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Douglas J, Bouckaert R, Carter CW, Wills P. Enzymic recognition of amino acids drove the evolution of primordial genetic codes. Nucleic Acids Res 2024; 52:558-571. [PMID: 38048305 PMCID: PMC10810186 DOI: 10.1093/nar/gkad1160] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/28/2023] [Accepted: 11/20/2023] [Indexed: 12/06/2023] Open
Abstract
How genetic information gained its exquisite control over chemical processes needed to build living cells remains an enigma. Today, the aminoacyl-tRNA synthetases (AARS) execute the genetic codes in all living systems. But how did the AARS that emerged over three billion years ago as low-specificity, protozymic forms then spawn the full range of highly-specific enzymes that distinguish between 22 diverse amino acids? A phylogenetic reconstruction of extant AARS genes, enhanced by analysing modular acquisitions, reveals six AARS with distinct bacterial, archaeal, eukaryotic, or organellar clades, resulting in a total of 36 families of AARS catalytic domains. Small structural modules that differentiate one AARS family from another played pivotal roles in discriminating between amino acid side chains, thereby expanding the genetic code and refining its precision. The resulting model shows a tendency for less elaborate enzymes, with simpler catalytic domains, to activate amino acids that were not synthesised until later in the evolution of the code. The most probable evolutionary route for an emergent amino acid type to establish a place in the code was by recruiting older, less specific AARS, rather than adapting contemporary lineages. This process, retrofunctionalisation, differs from previously described mechanisms through which amino acids would enter the code.
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Affiliation(s)
- Jordan Douglas
- Department of Physics, The University of Auckland, New Zealand
- Centre for Computational Evolution, The University of Auckland, New Zealand
| | - Remco Bouckaert
- Centre for Computational Evolution, The University of Auckland, New Zealand
- School of Computer Science, The University of Auckland, New Zealand
| | - Charles W Carter
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, USA
| | - Peter R Wills
- Department of Physics, The University of Auckland, New Zealand
- Centre for Computational Evolution, The University of Auckland, New Zealand
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2
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Identification and analysis of putative tRNA genes in baculovirus genomes. Virus Res 2022; 322:198949. [PMID: 36181979 DOI: 10.1016/j.virusres.2022.198949] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/26/2022] [Accepted: 09/27/2022] [Indexed: 12/24/2022]
Abstract
Transfer RNAs (tRNAs) genes are both coded for and arranged along some viral genomes representing the entire virosphere and seem to play different biological functions during infection, other than transferring the correct amino acid to a growing peptide chain. Baculovirus genome description and annotation has focused mostly on protein-coding genes, microRNA, and homologous regions. Here we carried out a large-scale in silico search for putative tRNA genes in baculovirus genomes. Ninety-six of 257 baculovirus genomes analyzed was found to contain at least one putative tRNA gene. We found great diversity in primary and secondary structure, in location within the genome, in intron presence and size, and in anti-codon identity. In some cases, genes of tRNA-containing genomes were found to have a bias for the codons specified by the tRNAs present in such genomes. Moreover, analysis revealed that most of the putative tRNA genes possessed conserved motifs for tRNA type 2 promoters, including the A-box and B-box motifs with few mismatches from the eukaryotic canonical motifs. From publicly available small RNA deep sequencing datasets of baculovirus-infected insect cells, we found evidence that a putative Autographa californica multiple nucleopolyhedrovirus Gln-tRNA gene was transcribed and modified with the addition of the non-templated 3'-CCA tail found at the end of all tRNAs. Further research is needed to determine the expression and functionality of these viral tRNAs.
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3
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tRNA modification profiles in obligate and moderate thermophilic bacilli. Extremophiles 2022; 26:11. [PMID: 35122547 PMCID: PMC8818000 DOI: 10.1007/s00792-022-01258-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 01/04/2022] [Indexed: 11/12/2022]
Abstract
Transfer RNAs (tRNAs) are the most ancient RNA molecules in the cell, modification pattern of which is linked to phylogeny. The aim of this study was to determine the tRNA modification profiles of obligate (Anoxybacillus, Geobacillus, Paragebacillus) and moderate (Bacillus, Brevibacillus, Ureibacillus, Paenibacillus) thermophilic aerobic bacilli strains to find out its linkage to phylogenetic variations between species. LC-MS was applied for the quantification of modified nucleosides using both natural and isotopically labeled standards. The presence of m2A and m7G modifications at high levels was determined in all species. Relatively high level of i6A and m5C modification was observed for Paenibacillus and Ureibacillus, respectively. The lowest level of Cm modification was found in Bacillus. The modification ms2i6A and m1G were absent in Brevibacillus and Ureibacillus, respectively, while modifications Am and m22G were observed only for Ureibacillus. While both obligate and moderate thermophilic species contain Gm, m1G and ms2i6A modifications, large quantities of them (especially Gm and ms2i6A modification) were detected in obligate thermophilic ones (Geobacillus, Paragebacillus and Anoxybacillus). The collective set of modified tRNA bases is genus-specific and linked to the phylogeny of bacilli. In addition, the dataset could be applied to distinguish obligate thermophilic bacilli from moderate ones.
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Yoffe L, Kuperman AA, Isakov O, Haguel D, Polsky AL, Farberov L, Pillar N, Gurevich V, Haviv I, Shomron N. Assessing the involvement of the placental microbiome and virome in preeclampsia using non coding RNA sequencing. J Perinat Med 2021; 49:1071-1083. [PMID: 34114389 DOI: 10.1515/jpm-2021-0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 04/29/2021] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Preeclampsia is a dangerous pregnancy complication. The source of preeclampsia is unknown, though the placenta is believed to have a central role in its pathogenesis. An association between maternal infection and preeclampsia has been demonstrated, yet the involvement of the placental microbiome in the etiology of preeclampsia has not been determined. In this study, we examined whether preeclampsia is associated with an imbalanced microorganism composition in the placenta. METHODS To this end, we developed a novel method for the identification of bacteria/viruses based on sequencing of small non-coding RNA, which increases the microorganism-to-host ratio, this being a major challenge in microbiome methods. We validated the method on various infected tissues and demonstrated its efficiency in detecting microorganisms in samples with extremely low bacterial/viral biomass. We then applied the method to placenta specimens from preeclamptic and healthy pregnancies. Since the placenta is a remarkably large and heterogeneous organ, we explored the bacterial and viral RNA at each of 15 distinct locations. RESULTS Bacterial RNA was detected at all locations and was consistent with previous studies of the placental microbiome, though without significant differences between the preeclampsia and control groups. Nevertheless, the bacterial RNA composition differed significantly between various areas of the placenta. Viral RNA was detected in extremely low quantities, below the threshold of significance, thus viral abundance could not be determined. CONCLUSIONS Our results suggest that the bacterial and viral abundance in the placenta may have only limited involvement in the pathogenesis of preeclampsia. The evidence of a heterogenic bacterial RNA composition in the various placental locations warrants further investigation to capture the true nature of the placental microbiome.
