LaDean Cooley '09 and Piero Sanfilippo '09
has two known modes for
termination of RNA transcription. One is intrinsic to the
function of RNA polymerase, which can spontaneously terminate
transcription in response to certain, limited sequences. The other mode
is dependent upon the action of an essential protein factor called Rho
and occurs at sequences that are specific for its function but that are
less constrained than the sequences for intrinsic termination .
Rho protein functions as a hexamer of a single
chain with 419 residues, which is the product of the rho
gene. It is an RNA-binding
protein with the capacity to hydrolyze ATP and other nucleoside
triphosphates. Rho acts to cause termination by first binding to a site
on the nascent transcript from the transcription holoenzyme and by
subsequently using its ATP hydrolysis
activity as a source of energy to mediate dissociation of the
transcript from RNA polymerase and the DNA template.
Its six identical subunits are arranged in a torus with six canonical
ATP binding sites located at the interfaces of the C-terminal domains
of adjacent subunits. Each ATP binding site is composed of adjacent
typical of RecA-like proteins that utilize NTP to perform mechanical
work in the cell After binding to a transcript at a
cytosine-rich rut (Rho utilization) site, Rho loads the
polynucleotide into its central channel before adopting a conformation
competent to processively translocate along the strand .
Rho protein is
made up of
that pack laterally into a
The subunits are peanut shaped and are almost
structure, each composed of an N-terminal
domain and a C-terminal
of two subdomains: a three-helix
Each of the six C-terminal
of a parallel
between several α
There are 3 key motifs located in the C-terminal domain. The P-loop
required for ATP binding and hydrolysis. The R-loop
believed to form the secondary RNA binding site 
conformation of Rho is held
together by lateral interactions between subunits. The interactions are
the same for every subunit set and occur both between the N and C
terminal domains. The main interaction is attained by the packing of an
on one subunit against the β7/α8
junctions on a neighboring subunit
distinct primary nucleic acid binding sites. The
primary mRNA binding sites are formed by the N-terminal domains, which
have the ability to bind either single-stranded DNA or RNA. Each N-terminal
a dinucleotide segment in a network
of contacts that explain the preference of Rho for cytosine. The first nucleotide base packs into a
formed by the side chains of Tyr 80,
Glue 108, Tyr 110,
and is too
small to comfortably hold purine bases.
the second nucleotide
cytosine base stacks on the aromatic side chain of Phe 64, while its O2,
N3, and N4 groups interact with the side chains of the neighboring Arg 66 and Asp 78
contacts are seen to the 2´ hydroxyl of the bound
nucleic acid, explaining why Rho is able to bind both ssDNA and ssRNA.
translocation and unwinding catalyzed at Rho's secondary RNA
binding site, located in the C-terminal
function depends on two sequence motifs known Q-loop
Both loops line the interior hole of the hexamer.
lies on the upper segment of the C-terminal
and extends into the center of the ring.
The constellation of the six Q-loops
in the hexamer together form the narrowest constriction of the interior
are implicated in both ATP and RNA binding. Each R-loop
resides on a segment located at the subunit-subunit interface between
and lies both adjacent to and above the The P-loop
the ATP binding
pocket. Part of each R-loop
the interior hole of the Rho hexamer . RNA binding to the secondary
state coincides with closure of the hexameric ring and stimulation of
the ATPase activity, presumably by introducing conformational changes
between subunits and residues around the ATP binding site .
binds to RNA (See Diagram) and then uses its ATPase activity to
provide the energy to translocate along the RNA until it reaches the
RNA-DNA helical region, where it unwinds the hybrid duplex
structure. Each ATP-binding pocket of Rho is formed at the interface
between two adjacent C-terminal domains.
six subunits are catalytically competent and hydrolyze ATP
sequentially. Translocation of RNA is driven by the weak to tight
binding transition of nucleotide in the catalytic site and hydrolysis
is coordinated between adjacent subunits by the transmission of stress
catalytic arginine finger .
in a ring-shaped motor
protein can regulate and coordinate the hydrolysis cycle
of neighboring subunits. This occurs both via interfacial
interactions between subunits of the protein and via
the RNA substrate during translocation. Although most
of the communication occurs between adjacent subunits,
stress can propagate around the ring producing
weaker—but still important—effects on nonnearest
neighbor subunits. That is, stress mediates both local
and long-range regulation of the catalytic cycle .
Y.J. Jeong, J.C. Liao, G. Patel, D.E. Kim, G. Oster and S.S. Patel,
Mechanochemistry of transcription termination factor Rho, Mol. Cell 22
(2006), pp. 611–621
2. Bogden, C.E.; Fass, D.; Bergman, N.; et al.
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E., and J. M. Berger. 2003. Structure of the Rho
transcription terminator: mechanism of mRNA recognition and helicase
loading. Cell 114:135-146
E., and J. M. Berger. 2006. Structural Insights into
RNA-Dependant Ring Closure and ATPase Acitivation by the Rho
Terminatino Factor. Cell 127:553-564