-
Články
- Časopisy
- Kurzy
- Témy
- Kongresy
- Videa
- Podcasty
Playing RNase P Evolution: Swapping the RNA Catalyst for a Protein Reveals Functional Uniformity of Highly Divergent Enzyme Forms
Many biocatalysts apparently evolved independently more than once, leading to structurally unrelated macromolecules catalyzing the same biochemical reaction. The RNase P enzyme family is an exceptional case of this phenomenon called convergent evolution. RNase P enzymes use not only unrelated, but chemically distinct macromolecules, either RNA or protein, to catalyze a specific step in the biogenesis of transfer RNAs, the ubiquitous adaptor molecules in protein synthesis. However, this fundamental difference in the identity of the actual catalyst, together with a broad variation in structural complexity of the diverse forms of RNase P, cast doubts on their functional equivalence. Here we compared two of the structurally most extreme variants of RNase P by replacing the yeast nuclear enzyme, a 10-subunit RNA-protein complex, with a single-protein from plants representing the apparently simplest form of RNase P. Surprisingly, the viability and fitness of these RNase P-swapped yeasts and their molecular analyses demonstrated the full functional exchangeability of the highly dissimilar enzymes. The RNase P family, with its combination of structural diversity and functional uniformity, thus not only truly represents an extraordinary case of convergent evolution, but also demonstrates that increased structural complexity does not necessarily entail broadened functionality, but may rather be the result of “neutral” evolutionary mechanisms.
Vyšlo v časopise: Playing RNase P Evolution: Swapping the RNA Catalyst for a Protein Reveals Functional Uniformity of Highly Divergent Enzyme Forms. PLoS Genet 10(8): e32767. doi:10.1371/journal.pgen.1004506
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004506Souhrn
Many biocatalysts apparently evolved independently more than once, leading to structurally unrelated macromolecules catalyzing the same biochemical reaction. The RNase P enzyme family is an exceptional case of this phenomenon called convergent evolution. RNase P enzymes use not only unrelated, but chemically distinct macromolecules, either RNA or protein, to catalyze a specific step in the biogenesis of transfer RNAs, the ubiquitous adaptor molecules in protein synthesis. However, this fundamental difference in the identity of the actual catalyst, together with a broad variation in structural complexity of the diverse forms of RNase P, cast doubts on their functional equivalence. Here we compared two of the structurally most extreme variants of RNase P by replacing the yeast nuclear enzyme, a 10-subunit RNA-protein complex, with a single-protein from plants representing the apparently simplest form of RNase P. Surprisingly, the viability and fitness of these RNase P-swapped yeasts and their molecular analyses demonstrated the full functional exchangeability of the highly dissimilar enzymes. The RNase P family, with its combination of structural diversity and functional uniformity, thus not only truly represents an extraordinary case of convergent evolution, but also demonstrates that increased structural complexity does not necessarily entail broadened functionality, but may rather be the result of “neutral” evolutionary mechanisms.
Zdroje
1. LaiLB, VioqueA, KirsebomLA, GopalanV (2010) Unexpected diversity of RNase P, an ancient tRNA processing enzyme: challenges and prospects. FEBS Lett 584 : 287–296.
2. Liu F, Altman S, editors (2010) Ribonuclease P. New York: Springer. 283 p.
3. EsakovaO, KrasilnikovAS (2010) Of proteins and RNA: the RNase P/MRP family. RNA 16 : 1725–1747.
4. HartmannRK, GöβringerM, SpäthB, FischerS, MarchfelderA (2009) The Making of tRNAs and More - RNase P and tRNase Z. Prog Nucleic Acid Res Mol Biol. 85 : 319–368.
5. Ellis JC, Brown JW (2010) The evolution of RNase P and its RNA. In: Liu F, Altman S, editors. Ribonuclease P. New York: Springer. pp. 17–40.
6. Walker SC, Marvin MC, Engelke D (2010) Eukaryote RNase P and RNase MRP. In: Liu F, Altman S, editors. Ribonuclease P. New York: Springer. pp. 173–202.
