1
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Domingo E, Witzany G. Quasispecies productivity. THE SCIENCE OF NATURE - NATURWISSENSCHAFTEN 2024; 111:11. [PMID: 38372790 DOI: 10.1007/s00114-024-01897-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/05/2024] [Accepted: 02/06/2024] [Indexed: 02/20/2024]
Abstract
The quasispecies theory is a helpful concept in the explanation of RNA virus evolution and behaviour, with a relevant impact on methods used to fight viral diseases. It has undergone some adaptations to integrate new empirical data, especially the non-deterministic nature of mutagenesis, and the variety of behavioural motifs in cooperation, competition, communication, innovation, integration, and exaptation. Also, the consortial structure of quasispecies with complementary roles of memory genomes of minority populations better fits the empirical data than did the original concept of a master sequence and its mutant spectra. The high productivity of quasispecies variants generates unique sequences that never existed before and will never exist again. In the present essay, we underline that such sequences represent really new ontological entities, not just error copies of previous ones. Their primary unique property, the incredible variant production, is suggested here as quasispecies productivity, which replaces the error-replication narrative to better fit into a new relationship between mankind and living nature in the twenty-first century.
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Affiliation(s)
- Esteban Domingo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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2
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Pham TM, Miffin T, Sun H, Sharp KK, Wang X, Zhu M, Hoshika S, Peterson RJ, Benner SA, Kahn JD, Mathews DH. DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters. ACS Synth Biol 2023; 12:2750-2763. [PMID: 37671922 PMCID: PMC10510751 DOI: 10.1021/acssynbio.3c00358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Indexed: 09/07/2023]
Abstract
We show that in silico design of DNA secondary structures is improved by extending the base pairing alphabet beyond A-T and G-C to include the pair between 2-amino-8-(1'-β-d-2'-deoxyribofuranosyl)-imidazo-[1,2-a]-1,3,5-triazin-(8H)-4-one and 6-amino-3-(1'-β-d-2'-deoxyribofuranosyl)-5-nitro-(1H)-pyridin-2-one, abbreviated as P and Z. To obtain the thermodynamic parameters needed to include P-Z pairs in the designs, we performed 47 optical melting experiments and combined the results with previous work to fit free energy and enthalpy nearest neighbor folding parameters for P-Z pairs and G-Z wobble pairs. We find G-Z pairs have stability comparable to that of A-T pairs and should therefore be included as base pairs in structure prediction and design algorithms. Additionally, we extrapolated the set of loop, terminal mismatch, and dangling end parameters to include the P and Z nucleotides. These parameters were incorporated into the RNAstructure software package for secondary structure prediction and analysis. Using the RNAstructure Design program, we solved 99 of the 100 design problems posed by Eterna using the ACGT alphabet or supplementing it with P-Z pairs. Extending the alphabet reduced the propensity of sequences to fold into off-target structures, as evaluated by the normalized ensemble defect (NED). The NED values were improved relative to those from the Eterna example solutions in 91 of 99 cases in which Eterna-player solutions were provided. P-Z-containing designs had average NED values of 0.040, significantly below the 0.074 of standard-DNA-only designs, and inclusion of the P-Z pairs decreased the time needed to converge on a design. This work provides a sample pipeline for inclusion of any expanded alphabet nucleotides into prediction and design workflows.
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Affiliation(s)
- Tuan M. Pham
- Department
of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, United States
| | - Terrel Miffin
- Department
of Chemistry & Biochemistry, University
of Maryland, College
Park, Maryland 20742, United States
| | - Hongying Sun
- Department
of Surgery, University of Rochester Medical
Center, Rochester, New York 14642, United States
| | - Kenneth K. Sharp
- Department
of Chemistry & Biochemistry, University
of Maryland, College
Park, Maryland 20742, United States
| | - Xiaoyu Wang
- Department
of Chemistry & Biochemistry, University
of Maryland, College
Park, Maryland 20742, United States
| | - Mingyi Zhu
- Department
of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, United States
| | - Shuichi Hoshika
- Foundation
for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | | | - Steven A. Benner
- Foundation
for Applied Molecular Evolution, Alachua, Florida 32615, United States
| | - Jason D. Kahn
- Department
of Chemistry & Biochemistry, University
of Maryland, College
Park, Maryland 20742, United States
| | - David H. Mathews
- Department
of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, United States
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3
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Pham TM, Miffin T, Sun H, Sharp KK, Wang X, Zhu M, Hoshika S, Peterson RJ, Benner SA, Kahn JD, Mathews DH. DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.06.543917. [PMID: 37333404 PMCID: PMC10274641 DOI: 10.1101/2023.06.06.543917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
We show that in silico design of DNA secondary structures is improved by extending the base pairing alphabet beyond A-T and G-C to include the pair between 2-amino-8-(1'-β-D-2'-deoxyribofuranosyl)-imidazo-[1,2- a ]-1,3,5-triazin-(8 H )-4-one and 6-amino-3-(1'-β-D-2'-deoxyribofuranosyl)-5-nitro-(1 H )-pyridin-2-one, simply P and Z. To obtain the thermodynamic parameters needed to include P-Z pairs in the designs, we performed 47 optical melting experiments and combined the results with previous work to fit a new set of free energy and enthalpy nearest neighbor folding parameters for P-Z pairs and G-Z wobble pairs. We find that G-Z pairs have stability comparable to A-T pairs and therefore should be considered quantitatively by structure prediction and design algorithms. Additionally, we extrapolated the set of loop, terminal mismatch, and dangling end parameters to include P and Z nucleotides. These parameters were incorporated into the RNAstructure software package for secondary structure prediction and analysis. Using the RNAstructure Design program, we solved 99 of the 100 design problems posed by Eterna using the ACGT alphabet or supplementing with P-Z pairs. Extending the alphabet reduced the propensity of sequences to fold into off-target structures, as evaluated by the normalized ensemble defect (NED). The NED values were improved relative to those from the Eterna example solutions in 91 of 99 cases where Eterna-player solutions were provided. P-Z-containing designs had average NED values of 0.040, significantly below the 0.074 of standard-DNA-only designs, and inclusion of the P-Z pairs decreased the time needed to converge on a design. This work provides a sample pipeline for inclusion of any expanded alphabet nucleotides into prediction and design workflows.
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Affiliation(s)
- Tuan M. Pham
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, NY
| | - Terrel Miffin
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD
| | - Hongying Sun
- Department of Surgery, University of Rochester Medical Center, Rochester, NY
| | - Kenneth K. Sharp
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD
| | - Xiaoyu Wang
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD
| | - Mingyi Zhu
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, NY
| | | | | | | | - Jason D. Kahn
- Department of Chemistry & Biochemistry, University of Maryland, College Park, MD
| | - David H. Mathews
- Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, NY
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4
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Random and Natural Non-Coding RNA Have Similar Structural Motif Patterns but Differ in Bulge, Loop, and Bond Counts. Life (Basel) 2023; 13:life13030708. [PMID: 36983865 PMCID: PMC10054693 DOI: 10.3390/life13030708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/15/2023] [Accepted: 02/27/2023] [Indexed: 03/08/2023] Open
Abstract
An important question in evolutionary biology is whether (and in what ways) genotype–phenotype (GP) map biases can influence evolutionary trajectories. Untangling the relative roles of natural selection and biases (and other factors) in shaping phenotypes can be difficult. Because the RNA secondary structure (SS) can be analyzed in detail mathematically and computationally, is biologically relevant, and a wealth of bioinformatic data are available, it offers a good model system for studying the role of bias. For quite short RNA (length L≤126), it has recently been shown that natural and random RNA types are structurally very similar, suggesting that bias strongly constrains evolutionary dynamics. Here, we extend these results with emphasis on much larger RNA with lengths up to 3000 nucleotides. By examining both abstract shapes and structural motif frequencies (i.e., the number of helices, bonds, bulges, junctions, and loops), we find that large natural and random structures are also very similar, especially when contrasted to typical structures sampled from the spaces of all possible RNA structures. Our motif frequency study yields another result, where the frequencies of different motifs can be used in machine learning algorithms to classify random and natural RNA with high accuracy, especially for longer RNA (e.g., ROC AUC 0.86 for L = 1000). The most important motifs for classification are the number of bulges, loops, and bonds. This finding may be useful in using SS to detect candidates for functional RNA within ‘junk’ DNA regions.
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5
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Villarreal L, Witzany G. Self-empowerment of life through RNA networks, cells and viruses. F1000Res 2023; 12:138. [PMID: 36785664 PMCID: PMC9918806 DOI: 10.12688/f1000research.130300.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/20/2023] [Indexed: 01/05/2024] Open
Abstract
Our understanding of the key players in evolution and of the development of all organisms in all domains of life has been aided by current knowledge about RNA stem-loop groups, their proposed interaction motifs in an early RNA world and their regulative roles in all steps and substeps of nearly all cellular processes, such as replication, transcription, translation, repair, immunity and epigenetic marking. Cooperative evolution was enabled by promiscuous interactions between single-stranded regions in the loops of naturally forming stem-loop structures in RNAs. It was also shown that cooperative RNA stem-loops outcompete selfish ones and provide foundational self-constructive groups (ribosome, editosome, spliceosome, etc.). Self-empowerment from abiotic matter to biological behavior does not just occur at the beginning of biological evolution; it is also essential for all levels of socially interacting RNAs, cells and viruses.
