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New paths explored for curbing genetic malfunctions

Investigators probe mechanisms of RNA synthesis



RNAPJan. 15, 2013 — One of the most extraordinary properties of living cells is their ability to precisely reproduce themselves through processes that transfer genetic information from one cell to the next. However, there are times when one of the steps of information transfer, transcription, goes awry at the cellular level, potentially producing diseases such as cancer and other health disorders. Unraveling how those processes work and how substandard transcription can be prevented is a major goal of biomedical science. Progress in this area may also lead the way toward development of drugs that target the genetic transcription process in disease-causing microbes.

ARTICLE CAPSULE


Control of transcription fidelity by active center tuning as derived from RNA polymerase endonuclease reaction 

Background: Factor-assisted co-transcriptional proofreading and precise selection of NTP substrates provide high transcription fidelity.

Results: Both processes can be achieved through active center tuning (ACT) from inactive to catalytic state in response to establishing of recognition contacts of the reactions substrates.

Conclusion: High transcription fidelity can be explained by ACT.

Significance: Suggested ACT mechanism represents exceptional example of substrate recognition coupling to catalysis.

A research team led by Arkady Mustaev, PhD, of the Public Health Research Institute (PHRI) at the University of Medicine and Dentistry of New Jersey-New Jersey Medical School, has published a study posted online by The Journal of Biological Chemistry, that describes an effort by the investigators to understand the underlying mechanisms of high precision (fidelity) of RNA synthesis by RNA polymerase, the major enzyme that promotes the transcription process. They attempted to influence the role of active center tuning (ACT) — a mechanism they first identified — in the process of transcription fidelity, which is the accurate copying of genetic information.

ACT is a rearrangement of the RNA polymerase catalytic center from an inactive to a catalytically proficient state. The investigators found that both reactions of NTP polymerization and hydrolytic RNA proofreading are performed by the same active center that includes two magnesium (Mg) ions coordinated by aspartate triad. The active center is normally “turned off” since it is missing one of Mg ions. Correct NTP substrates as well as misincorporated RNA residues can promote ACT by inclusion of the missing Mg ion through establishing recognition contacts in the active center. Incorrect substrates cannot trigger ACT and are rejected. The investigators also demonstrate that transcript cleavage factors Gre build on ACT mechanism by providing the residues for stabilization of catalytic Mg ion and for activation of the attacking water causing 3,000–4,000-fold reaction enhancement thereby strongly reinforcing proofreading.

The suggested ACT mechanism is fundamentally different from that proposed for DNA replication enzyme, DNA polymerase (DNAP) in which the active centers for DNA synthesis and proofreading are separated and discrimination between deoxy- and ribo-substrate is achieved through strict fitting requirements for the sugar rather than through active center rearrangement. In DNAP active center carboxylates stem from rigid scaffolds, while in multisubunit RNAP they reside in an apparently flexible loop. ACT is accompanied by significant re-shaping of the loop, which would not be possible in DNAP.

This study was supported by NIH grant RO1 GM-30717-21.

Press release courtesy of the University of Medicine & Dentistry of New Jersey.