1
|
Di Giulio M. A discriminative test among the different theories proposed to explain the origin of the genetic code: The coevolution theory finds additional support. Biosystems 2018; 169-170:1-4. [DOI: 10.1016/j.biosystems.2018.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/26/2018] [Accepted: 05/07/2018] [Indexed: 11/29/2022]
|
2
|
Di Giulio M. The aminoacyl-tRNA synthetases had only a marginal role in the origin of the organization of the genetic code: Evidence in favor of the coevolution theory. J Theor Biol 2017; 432:14-24. [DOI: 10.1016/j.jtbi.2017.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 08/01/2017] [Accepted: 08/03/2017] [Indexed: 10/19/2022]
|
3
|
Dasgupta S, Basu G. Evolutionary insights about bacterial GlxRS from whole genome analyses: is GluRS2 a chimera? BMC Evol Biol 2014; 14:26. [PMID: 24521160 PMCID: PMC3927822 DOI: 10.1186/1471-2148-14-26] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 02/07/2014] [Indexed: 12/21/2022] Open
Abstract
Background Evolutionary histories of glutamyl-tRNA synthetase (GluRS) and glutaminyl-tRNA synthetase (GlnRS) in bacteria are convoluted. After the divergence of eubacteria and eukarya, bacterial GluRS glutamylated both tRNAGln and tRNAGlu until GlnRS appeared by horizontal gene transfer (HGT) from eukaryotes or a duplicate copy of GluRS (GluRS2) that only glutamylates tRNAGln appeared. The current understanding is based on limited sequence data and not always compatible with available experimental results. In particular, the origin of GluRS2 is poorly understood. Results A large database of bacterial GluRS, GlnRS, tRNAGln and the trimeric aminoacyl-tRNA-dependent amidotransferase (gatCAB), constructed from whole genomes by functionally annotating and classifying these enzymes according to their mutual presence and absence in the genome, was analyzed. Phylogenetic analyses showed that the catalytic and the anticodon-binding domains of functional GluRS2 (as in Helicobacter pylori) were independently acquired from evolutionarily distant hosts by HGT. Non-functional GluRS2 (as in Thermotoga maritima), on the other hand, was found to contain an anticodon-binding domain appended to a gene-duplicated catalytic domain. Several genomes were found to possess both GluRS2 and GlnRS, even though they share the common function of aminoacylating tRNAGln. GlnRS was widely distributed among bacterial phyla and although phylogenetic analyses confirmed the origin of most bacterial GlnRS to be through a single HGT from eukarya, many GlnRS sequences also appeared with evolutionarily distant phyla in phylogenetic tree. A GlnRS pseudogene could be identified in Sorangium cellulosum. Conclusions Our analysis broadens the current understanding of bacterial GlxRS evolution and highlights the idiosyncratic evolution of GluRS2. Specifically we show that: i) GluRS2 is a chimera of mismatching catalytic and anticodon-binding domains, ii) the appearance of GlnRS and GluRS2 in a single bacterial genome indicating that the evolutionary histories of the two enzymes are distinct, iii) GlnRS is more widespread in bacteria than is believed, iv) bacterial GlnRS appeared both by HGT from eukarya and intra-bacterial HGT, v) presence of GlnRS pseudogene shows that many bacteria could not retain the newly acquired eukaryal GlnRS. The functional annotation of GluRS, without recourse to experiments, performed in this work, demonstrates the inherent and unique advantages of using whole genome over isolated sequence databases.
Collapse
Affiliation(s)
| | - Gautam Basu
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, India.
| |
Collapse
|
4
|
Abstract
The aminoacyl-tRNA synthetases (aaRSs) are essential components of the protein synthesis machinery responsible for defining the genetic code by pairing the correct amino acids to their cognate tRNAs. The aaRSs are an ancient enzyme family believed to have origins that may predate the last common ancestor and as such they provide insights into the evolution and development of the extant genetic code. Although the aaRSs have long been viewed as a highly conserved group of enzymes, findings within the last couple of decades have started to demonstrate how diverse and versatile these enzymes really are. Beyond their central role in translation, aaRSs and their numerous homologs have evolved a wide array of alternative functions both inside and outside translation. Current understanding of the emergence of the aaRSs, and their subsequent evolution into a functionally diverse enzyme family, are discussed in this chapter.
