Widespread occurrence of organelle genome-encoded 5S rRNAs including permuted molecules

Nucleic Acids Research - Tập 42 Số 22 - Trang 13764-13777 - 2014
Matus Valach1, Gertraud Burger1, Michael W. Gray2, B. Franz Lang1
1Department of Biochemistry and Robert-Cedergren Centre of Bioinformatics and Genomics, Université de Montréal, Montréal, QC, H3C 3J7, Canada
2Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4B2, Canada

Tóm tắt

Từ khóa


Tài liệu tham khảo

Ban, 2000, The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution, Science, 289, 905, 10.1126/science.289.5481.905

Zhang, 1999, Single gene circles in dinoflagellate chloroplast genomes, Nature, 400, 155, 10.1038/22099

Bullerwell, 2003, Discovery and characterization of Acanthamoeba castellanii mitochondrial 5S rRNA, RNA, 9, 287, 10.1261/rna.2170803

Sharma, 2009, Structure of a mitochondrial ribosome with minimal RNA, Proc. Natl. Acad. Sci. U.S.A., 106, 9637, 10.1073/pnas.0901631106

Greber, 2014, Architecture of the large subunit of the mammalian mitochondrial ribosome, Nature, 505, 515, 10.1038/nature12890

Greber, 2014, The complete structure of the large subunit of the mammalian mitochondrial ribosome, Nature, 10.1038/nature13895

Amunts, 2014, Structure of the yeast mitochondrial large ribosomal subunit, Science, 343, 1485, 10.1126/science.1249410

Brown, 2014, Structure of the large ribosomal subunit from human mitochondria, Science, 346, 718, 10.1126/science.1258026

Sharma, 2003, Structure of the mammalian mitochondrial ribosome reveals an expanded functional role for its component proteins, Cell, 115, 97, 10.1016/S0092-8674(03)00762-1

Yoshionari, 1994, Existence of nuclear-encoded 5S-rRNA in bovine mitochondria, FEBS Lett., 338, 137, 10.1016/0014-5793(94)80351-X

Magalhães, 1998, Evidence for the presence of 5S rRNA in mammalian mitochondria, Mol. Biol. Cell, 9, 2375, 10.1091/mbc.9.9.2375

Smirnov, 2011, Biological significance of 5S rRNA import into human mitochondria: role of ribosomal protein MRP-L18, Genes Dev., 25, 1289, 10.1101/gad.624711

Burger, 1995, The mitochondrial DNA of the amoeboid protozoon, Acanthamoeba castellanii: complete sequence, gene content and genome organization, J. Mol. Biol., 245, 522, 10.1006/jmbi.1994.0043

Eddy, 1994, RNA sequence analysis using covariance models, Nucleic Acids Res., 22, 2079, 10.1093/nar/22.11.2079

Nawrocki, 2013, Infernal 1.1: 100-fold faster RNA homology searches, Bioinformatics, 29, 2933, 10.1093/bioinformatics/btt509

Burge, 2013, Rfam 11.0: 10 years of RNA families, Nucleic Acids Res., 41, D226, 10.1093/nar/gks1005

Lang, 1996, A 5 S rRNA gene is present in the mitochondrial genome of the protist Reclinomonas americana but is absent from red algal mitochondrial DNA, J. Mol. Biol., 261, 607, 10.1006/jmbi.1996.0486

Edgar, 2004, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res., 32, 1792, 10.1093/nar/gkh340

Smith, 1994, The genetic data environment an expandable GUI for multiple sequence analysis, Comput. Appl. Biosci., 10, 671

Bernhart, 2008, RNAalifold: improved consensus structure prediction for RNA alignments, BMC Bioinformatics, 9, 474, 10.1186/1471-2105-9-474

Gerstein, 1994, Volume changes in protein evolution, J. Mol. Biol., 236, 1067, 10.1016/0022-2836(94)90012-4

Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 25, 3389, 10.1093/nar/25.17.3389

Grigoriev, 2012, The genome portal of the Department of Energy Joint Genome Institute, Nucleic Acids Res., 40, D26, 10.1093/nar/gkr947