7. JarrousN, GopalanV (2010) Archaeal/eukaryal RNase P: subunits, functions and RNA diversification. Nucleic Acids Res 38 : 7885–7894.
8. Lai LB, Cho I-M, Chen W-Y, Gopalan V (2010) Archaeal RNase P: a mosaic of its bacterial and eukaryal relatives. In: Liu F, Altman S, editors. Ribonuclease P. New York: Springer. pp. 153–172.
9. GobertA, GutmannB, TaschnerA, GöβringerM, HolzmannJ, et al. (2010) A single Arabidopsis organellar protein has RNase P activity. Nat Struct Mol Biol 17 : 740–744.
10. GutmannB, GobertA, GiegéP (2012) PRORP proteins support RNase P activity in both organelles and the nucleus in Arabidopsis. Genes Dev 26 : 1022–1027.
11. TaschnerA, WeberC, BuzetA, HartmannRK, HartigA, et al. (2012) Nuclear RNase P of Trypanosoma brucei: a single protein in place of the multi-component RNA-protein complex. Cell Rep 2 : 19–25.
12. HolzmannJ, FrankP, LöfflerE, BennettKL, GernerC, et al. (2008) RNase P without RNA: identification and functional reconstitution of the human mitochondrial tRNA processing enzyme. Cell 135 : 462–474.
13. MarvinMC, EngelkeDR (2009) Broadening the mission of an RNA enzyme. J Cell Biochem 108 : 1244–1251.
14. MarvinMC, EngelkeDR (2009) RNase P: increased versatility through protein complexity? RNA Biol 6 : 40–42.
15. HowardMJ, LiuX, LimWH, KlemmBP, KoutmosM, et al. (2013) RNase P enzymes: Divergent scaffolds for a conserved biological reaction. RNA Biol 10 : 909–914.
16. PavlovaLV, GöβringerM, WeberC, BuzetA, RossmanithW, et al. (2012) tRNA processing by protein-only versus RNA-based RNase P: kinetic analysis reveals mechanistic differences. ChemBioChem 13 : 2270–2276.
17. RuohonenL, AaltoMK, KeränenS (1995) Modifications to the ADH1 promoter of Saccharomyces cerevisiae for efficient production of heterologous proteins. J Biotechnol 39 : 193–203.
18. MüllederM, CapuanoF, PirP, ChristenS, SauerU, et al. (2012) A prototrophic deletion mutant collection for yeast metabolomics and systems biology. Nat Biotechnol 30 : 1176–1178.
19. MarvinMC, WalkerSC, FierkeCA, EngelkeDR (2011) Binding and cleavage of unstructured RNA by nuclear RNase P. RNA. 17 : 1429–1440.
20. CoughlinDJ, PleissJA, WalkerSC, WhitworthGB, EngelkeDR (2008) Genome-wide search for yeast RNase P substrates reveals role in maturation of intron-encoded box C/D small nucleolar RNAs. Proc Natl Acad Sci USA 105 : 12218–12223.
21. MarvinMC, Clauder-MünsterS, WalkerSC, SarkeshikA, YatesJR3rd, et al. (2011) Accumulation of noncoding RNA due to an RNase P defect in Saccharomyces cerevisiae. RNA 17 : 1441–1450.
22. MnaimnehS, DavierwalaAP, HaynesJ, MoffatJ, PengW-T, et al. (2004) Exploration of essential gene functions via titratable promoter alleles. Cell 118 : 31–44.
23. BrachmannCB, DaviesA, CostGJ, CaputoE, LiJ, et al. (1998) Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14 : 115–132.
24. van DijkenJP, BauerJ, BrambillaL, DubocP, FrancoisJM, et al. (2000) An interlaboratory comparison of physiological and genetic properties of four Saccharomyces cerevisiae strains. Enzyme Microb Technol 26 : 706–714.
25. NijkampJF, van den BroekM, DatemaE, de KokS, BosmanL, et al. (2012) De novo sequencing, assembly and analysis of the genome of the laboratory strain Saccharomyces cerevisiae CEN.PK113-7D, a model for modern industrial biotechnology. Microb Cell Fact 11 : 36.
