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1.
A Macintosh Hypertalk program (Hypercard stack)for use in phylogenetic comparative analysis of RNA structureis described. The program identifies covariations and compensatorychanges in RNA sequence alignments, for use in the constructionof secondary structure models or the identification of tertiaryinteractions. The results of an analysis are presented eitheras a list of positions in the alignment which covary, or asa 2-dimensional matrix in which potential helices in the secondarystructure appear as diagonal patterns.
Received on January 7, 1991; accepted on March 19, 1991 相似文献
2.
Rother K Rother M Boniecki M Puton T Bujnicki JM 《Journal of molecular modeling》2011,17(9):2325-2336
In analogy to proteins, the function of RNA depends on its structure and dynamics, which are encoded in the linear sequence.
While there are numerous methods for computational prediction of protein 3D structure from sequence, there have been very
few such methods for RNA. This review discusses template-based and template-free approaches for macromolecular structure prediction,
with special emphasis on comparison between the already tried-and-tested methods for protein structure modeling and the very
recently developed “protein-like” modeling methods for RNA. We highlight analogies between many successful methods for modeling
of these two types of biological macromolecules and argue that RNA 3D structure can be modeled using “protein-like” methodology.
We also highlight the areas where the differences between RNA and proteins require the development of RNA-specific solutions. 相似文献
3.
Computer simulation results of folding linear RNA moleculesinto secondaty structures are presented. The structure is formedby two interacting processes: the RNA molecular chain growth(beginning from an initial length, Lo), and the structuring(secondary structure sequential growth in the region of theexisting molecular chain, based on the local free energy minimizationby sequential addition of elementary substruc tures-stems).It was found that the final secondary structure formation isgreatly influenced by the structuring period T(the ratio of the molecular chain growth rate to the structuringrate), and the direction of RNA synthesis. The computer simulationhas been performed for 219 and 906 tRNA genes from two publishedcatalogues, on the whale two-dimensional domain (T,L0) parameters,by using four known free-energy models. Minimwn stem lengthand molecular chain growth direction have been also varied Thecalculated secondary structures have been compared to the naturaltRNA structures given in the catalogues, and the region of bestcoincidence for the model parameters has been determined. Ithas been proved that, on average, >86% of the paired basesof natural tRNA structures appear in the folding simulation. 相似文献
4.
Li B Chen X Ren H Li L Xiong J Bai J Chen Y Wu J Ying H 《Bioprocess and biosystems engineering》2012,35(3):415-422
During ribonucleic acid fermentation, the fermentative processes were researched at pH controlled at 4.0 and under natural
conditions. Unstructured models in a 50-L airlift fermentor were established for batch RNA production at pH 4.0 using the
Verhulst equation for microbial growth, the Luedeking–Piret equation for product formation and a Luedeking–Piret-like equation
for substrate uptake. Parameters of the kinetic models were determined using origin 7.5. Based on the models estimated above,
another batch fermentation experiment was conducted in a 300-L airlift fermentor, which demonstrated that the models could
be useful for RNA production on an industrial scale. Additionally, continuous fermentation based on kinetic models was proposed
to make full use of substrates and reduce the cost of waste water treatment. As a result, although the DCW and RNA concentration
were 11.5 and 1.68 g L−1, which were lower than that of batch fermentation, the sugar utilization increased by 14.3%, while the waste water decreased
by more than 90%. 相似文献
5.
Magarshak et al. represented an RNA molecule as a complex vector and an RNA secondary structure Γ as a complex matrix S
Γ in such a way that the molecule represented by was compatible with the secondary structure Γ if and only if . They only considered Watson-Crick base pairs and their representation cannot be extended to allow for G⋅U pairs. In this paper we study a generalization of Magarshak's representation that allows for these pairs, and in particular
we provide a family of algebraic structures where that generalization can be carried out. We also show that this representation
can be used to compare secondary structures, through transfer matrices which transform the representation of one secondary
structure into the representation of the other.
Received: 10 December 2001 / Revised version: 7 May 2002 /
Published online: 28 February 2003
Key words or phrases: RNA secondary structure – Algebra – Finite field 相似文献
6.