Collapse
|
5
|
Di Giulio M. An extension of the coevolution theory of the origin of the genetic code. Biol Direct 2008; 3:37. [PMID: 18775066 PMCID: PMC2538516 DOI: 10.1186/1745-6150-3-37] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Accepted: 09/05/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The coevolution theory of the origin of the genetic code suggests that the genetic code is an imprint of the biosynthetic relationships between amino acids. However, this theory does not seem to attribute a role to the biosynthetic relationships between the earliest amino acids that evolved along the pathways of energetic metabolism. As a result, the coevolution theory is unable to clearly define the very earliest phases of genetic code origin. In order to remove this difficulty, I here suggest an extension of the coevolution theory that attributes a crucial role to the first amino acids that evolved along these biosynthetic pathways and to their biosynthetic relationships, even when defined by the non-amino acid molecules that are their precursors. RESULTS It is re-observed that the first amino acids to evolve along these biosynthetic pathways are predominantly those codified by codons of the type GNN, and this observation is found to be statistically significant. Furthermore, the close biosynthetic relationships between the sibling amino acids Ala-Ser, Ser-Gly, Asp-Glu, and Ala-Val are not random in the genetic code table and reinforce the hypothesis that the biosynthetic relationships between these six amino acids played a crucial role in defining the very earliest phases of genetic code origin. CONCLUSION All this leads to the hypothesis that there existed a code, GNS, reflecting the biosynthetic relationships between these six amino acids which, as it defines the very earliest phases of genetic code origin, removes the main difficulty of the coevolution theory. Furthermore, it is here discussed how this code might have naturally led to the code codifying only for the domains of the codons of precursor amino acids, as predicted by the coevolution theory. Finally, the hypothesis here suggested also removes other problems of the coevolution theory, such as the existence for certain pairs of amino acids with an unclear biosynthetic relationship between the precursor and product amino acids and the collocation of Ala between the amino acids Val and Leu belonging to the pyruvate biosynthetic family, which the coevolution theory considered as belonging to different biosyntheses. REVIEWERS This article was reviewed by Rob Knight, Paul Higgs (nominated by Laura Landweber), and Eugene Koonin.
Collapse
Affiliation(s)
- Massimo Di Giulio
- Laboratory for Molecular Evolution, Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNR, Via P. Castellino, 111, 80131 Naples, Napoli, Italy.
| |
Collapse
|
6
|
Di Giulio M. The origin of the genetic code: theories and their relationships, a review. Biosystems 2004; 80:175-84. [PMID: 15823416 DOI: 10.1016/j.biosystems.2004.11.005] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Revised: 11/12/2004] [Accepted: 11/18/2004] [Indexed: 10/26/2022]
Abstract
A review of the main theories proposed to explain the origin of the genetic code is presented. I analyze arguments and data in favour of different theories proposed to explain the origin of the organization of the genetic code. It is possible to suggest a mechanism that makes compatible the different theories of the origin of the code, even if these are based on a historical or physicochemical determinism and thus appear incompatible by definition. Finally, I discuss the question of why a given number of synonymous codons was attributed to the amino acids in the genetic code.
Collapse
Affiliation(s)
- Massimo Di Giulio
- Institute of Genetics and Biophysics Adriano Buzzati-Traverso, CNR, Naples, Italy
| |
Collapse
|
7
|
|
8
|
Abstract
The coevolution theory of genetic code origin (Wong, J.T. 1975, Proc. Natl Acad. Sci. U.S.A.72, 1909-1912) is assumed here to be substantially correct. This theory is based on the strict parallelism of the biosynthetic relationships between amino acids and the organization of the genetic code and postulates that these relationships were mediated by tRNA-like molecules on which the biosynthetic transformations between precursor and product amino acids took place. These transformations underlay the mechanism that gave rise to genetic code organization. One of the pathways which represents these transformations found in current organisms, and which are thus probably molecular fossils, is the Met-tRNA(fMet)-->fMet-tRNA(fMet)pathway. This pathway is present only in the Bacteria domain. This along with other observations and arguments leads us to believe that this pathway is a clear violation of the universality of the genetic code. Furthermore, the presence of this pathway only in the Bacteria domain seems to imply that the translation apparatus was still rapidly evolving when this pathway was fixed. This, in turn, appears to imply that the last universal common ancestor was a progenote. Finally, the implications that the finding of this pathway has for the stereochemical theory of genetic code origin are discussed.
