias and protein structure in the genomes of four model organisms, Escherichia coli, yeast, fly, and mouse. Using both the Mantel-Haenszel procedure, which applies to categorical data, and a newly developed association test for continuous variables, we find that translationally optimal codons associate with buried residues and also with residues at sites where mutations lead to large changes in free energy (DeltaDeltaG). In each species, only a subset of all amino acids show this signal, but most amino acids show the signal in at least one species. By repeating the analysis on a reduced data set that excludes interdomain linkers, we show that our results are not caused by an association of rare codons with solvent-accessible linker regions. Finally, we find that our results depend weakly on expression level; the association between optimal codons and buried sites exists at all expression levels, but increases in strength as expression level increases.
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Affiliation(s)
- Tong Zhou
- Center for Computational Biology and Bioinformatics, The University of Texas at Austin, TX, USA
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120
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Zhang G, Ignatova Z. Generic algorithm to predict the speed of translational elongation: implications for protein biogenesis. PLoS One 2009; 4:e5036. [PMID: 19343177 PMCID: PMC2661179 DOI: 10.1371/journal.pone.0005036] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2009] [Accepted: 03/03/2009] [Indexed: 11/27/2022] Open
Abstract
Synonymous codon usage and variations in the level of isoaccepting tRNAs exert a powerful selective force on translation fidelity. We have developed an algorithm to evaluate the relative rate of translation which allows large-scale comparisons of the non-uniform translation rate on the protein biogenesis. Using the complete genomes of Escherichia coli and Bacillus subtilis we show that stretches of codons pairing to minor tRNAs form putative sites to locally attenuate translation; thereby the tendency is to cluster in near proximity whereas long contiguous stretches of slow-translating triplets are avoided. The presence of slow-translating segments positively correlates with the protein length irrespective of the protein abundance. The slow-translating clusters are predominantly located down-stream of the domain boundaries presumably to fine-tune translational accuracy with the folding fidelity of multidomain proteins. Translation attenuation patterns at highly structurally and functionally conserved domains are preserved across the species suggesting a concerted selective pressure on the codon selection and species-specific tRNA abundance in these regions.
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Affiliation(s)
- Gong Zhang
- Department of Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
| | - Zoya Ignatova
- Department of Biochemistry, Institute of Biochemistry and Biology, University of Potsdam, Potsdam-Golm, Germany
- * E-mail:
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121
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Welch M, Villalobos A, Gustafsson C, Minshull J. You're one in a googol: optimizing genes for protein expression. J R Soc Interface 2009; 6 Suppl 4:S467-76. [PMID: 19324676 DOI: 10.1098/rsif.2008.0520.focus] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A vast number of different nucleic acid sequences can all be translated by the genetic code into the same amino acid sequence. These sequences are not all equally useful however; the exact sequence chosen can have profound effects on the expression of the encoded protein. Despite the importance of protein-coding sequences, there has been little systematic study to identify parameters that affect expression. This is probably because protein expression has largely been tackled on an ad hoc basis in many independent projects: once a sequence has been obtained that yields adequate expression for that project, there is little incentive to continue work on the problem. Synthetic biology may now provide the impetus to transform protein expression folklore into design principles, so that DNA sequences may easily be designed to express any protein in any system. In this review, we offer a brief survey of the literature, outline the major challenges in interpreting existing data and constructing robust design algorithms, and propose a way to proceed towards the goal of rational sequence engineering.
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Affiliation(s)
- Mark Welch
- DNA 2.0, Inc., 1430 O'Brien Drive, Menlo Park, CA 94025, USA
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122
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Tartaglia GG, Pechmann S, Dobson CM, Vendruscolo M. A relationship between mRNA expression levels and protein solubility in E. coli. J Mol Biol 2009; 388:381-9. [PMID: 19281824 DOI: 10.1016/j.jmb.2009.03.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Revised: 02/26/2009] [Accepted: 03/03/2009] [Indexed: 10/21/2022]
Abstract
Each step in the process of gene expression, from the transcription of DNA into mRNA to the folding and posttranslational modification of proteins, is regulated by complex cellular mechanisms. At the same time, stringent conditions on the physicochemical properties of proteins, and hence on the nature of their amino acids, are imposed by the need to avoid aggregation at the concentrations required for optimal cellular function. A relationship is therefore expected to exist between mRNA expression levels and protein solubility in the cell. By investigating such a relationship, we formulate a method that enables the prediction of the maximal levels of mRNA expression in Escherichia coli with an accuracy of 83% and of the solubility of recombinant human proteins expressed in E. coli with an accuracy of 86%.
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Affiliation(s)
- Gian Gaetano Tartaglia
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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123
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Abstract
Many bacterial cellular processes interact intimately with the chromosome. Such interplay is the major driving force of genome structure or organization. Interactions take place at different scales-local for gene expression, global for replication-and lead to the differentiation of the chromosome into organizational units such as operons, replichores, or macrodomains. These processes are intermingled in the cell and create complex higher-level organizational features that are adaptive because they favor the interplay between the processes. The surprising result of selection for genome organization is that gene repertoires change much more quickly than chromosomal structure. Comparative genomics and experimental genomic manipulations are untangling the different cellular and evolutionary mechanisms causing such resilience to change. Since organization results from cellular processes, a better understanding of chromosome organization will help unravel the underlying cellular processes and their diversity.