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Affiliation(s)
- Liron Yoffe
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amir A Kuperman
- Blood Coagulation Service and Pediatric Hematology Clinic, Galilee Medical Center, Nahariya, Israel
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Ofer Isakov
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Department of Internal Medicine "T", Tel Aviv Medical Center, Tel Aviv, Israel
| | | | | | - Luba Farberov
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nir Pillar
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Izhak Haviv
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Noam Shomron
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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5
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Wang N, Dong WL, Zhang XJ, Zhou T, Huang XJ, Li BG, Liu JN, Ma XF, Li ZH. Evolutionary characteristics and phylogeny of cotton chloroplast tRNAs. PLANTA 2021; 254:116. [PMID: 34750674 DOI: 10.1007/s00425-021-03775-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 10/28/2021] [Indexed: 06/13/2023]
Abstract
The novel structural variations were identified in cotton chloroplast tRNAs and gene loss events were more obvious than duplications in chloroplast tRNAs. Transfer RNAs (tRNA) have long been believed an evolutionary-conserved molecular family, which play the key roles in the process of protein biosynthesis in plant life activities. In this study, we detected the evolutionary characteristics and phylogeny of chloroplast tRNAs in cotton plants, an economic and fibered important taxon in the world. We firstly annotated the chloroplast tRNAs of 27 Gossypium species to analyze their genetic composition, structural characteristics and evolution. Compared with the traditional view of evolutionary conservation of tRNA, some novel tRNA structural variations were identified in cotton plants. I.g., tRNAVal-UAC and tRNAIle-GAU only contained one intron in the anti-condon loop region of tRNA secondary structure, respectively. In the variable region, some tRNAs contained a circle structure with a few nucleotides. Interestingly, the calculation result of free energy indicated that the variation of novel tRNAs contributed to the stability of tRNA structure. Phylogenetic analysis suggested that chloroplast tRNAs have evolved from multiple common ancestors, and the tRNAMet seemed to be an ancestral tRNA, which can be duplicated and diversified to produce other tRNAs. The chloroplast tRNAs contained a group I intron in cotton plants, and the evolutionary analysis of introns indicated that group I intron of chloroplast tRNA originated from cyanobacteria. Analysis of gene duplication and loss events showed that gene loss events were more obvious than duplications in Gossypium chloroplast tRNAs. Additionally, we found that the rate of transition was higher than the ones of transversion in cotton chloroplast tRNAs. This study provided new insights into the structural characteristics and evolution of chloroplast tRNAs in cotton plants.
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Affiliation(s)
- Ning Wang
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Wan-Lin Dong
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Xiao-Jing Zhang
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Tong Zhou
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Xiao-Juan Huang
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Bao-Guo Li
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Jian-Ni Liu
- State Key Laboratory of Continental Dynamics, Department of Geology, Early Life Institute, Northwest University, Xi'an, 710069, China
| | - Xiong-Feng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhong-Hu Li
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China.
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6
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Sun J, Evans PN, Gagen EJ, Woodcroft BJ, Hedlund BP, Woyke T, Hugenholtz P, Rinke C. Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages. ISME COMMUNICATIONS 2021; 1:30. [PMID: 36739331 PMCID: PMC9723677 DOI: 10.1038/s43705-021-00032-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/02/2021] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
Asgardarchaeota have been proposed as the closest living relatives to eukaryotes, and a total of 72 metagenome-assembled genomes (MAGs) representing six primary lineages in this archaeal phylum have thus far been described. These organisms are predicted to be fermentative heterotrophs contributing to carbon cycling in sediment ecosystems. Here, we double the genomic catalogue of Asgardarchaeota by obtaining 71 MAGs from a range of habitats around the globe, including the deep subsurface, brackish shallow lakes, and geothermal spring sediments. Phylogenomic inferences followed by taxonomic rank normalisation confirmed previously established Asgardarchaeota classes and revealed four additional lineages, two of which were consistently recovered as monophyletic classes. We therefore propose the names Candidatus Sifarchaeia class nov. and Ca. Jordarchaeia class nov., derived from the gods Sif and Jord in Norse mythology. Metabolic inference suggests that both classes represent hetero-organotrophic acetogens, which also have the ability to utilise methyl groups such as methylated amines, with acetate as the probable end product in remnants of a methanogen-derived core metabolism. This inferred mode of energy conservation is predicted to be enhanced by genetic code expansions, i.e., stop codon recoding, allowing the incorporation of the rare 21st and 22nd amino acids selenocysteine (Sec) and pyrrolysine (Pyl). We found Sec recoding in Jordarchaeia and all other Asgardarchaeota classes, which likely benefit from increased catalytic activities of Sec-containing enzymes. Pyl recoding, on the other hand, is restricted to Sifarchaeia in the Asgardarchaeota, making it the first reported non-methanogenic archaeal lineage with an inferred complete Pyl machinery, likely providing members of this class with an efficient mechanism for methylamine utilisation. Furthermore, we identified enzymes for the biosynthesis of ester-type lipids, characteristic of bacteria and eukaryotes, in both newly described classes, supporting the hypothesis that mixed ether-ester lipids are a shared feature among Asgardarchaeota.
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Affiliation(s)
- Jiarui Sun
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Paul N Evans
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Emma J Gagen
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
- School of Earth and Environmental Sciences, The University of Queensland, St Lucia, QLD, Australia
| | - Ben J Woodcroft
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
- Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Australia
| | - Brian P Hedlund
- School of Life Sciences and Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV, USA
| | - Tanja Woyke
- DOE Joint Genome Institute, Berkeley, CA, USA
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Christian Rinke
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia.
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Sharko FS, Boulygina ES, Tsygankova SV, Slobodova NV, Alekseev DA, Krasivskaya AA, Rastorguev SM, Tikhonov AN, Nedoluzhko AV. Steller's sea cow genome suggests this species began going extinct before the arrival of Paleolithic humans. Nat Commun 2021; 12:2215. [PMID: 33850161 PMCID: PMC8044168 DOI: 10.1038/s41467-021-22567-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 03/11/2021] [Indexed: 12/28/2022] Open
Abstract
Anthropogenic activity is the top factor directly related to the extinction of several animal species. The last Steller's sea cow (Hydrodamalis gigas) population on the Commander Islands (Russia) was wiped out in the second half of the 18th century due to sailors and fur traders hunting it for the meat and fat. However, new data suggests that the extinction process of this species began much earlier. Here, we present a nuclear de novo assembled genome of H. gigas with a 25.4× depth coverage. Our results demonstrate that the heterozygosity of the last population of this animal is low and comparable to the last woolly mammoth population that inhabited Wrangel Island 4000 years ago. Besides, as a matter of consideration, our findings also demonstrate that the extinction of this marine mammal starts along the North Pacific coastal line much earlier than the first Paleolithic humans arrived in the Bering sea region.