Collapse
Affiliation(s)
- M Di Giulio
- International Institute of Genetics and Biophysics, CNR, Via G. Marconi 10, 80125 Naples, Italy.
| |
Collapse
|
9
|
Abstract
The correlation between the optimal growth temperature of organisms and a thermophily index based on the propensity of amino acids to enter more frequently into (hyper)thermophile proteins is used to conduct an analysis aiming to establish whether genetic code structuring took place at a low or a high temperature. If the number of codons attributed to the various amino acids in the genetic code constitutes an estimate of the mean amino acid composition of proteins produced when the genetic code was definitively structured, then the thermophily index can also be associated to the genetic code. This value and the sampling of the variable thermophily index of different alignments of protein sequences from mesophile, thermophile and hyperthermophile species make it possible to establish, with an extremely high statistical confidence, that the late stage of genetic code structuring took place in a hyperthermophile (or thermophile) 'organism'. Moreover the 95% confidence interval of the temperature at which the genetic code was fixed turned out to be 91+/-24 degrees C. These observations seem to support the hypothesis that the origin of life might have taken place at a high temperature.
Collapse
Affiliation(s)
- M Di Giulio
- International Institute of Genetics and Biophysics, CNR, Via G. Marconi 10, 80125 Naples, Napoli, Italy.
| |
Collapse
|
10
|
|
11
|
Abstract
Comparative path lengths in amino acid biosynthesis and other molecular indicators of the timing of codon assignment were examined to reconstruct the main stages of code evolution. The codon tree obtained was rooted in the 4 N-fixing amino acids (Asp, Glu, Asn, Gln) and 16 triplets of the NAN set. This small, locally phased (commaless) code evidently arose from ambiguous translation on a poly(A) collector strand, in a surface reaction network. Copolymerisation of these amino acids yields polyanionic peptide chains, which could anchor uncharged amide residues to a positively charged mineral surface. From RNA virus structure and replication in vitro, the first genes seemed to be RNA segments spliced into tRNA. Expansion of the code reduced the risk of mutation to an unreadable codon. This step was conditional on initiation at the 5'-codon of a translated sequence. Incorporation of increasingly hydrophobic amino acids accompanied expansion. As codons of the NUN set were assigned most slowly, they received the most nonpolar amino acids. The origin of ferredoxin and Gln synthetase was traced to mid-expansion phase. Surface metabolism ceased by the end of code expansion, as cells bounded by a proteo-phospholipid membrane, with a protoATPase, had emerged. Incorporation of positively charged and aromatic amino acids followed. They entered the post-expansion code by codon capture. Synthesis of efficient enzymes with acid-base catalysis was then possible. Both types of aminoacyl-tRNA synthetases were attributed to this stage. tRNA sequence diversity and error rates in RNA replication indicate the code evolved within 20 million yr in the preIsuan era. These findings on the genetic code provide empirical evidence, from a contemporaneous source, that a surface reaction network, centred on C-fixing autocatalytic cycles, rapidly led to cellular life on Earth.
