リケラボ論文検索は、全国の大学リポジトリにある学位論文・教授論文を一括検索できる論文検索サービスです。

リケラボ 全国の大学リポジトリにある学位論文・教授論文を一括検索するならリケラボ論文検索大学・研究所にある論文を検索できる

リケラボ 全国の大学リポジトリにある学位論文・教授論文を一括検索するならリケラボ論文検索大学・研究所にある論文を検索できる

大学・研究所にある論文を検索できる 「Monotreme-Specific Conserved Putative Proteins Derived from Retroviral Reverse Transcriptase」の論文概要。リケラボ論文検索は、全国の大学リポジトリにある学位論文・教授論文を一括検索できる論文検索サービスです。

コピーが完了しました

URLをコピーしました

論文の公開元へ論文の公開元へ
書き出し

Monotreme-Specific Conserved Putative Proteins Derived from Retroviral Reverse Transcriptase

Kitao, Koichi Miyazawa, Takayuki Nakagawa, So 京都大学 DOI:10.1093/ve/veac084

2022

概要

Endogenous retroviruses (ERVs) have played an essential role in the evolution of mammals. ERV-derived genes are reported in the therians, many of which are involved in placental development; however, the contribution of the ERV-derived genes in monotremes, which are oviparous mammals, remains to be uncovered. Here, we conducted a comprehensive search for possible ERV-derived genes in platypus and echidna genomes and identified three reverse transcriptase-like genes named RTOM1, RTOM2, and RTOM3 clustered in the GRIP2 intron. Comparative genomic analyses revealed that RTOM1, RTOM2, and RTOM3 are strongly conserved and are under purifying selection between these species. These could be generated by tandem duplications before the divergence of platypus and echidna. All RTOM transcripts were specifically expressed in the testis, possibly suggesting their physiological importance. This is the first study reporting monotreme-specific de novo gene candidates derived from ERVs, which provides new insights into the unique evolution of monotremes.

この論文で使われている画像

参考文献

Best, S. et al. (1996) ‘Positional Cloning of the Mouse Retrovirus

Restriction Gene Fvl’, Nature, 382: 826–9.

Eddy, S. R. (2011) ‘Accelerated Profile HMM Searches’, PLoS Computational Biology, 7: e1002195.

Emerson, R. O., and Thomas, J. H. (2011) ‘Gypsy and the Birth of the

SCAN Domain’, Journal of Virology, 85: 12043–52.

Finn, R. D., Clements, J., and Eddy, S. R. (2011) ‘HMMER Web Server:

Interactive Sequence Similarity Searching,’ Nucleic Acids Research,

39(suppl): W29–37.

Heidmann, O. et al. (2017) ‘HEMO, an Ancestral Endogenous Retroviral Envelope Protein Shed in the Blood of Pregnant Women and

Expressed in Pluripotent Stem Cells and Tumors’, Proceedings of the

National Academy of Sciences, 114: E6642–51.

Hoang, D. T. et al. (2018) ‘UFBoot2: Improving the Ultrafast Bootstrap

Approximation’, Molecular Biology and Evolution, 35: 518–22.

Ikeda, H., and Sugimura, H. (1989) ‘Fv-4 Resistance Gene: A Truncated

Endogenous Murine Leukemia Virus with Ecotropic Interference

Properties’, Journal of Virology, 63: 5405–12.

Imakawa, K., and Nakagawa, S. (2017) ‘The Phylogeny of Placental Evolution through Dynamic Integrations of Retrotransposons’, Progress in Molecular Biology and Translational Science, 145:

89–109.

Imakawa, K., Nakagawa, S., and Miyazawa, T. (2015) ‘Baton Pass

Hypothesis: Successive Incorporation of Unconserved Endogenous Retroviral Genes for Placentation during Mammalian Evolution’, Genes to Cells, 20: 771–88.

Johnson, W. E. (2019) ‘Origins and Evolutionary Consequences of

Ancient Endogenous Retroviruses’, Nature Reviews. Microbiology,

17: 355–70.

Katoh, K., and Standley, D. M. (2013) ‘MAFFT Multiple Sequence

Alignment Software Version 7: Improvements in Performance and

Usability’, Molecular Biology and Evolution, 30: 772–80.

