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INTRODUCTION |
tRNA genes in Escherichia coli are normally transcribed
as precursor molecules that require processing at both their 5'- and 3'-ends to generate the mature functional forms (1). Maturation of the
5'-end of tRNA precursors is carried out by a single endoribonuclease, RNase P, whereas 3'-processing generally is a multistep process requiring the action of both endo- and exoribonucleases to remove the
extra nucleotides following the encoded 3'-terminal -CCA sequence (1-3). A single pathway for 3'-maturation does not exist. Rather, it
appears to proceed in a stochastic manner such that any one of five
exoribonucleases (RNase II, D, BN, T, or PH) may act to complete the
3'-maturation process (2-4).
The process is more complicated in bacteriophage T4-infected
Escherichia coli. In this situation, eight new tRNAs encoded by the T4 genome are synthesized (6). Four of these tRNA precursors lack the usually encoded -CCA sequence, and during their 3'-maturation, the incorrect residues must be removed and be replaced by the -CCA
sequence through the action of tRNA nucleotidyltransferase (5, 6). In
certain mutant E. coli strains, BN and CAN, this process
does not occur (7, 8). Thus, these strains do not support the growth of
a mutant T4 phage (BU33) because a phage-encoded suppressor
tRNASer, required for the translation of an amber mutation
in a BU33 head protein, cannot be processed to its mature form due to a defect in 3'-maturation (9). The molecular basis for this phenotype in
strains BN and CAN is the deficiency of the exoribonuclease RNase BN
(10, 11). Thus, in contrast to uninfected cells, in which at least five
exoribonucleases can remove the extra residues following the -CCA
sequence during 3'-maturation of tRNA precursors, only RNase BN appears
able to remove incorrect residues within the -CCA sequence during phage
T4 tRNA maturation.
To learn more about the structure, function, and specificity of RNase
BN, we first identified and cloned the rbn gene encoding the
enzyme (12). We discovered that rbn is nonessential in
E. coli and that it encodes a polypeptide of 32.8 kDa (12).
In this paper, we describe the overexpression, purification, and characterization of RNase BN.
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EXPERIMENTAL PROCEDURES |
Strains and Plasmids--
Plasmid pBS(+) (Stratagene) is an
inducible multicopy vector. Plasmid pBSrbn+ (12)
was used to overexpress RNase BN. E. coli strain BL21(DE3) pLys (13) was used as the host for the aforementioned plasmid.
Culture Conditions--
Cells were routinely grown at 37 °C
in YT medium or on YT plates (14). Ampicillin, when added, was present
at a concentration of 200 or 300 µg/ml. Growth in liquid medium was
followed by absorbance measurements at 600 nm.
Materials--
[3H]Poly(A), blue dextran 2000, Ultrogel-AcA44, and DEAE-Sephadex A-50 were obtained from Amersham
Pharmacia Biotech. [14C]ATP and
[
-32P]ATP were obtained from NEN Life Science
Products. Unlabeled poly(A) used to dilute the radioactive material was
obtained from Sigma. Bacterial alkaline phosphatase was purchased from
Worthington. N-Ethylmaleimide, 5,5'-dithiobis(2-nitrobenzoic
acid), p-hydroxymercuribenzoate, and protein size markers
were obtained from Sigma. Mercuric chloride was obtained from J. T. Baker Inc. Hydroxylapatite HT, Affi-Gel blue, and cellulose were
purchased from Bio-Rad. All other chemicals were reagent-grade.
RNase BN Assay--
RNase BN removes the 3'-terminal
mononucleotide AMP from the phage tRNA precursor analogue
tRNA-C[14C]A. This substrate was prepared as described
previously (15). Reaction mixtures of 100 µl contained 20 mM Hepes, pH 6.5, 0.2 mM CoCl2, 200 mM KCl, 8 or 16 µg of tRNA-C[14C]A
(104 cpm/nmol), and cell extract or purified enzyme.
Samples were incubated for 30 min at 37 °C, and acid-soluble
radioactivity was determined. One unit of RNase BN is the amount of
enzyme that releases 1 nmol of AMP in 1 h.