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Affiliation(s)
- Luis Villarreal
- Center for Virus Research, University of California, Irvine, California, USA
| | - Guenther Witzany
- Telos - Philosophische Praxis, Buermoos, Salzburg, 5111, Austria
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6
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Villarreal L, Witzany G. Self-empowerment of life through RNA networks, cells and viruses. F1000Res 2023; 12:138. [PMID: 36785664 PMCID: PMC9918806 DOI: 10.12688/f1000research.130300.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/23/2023] [Indexed: 03/08/2023] Open
Abstract
Our understanding of the key players in evolution and of the development of all organisms in all domains of life has been aided by current knowledge about RNA stem-loop groups, their proposed interaction motifs in an early RNA world and their regulative roles in all steps and substeps of nearly all cellular processes, such as replication, transcription, translation, repair, immunity and epigenetic marking. Cooperative evolution was enabled by promiscuous interactions between single-stranded regions in the loops of naturally forming stem-loop structures in RNAs. It was also shown that cooperative RNA stem-loops outcompete selfish ones and provide foundational self-constructive groups (ribosome, editosome, spliceosome, etc.). Self-empowerment from abiotic matter to biological behavior does not just occur at the beginning of biological evolution; it is also essential for all levels of socially interacting RNAs, cells and viruses.
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Affiliation(s)
- Luis Villarreal
- Center for Virus Research, University of California, Irvine, California, USA
| | - Guenther Witzany
- Telos - Philosophische Praxis, Buermoos, Salzburg, 5111, Austria
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7
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Metrics for RNA Secondary Structure Comparison. Methods Mol Biol 2023; 2586:79-88. [PMID: 36705899 DOI: 10.1007/978-1-0716-2768-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
RNA secondary structure comparison is one of the important analyses for elucidating individual functions of RNAs since it is widely accepted that their functions and structures are strongly correlated. However, although the RNA secondary structures with pseudoknot play important roles in vivo, it is difficult to deal with such structures in silico due to their structural complexity, which is a major obstacle to the analysis of RNA functions.Here, we introduce an algorithm and a metric for comparing pseudoknotted RNA secondary structures based on topological centroid identification and tree edit distance and describe the usage protocol of a software enabling us to run the comparison. This software is publicly available and works on both Microsoft Windows and Apple macOS.
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8
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Dingle K, Novev JK, Ahnert SE, Louis AA. Predicting phenotype transition probabilities via conditional algorithmic probability approximations. J R Soc Interface 2022; 19:20220694. [PMID: 36514888 PMCID: PMC9748496 DOI: 10.1098/rsif.2022.0694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Unravelling the structure of genotype-phenotype (GP) maps is an important problem in biology. Recently, arguments inspired by algorithmic information theory (AIT) and Kolmogorov complexity have been invoked to uncover simplicity bias in GP maps, an exponentially decaying upper bound in phenotype probability with the increasing phenotype descriptional complexity. This means that phenotypes with many genotypes assigned via the GP map must be simple, while complex phenotypes must have few genotypes assigned. Here, we use similar arguments to bound the probability P(x → y) that phenotype x, upon random genetic mutation, transitions to phenotype y. The bound is [Formula: see text], where [Formula: see text] is the estimated conditional complexity of y given x, quantifying how much extra information is required to make y given access to x. This upper bound is related to the conditional form of algorithmic probability from AIT. We demonstrate the practical applicability of our derived bound by predicting phenotype transition probabilities (and other related quantities) in simulations of RNA and protein secondary structures. Our work contributes to a general mathematical understanding of GP maps and may facilitate the prediction of transition probabilities directly from examining phenotype themselves, without utilizing detailed knowledge of the GP map.
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Affiliation(s)
- Kamaludin Dingle
- Department of Chemical Engineering and Biotechnology, Cambridge University, Cambridge CB2 1TN, UK,Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125, USA,Department of Mathematics and Natural Sciences, Centre for Applied Mathematics and Bioinformatics (CAMB), Gulf University for Science and Technology, 32093, Kuwait
| | - Javor K. Novev
- Department of Chemical Engineering and Biotechnology, Cambridge University, Cambridge CB2 1TN, UK
| | - Sebastian E. Ahnert
- Department of Chemical Engineering and Biotechnology, Cambridge University, Cambridge CB2 1TN, UK
| | - Ard A. Louis
- Department of Physics, Rudolf Peierls Centre for Theoretical Physics, Oxford University, Oxford OX1 2JD, UK
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9
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Dingle K, Ghaddar F, Šulc P, Louis AA. Phenotype Bias Determines How Natural RNA Structures Occupy the Morphospace of All Possible Shapes. Mol Biol Evol 2022; 39:msab280. [PMID: 34542628 PMCID: PMC8763027 DOI: 10.1093/molbev/msab280] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Morphospaces-representations of phenotypic characteristics-are often populated unevenly, leaving large parts unoccupied. Such patterns are typically ascribed to contingency, or else to natural selection disfavoring certain parts of the morphospace. The extent to which developmental bias, the tendency of certain phenotypes to preferentially appear as potential variation, also explains these patterns is hotly debated. Here we demonstrate quantitatively that developmental bias is the primary explanation for the occupation of the morphospace of RNA secondary structure (SS) shapes. Upon random mutations, some RNA SS shapes (the frequent ones) are much more likely to appear than others. By using the RNAshapes method to define coarse-grained SS classes, we can directly compare the frequencies that noncoding RNA SS shapes appear in the RNAcentral database to frequencies obtained upon a random sampling of sequences. We show that: 1) only the most frequent structures appear in nature; the vast majority of possible structures in the morphospace have not yet been explored; 2) remarkably small numbers of random sequences are needed to produce all the RNA SS shapes found in nature so far; and 3) perhaps most surprisingly, the natural frequencies are accurately predicted, over several orders of magnitude in variation, by the likelihood that structures appear upon a uniform random sampling of sequences. The ultimate cause of these patterns is not natural selection, but rather a strong phenotype bias in the RNA genotype-phenotype map, a type of developmental bias or "findability constraint," which limits evolutionary dynamics to a hugely reduced subset of structures that are easy to "find."
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Affiliation(s)
- Kamaludin Dingle
- Centre for Applied Mathematics and Bioinformatics, Department of Mathematics and Natural Sciences, Gulf University for Science and Technology, Hawally, Kuwait
| | - Fatme Ghaddar
- Centre for Applied Mathematics and Bioinformatics, Department of Mathematics and Natural Sciences, Gulf University for Science and Technology, Hawally, Kuwait
| | - Petr Šulc
- School of Molecular Sciences and Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, United Kingdom
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10
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Manrubia S, Cuesta JA, Aguirre J, Ahnert SE, Altenberg L, Cano AV, Catalán P, Diaz-Uriarte R, Elena SF, García-Martín JA, Hogeweg P, Khatri BS, Krug J, Louis AA, Martin NS, Payne JL, Tarnowski MJ, Weiß M. From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics. Phys Life Rev 2021; 38:55-106. [PMID: 34088608 DOI: 10.1016/j.plrev.2021.03.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/01/2021] [Indexed: 12/21/2022]
Abstract
Understanding how genotypes map onto phenotypes, fitness, and eventually organisms is arguably the next major missing piece in a fully predictive theory of evolution. We refer to this generally as the problem of the genotype-phenotype map. Though we are still far from achieving a complete picture of these relationships, our current understanding of simpler questions, such as the structure induced in the space of genotypes by sequences mapped to molecular structures, has revealed important facts that deeply affect the dynamical description of evolutionary processes. Empirical evidence supporting the fundamental relevance of features such as phenotypic bias is mounting as well, while the synthesis of conceptual and experimental progress leads to questioning current assumptions on the nature of evolutionary dynamics-cancer progression models or synthetic biology approaches being notable examples. This work delves with a critical and constructive attitude into our current knowledge of how genotypes map onto molecular phenotypes and organismal functions, and discusses theoretical and empirical avenues to broaden and improve this comprehension. As a final goal, this community should aim at deriving an updated picture of evolutionary processes soundly relying on the structural properties of genotype spaces, as revealed by modern techniques of molecular and functional analysis.