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Affiliation(s)
- Eduardo P C Rocha
- Institut Pasteur, Microbial Evolutionary Genomics, F-75015 Paris, France.
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124
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Basak S, Banerjee R, Mukherjee I, Das S. Influence of domain architecture and codon usage pattern on the evolution of virulence factors of Vibrio cholerae. Biochem Biophys Res Commun 2009; 379:803-5. [PMID: 19159613 DOI: 10.1016/j.bbrc.2009.01.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Accepted: 01/05/2009] [Indexed: 11/29/2022]
Abstract
Cholera remains a heavy burden to human health in some developing countries including India where sanitation is poor and health care is limited. After the publication of the complete genome sequence of Vibrio cholerae, the etiological agent of cholera, extensive possibilities, earlier unavailable, have opened up to understand the genetic organization of V. cholerae. In the present study, we analyzed all the pathogenic non-horizontally transferred genes of V. cholerae to know the ancestral relationship and how the pathogenic genes have been evolved in V. cholerae genome. We observed that protein domain has important role in developing pathogenicity, and codon usage pattern of the pathogenic protein domain is also subject to selection. The present study unambiguously depict that the patterns of synonymous codon usage within a protein domain can change dramatically during the course of evolution to give rise to pathogenicity.
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Affiliation(s)
- Surajit Basak
- Biomedical Informatics Center, National Institute of Cholera and Enteric Diseases, P-33, CIT Road, Scheme-XM, Beliaghata, Kolkata 700010, West Bengal, India.
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125
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Danchin A. Bacteria as computers making computers. FEMS Microbiol Rev 2009; 33:3-26. [PMID: 19016882 PMCID: PMC2704931 DOI: 10.1111/j.1574-6976.2008.00137.x] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2008] [Revised: 09/20/2008] [Accepted: 09/21/2008] [Indexed: 12/13/2022] Open
Abstract
Various efforts to integrate biological knowledge into networks of interactions have produced a lively microbial systems biology. Putting molecular biology and computer sciences in perspective, we review another trend in systems biology, in which recursivity and information replace the usual concepts of differential equations, feedback and feedforward loops and the like. Noting that the processes of gene expression separate the genome from the cell machinery, we analyse the role of the separation between machine and program in computers. However, computers do not make computers. For cells to make cells requires a specific organization of the genetic program, which we investigate using available knowledge. Microbial genomes are organized into a paleome (the name emphasizes the role of the corresponding functions from the time of the origin of life), comprising a constructor and a replicator, and a cenome (emphasizing community-relevant genes), made up of genes that permit life in a particular context. The cell duplication process supposes rejuvenation of the machine and replication of the program. The paleome also possesses genes that enable information to accumulate in a ratchet-like process down the generations. The systems biology must include the dynamics of information creation in its future developments.
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Affiliation(s)
- Antoine Danchin
- Génétique des Génomes Bactériens, Institut Pasteur, Paris, France.
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126
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Cambray G, Mazel D. Synonymous genes explore different evolutionary landscapes. PLoS Genet 2008; 4:e1000256. [PMID: 19008944 PMCID: PMC2575237 DOI: 10.1371/journal.pgen.1000256] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2008] [Accepted: 10/07/2008] [Indexed: 11/18/2022] Open
Abstract
The evolutionary potential of a gene is constrained not only by the amino acid sequence of its product, but by its DNA sequence as well. The topology of the genetic code is such that half of the amino acids exhibit synonymous codons that can reach different subsets of amino acids from each other through single mutation. Thus, synonymous DNA sequences should access different regions of the protein sequence space through a limited number of mutations, and this may deeply influence the evolution of natural proteins. Here, we demonstrate that this feature can be of value for manipulating protein evolvability. We designed an algorithm that, starting from an input gene, constructs a synonymous sequence that systematically includes the codons with the most different evolutionary perspectives; i.e., codons that maximize accessibility to amino acids previously unreachable from the template by point mutation. A synonymous version of a bacterial antibiotic resistance gene was computed and synthesized. When concurrently submitted to identical directed evolution protocols, both the wild type and the recoded sequence led to the isolation of specific, advantageous phenotypic variants. Simulations based on a mutation isolated only from the synthetic gene libraries were conducted to assess the impact of sub-functional selective constraints, such as codon usage, on natural adaptation. Our data demonstrate that rational design of synonymous synthetic genes stands as an affordable improvement to any directed evolution protocol. We show that using two synonymous DNA sequences improves the overall yield of the procedure by increasing the diversity of mutants generated. These results provide conclusive evidence that synonymous coding sequences do experience different areas of the corresponding protein adaptive landscape, and that a sequence's codon usage effectively constrains the evolution of the encoded protein.
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Affiliation(s)
- Guillaume Cambray
- Unité Plasticité du Génome Bactérien, Institut Pasteur, CNRS URA 2171, Paris, France
| | - Didier Mazel
- Unité Plasticité du Génome Bactérien, Institut Pasteur, CNRS URA 2171, Paris, France
- * E-mail:
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127
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Komar AA. A pause for thought along the co-translational folding pathway. Trends Biochem Sci 2008; 34:16-24. [PMID: 18996013 DOI: 10.1016/j.tibs.2008.10.002] [Citation(s) in RCA: 250] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Revised: 10/09/2008] [Accepted: 10/13/2008] [Indexed: 11/26/2022]
Abstract
A unifying concept that combines the basic features governing self-organization of proteins into complex three-dimensional structures in vitro and in vivo is still lacking. Recent experimental results and theoretical in silico modeling studies provide evidence showing that mRNA might contain an additional layer of information, beyond the amino acid sequence, that fine-tunes in vivo protein folding, which is largely believed to start as a co-translational process. These findings indicate that translation kinetics might direct the co-translational folding pathway and that translational pausing at rare codons might provide a time delay to enable independent and sequential folding of the defined portions of the nascent polypeptide emerging from the ribosome.
