Molecular Cell
Article
Structural Aspects of RbfA Action
during Small Ribosomal Subunit Assembly
Partha P. Datta,1,9 Daniel N. Wilson,2,3,5,9 Masahito Kawazoe,4,9 Neil K. Swami,1 Tatsuya Kaminishi,4
Manjuli R. Sharma,1 Timothy M. Booth,1 Chie Takemoto,4 Paola Fucini,5,6 Shigeyuki Yokoyama,4,7
and Rajendra K. Agrawal1,8,*
1Laboratory of Structural Pathology, Division of Molecular Medicine, Wadsworth Center, New York State Department of Health,
Empire State Plaza, Albany, NY 12201-0509, USA
2Munich Center for Integrated Protein Science CiPS, University of Munich, 81377 Munich, Germany
3Gene Center and Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München,
Feodor-Lynen-Strasse 25, 81377 Munich, Germany
4Protein Research Group, Genomic Sciences Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama,
230-0045, Japan
5Max-Planck-Institute for Molecular Genetics, Ihnestrasse 73-75, 14195 Berlin, Germany
6J.W. Goethe-Universität Frankfurt am Main, Institut für Organische Chemie und Chemische Biologie,
60438 Frankfurt am Main, Germany
7Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku,
Tokyo 113-0033, Japan
8Department of Biomedical Sciences, School of Public Health, State University of New York at Albany, Albany, NY 12201, USA
9These authors contributed equally to this work.
*Correspondence: [email protected]
DOI 10.1016/j.molcel.2007.08.026
SUMMARY
Ribosome binding factor A (RbfA) is a bacterial
cold shock response protein, required for an efficient processing of the 50 end of the 16S ribosomal RNA (rRNA) during assembly of the small
(30S) ribosomal subunit. Here we present a crystal structure of Thermus thermophilus (Tth) RbfA
and a three-dimensional cryo-electron microscopic (EM) map of the Tth 30SRbfA complex.
RbfA binds to the 30S subunit in a position overlapping the binding sites of the A and P site
tRNAs, and RbfA’s functionally important C terminus extends toward the 50 end of the 16S
rRNA. In the presence of RbfA, a portion of
the 16S rRNA encompassing helix 44, which is
known to be directly involved in mRNA decoding
and tRNA binding, is displaced. These results
shed light on the role played by RbfA during maturation of the 30S subunit, and also indicate how
RbfA provides cells with a translational advantage under conditions of cold shock.
INTRODUCTION
Ribosomes are complex macromolecular machines that
are involved in translating an organism’s genetic information into polypeptides (reviewed by Ramakrishnan, 2002).
All ribosomes consist of two unequally sized subunits,
each composed of both ribosomal RNA (rRNA) and ribosomal protein (r-protein) molecules. The small 30S subunit
plays a direct role in decoding of the genetic message
(Ogle et al., 2003); in bacteria, such as Escherichia coli,
the small subunit is composed of one 16S rRNA molecule
and 21 r-proteins (designated S1–S21) (Wittmann-Liebold, 1986). In vitro, the 30S subunit can be assembled
from only its rRNA and r-protein components (Traub and
Nomura, 1968; Culver and Noller, 2000); however, the process requires nonphysiological conditions, namely, high
magnesium ion and salt concentrations (Traub and Nomura, 1968). In vivo, however, maturation of rRNAs and
assembly of the r-proteins into a functional ribosome appear to be highly complex processes (Culver, 2003), involving multiple accessory factors (Williamson, 2003).
While the involvement of many protein factors in ribosomal
assembly has been well characterized, including modification enzymes, such as methylases and pseudouridinylases (Decatur and Fournier, 2002), RNA helicases (Iost
and Dreyfus, 2006), and molecular chaperones (Alix and
Nierhaus, 2003; Maki et al., 2002), there appear to be
a number of additional protein factors, the exact roles of
which remain to be defined (reviewed by Wilson and Nierhaus, 2007). Protein factors implicated in 30S maturation
include the highly conserved GTPase Era (Sharma et al.,
2005), the PRC b-barrel protein RimM (Bylund et al.,
1998), the ribosome-activated GTPase RsgA (also called
YjeQ; Daigle and Brown, 2004; Himeno et al., 2004), and
the ribosome binding factor A (RbfA), the focus of our
study.
RbfA is a small protein (10.9 kDa in Thermus thermophilus [Tth]) required for efficient processing of the 16S rRNA
(Bylund et al., 1998; Xia et al., 2003). RbfA binds to the 30S
subunit, but not to the large (50S) subunit nor to the 70S
ribosome (Dammel and Noller, 1995; Xia et al., 2003).
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Interaction of RbfA with the 30S Ribosomal Subunit
NMR (Huang et al., 2003; Rubin et al., 2003) and X-ray
crystallographic (PDB ID, 1JOS) structures of RbfA
obtained from various bacterial species reveal a singledomain protein with a type-II KH-domain fold topology,
characteristic of a nucleic acid-binding protein family.