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Affiliation(s)
- Susanna Manrubia
- Department of Systems Biology, Centro Nacional de Biotecnología (CSIC), Madrid, Spain; Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain.
| | - José A Cuesta
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain; Departamento de Matemáticas, Universidad Carlos III de Madrid, Leganés, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BiFi), Universidad de Zaragoza, Spain; UC3M-Santander Big Data Institute (IBiDat), Getafe, Madrid, Spain
| | - Jacobo Aguirre
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain; Centro de Astrobiología, CSIC-INTA, ctra. de Ajalvir km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Sebastian E Ahnert
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, UK; The Alan Turing Institute, British Library, 96 Euston Road, London NW1 2DB, UK
| | | | - Alejandro V Cano
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Pablo Catalán
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain; Departamento de Matemáticas, Universidad Carlos III de Madrid, Leganés, Spain
| | - Ramon Diaz-Uriarte
- Department of Biochemistry, Universidad Autónoma de Madrid, Madrid, Spain; Instituto de Investigaciones Biomédicas "Alberto Sols" (UAM-CSIC), Madrid, Spain
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas, I(2)SysBio (CSIC-UV), València, Spain; The Santa Fe Institute, Santa Fe, NM, USA
| | | | - Paulien Hogeweg
- Theoretical Biology and Bioinformatics Group, Utrecht University, the Netherlands
| | - Bhavin S Khatri
- The Francis Crick Institute, London, UK; Department of Life Sciences, Imperial College London, London, UK
| | - Joachim Krug
- Institute for Biological Physics, University of Cologne, Köln, Germany
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, UK
| | - Nora S Martin
- Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, Cambridge, UK; Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Joshua L Payne
- Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | - Marcel Weiß
- Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, Cambridge, UK; Sainsbury Laboratory, University of Cambridge, Cambridge, UK
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11
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Villarreal LP, Witzany G. Social Networking of Quasi-Species Consortia drive Virolution via Persistence. AIMS Microbiol 2021; 7:138-162. [PMID: 34250372 PMCID: PMC8255905 DOI: 10.3934/microbiol.2021010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 04/25/2021] [Indexed: 12/31/2022] Open
Abstract
The emergence of cooperative quasi-species consortia (QS-C) thinking from the more accepted quasispecies equations of Manfred Eigen, provides a conceptual foundation from which concerted action of RNA agents can now be understood. As group membership becomes a basic criteria for the emergence of living systems, we also start to understand why the history and context of social RNA networks become crucial for survival and function. History and context of social RNA networks also lead to the emergence of a natural genetic code. Indeed, this QS-C thinking can also provide us with a transition point between the chemical world of RNA replicators and the living world of RNA agents that actively differentiate self from non-self and generate group identity with membership roles. Importantly the social force of a consortia to solve complex, multilevel problems also depend on using opposing and minority functions. The consortial action of social networks of RNA stem-loops subsequently lead to the evolution of cellular organisms representing a tree of life.
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12
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Wang F, Akutsu T, Mori T. Comparison of Pseudoknotted RNA Secondary Structures by Topological Centroid Identification and Tree Edit Distance. J Comput Biol 2020; 27:1443-1451. [PMID: 32058802 DOI: 10.1089/cmb.2019.0512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Comparison of RNA structures is one of the most crucial analysis for elucidating their individual functions and promoting medical applications. Because it is widely accepted that their functions and structures are strongly correlated, various methods for RNA secondary structure analysis have been proposed owing to the difficulty in predicting RNA three-dimensional structure directly from its sequence. However, there are few methods dealing with RNA secondary structures with a specific and complex partial structure called pseudoknot despite its significance to biological process, which is a big obstacle for analyzing their functions. In this study, we propose a novel tree representation of pseudoknotted RNA secondary structures by topological centroid identification and their comparison methods based on the tree edit distance. In the proposed method, a given graph representing an RNA secondary structure is transformed to a tree rooted at one of the vertices constituting the topological centroid that is identified by removing cycles with peeling processing for the graph. When comparing tree-represented RNA secondary structures collected from a public database using the tree edit distance and functional gene groups defined by Gene Ontology (GO), the proposed method showed better clustering results according to their GOs than canonical RNA sequence-based comparison. In addition, we also report a case that the combination of the tree edit distance and the sequence edit distance shows a better classification of the pseudoknotted RNA secondary structures.
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Affiliation(s)
- Feiqi Wang
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Tatsuya Akutsu
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan
| | - Tomoya Mori
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan
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13
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Oliver CG, Reinharz V, Waldispühl J. On the emergence of structural complexity in RNA replicators. RNA (NEW YORK, N.Y.) 2019; 25:1579-1591. [PMID: 31467146 PMCID: PMC6859851 DOI: 10.1261/rna.070391.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 08/19/2019] [Indexed: 06/10/2023]
Abstract
The RNA world hypothesis relies on the ability of ribonucleic acids to spontaneously acquire complex structures capable of supporting essential biological functions. Multiple sophisticated evolutionary models have been proposed for their emergence, but they often assume specific conditions. In this work, we explore a simple and parsimonious scenario describing the emergence of complex molecular structures at the early stages of life. We show that at specific GC content regimes, an undirected replication model is sufficient to explain the apparition of multibranched RNA secondary structures-a structural signature of many essential ribozymes. We ran a large-scale computational study to map energetically stable structures on complete mutational networks of 50-nt-long RNA sequences. Our results reveal that the sequence landscape with stable structures is enriched with multibranched structures at a length scale coinciding with the appearance of complex structures in RNA databases. A random replication mechanism preserving a 50% GC content may suffice to explain a natural enrichment of stable complex structures in populations of functional RNAs. In contrast, an evolutionary mechanism eliciting the most stable folds at each generation appears to help reaching multibranched structures at highest GC content.
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Affiliation(s)
- Carlos G Oliver
- School of Computer Science, McGill University, Montreal, QC H3A 2B3, Canada
| | - Vladimir Reinharz
- Center for Soft and Living Matter, Institute for Basic Science, Ulsan 34126, South Korea
| | - Jérôme Waldispühl
- School of Computer Science, McGill University, Montreal, QC H3A 2B3, Canada
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14
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Danaee P, Rouches M, Wiley M, Deng D, Huang L, Hendrix D. bpRNA: large-scale automated annotation and analysis of RNA secondary structure. Nucleic Acids Res 2019; 46:5381-5394. [PMID: 29746666 PMCID: PMC6009582 DOI: 10.1093/nar/gky285] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/11/2018] [Indexed: 01/04/2023] Open
Abstract
While RNA secondary structure prediction from sequence data has made remarkable progress, there is a need for improved strategies for annotating the features of RNA secondary structures. Here, we present bpRNA, a novel annotation tool capable of parsing RNA structures, including complex pseudoknot-containing RNAs, to yield an objective, precise, compact, unambiguous, easily-interpretable description of all loops, stems, and pseudoknots, along with the positions, sequence, and flanking base pairs of each such structural feature. We also introduce several new informative representations of RNA structure types to improve structure visualization and interpretation. We have further used bpRNA to generate a web-accessible meta-database, ‘bpRNA-1m’, of over 100 000 single-molecule, known secondary structures; this is both more fully and accurately annotated and over 20-times larger than existing databases. We use a subset of the database with highly similar (≥90% identical) sequences filtered out to report on statistical trends in sequence, flanking base pairs, and length. Both the bpRNA method and the bpRNA-1m database will be valuable resources both for specific analysis of individual RNA molecules and large-scale analyses such as are useful for updating RNA energy parameters for computational thermodynamic predictions, improving machine learning models for structure prediction, and for benchmarking structure-prediction algorithms.
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Affiliation(s)
| | | | | | - Dezhong Deng
- School of Electrical Engineering and Computer Science
| | - Liang Huang
- School of Electrical Engineering and Computer Science
| | - David Hendrix
- School of Electrical Engineering and Computer Science.,Department of Biochemistry and Biophysics
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15
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Villarreal LP, Witzany G. That is life: communicating RNA networks from viruses and cells in continuous interaction. Ann N Y Acad Sci 2019; 1447:5-20. [PMID: 30865312 DOI: 10.1111/nyas.14040] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/13/2019] [Accepted: 01/31/2019] [Indexed: 02/06/2023]
Abstract
All the conserved detailed results of evolution stored in DNA must be read, transcribed, and translated via an RNA-mediated process. This is required for the development and growth of each individual cell. Thus, all known living organisms fundamentally depend on these RNA-mediated processes. In most cases, they are interconnected with other RNAs and their associated protein complexes and function in a strictly coordinated hierarchy of temporal and spatial steps (i.e., an RNA network). Clearly, all cellular life as we know it could not function without these key agents of DNA replication, namely rRNA, tRNA, and mRNA. Thus, any definition of life that lacks RNA functions and their networks misses an essential requirement for RNA agents that inherently regulate and coordinate (communicate to) cells, tissues, organs, and organisms. The precellular evolution of RNAs occurred at the core of the emergence of cellular life and the question remained of how both precellular and cellular levels are interconnected historically and functionally. RNA networks and RNA communication can interconnect these levels. With the reemergence of virology in evolution, it became clear that communicating viruses and subviral infectious genetic parasites are bridging these two levels by invading, integrating, coadapting, exapting, and recombining constituent parts in host genomes for cellular requirements in gene regulation and coordination aims. Therefore, a 21st century understanding of life is of an inherently social process based on communicating RNA networks, in which viruses and cells continuously interact.
