-
Články
- Časopisy
- Kurzy
- Témy
- Kongresy
- Videa
- Podcasty
Transcriptional Control of an Essential Ribozyme in Reveals an Ancient Evolutionary Divide in Animals
The processing of the 5′ end of nascent tRNAs is catalyzed by ribonuclease P (RNase P), an essential enzyme. In the ribonucleoprotein form of this enzyme, the RNase P RNA (RPR) functions as a ribozyme aided by protein cofactors. All previously examined eukaryotic RPR genes are transcribed from their own promoters by RNA pol III. In contrast, the Drosophila RPR gene is embedded in an intron of a recipient gene. We have shown that the embedded sequence, the only copy of RPR in the genome, is transcribed by pol II from the promoter of its recipient gene and encodes the functional RPR. Analysis of other animal genomes revealed that an embedded RPR is also present in the genomes of other insects and crustaceans. This feature provides evidence that the mode of transcription of RPR changed as the result of insertion into a recipient gene approximately 500 million years ago. This new, inserted type of RPR must first have appeared in the arthropod lineage in a common ancestor of insects and crustaceans.
Vyšlo v časopise: Transcriptional Control of an Essential Ribozyme in Reveals an Ancient Evolutionary Divide in Animals. PLoS Genet 11(1): e32767. doi:10.1371/journal.pgen.1004893
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004893Souhrn
The processing of the 5′ end of nascent tRNAs is catalyzed by ribonuclease P (RNase P), an essential enzyme. In the ribonucleoprotein form of this enzyme, the RNase P RNA (RPR) functions as a ribozyme aided by protein cofactors. All previously examined eukaryotic RPR genes are transcribed from their own promoters by RNA pol III. In contrast, the Drosophila RPR gene is embedded in an intron of a recipient gene. We have shown that the embedded sequence, the only copy of RPR in the genome, is transcribed by pol II from the promoter of its recipient gene and encodes the functional RPR. Analysis of other animal genomes revealed that an embedded RPR is also present in the genomes of other insects and crustaceans. This feature provides evidence that the mode of transcription of RPR changed as the result of insertion into a recipient gene approximately 500 million years ago. This new, inserted type of RPR must first have appeared in the arthropod lineage in a common ancestor of insects and crustaceans.
Zdroje
1. Liu F, Altman S (2009) Ribonuclease P: Springer, New York.
2. ChamberlainJR, LeeY, LaneWS, EngelkeDR (1998) Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRP. Genes Dev 12 : 1678–1690.
3. RossmanithW (2011) Of P and Z: mitochondrial tRNA processing enzymes. Biochim Biophys Acta 1819 : 1017–1026.
4. HowardMJ, LiuX, LimWH, KlemmBP, FierkeCA, et al. (2013) RNase P enzymes: divergent scaffolds for a conserved biological reaction. RNA Biol 10 : 909–914.
5. LaiLB, VioqueA, KirsebomLA, GopalanV (2010) Unexpected diversity of RNase P, an ancient tRNA processing enzyme: challenges and prospects. FEBS Lett 584 : 287–296.
6. HolzmannJ, FrankP, LofflerE, BennettKL, GernerC, et al. (2008) RNase P without RNA: identification and functional reconstitution of the human mitochondrial tRNA processing enzyme. Cell 135 : 462–474.
7. GutmannB, GobertA, GiegeP (2012) PRORP proteins support RNase P activity in both organelles and the nucleus in Arabidopsis. Genes Dev 26 : 1022–1027.
8. GuentherUP, YandekLE, NilandCN, CampbellFE, AndersonD, et al. (2013) Hidden specificity in an apparently nonspecific RNA-binding protein. Nature 502 : 385–388.
9. SunL, HarrisME (2007) Evidence that binding of C5 protein to P RNA enhances ribozyme catalysis by influencing active site metal ion affinity. RNA 13 : 1505–1515.
10. MyslinskiE, AmeJC, KrolA, CarbonP (2001) An unusually compact external promoter for RNA polymerase III transcription of the human H1RNA gene. Nucleic Acids Res 29 : 2502–2509.