26. BertrandE, Houser-ScottF, KendallA, SingerRH, EngelkeDR (1998) Nucleolar localization of early tRNA processing. Genes Dev 12 : 2463–2468.
27. SunwooH, DingerME, WiluszJE, AmaralPP, MattickJS, et al. (2009) MEN ε/β nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res 19 : 347–359.
28. WiluszJE, FreierSM, SpectorDL (2008) 3′ end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell 135 : 919–932.
29. SamantaMP, TongprasitW, SethiH, ChinC-S, StolcV (2006) Global identification of noncoding RNAs in Saccharomyces cerevisiae by modulating an essential RNA processing pathway. Proc Natl Acad Sci USA 103 : 4192–4197.
30. Pagán-RamosE, LeeY, EngelkeDR (1996) A conserved RNA motif involved in divalent cation utilization by nuclear RNase P. RNA 2 : 1100–1109.
31. ReinerR, Ben-AsouliY, KrilovetzkyI, JarrousN (2006) A role for the catalytic ribonucleoprotein RNase P in RNA polymerase III transcription. Genes Dev 20 : 1621–1635.
32. ReinerR, Krasnov-YoeliN, DehtiarY, JarrousN (2008) Function and Assembly of a Chromatin-Associated RNase P that Is Required for Efficient Transcription by RNA Polymerase I. PLoS ONE 3: e4072.
33. IshiguroA, KassavetisGA, GeiduschekEP (2002) Essential roles of Bdp1, a subunit of RNA polymerase III initiation factor TFIIIB, in transcription and tRNA processing. Mol Cell Biol 22 : 3264–3275.
34. JarrousN, ReinerR (2007) Human RNase P: a tRNA-processing enzyme and transcription factor. Nucleic Acids Res 35 : 3519–3524.
35. StoltzfusA (1999) On the possibility of constructive neutral evolution. J Mol Evol 49 : 169–181.
36. LukesJ, ArchibaldJM, KeelingPJ, DoolittleWF, GrayMW (2011) How a neutral evolutionary ratchet can build cellular complexity. IUBMB Life 63 : 528–537.
37. KikovskaE, SvärdSG, KirsebomLA (2007) Eukaryotic RNase P RNA mediates cleavage in the absence of protein. Proc Natl Acad Sci USA 104 : 2062–2067.
38. WillCL, LührmannR (2001) Spliceosomal UsnRNP biogenesis, structure and function. Curr Opin Cell Biol 13 : 290–301.
39. RossmanithW (2012) Of P and Z: Mitochondrial tRNA processing enzymes. Biochim Biophys Acta 1819 : 1017–1026.
40. GalperinMY, KooninEV (2012) Divergence and convergence in enzyme evolution. J Biol Chem 287 : 21–28.
41. OmelchenkoMV, GalperinMY, WolfYI, KooninEV (2010) Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution. Biol Direct 5 : 31.
42. ChristianT, EviliaC, WilliamsS, HouYM (2004) Distinct origins of tRNA(m1G37) methyltransferase. J Mol Biol 339 : 707–719.
43. PopowJ, SchleifferA, MartinezJ (2012) Diversity and roles of (t)RNA ligases. Cell Mol Life Sci 69 : 2657–2670.
44. WachA, BrachatA, PöhlmannR, PhilippsenP (1994) New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae. Yeast 10 : 1793–1808.
45. GüldenerU, HeckS, FielderT, BeinhauerJ, HegemannJH (1996) A new efficient gene disruption cassette for repeated use in budding yeast. Nucleic Acids Res 24 : 2519–2524.
46. GueldenerU, HeinischJ, KoehlerGJ, VossD, HegemannJH (2002) A second set of loxP marker cassettes for Cre-mediated multiple gene knockouts in budding yeast. Nucleic Acids Res 30: e23.
47. GietzRD, SuginoA (1988) New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. Gene 74 : 527–534.
48. HuberA, KochJ, KraglerF, BrocardC, HartigA (2012) A subtle interplay between three Pex11 proteins shapes de novo formation and fission of peroxisomes. Traffic 13 : 157–167.