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Affiliation(s)
- Luis P Villarreal
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California
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Bellaousov S, Kayedkhordeh M, Peterson RJ, Mathews DH. Accelerated RNA secondary structure design using preselected sequences for helices and loops. RNA (NEW YORK, N.Y.) 2018; 24:1555-1567. [PMID: 30097542 PMCID: PMC6191713 DOI: 10.1261/rna.066324.118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 08/06/2018] [Indexed: 06/08/2023]
Abstract
Nucleic acids can be designed to be nano-machines, pharmaceuticals, or probes. RNA secondary structures can form the basis of self-assembling nanostructures. There are only four natural RNA bases, therefore it can be difficult to design sequences that fold to a single, specified structure because many other structures are often possible for a given sequence. One approach taken by state-of-the-art sequence design methods is to select sequences that fold to the specified structure using stochastic, iterative refinement. The goal of this work is to accelerate design. Many existing iterative methods select and refine sequences one base pair and one unpaired nucleotide at a time. Here, the hypothesis that sequences can be preselected in order to accelerate design was tested. To this aim, a database was built of helix sequences that demonstrate thermodynamic features found in natural sequences and that also have little tendency to cross-hybridize. Additionally, a database was assembled of RNA loop sequences with low helix-formation propensity and little tendency to cross-hybridize with either the helices or other loops. These databases of preselected sequences accelerate the selection of sequences that fold with minimal ensemble defect by replacing some of the trial and error of current refinement approaches. When using the database of preselected sequences as compared to randomly chosen sequences, sequences for natural structures are designed 36 times faster, and random structures are designed six times faster. The sequences selected with the aid of the database have similar ensemble defect as those sequences selected at random. The sequence database is part of RNAstructure package at http://rna.urmc.rochester.edu/RNAstructure.html.
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Affiliation(s)
- Stanislav Bellaousov
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | - Mohammad Kayedkhordeh
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
| | | | - David H Mathews
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, New York 14642, USA
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17
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Haney SA. High-Content Screening Approaches That Minimize Confounding Factors in RNAi, CRISPR, and Small Molecule Screening. Methods Mol Biol 2018; 1683:113-130. [PMID: 29082490 DOI: 10.1007/978-1-4939-7357-6_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Screening arrayed libraries of reagents, particularly small molecules began as a vehicle for drug discovery, but the in last few years it has become a cornerstone of biological investigation, joining RNAi and CRISPR as methods for elucidating functional relationships that could not be anticipated, and illustrating the mechanisms behind basic and disease biology, and therapeutic resistance. However, these approaches share some common challenges, especially with respect to specificity or selectivity of the reagents as they are scaled to large protein families or the genome. High-content screening (HCS) has emerged as an important complement to screening, mostly the result of a wide array of specific molecular events, such as protein kinase and transcription factor activation, morphological changes associated with stem cell differentiation or the epithelial-mesenchymal transition of cancer cells. Beyond the range of cellular events that can be screened by HCS, image-based screening introduces new processes for differentiating between specific and nonspecific effects on cells. This chapter introduces these complexities and discusses strategies available in image-based screening that can mitigate the challenges they can bring to screening.
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Affiliation(s)
- Steven A Haney
- Cancer Biology and the Tumor Microenvironment, Discovery Oncology, Lilly Research Laboratories/Lilly Corporate Center, Eli Lilly and Company, Indianapolis, IN, 46285, USA.
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18
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Witzany G. Two genetic codes: Repetitive syntax for active non-coding RNAs; non-repetitive syntax for the DNA archives. Commun Integr Biol 2017; 10:e1297352. [PMID: 29149223 PMCID: PMC5398208 DOI: 10.1080/19420889.2017.1297352] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 02/16/2017] [Indexed: 02/06/2023] Open
Abstract
Current knowledge of the RNA world indicates 2 different genetic codes being present throughout the living world. In contrast to non-coding RNAs that are built of repetitive nucleotide syntax, the sequences that serve as templates for proteins share-as main characteristics-a non-repetitive syntax. Whereas non-coding RNAs build groups that serve as regulatory tools in nearly all genetic processes, the coding sections represent the evolutionarily successful function of the genetic information storage medium. This indicates that the differences in their syntax structure are coherent with the differences of the functions they represent. Interestingly, these 2 genetic codes resemble the function of all natural languages, i.e., the repetitive non-coding sequences serve as appropriate tool for organization, coordination and regulation of group behavior, and the non-repetitive coding sequences are for conservation of instrumental constructions, plans, blueprints for complex protein-body architecture. This differentiation may help to better understand RNA group behavioral motifs.
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Witzany G. The biocommunication method: On the road to an integrative biology. Commun Integr Biol 2016; 9:e1164374. [PMID: 27195071 PMCID: PMC4857777 DOI: 10.1080/19420889.2016.1164374] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 03/01/2016] [Accepted: 03/07/2016] [Indexed: 02/06/2023] Open
Abstract
Although molecular biology, genetics, and related special disciplines represent a large amount of empirical data, a practical method for the evaluation and overview of current knowledge is far from being realized. The main concepts and narratives in these fields have remained nearly the same for decades and the more recent empirical data concerning the role of noncoding RNAs and persistent viruses and their defectives do not fit into this scenario. A more innovative approach such as applied biocommunication theory could translate empirical data into a coherent perspective on the functions within and between biological organisms and arguably lead to a sustainable integrative biology.
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20
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Crucial steps to life: From chemical reactions to code using agents. Biosystems 2016; 140:49-57. [DOI: 10.1016/j.biosystems.2015.12.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 12/05/2015] [Accepted: 12/07/2015] [Indexed: 01/21/2023]
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Dingle K, Schaper S, Louis AA. The structure of the genotype-phenotype map strongly constrains the evolution of non-coding RNA. Interface Focus 2015; 5:20150053. [PMID: 26640651 DOI: 10.1098/rsfs.2015.0053] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The prevalence of neutral mutations implies that biological systems typically have many more genotypes than phenotypes. But, can the way that genotypes are distributed over phenotypes determine evolutionary outcomes? Answering such questions is difficult, in part because the number of genotypes can be hyper-astronomically large. By solving the genotype-phenotype (GP) map for RNA secondary structure (SS) for systems up to length L = 126 nucleotides (where the set of all possible RNA strands would weigh more than the mass of the visible universe), we show that the GP map strongly constrains the evolution of non-coding RNA (ncRNA). Simple random sampling over genotypes predicts the distribution of properties such as the mutational robustness or the number of stems per SS found in naturally occurring ncRNA with surprising accuracy. Because we ignore natural selection, this strikingly close correspondence with the mapping suggests that structures allowing for functionality are easily discovered, despite the enormous size of the genetic spaces. The mapping is extremely biased: the majority of genotypes map to an exponentially small portion of the morphospace of all biophysically possible structures. Such strong constraints provide a non-adaptive explanation for the convergent evolution of structures such as the hammerhead ribozyme. These results present a particularly clear example of bias in the arrival of variation strongly shaping evolutionary outcomes and may be relevant to Mayr's distinction between proximate and ultimate causes in evolutionary biology.
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Affiliation(s)
- Kamaludin Dingle
- Rudolf Peierls Centre for Theoretical Physics , University of Oxford , Oxford OX1 3NP , UK ; Systems Biology DTC , University of Oxford , Oxford , UK ; Department of Mathematics and Natural Sciences , Gulf University for Science and Technology , Block 5, West Mishref , Kuwait
| | - Steffen Schaper
- Rudolf Peierls Centre for Theoretical Physics , University of Oxford , Oxford OX1 3NP , UK
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics , University of Oxford , Oxford OX1 3NP , UK
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22
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Abstract
Manfred Eigen extended Erwin Schroedinger's concept of "life is physics and chemistry" through the introduction of information theory and cybernetic systems theory into "life is physics and chemistry and information." Based on this assumption, Eigen developed the concepts of quasispecies and hypercycles, which have been dominant in molecular biology and virology ever since. He insisted that the genetic code is not just used metaphorically: it represents a real natural language. However, the basics of scientific knowledge changed dramatically within the second half of the 20th century. Unfortunately, Eigen ignored the results of the philosophy of science discourse on essential features of natural languages and codes: a natural language or code emerges from populations of living agents that communicate. This contribution will look at some of the highlights of this historical development and the results relevant for biological theories about life.
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Witzany G. RNA sociology: group behavioral motifs of RNA consortia. Life (Basel) 2014; 4:800-18. [PMID: 25426799 PMCID: PMC4284468 DOI: 10.3390/life4040800] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 11/11/2014] [Accepted: 11/12/2014] [Indexed: 02/07/2023] Open
Abstract
RNA sociology investigates the behavioral motifs of RNA consortia from the social science perspective. Besides the self-folding of RNAs into single stem loop structures, group building of such stem loops results in a variety of essential agents that are highly active in regulatory processes in cellular and non-cellular life. RNA stem loop self-folding and group building do not depend solely on sequence syntax; more important are their contextual (functional) needs. Also, evolutionary processes seem to occur through RNA stem loop consortia that may act as a complement. This means the whole entity functions only if all participating parts are coordinated, although the complementary building parts originally evolved for different functions. If complementary groups, such as rRNAs and tRNAs, are placed together in selective pressure contexts, new evolutionary features may emerge. Evolution initiated by competent agents in natural genome editing clearly contrasts with statistical error replication narratives.
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Affiliation(s)
- Guenther Witzany
- Telos-Philosophische Praxis, Vogelsangstraße 18c, 5111-Buermoos, Austria.
