Rr. Higgins et A. Becker, CHROMOSOME END FORMATION IN PHAGE-LAMBDA, CATALYZED BY TERMINASE, IS CONTROLLED BY 2 DNA ELEMENTS OF COS, COSN AND R3, AND BY ATP, EMBO journal, 13(24), 1994, pp. 6152-6161
The terminase enzyme of phage lambda is a site-specific endonuclease t
hat nicks DNA concatemers to regenerate the 12 nucleotide cohesive end
s of the mature chromosome. The enzyme's DNA target, cos, consists of
a nicking domain, cosN, and a binding domain, cosB. cosB, situated to
the right of cosN, comprises three 16 bp repeat sequences, R1, R2 and
R3. A similar sequence, R4, is present to the left of cosN. It is show
n here that terminase has an intrinsic specificity for cosN which is i
ndependent of the R sites. The interaction with cosN is mediated by bi
nding to target sites that include 12 bp on the 5', and 2-7 bp on the
3' side of the nick. Of the four R sites, only R3 is required for the
proper formation of ends. When R3 is present, an ATP-charged terminase
system correctly catalyzes the production of staggered nicks in cosN,
at sites N1 and N2 on the bottom and top strands, respectively. When
ATP is omitted, the bottom strand is nicked incorrectly, at the site N
x, 8 bp to the left of N1. If R3 is removed or disabled by a point mut
ation, nicking in cosN becomes dependent upon ATP but, even in the pre
sence of ATP, bottom strand nicking is divided between sites N1, the c
orrect site, and Nx, the incorrect one. Thus, R3 is an important regul
atory element and must reside in cis in respect to cosN. Furthermore,
cosN substrates bearing point mutations at N1 and N2 are nicked at sit
es Nx and Ny, 8 bp to the left of N1 and N2, respectively. When R3 is
present and ATP is added, nicking is redirected to the N1 and N2 posit
ions despite the mutations present. Thus, terminase binding to R3, on
one side of cosN, regulates the rotationally symmetric nicking reactio
ns on the bottom and top strands within cosN.