1
|
On the Base Composition of Transposable Elements. Int J Mol Sci 2022; 23:ijms23094755. [PMID: 35563146 PMCID: PMC9099904 DOI: 10.3390/ijms23094755] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/22/2022] [Accepted: 04/23/2022] [Indexed: 01/27/2023] Open
Abstract
Transposable elements exhibit a base composition that is often different from the genomic average and from hosts’ genes. The most common compositional bias is towards Adenosine and Thymine, although this bias is not universal, and elements with drastically different base composition can coexist within the same genome. The AT-richness of transposable elements is apparently maladaptive because it results in poor transcription and sub-optimal translation of proteins encoded by the elements. The cause(s) of this unusual base composition remain unclear and have yet to be investigated. Here, I review what is known about the nucleotide content of transposable elements and how this content can affect the genome of their host as well as their own replication. The compositional bias of transposable elements could result from several non-exclusive processes including horizontal transfer, mutational bias, and selection. It appears that mutation alone cannot explain the high AT-content of transposons and that selection plays a major role in the evolution of the compositional bias. The reason why selection would favor a maladaptive nucleotide content remains however unexplained and is an area of investigation that clearly deserves attention.
Collapse
|
2
|
Ruggiero RP, Boissinot S. Variation in base composition underlies functional and evolutionary divergence in non-LTR retrotransposons. Mob DNA 2020; 11:14. [PMID: 32280379 PMCID: PMC7140322 DOI: 10.1186/s13100-020-00209-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 03/24/2020] [Indexed: 12/03/2022] Open
Abstract
Background Non-LTR retrotransposons often exhibit base composition that is markedly different from the nucleotide content of their host’s gene. For instance, the mammalian L1 element is AT-rich with a strong A bias on the positive strand, which results in a reduced transcription. It is plausible that the A-richness of mammalian L1 is a self-regulatory mechanism reflecting a trade-off between transposition efficiency and the deleterious effect of L1 on its host. We examined if the A-richness of L1 is a general feature of non-LTR retrotransposons or if different clades of elements have evolved different nucleotide content. We also investigated if elements belonging to the same clade evolved towards different base composition in different genomes or if elements from different clades evolved towards similar base composition in the same genome. Results We found that non-LTR retrotransposons differ in base composition among clades within the same host but also that elements belonging to the same clade differ in base composition among hosts. We showed that nucleotide content remains constant within the same host over extended period of evolutionary time, despite mutational patterns that should drive nucleotide content away from the observed base composition. Conclusions Our results suggest that base composition is evolving under selection and may be reflective of the long-term co-evolution between non-LTR retrotransposons and their host. Finally, the coexistence of elements with drastically different base composition suggests that these elements may be using different strategies to persist and multiply in the genome of their host.
Collapse
Affiliation(s)
- Robert P Ruggiero
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates PO 129188
| | - Stéphane Boissinot
- New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates PO 129188
| |
Collapse
|
3
|
Serrano-Solís V, Toscano Soares PE, de Farías ST. Genomic Signatures Among Acanthamoeba polyphaga Entoorganisms Unveil Evidence of Coevolution. J Mol Evol 2018; 87:7-15. [PMID: 30456441 DOI: 10.1007/s00239-018-9877-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/09/2018] [Indexed: 11/30/2022]
Abstract
The definition of a genomic signature (GS) is "the total net response to selective pressure". Recent isolation and sequencing of naturally occurring organisms, hereby named entoorganisms, within Acanthamoeba polyphaga, raised the hypothesis of a common genomic signature despite their diverse and unrelated evolutionary origin. Widely accepted and implemented tests for GS detection are oligonucleotide relative frequencies (OnRF) and relative codon usage (RCU) surveys. A common pattern and strong correlations were unveiled from OnRFs among A. polyphaga's Mimivirus and virophage Sputnik. RCU showed a common A-T bias at third codon position. We expanded tests to the amoebal mitochondrial genome and amoeba-resistant bacteria, achieving strikingly coherent results to the aforementioned viral analyses. The GSs in these entoorganisms of diverse evolutionary origin are coevolutionarily conserved within an intracellular environment that provides sanctuary for species of ecological and biomedical relevance.