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24
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Formation of Cytoplasmic P-Bodies inSakeYeast during JapaneseSakeBrewing and Wine Making. Biosci Biotechnol Biochem 2014; 71:2800-7. [DOI: 10.1271/bbb.70417] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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25
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Mallatt J, Chittenden KD. The GC content of LSU rRNA evolves across topological and functional regions of the ribosome in all three domains of life. Mol Phylogenet Evol 2014; 72:17-30. [PMID: 24394731 DOI: 10.1016/j.ympev.2013.12.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 11/28/2013] [Accepted: 12/24/2013] [Indexed: 12/21/2022]
Abstract
Large-subunit rRNA is the ribozyme that catalyzes protein synthesis by translation, and many of its features vary along a deep-to-superficial gradient. By measuring the G+C proportions in this rRNA in all three domains of life (60 bacteria, 379 eukaryote, and 23 archaean sequences), we tested whether the proportion of GC nucleotides varies along this in-out gradient. The rRNA regions used were several zones identified by Bokov and Steinberg (2009) as being arranged from deep to superficial within the LSU. To the Bokov-Steinberg zones, we added the most superficial zone of all, the divergent domains (expansion segments), which are greatly enlarged in eukaryotes. Regression lines constructed from the hundreds of species of organisms revealed the expected in-out gradient, showing that species with high %GC (or high %AT) in their rRNA distribute more of these abundant nucleotides into the peripheral zones. This could be explained by the evolutionary rates of replacement of all nucleotides (A, C, G, T), because these latter rates are fastest at the periphery and slowest near the conserved core. As an overall explanation, we propose that when extrinsic factors (whole-genome nucleotide composition, or environmental temperature) demand the percentage of GC in the rRNA of a species be high or low, then the deep-lying zones are buffered against GC variation because they are the slowest to evolve. The deep, conserved zones are also the most involved in translation, hinting that stabilizing selection there prevents a high GC variability that would diminish LSU rRNA's core functions. We found only a few domain-specific trends in rRNA-GC distribution, which relate to many Archaea living at high temperatures or to the highly complex genes and adaptations of Eukaryota. Use of rRNA sequences in molecular phylogenetic studies, for reconstructing the relationships of organisms across the tree of life, requires accurate models of how rRNA evolves. The demonstration that GC distributes in regular patterns across rRNA regions can improve these tree-reconstruction models in the future and should yield phylogenies of greater accuracy.
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Affiliation(s)
- Jon Mallatt
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, United States.
| | - Kevin D Chittenden
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, United States
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26
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Novikova IV, Hennelly SP, Sanbonmatsu KY. Tackling structures of long noncoding RNAs. Int J Mol Sci 2013; 14:23672-84. [PMID: 24304541 PMCID: PMC3876070 DOI: 10.3390/ijms141223672] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 11/15/2013] [Accepted: 11/25/2013] [Indexed: 11/16/2022] Open
Abstract
RNAs are important catalytic machines and regulators at every level of gene expression. A new class of RNAs has emerged called long non-coding RNAs, providing new insights into evolution, development and disease. Long non-coding RNAs (lncRNAs) predominantly found in higher eukaryotes, have been implicated in the regulation of transcription factors, chromatin-remodeling, hormone receptors and many other processes. The structural versatility of RNA allows it to perform various functions, ranging from precise protein recognition to catalysis and metabolite sensing. While major housekeeping RNA molecules have long been the focus of structural studies, lncRNAs remain the least characterized class, both structurally and functionally. Here, we review common methodologies used to tackle RNA structure, emphasizing their potential application to lncRNAs. When considering the complexity of lncRNAs and lack of knowledge of their structure, chemical probing appears to be an indispensable tool, with few restrictions in terms of size, quantity and heterogeneity of the RNA molecule. Probing is not constrained to in vitro analysis and can be adapted to high-throughput sequencing platforms. Significant efforts have been applied to develop new in vivo chemical probing reagents, new library construction protocols for sequencing platforms and improved RNA prediction software based on the experimental evidence.
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27
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Villarreal LP, Witzany G. The DNA Habitat and its RNA Inhabitants: At the Dawn of RNA Sociology. GENOMICS INSIGHTS 2013; 6:1-12. [PMID: 26217106 PMCID: PMC4510605 DOI: 10.4137/gei.s11490] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Most molecular biological concepts derive from physical chemical assumptions about the genetic code that are basically more than 40 years old. Additionally, systems biology, another quantitative approach, investigates the sum of interrelations to obtain a more holistic picture of nucleotide sequence order. Recent empirical data on genetic code compositions and rearrangements by mobile genetic elements and noncoding RNAs, together with results of virus research and their role in evolution, does not really fit into these concepts and compel a reexamination. In this review, we try to find an alternate hypothesis. It seems plausible now that if we look at the abundance of regulatory RNAs and persistent viruses in host genomes, we will find more and more evidence that the key players that edit the genetic codes of host genomes are consortia of RNA agents and viruses that drive evolutionary novelty and regulation of cellular processes in all steps of development. This agent-based approach may lead to a qualitative RNA sociology that investigates and identifies relevant behavioral motifs of cooperative RNA consortia. In addition to molecular biological perspectives, this may lead to a better understanding of genetic code evolution and dynamics.
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Affiliation(s)
- Luis P Villarreal
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
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28
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Mallatt J, Craig CW, Yoder MJ. Nearly complete rRNA genes from 371 Animalia: Updated structure-based alignment and detailed phylogenetic analysis. Mol Phylogenet Evol 2012; 64:603-17. [DOI: 10.1016/j.ympev.2012.05.016] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Revised: 05/15/2012] [Accepted: 05/17/2012] [Indexed: 12/30/2022]
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Widmann J, Stombaugh J, McDonald D, Chocholousova J, Gardner P, Iyer MK, Liu Z, Lozupone CA, Quinn J, Smit S, Wikman S, Zaneveld JR, Knight R. RNASTAR: an RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs. RNA (NEW YORK, N.Y.) 2012; 18:1319-27. [PMID: 22645380 PMCID: PMC3383963 DOI: 10.1261/rna.032052.111] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Automated RNA alignment algorithms often fail to recapture the essential conserved sites that are critical for function. To assist in the refinement of these algorithms, we manually curated a set of 148 alignments with a total of 9600 unique sequences, in which each alignment was backed by at least one crystal or NMR structure. These alignments included both naturally and artificially selected molecules. We used principles of isostericity to improve the alignments from an average of 83%-94% isosteric base pairs. We expect that this alignment collection will assist in a wide range of benchmarking efforts and provide new insight into evolutionary principles governing change in RNA structural motifs. The improved alignments have been contributed to the Rfam database.
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Affiliation(s)
- Jeremy Widmann
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Jesse Stombaugh
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Daniel McDonald
- Biofrontiers Institute, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Jana Chocholousova
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague 6, Czech Republic
| | - Paul Gardner
- School of Biological Sciences, University of Canterbury, Christchurch 8140, New Zealand
| | - Matthew K. Iyer
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Zongzhi Liu
- Department of Pathology Informatics, School of Medicine, Yale University, New Haven, Connecticut 06510, USA
| | - Catherine A. Lozupone
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - John Quinn
- Thermo Fisher Scientific, Lafayette, Colorado 80026, USA
| | - Sandra Smit
- Laboratory of Bioinformatics, Wageningen University, 6700 AN Wageningen, The Netherlands
| | | | - Jesse R.R. Zaneveld
- Department of Microbiology, Oregon State University, Corvallis, Oregon 97331, USA
| | - Rob Knight
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309, USA
- Howard Hughes Medical Institute, Boulder, Colorado 80309, USA
- Corresponding authorE-mail
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30
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Wang Y, Manzour A, Shareghi P, Shaw TI, Li YW, Malmberg RL, Cai L. Stable stem enabled Shannon entropies distinguish non-coding RNAs from random backgrounds. BMC Bioinformatics 2012; 13 Suppl 5:S1. [PMID: 22537005 PMCID: PMC3358654 DOI: 10.1186/1471-2105-13-s5-s1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background The computational identification of RNAs in genomic sequences requires the identification of signals of RNA sequences. Shannon base pairing entropy is an indicator for RNA secondary structure fold certainty in detection of structural, non-coding RNAs (ncRNAs). Under the Boltzmann ensemble of secondary structures, the probability of a base pair is estimated from its frequency across all the alternative equilibrium structures. However, such an entropy has yet to deliver the desired performance for distinguishing ncRNAs from random sequences. Developing novel methods to improve the entropy measure performance may result in more effective ncRNA gene finding based on structure detection. Results This paper shows that the measuring performance of base pairing entropy can be significantly improved with a constrained secondary structure ensemble in which only canonical base pairs are assumed to occur in energetically stable stems in a fold. This constraint actually reduces the space of the secondary structure and may lower the probabilities of base pairs unfavorable to the native fold. Indeed, base pairing entropies computed with this constrained model demonstrate substantially narrowed gaps of Z-scores between ncRNAs, as well as drastic increases in the Z-score for all 13 tested ncRNA sets, compared to shuffled sequences. Conclusions These results suggest the viability of developing effective structure-based ncRNA gene finding methods by investigating secondary structure ensembles of ncRNAs.
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Affiliation(s)
- Yingfeng Wang
- Department of Computer Science, University of Georgia, Athens, Georgia 30602, USA.
