RNA virus genetic robustness: possible causes and some consequences

[EN] In general terms, robustness is the capacity of biological systems to function in spite of genetic or environmental perturbations. The small and compacted genomes and high mutation rates of RNA viruses, as well as the ever-changing environments wherein they replicate, create the conditions for robustness to be advantageous. In this review, I will enumerate possible mechanisms by which viral populations may acquire robustness, distinguishing between mechanisms that are inherent to virus replication and population dynamics and those that result from the interaction with host factors. Then, I will move to review some evidences that RNA virus populations are robust indeed. Finally, I will comment on the implications of robustness for virus evolvability, the emergence of new viruses and the efficiency of lethal mutagenesis as an antiviral strategyThis work was supported by the Spanish MICINN grant BFU2009-06993 and by the Santa Fe Institute. I thank Mark P. Zwart for critical reading of the manuscript.Elena Fito, SF. (2012). RNA virus genetic robustness: possible causes and some consequences. Current Opinion in Virology. 2(5):525-530. https://doi.org/10.1016/j.coviro.2012.06.008S5255302

Structure-function relationship in viral RNA genomes: The case of hepatitis C virus

The acquisition of a storage information system beyond the nucleotide sequence has been a crucial issue for the propagation and dispersion of RNA viruses. This system is composed by highly conserved, complex structural units in the genomic RNA, termed functional RNA domains. These elements interact with other regions of the viral genome and/or proteins to direct viral translation, replication and encapsidation. The genomic RNA of the hepatitis C virus (HCV) is a good model for investigating about conserved structural units. It contains functional domains, defined by highly conserved structural RNA motifs, mostly located in the 5’-untranslatable regions (5’UTRs) and 3’UTR, but also occupying long stretches of the coding sequence. Viral translation initiation is mediated by an internal ribosome entry site located at the 5’ terminus of the viral genome and regulated by distal functional RNA domains placed at the 3’ end. Subsequent RNA replication strongly depends on the 3’UTR folding and is also influenced by the 5’ end of the HCV RNA. Further increase in the genome copy number unleashes the formation of homodimers by direct interaction of two genomic RNA molecules, which are finally packed and released to the extracellular medium. All these processes, as well as transitions between them, are controlled by structural RNA elements that establish a complex, direct and long-distance RNARNA interaction network. This review summarizes current knowledge about functional RNA domains within the HCV RNA genome and provides an overview of the control exerted by direct, long-range RNA-RNA contacts for the execution of the viral cycle.Spanish Ministry of Economy and Competitiveness, No. BFU2012-31213; Junta de Andalucía, No. CVI-7430; and FEDER funds from the EUPeer reviewe

Describing the structural robustness landscape of bacterial small RNAs

<p>Abstract</p> <p>Background</p> <p>The potential role of RNA molecules as gene expression regulators has led to a new perspective on the intracellular control and genome organization. Because secondary structures are crucial for their regulatory role, we sought to investigate their robustness to mutations and environmental changes.</p> <p>Results</p> <p>Here, we dissected the structural robustness landscape of the small non-coding RNAs (sncRNAs) encoded in the genome of the bacterium <it>Escherichia coli</it>. We found that bacterial sncRNAs are not significantly robust to both mutational and environmental perturbations when compared against artificial, unbiased sequences. However, we found that, on average, bacterial sncRNAs tend to be significantly plastic, and that mutational and environmental robustness strongly correlate. We further found that, on average, epistasis in bacterial sncRNAs is significantly antagonistic, and positively correlates with plasticity. Moreover, the evolution of robustness is likely dependent upon the environmental stability of the cell, with more fluctuating environments leading to the emergence and fixation of more robust molecules. Mutational robustness also appears to be correlated with structural functionality and complexity.</p> <p>Conclusion</p> <p>Our study provides a deep characterization of the structural robustness landscape of bacterial sncRNAs, suggesting that evolvability could be evolved as a consequence of selection for more plastic molecules. It also supports that environmental fluctuations could promote mutational robustness. As a result, plasticity emerges to link robustness, functionality and evolvability.</p

RNA structures and their molecular evolution in HIV: evolution of robustness in RNA structures and theoretical systems