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Affiliation(s)
- Fedor S Sharko
- National Research Center "Kurchatov Institute", 1st Akademika Kurchatova Square, Moscow, Russia.,Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Eugenia S Boulygina
- National Research Center "Kurchatov Institute", 1st Akademika Kurchatova Square, Moscow, Russia
| | - Svetlana V Tsygankova
- National Research Center "Kurchatov Institute", 1st Akademika Kurchatova Square, Moscow, Russia
| | - Natalia V Slobodova
- National Research Center "Kurchatov Institute", 1st Akademika Kurchatova Square, Moscow, Russia
| | - Dmitry A Alekseev
- Russian Presidential Academy of National Economy and Public Administration, Prospect Vernadskogo, 82, Moscow, Russia
| | | | - Sergey M Rastorguev
- National Research Center "Kurchatov Institute", 1st Akademika Kurchatova Square, Moscow, Russia
| | - Alexei N Tikhonov
- Zoological Institute Russian Academy of Sciences, Universitetskaya nab., 1, Saint-Petersburg, Russia.,Institute of Applied Ecology of the North, North-Eastern Federal University, Yakutsk, Russia
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Ehrlich R, Davyt M, López I, Chalar C, Marín M. On the Track of the Missing tRNA Genes: A Source of Non-Canonical Functions? Front Mol Biosci 2021; 8:643701. [PMID: 33796548 PMCID: PMC8007984 DOI: 10.3389/fmolb.2021.643701] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/02/2021] [Indexed: 01/31/2023] Open
Abstract
Cellular tRNAs appear today as a diverse population of informative macromolecules with conserved general elements ensuring essential common functions and different and distinctive features securing specific interactions and activities. Their differential expression and the variety of post-transcriptional modifications they are subject to, lead to the existence of complex repertoires of tRNA populations adjusted to defined cellular states. Despite the tRNA-coding genes redundancy in prokaryote and eukaryote genomes, it is surprising to note the absence of genes coding specific translational-active isoacceptors throughout the phylogeny. Through the analysis of different releases of tRNA databases, this review aims to provide a general summary about those “missing tRNA genes.” This absence refers to both tRNAs that are not encoded in the genome, as well as others that show critical sequence variations that would prevent their activity as canonical translation adaptor molecules. Notably, while a group of genes are universally missing, others are absent in particular kingdoms. Functional information available allows to hypothesize that the exclusion of isodecoding molecules would be linked to: 1) reduce ambiguities of signals that define the specificity of the interactions in which the tRNAs are involved; 2) ensure the adaptation of the translational apparatus to the cellular state; 3) divert particular tRNA variants from ribosomal protein synthesis to other cellular functions. This leads to consider the “missing tRNA genes” as a source of putative non-canonical tRNA functions and to broaden the concept of adapter molecules in ribosomal-dependent protein synthesis.
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Affiliation(s)
- Ricardo Ehrlich
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay.,Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Marcos Davyt
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
| | - Ignacio López
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
| | - Cora Chalar
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
| | - Mónica Marín
- Biochemistry-Molecular Biology, Faculty of Science, Universidad de la República, Montevideo, Uruguay
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Infante-Rojas H, Marino-Ramirez L, Hernández-Fernández J. Structural analysis of leucine, lysine and tryptophan mitochondrial tRNA of nesting turtles Caretta caretta (Testudines: Chelonioidea) in the Colombian Caribbean. PeerJ 2020; 8:e9204. [PMID: 32596037 PMCID: PMC7306221 DOI: 10.7717/peerj.9204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 04/25/2020] [Indexed: 11/20/2022] Open
Abstract
The understanding of the functional properties of mitochondrial transfer RNA (mt tRNAs) depend on the knowledge of its structure. tRNA acts as an interface between polynucleotides and polypeptides thus, they are key molecules in protein biosynthesis. The tRNA molecule has a functional design and, given its importance in the translation of mitochondrial genes, it is plausible that modifications of the structure can affect the synthesis of proteins and the functional properties of the mitochondria. In a previous work, the mitochondrial genome of an individual of the nesting Caretta caretta of the Colombian Caribbean was obtained, where specific mutations were identified in the only tRNALeu (CUN), tRNATrp and tRNALys genes. In order to analyze the effect of these mutations on these three mt tRNAs, the prediction of 2D and 3D structures was performed. Genes were sequenced in 11 nesting loggerhead turtles from the Colombian Caribbean. Two-dimensional structures were inferred using the ARWEN program, and three-dimensional structures were obtained with the RNA Composer 3D program. Two polymorphisms were identified in tRNATrp and another one was located in tRNALys, both specific to C. caretta. The thymine substitution in nucleotide position 14 of tRNATrp could constitute an endemic polymorphism of the nesting colony of the Colombian Caribbean. Two 2D and three 3D patterns were obtained for tRNATrp. In the case of tRNALys and tRNALeu 2D and 3D structures were obtained respectively, which showed compliance to canonical structures, with 4 bp in the D-arm, 4-5 bp in the T-arm, and 5 bp in the anticodon arm. Moderate deviations were found, such as a change in the number of nucleotides, elongation in loops or stems and non-Watson-Crick base pairing: adenine-adenine in stem D of tRNATrp, uracil-uracil and adenine-cytosine in the acceptor arm of the tRNALys and cytosine-cytosine in the anticodon stem of the tRNALeu. In addition, distortions or lack of typical interactions in 3D structures gave them unique characteristics. According to the size of the variable region (4-5 nt), the three analyzed tRNAs belong to class I. The interactions in the three studied tRNAs occur mainly between D loop-variable region, and between spacer bases-variable region, which classifies them as tRNA of typology II. The polymorphisms and structural changes described can, apparently, be post-transcriptionally stabilized. It will be crucial to perform studies at the population and functional levels to elucidate the synthetic pathways affected by these genes. This article analyses for the first time the 1D, 2D and 3D structures of the mitochondrial tRNALys, tRNATrp and tRNALeu in the loggerhead turtle.
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Affiliation(s)
- Harvey Infante-Rojas
- Department of Natural and Environmental Sciences, Genetics, Molecular Biology and Bioinformatics Lab, Jorge Tadeo Lozano University, Bogotá, Cundinamarca, Colombia
| | | | - Javier Hernández-Fernández
- Department of Natural and Environmental Sciences, Genetics, Molecular Biology and Bioinformatics Lab, Jorge Tadeo Lozano University, Bogotá, Cundinamarca, Colombia
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10
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The complete mitochondrial genome of a parasite at the animal-fungal boundary. Parasit Vectors 2020; 13:81. [PMID: 32066491 PMCID: PMC7027106 DOI: 10.1186/s13071-020-3926-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 02/01/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sphaerothecum destruens is an obligate intracellular fish parasite which has been identified as a serious threat to freshwater fishes. Taxonomically, S. destruens belongs to the order Dermocystida within the class Ichthyosporea (formerly referred to as Mesomycetozoea), which sits at the animal-fungal boundary. Mitochondrial DNA (mtDNA) sequences can be valuable genetic markers for species detection and are increasingly used in environmental DNA (eDNA) based species detection. Furthermore, mtDNA sequences can be used in epidemiological studies by informing detection, strain identification and geographical spread. METHODS We amplified the entire mitochondrial (mt) genome of S. destruens in two overlapping long fragments using primers designed based on the cox1, cob and nad5 partial sequences. The mt-genome architecture of S. destruens was then compared to close relatives to gain insights into its evolution. RESULTS The complete mt-genome of Sphaerothecum destruens is 23,939 bp in length and consists of 47 genes including 21 protein-coding genes, 2 rRNA, 22 tRNA and two unidentified open reading frames. The mitochondrial genome of S. destruens is intronless and compact with a few intergenic regions and includes genes that are often missing from animal and fungal mt-genomes, such as, the four ribosomal proteins (small subunit rps13 and 14; large subunit rpl2 and 16), tatC (twin-arginine translocase component C), and ccmC and ccmF (cytochrome c maturation protein ccmC and heme lyase). CONCLUSIONS We present the first mt-genome of S. destruens which also represents the first mt-genome for the order Dermocystida. The availability of the mt-genome can assist the detection of S. destruens and closely related parasites in eukaryotic diversity surveys using eDNA and assist epidemiological studies by improving molecular detection and tracking the parasite's spread. Furthermore, as the only representative of the order Dermocystida, its mt-genome can be used in the study of mitochondrial evolution of the unicellular relatives of animals.