11. EderPS, SrinivasanA, FishmanMC, AltmanS (1996) The RNA subunit of ribonuclease P from the zebrafish, Danio rerio. J Biol Chem 271 : 21031–21036.
12. LeeJY, EvansCF, EngelkeDR (1991) Expression of RNase P RNA in Saccharomyces cerevisiae is controlled by an unusual RNA polymerase III promoter. Proc Natl Acad Sci U S A 88 : 6986–6990.
13. MarquezSM, ChenJL, EvansD, PaceNR (2006) Structure and function of eukaryotic Ribonuclease P RNA. Mol Cell 24 : 445–456.
14. PiccinelliP, RosenbladMA, SamuelssonT (2005) Identification and analysis of ribonuclease P and MRP RNA in a broad range of eukaryotes. Nucleic Acids Res 33 : 4485–4495.
15. TripoliG, D'EliaD, BarsantiP, CaggeseC (2005) Comparison of the oxidative phosphorylation (OXPHOS) nuclear genes in the genomes of Drosophila melanogaster, Drosophila pseudoobscura and Anopheles gambiae. Genome Biol 6: R11.
16. HernandezGJr, ValafarF, StumphWE (2007) Insect small nuclear RNA gene promoters evolve rapidly yet retain conserved features involved in determining promoter activity and RNA polymerase specificity. Nucleic Acids Res 35 : 21–34.
17. Davila LopezM, RosenbladMA, SamuelssonT (2009) Conserved and variable domains of RNase MRP RNA. RNA Biol 6 : 208–220.
18. MisofB, LiuS, MeusemannK, PetersRS, DonathA, et al. (2014) Phylogenomics resolves the timing and pattern of insect evolution. Science 346 : 763–767.
19. AmeJC, SchreiberV, FraulobV, DolleP, de MurciaG, et al. (2001) A bidirectional promoter connects the poly(ADP-ribose) polymerase 2 (PARP-2) gene to the gene for RNase P RNA. structure and expression of the mouse PARP-2 gene. J Biol Chem 276 : 11092–11099.
20. IsogaiY, TakadaS, TjianR, KelesS (2007) Novel TRF1/BRF target genes revealed by genome-wide analysis of Drosophila Pol III transcription. EMBO J 26 : 79–89.
21. KrasnowMA, SaffmanEE, KornfeldK, HognessDS (1989) Transcriptional activation and repression by Ultrabithorax proteins in cultured Drosophila cells. Cell 57 : 1031–1043.
22. BrandAH, PerrimonN (1993) Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 118 : 401–415.
23. LaiLB, ChanPP, CozenAE, BernickDL, BrownJW, et al. (2010) Discovery of a minimal form of RNase P in Pyrobaculum. Proc Natl Acad Sci U S A 107 : 22493–22498.
24. ColbourneJK, PfrenderME, GilbertD, ThomasWK, TuckerA, et al. (2011) The ecoresponsive genome of Daphnia pulex. Science 331 : 555–561.
25. TrautweinMD, WiegmannBM, BeutelR, KjerKM, YeatesDK (2012) Advances in insect phylogeny at the dawn of the postgenomic era. Annu Rev Entomol 57 : 449–468.
26. RegierJC, ShultzJW, ZwickA, HusseyA, BallB, et al. (2010) Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences. Nature 463 : 1079–1083.
27. OakleyTH, WolfeJM, LindgrenAR, ZaharoffAK (2013) Phylotranscriptomics to bring the understudied into the fold: monophyletic ostracoda, fossil placement, and pancrustacean phylogeny. Mol Biol Evol 30 : 215–233.
28. von ReumontBM, JennerRA, WillsMA, Dell'ampioE, PassG, et al. (2012) Pancrustacean phylogeny in the light of new phylogenomic data: support for Remipedia as the possible sister group of Hexapoda. Mol Biol Evol 29 : 1031–1045.