Consistent with a role in ribosome biogenesis, deletion
of the rbfA gene (DrbfA) causes a decrease in the quantity
of 70S ribosomes and polysomes, and a concomitant
increase in 30S and 50S ribosomal subunits (Dammel
and Noller, 1995; Jones and Inouye, 1996; Bylund et al.,
1998). Furthermore, DrbfA mutants display an accumulation of 17S rRNA, a precursor to the 16S rRNA (Bylund
et al., 1998; Inoue et al., 2003). RbfA was originally identified as a multicopy suppressor of the cold sensitivity of
a C23U mutation at the 50 -terminal helix (h1) of the 16S
rRNA (Dammel and Noller, 1993, 1995). The C23U mutation is predicted to significantly weaken the helix, enabling
formation of an alternative helix through base-pairing with
nucleotides located in the upstream region of the precursor 17S rRNA (see Figures S1A and S1B in the Supplemental Data available with this article online). Indeed, additional suppressors of the C23U mutation were identified
within the 16S rRNA that would appear to push the equilibrium back toward formation of h1 (Dammel and Noller,
1995). The cold sensitivity of the C23U mutant and DrbfA
strains suggests the existence of an energy barrier to
the formation of the canonical h1, which is provided by
high temperature at the permissive temperatures of these
strains, and by RbfA in the case of the C23U mutant strain
at cold shock temperatures. Thus, part of the role of RbfA
could be to facilitate correct folding and maturation of h1
at the 50 end of the 16S rRNA, which is particularly important under cold shock conditions.
Cold shock results in an increase in the level of nontranslating ribosomes and produces a temporary cessation of bacterial growth; growth is then restored through
the action of a set of cold shock response proteins (Jones
and Inouye, 1994; Graumann et al., 1996; Datta and Bhadra, 2003). The role of RbfA as a cold shock protein has
been well documented. In E. coli, RbfA is encoded in an
operon together with the cold shock protein NusA (Dammel and Noller, 1995). RbfA is expressed constitutively under normal growth conditions; however, the expression
level rapidly increases upon cold shock, due to an upregulation of the transcription of the rbfA mRNA (Jones and
Inouye, 1996), resulting in a several-fold increase in the
amount of 30S-bound RbfA (Xia et al., 2003). The elevated
levels of RbfA under cold shock conditions are necessary
to overcome the translational block at the reduced temperature, presumably by facilitating rapid maturation of
the 30S subunits. This role is in contrast to the action of
the cold shock protein pY; the latter has been proposed
to stabilize 70S ribosomes against dissociation, and thus
protect them from degradation, by binding to them (VilaSanjurjo et al., 2004).
Here we report a crystal structure of Tth RbfA and
a cryo-electron microscopic (EM) structure of a Tth
30SRbfA complex at resolutions of 1.84 Å and 12.5 Å,
respectively. Our analysis shows that RbfA binds at the
junction of the head and body, i.e., at the neck region of
the 30S subunit, with the C terminus of RbfA approaching
helix 1 located at the 50 end of the 16S rRNA. This strategic
location of RbfA on the 30S subunit, and interaction of
RbfA with multiple rRNA helices and r-proteins, is suggestive of an important role in a late step in maturation of the
30S subunit. In addition, we find that the presence of RbfA
maintains the decoding region of the 30S subunit in a conformation unsuitable for the subunit’s participation in protein synthesis. Specifically, RbfA appears to dramatically
alter the position and conformation of helix 44, a functionally important segment of the 16S rRNA that is known to
be directly involved in mRNA decoding and in the formation of two of the intersubunit bridges, B2a and B3 (Gabashvili et al., 2000; Yusupov et al., 2001). Our results
not only provide insight into the role of RbfA during maturation of the 30S subunit, but they also suggest
how RbfA confers a translational advantage to cells under
conditions of cold shock.
RESULTS AND DISCUSSION
Crystal Structure of the Tth RbfA
The crystal structure of RbfA from Thermus thermophilus
was determined at 1.84 Å resolution and is shown in
Figure 1A, and crystallographic and refinement data are
provided in Table 1. The asymmetric unit contains two
molecules (A and B), and 90 (4–94) and 89 (3–92) out of
the 95 residues comprising Tth RbfA could be unambiguously modeled, respectively. The refined models of the
two molecules can be superimposed with a root-meansquare deviation (rmsd) of 0.53 Å for the main-chain
atoms. The structure shows a single KH domain containing three a helices (a1–a3) and three b strands (b1–b3)
with an abbaab topology (Figure 1B). The a2 and a3 helices are arranged to form a helix-kink-helix (hkh) at the
strictly conserved Ala65 with a CH-p interaction between
Leu62 (a2) and Phe87 (b3) (Figure 1B). It is possible that
the kink serves to expand the space for an interaction
and to alter the direction of basic residues on a3. The
electrostatic surface potential reveals highly positively
charged regions, which encompass three loops between
b1-b2, b2-a2, and a3-b3, and the surface of a2-a3
(Figure 1C). A highly conserved sequence, 25DPRL28
(29DPRL32 in E. coli), forms a 310 helix both in molecules
A and B, as seen in the E. coli structure (see alignment
in Figure S2; Huang et al., 2003). While Asp25 and
Arg27 form an electrostatic interaction in molecule A,
the side-chain direction of Arg27 is different and the interaction is not observed in molecule B. The loop between
a3-b3, where the well-conserved Arg78 (Arg88 in
E. coli) is located, also shows a notable difference in
the two molecules. These conserved regions are likely
to possess functional importance due to the structural
flexibility.
