Identification of two lysine tRNA cistrons in Bacillus subtilis by hybridization of lysyl-tRNA with DNA

Identification of two lysine tRNA cistrons in Bacillus subtilis by hybridization of lysyl-tRNA with DNA

Vol. 43, No. 4, 1971 BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS IDENTIFICATION OF TWOLYSINE tRNA CISTRONSIN BACILLUSSUBTILIS BY HYBRIDIZA...

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Vol. 43, No. 4, 1971

BIOCHEMICAL

AND BIOPHYSICAL

RESEARCH COMMUNICATIONS

IDENTIFICATION OF TWOLYSINE tRNA CISTRONSIN BACILLUSSUBTILIS BY HYBRIDIZATIONOF LYSYL-tRNA WITH DNA Ronald Chuang, Toshio Yamakawa,and Roy H. Doi Department of Biochemistry and Biophysics University of California Davis, California 95616

Received February 2, 1971 Summary. Two lysyl-tRNA species were obtained from Bacillus subtilis by benzoylated-DEAE-cellulose column chromatography. They were found to hybridize in an additive fashion to 2. subtilis DNA. These results indicate that the base sequences of these two lysine tRNA species differ sufficiently to prevent the saturation of both genetic sites by either and indicate that there are at least two cistrons for lysine tRNA. Many examples of multiple reported (1,2).

Two general assumptions are that the tRNA species either

are products of different transcribed

tRNA species for an amino acid have been

genes or are different

modified forms of a tRNA

from one gene. In a sequence study it was found that two

serine tRNA.. from brewer's yeast differed the presence of two serine tRNA genes. that gene duplication

by 3 base changes (3) indicating In this particular

case it appears

had occurred followed by three mutations resulting

two serine tRNAs which were still

very similar

in structure

in

and function.

In previous studies of the lysine tRNA species of Bacillus subtilis during sporulation,

it was reported that two peaks of lysyl-tRNA

resolved by chromatographic columns (4-6). tRNA patterns and functions of -.B subtilis tRNA-DNAhybridization

cells

(7), we have found from

to DNAin an additive

of analysis allows one to distinguish sufficiently

In a continuing study of lysine

studies that two lysine tRNA species separated by

column chromatography hybridized

differ

were

two ieoaccepting

fashion.

This method

tRNA species which

in base sequence to prevent the saturation

of both

genetic sites by either. MATERIALSANDMETHODS Organism and medium: & subtilis

W23 was used as the source of tRNA, 710

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AND BIOPHYSICAL RESEARCH COMMUNICATIONS

and DNA. Cells were grown to a density of 5 x lo8

aminoacyl synthetase,

cells per ml in Penassay medium (Difco) at 37" C with vigorous shaking. Preparation of lysyl-tBNA:

The tBNA was prepared from cells as The aminoacyl synthetase was

described by von Ehrenstein and Lipmann (8). prepared generally

as described by Zubay (9) followed by chromatography

through Sephadex 675 and DSAE-sephadexA-50 to a stage where no RNaseactivity could be detected (Chuang and Doi, manuscript in preparation).

The reaction

mixture for the preparation

experiments

of lysyl-tBNA

contained in pmoles: 50, Tris-HCl buffer, ATP; 0.5, glutathione;

for the hybridization

pH 8.0; 2.5, MgC12; 5,

100-500 pg, tBNA; 58 pg, partially

purified

KCl;

0.5,

synthetase;

50 pg, bovine serum albumin; and 25 pCi 3H-lysine (50 Ci/mmole); in a total The reaction mixture was incubated at 37' C for 12 min.

volume of 0.20 ml.

The reaction was stopped by adding 0.2 ml of phenol saturated with 0.1 M sodium acetate buffer,

pH 5.

method (8) and the final buffer,

The lysyl-tl7NA was extracted

precipitate

was dissolved in 0.05 M sodium acetate

pH 5.0.

Column chromatography:

The benzoylated diethylaminoethyl-cellulose

(B-DEAE) column was prepared according to Gillam --et al. treatment of lysyl-tBNA cellulose

by the phenol

(10).

and chromatography of oligonucleotides

The Tl RNase on DEAE-

columns were performed by the method described by Ishida and

Miura (11). DNA-RNAhybridization: as described by Gillespie

DNA-RNAhybridization

was carried out essentially

and Spiegelman (12) and Weiss --et al.

denatured DNA (200 pg) was fixed onto nitrocellulose incubated in a total RNA, 2XSSCbuffer as indicated

filters

(13).

Alkaline

(27 mm) and

volume of 1.5 ml with 50%formamide, 1 mg/ml yeast pH 5.0, and 3H-lysyl-tBNA

(0.3 M NaCl + 0.03 M Na citrate),

for 3 hr at 30" C.

