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Frenkel-Pinter M, Petrov AS, Matange K, Travisano M, Glass JB, Williams LD. Adaptation and Exaptation: From Small Molecules to Feathers. J Mol Evol 2022; 90:166-175. [PMID: 35246710 PMCID: PMC8975760 DOI: 10.1007/s00239-022-10049-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 01/26/2022] [Indexed: 11/27/2022]
Abstract
Evolution works by adaptation and exaptation. At an organismal level, exaptation and adaptation are seen in the formation of organelles and the advent of multicellularity. At the sub-organismal level, molecular systems such as proteins and RNAs readily undergo adaptation and exaptation. Here we suggest that the concepts of adaptation and exaptation are universal, synergistic, and recursive and apply to small molecules such as metabolites, cofactors, and the building blocks of extant polymers. For example, adenosine has been extensively adapted and exapted throughout biological evolution. Chemical variants of adenosine that are products of adaptation include 2' deoxyadenosine in DNA and a wide array of modified forms in mRNAs, tRNAs, rRNAs, and viral RNAs. Adenosine and its variants have been extensively exapted for various functions, including informational polymers (RNA, DNA), energy storage (ATP), metabolism (e.g., coenzyme A), and signaling (cyclic AMP). According to Gould, Vrba, and Darwin, exaptation imposes a general constraint on interpretation of history and origins; because of exaptation, extant function should not be used to explain evolutionary history. While this notion is accepted in evolutionary biology, it can also guide the study of the chemical origins of life. We propose that (i) evolutionary theory is broadly applicable from the dawn of life to the present time from molecules to organisms, (ii) exaptation and adaptation were important and simultaneous processes, and (iii) robust origin of life models can be constructed without conflating extant utility with historical basis of origins.
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Affiliation(s)
- Moran Frenkel-Pinter
- NASA Center for the Origins of Life, Atlanta, GA, 30332-0400, USA.,NSF-NASA Center of Chemical Evolution, Atlanta, GA, 30332-0400, USA.,Institute of Chemistry, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Anton S Petrov
- NASA Center for the Origins of Life, Atlanta, GA, 30332-0400, USA.,NSF-NASA Center of Chemical Evolution, Atlanta, GA, 30332-0400, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA
| | - Kavita Matange
- NASA Center for the Origins of Life, Atlanta, GA, 30332-0400, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA
| | - Michael Travisano
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Jennifer B Glass
- NASA Center for the Origins of Life, Atlanta, GA, 30332-0400, USA.,School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA
| | - Loren Dean Williams
- NASA Center for the Origins of Life, Atlanta, GA, 30332-0400, USA. .,NSF-NASA Center of Chemical Evolution, Atlanta, GA, 30332-0400, USA. .,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332-0400, USA.
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2
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Blersch KF, Burchert JP, August SC, Welp L, Neumann P, Köster S, Urlaub H, Ficner R. Structural model of the M7G46 Methyltransferase TrmB in complex with tRNA. RNA Biol 2021; 18:2466-2479. [PMID: 34006170 DOI: 10.1080/15476286.2021.1925477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
TrmB belongs to the class I S-adenosylmethionine (SAM)-dependent methyltransferases (MTases) and introduces a methyl group to guanine at position 7 (m7G) in tRNA. In tRNAs m7G is most frequently found at position 46 in the variable loop and forms a tertiary base pair with C13 and U22, introducing a positive charge at G46. The TrmB/Trm8 enzyme family is structurally diverse, as TrmB proteins exist in a monomeric, homodimeric, and heterodimeric form. So far, the exact enzymatic mechanism, as well as the tRNA-TrmB crystal structure is not known. Here we present the first crystal structures of B. subtilis TrmB in complex with SAM and SAH. The crystal structures of TrmB apo and in complex with SAM and SAH have been determined by X-ray crystallography to 1.9 Å (apo), 2.5 Å (SAM), and 3.1 Å (SAH). The obtained crystal structures revealed Tyr193 to be important during SAM binding and MTase activity. Applying fluorescence polarization, the dissociation constant Kd of TrmB and tRNAPhe was determined to be 0.12 µM ± 0.002 µM. Luminescence-based methyltransferase activity assays revealed cooperative effects during TrmB catalysis with half-of-the-site reactivity at physiological SAM concentrations. Structural data retrieved from small-angle x-ray scattering (SAXS), mass-spectrometry of cross-linked complexes, and molecular docking experiments led to the determination of the TrmB-tRNAPhe complex structure.