Collapse
Affiliation(s)
- Víctor Serrano-Solís
- Laboratório de Genética Evolutiva Paulo Leminsk, Departamento de Biologia Molecular, Centro de Ciencias Exatas e da Natureza, Universidade Federal da Paraíba, João Pessoa, Brazil.
| | - Paulo Eduardo Toscano Soares
- Laboratório de Genética Evolutiva Paulo Leminsk, Departamento de Biologia Molecular, Centro de Ciencias Exatas e da Natureza, Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Sávio T de Farías
- Laboratório de Genética Evolutiva Paulo Leminsk, Departamento de Biologia Molecular, Centro de Ciencias Exatas e da Natureza, Universidade Federal da Paraíba, João Pessoa, Brazil
| |
Collapse
|
4
|
Luo XL, Xu JG, Ye CY. Analysis of synonymous codon usage inShigella flexneri2a strain 301 and otherShigellaandEscherichia colistrains. Can J Microbiol 2011; 57:1016-23. [DOI: 10.1139/w11-095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study, we analysed synonymous codon usage in Shigella flexneri 2a strain 301 (Sf301) and performed a comparative analysis of synonymous codon usage patterns in Sf301 and other strains of Shigella and Escherichia coli . Although there was a significant variety in codon usage bias among different Sf301 genes, there was a slight but observable codon usage bias that could primarily be attributable to mutational pressure and translational selection. In addition, the relative abundance of dinucleotides in Sf301 was observed to be independent of the overall base composition but was still caused by differential mutational pressure; this also shaped codon usage. By comparing the relative synonymous codon usage values across different Shigella and E. coli strains, we suggested that the synonymous codon usage pattern in the Shigella genomes was strain specific. This study represents a comprehensive analysis of Shigella codon usage patterns and provides a basic understanding of the mechanisms underlying codon usage bias.
Collapse
Affiliation(s)
- Xue Lian Luo
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, People’s Republic of China
| | - Jian Guo Xu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, People’s Republic of China
| | - Chang Yun Ye
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing 102206, People’s Republic of China
| |
Collapse
|
5
|
NYEO SULONG, YU JUIPING. LENGTH DISTRIBUTIONS OF SIMPLE TANDEM REPEATS IN GENOMES. J BIOL SYST 2011. [DOI: 10.1142/s0218339007002246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The length distributions of simple tandem repeats in the genomes of several organisms are evaluated and found to exhibit long-range correlations in A and T nucleotide bases related repeats for most eukaryotes. In particular, the length distributions of the mononucleotide A/T repeat units have longer tails than those of the C/G repeat units. Also, the length distributions of the dinucleotide repeat unit CG show a simple monotonously fast decreasing behavior, while those of repeat units AT, AG and AC have complicated structures at larger repeat lengths, especially for human, mouse and rat chromosomes. These distributive behaviors are due to the CpG deficiency in different genomes with different methylation activities. Especially, methyltransferases in vertebrates appear to methylate specifically the cytosine in CpG dinucleotides, and the methylated cytosines is prone to mutate to thymine by spontaneous deamination. The dinucleotide CpG would gradually decay into TpG and CpA. In addition, there is a peak in the distributions of repeat unit A at repeat-repeat separation 153 nt for humans and chimpanzees. We show that the long-tail behavior of mononucleotide repeat unit A and the peak at repeat separation 153 nt are due to the interspersed repetitive DNA sequences in humans and chimpanzees.