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Affiliation(s)
- Anton A Komar
- Department of Biological, Center for Gene Regulation in Health and Disease, Cleveland State University, Cleveland, OH 44115, USA.
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128
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Abstract
The persistent difficulties in the production of protein at high levels in heterologous systems, as well as the inability to understand pathologies associated with protein aggregation, highlight our limited knowledge on the mechanisms of protein folding in vivo. Attempts to improve yield and quality of recombinant proteins are diverse, frequently involving optimization of the cell growth temperature, the use of synonymous codons and/or the co-expression of tRNAs, chaperones and folding catalysts among others. Although protein secondary structure can be determined largely by the amino acid sequence, protein folding within the cell is affected by a range of factors beyond amino acid sequence. The folding pathway of a nascent polypeptide can be affected by transient interactions with other proteins and ligands, the ribosome, translocation through a pore membrane, redox conditions, among others. The translation rate as well as the translation machinery itself can dramatically affect protein folding, and thus the structure and function of the protein product. This review addresses current efforts to better understand how the use of synonymous codons in the mRNA and the availability of tRNAs can modulate translation kinetics, affecting the folding, the structure and the biological activity of proteins.
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Affiliation(s)
- Monica Marin
- Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay.
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129
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Abstract
Most amino acids are encoded by more than one codon. These synonymous codons are not used with equal frequency: in every organism, some codons are used more commonly, while others are more rare. Though the encoded protein sequence is identical, selective pressures favor more common codons for enhanced translation speed and fidelity. However, rare codons persist, presumably due to neutral drift. Here, we determine whether other, unknown factors, beyond neutral drift, affect the selection and/or distribution of rare codons. We have developed a novel algorithm that evaluates the relative rareness of a nucleotide sequence used to produce a given protein sequence. We show that rare codons, rather than being randomly scattered across genes, often occur in large clusters. These clusters occur in numerous eukaryotic and prokaryotic genomes, and are not confined to unusual or rarely expressed genes: many highly expressed genes, including genes for ribosomal proteins, contain rare codon clusters. A rare codon cluster can impede ribosome translation of the rare codon sequence. These results indicate additional selective pressures govern the use of synonymous codons, and specifically that local pauses in translation can be beneficial for protein biogenesis.
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Affiliation(s)
- Thomas F. Clarke
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Patricia L. Clark
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
- * E-mail:
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130
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Batey S, Nickson AA, Clarke J. Studying the folding of multidomain proteins. HFSP JOURNAL 2008; 2:365-77. [PMID: 19436439 DOI: 10.2976/1.2991513] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2008] [Indexed: 11/19/2022]
Abstract
There have been relatively few detailed comprehensive studies of the folding of protein domains (or modules) in the context of their natural covalently linked neighbors. This is despite the fact that a significant proportion of the proteome consists of multidomain proteins. In this review we highlight some key experimental investigations of the folding of multidomain proteins to draw attention to the difficulties that can arise in analyzing such systems. The evidence suggests that interdomain interactions can significantly affect stability, folding, and unfolding rates. However, preliminary studies suggest that folding pathways are unaffected-to this extent domains can be truly considered to be independent folding units. Nonetheless, it is clear that interactions between domains cannot be ignored, in particular when considering the effects of mutations.
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Affiliation(s)
- Sarah Batey
- Department of Chemistry, MRC Centre for Protein Engineering, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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131
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Heterologous expression of plasmodial proteins for structural studies and functional annotation. Malar J 2008; 7:197. [PMID: 18828893 PMCID: PMC2567985 DOI: 10.1186/1475-2875-7-197] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2008] [Accepted: 10/01/2008] [Indexed: 11/10/2022] Open
Abstract
Malaria remains the world's most devastating tropical infectious disease with as many as 40% of the world population living in risk areas. The widespread resistance of Plasmodium parasites to the cost-effective chloroquine and antifolates has forced the introduction of more costly drug combinations, such as Coartem®. In the absence of a vaccine in the foreseeable future, one strategy to address the growing malaria problem is to identify and characterize new and durable antimalarial drug targets, the majority of which are parasite proteins. Biochemical and structure-activity analysis of these proteins is ultimately essential in the characterization of such targets but requires large amounts of functional protein. Even though heterologous protein production has now become a relatively routine endeavour for most proteins of diverse origins, the functional expression of soluble plasmodial proteins is highly problematic and slows the progress of antimalarial drug target discovery. Here the status quo of heterologous production of plasmodial proteins is presented, constraints are highlighted and alternative strategies and hosts for functional expression and annotation of plasmodial proteins are reviewed.