Comparison of the two Tth RbfA structures with previously known RbfA structures reveals that, despite
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Interaction of RbfA with the 30S Ribosomal Subunit
Figure 1. Crystal Structure of Tth RbfA and Its Comparison with Known Atomic Structures of RbfA from Other Species
(A) Stereo representation of the Tth RbfA is shown in cartoon (PDB ID, 2DYJ).
(B) An enlarged view of the helix-kink-helix motif (cyan) with all residues in stick. Residues involved in notable interactions, Asp25 and Arg27 on the 310
helix (magenta) and the conserved Phe87, are also shown in stick.
(C) Stereo representation of Tth RbfA in the surface potential prepared by using APBS tools built in PyMOL.
(D) Superposition of structures of RbfA from T. Thermophilus (molecules A and B in the asymmetric unit are shown in dark and light blue colors,
respectively), H. influenzae (green, 1JOS), and M. pneumoniae (orange, 1PA4). In all panels, N, C, and hkh mean N terminus, C terminus, and
helix-kink-helix motif, respectively.
the low sequence conservation (20%), the overall topologies are remarkably similar (Figure 1D). Tth RbfA is
shorter than other known RbfA proteins, being 95
amino acids (aa) rather than the usual 111–150 aa (with
E. coli having 133 aa), and the residues appear to be
lacking from the C-terminal end (Figure S2). However,
significant differences between the structures are clearly
evident, especially when comparing the highly flexible
loop regions, as well as the N- and C-terminal ends
(Figure 1D).
Cryo-EM Structure of the 30SRbfA Complex
After ascertaining that Tth RbfA binds to the mature Tth
30S subunit (Figure 2A), we obtained a three-dimensional
(3D) cryo-EM map of the Tth 30SRbfA complex at 12.5 Å
resolution, according to the FSC criterion with a 0.5 cutoff
(Bottcher et al., 1997; Malhotra et al., 1998), or at 8.0 Å
according to the 3s cutoff (Orlova et al., 1997). The
map shows all of the recognizable features of the 30S
subunit, namely head with beak, body with spur, platform, and helix 44 (h44) of the 16S rRNA (Figure 2B). A
complex mass of extra density, with two protruding cylindrical features on the subunit interface side, was directly
visible within the cryo-EM map of the 30SRbfA complex,
located between the head and body of the 30S subunit. In
order to interpret this density, we docked the X-ray crystallographic structure of the 30S subunit (Wimberly et al.,
2000; PDB ID, 1J5E) into the cryo-EM map of the
30SRbfA complex. For an optimum fit, the X-ray coordinates were divided into four structural domains (head,
body, platform, and the 30 minor domain encompassing
h44 and h45 of the 16S rRNA), and then each domain
was fitted individually as a rigid body. Subsequently,
the fitted coordinates were filtered to match the resolution of the cryo-EM map and then subtracted from the
cryo-EM map of the 30SRbfA complex. This process
allowed the boundaries of the extra mass of density in
the 30SRbfA cryo-EM map to be delineated (Figure 2B).
Volumetric calculations indicate that the extra density
encloses a space (922 voxels z 19,384 Å3) much
larger than would be expected from the volume (512
voxels z 10,764 Å3) computed from the Tth RbfA structure. Possible explanations for this are that either two
molecules of RbfA are binding to each 30S subunit, or
binding of RbfA induces a conformational change within
the 30S subunit.
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Interaction of RbfA with the 30S Ribosomal Subunit
Table 1. X-Ray Crystallographic Structure
Determination Statistics
Crystal Characteristics
Space group
P1 21 1
Unit-cell parameters
a = 28.43,
b = 65.84, c = 43.17
b = 96.18
Molecules/asymmetric
unit
2
Data Collection
Wavelength (Å)
Resolution (Å)
1.0000
a
1.84 (1.96–1.84)
Unique reflections
13,813 (1383)
Completeness (%)a
100 (100)
I/s(I)
a
24.4 (3.22)
Redundancy
3.7 (3.7)
Rsyma,b
0.061 (0.312)
Refinement
Resolution range (Å)
43.03–1.84
Reflections
13,796
Rcryst/Rfreec
0.199/0.245
Rmsd
Bond lengths (Å)
0.008
Bond angles ( )
1.30
Dihedral angles ( )
21.50
Improper ( )
0.79
Average B factor
25.6
Figure 2. Binding of RbfA to the 30S Ribosomal Subunit
a
Numbers in parentheses are for the highest resolution shell.
P P
P P
Rsym = h ijIi(h) < I(h) >j / h I(h).
P
P
c
Rcryst = hjjFobsj jFcalcjj / hjFobsj. Rfree is Rcryst calculated
with only the test set (5%) of reflections.
b
Conformational Changes of the 30S Subunit Due
to RbfA Binding
Two pieces of evidence indicate that RbfA binds as
a monomer to the 30S subunit and thus must induce a dramatic conformational change in the 16S rRNA to produce
the additional density over that expected for a single
RbfA molecule. First, analysis of the density maps of the
30SRbfA complex reveals much weaker density for
where h45 and the top of h44 are located in the 30S control. Second, contouring to very high threshold values
leads to a loss of all but the extra bilobed density (see Figure S3). At such high thresholds only double-stranded
RNA helices are expected to be visible, whereas less
electron dense material, such as protein, is lost. This observation indicates that the two protruding cylindrical features of the extra density must originate from a shift in
rRNA helices h44 and h45, whereas the remainder of the
extra density, which disappears at high threshold values,
(A) SDS-PAGE results showing the binding of RbfA to the 30S subunit.
