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Zabolotskii AI, Kozlovskiy SV, Katrukha AG. The Influence of the Nucleotide Composition of Genes and Gene Regulatory Elements on the Efficiency of Protein Expression in Escherichia coli. BIOCHEMISTRY (MOSCOW) 2023; 88:S176-S191. [PMID: 37069120 DOI: 10.1134/s0006297923140109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Recombinant proteins expressed in Escherichia coli are widely used in biochemical research and industrial processes. At the same time, achieving higher protein expression levels and correct protein folding still remains the key problem, since optimization of nutrient media, growth conditions, and methods for induction of protein synthesis do not always lead to the desired result. Often, low protein expression is determined by the sequences of the expressed genes and their regulatory regions. The genetic code is degenerated; 18 out of 20 amino acids are encoded by more than one codon. Choosing between synonymous codons in the coding sequence can significantly affect the level of protein expression and protein folding due to the influence of the gene nucleotide composition on the probability of formation of secondary mRNA structures that affect the ribosome binding at the translation initiation phase, as well as the ribosome movement along the mRNA during elongation, which, in turn, influences the mRNA degradation and the folding of the nascent protein. The nucleotide composition of the mRNA untranslated regions, in particular the promoter and Shine-Dalgarno sequences, also affects the efficiency of mRNA transcription, translation, and degradation. In this review, we describe the genetic principles that determine the efficiency of protein production in Escherichia coli.
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Affiliation(s)
- Artur I Zabolotskii
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | | | - Alexey G Katrukha
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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2
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Lyu X, Yang Q, Zhao F, Liu Y. Codon usage and protein length-dependent feedback from translation elongation regulates translation initiation and elongation speed. Nucleic Acids Res 2021; 49:9404-9423. [PMID: 34417614 PMCID: PMC8450115 DOI: 10.1093/nar/gkab729] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 07/26/2021] [Accepted: 08/17/2021] [Indexed: 12/26/2022] Open
Abstract
Essential cellular functions require efficient production of many large proteins but synthesis of large proteins encounters many obstacles in cells. Translational control is mostly known to be regulated at the initiation step. Whether translation elongation process can feedback to regulate initiation efficiency is unclear. Codon usage bias, a universal feature of all genomes, plays an important role in determining gene expression levels. Here, we discovered that there is a conserved but codon usage-dependent genome-wide negative correlation between protein abundance and CDS length. The codon usage effects on protein expression and ribosome flux on mRNAs are influenced by CDS length; optimal codon usage preferentially promotes production of large proteins. Translation of mRNAs with long CDS and non-optimal codon usage preferentially induces phosphorylation of initiation factor eIF2α, which inhibits translation initiation efficiency. Deletion of the eIF2α kinase CPC-3 (GCN2 homolog) in Neurospora preferentially up-regulates large proteins encoded by non-optimal codons. Surprisingly, CPC-3 also inhibits translation elongation rate in a codon usage and CDS length-dependent manner, resulting in slow elongation rates for long CDS mRNAs. Together, these results revealed a codon usage and CDS length-dependent feedback mechanism from translation elongation to regulate both translation initiation and elongation kinetics.
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Affiliation(s)
- Xueliang Lyu
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA.,State Key Laboratory of Agricultural Microbiology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Qian Yang
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Fangzhou Zhao
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Yi Liu
- Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
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Lalanne J, Parker DJ, Li G. Spurious regulatory connections dictate the expression-fitness landscape of translation factors. Mol Syst Biol 2021; 17:e10302. [PMID: 33900014 PMCID: PMC8073009 DOI: 10.15252/msb.202110302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 12/21/2022] Open
Abstract
During steady-state cell growth, individual enzymatic fluxes can be directly inferred from growth rate by mass conservation, but the inverse problem remains unsolved. Perturbing the flux and expression of a single enzyme could have pleiotropic effects that may or may not dominate the impact on cell fitness. Here, we quantitatively dissect the molecular and global responses to varied expression of translation termination factors (peptide release factors, RFs) in the bacterium Bacillus subtilis. While endogenous RF expression maximizes proliferation, deviations in expression lead to unexpected distal regulatory responses that dictate fitness reduction. Molecularly, RF depletion causes expression imbalance at specific operons, which activates master regulators and detrimentally overrides the transcriptome. Through these spurious connections, RF abundances are thus entrenched by focal points within the regulatory network, in one case located at a single stop codon. Such regulatory entrenchment suggests that predictive bottom-up models of expression-fitness landscapes will require near-exhaustive characterization of parts.