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132
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Electrostatics in the ribosomal tunnel modulate chain elongation rates. J Mol Biol 2008; 384:73-86. [PMID: 18822297 DOI: 10.1016/j.jmb.2008.08.089] [Citation(s) in RCA: 244] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Revised: 08/22/2008] [Accepted: 08/27/2008] [Indexed: 11/24/2022]
Abstract
Electrostatic potentials along the ribosomal exit tunnel are nonuniform and negative. The significance of electrostatics in the tunnel remains relatively uninvestigated, yet they are likely to play a role in translation and secondary folding of nascent peptides. To probe the role of nascent peptide charges in ribosome function, we used a molecular tape measure that was engineered to contain different numbers of charged amino acids localized to known regions of the tunnel and measured chain elongation rates. Positively charged arginine or lysine sequences produce transient arrest (pausing) before the nascent peptide is fully elongated. The rate of conversion from transiently arrested to full-length nascent peptide is faster for peptides containing neutral or negatively charged residues than for those containing positively charged residues. We provide experimental evidence that extraribosomal mechanisms do not account for this charge-specific pausing. We conclude that pausing is due to charge-specific interactions between the tunnel and the nascent peptide.
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133
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Tsai CJ, Sauna ZE, Kimchi-Sarfaty C, Ambudkar SV, Gottesman MM, Nussinov R. Synonymous mutations and ribosome stalling can lead to altered folding pathways and distinct minima. J Mol Biol 2008; 383:281-91. [PMID: 18722384 DOI: 10.1016/j.jmb.2008.08.012] [Citation(s) in RCA: 187] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Revised: 07/31/2008] [Accepted: 08/06/2008] [Indexed: 01/08/2023]
Abstract
How can we understand a case in which a given amino acid sequence folds into structurally and functionally distinct molecules? Synonymous single-nucleotide polymorphisms in the MDR1 (multidrug resistance 1 or ABCB1) gene involving frequent-to-rare codon substitutions lead to identical protein sequences. Remarkably, these alternative sequences give a protein product with similar but different structures and functions. Here, we propose that long-enough ribosomal pause time scales may lead to alternate folding pathways and distinct minima on the folding free energy surface. While the conformational and functional differences between the native and alternate states may be minor, the MDR1 case illustrates that the barriers may nevertheless constitute sufficiently high hurdles in physiological time scales, leading to kinetically trapped states with altered structures and functions. Different folding pathways leading to conformationally similar trapped states may be due to swapping of (fairly symmetric) segments. Domain swapping is more likely in the no-pause case in which the chain elongates and folds simultaneously; on the other hand, sufficiently long pause times between such segments may be expected to lessen the chances of swapping events. Here, we review the literature in this light.
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Affiliation(s)
- Chung-Jung Tsai
- Basic Research Program, SAIC-Frederick, Inc., Center for Cancer Research Nanobiology Program, NCI-Frederick, Frederick, MD 21702, USA
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134
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Holloway AK, Begun DJ, Siepel A, Pollard KS. Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster. Genome Res 2008; 18:1592-601. [PMID: 18583644 DOI: 10.1101/gr.077131.108] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Recent genomic sequencing of 10 additional Drosophila genomes provides a rich resource for comparative genomics analyses aimed at understanding the similarities and differences between species and between Drosophila and mammals. Using a phylogenetic approach, we identified 64 genomic elements that have been highly conserved over most of the Drosophila tree, but that have experienced a recent burst of evolution along the Drosophila melanogaster lineage. Compared to similarly defined elements in humans, these regions of rapid lineage-specific evolution in Drosophila differ dramatically in location, mechanism of evolution, and functional properties of associated genes. Notably, the majority reside in protein-coding regions and primarily result from rapid adaptive synonymous site evolution. In fact, adaptive evolution appears to be driving substitutions to unpreferred codons. Our analysis also highlights interesting noncoding genomic regions, such as regulatory regions in the gene gooseberry-neuro and a putative novel miRNA.
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Affiliation(s)
- Alisha K Holloway
- Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, California 95691, USA.
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135
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Angov E, Hillier CJ, Kincaid RL, Lyon JA. Heterologous protein expression is enhanced by harmonizing the codon usage frequencies of the target gene with those of the expression host. PLoS One 2008; 3:e2189. [PMID: 18478103 PMCID: PMC2364656 DOI: 10.1371/journal.pone.0002189] [Citation(s) in RCA: 209] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2008] [Accepted: 04/04/2008] [Indexed: 11/24/2022] Open
Abstract
Synonymous codon replacement can change protein structure and function, indicating that protein structure depends on DNA sequence. During heterologous protein expression, low expression or formation of insoluble aggregates may be attributable to differences in synonymous codon usage between expression and natural hosts. This discordance may be particularly important during translation of the domain boundaries (link/end segments) that separate elements of higher ordered structure. Within such regions, ribosomal progression slows as the ribosome encounters clusters of infrequently used codons that preferentially encode a subset of amino acids. To replicate the modulation of such localized translation rates during heterologous expression, we used known relationships between codon usage frequencies and secondary protein structure to develop an algorithm (“codon harmonization”) for identifying regions of slowly translated mRNA that are putatively associated with link/end segments. It then recommends synonymous replacement codons having usage frequencies in the heterologous expression host that are less than or equal to the usage frequencies of native codons in the native expression host. For protein regions other than these putative link/end segments, it recommends synonymous substitutions with codons having usage frequencies matched as nearly as possible to the native expression system. Previous application of this algorithm facilitated E. coli expression, manufacture and testing of two Plasmodium falciparum vaccine candidates. Here we describe the algorithm in detail and apply it to E. coli expression of three additional P. falciparum proteins. Expression of the “recoded” genes exceeded that of the native genes by 4- to 1,000-fold, representing levels suitable for vaccine manufacture. The proteins were soluble and reacted with a variety of functional conformation-specific mAbs suggesting that they were folded properly and had assumed native conformation. Codon harmonization may further provide a general strategy for improving the expression of soluble functional proteins during heterologous expression in hosts other than E. coli.