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Xiao L, Zhang S, Long C, Guo Q, Xu J, Dai X, Wang J. Complete Mitogenome of a Leaf-Mining Buprestid Beetle, Trachys auricollis, and Its Phylogenetic Implications. Genes (Basel) 2019; 10:E992. [PMID: 31805706 PMCID: PMC6947639 DOI: 10.3390/genes10120992] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/26/2019] [Accepted: 11/28/2019] [Indexed: 11/16/2022] Open
Abstract
A complete mitogenome of Trachys auricollis is reported, and a mitogenome-based phylogenetic tree of Elateriformia with all protein-coding genes (PCGs), rRNAs, and tRNAs is presented for the first time. The complete mitochondrial genome of T. auricollis is 16,429 bp in size and contains 13 PCGs, two rRNA genes, 22 tRNA genes, and an A + T-rich region. The A + T content of the entire genome is approximately 71.1%, and the AT skew and GC skew are 0.10 and -0.20, respectively. According to the the nonsynonymous substitution rate to synonymous substitution rates (Ka/Ks) of all PCGs, the highest and lowest evolutionary rates were observed for atp8 and cox1, respectively, which is a common finding among animals. The start codons of all PCGs are the typical ATN. Ten PCGs have complete stop codons, but three have incomplete stop codons with T or TA. As calculated based on the relative synonymous codon usage (RSCU) values, UUA(L) is the codon with the highest frequency. Except for trnS1, all 22 tRNA genes exhibit typical cloverleaf structures. The A + T-rich region of T. auricollis is located between rrnS and the trnI-trnG-trnM gene cluster, with six 72-bp tandem repeats. Both maximum likelihood (ML) and Bayesian (BI) trees suggest that Buprestoidea is close to Byrrhoidea and that Buprestoidea and Byrrhoidea are sister groups of Elateroidea, but the position of Psephenidae is undetermined. The inclusion of tRNAs might help to resolve the phylogeny of Coleoptera.
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Affiliation(s)
- Lifang Xiao
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China;
| | - Shengdi Zhang
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
| | - Chengpeng Long
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
| | - Qingyun Guo
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
| | - Jiasheng Xu
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
| | - Xiaohua Dai
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
- National Navel-Orange Engineering Research Center, Ganzhou 341000, China
| | - Jianguo Wang
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China;
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12
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Schwartz MH, Wang H, Pan JN, Clark WC, Cui S, Eckwahl MJ, Pan DW, Parisien M, Owens SM, Cheng BL, Martinez K, Xu J, Chang EB, Pan T, Eren AM. Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis. Nat Commun 2018; 9:5353. [PMID: 30559359 PMCID: PMC6297222 DOI: 10.1038/s41467-018-07675-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 11/09/2018] [Indexed: 12/13/2022] Open
Abstract
Advances in high-throughput sequencing have facilitated remarkable insights into the diversity and functioning of naturally occurring microbes; however, current sequencing strategies are insufficient to reveal physiological states of microbial communities associated with protein translation dynamics. Transfer RNAs (tRNAs) are core components of protein synthesis machinery, present in all living cells, and are phylogenetically tractable, which make them ideal targets to gain physiological insights into environmental microbes. Here we report a direct sequencing approach, tRNA-seq, and a software suite, tRNA-seq-tools, to recover sequences, abundance profiles, and post-transcriptional modifications of microbial tRNA transcripts. Our analysis of cecal samples using tRNA-seq distinguishes high-fat- and low-fat-fed mice in a comparable fashion to 16S ribosomal RNA gene amplicons, and reveals taxon- and diet-dependent variations in tRNA modifications. Our results provide taxon-specific in situ insights into the dynamics of tRNA gene expression and post-transcriptional modifications within complex environmental microbiomes.
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Affiliation(s)
- Michael H Schwartz
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA.,Committee on Microbiology, University of Chicago, Chicago, IL, 60637, USA
| | - Haipeng Wang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA.,School of Computer Science and Technology, Shandong University of Technology, Zibo, Shandong, China.,Toyota Technological Institute at Chicago, Chicago, IL, 60637, USA
| | - Jessica N Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Wesley C Clark
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Steven Cui
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Matthew J Eckwahl
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - David W Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Marc Parisien
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Sarah M Owens
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA.,Argonne National Laboratory, Lemont, IL, 60439, USA
| | - Brian L Cheng
- Committee on Microbiology, University of Chicago, Chicago, IL, 60637, USA
| | - Kristina Martinez
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Jinbo Xu
- Toyota Technological Institute at Chicago, Chicago, IL, 60637, USA
| | - Eugene B Chang
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, 60637, USA. .,Committee on Microbiology, University of Chicago, Chicago, IL, 60637, USA.
| | - A Murat Eren
- Committee on Microbiology, University of Chicago, Chicago, IL, 60637, USA. .,Department of Medicine, University of Chicago, Chicago, IL, 60637, USA. .,Marine Biological Laboratory, Woods Hole, MA, 02543, USA.
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13
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Abstract
We advocate for a tRNA- rather than an mRNA-centric model for evolution of the genetic code. The mechanism for evolution of cloverleaf tRNA provides a root sequence for radiation of tRNAs and suggests a simplified understanding of code evolution. To analyze code sectoring, rooted tRNAomes were compared for several archaeal and one bacterial species. Rooting of tRNAome trees reveals conserved structures, indicating how the code was shaped during evolution and suggesting a model for evolution of a LUCA tRNAome tree. We propose the polyglycine hypothesis that the initial product of the genetic code may have been short chain polyglycine to stabilize protocells. In order to describe how anticodons were allotted in evolution, the sectoring-degeneracy hypothesis is proposed. Based on sectoring, a simple stepwise model is developed, in which the code sectors from a 1→4→8→∼16 letter code. At initial stages of code evolution, we posit strong positive selection for wobble base ambiguity, supporting convergence to 4-codon sectors and ∼16 letters. In a later stage, ∼5–6 letters, including stops, were added through innovating at the anticodon wobble position. In archaea and bacteria, tRNA wobble adenine is negatively selected, shrinking the maximum size of the primordial genetic code to 48 anticodons. Because 64 codons are recognized in mRNA, tRNA-mRNA coevolution requires tRNA wobble position ambiguity leading to degeneracy of the code.
