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Ojha R, Prajapati VK. Cognizance of posttranslational modifications in vaccines: A way to enhanced immunogenicity. J Cell Physiol 2021; 236:8020-8034. [PMID: 34170014 PMCID: PMC8427110 DOI: 10.1002/jcp.30483] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/21/2021] [Accepted: 06/14/2021] [Indexed: 12/25/2022]
Abstract
Vaccination is a significant advancement or preventative strategy for controlling the spread of various severe infectious and noninfectious diseases. The purpose of vaccination is to stimulate or activate the immune system by injecting antigens, i.e., either whole microorganisms or using the pathogen's antigenic part or macromolecules. Over time, researchers have made tremendous efforts to reduce vaccine side effects or failure by developing different strategies combining with immunoinformatic and molecular biology. These newly designed vaccines are composed of single or several antigenic molecules derived from a pathogenic organism. Although, whole‐cell vaccines are still in use against various diseases but due to their ineffectiveness, other vaccines like DNA‐based, RNA‐based, and protein‐based vaccines, with the addition of immunostimulatory agents, are in the limelight. Despite this, many researchers escape the most common fundamental phenomenon of protein posttranslational modifications during the development of vaccines, which regulates protein functional behavior, evokes immunogenicity and stability, etc. The negligence about post translational modification (PTM) during vaccine development may affect the vaccine's efficacy and immune responses. Therefore, it becomes imperative to consider these modifications of macromolecules before finalizing the antigenic vaccine construct. Here, we have discussed different types of posttranslational/transcriptional modifications that are usually considered during vaccine construct designing: Glycosylation, Acetylation, Sulfation, Methylation, Amidation, SUMOylation, Ubiquitylation, Lipidation, Formylation, and Phosphorylation. Based on the available research information, we firmly believe that considering these modifications will generate a potential and highly immunogenic antigenic molecule against communicable and noncommunicable diseases compared to the unmodified macromolecules.
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Affiliation(s)
- Rupal Ojha
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India
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Zheng S, Doucette AA. Preventing N- and O-formylation of proteins when incubated in concentrated formic acid. Proteomics 2016; 16:1059-68. [PMID: 26840995 DOI: 10.1002/pmic.201500366] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 12/11/2015] [Accepted: 01/26/2016] [Indexed: 12/28/2022]
Abstract
Concentrated formic acid is among the most effective solvents for protein solubilization. Unfortunately, this acid also presents a risk of inducing chemical modifications thereby limiting its use in proteomics. Previous reports have supported the esterification of serine and threonine residues (O-formylation) for peptides incubated in formic acid. However as shown here, exposure of histone H4 to 80% formic (1 h, 20(o) C) induces N-formylation of two independent lysine residues. Furthermore, incubating a mixture of Escherichia coli proteins in formic acid demonstrates a clear preference toward lysine modification over reactions at serine/threonine. N-formylation accounts for 84% of the 225 uniquely identified formylation sites. To prevent formylation, we provide a detailed investigation of reaction conditions (temperature, time, acid concentration) that define the parameters permitting the use of concentrated formic acid in a proteomics workflow for MS characterization. Proteins can be maintained in 80% formic acid for extended periods (24 h) without inducing modification, so long as the temperature is maintained at or below -20(o) C.
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Affiliation(s)
- Shi Zheng
- Department of Chemistry, Dalhousie University, Halifax, NS, Canada.,Key Laboratory of Pesticides and Chemical Biology, College of Chemistry, Central China Normal University, Wuhan, Hubei, P. R. China
| | - Alan A Doucette
- Department of Chemistry, Dalhousie University, Halifax, NS, Canada
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Zamir A, Leder P, Elson D. A ribosome-catalyzed reaction between N-formylmethionyl-trna and puromycin. Proc Natl Acad Sci U S A 2010; 56:1794-801. [PMID: 16591422 PMCID: PMC220182 DOI: 10.1073/pnas.56.6.1794] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- A Zamir
- BIOCHEMISTRY SECTION, THE WEIZMANN INSTITUTE OF SCIENCE, REHOVOTH, ISRAEL
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Vetro JA, Chang YH. Yeast methionine aminopeptidase type 1 is ribosome-associated and requires its N-terminal zinc finger domain for normal function in vivo. J Cell Biochem 2002; 85:678-88. [PMID: 11968008 DOI: 10.1002/jcb.10161] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Methionine aminopeptidase type 1 (MetAP1) cotranslationally removes N-terminal methionine from nascent polypeptides, when the second residue in the primary structure is small and uncharged. Eukaryotic MetAP1 has an N-terminal zinc finger domain not found in prokaryotic MetAPs. We hypothesized that the zinc finger domain mediates the association of MetAP1 with the ribosomes and have reported genetic evidence that it is important for the normal function of MetAP1 in vivo. In this study, the intracellular role of the zinc finger domain in yeast MetAP1 function was examined. Wild-type MetAP1 expressed in a yeast map1 null strain removed 100% of N-terminal methionine from a reporter protein, while zinc finger mutants removed only 31-35%. Ribosome profiles of map1 null expressing wild-type MetAP1 or one of three zinc finger mutants were compared. Wild-type MetAP1 was found to be an 80S translational complex-associated protein that primarily associates with the 60S subunit. Deletion of the zinc finger domain did not significantly alter the ribosome profile distribution of MetAP1. In contrast, single point mutations in the first or second zinc finger motif disrupted association of MetAP1 with the 60S subunit and the 80S translational complex. Together, these results indicate that the zinc finger domain is essential for the normal processing function of MetAP1 in vivo and suggest that it may be important for the proper functional alignment of MetAP1 on the ribosomes.