29. EsakovaO, KrasilnikovAS (2010) Of proteins and RNA: the RNase P/MRP family. RNA 16 : 1725–1747.
30. ZhuY, StribinskisV, RamosKS, LiY (2006) Sequence analysis of RNase MRP RNA reveals its origination from eukaryotic RNase P RNA. Rna 12 : 699–706.
31. SchneiderMD, BainsAK, RajendraTK, DominskiZ, MateraAG, et al. (2010) Functional characterization of the Drosophila MRP (mitochondrial RNA processing) RNA gene. Rna 16 : 2120–2130.
32. BaerM, NilsenTW, CostiganC, AltmanS (1990) Structure and transcription of a human gene for H1 RNA, the RNA component of human RNase P. Nucleic Acids Res. 18 : 97–103.
33. KimYK, KimVN (2007) Processing of intronic microRNAs. EMBO J 26 : 775–783.
34. HiroseT, ShuMD, SteitzJA (2003) Splicing-dependent and -independent modes of assembly for intron-encoded box C/D snoRNPs in mammalian cells. Mol Cell 12 : 113–123.
35. RichardP, KissAM, DarzacqX, KissT (2006) Cotranscriptional recognition of human intronic box H/ACA snoRNAs occurs in a splicing-independent manner. Mol Cell Biol 26 : 2540–2549.
36. HanJ, LeeY, YeomKH, KimYK, JinH, et al. (2004) The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev 18 : 3016–3027.
37. AebyE, UlluE, YepiskoposyanH, SchimanskiB, RoditiI, et al. (2010) tRNASec is transcribed by RNA polymerase II in Trypanosoma brucei but not in humans. Nucleic Acids Res 38 : 5833–5843.
38. DieciG, PretiM, MontaniniB (2009) Eukaryotic snoRNAs: a paradigm for gene expression flexibility. Genomics 94 : 83–88.
39. KatjuV (2012) In with the old, in with the new: the promiscuity of the duplication process engenders diverse pathways for novel gene creation. Int J Evol Biol 2012 : 341932.
40. LambowitzAM, BelfortM (1993) Introns as mobile genetic elements. Annu Rev Biochem 62 : 587–622.
41. SchneiderI (1972) Cell lines derived from late embryonic stages of Drosophila melanogaster. J Embryol Exp Morphol 27 : 353–365.
42. PaululatA, HeinischJJ (2012) New yeast/E. coli/Drosophila triple shuttle vectors for efficient generation of Drosophila P element transformation constructs. Gene 511 : 300–305.
43. ReeseMG, EeckmanFH, KulpD, HausslerD (1997) Improved splice site detection in Genie. J Comput Biol 4 : 311–323.
44. BonanoVI, OlteanS, Garcia-BlancoMA (2007) A protocol for imaging alternative splicing regulation in vivo using fluorescence reporters in transgenic mice. Nat Protoc 2 : 2166–2181.
45. ChildsJL, PooleAW, TurnerDH (2003) Inhibition of Escherichia coli RNase P by oligonucleotide directed misfolding of RNA. Rna 9 : 1437–1445.
46. GruegelsiepeH, WillkommDK, GoudinakisO, HartmannRK (2003) Antisense inhibition of Escherichia coli RNase P RNA: mechanistic aspects. Chembiochem 4 : 1049–1056.
47. NawrockiEP, EddySR (2013) Infernal 1.1 : 100-fold faster RNA homology searches. Bioinformatics 29 : 2933–2935.
48. ZukerM (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31 : 3406–3415.
49. YusufD, MarzM, StadlerPF, HofackerIL (2010) Bcheck: a wrapper tool for detecting RNase P RNA genes. BMC Genomics 11 : 432.
50. HusonDH, RichterDC, RauschC, DezulianT, FranzM, et al. (2007) Dendroscope: An interactive viewer for large phylogenetic trees. BMC Bioinformatics 8 : 460.
51. FrazerKA, PachterL, PoliakovA, RubinEM, DubchakI (2004) VISTA: computational tools for comparative genomics. Nucleic Acids Res 32: W273–279.