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Affiliation(s)
- Jean‐Benoît Lalanne
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
- Department of PhysicsMassachusetts Institute of TechnologyCambridgeMAUSA
- Present address:
Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
| | - Darren J Parker
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
- Present address:
Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Gene‐Wei Li
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMAUSA
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4
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Liu Y, Yang Q, Zhao F. Synonymous but Not Silent: The Codon Usage Code for Gene Expression and Protein Folding. Annu Rev Biochem 2021; 90:375-401. [PMID: 33441035 DOI: 10.1146/annurev-biochem-071320-112701] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Codon usage bias, the preference for certain synonymous codons, is found in all genomes. Although synonymous mutations were previously thought to be silent, a large body of evidence has demonstrated that codon usage can play major roles in determining gene expression levels and protein structures. Codon usage influences translation elongation speed and regulates translation efficiency and accuracy. Adaptation of codon usage to tRNA expression determines the proteome landscape. In addition, codon usage biases result in nonuniform ribosome decoding rates on mRNAs, which in turn influence the cotranslational protein folding process that is critical for protein function in diverse biological processes. Conserved genome-wide correlations have also been found between codon usage and protein structures. Furthermore, codon usage is a major determinant of mRNA levels through translation-dependent effects on mRNA decay and translation-independent effects on transcriptional and posttranscriptional processes. Here, we discuss the multifaceted roles and mechanisms of codon usage in different gene regulatory processes.
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Affiliation(s)
- Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA;
| | - Qian Yang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA;
| | - Fangzhou Zhao
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9040, USA;
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Chemla Y, Ozer E, Algov I, Alfonta L. Context effects of genetic code expansion by stop codon suppression. Curr Opin Chem Biol 2018; 46:146-155. [DOI: 10.1016/j.cbpa.2018.07.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 05/01/2018] [Accepted: 07/13/2018] [Indexed: 10/28/2022]
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Schlesinger O, Chemla Y, Heltberg M, Ozer E, Marshall R, Noireaux V, Jensen MH, Alfonta L. Tuning of Recombinant Protein Expression in Escherichia coli by Manipulating Transcription, Translation Initiation Rates, and Incorporation of Noncanonical Amino Acids. ACS Synth Biol 2017; 6:1076-1085. [PMID: 28230975 DOI: 10.1021/acssynbio.7b00019] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Protein synthesis in cells has been thoroughly investigated and characterized over the past 60 years. However, some fundamental issues remain unresolved, including the reasons for genetic code redundancy and codon bias. In this study, we changed the kinetics of the Eschrichia coli transcription and translation processes by mutating the promoter and ribosome binding domains and by using genetic code expansion. The results expose a counterintuitive phenomenon, whereby an increase in the initiation rates of transcription and translation lead to a decrease in protein expression. This effect can be rescued by introducing slow translating codons into the beginning of the gene, by shortening gene length or by reducing initiation rates. On the basis of the results, we developed a biophysical model, which suggests that the density of co-transcriptional-translation plays a role in bacterial protein synthesis. These findings indicate how cells use codon bias to tune translation speed and protein synthesis.
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Affiliation(s)
- Orr Schlesinger
- Department
of Life Sciences and Ilse Katz Institute for Nanoscale Science and
Technology, Ben-Gurion University of the Negev, PO Box 653, Beer-Sheva 8410501, Israel
| | - Yonatan Chemla
- Department
of Life Sciences and Ilse Katz Institute for Nanoscale Science and
Technology, Ben-Gurion University of the Negev, PO Box 653, Beer-Sheva 8410501, Israel
| | - Mathias Heltberg
- Niels
Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark
| | - Eden Ozer
- Department
of Life Sciences and Ilse Katz Institute for Nanoscale Science and
Technology, Ben-Gurion University of the Negev, PO Box 653, Beer-Sheva 8410501, Israel
| | - Ryan Marshall
- School
of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Vincent Noireaux
- School
of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Mogens Høgh Jensen
- Niels
Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark
| | - Lital Alfonta
- Department
of Life Sciences and Ilse Katz Institute for Nanoscale Science and
Technology, Ben-Gurion University of the Negev, PO Box 653, Beer-Sheva 8410501, Israel
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Wei Y, Wang J, Xia X. Coevolution between Stop Codon Usage and Release Factors in Bacterial Species. Mol Biol Evol 2016; 33:2357-67. [PMID: 27297468 PMCID: PMC4989110 DOI: 10.1093/molbev/msw107] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Three stop codons in bacteria represent different translation termination signals, and their usage is expected to depend on their differences in translation termination efficiency, mutation bias, and relative abundance of release factors (RF1 decoding UAA and UAG, and RF2 decoding UAA and UGA). In 14 bacterial species (covering Proteobacteria, Firmicutes, Cyanobacteria, Actinobacteria and Spirochetes) with cellular RF1 and RF2 quantified, UAA is consistently over-represented in highly expressed genes (HEGs) relative to lowly expressed genes (LEGs), whereas UGA usage is the opposite even in species where RF2 is far more abundant than RF1. UGA usage relative to UAG increases significantly with PRF2 [=RF2/(RF1 + RF2)] as expected from adaptation between stop codons and their decoders. PRF2 is > 0.5 over a wide range of AT content (measured by PAT3 as the proportion of AT at third codon sites), but decreases rapidly toward zero at the high range of PAT3. This explains why bacterial lineages with high PAT3 often have UGA reassigned because of low RF2. There is no indication that UAG is a minor stop codon in bacteria as claimed in a recent publication. The claim is invalid because of the failure to apply the two key criteria in identifying a minor codon: (1) it is least preferred by HEGs (or most preferred by LEGs) and (2) it corresponds to the least abundant decoder. Our results suggest a more plausible explanation for why UAA usage increases, and UGA usage decreases, with PAT3, but UAG usage remains low over the entire PAT3 range.