RNA–RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number
of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two interacting RNA
molecules have been proposed. Here joint structure means that in a diagram representation the intramolecular bonds of each
partner are pseudoknot-free, that the intermolecular binding pairs are noncrossing, and that there is no so-called “zigzag”
configuration. This paper presents the combinatorics of RNA interaction structures including their generating function, singularity
analysis as well as explicit recurrence relations. In particular, our results imply simple asymptotic formulas for the number
of joint structures. 相似文献
7.
The structure and function of polynucleotide phosphorylase (PNPase) and the exosome, as well as their associated RNA-helicases
proteins, are described in the light of recent studies. The picture raised is of an evolutionarily conserved RNA-degradation
machine which exonucleolytically degrades RNA from 3′ to 5′. In prokaryotes and in eukaryotic organelles, a trimeric complex
of PNPase forms a circular doughnut-shaped structure, in which the phosphorolysis catalytic sites are buried inside the barrel-shaped
complex, while the RNA binding domains create a pore where RNA enters, reminiscent of the protein degrading complex, the proteasome.
In some archaea and in the eukaryotes, several different proteins form a similar circle-shaped complex, the exosome, that
is responsible for 3′ to 5′ exonucleolytic degradation of RNA as part of the processing, quality control, and general RNA
degradation process. Both PNPase in prokaryotes and the exosome in eukaryotes are found in association with protein complexes
that notably include RNA helicase. 相似文献
8.
Heather D. Bean Frank A. L. Anet Ian R. Gould Nicholas V. Hud 《Origins of life and evolution of the biosphere》2006,36(1):39-63
The origin of the first RNA polymers is central to most current theories for the origin of life. Difficulties associated with
the prebiotic formation of RNA have lead to the general consensus that a simpler polymer preceded RNA. However, polymers proposed
as possible ancestors to RNA are not much easier to synthesize than RNA itself. One particular problem with the prebiotic
synthesis of RNA is the formation of phosphoester bonds in the absence of chemical activation. Here we demonstrate that glyoxylate
(the ionized form of glyoxylic acid), a plausible prebiotic molecule, represents a possible ancestor of the phosphate group
in modern RNA. Although in low yields (∼ 1%), acetals are formed from glyoxylate and nucleosides under neutral conditions,
provided that metal ions are present (e.g., Mg2+), and provided that water is removed by evaporation at moderate temperatures (e.g., 65 ∘C), i.e. under “drying conditions”. Such acetals are termed ga-dinucleotides and possess a linkage that is analogous to the backbone in RNA in both structure and electrostatic charge.
Additionally, an energy-minimized model of a gaRNA duplex predicts a helical structure similar to that of A-form RNA. We propose that glyoxylate-acetal linkages would have
had certain advantages over phosphate linkages for early self-replicating polymers, but that the distinct functional properties
of phosphoester and phosphodiester bonds would have eventually lead to the replacement of glyoxylate by phosphate. 相似文献
9.
10.
Prions and other misfolded proteins can impart their structure and functions to normal molecules. Based upon a thorough structural
assessment of RNA, prions and misfolded proteins, especially from the perspective of conformational diversity, we propose
a case for co-existence of these in the pre-biotic world. Analyzing the evolution of physical aspects of biochemical structures,
we put forward a case for an RNA–prion pre-biotic world, instead of, merely, the “RNA World”. 相似文献
11.
We present a method for improving the quality of nuclear magnetic resonance (NMR) spectra involving exchangeable protons near
the base of the stem of RNA hairpin molecules. NMR spectra of five different RNA hairpins were compared. These hairpins consisted
of a native RNA structure and four molecules each having different unpaired, or dangling, nucleotides at the 3′ end. NMR experiments
were acquired in water for each construct and the quality of the imino proton spectral regions were examined. The imino resonances
near the base of the stem of the wild type RNA structure were not observed due to breathing motions. However, a significant
increase in spectral quality for molecules with dangling 3′ adenosine or guanosine nucleotides was observed, with imino protons
detected in these constructs that were not observed in the wild type construct. A modest improvement in spectral quality was
seen for the construct with a 3′ unpaired uridine, whereas no significant improvement was observed for a 3′ unpaired cytidine.
This improvement in NMR spectral quality mirrors the increased thermodynamic stability observed for 3′ unpaired nucleotides
which is dependant on the stacking interactions of these nucleotides against the base of the stem. The use of a dangling 3′
adenosine nucleotide represents an easy method to significantly improve the quality of NMR spectra of RNA molecules.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
12.