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Affiliation(s)
- Daewoo Pak
- a Center for Statistical Training and Consulting , Michigan State University , E. Lansing , MI 48824 , USA
| | - Nan Du
- b Computer Science and Engineering , Michigan State University , E. Lansing , MI 48824
| | | | - Yanni Sun
- b Computer Science and Engineering , Michigan State University , E. Lansing , MI 48824
| | - Zachary F Burton
- d Department of Biochemistry and Molecular Biology , Michigan State University , E. Lansing , MI 48824-1319
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14
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Radhakrishnan S, Literman R, Mizoguchi B, Valenzuela N. MeDIP-seq and nCpG analyses illuminate sexually dimorphic methylation of gonadal development genes with high historic methylation in turtle hatchlings with temperature-dependent sex determination. Epigenetics Chromatin 2017; 10:28. [PMID: 28533820 PMCID: PMC5438563 DOI: 10.1186/s13072-017-0136-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 05/12/2017] [Indexed: 12/15/2022] Open
Abstract
Background DNA methylation alters gene expression but not DNA sequence and mediates some cases of phenotypic plasticity. Temperature-dependent sex determination (TSD) epitomizes phenotypic plasticity where environmental temperature drives embryonic sexual fate, as occurs commonly in turtles. Importantly, the temperature-specific transcription of two genes underlying gonadal differentiation is known to be induced by differential methylation in TSD fish, turtle and alligator. Yet, how extensive is the link between DNA methylation and TSD remains unclear. Here we test for broad differences in genome-wide DNA methylation between male and female hatchling gonads of the TSD painted turtle Chrysemys picta using methyl DNA immunoprecipitation sequencing, to identify differentially methylated candidates for future study. We also examine the genome-wide nCpG distribution (which affects DNA methylation) in painted turtles and test for historic methylation in genes regulating vertebrate gonadogenesis. Results Turtle global methylation was consistent with other vertebrates (57% of the genome, 78% of all CpG dinucleotides). Numerous genes predicted to regulate turtle gonadogenesis exhibited sex-specific methylation and were proximal to methylated repeats. nCpG distribution predicted actual turtle DNA methylation and was bimodal in gene promoters (as other vertebrates) and introns (unlike other vertebrates). Differentially methylated genes, including regulators of sexual development, had lower nCpG content indicative of higher historic methylation. Conclusions Ours is the first evidence suggesting that sexually dimorphic DNA methylation is pervasive in turtle gonads (perhaps mediated by repeat methylation) and that it targets numerous regulators of gonadal development, consistent with the hypothesis that it may regulate thermosensitive transcription in TSD vertebrates. However, further research during embryogenesis will help test this hypothesis and the alternative that instead, most differential methylation observed in hatchlings is the by-product of sexual differentiation and not its cause. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0136-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Srihari Radhakrishnan
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011 USA.,Department of Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011 USA
| | - Robert Literman
- Ecology and Evolutionary Biology Program, Iowa State University, Ames, IA 50011 USA.,Department of Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011 USA
| | - Beatriz Mizoguchi
- Interdepartmental Genetics and Genomics Program, Iowa State University, Ames, IA 50011 USA.,Department of Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011 USA
| | - Nicole Valenzuela
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011 USA
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15
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Mobile genes in the human microbiome are structured from global to individual scales. Nature 2016; 535:435-439. [PMID: 27409808 PMCID: PMC4983458 DOI: 10.1038/nature18927] [Citation(s) in RCA: 173] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 06/15/2016] [Indexed: 12/11/2022]
Abstract
Recent work has underscored the importance of the microbiome in human health, largely attributing differences in phenotype to differences in the species present across individuals1,2,3,4,5. But mobile genes can confer profoundly different phenotypes on different strains of the same species. Little is known about the function and distribution of mobile genes in the human microbiome, and in particular whether the gene pool is globally homogenous or constrained by human population structure. Here, we investigate this question by comparing the mobile genes found in the microbiomes of 81 metropolitan North Americans with that of 172 agrarian Fiji islanders using a combination of single-cell genomics and metagenomics. We find large differences in mobile gene content between the Fijian and North American microbiomes, with functional variation that mirrors known dietary differences such as the excess of plant-based starch degradation genes. Remarkably, differences are also observed between the mobile gene pools of proximal Fijian villages, even though microbiome composition across villages is similar. Finally, we observe high rates of recombination leading to individual-specific mobile elements, suggesting that the abundance of some genes may reflect environmental selection rather than dispersal limitation. Together, these data support the hypothesis that human activities and behaviors provide selective pressures that shape mobile gene pools, and that acquisition of mobile genes is important to colonizing specific human populations.
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16
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Bhattacharyya S, Varshney U. Evolution of initiator tRNAs and selection of methionine as the initiating amino acid. RNA Biol 2016; 13:810-9. [PMID: 27322343 DOI: 10.1080/15476286.2016.1195943] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Transfer RNAs (tRNAs) have been important in shaping biomolecular evolution. Initiator tRNAs (tRNAi), a special class of tRNAs, carry methionine (or its derivative, formyl-methionine) to ribosomes to start an enormously energy consuming but a highly regulated process of protein synthesis. The processes of tRNAi evolution, and selection of methionine as the universal initiating amino acid remain an enigmatic problem. We constructed phylogenetic trees using the whole sequence, the acceptor-TψC arm ('minihelix'), and the anticodon-dihydrouridine arm regions of tRNAi from 158 species belonging to all 3 domains of life. All the trees distinctly assembled into 3 domains of life. Large trees, generated using data for all the tRNAs of a vast number of species, fail to reveal the major evolutionary events and identity of the probable elongator tRNA sequences that could be ancestor of tRNAi. Therefore, we constructed trees using the minihelix or the whole sequence of species specific tRNAs, and iterated our analysis on 50 eubacterial species. We identified tRNA(Pro), tRNA(Glu), or tRNA(Thr) (but surprisingly not elongator tRNA(Met)) as probable ancestors of tRNAi. We then determined the factors imposing selection of methionine as the initiating amino acid. Overall frequency of occurrence of methionine, whose metabolic cost of synthesis is the highest among all amino acids, remains almost unchanged across the 3 domains of life. Our correlation analysis shows that its high metabolic cost is independent of many physicochemical properties of the side chain. Our results indicate that selection of methionine, as the initiating amino acid was possibly a consequence of the evolution of one-carbon metabolism, which plays an important role in regulating translation initiation.
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Affiliation(s)
- Souvik Bhattacharyya
- a Department of Microbiology and Cell Biology , Indian Institute of Science , Bangalore , India
| | - Umesh Varshney
- a Department of Microbiology and Cell Biology , Indian Institute of Science , Bangalore , India.,b Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur , Bangalore , India
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17
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Tran TTT, Belahbib H, Bonnefoy V, Talla E. A Comprehensive tRNA Genomic Survey Unravels the Evolutionary History of tRNA Arrays in Prokaryotes. Genome Biol Evol 2015; 8:282-95. [PMID: 26710853 PMCID: PMC4758250 DOI: 10.1093/gbe/evv254] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2015] [Indexed: 01/12/2023] Open
Abstract
Considering the importance of tRNAs in the translation machinery, scant attention has been paid to tRNA array units defined as genomic regions containing at least 20 tRNA genes with a minimal tRNA gene density of two tRNA genes per kilobase. Our analysis of Acidithiobacillus ferrivorans CF27 and Acidithiobacillus ferrooxidans ATCC 23270(T) genomes showed that both display a tRNA array unit with syntenic conservation which mainly contributed to the tRNA gene redundancy in these two organisms. Our investigations into the occurrence and distribution of tRNA array units revealed that 1) this tRNA organization is limited to few phyla and mainly found in Gram-positive bacteria; and 2) the presence of tRNA arrays favors the redundancy of tRNA genes, in particular those encoding the core tRNA isoacceptors. Finally, comparative array organization revealed that tRNA arrays were acquired through horizontal gene transfer (from Firmicutes or unknown donor), before being subjected to tRNA rearrangements, deletions, and duplications. In Bacilli, the most parsimonious evolutionary history involved two common ancestors and the acquisition of their arrays arose late in evolution, in the genera branches. Functional roles of the array units in organism lifestyle, selective genetic advantage and translation efficiency, as well as the evolutionary advantages of organisms harboring them were proposed. Our study offers new insight into the structural organization and evolution of tRNA arrays in prokaryotic organisms.
