One RNA plays three roles to provide catalytic activity to a group I intron lacking an endogenous internal guide sequence

RNA Structure: Past, Future, and Gene Therapy Applications

First believed to be a simple intermediary between the information encoded in deoxyribonucleic acid and that functionally displayed in proteins, ribonucleic acid (RNA) is now known to have many functions through its abundance and intricate, ubiquitous, diverse, and dynamic structure. About 70-90% of the human genome is transcribed into protein-coding and noncoding RNAs as main determinants along with regulatory sequences of cellular to populational biological diversity. From the nucleotide sequence or primary structure, through Watson-Crick pairing self-folding or secondary structure, to compaction via longer distance Watson-Crick and non-Watson-Crick interactions or tertiary structure, and interactions with RNA or other biopolymers or quaternary structure, or with metabolites and biomolecules or quinary structure, RNA structure plays a critical role in RNA's lifecycle from transcription to decay and many cellular processes. In contrast to the success of 3-dimensional protein structure prediction using AlphaFold, RNA tertiary and beyond structures prediction remains challenging. However, approaches involving machine learning and artificial intelligence, sequencing of RNA and its modifications, and structural analyses at the single-cell and intact tissue levels, among others, provide an optimistic outlook for the continued development and refinement of RNA-based applications. Here, we highlight those in gene therapy.

The RNA Revolution in the Central Molecular Biology Dogma Evolution

Human genome projects in the 1990s identified about 20,000 protein-coding sequences. We are now in the RNA revolution, propelled by the realization that genes determine phenotype beyond the foundational central molecular biology dogma, stating that inherited linear pieces of DNA are transcribed to RNAs and translated into proteins. Crucially, over 95% of the genome, initially considered junk DNA between protein-coding genes, encodes essential, functionally diverse non-protein-coding RNAs, raising the gene count by at least one order of magnitude. Most inherited phenotype-determining changes in DNA are in regulatory areas that control RNA and regulatory sequences. RNAs can directly or indirectly determine phenotypes by regulating protein and RNA function, transferring information within and between organisms, and generating DNA. RNAs also exhibit high structural, functional, and biomolecular interaction plasticity and are modified via editing, methylation, glycosylation, and other mechanisms, which bestow them with diverse intra- and extracellular functions without altering the underlying DNA. RNA is, therefore, currently considered the primary determinant of cellular to populational functional diversity, disease-linked and biomolecular structural variations, and cell function regulation. As demonstrated by RNA-based coronavirus vaccines' success, RNA technology is transforming medicine, agriculture, and industry, as did the advent of recombinant DNA technology in the 1980s.

The non-deterministic genotype-phenotype map of RNA secondary structure

Selection and variation are both key aspects in the evolutionary process. Previous research on the mapping between molecular sequence (genotype) and molecular fold (phenotype) has shown the presence of several structural properties in different biological contexts, implying that these might be universal in evolutionary spaces. The deterministic genotype-phenotype (GP) map that links short RNA sequences to minimum free energy secondary structures has been studied extensively because of its computational tractability and biologically realistic nature. However, this mapping ignores the phenotypic plasticity of RNA. We define a GP map that incorporates non-deterministic (ND) phenotypes, and take RNA as a case study; we use the Boltzmann probability distribution of folded structures and examine the structural properties of ND GP maps for RNA sequences of length 12 and coarse-grained RNA structures of length 30 (RNAshapes30). A framework is presented to study robustness, evolvability and neutral spaces in the ND map. This framework is validated by demonstrating close correspondence between the ND quantities and sample averages of their deterministic counterparts. When using the ND framework we observe the same structural properties as in the deterministic GP map, such as bias, negative correlation between genotypic robustness and evolvability, and positive correlation between phenotypic robustness and evolvability.

The simple emergence of complex molecular function

At odds with a traditional view of molecular evolution that seeks a descent-with-modification relationship between functional sequences, new functions can emerge de novo with relative ease. At early times of molecular evolution, random polymers could have sufficed for the appearance of incipient chemical activity, while the cellular environment harbours a myriad of proto-functional molecules. The emergence of function is facilitated by several mechanisms intrinsic to molecular organization, such as redundant mapping of sequences into structures, phenotypic plasticity, modularity or cooperative associations between genomic sequences. It is the availability of niches in the molecular ecology that filters new potentially functional proposals. New phenotypes and subsequent levels of molecular complexity could be attained through combinatorial explorations of currently available molecular variants. Natural selection does the rest. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.