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Affiliation(s)
- Joseph A Vetro
- Edward A. Doisy Department of Biochemistry and Molecular Biology, St. Louis University Health Sciences Center, St. Louis, Missouri 63104, USA
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Taira M, Iizasa T, Shimada H, Kudoh J, Shimizu N, Tatibana M. A human testis-specific mRNA for phosphoribosylpyrophosphate synthetase that initiates from a non-AUG codon. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(17)46249-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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6
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Nomura T, Fujita N, Ishihama A. Promoter selectivity of Escherichia coli RNA polymerase: alteration by fMet-tRNAfMet. Nucleic Acids Res 1986; 14:6857-70. [PMID: 3532031 PMCID: PMC311704 DOI: 10.1093/nar/14.17.6857] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
An in vitro mixed transcription system was employed to examine the possible alteration of the promoter selectivity of Escherichia coli RNA polymerase by specific tRNAs. Transcription in vitro was inhibited by most of the tRNAs examined, although the extent of the inhibition differed with the tRNA species. The inhibition by tRNAs was due to competition with DNA for binding RNA polymerase. This inhibitory effect remained after charging of the tRNAs with amino acids. The charging of tRNAfMet with fMet, but not with Met, abolished its inhibitory effect, and instead gave a stimulatory effect on the transcription from some promoters. These observations suggest that fMet-tRNAfMet plays a specific regulatory role in the coupling of transcription to translation.
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Lin F, Wishnia A. The protein synthesis inhibitor thermorubin. 2. Mechanism of inhibition of initiation on Escherichia coli ribosomes. Biochemistry 1982; 21:484-91. [PMID: 7039672 DOI: 10.1021/bi00532a011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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8
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Pre-ornithine transcarbamylase. Properties of the cytoplasmic precursor of a mitochondrial matrix enzyme. J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)68500-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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9
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Hoburg A, Aschhoff HJ, Kersten H, Manderschied U, Gassen HG. Function of modified nucleosides 7-methylguanosine, ribothymidine, and 2-thiomethyl-N6-(isopentenyl)adenosine in procaryotic transfer ribonucleic acid. J Bacteriol 1979; 140:408-14. [PMID: 115845 PMCID: PMC216664 DOI: 10.1128/jb.140.2.408-414.1979] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
To elucidate subtle functions of transfer ribonucleic acid (tRNA) modifications in protein synthesis, pairs of tRNA's that differ in modifications at specific positions were prepared from Bacillus subtilis. The tRNA's differ in modifications in the anticodon loop, the extra arm, and the TUC loop. The functional properties of these species were compared in aminoacylation, as well as in initiation and peptide bond formation, at programmed ribosomes. These experiments demonstrated the following. (i) In tRNA(f) (Met) the methylation of guanosine 46 in the extra arm to 7-methylguanosine by the 7-methylguanosine-forming enzyme from Escherichia coli changes the aminoacylation kinetics for the B. subtilis methionyl-tRNA synthetase. In repeated experiments the V(max) value is decreased by one-half. (ii) tRNA(f) (Met) species with ribothymidine at position 54 (rT54) or uridine at position 54 (U54) were obtained from untreated or trimethoprim-treated B. subtilis. The formylated fMet-tRNA(f) (Met) species with U54 and rT54, respectively, function equally well in an in vitro initiation system containing AUG, initiation factors, and 70s ribosomes. The unformylated Met-tRNA(t) (Met) species, however, differ from each other: "Met-tRNA(f) (Met) rT" is inactive, whereas the U54 counter-upart effectively forms the initiation complex. (iii) Two isoacceptors, tRNA(1) (Phe) and tRNA(2) (Phe), were obtained from B. subtilis. tRNA(1) (Phe) accumulates only under special growth conditions and is an incompletely modified precursor oftRNA(2) (Phe): in the first position of the anticodon, guanosine replaces Gm, and next to the 3' end of the anticodon (isopentenyl)adenosine replaces 2-thiomethyl-N(6)-(isopentenyl)adenosine. Both tRNA's behave identically in aminoacylation kinetics. In the factor-dependent AUGU(3)-directed formation of fMet-Phe, the undermodified tRNA(1) (Phe) is always less efficient at Mg(2+) concentrations between 5 and 15 mM than its mature counterpart.