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Affiliation(s)
- Tam T T Tran
- Aix Marseille Université, CNRS, IGS, UMR 7256, IMM, France
| | | | | | - Emmanuel Talla
- Aix Marseille Université, CNRS, IGS, UMR 7256, IMM, France
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18
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Diken E, Ozer T, Arikan M, Emrence Z, Oner ET, Ustek D, Arga KY. Genomic analysis reveals the biotechnological and industrial potential of levan producing halophilic extremophile, Halomonas smyrnensis AAD6T. SPRINGERPLUS 2015; 4:393. [PMID: 26251777 PMCID: PMC4523562 DOI: 10.1186/s40064-015-1184-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 07/27/2015] [Indexed: 01/21/2023]
Abstract
Halomonas smyrnensis AAD6T is a gram negative, aerobic, and moderately halophilic bacterium, and is known to produce high levels of levan with many potential uses in foods, feeds, cosmetics, pharmaceutical and chemical industries due to its outstanding properties. Here, the whole-genome analysis was performed to gain more insight about the biological mechanisms, and the whole-genome organization of the bacterium. Industrially crucial genes, including the levansucrase, were detected and the genome-scale metabolic model of H. smyrnensis AAD6T was reconstructed. The bacterium was found to have many potential applications in biotechnology not only being a levan producer, but also because of its capacity to produce Pel exopolysaccharide, polyhydroxyalkanoates, and osmoprotectants. The genomic information presented here will not only provide additional information to enhance our understanding of the genetic and metabolic network of halophilic bacteria, but also accelerate the research on systematical design of engineering strategies for biotechnology applications.
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Affiliation(s)
- Elif Diken
- />Department of Bioengineering, Marmara University, Goztepe, 34722 Istanbul, Turkey
| | - Tugba Ozer
- />Department of Bioengineering, Marmara University, Goztepe, 34722 Istanbul, Turkey
| | - Muzaffer Arikan
- />Department of Genetics, Institute for Experimental Medicine, Istanbul University, Capa, 34093 Istanbul, Turkey
| | - Zeliha Emrence
- />Department of Genetics, Institute for Experimental Medicine, Istanbul University, Capa, 34093 Istanbul, Turkey
| | - Ebru Toksoy Oner
- />Department of Bioengineering, Marmara University, Goztepe, 34722 Istanbul, Turkey
| | - Duran Ustek
- />Department of Medical Genetics, School of Medicine, REMER, Medipol University, 34810 Istanbul, Turkey
| | - Kazim Yalcin Arga
- />Department of Bioengineering, Marmara University, Goztepe, 34722 Istanbul, Turkey
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19
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Mitra S, Das P, Samadder A, Das S, Betai R, Chakrabarti J. Eukaryotic tRNAs fingerprint invertebrates vis-à-vis vertebrates. J Biomol Struct Dyn 2015; 33:2104-20. [PMID: 25581620 DOI: 10.1080/07391102.2014.990925] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
During translation, aminoacyl-tRNA synthetases recognize the identities of the tRNAs to charge them with their respective amino acids. The conserved identities of 58,244 eukaryotic tRNAs of 24 invertebrates and 45 vertebrates in genomic tRNA database were analyzed and their novel features extracted. The internal promoter sequences, namely, A-Box and B-Box, were investigated and evidence gathered that the intervention of optional nucleotides at 17a and 17b correlated with the optimal length of the A-Box. The presence of canonical transcription terminator sequences at the immediate vicinity of tRNA genes was ventured. Even though non-canonical introns had been reported in red alga, green alga, and nucleomorph so far, fairly motivating evidence of their existence emerged in tRNA genes of other eukaryotes. Non-canonical introns were seen to interfere with the internal promoters in two cases, questioning their transcription fidelity. In a first of its kind, phylogenetic constructs based on tRNA molecules delineated and built the trees of the vast and diverse invertebrates and vertebrates. Finally, two tRNA models representing the invertebrates and the vertebrates were drawn, by isolating the dominant consensus in the positional fluctuations of nucleotide compositions.
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Affiliation(s)
- Sanga Mitra
- a Computational Biology Group , Indian Association for the Cultivation of Science , Kolkata 700032 , India
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20
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Amrine KCH, Swingley WD, Ardell DH. tRNA signatures reveal a polyphyletic origin of SAR11 strains among alphaproteobacteria. PLoS Comput Biol 2014; 10:e1003454. [PMID: 24586126 PMCID: PMC3937112 DOI: 10.1371/journal.pcbi.1003454] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Accepted: 12/10/2013] [Indexed: 12/18/2022] Open
Abstract
Molecular phylogenetics and phylogenomics are subject to noise from horizontal gene transfer (HGT) and bias from convergence in macromolecular compositions. Extensive variation in size, structure and base composition of alphaproteobacterial genomes has complicated their phylogenomics, sparking controversy over the origins and closest relatives of the SAR11 strains. SAR11 are highly abundant, cosmopolitan aquatic Alphaproteobacteria with streamlined, A+T-biased genomes. A dominant view holds that SAR11 are monophyletic and related to both Rickettsiales and the ancestor of mitochondria. Other studies dispute this, finding evidence of a polyphyletic origin of SAR11 with most strains distantly related to Rickettsiales. Although careful evolutionary modeling can reduce bias and noise in phylogenomic inference, entirely different approaches may be useful to extract robust phylogenetic signals from genomes. Here we develop simple phyloclassifiers from bioinformatically derived tRNA Class-Informative Features (CIFs), features predicted to target tRNAs for specific interactions within the tRNA interaction network. Our tRNA CIF-based model robustly and accurately classifies alphaproteobacterial genomes into one of seven undisputed monophyletic orders or families, despite great variability in tRNA gene complement sizes and base compositions. Our model robustly rejects monophyly of SAR11, classifying all but one strain as Rhizobiales with strong statistical support. Yet remarkably, conventional phylogenetic analysis of tRNAs classifies all SAR11 strains identically as Rickettsiales. We attribute this discrepancy to convergence of SAR11 and Rickettsiales tRNA base compositions. Thus, tRNA CIFs appear more robust to compositional convergence than tRNA sequences generally. Our results suggest that tRNA-CIF-based phyloclassification is robust to HGT of components of the tRNA interaction network, such as aminoacyl-tRNA synthetases. We explain why tRNAs are especially advantageous for prediction of traits governing macromolecular interactions from genomic data, and why such traits may be advantageous in the search for robust signals to address difficult problems in classification and phylogeny. If gene products work well in the networks of foreign cells, their genes may transfer horizontally between unrelated genomes. What factors dictate the ability to integrate into foreign networks? Different RNAs and proteins must interact specifically in order to function well as a system. For example, tRNA functions are determined by the interactions they have with other macromolecules. We have developed ways to predict, from genomic data alone, how tRNAs distinguish themselves to their specific interaction partners. Here, as proof of concept, we built a robust computational model from these bioinformatic predictions in seven lineages of Alphaproteobacteria. We validated our model by classifying hundreds of diverse alphaproteobacterial taxa and tested it on eight strains of SAR11, a phylogenetically controversial group that is highly abundant in the world's oceans. We found that different strains of SAR11 are more distantly related, both to each other and to mitochondria, than widely believed. We explain conflicting results about SAR11 as an artifact of bias created by the variability in base contents of alphaproteobacterial genomes. While this bias affects tRNAs too, our classifier appears unexpectedly robust to it. More broadly, our results suggest that traits governing macromolecular interactions may be more faithfully vertically inherited than the macromolecules themselves.