Lorenz, 2011, ViennaRNA Package 2.0, Algorithms Mol. Biol., 6, 26, 10.1186/1748-7188-6-26

Lai, 2012, R-CHIE: a web server and R package for visualizing RNA secondary structures, Nucleic Acids Res., 40, e95, 10.1093/nar/gks241

Weinberg, 2011, R2R - software to speed the depiction of aesthetic consensus RNA secondary structures, BMC Bioinformatics, 12, 3, 10.1186/1471-2105-12-3

Burger, 2013, Strikingly bacteria-like and gene-rich mitochondrial genomes throughout jakobid protists, Genome Biol. Evol., 5, 418, 10.1093/gbe/evt008

Ewing, 1998, Base-calling of automated sequencer traces using Phred. I. Accuracy assessment, Genome Res., 8, 175, 10.1101/gr.8.3.175

Ewing, 1998, Base-calling of automated sequencer traces using Phred. II. Error probabilities, Genome Res., 8, 186, 10.1101/gr.8.3.186

Lang, 2007, Purification of mitochondrial and plastid DNA, Nat. Protoc., 2, 652, 10.1038/nprot.2007.58

Burger, 2007, Sequencing complete mitochondrial and plastid genomes, Nat. Protoc., 2, 603, 10.1038/nprot.2007.59

Liang, 2010, Identification of miRNA from Porphyra yezoensis by high-throughput sequencing and bioinformatics analysis, PLoS ONE, 5, e10698, 10.1371/journal.pone.0010698

Huang, 2011, Identification and characterization of microRNAs from Phaeodactylum tricornutum by high-throughput sequencing and bioinformatics analysis, BMC Genom., 12, 337, 10.1186/1471-2164-12-337

Norden-Krichmar, 2011, Characterization of the small RNA transcriptome of the diatom, Thalassiosira pseudonana, PLoS ONE, 6, e22870, 10.1371/journal.pone.0022870

Cock, 2010, The Ectocarpus genome and the independent evolution of multicellularity in brown algae, Nature, 465, 617, 10.1038/nature09016

Xu, 2013, Comparative characterization of microRNA profiles of different genotypes of Toxoplasma gondii, Parasitology, 140, 1111, 10.1017/S003118201300053X

Qutob, 2013, Transgenerational gene silencing causes gain of virulence in a plant pathogen, Nat. Commun., 4, 1349, 10.1038/ncomms2354

Martin, 2011, Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet. J., 17, 10, 10.14806/ej.17.1.200

Langmead, 2012, Fast gapped-read alignment with Bowtie 2, Nat. Methods, 9, 357, 10.1038/nmeth.1923

Carver, 2012, Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data, Bioinformatics, 28, 464, 10.1093/bioinformatics/btr703

Rutherford, 2000, Artemis: sequence visualization and annotation, Bioinformatics, 16, 944, 10.1093/bioinformatics/16.10.944

Gajria, 2008, ToxoDB: an integrated Toxoplasma gondii database resource, Nucleic Acids Res., 36, D553, 10.1093/nar/gkm981

Richardson, 2007, Horizontal gene transfer in plants, J. Exp. Bot., 58, 1, 10.1093/jxb/erl148

Smith, 2014, Mitochondrion-to-plastid DNA transfer: it happens, New Phytol., 202, 736, 10.1111/nph.12704

Karpov, 2006, Molecular phylogeny of Cercomonadidae and kinetid patterns of Cercomonas and Eocercomonas gen. nov. (Cercomonadida, Cercozoa), Protist, 157, 125, 10.1016/j.protis.2006.01.001

Gray, 2004, Mitochondria of protists, Annu. Rev. Genet., 38, 477, 10.1146/annurev.genet.37.110801.142526

Burger, 2003, Mitochondrial genomes: anything goes, Trends Genet., 19, 709, 10.1016/j.tig.2003.10.012