Tth 30S subunits were incubated alone (lanes 2–4), or with increasing
concentrations of RbfA (10-fold [lanes 5–7], 20-fold [lanes 8–10], and
40-fold [lanes 11–13] molar excess over 30S subunit), before being
centrifuged through a 10% sucrose cushion (see Experimental Procedures). As a control, reactions were also performed with RbfA in the
absence of 30S subunits (lanes 15–20). For each condition, aliquots
of the initial (pre) reaction, supernatant (S), and pellet (P) were subjected to 20% SDS-PAGE and stained with Coomassie blue. RbfA pellets only in the presence of the 30S subunit, and the stoichiometry of
binding increases with increasing initial excess of RbfA over 30S subunit. Lanes 1 and 14 are marker lanes, with 14, 20, and 33 kDa bands
indicated.
(B) Cryo-EM map showing extra mass of density that encompasses
the binding position of RbfA (red) on the Tth 30S subunit (yellow).
represents the bound RbfA protein. Closer inspection of
the cryo-EM map clearly suggests that the upper segment
of h44 (nucleotides 1400–1410 and 1490–1500) is what
must shift position in the RbfA-bound 30S subunit by
25 Å, to account for the lobe of extra density that is
closer to the body of 30S (Figure 3). Because h45 is contiguous with h44, and because the loop region of h45
makes intimate contacts with the minor groove at the
top of h44, it seems likely that the two regions move as
a single unit. This idea is also consistent with the excellent
fit of the respective RNA helices into the lobed densities,
which allowed satisfactory overall docking of the
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Interaction of RbfA with the 30S Ribosomal Subunit
Figure 3. Conformational Changes in the
30S Subunit upon RbfA Binding
A portion of the difference map (red) shown in
Figure 2B corresponds to a large positional
shift of the 30 minor domain of the 16S rRNA involving the decoding site helix 44. Both positions of helix 44 (h44), as well as those of helix
45 (h45), are shown. Purple ribbons, original
positions; red/orange ribbons, shifted positions. B2a and B3 indicate the positions of
the intersubunit bridges. Arrow indicates direction of the shift. The landmarks of the 30S subunit are: h, head; p, platform; and sp, spur.
h44-h45 region from the crystal structure into the cryo-EM
map (Figure 3). In the crystal structure of the 30S subunit,
the 30 minor domain of the 16S rRNA, encompassing h44
and h45, establishes limited contacts with the r-proteins
and utilizes non-sequence-specific backbone interactions
with the rest of the 30S subunit, thus indicating the potential flexibility within this domain (Brodersen et al., 2002).
Furthermore, such conformational changes are not without precedent, given that shifts in h44 have been observed
upon the binding of translation initiation factor IF1 (Carter
et al., 2001), as well as between different elongation states
of the ribosome (VanLoock et al., 2000). Note, however,
that the shifts in the two cases just mentioned were not
of the magnitude that is seen here.
Localization of RbfA on the 30S Subunit
We isolated the portion of the extra density that is directly
attributable to RbfA by converting the fitted coordinates of
h44 and h45 into electron densities and filtering them to
the resolution of the cryo-EM map. The resulting mass
was then subtracted from the total extra density mass
(Figure 4A), leaving a density feature that matches the
structure of Tth RbfA in volume and in overall shape
(Figure 4B). However, the homology model of the Tth
RbfA, which includes three additional amino acids at the
C terminus, shows a slightly better fit into the density (Figure 4C), as indicated by a cross-correlation coefficient
(CCF) of 0.79. The conclusion is that RbfA binds in the
neck region, buried deep within the cleft between the
head and body of the 30S subunit. This position of RbfA
is pivotal in that it is a junction point between all four domains of the 30S subunit, namely the ‘‘switch’’ region
where h1 of the 50 domain (body) base pairs with the single-stranded region between the central (platform) and
30 major (head) domains, as well as the linker between
the 30 major and 30 minor (h44-45) domains located at
the base of h27 (see Figures S1C and S1D). When the
complex is viewed from the intersubunit side, the side of
the 30S subunit that would face the 50S subunit in the
70S ribosome, RbfA is situated behind h44 and h45. The
inaccessibility of the RbfA binding site in the 30SRbfA
complex suggests that binding of RbfA to the 30S subunit
utilizes an induced fit-like mechanism, such that h44 and
h45 shift concomitantly with RbfA’s interaction with the
neck region of the 30S subunit. One surface of the KH
domain of RbfA forms a three-stranded b sheet, which in
the 30SRbfA complex is oriented toward the neck region,
whereas the RNA-binding hkh motif, encompassing a2
and a3, faces the junction between h44 and h45 (Figure 5A). The flexible C terminus of RbfA extends from the
end of b3, deep into the body of the 30S subunit, and
approaches h1 of the 16S rRNA (Figure 6A).