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Affiliation(s)
- Yulong Wei
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Juan Wang
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
| | - Xuhua Xia
- Department of Biology, University of Ottawa, Ottawa, ON, Canada Ottawa Institute of Systems Biology, Ottawa, ON, Canada
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8
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Liu H, Wang Q, He Y, Chen L, Hao C, Jiang C, Li Y, Dai Y, Kang Z, Xu JR. Genome-wide A-to-I RNA editing in fungi independent of ADAR enzymes. Genome Res 2016; 26:499-509. [PMID: 26934920 PMCID: PMC4817773 DOI: 10.1101/gr.199877.115] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/22/2016] [Indexed: 01/10/2023]
Abstract
Yeasts and filamentous fungi do not have adenosine deaminase acting on RNA (ADAR) orthologs and are believed to lack A-to-I RNA editing, which is the most prevalent editing of mRNA in animals. However, during this study with the PUK1(FGRRES_01058) pseudokinase gene important for sexual reproduction in Fusarium graminearum, we found that two tandem stop codons, UA(1831)GUA(1834)G, in its kinase domain were changed to UG(1831)GUG(1834)G by RNA editing in perithecia. To confirm A-to-I editing of PUK1 transcripts, strand-specific RNA-seq data were generated with RNA isolated from conidia, hyphae, and perithecia. PUK1 was almost specifically expressed in perithecia, and 90% of transcripts were edited to UG(1831)GUG(1834)G. Genome-wide analysis identified 26,056 perithecium-specific A-to-I editing sites. Unlike those in animals, 70.5% of A-to-I editing sites inF. graminearum occur in coding regions, and more than two-thirds of them result in amino acid changes, including editing of 69PUK1-like pseudogenes with stop codons in ORFs.PUK1orthologs and other pseudogenes also displayed stage-specific expression and editing in Neurospora crassa and F. verticillioides Furthermore,F. graminearum differs from animals in the sequence preference and structure selectivity of A-to-I editing sites. Whereas A's embedded in RNA stems are targeted by ADARs, RNA editing inF. graminearum preferentially targets A's in hairpin loops, which is similar to the anticodon loop of tRNA targeted by adenosine deaminases acting on tRNA (ADATs). Overall, our results showed that A-to-I RNA editing occurs specifically during sexual reproduction and mainly in the coding regions in filamentous ascomycetes, involving adenosine deamination mechanisms distinct from metazoan ADARs.
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Affiliation(s)
- Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Purdue-NWAFU Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qinhu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Purdue-NWAFU Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yi He
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lingfeng Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Purdue-NWAFU Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chaofeng Hao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Purdue-NWAFU Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Cong Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Purdue-NWAFU Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yang Li
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Yafeng Dai
- State Key Laboratory of Crop Stress Biology for Arid Areas, Purdue-NWAFU Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Purdue-NWAFU Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jin-Rong Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Purdue-NWAFU Joint Research Center, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China; Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
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9
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Horstick EJ, Jordan DC, Bergeron SA, Tabor KM, Serpe M, Feldman B, Burgess HA. Increased functional protein expression using nucleotide sequence features enriched in highly expressed genes in zebrafish. Nucleic Acids Res 2015; 43:e48. [PMID: 25628360 PMCID: PMC4402511 DOI: 10.1093/nar/gkv035] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/12/2015] [Indexed: 12/18/2022] Open
Abstract
Many genetic manipulations are limited by difficulty in obtaining adequate levels of protein expression. Bioinformatic and experimental studies have identified nucleotide sequence features that may increase expression, however it is difficult to assess the relative influence of these features. Zebrafish embryos are rapidly injected with calibrated doses of mRNA, enabling the effects of multiple sequence changes to be compared in vivo. Using RNAseq and microarray data, we identified a set of genes that are highly expressed in zebrafish embryos and systematically analyzed for enrichment of sequence features correlated with levels of protein expression. We then tested enriched features by embryo microinjection and functional tests of multiple protein reporters. Codon selection, releasing factor recognition sequence and specific introns and 3′ untranslated regions each increased protein expression between 1.5- and 3-fold. These results suggested principles for increasing protein yield in zebrafish through biomolecular engineering. We implemented these principles for rational gene design in software for codon selection (CodonZ) and plasmid vectors incorporating the most active non-coding elements. Rational gene design thus significantly boosts expression in zebrafish, and a similar approach will likely elevate expression in other animal models.