Downloaded from https://academic.oup.com/ve/article/8/2/veac084/6691461 by Kyoto University user on 24 November 2022

Expression analyses

Blaise, S. et al. (2003) ‘Genomewide Screening for Fusogenic Human

Endogenous Retrovirus Envelopes Identifies Syncytin 2, a Gene

Conserved on Primate Evolution’, Proceedings of the National

Academy of Sciences of the United States of America, 100: 13013–8.

Blond, J.-L. et al. (2000) ‘An Envelope Glycoprotein of the Human

Endogenous Retrovirus HERV-W Is Expressed in the Human Placenta and Fuses Cells Expressing the Type D Mammalian Retrovirus Receptor’, Journal of Virology, 74: 3321–9.

Boso, G. et al. (2021) ‘The Oldest Co-opted Gag Gene of a Human

Endogenous Retrovirus Shows Placenta-Specific Expression and Is

Upregulated in Diffuse Large B-Cell Lymphomas’, Molecular Biology

and Evolution, 38: 5453–71.

Camacho, C. et al. (2009) ‘BLAST+: Architecture and Applications’,

BMC Bioinformatics, 10: 421.

́ T. (2009)

Capella-Gutierrez,

S., Silla-Martínez, J. M., and Gabaldon,

‘trimAl: A Tool for Automated Alignment Trimming in Large-Scale

Phylogenetic Analyses’, Bioinformatics, 25: 1972–3.

Charlier, C. et al. (2001) ‘Human–Ovine Comparative Sequencing of

a 250-kb Imprinted Domain Encompassing the Callipyge (Clpg)

Locus and Identification of Six Imprinted Transcripts: DLK1,

DAT, GTL2, PEG11, antiPEG11, and MEG8’, Genome Research, 11:

850–62.

Chen, S. et al. (2018) ‘fastp: An Ultra-fast All-in-One FASTQ Preprocessor’, Bioinformatics, 34: i884–90.

Dupressoir, A. et al. (2009) ‘Syncytin-A Knockout Mice Demonstrate the Critical Role in Placentation of a Fusogenic, Endogenous Retrovirus-Derived, Envelope Gene’, Proceedings of the

National Academy of Sciences of the United States of America, 106:

12127–32.

Dupressoir, A. et al. (2011) ‘A Pair of Co-opted Retroviral Envelope Syncytin Genes Is Required for Formation of the Two-layered Murine

Placental Syncytiotrophoblast’, Proceedings of the National Academy

of Sciences, 108: E1164–73.

A Self-archived copy in

Kyoto University Research Information Repository

https://repository.kulib.kyoto-u.ac.jp

K. Kitao et al.

Naville, M. et al. (2016) ‘Not so Bad after All: Retroviruses and Long

Terminal Repeat Retrotransposons as a Source of New Genes in

Vertebrates’, Clinical Microbiology and Infection, 22: 312–23.

Nei, M., and Gojobori, T. (1986) ‘Simple Methods for Estimating the Numbers of Synonymous and Nonsynonymous

Nucleotide Substitutions’, Molecular Biology and Evolution, 3:

418–26.

Ono, R. et al. (2001) ‘A Retrotransposon-Derived Gene, PEG10, Is a

Novel Imprinted Gene Located on Human Chromosome 7aq21’,

Genomics, 73: 232–7.

Perelman, P. et al. (2011) ‘A Molecular Phylogeny of Living Primates’,

PLoS Genetics, 7: 1–17.

Pertea, M. et al. (2016) ‘Transcript-Level Expression Analysis of RNAseq Experiments with HISAT, StringTie and Ballgown’, Nature

Protocols, 11: 1650–67.

Rice, P., Longden, L., and Bleasby, A. (2000) ‘EMBOSS: The European

Molecular Biology Open Software Suite’, Trends in Genetics, 16:

276–7.

Sarafianos, S. G. et al. (2009) ‘Structure and Function of HIV-1

Reverse Transcriptase: Molecular Mechanisms of Polymerization and Inhibition’, Journal of Molecular Biology, 385:

693–713.

Stothard, P. (2000) ‘The Sequence Manipulation Suite: JavaScript Programs for Analyzing and Formatting Protein and DNA Sequences’,

BioTechniques, 28: 1102–4.