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Affiliation(s)
- Evelina Angov
- Molecular Parasitology, Division of Malaria Vaccine Development, Walter Reed Army Institute of Research, Silver Spring, Maryland, United States of America.
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136
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Widmann M, Clairo M, Dippon J, Pleiss J. Analysis of the distribution of functionally relevant rare codons. BMC Genomics 2008; 9:207. [PMID: 18457591 PMCID: PMC2391168 DOI: 10.1186/1471-2164-9-207] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2008] [Accepted: 05/05/2008] [Indexed: 11/20/2022] Open
Abstract
Background The substitution of rare codons with more frequent codons is a commonly applied method in heterologous gene expression to increase protein yields. However, in some cases these substitutions lead to a decrease of protein solubility or activity. To predict these functionally relevant rare codons, a method was developed which is based on an analysis of multisequence alignments of homologous protein families. Results The method successfully predicts functionally relevant codons in fatty acid binding protein and chloramphenicol acetyltransferase which had been experimentally determined. However, the analysis of 16 homologous protein families belonging to the α/β hydrolase fold showed that functionally rare codons share no common location in respect to the tertiary and secondary structure. Conclusion A systematic analysis of multisequence alignments of homologous protein families can be used to predict rare codons with a potential impact on protein expression. Our analysis showed that most genes contain at least one putative rare codon rich region. Rare codons located near to those regions should be excluded in an approach of improving protein expression by an exchange of rare codons by more frequent codons.
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Affiliation(s)
- Michael Widmann
- Institute of Technical Biochemistry, Allmandring 31, 70569 Stuttgart, Germany.
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137
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Dynamic covariation between gene expression and genome characteristics. Gene 2008; 410:53-66. [PMID: 18191345 DOI: 10.1016/j.gene.2007.11.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2007] [Revised: 11/13/2007] [Accepted: 11/29/2007] [Indexed: 11/21/2022]
Abstract
Gene and protein expression is controlled so that cells can react to changing intra- and extracellular signals by modulating biochemical networks and pathways. We have previously shown that gene expression and the properties of expressed proteins are dynamically correlated. Here we investigated correlations between gene related parameters and gene expression patterns, and found statistically significant correlations in microarray datasets for different cell types, organisms and processes, including human B and T cell stimulation, cell cycle in HeLa cells, infection in intestinal epithelial cells, Drosophila melanogaster life span, and Saccharomyces cerevisiae cell cycle. Our method was applied to time course datasets individually for each time point. We derived from sequence information numerous parameters for nucleotide composition, two-base composition, codon usage, skew parameters, and codon bias. In addition to coding regions, we also investigated correlations for complete genes and introns. Significant dynamic correlations were identified for each of the analyses. Our method also proved useful for detecting dynamic shifts in gene expression profiles, such as in the D. melanogaster dataset. Detection of changes in the properties of expressed genes and proteins might be useful for predicting or following biological processes, responses, growth, differentiation and possibly in related disorders.
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138
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On the origin of synonymous codon usage divergence between thermophilic and mesophilic prokaryotes. FEBS Lett 2007; 581:5825-30. [DOI: 10.1016/j.febslet.2007.11.054] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2007] [Revised: 11/14/2007] [Accepted: 11/16/2007] [Indexed: 01/24/2023]
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139
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Mukhopadhyay P, Basak S, Ghosh TC. Synonymous codon usage in different protein secondary structural classes of human genes: implication for increased non-randomness of GC3 rich genes towards protein stability. J Biosci 2007; 32:947-63. [PMID: 17914237 DOI: 10.1007/s12038-007-0095-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The relationship between the synonymous codon usage and different protein secondary structural classes were investigated using 401 Homo sapiens proteins extracted from Protein Data Bank (PDB). A simple Chi-square test was used to assess the significance of deviation of the observed and expected frequencies of 59 codons at the level of individual synonymous families in the four different protein secondary structural classes. It was observed that synonymous codon families show non-randomness in codon usage in four different secondary structural classes. However,when the genes were classified according to their GC3 levels there was an increase in non-randomness in high GC3 group of genes. The non-randomness in codon usage was further tested among the same protein secondary structures belonging to four different protein folding classes of high GC3 group of genes. The results show that in each of the protein secondary structural unit there exist some synonymous family that shows class specific codon-usage pattern. Moreover, there is an increased non-random behaviour of synonymous codons in sheet structure of all secondary structural classes in high GC3 group of genes. Biological implications of these results have been discussed.