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Affiliation(s)
- Eric J Horstick
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Diana C Jordan
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Sadie A Bergeron
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Kathryn M Tabor
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Mihaela Serpe
- Program in Cellular Regulation and Metabolism, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Benjamin Feldman
- Zebrafish Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
| | - Harold A Burgess
- Program in Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
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Lis E, Podkowik M, Schubert J, Bystroń J, Stefaniak T, Bania J. Production of staphylococcal enterotoxin R by Staphylococcus aureus strains. Foodborne Pathog Dis 2012; 9:762-6. [PMID: 22827454 DOI: 10.1089/fpd.2012.1185] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Staphylococcal enterotoxin D and R (SED, SER) production was determined in 24 S. aureus strains harboring sed gene. Seven of them were not able to produce SED as evidenced by enzyme-linked immunosorbent assay and Western blotting. Sequencing revealed that all these strains harbor a variant of sed gene. Expression of SER was detectable in 22 out of 24 isolates, with variance in productivity ranging from ∼40 to 450 ng/mL. Out of the seven isolates not able to produce SED, three produced high amounts of SER (249-396 ng/mL), two produced less than 200 ng/mL of SER, and two were found to express no detectable amount of SER. Three of those were assigned to spa type t1677 with two being of agr type III and one of agr type I. One strain was t084, agr type II, one t603, agr type II, one 2920, agr type III, one t2920, agr type III, and one t5160, agr type I. Because conventional screening procedures involve only the detection of classical enterotoxins in food, the isolates not able to produce SED presented in this study could pose a threat to human health due to SER production.
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Affiliation(s)
- Elżbieta Lis
- Department of Food Hygiene and Consumer Health Protection, Wrocław University of Environmental and Life Sciences, Wrocław, Poland
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11
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Hypomodification of the wobble base in tRNAGlu, tRNALys, and tRNAGln suppresses the temperature-sensitive phenotype caused by mutant release factor 1. J Bacteriol 2008; 191:1604-9. [PMID: 19103926 DOI: 10.1128/jb.01485-08] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Escherichia coli, release factor 1 (RF1) is one of two RFs that mediate termination; it specifically recognizes UAA and UAG stop codons. A mutant allele, prfA1, coding for an RF1 that causes temperature-sensitive (Ts) growth at 42 degrees C, was used to select for temperature-resistant (Ts(+)) suppressors. This study describes one such suppressor that is the result of an IS10 insertion into the cysB gene, giving a Cys(-) phenotype. CysB is a transcription factor regulating the cys regulon, mainly as an activator, which explains the Cys(-) phenotype. We have found that suppression is a consequence of the lost ability to donate sulfur to enzymes involved in the synthesis of thiolated nucleosides. From genetic analyses we conclude that it is the lack of the 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) modification of the wobble base of tRNA(Glu), tRNA(Lys), and/or tRNA(Gln) that causes the suppressor phenotype.
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Mora L, Heurgué-Hamard V, de Zamaroczy M, Kervestin S, Buckingham RH. Methylation of bacterial release factors RF1 and RF2 is required for normal translation termination in vivo. J Biol Chem 2007; 282:35638-45. [PMID: 17932046 DOI: 10.1074/jbc.m706076200] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacterial release factors RF1 and RF2 are methylated on the Gln residue of a universally conserved tripeptide motif GGQ, which interacts with the peptidyl transferase center of the large ribosomal subunit, triggering hydrolysis of the ester bond in peptidyl-tRNA and releasing the newly synthesized polypeptide from the ribosome. In vitro experiments have shown that the activity of RF2 is stimulated by Gln methylation. The viability of Escherichia coli K12 strains depends on the integrity of the release factor methyltransferase PrmC, because K12 strains are partially deficient in RF2 activity due to the presence of a Thr residue at position 246 instead of Ala. Here, we study in vivo RF1 and RF2 activity at termination codons in competition with programmed frameshifting and the effect of the Ala-246 --> Thr mutation. PrmC inactivation reduces the specific termination activity of RF1 and RF2(Ala-246) by approximately 3- to 4-fold. The mutation Ala-246 --> Thr in RF2 reduces the termination activity in cells approximately 5-fold. After correction for the decrease in level of RF2 due to the autocontrol of RF2 synthesis, the mutation Ala-246 --> Thr reduced RF2 termination activity by approximately 10-fold at UGA codons and UAA codons. PrmC inactivation had no effect on cell growth in rich media but reduced growth considerably on poor carbon sources. This suggests that the expression of some genes needed for optimal growth under such conditions can become growth limiting as a result of inefficient translation termination.