Overexpression of RNase BN--
Plasmid
pBSrbn+ carrying the rbn gene cloned
under control of a T7 promoter was transformed into strain
BL21(DE3) pLys. Bacteriophage DE3 contains the gene for T7
RNA polymerase controlled by the lacUV5 promoter, which is
inducible by isopropyl-
-D-thiogalactopyranoside. The
pLys plasmid carries the gene for T7 lysozyme, which
inhibits basal levels of T7 transcription in the uninduced
cell. Cells were grown to an absorbance of 0.5 at 600 nm in YT medium
containing 200 µg/ml ampicillin. To maintain the
rbn+ plasmid, cells were then harvested by
centrifugation at 5000 rpm for 5 min, washed with YT medium to remove
-lactamase, and then resuspended in fresh YT medium containing 300 µg/ml ampicillin. The culture was grown to an absorbance of just
under 1 at 600 nm. The cells were spun down, washed with YT medium, and
resuspended in YT medium containing 300 µg/ml ampicillin and 0.4 mM isopropyl-
-D-thiogalactopyranoside to
induce T7 RNA polymerase. Cells were then grown for an
additional 4 h before harvesting.
Preparation of Extracts--
All steps of the purification
procedure were carried out at 4 °C in the cold room. Ten grams of
induced cells (wet weight) were suspended in 2.5 volumes of Buffer A
(10 mM Tris-HCl, pH 7.5, 1 mM dithiothreitol,
0.1 mM EDTA, and 0.1 mM phenylmethylsulfonyl fluoride) and passed twice through an Amicon French press at 10,000 p.s.i. DNase I was added to the resulting extract at a concentration of
10 µg/ml, and the sample was incubated at 0 °C for 45 min. The
extract was then centrifuged at 20,000 rpm for 40 min, and the soluble
fraction obtained was centrifuged at 45,000 rpm for an additional 120 min in a Ti-70.1 rotor in a Beckman L8-70M ultracentrifuge.
DEAE-Sephadex Chromatography--
The supernatant fraction was
diluted 2-fold with Buffer A containing 10% glycerol to lower the
ionic strength and passed through a 0.22-µ syringe filter. The
resulting 12-ml sample was applied to a DEAE-Sephadex A-50 column
(2.8 × 13 cm) and washed with Buffer A containing 50 mM KCl until the A280 was <1. The
column was eluted using a linear gradient of 50-700 mM KCl
in Buffer A. Eighty 1-ml fractions were collected. Fractions 51-73,
with the highest RNase BN activity, were combined. This material was
concentrated 5-fold with an Amicon Diaflo YM-10 membrane and dialyzed
against 2 liters of Buffer B (5 mM potassium phosphate, pH
7.5, 1 mM dithiothreitol, 0.1 mM EDTA, and 0.1 mM phenylmethylsulfonyl fluoride).
Hydroxylapatite Chromatography--
The dialyzed 6.7-ml sample
was applied to a hydroxylapatite column (2.8 × 13 cm) that
contained 10% cellulose to improve flow rates and that had been
equilibrated with Buffer B. The column was eluted with a linear
gradient of 5-50 mM phosphate in Buffer B. Eighty 1-ml
fractions were collected. Fractions 35-55, with the highest activity,
were combined and concentrated ~10-fold to a final volume of 2 ml by
ultrafiltration as described above.
Ultrogel-AcA44 Chromatography--
The concentrated sample was
applied to an Ultrogel-AcA44 column (1.8 × 78 cm) equilibrated
with Buffer A containing 1 M KCl. The column was eluted
with the same buffer. Eighty 2-ml fractions were collected. Fractions
42-74, containing RNase BN activity, were combined, dialyzed against 2 liters of Buffer A, and concentrated ~30-fold by ultrafiltration to a
final volume of 2 ml.
Affi-Gel Blue Chromatography--
The sample was applied to an
Affi-Gel blue column (0.8 × 10 cm) and washed with Buffer A
containing 50 mM KCl until the A280 was <1. The column was eluted with a linear gradient of 0-1
M KCl in Buffer A. Fifty 75-µl fractions were collected,
and the active fractions, in tubes 25-27 (see Fig. 1), were combined
and frozen at
80 °C. Side fractions, 19-24 and 28-33, were also
combined and concentrated 2-fold by ultrafiltration. This latter sample was split into three portions and stored at
80,
20, and
20 °C
with 50% glycerol to ascertain the best storage conditions.