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Affiliation(s)
- Pamela Mukhopadhyay
- Bioinformatics Centre, Bose Institute, P 1/12, CIT Scheme VII M, Kolkata 700 054, India
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140
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Vladimirov NV, Likhoshvai VA, Matushkin YG. Correlation of codon biases and potential secondary structures with mRNA translation efficiency in unicellular organisms. Mol Biol 2007. [DOI: 10.1134/s0026893307050184] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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141
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Sunagawa M, Nakamura M, Kosugi T. Cloning of habutobin cDNA and antithrombotic activity of recombinant protein. Biochem Biophys Res Commun 2007; 362:899-904. [PMID: 17803962 DOI: 10.1016/j.bbrc.2007.08.103] [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] [Received: 08/08/2007] [Accepted: 08/13/2007] [Indexed: 11/19/2022]
Abstract
The habutobin cDNA was cloned from total RNA extracted from venom glands of Trimeresurus flavoviridis (the habu snake). The conceptual translation of 1539 bp of habutobin cDNA consists of 236 amino acids and its molecular weight is 25.7 kDa. Histidine (His)-tagged recombinant habutobin fusion protein, pET-r-habutobin and AcNPV-r-habutobin, was purified by bacterial system and baculoviral system, respectively. After refolding pET-r-habutobin, there were two protein bands at about 32 kDa and 65 kDa, indicating that habutobin might be produced as a monomer protein and processed to form two concatenated protein. Purified AcNPV-r-habutobin dose-dependently increased fibrin forming activity and inhibited collagen-induced aggregation of rabbit washed platelets. Thus, AcNPV-r-habutobin produced by baculoviral system is very useful for study on structure-function relationship, which is necessary for developing an antithrombotic drug from habutobin.
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Affiliation(s)
- Masanori Sunagawa
- 1st Department of Physiology, Unit of Physiological Science, School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa 903-0215, Japan.
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142
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Horjales S, Cota G, Señorale-Pose M, Rovira C, Román E, Artagaveytia N, Ehrlich R, Marín M. Translational machinery and protein folding: evidence of conformational variants of the estrogen receptor alpha. Arch Biochem Biophys 2007; 467:139-43. [PMID: 17900518 DOI: 10.1016/j.abb.2007.07.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2007] [Revised: 07/23/2007] [Accepted: 07/24/2007] [Indexed: 11/21/2022]
Abstract
As an approach to understand how translation may affect protein folding, we analyzed structural and functional properties of the human estrogen receptor alpha synthesized by different eukaryotic translation systems. A minimum of three conformations of the receptor were detected using limited proteolysis and a sterol ligand-binding assay. The receptor in vitro translated in rabbit reticulocyte lysate was rapidly degraded by protease, produced major bands of about 34kDa and showed a high affinity for estradiol. In a wheat germ translation system, the receptor was more slowly digested. Two soluble co-existing conformations were evident by different degradation patterns and estradiol binding. Our data show that differences in the translation machinery may result in alternative conformations of the receptor with distinct sterol binding properties. These studies suggest that components of the cellular translation machinery itself might influence the protein folding pathways and the relative abundance of different receptor conformers.
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Affiliation(s)
- Sofía Horjales
- Sección Bioquímica, Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay
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143
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Fluitt A, Pienaar E, Viljoen H. Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis. Comput Biol Chem 2007; 31:335-46. [PMID: 17897886 PMCID: PMC2727733 DOI: 10.1016/j.compbiolchem.2007.07.003] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Accepted: 07/30/2007] [Indexed: 11/27/2022]
Abstract
It is generally accepted that the translation rate depends on the availability of cognate aa-tRNAs. In this study it is shown that the key factor that determines translation rate is the competition between near-cognate and cognate aa-tRNAs. The transport mechanism in the cytoplasm is diffusion, thus the competition between cognate, near-cognate and non-cognate aa-tRNAs to bind to the ribosome is a stochastic process. Two competition measures are introduced; C(i) and R(i) (i=1, 64) are quotients of the arrival frequencies of near-cognates vs. cognates and non-cognates vs. cognates, respectively. Furthermore, the reaction rates of bound cognates differ from those of bound near-cognates. If a near-cognate aa-tRNA binds to the A site of the ribosome, it may be rejected at the anti-codon recognition step or proofreading step or it may be accepted. Regardless of its fate, the near-cognates and non-cognates have caused delays of varying duration to the observed rate of translation. Rate constants have been measured at a temperature of 20 degrees C by (Gromadski, K.B., Rodnina, M.V., 2004. Kinetic determinants of high-fidelity tRNA discrimination on the ribosome. Mol. Cell 13, 191-200). These rate constants have been re-evaluated at 37 degrees C, using experimental data at 24.5 degrees C and 37 degrees C (Varenne, S., et al., 1984. Translation in a non-uniform process: effect of tRNA availability on the rate of elongation of nascent polypeptide chains. J. Mol. Biol. 180, 549-576). The key results of the study are: (i) the average time (at 37 degrees C) to add an amino acid, as defined by the ith codon, to the nascent peptide chain is: tau(i)=9.06+1.445x[10.48C(i)+0.5R(i)] (in ms); (ii) the misreading frequency is directly proportional to the near-cognate competition, E(i)=0.0009C(i); (iii) the competition from near-cognates, and not the availability of cognate aa-tRNAs, is the most important factor that determines the translation rate - the four codons with highest near-cognate competition (in the case of E. coli) are [GCC]>[CGG]>[AGG]>[GGA], which overlap only partially with the rarest codons: [AGG]<[CCA]<[GCC]<[CAC]; (iv) based on the kinetic rates at 37 degrees C, the average time to insert a cognate amino acid is 9.06ms and the average delay to process a near-cognate aa-tRNA is 10.45ms and (vii) the model also provides estimates of the vacancy times of the A site of the ribosome - an important factor in frameshifting.
