Our Team

FfAME Our Team Clay Abraham

Researcher

Clay Abraham

Clay Abraham is a research scientist at FfAME and has been working here since 2018. Clay’s research explores anaerobic microbiology and metagenomics, synthetic biology, and prebiotic chemistry.
  • (386) 418-8085
  • 5+

Research Summary

My research at FfAME spans prebiotic chemistry, environmental microbiology, and synthetic biology. I investigate the role of basalt glass in prebiotic RNA formation and related chemical pathways. I also perform metagenomic and bioinformatic analyses of Arctic Ocean sediments and study anaerobic extremophiles. In synthetic biology, I engineer enzymes, develop functional assays, and apply sequencing technologies using artificial nucleotides.

Research Focus:
  • Astrobiology
  • Bioinformatics
  • Extremophiles
  • Microbiology
  • Prebiotic Chemistry
Education:
  • BAS in Industrial Biotechnology, Santa Fe College, United States (2018)
  • MS in Biology, University of St. Joseph, United States (2023)
  • Certificates in genomics and environmental science
Awards:
  • Clay A. Abraham. Arctic Microbes and the Quest for Analog Alien Life.The American Philosophical Society, Baruch Blumberg Grants in Astrobiology. 2025. (Awarded; $7,000)

Publications

Hirakawa, Y., Kim, H.-J., Furukawa, Y., Abraham, C., Peng, T.-W., Biondi, E., Benner, S. A. Proc. Natl. Acad. Sci. USA 122 (51) (2025) e2516418122, doi: 10.1073/pnas.2516418122

Models for prebiotic syntheses often have many steps, each separately validated by laboratory experiments. The challenge then asks whether these steps work together in natural geological environments, absent human intervention. Here, we analyze a six-step Discontinuous Synthesis Model (DSM) for the prebiotic formation of RNA, proposed to be the first informational molecule to support Darwinian evolution, and life, on Earth and/or Mars. DSM requires that borate in multiple steps guide the formation of pentoses from simple carbohydrates and control phosphorylation, in all cases by binding adjacent HO-groups on key intermediates. However, adjacent HO-groups must react in two other steps, which borate might inhibit. Experiments here show that borate does not inhibit these two other steps, but rather facilitates them. This makes the six-step DSM a “no human intervention” route from simple
precursors (1 to 3 carbons, 0 to 2 nitrogens) to oligomeric RNA with predominately 3’,5’
-linkages at least 6 nucleotides long, but possibly much longer. The process i) exploits privileged chemistry in ii) intermittently irrigated aquifers constrained by basalt that iii) have borate iv) above a redox-neutral mantle v) having access to an atmosphere transiently reduced by a Vesta-sized impactor. In a possible coincidence, such an impact occurred most likely ca. 4.3 billion years ago (Ga), ~100 Mya before some molecular clocks date the divergence of the three kingdoms of life on Earth (4.2 Ga), and ca. 200 Mya before isotopically “light” carbon is reported in zircons dated at 4.1 Ga. This carbon may be the oldest trace of life ever proposed.

Abraham, C., Ingvadottir, E.M., Bradley, K., Scully, S.M., Orlygsson, J., Dube, D., Benner, S.A Data In Brief 63, Elsevier 112192 (2025) doi: 10.1016/j.dib.2025.112192

Thermoanaerobacter uzonensis strain AK85 belongs to the Thermoanaerobacter genus, which comprises rod-shaped, Gram-positive, thermophilic, obligate anaerobic bacteria. Members of this genus exhibit unique fermentation qualities, such as prolific ethanol production, and can generate longer-chain alcohols from carbohydrate and amino acid sources. Here we present the draft genome sequence of Thermoanaerobacter uzonensis strain AK85, which was previously isolated from a hot spring in Graensdalur in Southwestern Iceland. The genome was sequenced with a 150 bp paired-end library on a MGISEQ-2000. The assembled genome comprises 2,577,794 bp and a GC ratio of 33.69 %. With an ANI of 96.9 % strain AK85 was determined to be a strain of Thermoanaerobacter uzonensis. Annotation was conducted with Prokka which revealed 41 enzymes related to carbohydrate, amino acid, and carboxylic acid metabolism. The genomic dataset establishes the biotechnological capacity and potential of strain AK85 for the production of alcohols and other bio-manufactured products. Further, the genomic dataset is coupled with a cofactor and substrate analysis of the three detected alcohol dehydrogenases. These enzymes were assessed via a lysate based colorimetric assay with NAD+ and NADP+. Under these conditions the native alcohol dehydrogenases are able to oxidize long chain primary alcohols such as 1-octanol and benzyl alcohol. The reads and assembled draft genome of AK85 were deposited into SRA and NCBI under Bioproject PRJNA1108289, Genbank JBDHNK000000000, and Biosample SAMN41233939.

Li Y, Abraham C, Suslov O, Yaren O, Shaw RW, Kim MJ, Wan S, Marliere P, Benner SA ACS Synthetic Biology 12 (6), American Chemical Society 1772-1781 (2023) PMCID: PMC10911313

One horizon in synthetic biology seeks alternative forms of DNA that store, transcribe, and support the evolution of biological information. Here, hydrogen bond donor and acceptor groups are rearranged within a Watson–Crick geometry to get 12 nucleotides that form 6 independently replicating pairs. Such artificially expanded genetic information systems (AEGIS) support Darwinian evolution in vitro. To move AEGIS into living cells, metabolic pathways are next required to make AEGIS triphosphates economically from their nucleosides, eliminating the need to feed these expensive compounds in growth media. We report that “polyphosphate kinases” can be recruited for such pathways, working with natural diphosphate kinases and engineered nucleoside kinases. This pathway in vitro makes AEGIS triphosphates, including third-generation triphosphates having improved ability to survive in living bacterial cells. In α-32P-labeled forms, produced here for the first time, they were used to study DNA polymerases, finding cases where third-generation AEGIS triphosphates perform better with natural enzymes than second-generation AEGIS triphosphates.