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Affiliation(s)
- Liliana Mora
- CNRS, UPR 9073, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, Paris 75005, France
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13
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Yu JS, Kokoska RJ, Khemici V, Steege DA. In‐frame overlapping genes: the challenges for regulating gene expression. Mol Microbiol 2006; 63:1158-72. [PMID: 17238928 DOI: 10.1111/j.1365-2958.2006.05572.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In-frame overlapping genes in phage, plasmid and bacterial genomes permit synthesis of more than one form of protein from the same gene. Having one gene entirely within another rather than two separate genes presumably precludes recombination events between the identical sequences. However, studies of such gene pairs indicate that the overlapping arrangement can make regulation of the genes more difficult. Here, we extend studies of in-frame overlapping genes II and X from filamentous phage f1 to determine if translational controls are required to regulate the gene properly. These genes encode proteins (pII and pX) with essential but opposing roles in phage DNA replication. They must be tightly regulated to maintain production of the proteins at relative steady state levels that permit continuous replication without killing the host. To determine why little or no pX appears to be made on the gene II/X mRNA, gene II translation was lowered by progressively deleting into the gene II initiator region. Increased pX translation resulted, suggesting that elongating ribosomes on the gene II mRNA interfere with internal initiation on the gene X ribosome binding site and limit gene X translation. As judged from systematically lowering the efficiency of suppression at a gene II amber codon upstream from the gene X start, the already modest level of gene II translation would have to be reduced by more than twofold to relieve all interference with internal initiation. Further downregulation of gene X expression proved to be required to maintain pX at levels relative to pII that are tolerated by the cell. Site-directed mutagenesis and nuclease mapping revealed that the gene X initiation site is sequestered in an extended RNA secondary structure that lowers gene X translation on the two mRNAs encoding it. The more general implications of the results for expression of in-frame overlapping genes are discussed.
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Affiliation(s)
- Jae-Sung Yu
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
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Ahn JH, Hwang MY, Lee KH, Choi CY, Kim DM. Use of signal sequences as an in situ removable sequence element to stimulate protein synthesis in cell-free extracts. Nucleic Acids Res 2006; 35:e21. [PMID: 17185295 PMCID: PMC1849898 DOI: 10.1093/nar/gkl917] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
This study developed a method to boost the expression of recombinant proteins in a cell-free protein synthesis system without leaving additional amino acid residues. It was found that the nucleotide sequences of the signal peptides serve as an efficient downstream box to stimulate protein synthesis when they were fused upstream of the target genes. The extent of stimulation was critically affected by the identity of the second codons of the signal sequences. Moreover, the yield of the synthesized protein was enhanced by as much as 10 times in the presence of an optimal second codon. The signal peptides were in situ cleaved and the target proteins were produced in their native sizes by carrying out the cell-free synthesis reactions in the presence of Triton X-100, most likely through the activation of signal peptidase in the S30 extract. The amplification of the template DNA and the addition of the signal sequences were accomplished by PCR. Hence, elevated levels of recombinant proteins were generated within several hours.
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Affiliation(s)
- Jin-Ho Ahn
- Interdisciplinary Program for Biochemical Engineering and Biotechnology, College of Engineering, Seoul National UniversitySeoul 151-742, Korea
| | - Mi-Yeon Hwang
- School of Chemical and Biological Engineering, College of Engineering, Seoul National UniversitySeoul 151-742, Korea
| | - Kyung-Ho Lee
- Department of Fine Chemical Engineering and Chemistry, Chungnam National UniversityDaejeon 305-764, Korea
| | - Cha-Yong Choi
- Interdisciplinary Program for Biochemical Engineering and Biotechnology, College of Engineering, Seoul National UniversitySeoul 151-742, Korea
- School of Chemical and Biological Engineering, College of Engineering, Seoul National UniversitySeoul 151-742, Korea
| | - Dong-Myung Kim
- Department of Fine Chemical Engineering and Chemistry, Chungnam National UniversityDaejeon 305-764, Korea
- To whom correspondence should be addressed. Tel: +82 42 821 5899; Fax: +82 42 823 7692;
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15
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Jin H, Zhao Q, Gonzalez de Valdivia EI, Ardell DH, Stenström M, Isaksson LA. Influences on gene expression in vivo by a Shine-Dalgarno sequence. Mol Microbiol 2006; 60:480-92. [PMID: 16573696 DOI: 10.1111/j.1365-2958.2006.05110.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Shine-Dalgarno (SD+: 5'-AAGGAGG-3') sequence anchors the mRNA by base pairing to the 16S rRNA in the small ribosomal subunit during translation initiation. We have here compared how an SD+ sequence influences gene expression, if located upstream or downstream of an initiation codon. The positive effect of an upstream SD+ is confirmed. A downstream SD+ gives decreased gene expression. This effect is also valid for appropriately modified natural Escherichia coli genes. If an SD+ is placed between two potential initiation codons, initiation takes place predominantly at the second start site. The first start site is activated if the distance between this site and the downstream SD+ is enlarged and/or if the second start site is weakened. Upstream initiation is eliminated if a stable stem-loop structure is placed between this SD+ and the upstream start site. The results suggest that the two start sites compete for ribosomes that bind to an SD+ located between them. A minor positive contribution to upstream initiation resulting from 3' to 5' ribosomal diffusion along the mRNA is suggested. Analysis of the E. coli K12 genome suggests that the SD+ or SD-like sequences are systematically avoided in the early coding region suggesting an evolutionary significance.
