Active and passive mechanisms of helicases -
Manosas, Maria and Xi, Xu Guang and Bensimon, David and Croquette, VincentNUCLEIC ACIDS RESEARCH 38,
5518-5526 (2010) LPS
Abstract : In this work, we discuss the active or passive character of helicases.
In the past years, several studies have used the theoretical framework
proposed by Betterton and Julicher [Betterton, M.D. and Julicher, F.
(2005) Opening of nucleic-acid double strands by helicases: active
versus passive opening. Phys. Rev. E, 71, 11904-11911.] to analyse the
unwinding data and assess the mechanism of the helicase under study
(active versus passive). However, this procedure has given rise to
apparently contradictory interpretations: helicases exhibiting similar
behaviour have been classified as both active and passive enzymes
[Johnson, D.S., Bai, L. Smith, B.Y., Patel, S.S. and Wang, M.D. (2007)
Single-molecule studies reveal dynamics of DNA unwinding by the
ring-shaped T7 helicase. Cell, 129, 1299-1309; Lionnet, T., Spiering,
M.M., Benkovic, S.J., Bensimon, D. and Croquette, V. (2007) Real-time
observation of bacteriophage T4 gp41 helicase reveals an unwinding
mechanism Proc. Natl Acid. Sci., 104, 19790-19795]. In this work, we
show that when the helicase under study has not been previously well
characterized (namely, if its step size and rate of slippage are
unknown) a multi-parameter fit to the afore-mentioned model can indeed
lead to contradictory interpretations. We thus propose to differentiate
between active and passive helicases on the basis of the comparison
between their observed translocation velocity on single-stranded nucleic
acid and their unwinding rate of double-stranded nucleic acid (with
various GC content and under different tensions). A threshold separating
active from passive behaviour is proposed following an analysis of the
reported activities of different helicases. We study and contrast the
mechanism of two helicases that exemplify these two behaviours: active
for the RecQ helicase and passive for the gp41 helicase.