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Grasmuk H, Nolan RD, Drews J. A new concept of the function of elongation factor 1 in peptid chain elongation. EUROPEAN JOURNAL OF BIOCHEMISTRY 1976; 71:271-9. [PMID: 1009951 DOI: 10.1111/j.1432-1033.1976.tb11113.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
An entirely new model for the mechanism of elongation factor 1 (EF-1) function is presented. Experiments in which mixtures of [3H]EF-1, ribosomes from Drebs II ascites cells and various additional co-factors were analyzed by chromatography on Sepharose 6B, show that EF-1 binds to the ribosome early in the translation process and remains bound on the ribosome during translation. Optimal EF-1 binding occurs on polynucleotide-programmed ribosomes carrying a tRNA in their P-site. On the other hand it was clearly shown that EF-2 attached at each translocation event and was then released before a new Phe-tRNA could be bound.
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Grasmuk H, Nolan RD, Drews J. The stimulation of labelled polynucleotide binding to Krebs II ascites and Escheria coli ribosomes by deacylated tRNAs. FEBS Lett 1975; 53:229-33. [PMID: 1095415 DOI: 10.1016/0014-5793(75)80026-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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12
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Harvey RJ. Growth and initiation of protein synthesis in Escherichia coli in the presence of trimethoprim. J Bacteriol 1973; 114:309-22. [PMID: 4572717 PMCID: PMC251769 DOI: 10.1128/jb.114.1.309-322.1973] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Escherichia coli grew exponentially at a reduced rate in the presence of 50 or 100 mug of trimethoprim/ml if the low-molecular-weight products of folate metabolism or their precursors (thymidine, purines, methionine, glycine, and pantothenate) were supplied in the medium. Folate metabolism was inhibited 99.9% by these concentrations of trimethoprim, but a low level of formylation of methionyl transfer ribonucleic acid (met-tRNA(F)) could be detected. However, in a medium containing all major amino acids, nucleosides, and vitamins, formylation of met-tRNA(F) was undetectable in the presence of trimethoprim. No other amino-masked amino acids were detected, and methionine remained a major amino-terminal amino acid of mature proteins. met-tRNA(F) was rapidly labeled with exogenous methionine and was associated with 30s ribosomal subunits and 70s ribosomes. It was concluded that initiation of protein synthesis can occur with unformylated met-tRNA(F) in E. coli. Changes in macromolecular composition were associated with the lack of formylation, in particular a fourfold increase in both met-tRNA(F) and ribosomal subunits. These changes would tend to compensate for the low specific rate of initiation with unformylated met-tRNA(F).
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Lapidot Y, de Groot N. The chemical synthesis and the biochemical properties of peptidyl-tRNA. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1972; 12:189-228. [PMID: 4557056 DOI: 10.1016/s0079-6603(08)60663-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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16
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17
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Migita LK, Doi RH. The Amino-terminal Residues of Bacillus subtilis Proteins Made in Vitro. J Biol Chem 1970. [DOI: 10.1016/s0021-9258(18)63198-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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18
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Leder P, Skogerson LE, Nau MM. Translocation of mRNA codons. I. The preparation and characteristics of a homogeneous enzyme. Proc Natl Acad Sci U S A 1969; 62:454-60. [PMID: 4307715 PMCID: PMC277820 DOI: 10.1073/pnas.62.2.454] [Citation(s) in RCA: 46] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
This report describes a convenient scheme for the further purification of an E. coli enzyme which is required for the translocation step in protein biosynthesis. The homogeneous enzyme translocase appears to be a relatively large monomeric protein, having a molecular weight of approximately 72,000, and acts in a catalytic fashion during protein synthesis. It is also one of the major soluble macromolecular constituents of rapidly growing E. coli, comprising more than 2 per cent of the protein in ribosome-free extracts. Further, the rate of in vitro protein synthesis is linearly dependent upon the concentration of the pure enzyme until approximately one molecule of translocase is present per ribosome in reaction mixtures.
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19
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Vogel Z, Zamir A, Elson D. On the specificity and stability of an enzyme that hydrolyzes N-substituted aminoacyl-transfer RNA's. Proc Natl Acad Sci U S A 1968; 61:701-7. [PMID: 4879402 PMCID: PMC225216 DOI: 10.1073/pnas.61.2.701] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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21
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The Genetic Code After The Excitement. ADVANCES IN GENETICS 1968. [DOI: 10.1016/s0065-2660(08)60429-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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22
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Anderson JS, Dahlberg JE, Bretscher MS, Revel M, Clark BF. GTP-stimulated binding of initiator-tRNA to ribosomes directed by f2 bacteriophage RNA. Nature 1967; 216:1072-6. [PMID: 6075248 DOI: 10.1038/2161072a0] [Citation(s) in RCA: 51] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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23
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Economou AE, Nakamoto T. Further studies on the initiation of protein synthesis with N-formylmethionine in E. coli extracts. Proc Natl Acad Sci U S A 1967; 58:1033-9. [PMID: 4861303 PMCID: PMC335743 DOI: 10.1073/pnas.58.3.1033] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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24
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Leder P, Nau MM. Initiation of protein synthesis. 3. Factor-GTP-codon-dependent binding of F-met-tRNA to ribosomes. Proc Natl Acad Sci U S A 1967; 58:774-81. [PMID: 4860758 PMCID: PMC335700 DOI: 10.1073/pnas.58.2.774] [Citation(s) in RCA: 50] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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