Collapse
Affiliation(s)
- SU-LONG NYEO
- Department of Physics, National Cheng Kung University, Tainan, Taiwan 701, R.O.C
| | - JUI-PING YU
- Department of Physics, National Cheng Kung University, Tainan, Taiwan 701, R.O.C
| |
Collapse
|
6
|
Infra- and Transspecific Clues to Understanding the Dynamics of Transposable Elements. TRANSPOSONS AND THE DYNAMIC GENOME 2009. [DOI: 10.1007/7050_2009_044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
7
|
The correlation between recombination rate and dinucleotide bias in Drosophila melanogaster. J Mol Evol 2008; 67:358-67. [PMID: 18797953 DOI: 10.1007/s00239-008-9150-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Revised: 06/12/2008] [Accepted: 06/23/2008] [Indexed: 10/21/2022]
Abstract
Revealing how recombination affects genomic sequence is of great significance to our understanding of genome evolution. The present paper focuses on the correlation between recombination rate and dinucleotide bias in Drosophila melanogaster genome. Our results show that the overall dinucleotide bias is positively correlated with recombination rate for genomic sequences including untranslated regions, introns, intergenic regions, and coding sequences. The correlation patterns of individual dinucleotide biases with recombination rate are presented. Possible mechanisms of interaction between recombination and dinucleotide bias are discussed. Our data indicate that there may be a genome-wide universal mechanism acting between recombination rate and dinucleotide bias, which is likely to be neighbor-dependent biased gene conversion.
Collapse
|
8
|
Identification of prophages in bacterial genomes by dinucleotide relative abundance difference. PLoS One 2007; 2:e1193. [PMID: 18030328 PMCID: PMC2075365 DOI: 10.1371/journal.pone.0001193] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2007] [Accepted: 10/27/2007] [Indexed: 12/23/2022] Open
Abstract
Background Prophages are integrated viral forms in bacterial genomes that have been found to contribute to interstrain genetic variability. Many virulence-associated genes are reported to be prophage encoded. Present computational methods to detect prophages are either by identifying possible essential proteins such as integrases or by an extension of this technique, which involves identifying a region containing proteins similar to those occurring in prophages. These methods suffer due to the problem of low sequence similarity at the protein level, which suggests that a nucleotide based approach could be useful. Methodology Earlier dinucleotide relative abundance (DRA) have been used to identify regions, which deviate from the neighborhood areas, in genomes. We have used the difference in the dinucleotide relative abundance (DRAD) between the bacterial and prophage DNA to aid location of DNA stretches that could be of prophage origin in bacterial genomes. Prophage sequences which deviate from bacterial regions in their dinucleotide frequencies are detected by scanning bacterial genome sequences. The method was validated using a subset of genomes with prophage data from literature reports. A web interface for prophage scan based on this method is available at http://bicmku.in:8082/prophagedb/dra.html. Two hundred bacterial genomes which do not have annotated prophages have been scanned for prophage regions using this method. Conclusions The relative dinucleotide distribution difference helps detect prophage regions in genome sequences. The usefulness of this method is seen in the identification of 461 highly probable loci pertaining to prophages which have not been annotated so earlier. This work emphasizes the need to extend the efforts to detect and annotate prophage elements in genome sequences.
Collapse
|
9
|
Bui QT, Delaurière L, Casse N, Nicolas V, Laulier M, Chénais B. Molecular characterization and phylogenetic position of a new mariner-like element in the coastal crab, Pachygrapsus marmoratus. Gene 2007; 396:248-56. [PMID: 17490833 DOI: 10.1016/j.gene.2007.03.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2006] [Revised: 03/01/2007] [Accepted: 03/12/2007] [Indexed: 11/17/2022]
Abstract
Mariner-like elements (MLEs) are class-II transposable elements that move within the genome of their hosts by means of a DNA-mediated "cut and paste" mechanism. MLEs have been identified in several organisms, from most of the phyla. Nevertheless, only a few of the sequences characterized contain an intact open reading frame. Investigation of the genome of a coastal crab, Pachygrapsus marmoratus, has identified nine Pacmmar elements, two of which have an open reading frame encoding a putatively functional transposase. Nucleic acid analyses and comparison with the previous data showed that the GC contents of MLEs derived from coastal organisms such as P. marmoratus are significantly higher than those of terrestrial MLEs and significantly lower than those of hydrothermal ones. Furthermore, molecular phylogeny analyses have shown that Pacmmar elements constitute a new lineage of the irritans subfamily within the mariner family.