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Affiliation(s)
- Aaron Fluitt
- Department of Chemical Engineering, University of Nebraska, Lincoln, NE 68588, USA
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144
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Abstract
While it has often been assumed that, in humans, synonymous mutations would have no effect on fitness, let alone cause disease, this position has been questioned over the last decade. There is now considerable evidence that such mutations can, for example, disrupt splicing and interfere with miRNA binding. Two recent publications suggest involvement of additional mechanisms: modification of protein abundance most probably mediated by alteration in mRNA stability and modification of protein structure and activity, probably mediated by induction of translational pausing. These case histories put a further nail into the coffin of the assumption that synonymous mutations must be neutral.
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Affiliation(s)
- Joanna L Parmley
- Department of Biology and Biochemistry, University of Bath, Bath, UK
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145
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Neafsey DE, Galagan JE. Positive selection for unpreferred codon usage in eukaryotic genomes. BMC Evol Biol 2007; 7:119. [PMID: 17640368 PMCID: PMC1936986 DOI: 10.1186/1471-2148-7-119] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2006] [Accepted: 07/18/2007] [Indexed: 01/17/2023] Open
Abstract
Background Natural selection has traditionally been understood as a force responsible for pushing genes to states of higher translational efficiency, whereas lower translational efficiency has been explained by neutral mutation and genetic drift. We looked for evidence of directional selection resulting in increased unpreferred codon usage (and presumably reduced translational efficiency) in three divergent clusters of eukaryotic genomes using a simple optimal-codon-based metric (Kp/Ku). Results Here we show that for some genes natural selection is indeed responsible for causing accelerated unpreferred codon substitution, and document the scope of this selection. In Cryptococcus and to a lesser extent Drosophila, we find many genes showing a statistically significant signal of selection for unpreferred codon usage in one or more lineages. We did not find evidence for this type of selection in Saccharomyces. The signal of positive selection observed from unpreferred synonymous codon substitutions is coincident in Cryptococcus and Drosophila with the distribution of upstream open reading frames (uORFs), another genic feature known to reduce translational efficiency. Functional enrichment analysis of genes exhibiting low Kp/Ku ratios reveals that genes in regulatory roles are particularly subject to this type of selection. Conclusion Through genome-wide scans, we find recent selection for unpreferred codon usage at approximately 1% of genetic loci in a Cryptococcus and several genes in Drosophila. Unpreferred codons can impede translation efficiency, and we find that genes with translation-impeding uORFs are enriched for this selection signal. We find that regulatory genes are particularly likely to be subject to selection for unpreferred codon usage. Given that expression noise can propagate through regulatory cascades, and that low translational efficiency can reduce expression noise, this finding supports the hypothesis that translational efficiency may be suppressed in some cases to reduce stochastic noise in gene expression.
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Affiliation(s)
- Daniel E Neafsey
- Microbial Analysis Group, Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
| | - James E Galagan
- Microbial Analysis Group, Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
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146
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Translational control of recombinant human acetylcholinesterase accumulation in plants. BMC Biotechnol 2007; 7:27. [PMID: 17537261 PMCID: PMC1913049 DOI: 10.1186/1472-6750-7-27] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2007] [Accepted: 05/30/2007] [Indexed: 11/10/2022] Open
Abstract
Background Codon usage differences are known to regulate the levels of gene expression in a species-specific manner, with the primary factors often cited to be mRNA processing and accumulation. We have challenged this conclusion by expressing the human acetylcholinesterase coding sequence in transgenic plants in its native GC-rich sequence and compared to a matched sequence with (dicotyledonous) plant-optimized codon usage and a lower GC content. Results We demonstrate a 5 to 10 fold increase in accumulation levels of the "synaptic" splice variant of human acetylcholinesterase in Nicotiana benthamiana plants expressing the optimized gene as compared to the native human sequence. Both transient expression assays and stable transformants demonstrated conspicuously increased accumulation levels. Importantly, we find that the increase is not a result of increased levels of acetylcholinesterase mRNA, but rather its facilitated translation, possibly due to the reduced energy required to unfold the sequence-optimized mRNA. Conclusion Our findings demonstrate that codon usage differences may regulate gene expression at different levels and anticipate translational control of acetylcholinesterase gene expression in its native mammalian host as well.
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147
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Elcock AH. Molecular simulations of cotranslational protein folding: fragment stabilities, folding cooperativity, and trapping in the ribosome. PLoS Comput Biol 2006; 2:e98. [PMID: 16789821 PMCID: PMC1523309 DOI: 10.1371/journal.pcbi.0020098.eor] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2006] [Accepted: 06/14/2006] [Indexed: 11/19/2022] Open
Abstract
Although molecular simulation methods have yielded valuable insights into mechanistic aspects of protein refolding in vitro, they have up to now not been used to model the folding of proteins as they are actually synthesized by the ribosome. To address this issue, we report here simulation studies of three model proteins: chymotrypsin inhibitor 2 (CI2), barnase, and Semliki forest virus protein (SFVP), and directly compare their folding during ribosome-mediated synthesis with their refolding from random, denatured conformations. To calibrate the methodology, simulations are first compared with in vitro data on the folding stabilities of N-terminal fragments of CI2 and barnase; the simulations reproduce the fact that both the stability and thermal folding cooperativity increase as fragments increase in length. Coupled simulations of synthesis and folding for the same two proteins are then described, showing that both fold essentially post-translationally, with mechanisms effectively identical to those for refolding. In both cases, confinement of the nascent polypeptide chain within the ribosome tunnel does not appear to promote significant formation of native structure during synthesis; there are however clear indications that the formation of structure within the nascent chain is sensitive to location within the ribosome tunnel, being subject to both gain and loss as the chain lengthens. Interestingly, simulations in which CI2 is artificially stabilized show a pronounced tendency to become trapped within the tunnel in partially folded conformations: non-cooperative folding, therefore, appears in the simulations to exert a detrimental effect on the rate at which fully folded conformations are formed. Finally, simulations of the two-domain protease module of SFVP, which experimentally folds cotranslationally, indicate that for multi-domain proteins, ribosome-mediated folding may follow different pathways from those taken during refolding. Taken together, these studies provide a first step toward developing more realistic methods for simulating protein folding as it occurs in vivo.