52. GraveleyBR, BrooksAN, CarlsonJW, DuffMO, LandolinJM, et al. (2011) The developmental transcriptome of Drosophila melanogaster. Nature 471 : 473–479.
53. RoyS, ErnstJ, KharchenkoPV, KheradpourP, NegreN, et al. (2010) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330 : 1787–1797.
54. RobinsonJT, ThorvaldsdottirH, WincklerW, GuttmanM, LanderES, et al. (2011) Integrative genomics viewer. Nat Biotechnol 29 : 24–26.
55. LiH, HandsakerB, WysokerA, FennellT, RuanJ, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25 : 2078–2079.
56. TarazonaS, Garcia-AlcaldeF, DopazoJ, FerrerA, ConesaA (2011) Differential expression in RNA-seq: a matter of depth. Genome Res 21 : 2213–2223.
57. LeinonenR, SugawaraH, ShumwayM (2011) International Nucleotide Sequence Database C (2011) The sequence read archive. Nucleic Acids Res 39: D19–21.
58. LangmeadB, SalzbergSL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9 : 357–359.
59. TrapnellC, PachterL, SalzbergSL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25 : 1105–1111.
60. TrapnellC, WilliamsBA, PerteaG, MortazaviA, KwanG, et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28 : 511–515.
61. CamachoC, CoulourisG, AvagyanV, MaN, PapadopoulosJ, et al. (2009) BLAST+: architecture and applications. BMC Bioinformatics 10 : 421.
62. LarkinMA, BlackshieldsG, BrownNP, ChennaR, McGettiganPA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23 : 2947–2948.
63. LiXY, MacArthurS, BourgonR, NixD, PollardDA, et al. (2008) Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol 6: e27.
64. MacArthurS, LiXY, LiJ, BrownJB, ChuHC, et al. (2009) Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biol 10: R80.
65. GiribetG, EdgecombeGD (2012) Reevaluating the arthropod tree of life. Annu Rev Entomol 57 : 167–186.
66. GlennerH, ThomsenPF, HebsgaardMB, SorensenMV, WillerslevE (2006) Evolution. The origin of insects. Science 314 : 1883–1884.
67. LeuJH, ChenSH, WangYB, ChenYC, SuSY, et al. (2011) A review of the major penaeid shrimp EST studies and the construction of a shrimp transcriptome database based on the ESTs from four penaeid shrimp. Mar Biotechnol (NY) 13 : 608–621.
68. EddySR (2002) A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure. BMC Bioinformatics 3 : 18.
69. AltschulSF, MaddenTL, SchafferAA, ZhangJ, ZhangZ, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25 : 3389–3402.
70. BurgeCB, KarlinS (1998) Finding the genes in genomic DNA. Curr Opin Struct Biol 8 : 346–354.
71. Graveley BR, May G, Brooks AN, Carlson JW, Cherbas L, et al. (2011) The D. melanogaster transcriptome: modENCODE RNA-Seq data for dissected tissues.
72. BehrensS, PeussR, MilutinovicB, EggertH, EsserD, et al. (2014) Infection routes matter in population-specific responses of the red flour beetle to the entomopathogen Bacillus thuringiensis. BMC Genomics 15 : 445.
73. HepatR, SongJJ, LeeD, KimY (2013) A viral histone h4 joins to eukaryotic nucleosomes and alters host gene expression. J Virol 87 : 11223–11230.
Štítky
Genetika Reprodukčná medicína
Článek Phosphorylation of Elp1 by Hrr25 Is Required for Elongator-Dependent tRNA Modification in YeastČlánek Naturally Occurring Differences in CENH3 Affect Chromosome Segregation in Zygotic Mitosis of HybridsČlánek Insight in Genome-Wide Association of Metabolite Quantitative Traits by Exome Sequence AnalysesČlánek ALIX and ESCRT-III Coordinately Control Cytokinetic Abscission during Germline Stem Cell DivisionČlánek Deciphering the Genetic Programme Triggering Timely and Spatially-Regulated Chitin Deposition
Článok vyšiel v časopisePLOS Genetics
Najčítanejšie tento týždeň
2015 Číslo 1- Gynekologové a odborníci na reprodukční medicínu se sejdou na prvním virtuálním summitu
- Je „freeze-all“ pro všechny? Odborníci na fertilitu diskutovali na virtuálním summitu
-
Všetky články tohto čísla
- The Combination of Random Mutagenesis and Sequencing Highlight the Role of Unexpected Genes in an Intractable Organism
- Ataxin-3, DNA Damage Repair, and SCA3 Cerebellar Degeneration: On the Path to Parsimony?