Contacts of Bound RbfA with Components
of the 30S Subunit
The low sequence identity between different RbfA homologs suggests that RbfA interacts with the 30S subunit utilizing general electrostatic interactions, rather than specific conserved contacts (Figure S4). RbfA interacts with
three of the four domains in the 30S subunit, the head,
body, and 30 minor (h44-45) domains. The most prominent
interaction with the 30S subunit involves the highly basic
region on one side of RbfA, formed from the N terminus,
the hkh motif (a2-a3), and the flexible loop regions located
between b1-b2 and a3-b3 (Figures 5A and 5B, also see
Figure S5). The positively charged residues located in
the hkh motif are positioned so as to interact with the negatively charged phosphate-oxygen backbone of nucleotides located in the single-stranded linker region that
spans between the top of h44 and the base of h45. Similarly, the N terminus and loop regions form a positive surface with which the backbone of h28, h29, and to a lesser
extent h30 can interact. In contrast, it is interesting that
a large negative area, derived from the terminal end of
a1 and start of b1, is oriented toward where the top of
h44 is located in the native 30S subunit (Figure 5B, see
Figure S5C). Therefore, the charge distribution supports
not only our placement of RbfA and its interaction with
rRNA, but also the necessity of a shift in the h44-45 region,
to avoid electrostatic repulsion. In addition, the long C-terminal extensions of r-proteins S9 and S13 wind their way
into the P site of the 30S subunit and interact with RbfA
(Figure 6B) at the periphery of the highly basic region. Deletion of either of these extensions in E. coli shows that
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Interaction of RbfA with the 30S Ribosomal Subunit
Figure 4. Localization of RbfA on the 30S
Subunit, and Comparison of the Atomic
Structure of RbfA with the Cryo-EM
Density Map
(A) Interpretation of the extra mass in terms of
30S subunit conformational change, involving
16S rRNA helices 44 and 45 (orange), and RbfA
mass (red). The mass attributable to RbfA was
derived after subtraction of the density corresponding to shifted positions of helices 44 (h440 )
and 45 (h450 ) from the total extra mass shown
in Figure 2B.
(B and C) Stereo representations of the fittings
of (B) the X-ray crystallographic structure
(CCF, 0.78) and (C) the homology model (CCF,
0.79) of the Tth RbfA into the corresponding
cryo-EM density. The asterisk (*) in (B) points
to an unoccupied region of the cryo-EM density, due to absence of three amino acid residues and a different orientation of the tail in
the X-ray structure. However, the same density
region is nicely accounted for by the homology
model (C). Thumbnails to the left of the panels
depict the orientations of the 30S subunit, with
body (b), head (h), and platform (p) identified.
these extensions are not essential for viability; however,
the deletion strains exhibit reduced growth rates, and
the 30S subunits have a lower affinity for tRNA (Hoang
et al., 2004). The other major site of contact between
RbfA and the 30S subunit overlaps with the binding site
of IF1 (Carter et al., 2001), encompassing h18 and r-protein S12. The loop region between b2-a2 approaches
the backbone of nucleotides located at the top of h18
and is directly proximal to the long flexible loop linking
b1-b2 of the OB fold of S12 (Figure 6B). This loop contains
highly conserved residues involved in mRNA-tRNA codon-anticodon discrimination at the A site; mutations
within the loop affect translational fidelity (see Ogle et al.,
2001).
In the 30SRbfA complex, rigid body docking of RbfA
into the cryo-EM density places the C terminus of RbfA
in a position at the neck of the 30S subunit where it clashes
with the single-stranded region linking h28 with the top of
h44 and the upper region of h18 (Figure 6B). However,
given the flexibility of this region in the known RbfA structures (Figure 1D), it is conceivable that the C-terminal
amino acids relocate toward h18, such that the C-terminal
end of the protein comes into close proximity with the loop
region of h1 at the 50 end of the 16S rRNA (Figure 6A).
Molecular Basis for the Overlapping Function
between 30S Assembly Factors
There appears to be a complicated interplay, as well as
partial overlaps in function, among a number of the 30S
subunit assembly factors. It has been reported that overexpression of Era, a GTP-binding protein also involved in
the 16S rRNA maturation, suppresses (at least partially),
the cold-sensitive cell growth and defective ribosome assembly in a DrbfA strain (Inoue et al., 2003). Overexpression of RbfA, but not Era, can rescue a slow-growth phenotype and assembly defects associated with deletion of
the rimM gene, which encodes another ribosome maturation factor, RimM (Bylund et al., 1998; Inoue et al., 2003).
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Interaction of RbfA with the 30S Ribosomal Subunit
Figure 5. Interactions of RbfA with 16S
rRNA Helices 44 and 45
(A) Stereo-view presentation of the interaction
between the hkh motif of RbfA (red) and the
linker region between the shifted positions of
helices 44 (h440 ) and 45 (h450 ). The hkh motif
is shown in cyan.
(B) Correlation between the electrostatic distribution of RbfA (shown with regions of positive
and negative potentials, in blue and red, respectively) and interaction of RbfA with h44
and h45. Both positions of h44 and h45 are
shown: light purple ribbons, original positions;
brown ribbons, shifted positions (marked as
h440 and h450 ). (B) was made with PyMOL
(http://www.pymol.org). In both panels, the
RbfA-30S complex is viewed from the platform
side, as depicted in the thumbnail to the lower
right.