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Affiliation(s)
- Katherine C. H. Amrine
- Program in Quantitative and Systems Biology, University of California, Merced, Merced, California, United States of America
| | - Wesley D. Swingley
- Program in Quantitative and Systems Biology, University of California, Merced, Merced, California, United States of America
| | - David H. Ardell
- Program in Quantitative and Systems Biology, University of California, Merced, Merced, California, United States of America
- * E-mail:
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21
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Yona AH, Bloom-Ackermann Z, Frumkin I, Hanson-Smith V, Charpak-Amikam Y, Feng Q, Boeke JD, Dahan O, Pilpel Y. tRNA genes rapidly change in evolution to meet novel translational demands. eLife 2013; 2:e01339. [PMID: 24363105 PMCID: PMC3868979 DOI: 10.7554/elife.01339] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Changes in expression patterns may occur when organisms are presented with new environmental challenges, for example following migration or genetic changes. To elucidate the mechanisms by which the translational machinery adapts to such changes, we perturbed the tRNA pool of Saccharomyces cerevisiae by tRNA gene deletion. We then evolved the deletion strain and observed that the genetic adaptation was recurrently based on a strategic mutation that changed the anticodon of other tRNA genes to match that of the deleted one. Strikingly, a systematic search in hundreds of genomes revealed that anticodon mutations occur throughout the tree of life. We further show that the evolution of the tRNA pool also depends on the need to properly couple translation to protein folding. Together, our observations shed light on the evolution of the tRNA pool, demonstrating that mutation in the anticodons of tRNA genes is a common adaptive mechanism when meeting new translational demands. DOI:http://dx.doi.org/10.7554/eLife.01339.001 Genes contain the blueprints for the proteins that are essential for countless biological functions and processes, and the path that leads from a particular gene to the corresponding protein is long and complex. The genetic information stored in the DNA must first be transcribed to produce a messenger RNA molecule, which then has to be translated to produce a string of amino acids that fold to form a protein. The translation step is performed by a molecular machine called the ribosome, with transfer RNA molecules bringing the amino acids that are needed to make the protein. The information in messenger RNA is stored as a series of letters, with groups of three letters called codons representing the different amino acids. Since there are four letters—A, C, G and U—it is possible to form 64 different codons. And since there are only 20 amino acids, two or more different codons can specify the same amino acid (for example, AGU and AGC both specify serine), and two or more different transfer RNA molecules can take this amino acid to the ribosome. Moreover, some codons are found more often than others in the messenger RNA molecules, so the genes that encode the related transfer RNA molecules are more common than the genes for other transfer RNA molecules. Environmental pressures mean that organisms must adapt to survive, with some genes and proteins increasing in importance, and others becoming less important. Clearly the relative numbers of the different transfer RNA molecules will also need to change to reflect these evolutionary changes, but the details of how this happens were not understood. Now Yona et al. have explored this issue by studying yeast cells that lack a gene for one of the less common transfer RNA molecules (corresponding to the codon AGG, which specifies the amino acid arginine). At first this mutation resulted in slower growth of the yeast cells, but after being allowed to evolve over 200 generations, the rate of growth matched that of a normal strain with all transfer RNA genes. Yona et al. found that the gene for a more common transfer RNA molecule, corresponding to the codon AGA, which also specifies arginine, had mutated to AGG. As a result, the mutated yeast was eventually able to produce proteins as quickly as wild type yeast. Moreover, further experiments showed that the levels of some transfer RNAs are kept deliberately low in order to slow down the production of proteins so as to ensure that the proteins assume their correct structure. But does the way these cells evolved in the lab resemble what happened in nature? To address this question Yona et al. examined a database of transfer RNA sequences from more than 500 species, and found evidence for the same codon-based switching mechanism in many species across the tree of life. DOI:http://dx.doi.org/10.7554/eLife.01339.002
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Affiliation(s)
- Avihu H Yona
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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22
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Maute RL, Dalla-Favera R, Basso K. RNAs with multiple personalities. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:1-13. [DOI: 10.1002/wrna.1193] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 07/19/2013] [Accepted: 07/25/2013] [Indexed: 02/05/2023]
Affiliation(s)
- Roy L. Maute
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center; Columbia University; New York NY USA
- Department of Genetics and Development; Columbia University; New York NY USA
| | - Riccardo Dalla-Favera
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center; Columbia University; New York NY USA
- Department of Genetics and Development; Columbia University; New York NY USA
- Department of Pathology and Cell Biology; Columbia University; New York NY USA
- Department of Microbiology and Immunology; Columbia University; New York NY USA
| | - Katia Basso
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center; Columbia University; New York NY USA
- Department of Pathology and Cell Biology; Columbia University; New York NY USA
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23
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Fischer C, Koblmüller S, Gülly C, Schlötterer C, Sturmbauer C, Thallinger GG. Complete mitochondrial DNA sequences of the threadfin cichlid (Petrochromis trewavasae) and the blunthead cichlid (Tropheus moorii) and patterns of mitochondrial genome evolution in cichlid fishes. PLoS One 2013; 8:e67048. [PMID: 23826193 PMCID: PMC3691221 DOI: 10.1371/journal.pone.0067048] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 05/13/2013] [Indexed: 01/28/2023] Open
Abstract
The cichlid fishes of the East African Great Lakes represent a model especially suited to study adaptive radiation and speciation. With several African cichlid genome projects being in progress, a promising set of closely related genomes is emerging, which is expected to serve as a valuable data base to solve questions on genotype-phenotype relations. The mitochondrial (mt) genomes presented here are the first results of the assembly and annotation process for two closely related but eco-morphologically highly distinct Lake Tanganyika cichlids, Petrochromis trewavasae and Tropheus moorii. The genomic sequences comprise 16,588 bp (P. trewavasae) and 16,590 bp (T. moorii), and exhibit the typical mitochondrial structure, with 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a non-coding control region. Analyses confirmed that the two species are very closely related with an overall sequence similarity of 96%. We analyzed the newly generated sequences in the phylogenetic context of 21 published labroid fish mitochondrial genomes. Consistent with other vertebrates, the D-loop region was found to evolve faster than protein-coding genes, which in turn are followed by the rRNAs; the tRNAs vary greatly in the rate of sequence evolution, but on average evolve the slowest. Within the group of coding genes, ND6 evolves most rapidly. Codon usage is similar among examined cichlid tribes and labroid families; although a slight shift in usage patterns down the gene tree could be observed. Despite having a clearly different nucleotide composition, ND6 showed a similar codon usage. C-terminal ends of Cox1 exhibit variations, where the varying number of amino acids is related to the structure of the obtained phylogenetic tree. This variation may be of functional relevance for Cox1 synthesis.
