Human α-chain globin messenger: Prediction of a nucleotide sequence

Vol. 54, No. 3, 1973

BIOCHEMICAL

AND BIOPHYSICAL RESEARCH COMMUNICATIONS

HUMAN a-CHAIN GLOBIN MESSENGER: PREDICTION OF A NUCLEOTIDE SEQUENCE Brian Department Received

Laux,

Don Dennis,

of Chemistry, August

and Harold

University

B. White,

of Delaware,

III* Newark 19711

3, 1973

Summary: All nucleotide sequences consistent with the amino acid sequence of the a-chain of human hemoglobin were tested for their complementarity with a known 26-nucleotide sequence from the a-chain messenger. The region with the highest pairing potential is immediately adjacent to the known nucleotide sequence. The existence of this potential hairpin loop requires the specification of nucleotides in at least 6 degenerate positions.

Secondary

structure

is

and rRNA2.

The degeneracy

possibility

for

we113-6.

Certainly

structure

is very

messengers

a characteristic of the genetic

extensive

secondary

for

the MS2 coat 7 evident . Whether

are favored

feature

generally

of

code allows

structure

tRNA's1

the

in mRNA's as

protein

messenger,

secondary

such base-paired

by natural

selection

is yet

to be determined. Double-standed

RNA inhibits

reticulocytes

by binding

This

that

suggests

region a-chain is

coding dictions

to initiation normally

factor

binds

The hyperchromicity

synthesis

to

a

in rabbit

3(IF-3j8. double-standed

exhibited

by rabbit

globin

messenger indicates that secondary structure 9 two possible in this molecule . We have predicted

present

hairpin

*

in mRNA.

IF-3

protein

loops for

for

the portion

the C-terminal

were made possible

To whom inquiries

should

of

region

the human a-chain 5. of the protein

by the amino acid be addressed.

messenger These pre-

sequence

of

the

BIOCHEMICAL

Vol. 54, No. 3,1973

chain-termination

variant,

discovery

of

permitted

the unambiguous

tides

in

This

this

third

structures5,

This maximal

base-pairing

coding

for

loop

for

All

the amino acid

using

a pattern

base-pairing

stable

secondary Several

This

with

agreement

which

the

with

a

provided

26-nucleotide all

sequence

regions

nucleotide

selection

recognition

of this

of

of

the mRNA

sequences

sequence of human a-chain

possibilities 12 structure .

features

both

1).

deduced

possible

were considered.

computer

(Fig.

nucleo-

communication).

with

in striking

complementarity

with

personal

the structure

when the

protein.

compatible globin

hairpin

The recent 11 Wayne , has

of 26 consecutive

incompatible is

.

variant,

assignment

but

loop represents

was checked

deletion

is

10

Spring

(W. P. Winter,

sequence

potential

Constant

frame-shift

region

nucleotide

predicted

only

the

AND BIOPHYSICAL RESEARCH COMMUNICATIONS

was performed algorithm

which

would

proposed

by

which

retains

contribute

loop

should

to

be

noted: a.

The region with

that

the

provides

26-nucleotide

maximum complementarity sequence

the mRNA immediately

adjacent

quence.

loop which

The hairpin

intrinsically

more stable

complementary

segments remote

(The region codes for nucleotides

with

is

a segment of

to that

than

this

known secreates

a structure

is with

from each other.

the second-best

pairing

Leu 80 to Leu 86 and is

potential

located

156

away from the known 26-nucleotide

sequence.) b.

The size comparable

and stability to those

of

this

in the MS2

895

hairpin RNA'.

loop

is

We have

Vol. 54, No. 3,1973

BIOCHEMICAL

AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Fig. 1. Predicted hairpin loop for the C-terminal region of human cl-chain globin. Circles indicate known nucleotides. Boxes indicate nucleotides in degenerate positions which have been selected to maximize basepairing. Unspecified nucleotides are indicated by X. The amino acid sequence beyond the termination codon is that of the chain-termination variant, Constant Springlo. The nucleotide sequence from Tyr 140 to Val 147 was deduced by a comparison of the amino acid sequences of the Constant Spring variant and the frameThe shift deletion variant, Waynell. Wayne variant can be explained by a deletion of any one of the three nucleotides coding for Lys 139 or either of the last two nucleotides of Ser 138. In order to maximize base-pairing, we have assumed that the Wayne variant results from a deletion of G from the Lys 139 codon. (The other possible deletions for the Wayne variant require an A in this position.) The first nucleotide of the Leu 136 codon is likely to be C since the hemoglobin variant Bibba (Leu 136a+Pro)16 would then be oossibleith a single nucleotide substitution. &

calculated to be -17.6 ing

the

stabilization energy of this 13 kcal/mole or -10.8 kcal/molel*

upon the method of

calculation

896

used.

loop dependThe

BIOCHEMICAL

Vol. 54, No. 3, 1973

loop

AND BIOPHYSICAL RESEARCH COMMUNICATIONS

as shown in Fig.

there

are four

1 is

interior

25-nucleotide

loops but

pairs

no bulge

long: 14

loops

.

