In a recent paper published in the journal ACS Omega, Prof. Sudha Rajamani’s group explored how life may have originated on early Earth by testing if a nucleotide analogue made of barbituric acid could be used to make RNA. What they found prompted them to propose that barbituric acid could have served as an ancestor for modern RNA bases. They carried out this work in collaboration with Prof. Sanjeev Galande's group from IISER Pune which is presently at Shiv Nadar University.
In an explanatory article below, Dr. Anupam Sawant and Prof. Sudha Rajamani describe the field of origins of life and their ongoing research on exploring how life might have evolved on Earth billions of years ago. Illustration credit: Dr. Sneha Tripathi.
This work was supported by research grants from DST’s Science and Engineering Research Board, GoI and the Department of Biotechnology, GoI.
Citation
Anupam A. Sawant, Sneha Tripathi, Sanjeev Galande, and Sudha Rajamani (2024). A prebiotic genetic nucleotide as an early Darwinian ancestor for pre-RNA evolution. ACS Omega 2024, 9, 16, 18072–18082.
https://doi.org/10.1021/acsomega.3c09949
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Authors of the research paper (Left to Right):
Dr. Anupam A. Sawant is a Senior Research Associate with Prof. Sudha Rajamani, Department of Biology, IISER Pune.
Dr. Sneha Tripathi was a PhD student at IISER Pune when she carried out this work. She is presently a Research Associate at the Weizmann Inst of Science, Israel and is a freelance scientific illustrator.
Prof. Sanjeev Galande was a faculty member at IISER Pune until recently and is presently the Dean of the School of Natural Sciences, Shiv Nadar University, Delhi-NCR.
Prof. Sudha Rajamani is a faculty member in the Department of Biology at IISER Pune.
Explanatory Article by Dr. Anupam Sawant and Prof. Sudha Rajamani
Illustration by Dr. Sneha Tripathi
Life’s oldest signatures on the planet Earth can be traced back to at least 3.5 billion years ago. In the past few decades, researching how life actually originated on the ‘pale blue dot’ has gained enormous importance. This renewed interest can be ascribed mainly to humankind’s imminent need to find the next “habitable” planet (or moon), either in our solar system or in planets of other galaxies (referred to as exoplanets). It has, therefore, become vital to understand how life came about on Earth, post its formation nearly 4.6 billion years ago.
Notably, elements like carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur are fundamental constituents of the complex extant life that we see today. This is mainly because they form the molecules fundamental to life including proteins, nucleic acids, and lipids, all of which are necessary for the functioning of a cell.
In the above context, the famous Urey-Miller experiment in 1953 demonstrated the formation of amino acids (the building blocks of protein), from inorganic molecules like hydrogen, ammonia and methane, with water being the vital solvent. They simulated reaction conditions that mimicked plausible early Earth scenario.
This resulted in versions of ‘prebiotic soup’, a coin termed by the famous J.B.S. Haldane who had a prominent connection with our subcontinent. Subsequent to Urey-Miller’s successful work, many research groups have undertaken studies to discern the emergence of other important biomolecules, including nucleic acids, amino acids and lipids, and studying their cross-talk as answers to these are essential to characterizing the emergence and propagation of early life.
Two of the important hallmarks of life that are defined by two important traits are information storage and reaction catalysis. Nucleic acids are informational polymers that are central to life as they store heritable genetic information. In most extant life, the information is encoded in the DNA and transferred to RNA, which is then read by the ribosomes to synthesize proteins that facilitate cellular reactions.
RNA, which is very similar to DNA but more ‘special’, are known to encode information in RNA viruses including the infamous SARS-CoV-2. RNAs are special as they can also facilitate reactions like proteins do. Such RNA enzymes are known as ribozymes and given this ‘dual ability’, it has been postulated that RNA molecules could have paved the way for the emergence of primordial life.
In this backdrop, our research group (the COoL group at IISER Pune) has been studying how nucleic acids could have formed from the prebiotic soup on the early Earth.
Typically, RNA-based evolution requires the formation of monomers or precursors called nucleotides. These result from the coming together of three basic components; a nucleobase (adenine, guanine, cytosine, uracil), a ribose pentose sugar and a phosphate. Pertinently, early Earth conditions were not conducive for forming nucleotide monomers that are similar to what is used in present-day cells.
This persuaded the origins of life community to delve into the idea of ‘molecular ancestry’ in nucleic acids. This posits that prior to the emergence of RNA and DNA as we know them, there were pre-RNAs that comprised of nucleobases that readily formed nucleotides and, subsequently, nucleic acids. This is strengthened by the fact that more than a hundred nucleobase modifications have been identified to date in various functional and non-functional RNA molecules.
Relevantly, the heterogenous prebiotic soup would have provided an opportunity for the various heterocycles that resulted under early Earth conditions, to evolve into nucleobases (and possibly nucleic acids too). Notably, few non-canonical heterocycles like barbituric acid, cyanuric acid and orotic acid, which have structures similar to canonical bases, have been shown to readily form nucleotide monomers.
Previously, our group successfully showed the formation of a nucleotide and RNA oligomers, which contain barbituric acid (BA) as the nucleobase. Given this, the next big challenge for us was to test whether this ‘alternate nucleotide analogue’, could have been utilized in processes that allowed for the transition from non-life to life on the early Earth. If yes, BA would truly fulfil the credential of being a potential ancestor to modern nucleotides.
This is precisely what we illustrated in our recently published work in ACS Omega. This was done by testing if present-day enzymes could use BA nucleotides instead of uracil, to make RNA via transcription reaction in a test tube (information transfer from DNA template to RNA is called transcription). Further, the RNA that contained these alternate nucleotides, were tested for their capacity to evolve into a ‘functional’ RNA (e.g. form an aptamer). Finally, we also checked if information could be transferred back from this modified RNA to DNA, via a process called reverse transcription (which is the opposite of transcription). Rewardingly for us, the barbituric acid nucleotide accomplished all the tests successfully, allowing us to propose that this, indeed, could have been an ancestor of our modern RNA bases.
In addition to being a really exciting outcome in itself, these results are very interesting as they not only widen our understanding of how informational polymers could have evolved during life’s emergence and early evolution, but also opens up new avenues in synthetic biology for manufacturing novel nucleic acid therapeutics that could potentially result in a cure for future pandemics.