Other Assays--
Protein was determined by the method of
Bradford (16) with bovine serum albumin as a standard or by absorbance
at 280 nm.
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RESULTS |
Overexpression and Purification of RNase BN--
Overexpression of
RNase BN is deleterious to cell growth and generally leads to loss of
the expression plasmid.1
However, use of the inducible T7 expression system (with
changing of the medium to remove
-lactamase and to restore
ampicillin levels) resulted in a 25-fold overproduction of RNase BN
during the 4-h induction period. In several experiments, it was found that this amount of time gave maximum expression of RNase BN.
As shown in Table I, RNase BN was
purified from a high-speed supernatant fraction using a series of four
chromatographic steps. The overall purification from the overexpressed
extract was 46-fold, equivalent to ~1000-fold from a normal extract.
The apparent recovery was 50%; however, as is clear from the increased activity in steps 2 and 3, RNase BN activity in the supernatant fraction actually is inhibited 2-3-fold, presumably by the large amount of nucleic acid present. This inhibition was verified directly by mixing of purified RNase BN with the initial supernatant fraction (data not shown).
Purified RNase BN was stored for 1 month under a variety of conditions
and then re-assayed to determine optimal conditions for storage.
Although the enzyme was relatively stable under all the conditions
tested, it was most stable at
20 °C in the presence of 50%
glycerol or at
80 °C after rapid freezing in a dry ice/ethanol bath. Under these conditions essentially no RNase BN activity was lost
during the period of storage.
Purity of RNase BN--
Based on the close correspondence between
RNase BN activity and absorbance at 280 nm upon elution from Affi-Gel
blue (Fig. 1), it was apparent that RNase
BN was quite pure. This was confirmed by SDS-polyacrylamide gel
electrophoresis (Fig. 2). Overexpression of RNase BN is evident by comparison of lanes 6 and
7. The progressive purification of RNase BN can be seen in
lanes 6 to 2. We estimate that the most purified
material (lane 2) was at least 95% pure.

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Fig. 1.
Affi-Gel blue chromatography. The
concentrated and dialyzed RNase BN-containing fractions from
Ultrogel-AcA44 chromatography were applied to a column of Affi-Gel blue
equilibrated with Buffer A. Samples were washed with the starting
buffer and were eluted with a linear gradient of 0-1 M KCl
in Buffer A. Fractions of 75 µl were collected, and aliquots of 1 µl were assayed for 30 min. Protein was determined by absorbance at
280 nm.
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Fig. 2.
SDS-polyacrylamide gel electrophoresis
of RNase BN purification fractions. Lane 1,
protein size markers of the masses indicated (from top to bottom:
ovalbumin, carbonic anhydrase, -lactoglobulin, and lysozyme);
lane 2, Affi-Gel blue combined fractions; lane 3,
Ultrogel-AcA44 combined fractions; lane 4, hydroxylapatite
combined fractions; lane 5, DEAE-Sephadex A-50 combined
fractions; lane 6, supernatant from induced cells;
lane 7, supernatant from uninduced cells.
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Spectral analysis of RNase BN, carried out in the range of 200-350 nm,
revealed no unusual peaks (data not shown). The
A280/A260 ratio was 1.89, indicating that purified RNase BN is free of nucleic acid. Thus, RNase
BN does not require nucleic acid for activity.
Molecular Mass and Subunit Structure--
SDS-polyacrylamide gel
electrophoresis (Fig. 2) indicated that purified RNase BN contains only
a single species of polypeptide chain with a molecular mass of ~37
kDa. This is in good agreement with the predicted size of RNase BN of
32.8 kDa based on the sequence of the rbn gene (12).
Based on gel filtration on Ultrogel-AcA44 (step 4 of the purification
procedure) and assuming that it is a globular protein, the native
molecular mass of RNase BN is ~65 kDa. These data strongly support
the conclusion that RNase BN functions as an
2-dimer, as
previously suggested from earlier genetic studies in which an
interruption-deletion mutant of RNase BN displayed a strong dominant-negative effect (12).