49. JankeC, MagieraMM, RathfelderN, TaxisC, ReberS, et al. (2004) A versatile toolbox for PCR-based tagging of yeast genes: new fluorescent proteins, more markers and promoter substitution cassettes. Yeast 21 : 947–962.
50. Amberg DC, Burke DJ, Strathern JN (2005) Methods in yeast genetics : a Cold Spring Harbor Laboratory course manual. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press. 230 p.
51. ShermanF (2002) Getting started with yeast. Methods Enzymol 350 : 3–41.
52. GietzRD, WoodsRA (2002) Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method. Methods Enzymol 350 : 87–96.
53. JohnstonM, RilesL, HegemannJH (2002) Gene disruption. Methods Enzymol 350 : 290–315.
54. ToussaintM, ConconiA (2006) High-throughput and sensitive assay to measure yeast cell growth: a bench protocol for testing genotoxic agents. Nat Protoc 1 : 1922–1928.
55. WarringerJ, BlombergA (2003) Automated screening in environmental arrays allows analysis of quantitative phenotypic profiles in Saccharomyces cerevisiae. Yeast 20 : 53–67.
Štítky
Genetika Reprodukčná medicína
Článok vyšiel v časopisePLOS Genetics
Najčítanejšie tento týždeň
2014 Číslo 8- 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
- DNA Double Strand Break Repair in Mitosis Is Suppressed by Phosphorylation of XRCC4
- Inference of Transposable Element Ancestry
- The Population Genetics of Evolutionary Rescue
- Retinoic Acid Activates Two Pathways Required for Meiosis in Mice
- Pooled Segregant Sequencing Reveals Genetic Determinants of Yeast Pseudohyphal Growth
- Comprehensive Identification of Single Nucleotide Polymorphisms Associated with Beta-lactam Resistance within Pneumococcal Mosaic Genes
- SMA-Causing Missense Mutations in Display a Wide Range of Phenotypes When Modeled in
- Branch Migration Prevents DNA Loss during Double-Strand Break Repair
- Transcriptome Sequencing from Diverse Human Populations Reveals Differentiated Regulatory Architecture
- Genetic Deletion of SEPT7 Reveals a Cell Type-Specific Role of Septins in Microtubule Destabilization for the Completion of Cytokinesis
- Tethering Sister Centromeres to Each Other Suggests the Spindle Checkpoint Detects Stretch within the Kinetochore
- Global Genetic Variations Predict Brain Response to Faces
- Demography and the Age of Rare Variants
- The Response to High CO Levels Requires the Neuropeptide Secretion Component HID-1 to Promote Pumping Inhibition
- Sp6 and Sp8 Transcription Factors Control AER Formation and Dorsal-Ventral Patterning in Limb Development
- The Groucho Co-repressor Is Primarily Recruited to Local Target Sites in Active Chromatin to Attenuate Transcription
- A Transposable Element Insertion Confers Xenobiotic Resistance in Drosophila
- The Genomic Architecture of Population Divergence between Subspecies of the European Rabbit
- Human Social Genomics
- Gene Expansion Shapes Genome Architecture in the Human Pathogen : An Evolutionary Genomics Analysis in the Ancient Terrestrial Mucorales (Mucoromycotina)
- Canonical Non-Homologous End Joining in Mitosis Induces Genome Instability and Is Suppressed by M-phase-Specific Phosphorylation of XRCC4
- Roles of Type 1A Topoisomerases in Genome Maintenance in
- The TRIM-NHL Protein LIN-41 Controls the Onset of Developmental Plasticity in
- Wnt-Mediated Repression via Bipartite DNA Recognition by TCF in the Hematopoietic System
- KDM6 Demethylase Independent Loss of Histone H3 Lysine 27 Trimethylation during Early Embryonic Development
- Integration of UPR and Oxidative Stress Signaling in the Control of Intestinal Stem Cell Proliferation
- miR171-Targeted Scarecrow-Like Proteins Bind to GT -Elements and Mediate Gibberellin-Regulated Chlorophyll Biosynthesis under Light Conditions