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Affiliation(s)
- Christoph Fischer
- Institute for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria
| | | | - Christian Gülly
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - Christian Schlötterer
- Institute of Population Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | | | - Gerhard G. Thallinger
- Institute for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria
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Yokobori SI, Kitamura A, Grosjean H, Bessho Y. Life without tRNAArg-adenosine deaminase TadA: evolutionary consequences of decoding the four CGN codons as arginine in Mycoplasmas and other Mollicutes. Nucleic Acids Res 2013; 41:6531-43. [PMID: 23658230 PMCID: PMC3711424 DOI: 10.1093/nar/gkt356] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In most bacteria, two tRNAs decode the four arginine CGN codons. One tRNA harboring a wobble inosine (tRNA(Arg)ICG) reads the CGU, CGC and CGA codons, whereas a second tRNA harboring a wobble cytidine (tRNA(Arg)CCG) reads the remaining CGG codon. The reduced genomes of Mycoplasmas and other Mollicutes lack the gene encoding tRNA(Arg)CCG. This raises the question of how these organisms decode CGG codons. Examination of 36 Mollicute genomes for genes encoding tRNA(Arg) and the TadA enzyme, responsible for wobble inosine formation, suggested an evolutionary scenario where tadA gene mutations first occurred. This allowed the temporary accumulation of non-deaminated tRNA(Arg)ACG, capable of reading all CGN codons. This hypothesis was verified in Mycoplasma capricolum, which contains a small fraction of tRNA(Arg)ACG with a non-deaminated wobble adenosine. Subsets of Mollicutes continued to evolve by losing both the mutated tRNA(Arg)CCG and tadA, and then acquired a new tRNA(Arg)UCG. This permitted further tRNA(Arg)ACG mutations with tRNA(Arg)GCG or its disappearance, leaving a single tRNA(Arg)UCG to decode the four CGN codons. The key point of our model is that the A-to-I deamination activity had to be controlled before the loss of the tadA gene, allowing the stepwise evolution of Mollicutes toward an alternative decoding strategy.
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Affiliation(s)
- Shin-ichi Yokobori
- Laboratory of Extremophiles, Department of Applied Life Sciences, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan.
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Ancient origin of the divergent forms of leucyl-tRNA synthetases in the Halobacteriales. BMC Evol Biol 2012; 12:85. [PMID: 22694720 PMCID: PMC3436685 DOI: 10.1186/1471-2148-12-85] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 04/27/2012] [Indexed: 02/01/2023] Open
Abstract
Background Horizontal gene transfer (HGT) has greatly impacted the genealogical history of many lineages, particularly for prokaryotes, with genes frequently moving in and out of a line of descent. Many genes that were acquired by a lineage in the past likely originated from ancestral relatives that have since gone extinct. During the course of evolution, HGT has played an essential role in the origin and dissemination of genetic and metabolic novelty. Results Three divergent forms of leucyl-tRNA synthetase (LeuRS) exist in the archaeal order Halobacteriales, commonly known as haloarchaea. Few haloarchaeal genomes have the typical archaeal form of this enzyme and phylogenetic analysis indicates it clusters within the Euryarchaeota as expected. The majority of sequenced halobacterial genomes possess a bacterial form of LeuRS. Phylogenetic reconstruction puts this larger group of haloarchaea at the base of the bacterial domain. The most parsimonious explanation is that an ancient transfer of LeuRS took place from an organism related to the ancestor of the bacterial domain to the haloarchaea. The bacterial form of LeuRS further underwent gene duplications and/or gene transfers within the haloarchaea, with some genomes possessing two distinct types of bacterial LeuRS. The cognate tRNALeu also reveals two distinct clusters for the haloarchaea; however, these tRNALeu clusters do not coincide with the groupings found in the LeuRS tree, revealing that LeuRS evolved independently of its cognate tRNA. Conclusions The study of leucyl-tRNA synthetase in haloarchaea illustrates the importance of gene transfer originating in lineages that went extinct since the transfer occurred. The haloarchaeal LeuRS and tRNALeu did not co-evolve.
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Krammer H, Möller FM, Braun D. Thermal, autonomous replicator made from transfer RNA. PHYSICAL REVIEW LETTERS 2012; 108:238104. [PMID: 23003995 DOI: 10.1103/physrevlett.108.238104] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Indexed: 06/01/2023]
Abstract
Evolving systems rely on the storage and replication of genetic information. Here we present an autonomous, purely thermally driven replication mechanism. A pool of hairpin molecules, derived from transfer RNA replicates the succession of a two-letter code. Energy is first stored thermally in metastable hairpins. Thereafter, energy is released by a highly specific and exponential replication with a duplication time of 30 s, which is much faster than the tendency to produce false positives in the absence of template. Our experiments propose a physical rather than a chemical scenario for the autonomous replication of protein encoding information in a disequilibrium setting.
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Affiliation(s)
- Hubert Krammer
- Systems Biophysics, Physics Department, Center for Nanoscience, Ludwig Maximilians Universität München, Amalienstrasse 54, 80799 München, Germany
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Jühling F, Pütz J, Bernt M, Donath A, Middendorf M, Florentz C, Stadler PF. Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements. Nucleic Acids Res 2011; 40:2833-45. [PMID: 22139921 PMCID: PMC3326299 DOI: 10.1093/nar/gkr1131] [Citation(s) in RCA: 169] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Transfer RNAs (tRNAs) are present in all types of cells as well as in organelles. tRNAs of animal mitochondria show a low level of primary sequence conservation and exhibit 'bizarre' secondary structures, lacking complete domains of the common cloverleaf. Such sequences are hard to detect and hence frequently missed in computational analyses and mitochondrial genome annotation. Here, we introduce an automatic annotation procedure for mitochondrial tRNA genes in Metazoa based on sequence and structural information in manually curated covariance models. The method, applied to re-annotate 1876 available metazoan mitochondrial RefSeq genomes, allows to distinguish between remaining functional genes and degrading 'pseudogenes', even at early stages of divergence. The subsequent analysis of a comprehensive set of mitochondrial tRNA genes gives new insights into the evolution of structures of mitochondrial tRNA sequences as well as into the mechanisms of genome rearrangements. We find frequent losses of tRNA genes concentrated in basal Metazoa, frequent independent losses of individual parts of tRNA genes, particularly in Arthropoda, and wide-spread conserved overlaps of tRNAs in opposite reading direction. Direct evidence for several recent Tandem Duplication-Random Loss events is gained, demonstrating that this mechanism has an impact on the appearance of new mitochondrial gene orders.
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Affiliation(s)
- Frank Jühling
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany
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Giegé R, Jühling F, Pütz J, Stadler P, Sauter C, Florentz C. Structure of transfer RNAs: similarity and variability. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:37-61. [DOI: 10.1002/wrna.103] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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29
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Fabret C, Dervyn E, Dalmais B, Guillot A, Marck C, Grosjean H, Noirot P. Life without the essential bacterial tRNAIle2-lysidine synthetase TilS: a case of tRNA gene recruitment in Bacillus subtilis. Mol Microbiol 2011; 80:1062-74. [DOI: 10.1111/j.1365-2958.2011.07630.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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