P oc.
Na l.
Acad.
Sci.
USA
Vol.
93,
pp.
8485-8489,
Augus
1996
E olu ion
T ansloca ion
e en s
in
he
e olu ion
o
aminoacyl-
RNA
syn he ases
(his idyl- RNA
syn he ase/Fugu
ub ipes)
SYDNEY
BRENNER*
AND
Luis
M.
CORROCHANO
Molecula
Gene ics,
Depa men
o
Medicine,
Uni e si y
o
Camb idge
School
o
Clinical
Medicine,
Hills
Road,
Camb idge
CB2
2QQ,
Uni ed
Kingdom
Con ibu ed
by
Syndey
B enne ,
Ma ch
19,
1996
ABSTRACT
We
ha e
cha ac e ized
hisS,
he
gene
encod-
ing
he
his idyl- RNA
syn he ase
(HisRS)
om
he
e aodon-
oid
ish
Fugu
ub ipes.
The
hisS
gene
is
abou
3.5
kbp
long
and
con ains
13
exons
and
12
in ons
o
172
bp,
on
a e age.
The
Fugu
hisS
gene
encodes
a
pu a i e
p o ein
o
519
amino
acids
wi h
he
h ee
mo i s
iden i ied
as
signa u es
o
class
2
aminoacyl- RNA
syn he ases.
A
model
o
he
shi ing
o
in on
8
be ween
Fugu
and
hams e
is
p oposed
based
on
he
successi e
appea ance
o
a
c yp ic
splicing
si e
ollowed
by
an
inse ion
mu a ion
ha
c ea ed
a
new
accep o
si e.
In
addi-
ion,
sequence
compa isons
sugges
ha
he
hisS
gene
has
unde gone
a
ansloca ion
h ough
he
i s
in on.
As
a
esul ,
he
Fugu
HisRS
has
an
N- e minal
sequence
ma kedly
di e en
om
ha
in
he
human
and
hams e
enzymes.
We
p opose
ha
simila
e en s
ha e
been
esponsible
o
a ia-
ions
a
he
N- e minal
end
o
o he
aminoacyl- RNA
syn-
he ases.
Ou
analysis
sugges s
ha
his
in ol es
exchanges
h ough
in ons
o
wo
exons
encoding
an
ances al
32-amino
acid
mo i .
Aminoacyl- RNA
syn he ases
join
an
amino
acid
o
i s
co e-
sponding
RNA
and
a e
esponsible
o
he
speci ici y
o
he
ansla ion
p ocess
(1,
2).
Since
aminoacyl- RNA
syn he ases
a e
key
componen s
o
he
con empo a y
p o ein-syn hesis
appa a us,
i
is
possible
ha
knowledge
o
he
s uc u e
o
genes
encoding
hese
enzymes
migh
con ain
clues
o
he
e olu ion
o
p o ein
syn hesis.
I
is
known
ha
many
o
he
aminoacyl- RNA
syn he ases
ha e
ela ed
sequences,
and
he
20
enzymes
ha e
been
g ouped
in o
wo
classes
based
on
exclusi e
se s
o
sequence
mo i s
(3).
Class
1
is
cha ac e ized
by
he
amino
acid
sequences
"HIGH"
and
"KMSKS"
and
ha e
a
nucleo ide
binding
old
simila
o
ha
ound
in
o he
nucleo ide-binding
p o eins;
class
2
syn he ases
ha e
h ee
consecu i e
mo i s
and
an
ac i e
si e
based
on
a
se en-s anded
an ipa allel
13-shee
(2,
4-7).
Aminoacyl- RNA
syn he ases
con ain
sepa able
s uc u al
domains
wi h
di e en
unc ions
(8).
Sequence
compa isons
and
phylogene ic
analysis
ha e
been
used
o
deduce
he
likely
e olu iona y
his o y
o
aminoacyl-
RNA
syn he ases
and
sugges s
ha
he
con empo a y
en-
zymes
in
he
wo
classes
migh
ha e
a isen
by
gene
duplica ion
om
single
ances o s
(9).