Catalysts, autocatalysis and the origin of metabolism

If life on Earth started out in geochemical environments like hydrothermal vents, then it started out from gasses like CO₂, N₂ and H₂. Anaerobic autotrophs still live from these gasses today, and they still inhabit the Earth's crust. In the search for connections between abiotic processes in ancient geological systems and biotic processes in biological systems, it becomes evident that chemical activation (catalysis) of these gasses and a constant source of energy are key. The H₂–CO₂ redox reaction provides a constant source of energy and anabolic inputs, because the equilibrium lies on the side of reduced carbon compounds. Identifying geochemical catalysts that activate these gasses en route to nitrogenous organic compounds and small autocatalytic networks will be an important step towards understanding prebiotic chemistry that operates only on the basis of chemical energy, without input from solar radiation. So, if life arose in the dark depths of hydrothermal vents, then understanding reactions and catalysts that operate under such conditions is crucial for understanding origins.

Riboswitch distribution, structure, and function in bacteria

Riboswitches are gene control elements that directly bind to specific ligands to regulate gene expression without the need for proteins. They are found in all three domains of life, including Bacteria, Archaea, and Eukaryota. Riboswitches are mostly spread in bacteria and archaea. In this paper, we discuss the general distribution, structure, and function of 28 different riboswitch classes as we focus our attention on riboswitches in bacteria. Bacterial riboswitches regulate gene expression by four distinct mechanisms. They regulate the expression of a limited number of genes. However, most of these genes are responsible for the synthesis of essential metabolites without which the cell cannot function. Therefore, riboswitch distribution is also important for antibacterial drug development.

On the networked architecture of genotype spaces and its critical effects on molecular evolution

Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at the macroevolutionary, ecological and molecular level. Actually, when the complex architecture of genotype spaces is taken into account, the evolutionary dynamics of molecular populations becomes intrinsically non-uniform, sharing deep qualitative and quantitative similarities with slowly driven physical systems: nonlinear responses analogous to critical transitions, sudden state changes or hysteresis, among others. Furthermore, the phenotypic plasticity inherent to genotypes transforms classical fitness landscapes into multiscapes where adaptation in response to an environmental change may be very fast. The quantitative nature of adaptive molecular processes is deeply dependent on a network-of-networks multilayered structure of the map from genotype to function that we begin to unveil.

Adaptive multiscapes: an up-to-date metaphor to visualize molecular adaptation

Background

Wright’s metaphor of the fitness landscape has shaped and conditioned our view of the adaptation of populations for almost a century. Since its inception, and including criticism raised by Wright himself, the concept has been surrounded by controversy. Among others, the debate stems from the intrinsic difficulty to capture important features of the space of genotypes, such as its high dimensionality or the existence of abundant ridges, in a visually appealing two-dimensional picture. Two additional currently widespread observations come to further constrain the applicability of the original metaphor: the very skewed distribution of phenotype sizes (which may actively prevent, due to entropic effects, the achievement of fitness maxima), and functional promiscuity (i.e. the existence of secondary functions which entail partial adaptation to environments never encountered before by the population).

Results

Here we revise some of the shortcomings of the fitness landscape metaphor and propose a new “scape” formed by interconnected layers, each layer containing the phenotypes viable in a given environment. Different phenotypes within a layer are accessible through mutations with selective value, while neutral mutations cause displacements of populations within a phenotype. A different environment is represented as a separated layer, where phenotypes may have new fitness values, other phenotypes may be viable, and the same genotype may yield a different phenotype, representing genotypic promiscuity. This scenario explicitly includes the many-to-many structure of the genotype-to-phenotype map. A number of empirical observations regarding the adaptation of populations in the light of adaptive multiscapes are reviewed.

Conclusions

Several shortcomings of Wright’s visualization of fitness landscapes can be overcome through adaptive multiscapes. Relevant aspects of population adaptation, such as neutral drift, functional promiscuity or environment-dependent fitness, as well as entropic trapping and the concomitant impossibility to reach fitness peaks are visualized at once. Adaptive multiscapes should aid in the qualitative understanding of the multiple pathways involved in evolutionary dynamics.

Reviewers

This article was reviewed by Eugene Koonin and Ricard Solé.