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MESH Headings
- Base Sequence
- Binding Sites
- Codon, Initiator/genetics
- Codon, Initiator/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression Regulation, Bacterial
- Genes, Bacterial/genetics
- Genes, Reporter
- Molecular Sequence Data
- Nucleic Acid Conformation
- Protein Biosynthesis/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/metabolism
- RNA, Ribosomal, 16S/metabolism
- RNA, Transfer, Amino Acyl/chemistry
- RNA, Transfer, Amino Acyl/metabolism
- Ribosomes/metabolism
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Affiliation(s)
- Haining Jin
- Department of Genetics, Microbiology and Toxicology, Stockholm University, S-106 91 Stockholm, Sweden
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16
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Cridge AG, Major LL, Mahagaonkar AA, Poole ES, Isaksson LA, Tate WP. Comparison of characteristics and function of translation termination signals between and within prokaryotic and eukaryotic organisms. Nucleic Acids Res 2006; 34:1959-73. [PMID: 16614446 PMCID: PMC1435984 DOI: 10.1093/nar/gkl074] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Six diverse prokaryotic and five eukaryotic genomes were compared to deduce whether the protein synthesis termination signal has common determinants within and across both kingdoms. Four of the six prokaryotic and all of the eukaryotic genomes investigated demonstrated a similar pattern of nucleotide bias both 5′ and 3′ of the stop codon. A preferred core signal of 4 nt was evident, encompassing the stop codon and the following nucleotide. Codons decoded by hyper-modified tRNAs were over-represented in the region 5′ to the stop codon in genes from both kingdoms. The origin of the 3′ bias was more variable particularly among the prokaryotic organisms. In both kingdoms, genes with the highest expression index exhibited a strong bias but genes with the lowest expression showed none. Absence of bias in parasitic prokaryotes may reflect an absence of pressure to evolve more efficient translation. Experiments were undertaken to determine if a correlation existed between bias in signal abundance and termination efficiency. In Escherichia coli signal abundance correlated with termination efficiency for UAA and UGA stop codons, but not in mammalian cells. Termination signals that were highly inefficient could be made more efficient by increasing the concentration of the cognate decoding release factor.
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Affiliation(s)
| | | | | | | | - Leif A. Isaksson
- Department of Genetics, Microbiology and Toxicology, Stockholm UniversityS-10691 Stockholm, Sweden
| | - Warren P. Tate
- To whom correspondence should be addressed. Tel: +64 3 479 7864; Fax: +64 3 479 7866;
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17
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Gonzalez de Valdivia EI, Isaksson LA. Abortive translation caused by peptidyl-tRNA drop-off at NGG codons in the early coding region of mRNA. FEBS J 2005; 272:5306-16. [PMID: 16218960 DOI: 10.1111/j.1742-4658.2005.04926.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In Escherichia coli the codons CGG, AGG, UGG or GGG (NGG codons) but not GGN or GNG (where N is non-G) are associated with low expression of a reporter gene, if located at positions +2 to +5. Induction of a lacZ reporter gene with any one of the NGG codons at position +2 to +5 does not influence growth of a normal strain, but growth of a strain with a defective peptidyl-tRNA hydrolase (Pth) enzyme is inhibited. The same codons, if placed at position +7, did not give this effect. Other codons, such as CGU and AGA, at location +2 to +5, did not give any growth inhibition of either the wild-type or the mutant strain. The inhibitory effect on the pth mutant strain by NGG codons at location +5 was suppressed by overexpression of the Pth enzyme from a plasmid. However, the overexpression of cognate tRNAs for AGG or GGG did not rescue from the growth inhibition associated with these codons early in the induced model gene. The data suggest that the NGG codons trigger peptidyl-tRNA drop-off if located at early coding positions in mRNA, thereby strongly reducing gene expression. This does not happen if these codons are located further down in the mRNA at position +7, or later.