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31
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Labean TH, Butt TR, Kauffman SA, Schultes EA. Protein folding absent selection. Genes (Basel) 2011; 2:608-26. [PMID: 24710212 PMCID: PMC3927614 DOI: 10.3390/genes2030608] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2011] [Revised: 08/05/2011] [Accepted: 08/11/2011] [Indexed: 11/16/2022] Open
Abstract
Biological proteins are known to fold into specific 3D conformations. However, the fundamental question has remained: Do they fold because they are biological, and evolution has selected sequences which fold? Or is folding a common trait, widespread throughout sequence space? To address this question arbitrary, unevolved, random-sequence proteins were examined for structural features found in folded, biological proteins. Libraries of long (71 residue), random-sequence polypeptides, with ensemble amino acid composition near the mean for natural globular proteins, were expressed as cleavable fusions with ubiquitin. The structural properties of both the purified pools and individual isolates were then probed using circular dichroism, fluorescence emission, and fluorescence quenching techniques. Despite this necessarily sparse "sampling" of sequence space, structural properties that define globular biological proteins, namely collapsed conformations, secondary structure, and cooperative unfolding, were found to be prevalent among unevolved sequences. Thus, for polypeptides the size of small proteins, natural selection is not necessary to account for the compact and cooperative folded states observed in nature.
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Affiliation(s)
- Thomas H Labean
- Sequenomics LLC, 1428 Chanterelle Lane, Hillsborough, NC 27278, USA.
| | - Tauseef R Butt
- LifeSensors Inc., 271 Great Valley Parkway, Suite 100, Malvern, PA 19355, USA.
| | - Stuart A Kauffman
- Complex Systems Center University of Vermont, 200C Farrell Hall, 210 Colchester Ave., Burlington, VT 05405, USA.
| | - Erik A Schultes
- Sequenomics LLC, 1428 Chanterelle Lane, Hillsborough, NC 27278, USA.
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32
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Schudoma C, Larhlimi A, Walther D. The influence of the local sequence environment on RNA loop structures. RNA (NEW YORK, N.Y.) 2011; 17:1247-57. [PMID: 21628431 PMCID: PMC3138562 DOI: 10.1261/rna.2550211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
RNA folding is assumed to be a hierarchical process. The secondary structure of an RNA molecule, signified by base-pairing and stacking interactions between the paired bases, is formed first. Subsequently, the RNA molecule adopts an energetically favorable three-dimensional conformation in the structural space determined mainly by the rotational degrees of freedom associated with the backbone of regions of unpaired nucleotides (loops). To what extent the backbone conformation of RNA loops also results from interactions within the local sequence context or rather follows global optimization constraints alone has not been addressed yet. Because the majority of base stacking interactions are exerted locally, a critical influence of local sequence on local structure appears plausible. Thus, local loop structure ought to be predictable, at least in part, from the local sequence context alone. To test this hypothesis, we used Random Forests on a nonredundant data set of unpaired nucleotides extracted from 97 X-ray structures from the Protein Data Bank (PDB) to predict discrete backbone angle conformations given by the discretized η/θ-pseudo-torsional space. Predictions on balanced sets with four to six conformational classes using local sequence information yielded average accuracies of up to 55%, thus significantly better than expected by chance (17%-25%). Bases close to the central nucleotide appear to be most tightly linked to its conformation. Our results suggest that RNA loop structure does not only depend on long-range base-pairing interactions; instead, it appears that local sequence context exerts a significant influence on the formation of the local loop structure.
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Affiliation(s)
- Christian Schudoma
- Bioinformatics Group, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany.
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Escobar JS, Glémin S, Galtier N. GC-Biased Gene Conversion Impacts Ribosomal DNA Evolution in Vertebrates, Angiosperms, and Other Eukaryotes. Mol Biol Evol 2011; 28:2561-75. [DOI: 10.1093/molbev/msr079] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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Werner A. Predicting translational diffusion of evolutionary conserved RNA structures by the nucleotide number. Nucleic Acids Res 2010; 39:e17. [PMID: 21068070 PMCID: PMC3035447 DOI: 10.1093/nar/gkq808] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Ribonucleic acids are highly conserved essential parts of cellular life. RNA function is determined to a large extent by its hydrodynamic behaviour. The presented study proposes a strategy to predict the hydrodynamic behaviour of RNA single strands on the basis of the polymer size. By atom-level shell-modelling of high-resolution structures, hydrodynamic radius and diffusion coefficient of evolutionary conserved RNA single strands (ssRNA) were calculated. The diffusion coefficients D of 17–174 nucleotides (nt) containing ssRNA depended on the number of nucleotides N with D = 4.56 × 10−10 N−0.39 m2 s−1. The hydrodynamic radius RH depended on N with RH = 5.00 × 10−10N0.38 m. An average ratio of the radius of gyration and the hydrodynamic radius of 0.98 ± 0.08 was calculated in solution. The empirical law was tested by in solution measured hydrodynamic radii and radii of gyration and was found to be highly consistent with experimental data of evolutionary conserved ssRNA. Furthermore, the hydrodynamic behaviour of several evolutionary unevolved ribonucleic acids could be predicted. Based on atom-level shell-modelling of high-resolution structures and experimental hydrodynamic data, empirical models are proposed, which enable to predict the translational diffusion coefficient and molecular size of short RNA single strands solely on the basis of the polymer size.
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Affiliation(s)
- Arne Werner
- Experimental Biomolecular Physics, Applied Physics, Royal Institute of Technology, Stockholm, SE-10691, Sweden.
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Kennedy R, Lladser ME, Wu Z, Zhang C, Yarus M, De Sterck H, Knight R. Natural and artificial RNAs occupy the same restricted region of sequence space. RNA (NEW YORK, N.Y.) 2010; 16:280-9. [PMID: 20032164 PMCID: PMC2811657 DOI: 10.1261/rna.1923210] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Different chemical and mutational processes within genomes give rise to sequences with different compositions and perhaps different capacities for evolution. The evolution of functional RNAs may occur on a "neutral network" in which sequences with any given function can easily mutate to sequences with any other. This neutral network hypothesis is more likely if there is a particular region of composition that contains sequences that are functional in general, and if many different functions are possible within this preferred region of composition. We show that sequence preferences in active sites recovered by in vitro selection combine with biophysical folding rules to support the neutral network hypothesis. These simple active-site specifications and folding preferences obtained by artificial selection experiments recapture the previously observed purine bias and specific spread along the GC axis of naturally occurring aptamers and ribozymes isolated from organisms, although other types of RNAs, such as miRNA precursors and spliceosomal RNAs, that act primarily through complementarity to other amino acids do not share these preferences. These universal evolved sequence features are therefore intrinsic in RNA molecules that bind small-molecule targets or catalyze reactions.
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MESH Headings
- Aptamers, Nucleotide/chemistry
- Aptamers, Nucleotide/genetics
- Aptamers, Nucleotide/metabolism
- Base Composition
- Base Sequence
- Binding Sites/genetics
- Biophysical Phenomena
- Computational Biology
- Models, Genetic
- Models, Molecular
- Models, Statistical
- Mutation
- Nucleic Acid Conformation
- Poisson Distribution
- RNA/chemistry
- RNA/genetics
- RNA/metabolism
- RNA, Catalytic/chemistry
- RNA, Catalytic/genetics
- RNA, Catalytic/metabolism
- SELEX Aptamer Technique
- Selection, Genetic
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Affiliation(s)
- Ryan Kennedy
- Department of Computer Science, University of Colorado, Boulder, Colorado 80309, USA
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Jermiin LS, Ho JWK, Lau KW, Jayaswal V. SeqVis: a tool for detecting compositional heterogeneity among aligned nucleotide sequences. Methods Mol Biol 2009; 537:65-91. [PMID: 19378140 DOI: 10.1007/978-1-59745-251-9_4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
Compositional heterogeneity is a poorly appreciated attribute of aligned nucleotide and amino acid sequences. It is a common property of molecular phylogenetic data, and it has been found to occur across sequences and/or across sites. Most molecular phylogenetic methods assume that the sequences have evolved under globally stationary, reversible, and homogeneous conditions, implying that the sequences should be compositionally homogeneous. The presence of the above-mentioned compositional heterogeneity implies that the sequences must have evolved under more general conditions than is commonly assumed. Consequently, there is a need for reliable methods to detect under what conditions alignments of nucleotides or amino acids may have evolved. In this chapter, we describe one such program. SeqVis is designed to survey aligned nucleotide sequences. We discuss pros-et-cons of this program in the context of other methods to detect compositional heterogeneity and violated phylogenetic assumptions. The benefits provided by SeqVis are demonstrated in two studies of alignments of nucleotides, one of which contained 7542 nucleotides from 53 species.
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Affiliation(s)
- Lars Sommer Jermiin
- School of Biological Sciences, Centre for Mathematical Biology and Sydney Bioinformatics, University of Sydney, Sydney, Australia
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Smit S, Knight R, Heringa J. RNA structure prediction from evolutionary patterns of nucleotide composition. Nucleic Acids Res 2009; 37:1378-86. [PMID: 19129237 PMCID: PMC2655677 DOI: 10.1093/nar/gkn987] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Structural elements in RNA molecules have a distinct nucleotide composition, which changes gradually over evolutionary time. We discovered certain features of these compositional patterns that are shared between all RNA families. Based on this information, we developed a structure prediction method that evaluates candidate structures for a set of homologous RNAs on their ability to reproduce the patterns exhibited by biological structures. The method is named SPuNC for ‘Structure Prediction using Nucleotide Composition’. In a performance test on a diverse set of RNA families we demonstrate that the SPuNC algorithm succeeds in selecting the most realistic structures in an ensemble. The average accuracy of top-scoring structures is significantly higher than the average accuracy of all ensemble members (improvements of more than 20% observed). In addition, a consensus structure that includes the most reliable base pairs gleaned from a set of top-scoring structures is generally more accurate than a consensus derived from the full structural ensemble. Our method achieves better accuracy than existing methods on several RNA families, including novel riboswitches and ribozymes. The results clearly show that nucleotide composition can be used to reveal the quality of RNA structures and thus the presented technique should be added to the set of prediction tools.