A review on architecture of the gag-pol ribosomal frameshifting RNA in human immunodeficiency virus: a variability survey of virus genotypes

Programmed '-1' ribosomal frameshifting is necessary for expressing the pol gene overlapped from a gag of human immunodeficiency virus. A viral RNA structure that requires base pairing across the overlapping sequence region suggests a mechanism of regulating ribosome and helicase traffic during expression. To get precise roles of an element around the frameshift site, a review on architecture of the frameshifting RNA is performed in combination of reported information with augments of a representative set of 19 viral samples. In spite of a different length for the viral RNAs, a canonical comparison on the element sequence allocation is performed for viewing variability associations between virus genotypes. Additionally, recent and historical insights recognized in frameshifting regulation are looked back as for indel and single nucleotide polymorphism of RNA. As specially noted, structural changes at a frameshift site, the spacer sequence, and a three-helix junction element, as well as two Watson-Crick base pairs near a bulge and a C-G pair close a loop, are the most vital strategies for the virus frameshifting regulations. All of structural changes, which are dependent upon specific sequence variations, facilitate an elucidation about the RNA element conformation-dependent mechanism for frameshifting. These facts on disrupting base pair interactions also allow solving the problem of competition between ribosome and helicase on a same RNA template, common to single-stranded RNA viruses. In a broad perspective, each new insight of frameshifting regulation in the competition systems introduced by the RNA element construct changes will offer a compelling target for antiviral therapy.

Recycling of informational units leads to selection of replicators in a prebiotic soup

Prebiotic chemical reactions would have been greatly aided by a process whereby living materials could have been recycled under conditions of limiting resources. Recombination of RNA fragments is a viable means of recycling but has not been demonstrated. Using systems based on the Azoarcus group I intron ribozyme, computational Monte Carlo studies indicate that a moderate level of recycling activity, spontaneous or catalyzed, leads to the most robust selection scenarios. It is interesting that recycling leads to a threshold effect where a dominant species suddenly jumps to fixation. In conjunction, laboratory studies with the Azoarcus ribozyme corroborate these results, showing that mixtures of scrambled and/or deleteriously mutated molecules can recycle their component fragments to generate fully functional recombinase ribozymes. These studies highlight the importance of recombination and recycling jointly in the advent of living systems.

A model for the origin of life through rearrangements among prebiotic phosphodiester polymers

This model proposes that the origin of life on Earth occurred as a result of a process of alteration of the chemical composition of prebiotic macromolecules. The stability of organic compounds assembled into polymers generally exceeded the stability of the same compounds as free monomers. This difference in stability stimulated accumulation of prebiotic macromolecules. The prebiotic circulation of matter included constant formation and decomposition of polymers. Spontaneous chemical reactions between macromolecules with phosphodiester backbones resulted in a non-Darwinian selection for chemical stability, while formation of strong structures provided an advantage in the struggle for stability. Intermolecular structures between nucleotide-containing polymers were further stabilized by occasional acquisition of complementary nucleotides. Less stable macromolecules provided the source of nucleotides. This process resulted first in the enrichment of nucleotide content in prebiotic polymers, and subsequently in the accumulation of complementary oligonucleotides. Finally, the role of complementary copy molecules changed from the stabilization of the original templates to the de novo production of template-like molecules. I associate this stage with the origin of life in the form of cell-free molecular colonies. Original life acquired ready-to-use substrates from constantly forming prebiotic polymers. Metabolism started to develop when life began to consume more substrates than the prebiotic cycling produced. The developing utilization of non-polymeric compounds stimulated the formation of the first membrane-enveloped cells that held small soluble molecules. Cells "digested" the nucleotide-containing prebiotic macromolecules to nucleotide monomers and switched the mode of replication to the polymerization of nucleotide triphosphates.

Group I intron ribozymes

Group I intron ribozymes constitute one of the main classes of ribozymes and have been a particularly important model in the discovery of key concepts in RNA biology as well as in the development of new methods. Compared to other ribozyme classes, group I intron ribozymes display considerable variation both in their structure and the reactions they catalyze. The best described pathway is the splicing pathway that results in a spliced out intron and ligated exons. This is paralleled by the circularization pathway that leads to full-length circular intron and un-ligated exons. In addition, the intronic products of these pathways have the potential to integrate into targets and to form various types of circular RNA molecules. Thus, group I intron ribozymes and associated elements found within group I introns is a rich source of biological phenomena. This chapter provides a strategy and protocols for initial characterization of new group I intron ribozymes.