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TAC Seminar Explores Y-Family Polymerases

By Brian Chorley
April 2009

Woodgate's research on Y-family polymerases has utilized a number of diverse model systems.
Woodgate's research on Y-family polymerases has utilized a number of diverse model systems which have related back to the human condition. “We started studying E. coli mutagenesis in bacteria and ended up with homologues that are involved in mutagenesis and carcinogenesis in humans.” (Photo courtesy of Steve McCaw)

Abdulovic introduced Woodgate.
Abdulovic introduced Woodgate as a “guru on the biochemical and enzymatic properties of Y-family polymerases,” which became evident during his talk. (Photo courtesy of Steve McCaw)

During the seminar, Woodgate presented a slide.
During the seminar, Woodgate presented a slide generated in 2001 that outlined fifty-two known orthologues of the Y-family polymerases at that time. Today, he stated, there are nearly three hundred, illustrating the ubiquitous nature of these enzymes in many species. (Photo courtesy of Steve McCaw)

LMG Principal Investigator Bill Copeland, Ph.D., center pondered Woodgate's findings.
LMG Principal Investigator Bill Copeland, Ph.D., center pondered Woodgate's findings as he sat with LMG Chief Jan Drake, Ph.D., right, Principal Investigator Mike Resnick, Ph.D., far left, and Principal Investigator Sam Wilson, M.D. (Photo courtesy of Steve McCaw)

On March 9, the NIEHS Trainee Action Committee (TAC) of the Laboratory of Molecular Genetics welcomed Roger Woodgate, Ph.D., chief of the Laboratory of Genomic Integrity( Exit NIEHS at the National Institute of Child Health and Development. Woodgate spoke about a special group of DNA polymerases, known as the Y-family, and their role in DNA replication and mutagenesis. Amy Abdulovic, Ph.D., a postdoctoral fellow in the DNA Replication Fidelity Group, hosted Woodgate's morning seminar.

Woodgate's lecture, “Y-Family DNA Polymerases: Facilitators and Suppressors of Mutagenesis and Carcinogenesis,” focused on the process of genome replication, a key aspect of an organism's survival. Not only is this process essential for cell replication and continual function, it is also critical for passing genetic information to offspring. There are more than six billion nucleotides in the human genome and the machinery responsible for genome replication needs to be not only accurate, but also consistent.

The enzymes central to genomic replication are DNA polymerases. These polymerases and other enzymes involved in proofreading and base mismatch repair all cooperate to make DNA replication a near error-free event. By some measurements, Woodgate explained, this process is marked by less than one mistake per billion nucleotide replication events. The result is what could otherwise be touted by audiophiles referring to quality sound production as “high fidelity.”

In addition to an organism's need for high fidelity genome replication, there are multiple situations where “hi-fi” is not always a good thing. Woodgate offered an example, pointing to environmental stressors, such as UV radiation and oxidative stress, that can damage DNA. Because of the very biochemical properties possessed by the polymerases that allow for high fidelity replication, these lesions would go unrecognized by these enzymes and replication would fail. Luckily, Woodgate explained there are translesion synthesis (TLS) polymerases — the cassette tapes of DNA replication.

TLS polymerases are mostly grouped into a special class of polymerases known as the Y-family. During his seminar, Woodgate delved into the world of Y-family polymerases, which have been central to his laboratory's ground-breaking research for nearly 25 years. He demonstrated the consistent presence of the Y-family polymerases in multiple organisms by presenting a slide that outlined approximately 300 orthologues known to exist in multiple species. As he explained, “The conservation of proteins from E. coli, through yeast and Archaea, and on to humans suggests that mechanisms of translesion synthesis...are conserved [as well].”

TLS polymerases can read through lesion-laden DNA without interrupting the replication event; however not without some cost to replication fidelity.

Woodgate stressed the importance of balance and interplay of these enzymatic members of the Y-family and their high fidelity brethren. He demonstrated in an E. coli model that by altering the activity of TLS polymerases and high fidelity polymerases, the rates of certain types of mutagenesis occurring at sites of DNA damage also change. Woodgate explained that while all polymerases affect mutagenesis to certain degrees, it is clear that members of the Y-family coordinate primarily “transversion mutations.” Tranversions substitute purine residues for pyrimidine residues, or vise versa, and are the most dramatic mutation at the nucleotide level — hence the brand “low fidelity.”

The processes of spontaneous mutagenesis coordinated by these enzymes are central to evolutionary adaptability and stress response. They also help us understand disease morphogenesis when these polymerases fail. Woodgate gave an example of a novel, “more efficient” Y-family polymerase called Rad30 his lab had discovered in yeast. He explained that soon after its discovery, it was found that homologues of this polymerase are defective in humans with the variant form of xeroderma pigmentosum, and that the defect predisposes affected individuals to sunlight-induced skin cancers.

Woodgate cited ongoing studies in his lab focused on isolation and structural characterization of the Y-family polymerases. He expects his work will lead to a more complete understanding of how this essential family of polymerases function and operate.

(Brian Chorley, Ph.D., is a postdoctoral fellow in the NIEHS Laboratory of Molecular Genetics Environmental Genomics Group.)

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