Effect of Sulfhydryl Reagents--
Based on the nucleotide
sequence of the rbn gene, RNase BN contains 2 cysteine
residues/polypeptide chain (12). To ascertain whether these residues
are present in their reduced form and whether they might play a role in
enzyme activity, purified RNase BN was incubated with the sulfhydryl
reagents N-ethylmaleimide, 5,5'-dithiobis(2-nitrobenzoic acid), p-hydroxymercuribenzoate, and mercuric chloride. As
presented in Table II, each of these
reagents was found to be a potent inhibitor of RNase BN, decreasing
RNase BN activity ~90% upon preincubation for 30 min at 37 °C.
These data show that at least 2 of the cysteine residues in native
RNase BN are in the reduced form and that cysteine residues are
required for enzyme activity. Whether these residues are directly
required for catalysis or indirectly by maintaining structure, such as
the dimeric form, remains to be determined.
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Table II
Effect of sulfhydryl reagents on RNase BN activity
Purified enzyme from the Affi-Gel blue combined fractions was used. The
enzyme was incubated at 37 °C with a 0.2 mM
concentration of the indicated sulfhydryl reagent for 30 min prior to
assay. Data shown are the averages of two experiments.
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Temperature Sensitivity of RNase BN--
Samples of RNase BN were
incubated at various temperatures for 10 min prior to determining the
amount of activity remaining. The data in Fig.
3 show that RNase BN remained stable for
10 min at temperatures up to 45 °C, and at 50 °C, still retained
66% of its activity. However, at 60 °C, 90% of the activity was
lost in 10 min. Additional experiments revealed that RNase BN retained ~25% of its activity upon incubation for 40 min at 50 °C (data not shown). These data indicate that RNase BN is moderately stable at
elevated temperatures.

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Fig. 3.
Temperature sensitivity of RNase BN.
Purified enzyme from the Affi-Gel blue combined fractions in Buffer A
was used. Samples of the enzyme were assayed as described under
"Experimental Procedures" after portions were first incubated for
10 min at the indicated temperatures.
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Optimal Conditions for RNase BN Activity--
RNase BN was assayed
under a variety of conditions to assess the requirements for optimal
activity. Assay at pH values between 6.0 and 8.0 in
Mes2 and Hepes buffers
indicated that RNase BN is most active at pH 6.5. Activity at pH 8.0 was 70% of that at pH 6.5, whereas that at pH 6.0 was 95% of that at
pH 6.5. The relatively low pH optimum for RNase BN is unusual among the
exoribonucleases of E. coli, which generally function
optimally at more alkaline pH values.
Among the divalent cations tested, significant activity was observed
only with Co2+ and Mg2+, with Co2+
being considerably more effective at 0.2 mM (Table
III). A more detailed examination of
these two cations (Fig. 4) revealed that at its optimum (0.2 mM), Co2+ was approximately
twice as effective as Mg2+ at its optimum (1 mM). Both cations displayed quite sharp optima. These
findings are quite unusual as Co2+ has not been observed
previously to function as such an effective cofactor for RNases.
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Table III
Divalent cation requirement for RNase BN activity
Purified RNase BN (0.025 µg) was assayed as described under
"Experimental Procedures" using 8 µg of substrate. The indicated
divalent cation as the chloride salt was present at 0.2 mM.
EDTA was added at 4 mM.
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Fig. 4.
Effect of Co2+ or
Mg2+ concentration on RNase BN activity. Purified
RNase BN (0.05 µg) was assayed with 16 µg of
tRNA-C[14C]A and the indicated concentrations of divalent
cation as described under "Experimental Procedures."
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RNase BN also requires a monovalent cation for activity. With
K+ as the cation, the optimal concentration was 200-400
mM (Fig. 5). At 200 mM, the monovalent cation requirement could be satisfied by
Li+, which was as effective as K+;
Na+ and Rb+ were ~70% as effective, and
Cs+ was ~30% as effective. A monovalent cation is also
required when Mg2+ is the divalent cation. Although a
number of other E. coli exoribonucleases are stimulated by
monovalent cations, the absolute requirement of RNase BN for a
monovalent cation is unusual.

