Conducting Miller-Urey Experiments

In 1953, Stanley Miller reported the production of biomolecules from simple gaseous starting materials, using an apparatus constructed to simulate the ...

NASA Johnson Space Center

RNA-directed recombination can be used to catalyze a disproportionation reaction among small RNA substrates to create new combinations of sequences. But the accommodation of secondary and tertiary structural constraints in the substrates by recombinase ribozymes has not been explored. Here, we show that the Azoarcus group I intron can recombine oligoribonucleotides to construct class I ligase ribozymes, which are catalytically active upon synthesis. The substrate oligonucleotides, ranging in size from 58 to 104 nucleotides (nt), along with the 152-nt ligase ribozymes they reconstitute, can contain significant amounts of secondary structure. However, substrate recognition by the Azoarcus ribozyme depends on the existence of a single accessible CAU triplet for effective recombination. A biphasic temperature reaction profile was designed such that the sequential recombination/ligation events could take place in a thermocycler without human intervention. A temperature-dependent pH shift of the reaction buffer contributes to the success of the net reaction. When the substrate for the ligase ribozyme is introduced into the reaction mixture, as much as 11% can be observed being converted to product by the recombined ligase in the same reaction vessel. Recombination followed by ligation can also occur under isothermal conditions at 37 degrees C. Tertiary structure formation of the ligase upon construction can provide some protection from cleavage by the Azoarcus ribozyme when compared to the constituent substrates. These data suggest that RNA-directed recombination can, in fact, articulate complex ribozymes, and that there are logical rules that can guide the optimal placement of the CAU recognition sequence.

RNA-directed construction of structurally complex and active ligase ribozymes through recombination.

Group I intron ribozymes isolated from natural sources have a strict dependence on the divalent metal cations Mg(II) or Mn(II) for catalytic activity. However, mutant versions of the Tetrahymena ribozyme have been previously isolated in the laboratory that show demonstrable activity in 10 mM CaCl(2) as the only supplied salt. Here, we sought to discover similar variants of another group I intron that is likely more evolutionarily specialized. We used in vitro selection to isolate a Ca(II)-dependent variant of the naturally-occurring form of the Azoarcus ribozyme, which is half the size of the Tetrahymena ribozyme and possesses an extremely high G+C content of 71%. A mutation of G to A at position 118 was selected in multiple independent trials. Activity of the mutant is very poor in Ca(II) and can only be observed after RT-PCR, highlighting the power of in vitro selection to isolate molecules with rare and low-level activities. The mutation likely confers an alternate but rare folded conformation that permits accommodation of Ca(II) ions and catalysis. This work also serves to caution that although a selection may be successful, isolates may not be catalytically proficient enough to provide useful levels of activity.

Calcium(II)-dependent catalytic activity of the Azoarcus ribozyme: testing the limits of resolution for in vitro selection.

An RNA-DNA World could arise from an all-RNA system with the development of as few as three ribozymes-a DNA-dependent RNA polymerase, an RNA-dependent DNA polymerase, and a catalyst for the production of DNA nucleotides. A significant objection to DNA preceding proteins is that RNA has not been shown to catalyze the production of DNA. However, RNA- and DNAzymes have been recently discovered that catalyze chemical reactions capable of forming deoxyribose, such as mixed aldol condensation of 5'-glyceryl- and 3'-glycoaldehyde-terminated DNA strands. Thus, the only remaining obstacles to RNA-catalyzed in vitro DNA synthesis are alterations of substrate and template specificities of known ribozymes. The RNA-DNA World lessens genomic size constraints through a relaxed error threshold, affording the evolutionary time needed to develop protein synthesis. Separation of information from catalyst enables genotype and phenotype to be readily discriminated by absence or presence, respectively, of the 2'-OH. Novel ribozymes that arise through mutation can be preserved in DNA by reverse transcription, which makes them much more likely to be retained than in an RNA-genome milieu. The extra degree of separation between protein and mRNA, in terms of identifying and then retaining a useful enzyme, may have in fact necessitated storing information in DNA prior to the advent of translation.

DNA before proteins? Recent discoveries in nucleic acid catalysis strengthen the case.

RNA and DNA oligonucleotides radiolabeled with (32)P or (33)P often require gel electrophoresis to remove undesired side and/or degradation products. Common ways to visualize these molecules after electrophoresis are by ultraviolet (UV) shadowing, which necessarily reduces the specific activity of the oligonucleotide, and by autoradiography using film, which is cumbersome and increases the cost of generating the radiolabeled molecule. A more cost-effective method is to physically inject the gel with a "Dip-N-Dot" solution of dye and radionuclide after electrophoresis but prior to phosphorimaging. The gel can be overlaid on its computer-generated image, allowing the labeled molecules to be visualized quickly.