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MESH Headings
- Base Sequence
- Carboxylic Ester Hydrolases/genetics
- Carboxylic Ester Hydrolases/metabolism
- Cell Division/genetics
- Codon/genetics
- Escherichia coli/genetics
- Gene Expression Regulation, Bacterial/genetics
- Genes, Reporter/genetics
- Lac Operon/genetics
- Molecular Sequence Data
- Mutation/genetics
- Plasmids/genetics
- Protein Biosynthesis/genetics
- RNA, Messenger/genetics
- RNA, Transfer, Amino Acyl/genetics
- RNA, Transfer, Amino Acyl/metabolism
- RNA, Transfer, Arg/genetics
- RNA, Transfer, Arg/metabolism
- RNA, Transfer, Gly/genetics
- RNA, Transfer, Gly/metabolism
- Staphylococcal Protein A/genetics
- Temperature
- Transformation, Bacterial
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18
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Hirokawa G, Inokuchi H, Kaji H, Igarashi K, Kaji A. In vivo effect of inactivation of ribosome recycling factor - fate of ribosomes after unscheduled translation downstream of open reading frame. Mol Microbiol 2005; 54:1011-21. [PMID: 15522083 DOI: 10.1111/j.1365-2958.2004.04324.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The post-termination ribosomal complex is disassembled by ribosome recycling factor (RRF) and elongation factor G. Without RRF, the ribosome is not released from mRNA at the termination codon and reinitiates translation downstream. This is called unscheduled translation. Here, we show that at the non-permissive temperature of a temperature-sensitive RRF strain, RRF is lost quickly, and some ribosomes reach the 3' end of mRNA. However, instead of accumulating at the 3' end of mRNA, ribosomes are released as monosomes. Some ribosomes are transferred to transfer-messenger RNA from the 3' end of mRNA. The monosomes thus produced are able to translate synthetic homopolymer but not natural mRNA with leader and canonical initiation signal. The pellet containing ribosomes appears to be responsible for rapid but reversible inhibition of most but not all of protein synthesis in vivo closely followed by decrease of cellular RNA and DNA synthesis.
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Affiliation(s)
- Go Hirokawa
- Department of Clinical Biochemistry, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan
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19
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Laursen BS, Sørensen HP, Mortensen KK, Sperling-Petersen HU. Initiation of protein synthesis in bacteria. Microbiol Mol Biol Rev 2005; 69:101-23. [PMID: 15755955 PMCID: PMC1082788 DOI: 10.1128/mmbr.69.1.101-123.2005] [Citation(s) in RCA: 415] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Valuable information on translation initiation is available from biochemical data and recently solved structures. We present a detailed description of current knowledge about the structure, function, and interactions of the individual components involved in bacterial translation initiation. The first section describes the ribosomal features relevant to the initiation process. Subsequent sections describe the structure, function, and interactions of the mRNA, the initiator tRNA, and the initiation factors IF1, IF2, and IF3. Finally, we provide an overview of mechanisms of regulation of the translation initiation event. Translation occurs on ribonucleoprotein complexes called ribosomes. The ribosome is composed of a large subunit and a small subunit that hold the activities of peptidyltransfer and decode the triplet code of the mRNA, respectively. Translation initiation is promoted by IF1, IF2, and IF3, which mediate base pairing of the initiator tRNA anticodon to the mRNA initiation codon located in the ribosomal P-site. The mechanism of translation initiation differs for canonical and leaderless mRNAs, since the latter is dependent on the relative level of the initiation factors. Regulation of translation occurs primarily in the initiation phase. Secondary structures at the mRNA ribosomal binding site (RBS) inhibit translation initiation. The accessibility of the RBS is regulated by temperature and binding of small metabolites, proteins, or antisense RNAs. The future challenge is to obtain atomic-resolution structures of complete initiation complexes in order to understand the mechanism of translation initiation in molecular detail.
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Affiliation(s)
- Brian Søgaard Laursen
- Department of Molecular Biology, Aarhus University, Gustav Wieds vej 10C, DK-8000 Aarhus C, Denmark
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20
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Gonzalez de Valdivia EI, Isaksson LA. A codon window in mRNA downstream of the initiation codon where NGG codons give strongly reduced gene expression in Escherichia coli. Nucleic Acids Res 2004; 32:5198-205. [PMID: 15459289 PMCID: PMC521668 DOI: 10.1093/nar/gkh857] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The influences on gene expression by codons at positions +2, +3, +5 and +7 downstream of the initiation codon have been compared. Most of the +2 codons that are known to give low gene expression are associated with a higher expression if placed at the later positions. The NGG codons AGG, CGG, UGG and GGG, but not GGN or GNG (where N is non-G), are unique since they are associated with a very low gene expression also if located at positions +2, +3 and +5. All codons, including NGG, give a normal gene expression if placed at positions +7. The negative effect by the NGG codons is true for both the lacZ and 3A' model genes. The low expression is suggested to originate at the translational level, although it is not the result of mRNA secondary structure or a lowered intracellular mRNA pool.