- α-Actinin-3: Why Gene Loss Is an Evolutionary Gain
- Origins of Context-Dependent Gene Repression by Capicua
- Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress
- No Evidence for Association of Autism with Rare Heterozygous Point Mutations in Contactin-Associated Protein-Like 2 (), or in Other Contactin-Associated Proteins or Contactins
- Nur1 Dephosphorylation Confers Positive Feedback to Mitotic Exit Phosphatase Activation in Budding Yeast
- A Regulatory Hierarchy Controls the Dynamic Transcriptional Response to Extreme Oxidative Stress in Archaea
- Genetic Variants Modulating CRIPTO Serum Levels Identified by Genome-Wide Association Study in Cilento Isolates
- Small RNA Sequences Support a Host Genome Origin of Satellite RNA
- Phosphorylation of Elp1 by Hrr25 Is Required for Elongator-Dependent tRNA Modification in Yeast
- Genetic Mapping of MAPK-Mediated Complex Traits Across
- An AP Endonuclease Functions in Active DNA Demethylation and Gene Imprinting in
- Developmental Regulation of the Origin Recognition Complex
- End of the Beginning: Elongation and Termination Features of Alternative Modes of Chromosomal Replication Initiation in Bacteria
- Naturally Occurring Differences in CENH3 Affect Chromosome Segregation in Zygotic Mitosis of Hybrids
- Imputation of the Rare G84E Mutation and Cancer Risk in a Large Population-Based Cohort
- Polycomb Protein SCML2 Associates with USP7 and Counteracts Histone H2A Ubiquitination in the XY Chromatin during Male Meiosis
- A Genetic Strategy for Probing the Functional Diversity of Magnetosome Formation
- Interactions of Chromatin Context, Binding Site Sequence Content, and Sequence Evolution in Stress-Induced p53 Occupancy and Transactivation
- The Yeast La Related Protein Slf1p Is a Key Activator of Translation during the Oxidative Stress Response
- Integrative Analysis of DNA Methylation and Gene Expression Data Identifies as a Key Regulator of COPD
- Proteasomes, Sir2, and Hxk2 Form an Interconnected Aging Network That Impinges on the AMPK/Snf1-Regulated Transcriptional Repressor Mig1
- Functional Interplay between the 53BP1-Ortholog Rad9 and the Mre11 Complex Regulates Resection, End-Tethering and Repair of a Double-Strand Break
- Estrogenic Exposure Alters the Spermatogonial Stem Cells in the Developing Testis, Permanently Reducing Crossover Levels in the Adult
- Protein Poly(ADP-ribosyl)ation Regulates Immune Gene Expression and Defense Responses
- Sumoylation Influences DNA Break Repair Partly by Increasing the Solubility of a Conserved End Resection Protein
- A Discrete Transition Zone Organizes the Topological and Regulatory Autonomy of the Adjacent and Genes
- Elevated Mutation Rate during Meiosis in
- The Intersection of the Extrinsic Hedgehog and WNT/Wingless Signals with the Intrinsic Hox Code Underpins Branching Pattern and Tube Shape Diversity in the Airways
- MiR-24 Is Required for Hematopoietic Differentiation of Mouse Embryonic Stem Cells
- Tissue-Specific Effects of Genetic and Epigenetic Variation on Gene Regulation and Splicing
- Heterologous Aggregates Promote Prion Appearance via More than One Mechanism
- The Tumor Suppressor BCL7B Functions in the Wnt Signaling Pathway
- , A -Acting Locus that Controls Chromosome-Wide Replication Timing and Stability of Human Chromosome 15
- Regulating Maf1 Expression and Its Expanding Biological Functions