Thorvaldsdottir,

H., Robinson, J. T., and Mesirov, J. P. (2013) ‘Integrative Genomics Viewer (IGV): High-Performance Genomics Data

Visualization and Exploration’, Briefings in Bioinformatics, 14:

178–92.

Ueda, M. T. et al. (2020) ‘Comprehensive Genomic Analysis

Reveals Dynamic Evolution of Endogenous Retroviruses that

Code for Retroviral-like Protein Domains’, Mobile DNA, 11:

29.

Wang, J., and Han, G. Z. (2020) ‘Frequent Retroviral Gene Co-option

during the Evolution of Vertebrates’, Molecular Biology and Evolution, 37: 3232–42.

Warren, W. C. et al. (2008) ‘Genome Analysis of the Platypus Reveals

Unique Signatures of Evolution’, Nature, 453: 175–83.

Zhou, Y. et al. (2021) ‘Platypus and Echidna Genomes

Reveal Mammalian Biology and Evolution’, Nature, 592:

756–62.

Downloaded from https://academic.oup.com/ve/article/8/2/veac084/6691461 by Kyoto University user on 24 November 2022

Kent, W. J. (2002) ‘BLAT—The BLAST-Like Alignment Tool’, Genome

Research, 12: 656–64.

Kiełbasa, S. M. et al. (2011) ‘Adaptive Seeds Tame Genomic Sequence

Comparison’, Genome Research, 21: 487–93.

Kjeldbjerg, A. L. et al. (2008) ‘Gene Conversion and Purifying Selection of a Placenta-Specific ERV-V Envelope Gene during Simian

Evolution’, BMC Evolutionary Biology, 8: 266.

Kovaka, S. et al. (2019) ‘Transcriptome Assembly from Long-read

RNA-seq Alignments with StringTie2’, Genome Biology, 20: 278.

Kumar, S. et al. (2018) ‘MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms’, Molecular Biology and

Evolution, 35: 1547–9.

Larder, B. A. et al. (1987) ‘Site-Specific Mutagenesis of AIDS Virus

Reverse Transcriptase’, Nature, 327: 716–7.

Li, W., and Godzik, A. (2006) ‘Cd-hit: A Fast Program for Clustering

and Comparing Large Sets of Protein or Nucleotide Sequences’,

Bioinformatics, 22: 1658–9.

Llorens, C. et al. (2011) ‘The Gypsy Database (Gydb) of Mobile Genetic

Elements: Release 2.0’, Nucleic Acids Research, 39(Database):

D70–74.

Llorens, C. et al. (2009) ‘Network Dynamics of Eukaryotic LTR

Retroelements beyond Phylogenetic Trees’, Biology Direct, 4: 41.

Marco, A., and Marin, I. (2009) ‘CGIN1: A Retroviral Contribution to

Mammalian Genomes’, Molecular Biology and Evolution, 26: 2167–70.

Marin, R. et al. (2017) ‘Convergent Origination of a Drosophila-like

Dosage Compensation Mechanism in a Reptile Lineage’, Genome

Research, 27: 1974–87.

Matsui, T. et al. (2011) ‘SASPase Regulates Stratum Corneum Hydration through Profilaggrin-to-Filaggrin Processing’, EMBO Molecular

Medicine, 3: 320–33.

Mi, S. et al. (2000) ‘Syncytin Is a Captive Retroviral Envelope Protein

Involved in Human Placental Morphogenesis’, Nature, 403: 785–9.

Minh, B. Q. et al. (2020) ‘IQ-TREE 2: New Models and Efficient Methods

for Phylogenetic Inference in the Genomic Era’, Molecular Biology

and Evolution, 37: 1530–4.

Mistry, J. et al. (2021) ‘Pfam: The Protein Families Database in 2021’,

Nucleic Acids Research, 49: D412–9.

Nakagawa, S., and Takahashi, M. U. (2016) ‘gEVE: A Genomebased Endogenous Viral Element Database Provides Comprehensive Viral Protein-Coding Sequences in Mammalian Genomes’,

Database, 2016: 1–8.

...

参考文献をもっと見る

全国の大学の
卒論・修論・学位論文

一発検索!

この論文の関連論文を見る