Collapse
Affiliation(s)
- Quynh-Trang Bui
- Laboratoire de Biologie et Génétique Evolutive (EA3265), Avenue Olivier Messiaen, 72085 Le Mans cedex, France
| | | | | | | | | | | |
Collapse
|
10
|
Andrieu O, Fiston AS, Anxolabéhère D, Quesneville H. Detection of transposable elements by their compositional bias. BMC Bioinformatics 2004; 5:94. [PMID: 15251040 PMCID: PMC497039 DOI: 10.1186/1471-2105-5-94] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2004] [Accepted: 07/13/2004] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transposable elements (TE) are mobile genetic entities present in nearly all genomes. Previous work has shown that TEs tend to have a different nucleotide composition than the host genes, either considering codon usage bias or dinucleotide frequencies. We show here how these compositional differences can be used as a tool for detection and analysis of TE sequences. RESULTS We compared the composition of TE sequences and host gene sequences using probabilistic models of nucleotide sequences. We used hidden Markov models (HMM), which take into account the base composition of the sequences (occurrences of words n nucleotides long, with n ranging here from 1 to 4) and the heterogeneity between coding and non-coding parts of sequences. We analyzed three sets of sequences containing class I TEs, class II TEs and genes respectively in three species: Drosophila melanogaster, Caenorhabditis elegans and Arabidopsis thaliana. Each of these sets had a distinct, homogeneous composition, enabling us to distinguish between the two classes of TE and the genes. However the particular base composition of the TEs differed in the three species studied. CONCLUSIONS This approach can be used to detect and annotate TEs in genomic sequences and complements the current homology-based TE detection methods. Furthermore, the HMM method is able to identify the parts of a sequence in which the nucleotide composition resembles that of a coding region of a TE. This is useful for the detailed annotation of TE sequences, which may contain an ancient, highly diverged coding region that is no longer fully functional.
Collapse
Affiliation(s)
- Olivier Andrieu
- Laboratoire Dynamique du Génome et Évolution, Institut Jacques Monod, Tour 42-32, 5 place Jussieu, 75251 PARIS cedex 05, FRANCE
| | - Anna-Sophie Fiston
- Laboratoire Dynamique du Génome et Évolution, Institut Jacques Monod, Tour 42-32, 5 place Jussieu, 75251 PARIS cedex 05, FRANCE
| | - Dominique Anxolabéhère
- Laboratoire Dynamique du Génome et Évolution, Institut Jacques Monod, Tour 42-32, 5 place Jussieu, 75251 PARIS cedex 05, FRANCE
| | - Hadi Quesneville
- Laboratoire Dynamique du Génome et Évolution, Institut Jacques Monod, Tour 42-32, 5 place Jussieu, 75251 PARIS cedex 05, FRANCE
| |
Collapse
|
11
|
Lerat E, Rizzon C, Biémont C. Sequence divergence within transposable element families in the Drosophila melanogaster genome. Genome Res 2003; 13:1889-96. [PMID: 12869581 PMCID: PMC403780 DOI: 10.1101/gr.827603] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The availability of the sequenced Drosophila melanogaster genome provides an opportunity to study sequence variation between copies within transposable element families. In this study,we analyzed the 624 copies of 22 transposable element (TE) families (14 LTR retrotransposons, five non-LTR retrotransposons, and three transposons). LTR and non-LTR retrotransposons possessed far fewer divergent elements than the transposons,suggesting that the difference depends on the transposition mechanism. However,there was not a continuous range of divergence of the copies in each class,which were either very similar to the canonical elements,or very divergent from them. This sequence homogeneity among TE family copies matches the theoretical models of the dynamics of these repeated sequences. The sequenced Drosophila genome thus appears to be composed of a mixture of TEs that are still active and of ancient relics that have degenerated and the distribution of which along the chromosomes results from natural selection. This clearly demonstrates that the TEs are highly active within the genome,suggesting that the genetic variability of the Drosophila genome is still being renewed by the action of TEs.
Collapse
Affiliation(s)
- Emmanuelle Lerat
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, 69622 Villeurbanne cedex, France
| | | | | |
Collapse
|