The filters

were washed with ZXSSC, treated

with BNaseT1 (2.5 Dg/ml) for 30 min at room temperature, washed again with ZXSSC, dried, E.

coli

and then counted in a scintillation

DNAor without

counter.

any DNAwere used as controls.

711

The filters

with

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AND BIOPHYSICAL RESEARCH COMMUNICATIONS

RESULTS When tRNA obtained from log phase cells of z. subtilis

was charged with

3 H-lysine and chromatographed through a B-DEAE-cellulose column, two peaks of 31i-lysyl-tRNA were obtained as illustrated

in Figure 1.

The fractions

in these peaks were pooled, concentrated by flash evaporation,

deacylated

by treatment at pH 8.8, and recharged with 3H-lysine illustrating were both functionally

active

tRNA fractions.

that they

Furthermore when the first

or second peak was passed through a B-DEAE-cellulose column a second time, it eluted from the column in the original peaks 1 (fractions

position.

130-150) and 2 (fractions

The lysine tRNA from

186-220) are designated as

lysine tRNAl and lysine tRNA2 through the rest of this paper.

6

FRACTION

Figure 1.

NUMBER

Elution profile of 3H-lysyl-tRNA from a B-DEAE-cellulose column. The open and closed CirCles represent A260 and Counts per minute, respectively. The squares indicate NaCl molarity for the elution gradient.

In a preliminary

test to determine whether the two lysine tRNA species

were different

in sequence, lysine tRNAl and lysine tRNA2 were charged with 14 3H-lysine and C-lysine, respectively, mixed together, and then digested 712

BIOCHEMICAL

Vol. 43, No. 4, 1971

with Tl BNase; the resulting

AND BIOPHYSICAL RESEARCH COMMUNICATIONS

lysyl-oligonucleotides

were chromatographed

through a DEAE-cellulose column to determine whether the two lysine tBNAs differed

in sequence from the first

guanine residue from the 3'terminus.

The results showed that lysyl-oligonucleotides

(with a chain length of 3

bases) from lysine tENAl and lysine tENA eluted in exactly These results in contrast tRNA (14) indicated

the sameposition.

to the previous results with g. subtilis

that the lysine tRNA species had identical

valine

T1 RNase

susceptible sequences near the amino acid accepting terminus. To test whether lysine tENAl and lysine tENA contained different sequences in the rest of the molecule, hybridization and lysyl-tBNA2

base

between lysyl-tENA

and DNAwas tested by the method of Weiss -et g.

(13).

Each of the pooled fractions

from the B-DEAE-cellulose column (Fig. 1) was 3 charged separately with 3H-lysine and the amount of H-lysyl-tENAl and of 3Ii-lysyl-tRNA2

which would hybridize

results are shown in Figure 2.

with DNAwas determined.

The ratio

of tENA to DNAabove 0.3 (i.e.

of tENA to 200 ng of DNA) resulted in saturation preparations

under the conditions used.

0

Since the samespecific

activity

of

the almost

counts with both tBNA preparations suggested

20

40 ,,g

Figure 2.

60 ng

of DNAsites for both tBNA

3H-lysine was used during charging of both tBNA preparations, equal number of hybridized

These

60 so of %I-lyryl-tRNA

100

120

Hybridization of 3H-lysyl-tENAl and 3H-lysyl-tRNA2 with 5. subtilis W23 DNA. The open and closed circles represent 3H-lysyl-tBNA1 (760 cpm per ng) and 3H-lysyl-tENA2 (1,170 cpm per ng), respectively. 713

Vol. 43, No. 4, 1971

BIOCHEMICAL

AND BIOPHYSICAL RESEARCH COMMUNICATIONS

that equal amounts of lysyl-tRNA1 14%deacylation

and lysyl-tRNA2 were hybridized.

occurred with control

samples of both tRNA preparations

during the experiment under incubation conditions identical hybridization

Only

of the

to that

reactions.

To determine whether the two lysine tRNA species were hybridizing two distinct

DNAsites,

the additive

nature of hybridization

adding saturating

levels of lysyl-tRNA1 and lysyl-tRNA2

the hybridization

reaction

presented in Table 1. tested first

Table 1.

Exp. No.

mixture.