The known functions of RNA structures have expanded of late, such that RNA is considered a more active player in molecular biology. The presence of RNA secondary structure in a sequence should constrain evolution of its constituent nucleotides because of the requirement to maintain the base-pairing regions in the structure. In a previous work, we found support for this hypothesis in nine molecules from various organisms, the exception being a structure found in a protein-coding region of the HIV-1 genome. In this work, I examine the interaction of constraints imposed by RNA structures and host-induced hypermutation on molecular evolution in HIV-1. I conclude that RNA structures in HIV do evolve via compensatory evolution, but that hypermutation can obscure the expected signal. Since RNA's known roles have increased, so have the methods for identification and prediction of RNA structures in genetic sequence. I use a method adapted for searching in multiple coding regions to identify conserved RNA structures throughout the HIV-1 and HIV-2 genomes. I find evidence for several new, small structures in HIV-1, but evidence is less strong for HIV-2. Finally, I consider the evolution of robustness, the property of phenotypic constancy, using RNA structures and two other theoretical model systems. I find that pervasive environmental variation can select for environmental and genetic robustness in all three systems, and conclude that it may be a generic mechanism for the evolution of robustness

Short interval change in hepatitis C hypervariable region 1 in chronic infection. Are there treatment windows in the envelope?

Hepatitis C Virus (HCV), an RNA virus, is one of the leading causes of cirrhosis worldwide and, remains the leading indication for orthoptic liver transplantation in the United States. Dual treatment with pegylated interferon and ribavirin has until 2010 been the mainstay of treatment. The emergence of newer agents with direct activity against specific virus proteins has revolutionised HCV treatment but, the high cost of these medications are likely to prevent universal access, particularly in developing countries and, strategies to optimise response to cheaper combination treatments are required. The Irish Hepatitis C outcomes research network (ICORN) has proposed a target of 2025 for the complete eradication of Hepatitis C from Ireland. HCV replicates in an error prone fashion resulting in mutant progeny known as quasispecies(QS), thought to form an important mechanism of host immune evasion in the establishment and maintenance of chronic infection, which develops in 50-80% of those acutely infected. HCV has three hypervariable regions (sections of the virus genome that appear to tolerate higher substitution rates) and one of these, Hypervariable region 1 (HVR1) has been recognised as a major target of the adaptive immune response. HVR1 quasispecies complexity and diversity have been implicated as predictive of response to dual therapy. Little, however, is known about the natural history of these parameters in chronic infection. We discuss evolutionary concepts and how they apply to quasispecies and hypothesise how viruses might select a setting appropriate mutation rate in order to optimise adaptation, advancing the theory of replicative homeostasis. We prospectively study 23 patients with chronic HCV infections and, differing degrees of liver fibrosis fortnightly for a 16 week period prior to commencement of treatment. Using amplicon sequencing, cloning and next generation sequencing we explore the behaviour of HVR1 QS, establishing the utility of each technique in describing QS change. We identify variable and unpredictable HVR1 change in our cloning data which precludes the use of these metrics in pre treatment prediction models. HVR1 change is far greater in non cirrhotic patients and the transition to cirrhosis appears to be associated with a change from positive to purifying selection. Using molecular clock techniques we illustrate differing substitution rates within HVR1 among cirrhotic and non cirrhotic patients. We identify, by including an additional retrospective sample, that the patterns we describe are sustained over prolonged periods and further clarify the mode and tempo of HVR1 change by estimating the substitution rates. Using next generation sequencing techniques we identify similar patterns of HCV change when compared with our cloning data. However, the sequence depth provided permits the description of time specific network of HVR1 clones, all connected by a single amino acid substitution to a central node. By separating our samples into immunoglobulin bound and free fractions we describe the importance of host immune mediated change driving the changes seen in our pyrosequencing and cloning data. Finally, using known viral and host molecular markers predictive of treatment response we explore unsuccessfully for models predictive of treatment response