- A Polyubiquitin Chain Reaction: Parkin Recruitment to Damaged Mitochondria
- RecFOR Is Not Required for Pneumococcal Transformation but Together with XerS for Resolution of Chromosome Dimers Frequently Formed in the Process
- An Intracellular Transcriptomic Atlas of the Giant Coenocyte
- Insight in Genome-Wide Association of Metabolite Quantitative Traits by Exome Sequence Analyses
- The Role of the Mammalian DNA End-processing Enzyme Polynucleotide Kinase 3’-Phosphatase in Spinocerebellar Ataxia Type 3 Pathogenesis
- The Global Regulatory Architecture of Transcription during the Cell Cycle
- Identification and Functional Characterization of Coding Variants Influencing Glycemic Traits Define an Effector Transcript at the Locus
- Altered Ca Kinetics Associated with α-Actinin-3 Deficiency May Explain Positive Selection for Null Allele in Human Evolution
- Genetic Variation in the Nuclear and Organellar Genomes Modulates Stochastic Variation in the Metabolome, Growth, and Defense
- PRDM9 Drives Evolutionary Erosion of Hotspots in through Haplotype-Specific Initiation of Meiotic Recombination
- Transcriptional Control of an Essential Ribozyme in Reveals an Ancient Evolutionary Divide in Animals
- ALIX and ESCRT-III Coordinately Control Cytokinetic Abscission during Germline Stem Cell Division
- Century-scale Methylome Stability in a Recently Diverged Lineage
- A Re-examination of the Selection of the Sensory Organ Precursor of the Bristle Sensilla of
- Antagonistic Cross-Regulation between Sox9 and Sox10 Controls an Anti-tumorigenic Program in Melanoma
- A Dependent Pool of Phosphatidylinositol 4,5 Bisphosphate (PIP) Is Required for G-Protein Coupled Signal Transduction in Photoreceptors
- Deciphering the Genetic Programme Triggering Timely and Spatially-Regulated Chitin Deposition
- Aberrant Gene Expression in Humans
- Fascin1-Dependent Filopodia are Required for Directional Migration of a Subset of Neural Crest Cells
- The SWI2/SNF2 Chromatin Remodeler BRAHMA Regulates Polycomb Function during Vegetative Development and Directly Activates the Flowering Repressor Gene
- Evolutionary Constraint and Disease Associations of Post-Translational Modification Sites in Human Genomes
- A Truncated NLR Protein, TIR-NBS2, Is Required for Activated Defense Responses in the Mutant
- The Genetic and Mechanistic Basis for Variation in Gene Regulation
- Inactivation of PNKP by Mutant ATXN3 Triggers Apoptosis by Activating the DNA Damage-Response Pathway in SCA3
- DNA Damage Response Factors from Diverse Pathways, Including DNA Crosslink Repair, Mediate Alternative End Joining
- hnRNP K Coordinates Transcriptional Silencing by SETDB1 in Embryonic Stem Cells
- PLOS Genetics
- Archív čísel
- Aktuálne číslo
- Informácie o časopise
Najčítanejšie v tomto čísle- The Global Regulatory Architecture of Transcription during the Cell Cycle
- A Truncated NLR Protein, TIR-NBS2, Is Required for Activated Defense Responses in the Mutant
- Proteasomes, Sir2, and Hxk2 Form an Interconnected Aging Network That Impinges on the AMPK/Snf1-Regulated Transcriptional Repressor Mig1
- The SWI2/SNF2 Chromatin Remodeler BRAHMA Regulates Polycomb Function during Vegetative Development and Directly Activates the Flowering Repressor Gene
Prihlásenie#ADS_BOTTOM_SCRIPTS#Zabudnuté hesloZadajte e-mailovú adresu, s ktorou ste vytvárali účet. Budú Vám na ňu zasielané informácie k nastaveniu nového hesla.
- Časopisy