However, overexpression of RimM cannot complement
the DrbfA strain, suggesting that some sort of hierarchy
exists during 30S assembly (Bylund et al., 1998). In light
of the binding position of RbfA determined here, we suggest an explanation for the partial functional redundancy
of RbfA with Era and RimM.
Although the principal known function of RbfA is to facilitate processing of the 50 ends of precursor 17S rRNA,
while that of Era is to facilitate processing of 30 ends, our
study shows that RbfA binds in the immediate vicinity of
Era’s binding position on the 30S subunit (Sharma et al.,
2005; Figure 7A). We suggest that Era can partially compensate for RbfA function through interaction with common structural elements of the ribosome, specifically
h28 (Figure 7B), which is directly base-paired through
a pseudoknot interaction with nucleotides located in the
loop of h1 at the 50 terminus of the 16S rRNA (Figures
S1A and S1B). Thus, the interaction of Era with h28 could
stabilize h1 indirectly, in a manner that RbfA normally performs through direct interaction.
Although the structure of RimM bound to the 30S subunit is not known, biochemical data indicate that this maturation factor interacts directly with the head region, in the
vicinity of r-proteins S13 and S19, and helices 31 and 33b
of the 16S rRNA, leading to the suggestion that RimM
plays a role in assembly of the head region (Lovgren
et al., 2004). RbfA also participates in multiple interactions
with components of the head, including r-protein S13 and
neighboring rRNA helices. Therefore, as compared to
bound Era, bound RbfA is better positioned to bring regions of the head, body, and 30 minor domain together
at a late assembly stage; in this way the factor could
compensate for the absence of RimM.
The Mechanisms of Action of RbfA during Small
Subunit Assembly and Cold Shock
The binding position of RbfA on the 30S subunit supports
a role for the factor during the final steps in the maturation
of the 30S subunit (Jiang et al., 2007). In particular, the
binding position is consistent with the proposal that
RbfA facilitates correct formation of h1 at the 50 end of
the 16S rRNA through interaction between the C terminus
of RbfA and the loop region of h1 (Figures S1A and S1B;
Dammel and Noller, 1995). The significantly longer C-terminal extensions present in RbfA from other bacteria,
such as E. coli, rather than Tth, suggest that the interaction
with h1 may be even more extensive in these species. One
possible explanation for the shortened tail in Tth may be
related to the high temperatures at which this organism
grows, by enabling efficient transition of the alternate
competing conformation for h1 in the precursor 17S
rRNA into the canonical h1 found in the mature 16S rRNA.
It appears that, in E. coli for example, under normal growth
temperatures (37 C) RbfA is partially dispensable for this
440 Molecular Cell 28, 434–445, November 9, 2007 ª2007 Elsevier Inc.
Molecular Cell
Interaction of RbfA with the 30S Ribosomal Subunit
Figure 6. Interactions of RbfA with Other Components of the 30S Subunit
(A) Proximity of the C terminus of RbfA (red) to helix 1, central pseudoknot helix 27, and helix 28 of the 16S rRNA.
(B) Other neighbors of RbfA within the subunit. Positions of 16S rRNA segments and r-proteins were defined by docking of the crystallographic structure (Wimberly et al., 2000) into the cryo-EM map. Numbers prefixed by h and S identify 16S rRNA helices and 30S small subunit proteins, respectively. The C terminus was positioned as in the Tth RbfA homology model because in the Tth RbfA crystallographic structure the C-terminal end would
clash with the 16S rRNA. Thumbnails to the left depict the orientations of the 30S subunit.
transition, although clearly the accumulation of 30S subunits containing 17S precursor observed in the DrbfA
strain indicates that RbfA stimulates the process (Dammel
and Noller, 1995; Bylund et al., 1998; Inoue et al., 2003).
Indeed, the presence of a C23U mutation in the stem of
h1 has been proposed to weaken formation of the helix
to such an extent that under cold shock conditions, the
phenotype of the mutant strain is reminiscent of the DrbfA
strain (Dammel and Noller, 1993). The latter phenotype
can be rescued by overexpression of RbfA (Dammel and
Noller, 1995). The detection of other suppression mutations in the 16S rRNA, which appear to work through
stabilization of h1, supports the idea that RbfA operates
in an analogous manner (Dammel and Noller, 1995).
We believe that our complex most closely represents the
postprocessing of the 30S subunit, just prior to RbfA dissociation. However, one of the surprising findings that binding of RbfA induces dramatic conformational changes in
h44 and h45 of the 30S subunit may have important implications during maturation: the large shift of h44 signifi-
cantly alters the locations of two important intersubunit
bridges, namely B2a and B3 (Figure 3; Gabashvili et al.,
2000; Yusupov et al., 2001), such that the association of
the precursor-30SRbfA complex with the 50S subunit
would be prohibited (Dammel and Noller, 1995). Furthermore, the position of bound RbfA on the 30S subunit overlaps that of IF1 (Carter et al., 2001), as well as with the
positions of the anticodon stem loops of A and P site bound
tRNAs (Agrawal et al., 2000; Selmer et al., 2006; see
Figure S6). In addition, RbfA is expected to block the
path of mRNA through the 30S subunit (Yusupova et al.,
2001); and due to the shift in the 30 end of the 16S rRNA,
the anti-Shine-Dalgarno (SD) sequence is placed in an unfavorable location for base-pairing with the SD sequence
present in the 50 UTRs of many bacterial mRNAs. Interestingly, the cold shock protein pY binds in a location similar
to that of RbfA and has been shown to inactivate translation by preventing binding of A and P site tRNAs (Vila-Sanjurjo et al., 2004; Wilson and Nierhaus, 2004). Thus, we
believe that RbfA prevents precursor 30S subunits, in
Molecular Cell 28, 434–445, November 9, 2007 ª2007 Elsevier Inc. 441
Molecular Cell
Interaction of RbfA with the 30S Ribosomal Subunit
EXPERIMENTAL PROCEDURES
Figure 7. Comparison of the Binding Positions of RbfA and
Era on the 30S Subunit
(A) Binding position of RbfA (red) and Era (magenta; Sharma et al.,
2005) on the 30S subunit.
