Bacterial Proteomics

The association of the essential Escherichia coli protein
NusA with RNA polymerase increases pausing
and the efÆciency of termination at intrinsic terminators.
NusA is also part of the phage l N protein-modiÆed
antitermination complex that functions to
prevent transcriptional termination. We have investigated
the structure of NusA using various deletion
fragments of NusA in a variety of in vitro assays.
Sequence and structural alignments have suggested
that NusA has both S1 and KH homology regions
that are thought to bind RNA. We show here that
the portion of NusA containing the S1 and KH homology
regions is important for NusA to enhance both
termination and antitermination. There are two RNA
polymerase-binding regions in NusA, one in the
amino-terminal 137 amino acids and the other in the
carboxy-terminal 264 amino acids; only the aminoterminal
RNA polymerase-binding region provides
a functional contact that enhances termination at
an intrinsic terminator or antitermination by N. The
carboxy-terminal region of NusA is also required for
interaction with N and is important for the formation
of an N±NusA±nut site or N±NusA±RNA polymerase
±nut site complex; the instability of complexes
lacking this carboxy-terminal region of NusA that
binds N and RNA polymerase can be compensated
for by the presence of the additional E. coli elongation
factors, NusB, NusG and ribosomal protein S10.