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Affiliation(s)
- Katharina F Blersch
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg August University Göttingen, Göttingen, Germany
| | - Jan-Philipp Burchert
- Institute for X-Ray Physics, Georg August University Göttingen, Göttingen, Germany
| | | | - Luisa Welp
- Bioanalytical Mass Spectrometry Research Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg August University Göttingen, Göttingen, Germany
| | - Sarah Köster
- Institute for X-Ray Physics, Georg August University Göttingen, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Research Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg August University Göttingen, Göttingen, Germany
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Thapar R, Bacolla A, Oyeniran C, Brickner JR, Chinnam NB, Mosammaparast N, Tainer JA. RNA Modifications: Reversal Mechanisms and Cancer. Biochemistry 2018; 58:312-329. [PMID: 30346748 DOI: 10.1021/acs.biochem.8b00949] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
An emerging molecular understanding of RNA alkylation and its removal is transforming our knowledge of RNA biology and its interplay with cancer chemotherapy responses. DNA modifications are known to perform critical functions depending on the genome template, including gene expression, DNA replication timing, and DNA damage protection, yet current results suggest that the chemical diversity of DNA modifications pales in comparison to those on RNA. More than 150 RNA modifications have been identified to date, and their complete functional implications are still being unveiled. These include intrinsic roles such as proper processing and RNA maturation; emerging evidence has furthermore uncovered RNA modification "readers", seemingly analogous to those identified for histone modifications. These modification recognition factors may regulate mRNA stability, localization, and interaction with translation machinery, affecting gene expression. Not surprisingly, tumors differentially modulate factors involved in expressing these marks, contributing to both tumorigenesis and responses to alkylating chemotherapy. Here we describe the current understanding of RNA modifications and their removal, with a focus primarily on methylation and alkylation as functionally relevant changes to the transcriptome. Intriguingly, some of the same RNA modifications elicited by physiological processes are also produced by alkylating agents, thus blurring the lines between what is a physiological mark and a damage-induced modification. Furthermore, we find that a high level of gene expression of enzymes with RNA dealkylation activity is a sensitive readout for poor survival in four different cancer types, underscoring the likely importance of examining RNA dealkylation mechanisms to cancer biology and for cancer treatment and prognosis.
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Affiliation(s)
- Roopa Thapar
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
| | - Clement Oyeniran
- Department of Pathology and Immunology, Siteman Cancer Center , Washington University in St. Louis School of Medicine , St. Louis , Missouri 63110 , United States
| | - Joshua R Brickner
- Department of Pathology and Immunology, Siteman Cancer Center , Washington University in St. Louis School of Medicine , St. Louis , Missouri 63110 , United States
| | - Naga Babu Chinnam
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Siteman Cancer Center , Washington University in St. Louis School of Medicine , St. Louis , Missouri 63110 , United States
| | - John A Tainer
- Department of Molecular and Cellular Oncology , University of Texas M. D. Anderson Cancer Center , Houston , Texas 77030 , United States
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4
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Structural aspects of messenger RNA reading frame maintenance by the ribosome. Nat Struct Mol Biol 2010; 17:555-60. [PMID: 20400952 DOI: 10.1038/nsmb.1790] [Citation(s) in RCA: 236] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2009] [Accepted: 02/22/2010] [Indexed: 11/09/2022]
Abstract
One key question in protein biosynthesis is how the ribosome couples mRNA and tRNA movements to prevent disruption of weak codon-anticodon interactions and loss of the translational reading frame during translocation. Here we report the complete path of mRNA on the 70S ribosome at the atomic level (3.1-A resolution), and we show that one of the conformational rearrangements that occurs upon transition from initiation to elongation is a narrowing of the downstream mRNA tunnel. This rearrangement triggers formation of a network of interactions between the mRNA downstream of the A-site codon and the elongating ribosome. Our data elucidate the mechanism by which hypermodified nucleoside 2-methylthio-N6 isopentenyl adenosine at position 37 (ms(2)i(6)A37) in tRNA(Phe)(GAA) stabilizes mRNA-tRNA interactions in all three tRNA binding sites. Another network of contacts is formed between this tRNA modification and ribosomal elements surrounding the mRNA E/P kink, resulting in the anchoring of P-site tRNA. These data allow rationalization of how modification deficiencies of ms(2)i(6)A37 in tRNAs may lead to shifts of the translational reading frame.