(B) RbfA (red) and Era (magenta) interact with a common structural element, h28, of the 16S rRNA (cyan). The thumbnail to the left depicts
the orientation of the 30S subunit.
which h1 has not formed and the 50 end has not been
processed, from entering the translation initiation cycle.
However, we do not think this is the case for mature 30S
subunits, as overexpression of RbfA in vivo does not inhibit
growth (Xia et al., 2003), and addition of RbfA does not
inhibit protein synthesis in vitro (M.K., C.T., and S.Y., unpublished data). This may suggest that binding of RbfA
to precursor 30S subunits is much tighter than to mature
30S subunits, and/or that RbfA may be easily released
from mature, but not precursor, 30S subunits during translation initiation complex formation. Moreover, RbfA is present at very low concentrations during normal growth conditions (Xia et al., 2003), but under cold shock conditions,
when many precursor 30S subunits are trapped with an alternate h1 conformation, RbfA expression is upregulated
(Jones et al., 1996). Thus, we believe that RbfA stimulates
protein synthesis indirectly, by facilitating a more rapid
supply of active 30S subunits under cold shock conditions,
rather than by promoting translation of specific mRNAs.
Purification, Crystallization, and Structure Determination of
the Tth RbfA
Tth HB8 rbfA gene (TTHA0907) was cloned to expression vector
pET11a (Novagen) by the RIKEN Structural Genomics Initiative (Yokoyama et al., 2000), and recombinant RbfA was expressed in E. coli
strain BL21 (DE3). The cell lysate was incubated at 55 C, and RbfA
was precipitated by the addition of 70%-saturated ammonium sulfate
(AS) to the supernatant. The precipitate was dissolved in 20 mM TrisHCl buffer (pH 8.0) containing 1.5 M NaCl and 1.2 M AS, and loaded on
hydrophobic column chromatography (HiPrep Buthyl). Further purification was performed by cation exchange chromatography (monoS
column) and by size-exclusion chromatography (Superdex-75). The final buffer is 20 mM Tris-HCl buffer containing 250 mM KCl (pH 8.0).
The protein yield was 1 mg per 1 g of cells. Crystals were obtained
in drops composed of 0.5 ml protein solution (2.5 mg/ml) and 0.5 ml reservoir solution (1.2 M ammonium dihydrogen phosphate, 80 mM Tris/
HCl [pH 8.5], 9.6% glycerol, 80 mM magnesium formate, 20 mM BisTris propane [pH 7.0]), by the sitting drop vapor diffusion technique
at 20 C. The diffraction data were collected at BL-5A beamline in Photon Factory (Tsukuba, Japan) from a single crystal up to 1.84 Å resolution and processed using the HKL2000 suite and SCALEPACK programs (Otwinowski and Minor, 1997). General handling of the scaled
data was carried out with programs in the CCP4 suite (CCP4, 1994).
The phase was determined by the method of molecular replacement
with program molrep, using a homology model for Tth RbfA (SWISS
MODEL, http://swissmodel.expasy.org/; Schwede et al., 2003) as
a search model, which was generated from 1JOS (Haemophilus influenzae) with ClustalW (Higgins et al., 1994). Models were rebuilt by
combining the auto-model-building results of ARP-wARP, improved
using O (Jones et al., 1991) and refined with CNS (Brunger et al.,
1998). The structures were refined to R factor of 19.9% (Rfree =
24.5%) at 1.84 Å resolution. Protein secondary structure was defined
by the DSSP algorithm (Kabsch and Sander, 1983). Figures were prepared with PyMOL (DeLano, 2002; http://www.pymol.org).
Preparation of the Tth 30S Subunit and the
30SRbfA Complex
The S1-depleted 30S ribosomal subunits were isolated as described
earlier (Sharma et al., 2005). The 30SRbfA complex was prepared
by incubation of RbfA (a 10- to 40-fold excess) with 30S ribosomal subunits (360 nM) for 20 min at 65 C in a buffer A, containing 20 mM
HEPES-KOH (pH 7.8), 10 mM Mg(OAc)2, 200 mM NH4Cl, and 65 mM
KCl. Reactions were stopped by incubation on ice and precentrifuged
for 10 min at 10,000 rpm, and an aliquot was removed before the remainder was loaded onto a 10% sucrose cushion in buffer A and
centrifuged in a TLN100 rotor at 78,000 rpm for 30 min. Binding of
RbfA to the 30S was checked by running the initial reaction, and the
TLN100 supernatant and pellet fractions, on 20% SDS-PAGE, with
Coomassie blue staining (as seen in Figure 2A).
