Biology Reference
In-Depth Information
the SN-BER proteins PNKP, Pol
b
, LigIII
a
, and XRCC1, as well as LP-BER-
specific DNA replication proteins including PCNA and FEN-1,
11,32,76,77
with
which the NEILs also interact in a pairwise fashion in the absence of DNA.
Direct interaction of NEILs with LigIII
a
, the last enzyme in SN-BER, indicates
that the repair is regulated by the initiating DG, which appears to act as a hub
protein. This has led us to propose a new BER paradigm in which collaboration
of multiple proteins in a coordinated fashion involving dynamic protein-protein
interactions enhances repair efficiency. Although the
in vivo
role of sequential
engagement of individual BER proteins versus coordinated action of a pre-
formed BER complex is not determined yet, we propose that the preformed
BER complexes repair endogenous base lesions, while repair via hand-off
mechanism by sequential recruitment could occur for induced DNA damage.
Further characterization of the dynamics of such preformed ''BERosomes'' is
required to unravel the precise repair processes.
III. Nonconserved Terminal Extensions in Mammalian
Early BER Proteins
Mammalian DGs possess unique structural features absent in their homo-
logs in lower organisms because of the presence of a nonconserved extension at
the N or C terminus (reviewed in
Ref. 90
). These might have been acquired
during evolution via terminal fusion of a non-BER gene (
Fig. 2
). The sequence
alignment of human (h) NTH1 with its prototype Nth in
E. coli
and NTHs in
other lower organisms clearly defines hNTH1's unique N-terminal extension.
HNTH1 was also shown to have reduced activity compared to
E. coli
Nth
prototype, which appears to be due to the inhibitory role of the N-terminal
tail.
27,91
This extension reduces the rate of product release without affecting
base excision or AP lyase activities.
92
Similarly, the crystal structure of the
catalytically active deletion construct of hNEIL1 (lacking 56 C-terminal resi-
dues) indicated that hNEIL1 has C-terminal extension (
100 residues), which
is absent in the
E. coli
prototype Nei.
90,93
Furthermore, PONDR, the
p
redictor
o
f
n
aturally
d
isordered
r
egions in proteins, and other modeling studies showed
that the terminal extensions in mammalian DGs are mostly disordered.
A sequence comparison of hMYH and its prototype MutY in
E. coli
shows
the presence of N-terminal disordered segment in the former.
90,94
Similar
disordered terminal sequences may also be present in other human DGs, for
example, UNG2 and TDG. In the case of APE, the nonconserved N-terminal
segment (
65 residues) in hAPE1, absent in the
E. coli
prototype Xth, appears
to be mostly disordered. Although the unfolded sequence generally exists at the
N or C terminus, this could also exist internally as in hNEIL2, where it may
serve as a linker of two domains.
90