13.
Piotr Lukasiak Maciej Antczak Tomasz Ratajczak Janusz M. Bujnicki Marta Szachniuk Ryszard W. Adamiak Mariusz Popenda Jacek Blazewicz 《Nucleic acids research》2013,41(12):5978-5990
The continuously increasing amount of RNA sequence and experimentally determined 3D structure data drives the development of computational methods supporting exploration of these data. Contemporary functional analysis of RNA molecules, such as ribozymes or riboswitches, covers various issues, among which tertiary structure modeling becomes more and more important. A growing number of tools to model and predict RNA structure calls for an evaluation of these tools and the quality of outcomes their produce. Thus, the development of reliable methods designed to meet this need is relevant in the context of RNA tertiary structure analysis and can highly influence the quality and usefulness of RNA tertiary structure prediction in the nearest future. Here, we present RNAlyzer—a computational method for comparison of RNA 3D models with the reference structure and for discrimination between the correct and incorrect models. Our approach is based on the idea of local neighborhood, defined as a set of atoms included in the sphere centered around a user-defined atom. A unique feature of the RNAlyzer is the simultaneous visualization of the model-reference structure distance at different levels of detail, from the individual residues to the entire molecules. 相似文献
14.
Lozada-Chávez I Stadler PF Prohaska SJ 《Origins of life and evolution of the biosphere》2011,41(6):587-607
The transitions to multicellularity mark the most pivotal and distinctive events in life’s history on Earth. Although several
transitions to “simple” multicellularity (SM) have been recorded in both bacterial and eukaryotic clades, transitions to complex
multicellularity (CM) have only happened a few times in eukaryotes. A large number of cell types (associated with large body
size), increased energy consumption per gene expressed, and an increment of non-protein-coding DNA positively correlate with
CM. These three factors can indeed be understood as the causes and consequences of the regulation of gene expression. Here,
we discuss how a vast expansion of non-protein-coding RNA (ncRNAs) regulators rather than large numbers of novel protein regulators
can easily contribute to the emergence of CM. We also propose that the evolutionary advantage of RNA-based gene regulation
derives from the robustness of the RNA structure that makes it easy to combine genetic drift with functional exploration.
We describe a model which aims to explain how the evolutionary dynamic of ncRNAs becomes dominated by the accessibility of
advantageous mutations to innovate regulation in complex multicellular organisms. The information and models discussed here
outline the hypothesis that pervasive ncRNA-based regulatory systems, only capable of being expanded and explored in higher
eukaryotes, are prerequisite to complex multicellularity. Thereby, regulatory RNA molecules in Eukarya have allowed intensification
of morphological complexity by stabilizing critical phenotypes and controlling developmental precision. Although the origin
of RNA on early Earth is still controversial, it is becoming clear that once RNA emerged into a protocellular system, its
relevance within the evolution of biological systems has been greater than we previously thought. 相似文献
15.
Background
Owing to the rapid expansion of RNA structure databases in recent years, efficient methods for structure comparison are in demand for function prediction and evolutionary analysis. Usually, the similarity of RNA secondary structures is evaluated based on tree models and dynamic programming algorithms. We present here a new method for the similarity analysis of RNA secondary structures. 相似文献16.
Bahrami A Clos LJ Markley JL Butcher SE Eghbalnia HR 《Journal of biomolecular NMR》2012,52(4):289-302
The significant biological role of RNA has further highlighted the need for improving the accuracy, efficiency and the reach
of methods for investigating RNA structure and function. Nuclear magnetic resonance (NMR) spectroscopy is vital to furthering
the goals of RNA structural biology because of its distinctive capabilities. However, the dispersion pattern in the NMR spectra
of RNA makes automated resonance assignment, a key step in NMR investigation of biomolecules, remarkably challenging. Herein
we present RNA Probabilistic Assignment of Imino Resonance Shifts (RNA-PAIRS), a method for the automated assignment of RNA
imino resonances with synchronized verification and correction of predicted secondary structure. RNA-PAIRS represents an advance
in modeling the assignment paradigm because it seeds the probabilistic network for assignment with experimental NMR data,
and predicted RNA secondary structure, simultaneously and from the start. Subsequently, RNA-PAIRS sets in motion a dynamic
network that reverberates between predictions and experimental evidence in order to reconcile and rectify resonance assignments
and secondary structure information. The procedure is halted when assignments and base-parings are deemed to be most consistent
with observed crosspeaks. The current implementation of RNA-PAIRS uses an initial peak list derived from proton-nitrogen heteronuclear
multiple quantum correlation (1H–15N 2D HMQC) and proton–proton nuclear Overhauser enhancement spectroscopy (1H–1H 2D NOESY) experiments. We have evaluated the performance of RNA-PAIRS by using it to analyze NMR datasets from 26 previously
studied RNAs, including a 111-nucleotide complex. For moderately sized RNA molecules, and over a range of comparatively complex
structural motifs, the average assignment accuracy exceeds 90%, while the average base pair prediction accuracy exceeded 93%.