Collapse
Affiliation(s)
- B K Davis
- Research Foundation of Southern California Inc., La Jolla 92037, USA
| |
Collapse
|
12
|
Curnow AW, Tumbula DL, Pelaschier JT, Min B, Söll D. Glutamyl-tRNA(Gln) amidotransferase in Deinococcus radiodurans may be confined to asparagine biosynthesis. Proc Natl Acad Sci U S A 1998; 95:12838-43. [PMID: 9789001 PMCID: PMC23620 DOI: 10.1073/pnas.95.22.12838] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/1998] [Indexed: 11/18/2022] Open
Abstract
Asparaginyl-tRNA (Asn-tRNA) and glutaminyl-tRNA (Gln-tRNA) are essential components of protein synthesis. They can be formed by direct acylation by asparaginyl-tRNA synthetase (AsnRS) or glutaminyl-tRNA synthetase (GlnRS). The alternative route involves transamidation of incorrectly charged tRNA. Examination of the preliminary genomic sequence of the radiation-resistant bacterium Deinococcus radiodurans suggests the presence of both direct and indirect routes of Asn-tRNA and Gln-tRNA formation. Biochemical experiments demonstrate the presence of AsnRS and GlnRS, as well as glutamyl-tRNA synthetase (GluRS), a discriminating and a nondiscriminating aspartyl-tRNA synthetase (AspRS). Moreover, both Gln-tRNA and Asn-tRNA transamidation activities are present. Surprisingly, they are catalyzed by a single enzyme encoded by three ORFs orthologous to Bacillus subtilis gatCAB. However, the transamidation route to Gln-tRNA formation is idled by the inability of the discriminating D. radiodurans GluRS to produce the required mischarged Glu-tRNAGln substrate. The presence of apparently redundant complete routes to Asn-tRNA formation, combined with the absence from the D. radiodurans genome of genes encoding tRNA-independent asparagine synthetase and the lack of this enzyme in D. radiodurans extracts, suggests that the gatCAB genes may be responsible for biosynthesis of asparagine in this asparagine prototroph.
Collapse
Affiliation(s)
- A W Curnow
- Department of Molecular Biophysics and Biochemistry, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520-8114, USA
| | | | | | | | | |
Collapse
|
13
|
Richards NG, Schuster SM. Mechanistic issues in asparagine synthetase catalysis. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 1998; 72:145-98. [PMID: 9559053 DOI: 10.1002/9780470123188.ch5] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The enzymatic synthesis of asparagine is an ATP-dependent process that utilizes the nitrogen atom derived from either glutamine or ammonia. Despite a long history of kinetic and mechanistic investigation, there is no universally accepted catalytic mechanism for this seemingly straightforward carboxyl group activating enzyme, especially as regards those steps immediately preceding amide bond formation. This chapter considers four issues dealing with the mechanism: (a) the structural organization of the active site(s) partaking in glutamine utilization and aspartate activation; (b) the relationship of asparagine synthetase to other amidotransferases; (c) the way in which ATP is used to activate the beta-carboxyl group; and (d) the detailed mechanism by which nitrogen is transferred.
Collapse
Affiliation(s)
- N G Richards
- Department of Chemistry, University of Florida, Gainesville 32611, USA
| | | |
Collapse
|
14
|
|
15
|
Di Giulio M. The beta-sheets of proteins, the biosynthetic relationships between amino acids, and the origin of the genetic code. ORIGINS LIFE EVOL B 1996; 26:589-609. [PMID: 9008882 DOI: 10.1007/bf01808222] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Two forces are generally hypothesised as being responsible for conditioning the origin of the organization of the genetic code: the physicochemical properties of amino acids and their biosynthetic relationships (relationships between precursor and product amino acids). If we assume that the biosynthetic relationships between amino acids were fundamental in defining the genetic code, then it is reasonable to expect that the distribution of physicochemical properties among the amino acids in precursor-product relationships cannot be random but must, rather, be affected by some selective constraints imposed by the structure of primitive proteins. Analysis shows that measurements representing the 'size' of amino acids, e.g. bulkiness, are specifically associated to the pairs of amino acids in precurso-product relationships. However, the size of amino acids cannot have been selected per se but, rather, because it reflects the beta-sheets of proteins which are, therefore, identified as the main adaptive theme promoting the origin of genetic code organization. Whereas there are no traces of the alpha-helix in the genetic code table. The above considerations make it necessary to re-examine the relationship linking the hydrophilicity of the dinucleoside monophosphates of anticodons and the polarity and bulkiness of amino acids. It can be concluded that this relationship seems to be meaningful only between the hydrophilicity of anticodons and the polarity of amino acids. The latter relationship is supposed to have been operative on hairpin structures, ancestors of the tRNA molecule. Moreover, it is on these very structures that the biosynthetic links between precursor and product amino acids might have been achieved, and the interaction between the hydrophilicity of anticodons and the polarity of amino acids might have had a role in the concession of codons (anticodons) from precursors to products.