The results from two experiments are

to determine the concentration

of lysyl-tRNA1

T

DNAon filter

was tested by

simultaneously to

For each experiment, the lysyl-tRNA

Hybridization

with

preparations were

of tRNA required for saturation

and lysyl-tRNA2

to DNA

1

3H-lysyl-tRNA hybridized tRNAy

1 tRNAys let cpm

la b C

2a

b

C

no DNA g. subtilis

W23

130

no DNA B. subtilis

W23

148

no DNA j& subtilis

W23

303

no DNA E. coli -. subtilis

W23

123

no DNA E. coli 5. subtilis

W23

121

no DNA E. coli z. subtilis

567*

320 339 533

W23 3

213

3H-lys~l-tRNAl (80 up) and H-lysyl-tRNA2 at saturating concentrations (80 ug or 100 ng ) were hybridized with denatured DNA (200 ng), respectively. In Exps. lc and 2c, both aminoacyl-tRNAs were added to the incubation mixture. 714

Vol. 43, No. 4, 1971

BIOCHEMICAL

AND BIOPHYSICAL

RESEARCH COMMUNICATIONS

of the DNAbefore testing

for additive

hybridization.

were used for the results

reported in Figure 2 and Table 1.

experiments no aberrant hybridization

The samepreparations

was noted when up to 200 ng of lysyl-

tRNA was added to the reaction mixture,

i.e.

did not result

than the saturation

in greater hybridization

Figure 2.

These results

hybridized

to a given saturation

to the reaction mixture,

illustrate

In other

a large excess of lysyl-tRNA levels noted in

that lysine tRNAl and lysine

tRNA2 each

level and that when they were added together

they hybridized

in an additive

fashion.

DISCUSSION Two significant 1)

conclusions can be reached from these data:

These results indicate

whose base sequences differ two isoaccepting duplication,

that two lysine tRNA genes are present

sufficiently

to allow additive

If the genes were originally

tRNA species.

these results suggest that sufficient

during evolution

to prevent hybridization

locus of the other.

At first

hybridization

with

derived by gene

base changes have occurred

of one tRNA species to the genetic

glance these results are surprising;

however,

a change of only a few bases could lead to unstable heterologous hybrid formation in the usual manner or the base changes could give rise to two tRNA species which are modified quite differently

by the various base-modifying

enzymes with subsequent enhanced loss of stable hybrid formation with the heterologous DNAsequence. 2)

In this particular

distinguish

the origin

case the hybridization

of two isoaccepting

technique was able to

tRNA species.

Although this may

not be the case with other isoaccepting tRNAs, it would be judicious this additive

hybridization

test to other bacterial

systems, in which iso-

accepting tRNAs have been reported to determine their Obviously those isoaccepting may still distinguish

tRNAs which differ

genetic origin.

by only one or a few bases

bind to heterologous sites and this particular their

in this particular

origin.

However, the clear and readily

case indicate

test will

715

not

obtained results

that it is worth the effort

this basic information.

to apply

to acquire

Vol. 43, No. 4, 1971

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AND BIOPHYSICAL RESEARCH COMMUNICATIONS

ACKNOWLEDGMENTS This research was supported by National Science Foundation Grant No. GB-8405 and U. S. Atomic Energy CommissionGrant No. AT(O4-3)-34.

REFERENCES 1. 2. 3. 4. 5. 6. 7. 8.

9. 10. 11. 12. 13. 14.

N. Sueoka and T. Kano-Sueoka, Prog. Nucleic Acid Res. & Molec. Biol. l& 23 (1970). G. D. Novelli, Ann. Rev. Biochem. 36, Part II, 449 (1967). H. G. Zachau, D. ktting, and H. Feldman, Angew. Chemie. Intern. Ed. Engl. 2, 422 (1966). R. A. Lazzarini, Proc. Natl. Acad. Sci. U. S. 56, 185 (1966). R. A. Lazzarini and E. Santangelo, J. Bacterial. 94, 125 (1967). B. Vold, J. Bacterial. 102, 711 (1970). B. Goehler and R. H. Doi, Proc. Natl. Acad. Sci. U. S. 56, 1047 (1966). G. Von Ehrenstein and F. Lipmann, Proc. Natl. Acad. Sci. U. S. 47, 941 (1961). G. Zubay, J. Mol. Biol. 4, 347 (1962). I. Gillam, S. Millward, D. Blew, M. von Tigerstrom, E. Wimmer, and G. M. Tener, Biochemistry 2, 3043 (1967). T. Ishida and K. Miura, J. Mol. Biol. 11, 341 (1965). D. Gillespie and S. Spiegelman, J. Mol. Biol. 2, 829 (1965). S. B. Weiss, W.-T. Hsu, J. W. Foft, and N. H. Scherberg, Proc. Natl. Acad. Sci. U. S. 61, 114 (1968). R. H. Doi, I. Kaneko, and R. T. Igarashi, J. Bfol. Chem.243, 945 (1968).

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