RNA-PAIRS yielded accurate assignments and base pairings consistent with imino resonances for a majority of the NMR resonances,
even when the initial predictions are only modestly accurate. RNA-PAIRS is available as a public web-server at . 相似文献
17.
Turnip yellow mosaic virus (TYMV) is a spherical plant virus that has a single 6.3 kb positive strand RNA. The genomic RNA
has a tRNA-like structure (TLS) at the 3′-end. The 3′-TLS and hairpins in the 5′-untranslated region supposedly serve as packaging
signals; however, recent studies have shown that they do not play a role in TYMV RNA packaging. In this study, we focused
on packaging signals by examining a series of deletion mutants of TYMV. Analysis of encapsidated viral RNA after agroinfiltration
of the deletion constructs into Nicotiana benthamiana showed that the mutant RNA lacking the protease (Pro)/helicase (Hel) region was not encapsidated by the coat proteins provided
in trans, implicating that a packaging signal lies in the Pro/Hel region. Examination of two Pro−Hel− mutants showed that protein activity from the Pro/Hel domains was dispensable for the packaging of the non-replicating TYMV
RNA. In contrast, the mutant TYMV RNA lacking the Pro/Hel region was efficiently encapsidated when the mutant TYMV was co-introduced
with a wild-type TYMV, suggesting that packaging mechanisms might differ depending on whether the virus is replicating or
not. 相似文献
18.
Gadgil S 《Journal of mathematical biology》2009,59(1):123-142
We study the secondary structure of RNA determined by Watson–Crick pairing without pseudo-knots using Milnor invariants of
links. We focus on the first non-trivial invariant, which we call the Heisenberg invariant. The Heisenberg invariant, which
is an integer, can be interpreted in terms of the Heisenberg group as well as in terms of lattice paths. We show that the
Heisenberg invariant gives a lower bound on the number of unpaired bases in an RNA secondary structure. We also show that
the Heisenberg invariant can predict allosteric structures for RNA. Namely, if the Heisenberg invariant is large, then there are widely separated local maxima (i.e., allosteric structures)
for the number of Watson–Crick pairs found.
Partially supported by DST (under grant DSTO773) and UGC (under SAP-DSA Phase IV). 相似文献
19.
Background
Pseudouridine (Ψ) is an abundant modified nucleoside in RNA and a number of studies have shown that the presence of Ψ affects RNA structure and function. The positions of Ψ in spliceosomal small nuclear RNAs (snRNAs) have been determined for a number of species but not for the snRNAs from Caenorhabditis elegans (C. elegans), a popular experimental model system of development. 相似文献20.
O. Hammouda 《Folia microbiologica》1996,41(4):357-362
Purification of DNA-dependent RNA polymerase from exponentially growing cells of the cyanobacteriumSynechococcus sp. is described in cultures grown at normal temperature (39°C) and after heat shock (HS) (47°C). Polyethyleneimine precipitation
followed by chromatography and gel filtration steps results in a 39% yield. The enzyme has a component of molar mass of 43
kDa, designated σ, in addition to the typical procaryotic β’β∝2 and γ. The results suggest thatSynechococcus RNA polymerase is similar to that of cyanobacterial andE. coli RNA polymerases. Electrophoresis of the HS preparation showed that the enzyme has a component of 18 kDa. This suggests the
existence of a functional relationship between this protein and the HS response ofSynechococcus RNA polymerase, probably in salvaging denatured RNA polymerase or helping to regain its native structure. 相似文献