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Affiliation(s)
- Adrian H Elcock
- Department of Biochemistry, University of Iowa, Iowa City, Iowa, USA.
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148
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Song J, Wang M, Burrage K. Exploring synonymous codon usage preferences of disulfide-bonded and non-disulfide bonded cysteines in the E. coli genome. J Theor Biol 2006; 241:390-401. [PMID: 16427089 DOI: 10.1016/j.jtbi.2005.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2005] [Revised: 10/31/2005] [Accepted: 12/05/2005] [Indexed: 11/27/2022]
Abstract
High-quality data about protein structures and their gene sequences are essential to the understanding of the relationship between protein folding and protein coding sequences. Firstly we constructed the EcoPDB database, which is a high-quality database of Escherichia coli genes and their corresponding PDB structures. Based on EcoPDB, we presented a novel approach based on information theory to investigate the correlation between cysteine synonymous codon usages and local amino acids flanking cysteines, the correlation between cysteine synonymous codon usages and synonymous codon usages of local amino acids flanking cysteines, as well as the correlation between cysteine synonymous codon usages and the disulfide bonding states of cysteines in the E. coli genome. The results indicate that the nearest neighboring residues and their synonymous codons of the C-terminus have the greatest influence on the usages of the synonymous codons of cysteines and the usage of the synonymous codons has a specific correlation with the disulfide bond formation of cysteines in proteins. The correlations may result from the regulation mechanism of protein structures at gene sequence level and reflect the biological function restriction that cysteines pair to form disulfide bonds. The results may also be helpful in identifying residues that are important for synonymous codon selection of cysteines to introduce disulfide bridges in protein engineering and molecular biology. The approach presented in this paper can also be utilized as a complementary computational method and be applicable to analyse the synonymous codon usages in other model organisms.
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Affiliation(s)
- Jiangning Song
- Advanced Computational Modelling Centre, The University of Queensland, Brisbane, Qld 4072, Australia.
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149
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Elcock AH. Molecular simulations of cotranslational protein folding: fragment stabilities, folding cooperativity, and trapping in the ribosome. PLoS Comput Biol 2006. [PMID: 16789821 PMCID: PMC1523309 DOI: 10.1371/journal.pcbi.0020098] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Although molecular simulation methods have yielded valuable insights into mechanistic aspects of protein refolding in vitro, they have up to now not been used to model the folding of proteins as they are actually synthesized by the ribosome. To address this issue, we report here simulation studies of three model proteins: chymotrypsin inhibitor 2 (CI2), barnase, and Semliki forest virus protein (SFVP), and directly compare their folding during ribosome-mediated synthesis with their refolding from random, denatured conformations. To calibrate the methodology, simulations are first compared with in vitro data on the folding stabilities of N-terminal fragments of CI2 and barnase; the simulations reproduce the fact that both the stability and thermal folding cooperativity increase as fragments increase in length. Coupled simulations of synthesis and folding for the same two proteins are then described, showing that both fold essentially post-translationally, with mechanisms effectively identical to those for refolding. In both cases, confinement of the nascent polypeptide chain within the ribosome tunnel does not appear to promote significant formation of native structure during synthesis; there are however clear indications that the formation of structure within the nascent chain is sensitive to location within the ribosome tunnel, being subject to both gain and loss as the chain lengthens. Interestingly, simulations in which CI2 is artificially stabilized show a pronounced tendency to become trapped within the tunnel in partially folded conformations: non-cooperative folding, therefore, appears in the simulations to exert a detrimental effect on the rate at which fully folded conformations are formed. Finally, simulations of the two-domain protease module of SFVP, which experimentally folds cotranslationally, indicate that for multi-domain proteins, ribosome-mediated folding may follow different pathways from those taken during refolding. Taken together, these studies provide a first step toward developing more realistic methods for simulating protein folding as it occurs in vivo.
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Affiliation(s)
- Adrian H Elcock
- Department of Biochemistry, University of Iowa, Iowa City, Iowa, USA.
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150
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Chamary JV, Parmley JL, Hurst LD. Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat Rev Genet 2006; 7:98-108. [PMID: 16418745 DOI: 10.1038/nrg1770] [Citation(s) in RCA: 590] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Although the assumption of the neutral theory of molecular evolution - that some classes of mutation have too small an effect on fitness to be affected by natural selection - seems intuitively reasonable, over the past few decades the theory has been in retreat. At least in species with large populations, even synonymous mutations in exons are not neutral. By contrast, in mammals, neutrality of these mutations is still commonly assumed. However, new evidence indicates that even some synonymous mutations are subject to constraint, often because they affect splicing and/or mRNA stability. This has implications for understanding disease, optimizing transgene design, detecting positive selection and estimating the mutation rate.
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Affiliation(s)
- J V Chamary
- Center for Integrative Genomics, University of Lausanne, Switzerland.
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