Cryo-EM and 3D Reconstruction
Cryo-EM grids were prepared following standard procedures (Wagenknecht et al., 1988). EM data were collected under low-dose conditions on a Philips Tecnai F20 field emission gun electron microscope
at 200 kV, at a magnification of 50,7603. Images were recorded between 0.7 and 3.5 mm under focus. A total of 131 micrographs were
used. The micrographs were digitized on a Zeiss/Imaging scanner
(Z/I Imaging Corporation, Huntsville, AL) with a step size of 14 mm, corresponding to 2.76 Å on the object scale. The 3D reconstructions were
calculated using a 3D projection alignment procedure (Penczek et al.,
1994). Each data set was subdivided into defocus groups and then analyzed with SPIDER software (Frank et al., 1996) to generate CTF-corrected 3D cryo-EM maps (Penczek et al., 1997). Initially, 154,476 particles were manually selected. The first 3D map obtained from all of the
manually selected particle images showed a fragmented mass of extra
442 Molecular Cell 28, 434–445, November 9, 2007 ª2007 Elsevier Inc.
Molecular Cell
Interaction of RbfA with the 30S Ribosomal Subunit
density in the neck region of the 30S subunit, suggesting a substoichiometric binding of RbfA to the 30S subunit. Therefore, the data set was
subjected to supervised classification (Valle et al., 2002), by use of the
3D map from the total image set as one of the references. The other
reference was the map of the Tth control 30S subunit (Sharma et al.,
2005). Finally, 61,207 particles that classified with the new reference
map were used to calculate the 3D reconstructions of the 30SRbfA
complex. The classification helped to enrich the population of RbfAbound 30S images. However, the possibility that the classified population was still contaminated with images of free (uncomplexed) 30S
subunits could not be ruled out. The resolution of the final 3D cryoEM map of the 30SRbfA complex was 12.5 Å, according to the FSC
criterion with a 0.5 cutoff (Bottcher et al., 1997; Malhotra et al.,
1998), or 8.9 Å, according to the 3s cutoff criterion (Orlova et al., 1997).
Fitting of X-Ray Crystallographic Structures
To attain an optimum fitting of the X-ray crystallographic structure of
the Tth 30S subunit (Wimberly et al., 2000; PDB ID, 1J5E), we divided
the X-ray coordinates into four structural domains (head, body, platform, and 16S rRNA 30 minor domain) and then fitted each domain individually into the cryo-EM map of the 30SRbfA complex. Subsequently, portions of the h44 and h45 rRNA helices from the 30 minor
domain of the X-ray crystallographic structure were separately fitted
into the protruding cylindrical features of the extra mass visible in the
cryo-EM map of the 30SRbfA complex. Fitted coordinates were converted into electron density maps with a pixel size of 2.76 Å, and the
resulting maps were filtered to match the resolution of the cryo-EM
map. The density assigned to RbfA was isolated through comparison
of the cryo-EM map of the 30SRbfA complex and the density map
obtained from the fitting of the 30S X-ray coordinates into the cryoEM map of the 30SRbfA complex. The cross correlation coefficient
(CCF) values between the fitted coordinates for Tth RbfA and the corresponding cryo-EM density maps were determined after conversion
of the fitted coordinates into the density map, through computation
of averaged densities within volume elements scale matched to those
of the cryo-EM map (i.e., with a pixel size of 2.76 Å, and after filtration of
the X-ray map to the resolution of the cryo-EM density map). Visualization of the fitted atomic structures and the cryo-EM density maps was
done with Ribbons (Carson, 1991) and IRIS EXPLORER (Numerical
Algorithms Group, Inc., Downers Grove, IL), respectively.
Supplemental Data
Supplemental Data include six figures and Supplemental References
and can be found with this article online at http://www.molecule.org/
cgi/content/full/28/3/434/DC1/.
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ACKNOWLEDGMENTS
We thank S. Wakatsuki for the use of BL-5A at the Photon Factory and
R. Nakayama-Ushikoshi, T. Terada, and M. Shirouzu for sample preparation. This work was supported by NIH R01 grant GM61576 (to
R.K.A.); by the RIKEN Structural Genomics/Proteomics Initiative
(RSGI) and the National Project on Protein Structural and Functional
Analysis, Ministry of Education, Culture, Sports, Science and Technology of Japan (to S.Y.); and by Deutsche Forschungsgemeinschaft
grant FU579/1-2 (to P.F.). The authors acknowledge use of the Wadsworth Center’s EM infrastructure.
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Received: May 14, 2007
Revised: June 28, 2007
Accepted: August 24, 2007
Published: November 8, 2007
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Accession Numbers
The cryo-EM map of the 30SRbfA complex has been deposited in the
EM database (http://www.ebi.ac.uk) under ID code EMD-1413. The
coordinates of the Tth RbfA crystal structure, the homology model of
RbfA as fitted into the cryo-EM map, and components of 30S ribosomal subunit located in RbfA neighborhood, have been deposited
in the Protein Data Bank (http://www.rcsb.org) under the accession
codes 2DYJ, 2R1C, and 2R1G, respectively.
Molecular Cell 28, 434–445, November 9, 2007 ª2007 Elsevier Inc. 445