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Affiliation(s)
- S Smit
- Centre for Integrative Bioinformatics VU (IBIVU), Vrije Universiteit, 1081 HV Amsterdam, The Netherlands.
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38
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Boots JL, Canny MD, Azimi E, Pardi A. Metal ion specificities for folding and cleavage activity in the Schistosoma hammerhead ribozyme. RNA (NEW YORK, N.Y.) 2008; 14:2212-22. [PMID: 18755844 PMCID: PMC2553736 DOI: 10.1261/rna.1010808] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Accepted: 07/02/2008] [Indexed: 05/20/2023]
Abstract
The effects of various metal ions on cleavage activity and global folding have been studied in the extended Schistosoma hammerhead ribozyme. Fluorescence resonance energy transfer was used to probe global folding as a function of various monovalent and divalent metal ions in this ribozyme. The divalent metals ions Ca(2+), Mg(2+), Mn(2+), and Sr(2+) have a relatively small variation (less than sixfold) in their ability to globally fold the hammerhead ribozyme, which contrasts with the very large difference (>10,000-fold) in apparent rate constants for cleavage for these divalent metal ions in single-turnover kinetic experiments. There is still a very large range (>4600-fold) in the apparent rate constants for cleavage for these divalent metal ions measured in high salt (2 M NaCl) conditions where the ribozyme is globally folded. These results demonstrate that the identity of the divalent metal ion has little effect on global folding of the Schistosoma hammerhead ribozyme, whereas it has a very large effect on the cleavage kinetics. Mechanisms by which the identity of the divalent metal ion can have such a large effect on cleavage activity in the Schistosoma hammerhead ribozyme are discussed.
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Affiliation(s)
- Jennifer L Boots
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309-0215, USA
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Kang S, Hong YS. RNA interference in infectious tropical diseases. THE KOREAN JOURNAL OF PARASITOLOGY 2008; 46:1-15. [PMID: 18344671 DOI: 10.3347/kjp.2008.46.1.1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Introduction of double-stranded RNA (dsRNA) into some cells or organisms results in degradation of its homologous mRNA, a process called RNA interference (RNAi). The dsRNAs are processed into short interfering RNAs (siRNAs) that subsequently bind to the RNA-induced silencing complex (RISC), causing degradation of target mRNAs. Because of this sequence-specific ability to silence target genes, RNAi has been extensively used to study gene functions and has the potential to control disease pathogens or vectors. With this promise of RNAi to control pathogens and vectors, this paper reviews the current status of RNAi in protozoans, animal parasitic helminths and disease-transmitting vectors, such as insects. Many pathogens and vectors cause severe parasitic diseases in tropical regions and it is difficult to control once the host has been invaded. Intracellularly, RNAi can be highly effective in impeding parasitic development and proliferation within the host. To fully realize its potential as a means to control tropical diseases, appropriate delivery methods for RNAi should be developed, and possible off-target effects should be minimized for specific gene suppression. RNAi can also be utilized to reduce vector competence to interfere with disease transmission, as genes critical for pathogenesis of tropical diseases are knockdowned via RNAi.
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Affiliation(s)
- Seokyoung Kang
- Department of Tropical Medicine, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA.
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40
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Varriale A, Torelli G, Bernardi G. Compositional properties and thermal adaptation of 18S rRNA in vertebrates. RNA (NEW YORK, N.Y.) 2008; 14:1492-500. [PMID: 18567811 PMCID: PMC2491464 DOI: 10.1261/rna.957108] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
In order to investigate the influence of temperature on the GC level of the paired sequences of ribosomal 18S RNAs in vertebrates, we have studied their base composition in cold- and warm-blooded vertebrates using a stem-by-stem comparison. We observed that a number of stems of 18S ribosomal RNAs (rRNAs) are variable among species and that the majority of such stems are GC richer in warm-blooded than in cold-blooded vertebrates. We also constructed the secondary structures of the 18S rRNAs of a polar fish, a marsupial, and a monotreme to compare them with those of temperate/tropical fishes and of eutherians, respectively. In these cases, differences similar to those already mentioned were found. We conclude that there is a correlation between stem stability and body temperature even within the relatively limited temperature range of vertebrates.
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Affiliation(s)
- Annalisa Varriale
- Laboratory of Molecular Evolution, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy
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LaPan P, Zhang J, Pan J, Hill A, Haney SA. Single cell cytometry of protein function in RNAi treated cells and in native populations. BMC Cell Biol 2008; 9:43. [PMID: 18673568 PMCID: PMC2529295 DOI: 10.1186/1471-2121-9-43] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2007] [Accepted: 08/01/2008] [Indexed: 01/10/2023] Open
Abstract
Background High Content Screening has been shown to improve results of RNAi and other perturbations, however significant intra-sample heterogeneity is common and can complicate some analyses. Single cell cytometry can extract important information from subpopulations within these samples. Such approaches are important for immune cells analyzed by flow cytometry, but have not been broadly available for adherent cells that are critical to the study of solid-tumor cancers and other disease models. Results We have directly quantitated the effect of resolving RNAi treatments at the single cell level in experimental systems for both exogenous and endogenous targets. Analyzing the effect of an siRNA that targets GFP at the single cell level permits a stronger measure of the absolute function of the siRNA by gating to eliminate background levels of GFP intensities. Extending these methods to endogenous proteins, we have shown that well-level results of the knockdown of PTEN results in an increase in phospho-S6 levels, but at the single cell level, the correlation reveals the role of other inputs into the pathway. In a third example, reduction of STAT3 levels by siRNA causes an accumulation of cells in the G1 phase of the cell cycle, but does not induce apoptosis or necrosis when compared to control cells that express the same levels of STAT3. In a final example, the effect of reduced p53 levels on increased adriamycin sensitivity for colon carcinoma cells was demonstrated at the whole-well level using siRNA knockdown and in control and untreated cells at the single cell level. Conclusion We find that single cell analysis methods are generally applicable to a wide range of experiments in adherent cells using technology that is becoming increasingly available to most laboratories. It is well-suited to emerging models of signaling dysfunction, such as oncogene addition and oncogenic shock. Single cell cytometry can demonstrate effects on cell function for protein levels that differ by as little as 20%. Biological differences that result from changes in protein level or pathway activation state can be modulated directly by RNAi treatment or extracted from the natural variability intrinsic to cells grown under normal culture conditions.
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Affiliation(s)
- Peter LaPan
- Department of Biological Technologies, Oncology Research, Wyeth Research, 87 Cambridge Park Drive, Cambridge, MA 02140, USA.
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Smit S, Rother K, Heringa J, Knight R. From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal. RNA (NEW YORK, N.Y.) 2008; 14:410-6. [PMID: 18230758 PMCID: PMC2248259 DOI: 10.1261/rna.881308] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Pseudoknots are abundant in RNA structures. Many computational analyses require pseudoknot-free structures, which means that some of the base pairs in the knotted structure must be disregarded to obtain a nested structure. There is a surprising diversity of methods to perform this pseudoknot removal task, but these methods are often poorly described and studies can therefore be difficult to reproduce (in part, because different procedures may be intuitively obvious to different investigators). Here we provide a variety of algorithms for pseudoknot removal, some of which can incorporate sequence or alignment information in the removal process. We demonstrate that different methods lead to different results, which might affect structure-based analyses. This work thus provides a starting point for discussion of the extent to which these different methods recapture the underlying biological reality. We provide access to reference implementations through a web interface (at http://www.ibi.vu.nl/programs/k2nwww), and the source code is available in the PyCogent project.
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Affiliation(s)
- Sandra Smit
- Centre for Integrative Bioinformatics VU (IBIVU), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
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Abstract
RNAi screening in mammalian cells has become a valuable method to identify and describe genetic relationships in both basic biology and disease mechanisms. Multiple efforts are underway to standardize how RNAi screening data are reported, including establishing experimental criteria for defining a validated hit from a screen, and the extent to which the primary screening data themselves are reported. These discussions have identified several key areas that require consistency, or at least understanding, before RNAi screening data can be used generally. Successfully addressing these targeted areas would broaden the use of RNAi screening data beyond advancing one or a few hits into validation experiments, to enable verification of primary screening data, and to facilitate comparisons between sample groups based on screening profiles. Areas for improving RNAi screening include general guidelines for validating hits from screens, the creation of standardized reporting structures for RNAi screening data, such as Minimum Information About an RNAi Experiment (MIARE), statistical methods for analyzing screening data that explicitly account for differences between screening RNAi reagents versus small molecules, and technical improvements to RNAi screening that improve the analysis of gene knockdowns, including multiparametric approaches, such as high-content screening. This review will discuss how these approaches can improve RNAi screening data at the community level and for an individual researcher trying to manage an RNAi screen.