Silberfeld, 2010, A multi-locus time-calibrated phylogeny of the brown algae (Heterokonta, Ochrophyta, Phaeophyceae): investigating the evolutionary nature of the ‘brown algal crown radiation’, Mol. Phylogenet. Evol., 56, 659, 10.1016/j.ympev.2010.04.020

Bullerwell, 2010, Abundant 5S rRNA-like transcripts encoded by the mitochondrial genome in Amoebozoa, Eukaryot. Cell, 9, 762, 10.1128/EC.00013-10

Adl, 2012, The revised classification of eukaryotes, J. Eukaryot. Microbiol., 59, 429, 10.1111/j.1550-7408.2012.00644.x

Zhong, 2011, Systematic error in seed plant phylogenomics, Genome Biol. Evol., 3, 1340, 10.1093/gbe/evr105

Lang, 1997, An ancestral mitochondrial DNA resembling a eubacterial genome in miniature, Nature, 387, 493, 10.1038/387493a0

Condon, 2001, Identification of the gene encoding the 5S ribosomal RNA maturase in Bacillus subtilis: mature 5S rRNA is dispensable for ribosome function, RNA, 7, 242, 10.1017/S1355838201002163

Verbruggen, 2010, Data mining approach identifies research priorities and data requirements for resolving the red algal tree of life, BMC Evol. Biol., 10, 16, 10.1186/1471-2148-10-16

Ohta, 1998, Structure and organization of the mitochondrial genome of the unicellular red alga Cyanidioschyzon merolae deduced from the complete nucleotide sequence, Nucleic Acids Res., 26, 5190, 10.1093/nar/26.22.5190

Gray, 1998, Genome structure and gene content in protist mitochondrial DNAs, Nucleic Acids Res., 26, 865, 10.1093/nar/26.4.865

Burger, 1999, Complete sequence of the mitochondrial DNA of the red alga Porphyra purpurea. Cyanobacterial introns and shared ancestry of red and green algae, Plant Cell, 11, 1675, 10.1105/tpc.11.9.1675

Soma, 2014, Circularly permuted tRNA genes: their expression and implications for their physiological relevance and development, Front Genet., 5, 63, 10.3389/fgene.2014.00063

Soma, 2007, Permuted tRNA genes expressed via a circular RNA intermediate in Cyanidioschyzon merolae, Science, 318, 450, 10.1126/science.1145718

Keiler, 2000, tmRNAs that encode proteolysis-inducing tags are found in all known bacterial genomes: A two-piece tmRNA functions in Caulobacter, Proc. Natl. Acad. Sci. U.S.A., 97, 7778, 10.1073/pnas.97.14.7778

Jacob, 2004, Loss of the mRNA-like region in mitochondrial tmRNAs of jakobids, RNA, 10, 605, 10.1261/rna.5227904

Hafez, 2013, A second eukaryotic group with mitochondrion-encoded tmRNA. In silico identification and experimental confirmation, RNA Biol., 10, 1117, 10.4161/rna.25376

de la Peña, 2010, Ubiquitous presence of the hammerhead ribozyme motif along the tree of life, RNA, 16, 1943, 10.1261/rna.2130310

Perreault, 2011, Identification of hammerhead ribozymes in all domains of life reveals novel structural variations, PLoS Comput. Biol., 7, e1002031, 10.1371/journal.pcbi.1002031

Roth, 2014, A widespread self-cleaving ribozyme class is revealed by bioinformatics, Nat. Chem. Biol., 10, 56, 10.1038/nchembio.1386

Vu, 2012, Convergent evolution of adenosine aptamers spanning bacterial, human, and random sequences revealed by structure-based bioinformatics and genomic SELEX, Chem. Biol., 19, 1247, 10.1016/j.chembiol.2012.08.010

Yusupov, 2001, Crystal structure of the ribosome at 5.5 Å resolution, Science, 292, 883, 10.1126/science.1060089

Gawryluk, 2014, Compositional complexity of the mitochondrial proteome of a unicellular eukaryote (Acanthamoeba castellanii, supergroup Amoebozoa) rivals that of animals, fungi, and plants, J. Proteomics, 109, 400, 10.1016/j.jprot.2014.07.005