- Syndecan-1 Is Required to Maintain Intradermal Fat and Prevent Cold Stress
- LIN-3/EGF Promotes the Programmed Cell Death of Specific Cells in by Transcriptional Activation of the Pro-apoptotic Gene
- A System for Genome-Wide Histone Variant Dynamics In ES Cells Reveals Dynamic MacroH2A2 Replacement at Promoters
- Multiple Regulation of Rad51-Mediated Homologous Recombination by Fission Yeast Fbh1
- A Genome-Wide Association Study of the Maize Hypersensitive Defense Response Identifies Genes That Cluster in Related Pathways
- The RNA Helicases AtMTR4 and HEN2 Target Specific Subsets of Nuclear Transcripts for Degradation by the Nuclear Exosome in
- Asymmetric Division and Differential Gene Expression during a Bacterial Developmental Program Requires DivIVA
- A Model-Based Approach for Identifying Signatures of Ancient Balancing Selection in Genetic Data
- Chromatin Insulator Factors Involved in Long-Range DNA Interactions and Their Role in the Folding of the Drosophila Genome
- Conditional Inactivation of Upstream Binding Factor Reveals Its Epigenetic Functions and the Existence of a Somatic Nucleolar Precursor Body
- Evidence for Divisome Localization Mechanisms Independent of the Min System and SlmA in
- Patterns of Admixture and Population Structure in Native Populations of Northwest North America
- Response Regulator Heterodimer Formation Controls a Key Stage in S Development
- A Genetic Strategy to Measure Circulating Insulin Reveals Genes Regulating Insulin Production and Secretion
- EVA-1 Functions as an UNC-40 Co-receptor to Enhance Attraction to the MADD-4 Guidance Cue in
- Dysfunction of the CNS-Heart Axis in Mouse Models of Huntington's Disease
- An Otx/Nodal Regulatory Signature for Posterior Neural Development in Ascidians
- Phosphorylation of a Central Clock Transcription Factor Is Required for Thermal but Not Photic Entrainment
- Genome-Wide Patterns of Genetic Variation within and among Alternative Selective Regimes
- EF-P Dependent Pauses Integrate Proximal and Distal Signals during Translation
- Ku-Mediated Coupling of DNA Cleavage and Repair during Programmed Genome Rearrangements in the Ciliate
- Functional Specialization Among Members Of Knickkopf Family Of Proteins In Insect Cuticle Organization
- Playing RNase P Evolution: Swapping the RNA Catalyst for a Protein Reveals Functional Uniformity of Highly Divergent Enzyme Forms
- The Translational Regulators GCN-1 and ABCF-3 Act Together to Promote Apoptosis in
- Meta-Analysis of Genome-Wide Association Studies in African Americans Provides Insights into the Genetic Architecture of Type 2 Diabetes
- A -Regulatory Mutation of Causes Silky-Feather in Chickens
- VIB1, a Link between Glucose Signaling and Carbon Catabolite Repression, Is Essential for Plant Cell Wall Degradation by
- A Population Genetic Signal of Polygenic Adaptation
- A Conserved Dopamine-Cholecystokinin Signaling Pathway Shapes Context–Dependent Behavior
- The MAP Kinase p38 Is Part of Circadian Clock
- The Cohesin Subunit Rad21 Is Required for Synaptonemal Complex Maintenance, but Not Sister Chromatid Cohesion, during Drosophila Female Meiosis
- PLOS Genetics
- Archív čísel
- Aktuálne číslo
- Informácie o časopise
Najčítanejšie v tomto čísle- Meta-Analysis of Genome-Wide Association Studies in African Americans Provides Insights into the Genetic Architecture of Type 2 Diabetes
- KDM6 Demethylase Independent Loss of Histone H3 Lysine 27 Trimethylation during Early Embryonic Development
- The RNA Helicases AtMTR4 and HEN2 Target Specific Subsets of Nuclear Transcripts for Degradation by the Nuclear Exosome in
- EF-P Dependent Pauses Integrate Proximal and Distal Signals during Translation
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