The codons are in 2:2 registry5. It start

is

at the third

at the the it

first

that

the hairpin

could

of Ala

130 and end

nucleotide

nucleotide

of Ala

145.

loop would be 19 nucleotides is

third

possible

that

nucleotide

nucleotide hairpin there

of is

The loop

bility

at

of Ser 133 and end at the

first

codon.

more stable factors

While

the

the

longest

theoretically,

which

would

favor

these

loops.

in Fig.

1 permits

in degenerate

of the

tides

start

slightly

nucleotides

case

Likewise,

could

the termination

hairpin

In this

long.

the hairpin

may be other

shorter C.

conceivable

the prediction positions.

random occurrence

in the positions

The proba-

of

indicated

of 15

these

is

nucleo-

less

than

lQ-? d.

The proposed of the

a-chain

sequence It

loop

is

globin,

rather

may be that

contributes

If

will

secondary

loop

constant

is

region

whose amino acid 1.

among vertebrates

segment of a messenger of a particular

sequence. of human globin

confirm

our prediction

hairpin

a region

a stable

The sequencing 15

the C-terminal

to the retention

amino acid

progress

codes for

or refute

is confirmed, present.

structure

methods used in this

is

messengers our predicted

it

is highly

Furthermore, also

paper

important

it for

combined with

897

now in sequence.

likely

would

that

suggest

nonviral additional

mRNA.

a that The

selection

Vol. 54, No. 3,1973

rules

may then

BIOCHEMICAL

make it

from the many protein We thank their

Drs.

possible

to predict

sequences

availablei.

Jean S. White

comments and criticisms.

the University

AND BIOPHYSICAL

and William

RESEARCH COMMUNICATIONS

messenger sequences

P. Winter

This work was supported

for by

of Delaware.

REFERENCES 1. 2. 3. 4. 5. 6. 7. 8. 9. 10 . 11. 12. 13. 14. 15. 16.

Dayhoff, M. O., Atlas of Protein Sequence and Structure, Nationalmedical Research Foundation, Silver vol. 4. Spring, Md. 543 pp (1972). Fellner, P., Ehresmann, C., Stiegler, P., and Ebel, J.-P., Nature New Biology, 239, 1 (1972). -Adams, J. M., Jeppeson, P. G. N., Sanger, F., Barrell, B. C., Cold e. Harb. e. 34, 611 (1969). -Quant. Biol., Fitch, W. M. and Margoliash, E., Evol. Biol., =$, 67 (1970). -White, III, H. B., Laux, B. E., and Dennis, D., Science, 175, 1264 (1972). Mark, A. J. and Petruska, J. A., J. Mol. Biol., 72, 609 (1972). Min Jou, W., Haegeman, G., Ysebae&,x, and FieE, W., Nature, 237, 82 (1972). Natl. Acad. Sci. U.S., Kaempfer,. and Kaufman, J., PE. ---70, 1222 (1973). Eanni, A. M., Giglioni, B., Ottolenghi, S., and Comi, P., Nature New Biology, 240, 183 (1972). -Clegg, J. B., Weatherall, D. J., and Milnor, P. F., Nature, 234, 337 (1971). ad-Akhavan, M., Winter, W. P., Abramson, R. K., and Rucknagel, D. L., Blood, 40, 927 (1972). Fitch, W. M., J. Molec. Evolution, 1, 185 (1972). Sci U.S., Delisi, C. and-Crothers, D. M., 6. Natl. e. -. 68, 2682 (1971). %oco Jun, I., Uhlenbeck, 0. C., and Levine, M. D., Nature, 230, 362 (1972). zotta, C. A., Verma, I. M., McCaffery, R. P., and Forget, B. G., -Fed. Proc. 32, 455 (1973). Kleinauer, E. F., Reynolds, C. A., Duzy, A. M., Wilson, J. B., Moores, R. R., Berenson, M. P., Wright, C. S., Hnisnan, T. H. J., Biochem. Biophys. Acta, 154, 220 (1968). -x

898