Identification of functional RNA structures in sequence data

Thesis advisor: Michelle M. MeyerThesis advisor: Peter CloteStructured RNAs have many biological functions ranging from catalysis of chemical reactions to gene regulation. Many of these homologous structured RNAs display most of their conservation at the secondary or tertiary structure level. As a result, strategies for natural structured RNA discovery rely heavily on identification of sequences sharing a common stable secondary structure. However, correctly identifying the functional elements of the structure continues to be challenging. In addition to studying natural RNAs, we improve our ability to distinguish functional elements by studying sequences derived from in vitro selection experiments to select structured RNAs that bind specific proteins. In this thesis, we seek to improve methods for distinguishing functional RNA structures from arbitrarily predicted structures in sequencing data. To do so, we developed novel algorithms that prioritize the structural properties of the RNA that are under selection. In order to identify natural structured ncRNAs, we bring concepts from evolutionary biology to bear on the de novo RNA discovery process. Since there is selective pressure to maintain the structure, we apply molecular evolution concepts such as neutrality to identify functional RNA structures. We hypothesize that alignments corresponding to structured RNAs should consist of neutral sequences. During the course of this work, we developed a novel measure of neutrality, the structure ensemble neutrality (SEN), which calculates neutrality by averaging the magnitude of structure retained over all single point mutations to a given sequence. In order to analyze in vitro selection data for RNA-protein binding motifs, we developed a novel framework that identifies enriched substructures in the sequence pool. Our method accounts for both sequence and structure components by abstracting the overall secondary structure into smaller substructures composed of a single base-pair stack. Unlike many current tools, our algorithm is designed to deal with the large data sets coming from high-throughput sequencing. In conclusion, our algorithms have similar performance to existing programs. However, unlike previous methods, our algorithms are designed to leverage the evolutionary selective pressures in order to emphasize functional structure conservation.Thesis (PhD) — Boston College, 2016.Submitted to: Boston College. Graduate School of Arts and Sciences.Discipline: Biology

Evolutionary responses of fast adapting populations to opposing selection pressures

This thesis deals with the mathematical modeling of evolutionary processes that take place in heterogeneous populations. Its leitmotif is the response of complex ensembles of replicating entities to multiple (and often opposite) selection pressures. Even though the specific problems addressed in different chapters belong to different organizational levels—genome, population, and community—all of them can be conceptualized as the evolution of a heterogeneous population—let it be a population of genomic elements, viruses, or prokaryotic hosts and phages—facing a complex environment. As a result, the mathematical tools required for their study are quite similar. In contrast, the strategies that each population has discovered to perpetuate vary according to the different evolutionary challenges and environmental constraints that the population experiences. Along this thesis, there has been a special interest on connecting theoretical models with experimental results. To that end, most of the work presented here has been motivated either by laboratory findings or by the bioinformatic analysis of sequenced genomes. We strongly believe that such a multidisciplinary approach is necessary in order to improve our knowledge on how evolution works. Moreover, experiments are a must when it comes to propose antiviral strategies based on theoretical predictions, as we do in Chapter 3. This thesis is structured in two main blocks. The first one focuses on studying instances of viral evolution under the action of mutagenic drugs, paying particular attention to their possible application to the development of novel antiviral therapies. This block comprises chapters 2 and 3; the former dicussing the phenomenon of lethal defection and stochastic viral extinction; the latter dealing with the optimal way to combine mutagens and inhibitors in multidrug antiviral treatments. The second block is devoted to the study of the evolutionary forces underlying genome structure. In chapter 4, we propose a mechanism through which multipartite viruses could have originated. Interestingly, the pathway leading to genome segmentation shares some steps with lethal defection, but each outcome is reached at specific environmental conditions. Chapter 5 analyses the abundance distributions of transposable elements in prokaryotic genomes, with the aim of determining the key processes involved in their spreading. We explicitly explore the hypothesis that transposable elements follow a neutral dynamics, with a negligible fitness cost for their host genomes. A higher level of organization is studied in Chapter 6, where an agent based coevolutionary model based on Lotka-Volterra interactions is used to investigate the evolutionary dynamics of the prokaryotic antiviral immunity system CRISPR-Cas. This chapter also examines the environmental factors that are responsible for its maintenance or loss. Finally, Chapter 7 summarizes the main results obtained along the thesis and sketches possible lines of work based on them