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Björk GR. Genetic dissection of synthesis and function of modified nucleosides in bacterial transfer RNA. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1995; 50:263-338. [PMID: 7538683 DOI: 10.1016/s0079-6603(08)60817-x] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- G R Björk
- Department of Microbiology, Umeå University, Sweden
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Chapter 1 Synthesis and Function of Modified Nucleosides in tRNA. ACTA ACUST UNITED AC 1990. [DOI: 10.1016/s0301-4770(08)61487-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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7
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Wilson RK, Roe BA. Presence of the hypermodified nucleotide N6-(delta 2-isopentenyl)-2-methylthioadenosine prevents codon misreading by Escherichia coli phenylalanyl-transfer RNA. Proc Natl Acad Sci U S A 1989; 86:409-13. [PMID: 2643111 PMCID: PMC286479 DOI: 10.1073/pnas.86.2.409] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The overall structure of transfer RNA is optimized for its various functions by a series of unique post-transcriptional nucleotide modifications. Since many of these modifications are conserved from prokaryotes through higher eukaryotes, it has been proposed that most modified nucleotides serve to optimize the ability of the tRNA to accurately interact with other components of the protein synthesizing machinery. When a cloned synthetic Escherichia coli tRNAPhe gene was transfected into a bacterial host that carried a defective phenylalanine tRNA-synthetase gene, tRNAPhe was overexpressed by 11-fold. As a result of this overexpression, an undermodified tRNAPhe species was produced that lacked only N6-(delta 2-isopentenyl)-2-methylthioadenosine (ms2i6A), a hypermodified nucleotide found immediately 3' to the anticodon of all major E. coli tRNAs that read UNN codons. To investigate the role of ms2i6A in E. coli tRNA, we compared the aminoacylation kinetics and in vitro codon-reading properties of the ms2i6A-lacking and normal fully modified tRNAPhe species. The results of these experiments indicate that while ms2i6A is not required for normal aminoacylation of tRNAPhe, its presence stabilizes codon-anticodon interaction and thereby prevents misreading of the genetic code.
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MESH Headings
- Adenosine/analogs & derivatives
- Amino Acid Sequence
- Base Sequence
- Chemical Fractionation
- Chromatography, Thin Layer
- Cloning, Molecular
- Codon/genetics
- Escherichia coli/genetics
- Gene Expression Regulation
- Isopentenyladenosine/analogs & derivatives
- Isopentenyladenosine/genetics
- Isopentenyladenosine/metabolism
- Kinetics
- Molecular Sequence Data
- Phenylalanine-tRNA Ligase/genetics
- Protein Biosynthesis
- RNA Processing, Post-Transcriptional
- RNA, Messenger/genetics
- RNA, Transfer, Amino Acid-Specific/metabolism
- RNA, Transfer, Phe/biosynthesis
- RNA, Transfer, Phe/genetics
- RNA, Transfer, Phe/isolation & purification
- RNA, Transfer, Phe/metabolism
- Transcription, Genetic
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Affiliation(s)
- R K Wilson
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman 73019
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Ajitkumar P, Cherayil JD. Thionucleosides in transfer ribonucleic acid: diversity, structure, biosynthesis, and function. Microbiol Rev 1988; 52:103-13. [PMID: 3280963 PMCID: PMC372707 DOI: 10.1128/mr.52.1.103-113.1988] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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9
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10
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Vani BR, Ramakrishnan T. Studies on the effects ofin vitro methyiation on aminoacylation of transfer RNA. J Biosci 1984. [DOI: 10.1007/bf02702643] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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11
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Kersten H. On the biological significance of modified nucleosides in tRNA. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1984; 31:59-114. [PMID: 6397775 DOI: 10.1016/s0079-6603(08)60375-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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12
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Colonna A, Ciliberto G, Santamaria R, Cimino F, Salvatore F. Isolation and characterization of a tRNA(guanine-7-)-methyltransferase from Salmonella typhimurium. Mol Cell Biochem 1983; 52:97-106. [PMID: 6348510 DOI: 10.1007/bf00224919] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The tRNA modifying enzyme, S-adenosylmethionine:tRNA(guanine-7-)-methyltransferase, has been extensively purified from Salmonella typhimurium. A rapid and efficient purification method using phosphocellulose chromatography followed by ammonium sulfate precipitation and Sephadex G-100 gel filtration is described. The enzyme appears to be a single polypeptide chain with a molecular weight of approximately 25 000--30 000 daltons. The Km for S-adenosylmethionine and for undermethylated tRNA is 53 microM and 3.4 microM, respectively. The methylation reaction is dependent on added monovalent or divalent cations; 5 mM spermidine, 3 mM MgCl2 and 1 mM spermine are the most effective. The enzyme, though not homogeneous, is free from contaminating ribonucleases and other tRNA methyltransferases.