Gel purification of radiolabeled nucleic acids via phosphorimaging: Dip-N-Dot.

An in vitro form of the self-splicing group-I intron interrupting the Azoarcus tRNA(Ile) was shortened by ~10% with the removal of helix P6a. This deletion reduced the reverse-splicing activity of the ribozyme about 10-fold. Through in vitro selection, this activity was restored in several low-error mutants. A number of mutations were found that improved reverse-splicing activity through both increased k (obs) and better folding. The deletion mutant could be fragmented into as many as three discrete pieces, which, when incubated together, were capable of covalent self-assembly through energy-neutral transesterification reactions, a process called autorecombination. A subset of the mutations identified through in vitro selection for reverse-splicing were exaptations in that they were also shown to augment the autorecombination reactions, leading to higher yields of covalently self-assembled products, making this the smallest such system yet discovered.

Enhancing the prebiotic relevance of a set of covalently self-assembling, autorecombining RNAs through in vitro selection.

A "warm formamide" scenario for the origins of life might not be so hot: Comment on "Formamide and the origin of life" by E. Di Mauro et al.

The discoveries of amino acids of extraterrestrial origin in many meteorites over the last 50 years have revolutionized the Astrobiology field. A variety of non-terrestrial amino acids similar to those found in life on Earth have been detected in meteorites. A few amino acids have even been found with chiral excesses, suggesting that meteorites could have contributed to the origin of homochirality in life on Earth. In addition to amino acids, which have been productively studied for years, sugar-like molecules, activated phosphates, and nucleobases have also been determined to be indigenous to numerous meteorites. Because these molecules are essential for life as we know it, and meteorites have been delivering them to the Earth since accretion, it is plausible that the origin(s) of life on Earth were aided by extraterrestrially-synthesized molecules. Understanding the origins of life on Earth guides our search for life elsewhere, helping to answer the question of whether biology is unique to Earth. This tutorial review focuses on meteoritic amino acids and nucleobases, exploring modern analytical methods and possible formation mechanisms. We will also discuss the unique window that meteorites provide into the chemistry that preceded life on Earth, a chemical record we do not have access to on Earth due to geologic recycling of rocks and the pervasiveness of biology across the planet. Finally, we will address the future of meteorite research, including asteroid sample return missions.

Understanding prebiotic chemistry through the analysis of extraterrestrial amino acids and nucleobases in meteorites.

Doppler weather radar imaging enabled the rapid recovery of the Sutter's Mill meteorite after a rare 4-kiloton of TNT-equivalent asteroid impact over the foothills of the Sierra Nevada in northern California. The recovered meteorites survived a record high-speed entry of 28.6 kilometers per second from an orbit close to that of Jupiter-family comets (Tisserand's parameter = 2.8 ± 0.3). Sutter's Mill is a regolith breccia composed of CM (Mighei)-type carbonaceous chondrite and highly reduced xenolithic materials. It exhibits considerable diversity of mineralogy, petrography, and isotope and organic chemistry, resulting from a complex formation history of the parent body surface. That diversity is quickly masked by alteration once in the terrestrial environment but will need to be considered when samples returned by missions to C-class asteroids are interpreted.

Article	Year
RNA-directed construction of structurally complex and active ligase ribozymes through recombination. RNA (New York, N.Y.)\| PubMed ID: 16177133	2005
Calcium(II)-dependent catalytic activity of the Azoarcus ribozyme: testing the limits of resolution for in vitro selection. Biochimie\| PubMed ID: 16494986	2006
DNA before proteins? Recent discoveries in nucleic acid catalysis strengthen the case. Astrobiology\| PubMed ID: 19215202	2009
Gel purification of radiolabeled nucleic acids via phosphorimaging: Dip-N-Dot. Analytical biochemistry\| PubMed ID: 19232314	2009
Enhancing the prebiotic relevance of a set of covalently self-assembling, autorecombining RNAs through in vitro selection. Journal of molecular evolution\| PubMed ID: 20198367	2010
A "warm formamide" scenario for the origins of life might not be so hot: Comment on "Formamide and the origin of life" by E. Di Mauro et al. Physics of life reviews\| PubMed ID: 22222771	2012
Understanding prebiotic chemistry through the analysis of extraterrestrial amino acids and nucleobases in meteorites. Chemical Society reviews\| PubMed ID: 22706603	2012
Radar-enabled recovery of the Sutter's Mill meteorite, a carbonaceous chondrite regolith breccia. Science (New York, N.Y.)\| PubMed ID: 23258889	2012

Aaron S. Burton

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