I. Moll et al., Evidence against an interaction between the mRNA downstream box and 16S rRNA in translation initiation, J BACT, 183(11), 2001, pp. 3499-3505
Based on the complementarity of the initial coding region (downstream box [
db]) of several bacterial and phage mRNAs to bases 1469 to 1483 in helix 44
of 16S rRNA (anti-downstream box [adb]), it has been proposed that db-adb
base pairing enhances translation in a way that is similar to that of the S
hine-Dalgarno (SD)/anti-Shine-Dalgarno (aSD) interaction. Computer modeling
of helix 44 on the 308 subunit shows that the topography of the 308 riboso
me does not allow a simultaneous db-adb interaction and placement of the in
itiation codon in the ribosomal P site. Thus, the db-adb interaction cannot
substitute for the SD-aSD interaction in translation initiation. We have a
lways argued that any contribution of the db-adb interaction should be most
apparent on mRNAs devoid of an SD sequence. Here, we show that 30S ribosom
es do not bind to leaderless mRNA in the absence of initiator tRNA, even wh
en the initial coding region shows a 15-nucleotide complementarity (optimal
fit) with the putative adb. In addition, an optimized db did not affect th
e translational efficiency of a leaderless lambda cI-lacZ reporter construc
t. Thus, the db-adb interaction can hardly serve as an initial recruitment
signal for ribosomes. Moreover, we show that different leaderless mRNAs are
translated in heterologous systems although the sequence of the putative a
db's within helix 44 of the 308 subunits of the corresponding bacteria diff
er largely. Taken our data together with those of others (M, O'Connor, T. A
sai, C. L. Squires, and A. E. Dahlberg, Proc. Natl. Acad. Sci. USA 96:8973-
8978, 1999; A. La Teana, A. Brandi, M. O'Connor, S. Freddi, and C. L. Pon,
RNA 6:1393-1402, 2000), we conclude that the db does not base pair with the
adb.