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Fig. 5.
Effect of KCl concentration on RNase BN
activity. Purified RNase BN (0.025 µg) was assayed with 8 µg
of tRNA-C[14C]A and the indicated concentrations of KCl
as described under "Experimental Procedures."
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Substrate Specificity of RNase BN--
RNase BN is highly specific
in its mode of action (Table IV). tRNA
molecules in which a nucleotide residue within the normal 3'-terminal
-CCA sequence has been replaced such as tRNA-CA and tRNA-CU were highly
active as substrates, whereas all the other RNA molecules tested, even
those with very similar structures, were essentially inactive. Thus,
intact tRNA-CCA, diesterase-treated tRNA (which lacks 3'-terminal
residues), and tRNA-CCA-Cn (which contains residues following the
normal 3' terminus) were all extremely poor substrates. Even the
closely related tRNA-CC, which differs from the active substrates by a
single terminal residue, was almost inactive. Given this high degree of
specificity against such similar molecules, it is not surprising that
rRNA and poly(A) also were poor substrates (Table IV).
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Table IV
Substrate specificity of RNase BN
Purified RNase BN (0.05 µg) was assayed as described under
"Experimental Procedures" using 800 pmol of each RNA substrate.
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A second group of substrates consisting of RNA and DNA oligonucleotides
11-17 residues in length were also tested as substrates (Table
V). The sequences of the RNA
oligonucleotides are those of the 3' terminus of E. coli
tRNA1Tyr and its precursor molecules
with 3 or 6 extra 3'-residues. These molecules were labeled at their 5'
termini with 32P, and RNase BN action was assessed on a
20% acrylamide gel, which can detect shortening by even a single
nucleotide residue. Based on this analysis, none of these molecules
were substrates for RNase BN under standard assay conditions.
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Table V
Action of RNase BN on oligonucleotides
Purified RNase BN (0.025 µg) was assayed as described under
"Experimental Procedures" using 3 pmol of each substrate.
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Products of RNase BN Action--
Based on earlier work in which
relatively crude preparations of RNase BN were found to release UMP
from tRNA-CU, it was suggested that this enzyme is an exoribonuclease
(10). To confirm this conclusion and to ensure that the release of
mononucleotide was not due to a secondary reaction resulting from the
presence of a contaminating activity, the products of the reaction
catalyzed by highly purified RNase BN were examined. Thus, using
tRNA-C[14C]A as a substrate, both the acid-soluble and
tRNA products were determined (Table
VI).
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Table VI
Products of RNase BN treatment of tRNA-C[14C]A
tRNA-C[14C]A was treated with RNase BN (0.05 µg) for 30 min
as described under "Experimental Procedures." Half of each reaction
mixture was used to determine acid-soluble radioactivity, as usual. The
other half was heated at 70 °C for 10 min to inactivate RNase BN,
followed by the addition of 50 mM glycine-NaOH, pH 9.4, 5 mM MgCl2, 0.5 mM [3H]CTP, and
excess tRNA nucleotidyltransferase. After incubation at 37 °C for 30 min, acid-precipitable radioactivity was determined. In a separate
scaled-up experiment using 80 µg of tRNA-C[14C]A and 0.125 µg of RNase BN, the acid-soluble fraction was extracted four times
with ether; adjusted to 10 mM NH4HCO3, pH
8.8, and 5 mM MgCl2; and incubated with 0.5 unit of
bacterial alkaline phosphatase for 30 min at 45 °C. The pH of the
sample was adjusted to 7, and the sample was added to a 1-ml column of
Dowex AG 1-X2. Nucleosides were eluted with seven 1-ml portions of
H2O, and nucleotide material was eluted with five 1-ml portions
of 0.1 N HCl. Data shown are the averages of two
experiments.
