Putative intermediary stages for the molecular evolution from a ribozyme to a catalytic RNP

Pairwise Engineering of Tandemly Aligned Self-Splicing Group I Introns for Analysis and Control of Their Alternative Splicing

Alternative splicing is an important mechanism in the process of eukaryotic nuclear mRNA precursors producing multiple protein products from a single gene. Although group I self-splicing introns usually perform regular splicing, limited examples of alternative splicing have also been reported. The exon-skipping type of splicing has been observed in genes containing two group I introns. To characterize splicing patterns (exon-skipping/exon-inclusion) of tandemly aligned group I introns, we constructed a reporter gene containing two Tetrahymena introns flanking a short exon. To control splicing patterns, we engineered the two introns in a pairwise manner to design pairs of introns that selectively perform either exon-skipping or exon-inclusion splicing. Through pairwise engineering and biochemical characterization, the structural elements important for the induction of exon-skipping splicing were elucidated.

Prebiotic Peptides: Molecular Hubs in the Origin of Life

The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.

A maturase that specifically stabilizes and activates its cognate group I intron at high temperatures

Folding of large structured RNAs into their functional tertiary structures at high temperatures is challenging. Here we show that I-TnaI protein, a small LAGLIDADG homing endonuclease encoded by a group I intron from a hyperthermophilic bacterium, acts as a maturase that is essential for the catalytic activity of this intron at high temperatures and physiological cationic conditions. I-TnaI specifically binds to and induces tertiary packing of the P4-P6 domain of the intron; this RNA-protein complex might serve as a thermostable platform for active folding of the entire intron. Interestingly, the binding affinity of I-TnaI to its cognate intron RNA largely increases with temperature; over 30-fold stronger binding at higher temperatures relative to 37 °C correlates with a switch from an entropy-driven (37 °C) to an enthalpy-driven (55-60 °C) interaction mode. This binding mode may represent a novel strategy how an RNA binding protein can promote the function of its target RNA specifically at high temperatures.

Coordinated control of a designed trans-acting ligase ribozyme by a loop-receptor interaction

We previously developed a synthetic cis-acting RNA ligase ribozyme with 3'-5' joining activity termed "DSL" (designed and selected ligase). DSL was easily transformed into a trans-acting form because of its highly modular architecture. In this study, we investigated the modular properties and turnover capabilities of a trans-acting DSL, tDSL-1/GUAA. tDSL-1/GUAA exhibited remarkably high activity compared with the parental cis-acting DSL, and it attained a high turnover number. Taken together, the results indicate that a loop-receptor interaction plays a significant role in determining the activity of the trans-acting ribozyme and in its ability to perform multiple turnovers of the reaction.

Primitive templated catalysis of a peptide ligation by self-folding RNAs

RNA–polypeptide complexes (RNPs), which play various roles in extant biological systems, have been suggested to have been important in the early stages of the molecular evolution of life. At a certain developmental stage of ancient RNPs, their RNA and polypeptide components have been proposed to evolve in a reciprocal manner to establish highly elaborate structures and functions. We have constructed a simple model system, from which a cooperative evolution system of RNA and polypeptide components could be developed. Based on the observation that several RNAs modestly accelerated the chemical ligation of the two basic peptides. We have designed an RNA molecule possessing two peptide binding sites that capture the two peptides. This designed RNA can also accelerate the peptide ligation. The resulting ligated peptide, which has two RNA-binding sites, can in turn function as a trans-acting factor that enhances the endonuclease activity catalyzed by the designed RNA.

Bacteriophage P22 antitermination boxB sequence requirements are complex and overlap with those of lambda

Transcription antitermination in phages lambda and P22 uses N proteins that bind to similar boxB RNA hairpins in regulated transcripts. In contrast to the lambda N-boxB interaction, the P22 N-boxB interaction has not been extensively studied. A nuclear magnetic resonance structure of the P22 N peptide boxB(left) complex and limited mutagenesis have been reported but do not reveal a consensus sequence for boxB. We have used a plasmid-based antitermination system to screen boxBs with random loops and to test boxB mutants. We find that P22 N requires boxB to have a GNRA-like loop with no simple requirements on the remaining sequences in the loop or stem. U:A or A:U base pairs are strongly preferred adjacent to the loop and appear to modulate N binding in cooperation with the loop and distal stem. A few GNRA-like hexaloops have moderate activity. Some boxB mutants bind P22 and lambda N, indicating that the requirements imposed on boxB by P22 N overlap those imposed by lambda N. Point mutations can dramatically alter boxB specificity between P22 and lambda N. A boxB specific for P22 N can be mutated to lambda N specificity by a series of single mutations via a bifunctional intermediate, as predicted by neutral theories of evolution.

RNA and RNP as new molecular parts in synthetic biology

Synthetic biology has a promising outlook in biotechnology and for understanding the self-organizing principle of biological molecules in life. However, synthetic biologists have been looking for new molecular "parts" that function as modular units required in designing and constructing new "devices" and "systems" for regulating cell function because the number of such parts is strictly limited at present. In this review, we focus on RNA/ribonucleoprotein (RNP) architectures that hold promise as new "parts" for synthetic biology. They are constructed with molecular design and an experimental evolution technique. So far, designed self-folding RNAs, RNA (RNP) enzymes, and nanoscale RNA architectures have been successfully constructed by utilizing Watson-Crick base-pairs together with specific RNA-RNA or RNA-protein binding motifs of known defined 3D structures. Riboregulators for regulating targeted gene expression have also been designed and produced in vitro as well as in vivo. Lately, RNA and ribonucleoprotein complexes have been strongly attracting the attention of molecular biologists because a variety of noncoding RNAs discovered in nature perform spatiotemporal gene expressions. Thus we hope that newly accumulating knowledge on naturally occurring RNAs and RNP complexes will provide a variety of new parts, devices and systems for synthetic biology.