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Affiliation(s)
- Steven A Haney
- Department of Biological Technologies, Wyeth Research, 35 Cambridge Park Drive, Cambridge, MA 02140, USA.
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Abstract
Understanding patterns of rRNA evolution is critical for a number of fields, including structure prediction and phylogeny. The standard model of RNA evolution is that compensatory mutations in stems make up the bulk of the changes between homologous sequences, while unpaired regions are relatively homogeneous. We show that considerable heterogeneity exists in the relative rates of evolution of different secondary structure categories (stems, loops, bulges, etc.) within the rRNA, and that in eukaryotes, loops actually evolve much faster than stems. Both rates of evolution and abundance of different structural categories vary with distance from functionally important parts of the ribosome such as the tRNA path and the peptidyl transferase center. For example, fast-evolving residues are mainly found at the surface; stems are enriched at the subunit interface, and junctions near the peptidyl transferase center. However, different secondary structure categories evolve at different rates even when these effects are accounted for. The results demonstrate that relative rates and patterns of evolution are lineage specific, suggesting that phylogenetically and structurally specific models will improve evolutionary and structural predictions.
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Affiliation(s)
| | | | - R. Knight
- *To whom correspondence should be addressed. Tel: 303-492-1984; Fax: 303-492-7744;
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45
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Silva AL, Pereira FJC, Morgado A, Kong J, Martins R, Faustino P, Liebhaber SA, Romão L. The canonical UPF1-dependent nonsense-mediated mRNA decay is inhibited in transcripts carrying a short open reading frame independent of sequence context. RNA (NEW YORK, N.Y.) 2006; 12:2160-70. [PMID: 17077274 PMCID: PMC1664719 DOI: 10.1261/rna.201406] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism that degrades mRNAs carrying premature translation termination codons. Generally, NMD is elicited if translation terminates >50-54 nucleotides (nt) upstream of an exon-exon junction. We have previously reported that human beta-globin mRNAs carrying 5'-proximal nonsense mutations (e.g., beta15) accumulate to normal levels, suggesting an exception to the "50-54-nt boundary rule." In the present report, we demonstrate that the strength of the UPF1-dependent NMD of mutant beta-globin mRNAs is specifically determined by the proximity of the nonsense codon to the initiation AUG. This conclusion is supported by a parallel effect of the short ORF size on NMD of nonsense-containing alpha-globin mRNAs. To determine whether the short-ORF effect on NMD response is conserved in heterologous transcripts, we assessed its effects on a set of beta-globin/triosephosphate isomerase (TPI) hybrid mRNAs and on the TPI mRNA. Our data support the conclusion that nonsense mutations resulting in a short ORF are able to circumvent the full activity of the canonical UPF1-dependent NMD pathway.
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Affiliation(s)
- Ana Luísa Silva
- Centro de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, 1649-016 Lisboa, Portugal
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Using the nucleotide substitution rate matrix to detect horizontal gene transfer. BMC Bioinformatics 2006; 7:476. [PMID: 17067382 PMCID: PMC1657035 DOI: 10.1186/1471-2105-7-476] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Accepted: 10/26/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Horizontal gene transfer (HGT) has allowed bacteria to evolve many new capabilities. Because transferred genes perform many medically important functions, such as conferring antibiotic resistance, improved detection of horizontally transferred genes from sequence data would be an important advance. Existing sequence-based methods for detecting HGT focus on changes in nucleotide composition or on differences between gene and genome phylogenies; these methods have high error rates. RESULTS First, we introduce a new class of methods for detecting HGT based on the changes in nucleotide substitution rates that occur when a gene is transferred to a new organism. Our new methods discriminate simulated HGT events with an error rate up to 10 times lower than does GC content. Use of models that are not time-reversible is crucial for detecting HGT. Second, we show that using combinations of multiple predictors of HGT offers substantial improvements over using any single predictor, yielding as much as a factor of 18 improvement in performance (a maximum reduction in error rate from 38% to about 3%). Multiple predictors were combined by using the random forests machine learning algorithm to identify optimal classifiers that separate HGT from non-HGT trees. CONCLUSION The new class of HGT-detection methods introduced here combines advantages of phylogenetic and compositional HGT-detection techniques. These new techniques offer order-of-magnitude improvements over compositional methods because they are better able to discriminate HGT from non-HGT trees under a wide range of simulated conditions. We also found that combining multiple measures of HGT is essential for detecting a wide range of HGT events. These novel indicators of horizontal transfer will be widely useful in detecting HGT events linked to the evolution of important bacterial traits, such as antibiotic resistance and pathogenicity.
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Jiang W, Pisetsky DS. The role of IFN-alpha and nitric oxide in the release of HMGB1 by RAW 264.7 cells stimulated with polyinosinic-polycytidylic acid or lipopolysaccharide. THE JOURNAL OF IMMUNOLOGY 2006; 177:3337-43. [PMID: 16920974 DOI: 10.4049/jimmunol.177.5.3337] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
High mobility group protein 1 (HMGB1) is a nonhistone nuclear protein with a dual function. Inside the cell, HMGB1 binds to DNA and modulates a variety of processes, including transcription. Outside the cell, HMGB1 displays cytokine activity and can promote inflammation, serving as a mediator in models of shock and arthritis. In in vitro studies, proinflammatory molecules such as LPS, lipoteichoic acid, dsRNA, TNF-alpha, and IFN-gamma can induce HMGB1 release from macrophages. To define further the release process, we investigated the role of the downstream mediators, NO and IFN-alpha, in the release of HMGB1 from RAW 264.7 macrophage cells stimulated with LPS or polyinosinic-polycytidylic acid (poly(I:C)). In these experiments, 1400W, an inhibitor of NO production by the inducible NO synthase, reduced HMGB1 release stimulated by LPS, but not poly(I:C), whereas neutralizing IFN-alpha prevented HMGB1 release induced by poly(I:C), but not LPS. The addition of an NO donor and rIFN-alpha to RAW 264.7 cells caused HMGB1 release. Furthermore, inhibition of JNK activation attenuated HMGB1 release induced by either LPS or poly(I:C). Analysis of bone marrow-derived macrophages stimulated by LPS or poly(I:C) showed patterns of HMGB1 release similar to those of RAW 264.7 cells. Together, these experiments indicate that, although both LPS and poly(I:C) induce HMGB1 release from RAW 264.7 cells and murine macrophages, the response is differentially dependent on NO and IFN-alpha.
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Affiliation(s)
- Weiwen Jiang
- Division of Rheumatology and Immunology, Department of Medicine, Duke University, Durham, NC 27710, USA
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48
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Paschoud S, Dogar AM, Kuntz C, Grisoni-Neupert B, Richman L, Kühn LC. Destabilization of interleukin-6 mRNA requires a putative RNA stem-loop structure, an AU-rich element, and the RNA-binding protein AUF1. Mol Cell Biol 2006; 26:8228-41. [PMID: 16954375 PMCID: PMC1636780 DOI: 10.1128/mcb.01155-06] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Interleukin-6 mRNA is unstable and degraded with a half-life of 30 min. Instability determinants can entirely be attributed to the 3' untranslated region. By grafting segments of this region to stable green fluorescent protein mRNA and subsequent scanning mutagenesis, we have identified two conserved elements, which together account for most of the instability. The first corresponds to a short noncanonical AU-rich element. The other, 80 nucleotides further 5', comprises a sequence predicted to form a stem-loop structure. Neither element alone was sufficient to confer full instability, suggesting that they might cooperate. Overexpression of myc-tagged AUF1 p37 and p42 isoforms as well as suppression of endogenous AUF1 by RNA interference stabilized interleukin-6 mRNA. Both effects required the AU-rich instability element. Similarly, the proteasome inhibitor MG132 stabilized interleukin-6 mRNA probably through an increase of AUF1 levels. The mRNA coimmunoprecipitated specifically with myc-tagged AUF1 p37 and p42 in cell extracts but only when the AU-rich instability element was present. These results indicate that AUF1 binds to the AU-rich element in vivo and promotes IL-6 mRNA degradation.
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Affiliation(s)
- Serge Paschoud
- Swiss Institute for Experimental Cancer Research, Genetics Unit, Chemin des Boveresses 155, CH-1066 Epalinges, Switzerland.
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49
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Abstract
Chromosome stability requires a dynamic balance of DNA loss and gain in each terminal tract of telomeric repeats. Repeat addition by a specialized reverse transcriptase, telomerase, has an important role in maintaining this equilibrium. Insights that have been gained into the cellular pathways for biogenesis and regulation of telomerase ribonucleoproteins raise new questions, particularly concerning the dynamic nature of this unique polymerase.
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Affiliation(s)
- Kathleen Collins
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3204, USA.
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50
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Brown K, Samarsky D. RNAi off-targeting: Light at the end of the tunnel. JOURNAL OF RNAI AND GENE SILENCING : AN INTERNATIONAL JOURNAL OF RNA AND GENE TARGETING RESEARCH 2006; 2:175-7. [PMID: 19771224 PMCID: PMC2737219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/19/2006] [Indexed: 10/28/2022]
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