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If RNase BN were an exoribonuclease, the 14C-labeled
acid-soluble product would be expected to be AMP, which, upon treatment with alkaline phosphatase, would be converted to the uncharged molecule
[14C]adenosine. If, on the other hand, RNase BN were an
endoribonuclease, any acid-soluble oligonucleotides produced would
remain charged after treatment with the phosphatase and would elute
with the "nucleotide" fraction. Columns of the anion exchanger
Dowex AG 1-X2 were used to separate radioactive nucleoside from
nucleotide species. As shown in Table VI, after phosphatase treatment,
93% of the acid-soluble radioactivity was eluted from the ion-exchange column with water, consistent with its being the nucleoside adenosine.
To further verify the exoribonucleolytic action of RNase BN, the tRNA
product was treated with tRNA nucleotidyltransferase in the presence of
[3H]CTP. Removal of AMP from tRNA-CA would generate
tRNA-C, a substrate for the incorporation of CMP by tRNA
nucleotidyltransferase. As also shown in Table VI, release of 14 pmol
of acid-soluble radioactivity from tRNA-C[14C]A by RNase
BN resulted in the incorporation of 13 pmol of [3H]CTP
over and above that incorporated in the absence of RNase BN action. The
incorporation of [3H]CTP in the absence of RNase BN
treatment is due to the fact that the preparation of the
tRNA-C[14C]A substrate from tRNA-C is not quantitative,
and some residual tRNA-C remains. Nevertheless, these data support the
conclusion that RNase BN removed a single nucleotide residue from
tRNA-C[14C]A to generate [14C]AMP and
tRNA-C, as expected if it were an exoribonuclease.
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DISCUSSION |
In this paper, the purification of RNase BN in its native untagged
form has been described. RNase BN is now the seventh of the eight known
E. coli exoribonucleases (all except RNase R) to have been
purified to near homogeneity. Interestingly, RNase BN is the sixth of
the eight enzymes to exist as a multimer and the fifth to be an
2-dimer (polynucleotide phosphorylase is a trimer).
Inasmuch as there is relatively little overall sequence similarity or
similarity in size among the exoribonucleases as a group, it is
intriguing that there is commonality in their quaternary structure.
Perhaps, this represents some consistency among these enzymes in their
interactions with substrate. As yet, there is very little detailed
structural information about this class of enzymes, so the significance
of their multimeric forms will have to await further work.
In contrast to its shared structural similarity, RNase BN is unique
among the E. coli exoribonucleases in a number of its catalytic properties. These include a low pH optimum of 6.5, a strong
preference for Co2+ as the required divalent cation, and a
requirement for a high concentration of monovalent ions or for elevated
ionic strength. In addition, RNase BN displays a highly unusual and
strict substrate specificity. Of the molecules tested, only those
containing alterations within the 3'-terminal -CCA sequence serve as
effective substrates, resulting in removal of the incorrect nucleotide.
Other closely related molecules, even tRNA-CC, are inactive or very
poorly active as substrates. This unusual substrate specificity makes
RNase BN ideally suited for its, so far, only known biological role: the maturation of a subset of bacteriophage T4 tRNA precursors that
lack the -CCA sequence (5). RNase BN is essential for the 3'-processing
of at least some of this group of tRNAs (6, 9).
This, of course, raises the interesting question of what the role of
RNase BN is in the uninfected E. coli cell. Clearly, this
enzyme has not been maintained solely for its role during phage
infection. It is known that RNase BN can contribute to the maturation
of cellular tRNAs when other processing exoribonucleases are absent (3,
4). However, it is the poorest of all the exoribonucleases in this
regard. RNase BN is not an essential enzyme in E. coli, and
its absence has no effect on cell growth under usual laboratory
conditions (12). It is possible that RNase BN is important during a
stress response. In fact, RNase BN expression is affected by
manipulation of certain proteins altered during heat
shock,1 but further work is necessary to clarify this
effect. One might expect that the unusual substrate specificity of
RNase BN would be a clue to its cellular function. Yet in E. coli, in contrast to higher organisms, all tRNA genes encode the
universal -CCA sequence (17). Thus, there are no known conditions in
which incorrect residues would be present in this sequence other than in the case of errors during transcription.
From the foregoing discussion, it is evident that there is much
remaining to be learned about the structure and function of RNase BN.
Now, with the availability of purified protein and of mutant strains
lacking RNase BN (12), continued progress can be expected in studies of
this interesting enzyme.