Collapse
Affiliation(s)
- M Di Giulio
- International Institute of Genetics and Biophysics, CNR, Napoli, Italy
| |
Collapse
|
16
|
Di Giulio M. The phylogeny of tRNAs seems to confirm the predictions of the coevolution theory of the origin of the genetic code. ORIGINS LIFE EVOL B 1995; 25:549-64. [PMID: 7494635 DOI: 10.1007/bf01582024] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
An extensive analysis of the evolutionary relationships existing between transfer RNAs, performed using parsimony algorithms, is presented. After building up an estimate of the tRNA ancestral sequences, these sequences are then compared using certain methods. The results seem to suggest that the coevolution hypothesis (Wong, J.T., 1975, Proc. Natl. Acad. Sci. USA 72, 1909-1912) that sees the genetic code as a map of the biosynthetic relationships between amino acids is further supported by these results, as compared to the hypotheses that see the physicochemical properties of amino acids as the main adaptative theme that led to the structuring of the genetic code.
Collapse
Affiliation(s)
- M Di Giulio
- International Institute of Genetics and Biophysics, CNR, Napoli, Italy
| |
Collapse
|
17
|
Eriani G, Cavarelli J, Martin F, Ador L, Rees B, Thierry JC, Gangloff J, Moras D. The class II aminoacyl-tRNA synthetases and their active site: evolutionary conservation of an ATP binding site. J Mol Evol 1995; 40:499-508. [PMID: 7783225 DOI: 10.1007/bf00166618] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Previous sequence analyses have suggested the existence of two distinct classes of aminoacyl-tRNA synthetase. The partition was established on the basis of exclusive sets of sequence motifs (Eriani et al. [1990] Nature 347:203-306). X-ray studies have now well defined the structural basis of the two classes: the class I enzymes share with dehydrogenases and kinases the classic nucleotide binding fold called the Rossmann fold, whereas the class II enzymes possess a different fold, not found elsewhere, built around a six-stranded antiparallel beta-sheet. The two classes of synthetases catalyze the same global reaction that is the attachment of an amino acid to the tRNA, but differ as to where on the terminal adenosine of the tRNA the amino acid is placed: class I enzymes act on the 2' hydroxyl whereas the class II enzymes prefer the 3' hydroxyl group. The three-dimensional structure of aspartyl-tRNA synthetase from yeast, a typical class II enzyme, is described here, in relation to its function. The crucial role of the sequence motifs in substrate binding and enzyme structure is high-lighted. Overall these results underline the existence of an intimate evolutionary link between the aminoacyl-tRNA synthetases, despite their actual structural diversity.
Collapse
Affiliation(s)
- G Eriani
- UPR 9002, Structure des Macromolécules Biologiques et Mécanismes de Reconnaissance, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
| | | | | | | | | | | | | | | |
Collapse
|
18
|
Abstract
The evolutionary relationships between transfer RNA (tRNA) molecules are analyzed by parsimony algorithms. The position of the topologies expected on the basis of the hypotheses made to explain the origin of the genetic code, on the frequency distribution of all the possible tree topologies of the evolutionary relationships between tRNAs seems to lead to the following conclusion: The hypothesis (Wong, J. T., Proc. Natl. Acad. Sci. USA, 1975, 72: 1909-1912) that sees the genetic code as a map of the biosynthetic relationships between amino acids seems to occupy a statistically significant position on these frequency distributions, thus reflecting a significant part of the tRNA phylogeny.
Collapse
Affiliation(s)
- M Di Giulio
- International Institute of Genetics and Biophysics, CNR, Naples, Italy
| |
Collapse
|