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21
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Chen G, Yanofsky C. Features of a leader peptide coding region that regulate translation initiation for the anti-TRAP protein of B. subtilis. Mol Cell 2004; 13:703-11. [PMID: 15023340 DOI: 10.1016/s1097-2765(04)00085-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2003] [Revised: 01/06/2004] [Accepted: 01/09/2004] [Indexed: 11/20/2022]
Abstract
The rtpA gene of Bacillus subtilis encodes the Anti-TRAP protein, AT. AT can bind and inhibit the TRAP regulatory protein, preventing TRAP from promoting transcription termination in the trpEDCFBA operon leader region. AT synthesis is upregulated transcriptionally and translationally in response to the accumulation of uncharged tRNA(Trp). Here we analyze AT's translational regulation by rtpLP, a 10 residue leader peptide coding region located immediately preceding the rtpA Shine-Dalgarno sequence. Our findings suggest that, whenever the charged tRNA(Trp) level is sufficient to allow the ribosome translating rtpLP to reach its stop codon, it blocks the adjacent rtpA Shine-Dalgarno sequence, inhibiting AT synthesis. However, when there is a charged tRNA(Trp) deficiency, the translating ribosome presumably stalls at one of three adjacent rtpLP Trp codons. This stalling exposes the rtpA Shine-Dalgarno sequence, permitting AT synthesis. RNA-RNA pairing may also influence AT synthesis. Production of AT would inactivate TRAP, thereby increasing trp operon expression.
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Affiliation(s)
- Guangnan Chen
- Department of Biological Sciences, Stanford University, Stanford, CA 94305 USA
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22
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Lithwick G, Margalit H. Hierarchy of sequence-dependent features associated with prokaryotic translation. Genome Res 2004; 13:2665-73. [PMID: 14656971 PMCID: PMC403808 DOI: 10.1101/gr.1485203] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Protein expression in the cell is affected by various sequence-dependent features. Several such sequence-dependent features have been individually studied,yet they have not been compared quantitatively in terms of their relative influence on protein expression,and a hierarchy of these elements has not been determined. Here we present a quantitative analysis examining sequence-dependent features involved in prokaryotic translation,namely,the base-pairing potential between the mRNA Shine-Dalgarno sequence and the ribosomal RNA,codon bias,and the identity of the stop codon. We analyzed these features both at intra- and intergenomic levels using the Escherichia coli and Haemophilus influenzae genomes. Within each genome,we examined the relationship between each feature and protein expression levels determined by 2D-gel analyses. At the intergenomic level,comparative genomic principles were applied to study the relative preservation of the different sequence-dependent properties between orthologs. From these analyses,we determined that biased codon usage is the property that is most highly associated with protein expression and that is most conserved. The identity of the stop codon and the base-pairing potential of the mRNA Shine-Dalgarno sequence and the rRNA seem to have less of an effect on protein expression.
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Affiliation(s)
- Gila Lithwick
- Department of Molecular Genetics and Biotechnology, Faculty of Medicine, The Hebrew University, Jerusalem 91120, Israel
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23
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Nilsson M, Rydén-Aulin M. Glutamine is incorporated at the nonsense codons UAG and UAA in a suppressor-free Escherichia coli strain. BIOCHIMICA ET BIOPHYSICA ACTA 2003; 1627:1-6. [PMID: 12759186 DOI: 10.1016/s0167-4781(03)00050-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Readthrough of the nonsense codons UAG, UAA, and UGA is seen in Escherichia coli strains lacking tRNA suppressors. Earlier results indicate that UGA is miscoded by tRNA(Trp). It has also been shown that tRNA(Tyr) and tRNA(Gln) are involved in UAG and UAA decoding in several eukaryotic viruses as well as in yeast. Here we have investigated which amino acid(s) is inserted in response to the nonsense codons UAG and UAA in E. coli. To do this, the stop codon in question was introduced into the staphylococcal protein A gene. Protein A binds to IgG, which facilitates purification of the readthrough product. We have shown that the stop codons UAG and UAA direct insertion of glutamine, indicating that tRNA(Gln) can read the two codons. We have also confirmed that tryptophan is inserted in response to UGA, suggesting that it is read by tRNA(Trp).
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Affiliation(s)
- Michaela Nilsson
- Department of Microbiology, Stockholm University, S-106 91, Stockholm, Sweden
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