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13
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Dirheimer G. Chemical nature, properties, location, and physiological and pathological variations of modified nucleosides in tRNAs. Recent Results Cancer Res 1983; 84:15-46. [PMID: 6342070 DOI: 10.1007/978-3-642-81947-6_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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14
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Buck M, McCloskey JA, Basile B, Ames BN. cis 2-Methylthio-ribosylzeatin (ms2io6A) is present in the transfer RNA of Salmonella typhimurium, but not Escherichia coli. Nucleic Acids Res 1982; 10:5649-62. [PMID: 6755395 PMCID: PMC320913 DOI: 10.1093/nar/10.18.5649] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
We have identified the cis isomer of N6-(4-hydroxy-isopentenyl)-2-methylthioadenosine (ms2io6A) as a component of the tRNA of Salmonella typhimurium. This is the first report of this compound in the tRNA of any member of the enterobacteriaceae: the nucleoside was previously thought to be found exclusively in plants or plant associated bacteria. Interestingly, all E. coli strains examined were found to lack ms2io6A. Evidence is presented which suggests S. typhimurium tRNA also contains low levels of 5-carboxymethylaminomethyl-2-thiouridine (cmnm5s2U) in addition to 5-methylaminomethyl-2-thiouridine (mnm5s2U).
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15
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Buck M, Griffiths E. Iron mediated methylthiolation of tRNA as a regulator of operon expression in Escherichia coli. Nucleic Acids Res 1982; 10:2609-24. [PMID: 7043398 PMCID: PMC320637 DOI: 10.1093/nar/10.8.2609] [Citation(s) in RCA: 72] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
E. coli growing in the presence of iron-binding proteins produced tRNAtrp and tRNAphe molecules containing i6A instead of ms2i6A adjacent to the anticodon. These undermodified tRNAs functioned less efficiently than the fully modified molecules when translating synthetic polynucleotides containing contiguous codons in an in vitro system, but did not limit the translation of MS2 RNA. We examined the possibility that the altered tRNAs with lowered translational efficiencies could relieve transcription termination at the trp and phe attenuators and lead to increased operon expression under iron restricted conditions. Using trpR mutants we found that there was indeed greater expression of the trp operon during iron restricted growth. This increase was attributable solely to the tRNA alteration induced by iron restriction.
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Cedergren RJ, Sankoff D, LaRue B, Grosjean H. The evolving tRNA molecule. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1981; 11:35-104. [PMID: 7030617 DOI: 10.3109/10409238109108699] [Citation(s) in RCA: 74] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The study of tRNA molecular evolution is crucial to understanding the origin and establishment of the genetic code as well as the differentiation and refinement of the machinery of protein synthesis in prokaryotes, eukaryotes, organelles, and phage systems. The small size of the molecule and its critical involvement in a multiplicity of roles distinguish its study from classical protein molecular evolution with respect to goals and methods. Here, the authors assess available and missing data, existing and needed methodology, and the impact of tRNA studies on current theories both of genetic code evolution and of the evolution of species. They analyze mutational "hot spots", the role of base modification, synthetase recognition, codon-anticodon interactions and the status of organelle tRNA.
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17
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Grosjean H, Chantrenne H. On codon- anticodon interactions. MOLECULAR BIOLOGY, BIOCHEMISTRY, AND BIOPHYSICS 1980; 32:347-67. [PMID: 7003350 DOI: 10.1007/978-3-642-81503-4_27] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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