The
genomic
s uc u e
o
he
genes
encoding
hese
enzymes
is
likely
o
help
in
he
elucida ion
o
hei
e olu iona y
o igins,
and
he
posi ion
o
in ons
migh
e eal
ela ionships
no
easily
ound
in
sequence
compa isons.
In on
posi ions
a e
only
known
o
he
human
glu amyl-p olyl- RNA
syn he ase
(Glu-
P oRS),
a
single
gene
encoding
he
wo
ac i i ies
in
a
usion
p o ein
(10),
human
yp ophanyl- RNA
syn he ase
(T pRS)
(11),
Caeno habdi is
elegans
his idyl- RNA
syn he ase
(HisRS)
(12),
and
hams e
HisRS
(13).
The
genome
o
he
e aodon oid
ish
Fugu
ub ipes,
wi h
abou
400
Mbp
and
small
in ons,
is
7.5
imes
smalle
han
he
human
genome
(14).
The
ela i e
small
size
o
his
e eb a e
genome
allows
he
easy
cloning
and
sequencing
o
genes
om
genomic
lib a ies,
and
genomic
s uc u es
can
be
apidly
ound.
To
alida e
his
app oach
o
aminoacyl- RNA
syn-
he ases,
we
selec ed
he
HisRS
encoding
gene
whose
in on
s uc u e
is
known
in
hams e
and
C.
elegans
(12,
13).
We
epo
he
genomic
s uc u e
o
he
Fugu
HisRS
gene.
A
compa ison
o
he
in on
posi ions
in
HisRS
wi h
o he
aminoacyl- RNA
syn he ases
p o ides
e idence
o
ela i ely
ecen
ansloca ion
e en s
in
he
e olu ion
o
hese
enzymes.
MATERIALS
AND
METHODS
Cloning
and
Sequencing
he
Fugu
hisS
Gene.
PCR
(15)
was
pe o med
wi h
wo
se s
o
nes ed
p ime s
designed
o
anneal
o
conse ed
a eas
o
hisS,
he
gene
encoding
HisRS.
The
p ime s
used
we e
HislF,
5'-GAYACNCCNGTNTTYGA-3',
co esponding
o
he
amino
acid
sequence,
DTPVFE,
in
he
human
HisRS
(13,
16);
His1R,
5'-CCNGTRTARTARTC-3',
GTYYD;
His2F,
5'-TAYCAYATHGCNAARGT,
YHIAKV;
and
His2R,
5'-TTYTTNACYKCYTCCCA-3',
K/NKVE/
AEW.
Taq
polyme ase
(Pe kin-Elme /Ce us)
was
used
wi h
1.5
mM
Mg2+
o
ampli y
and
clone
a
segmen
o
he
Fugu
hisS
gene,
which
was
e i ied
by
sequencing.
A
A2001
Sau3AI
Fugu
genomic
lib a y
(14)
was
sc eened wi h
he
hisS
agmen
using
he
me hod
o
Chu ch
and
Gilbe
(17).
A
phage
designa ed
AHis
was
ob ained
ha
con ained
he
Fugu
hisS
gene
and
was
con i med
by
PCR.
The
15
kbp
o
Fugu
DNA
om
AHis
was
subcloned
and
sequenced
by
he
chain- e mina ion
me hod
(18)
using
syn he ic
oligonucleo ides
as
p ime s.
The
hisS
coding
sequences
we e
iden i ied
by
simila i ies
wi h
o he
HisRS
by
using
he
p og am
BLAST
(19)
accessed
om
he
Human
Genome
Mapping
P og am
Resou ce
Cen e
(Ha -
ow,
U.K.).
Cloning
cDNAs
Encoding
Fugu
HisRS
by
PCR.
To al
Fugu
RNA
isola ed
om
muscle
was
used
o
cDNA
syn hesis
as
desc ibed
(20).
PCR
was
pe o med
using
1-2
,ul
o
he
cDNA
mix
and
se e al
se
o
p ime s:
His7W5
(5'-CATAGCGTT-
TCCTGTTC-3')
and
His2W2
(5'-ATAAAACTCTCTATA-
ACGTC-3'),
His7W8
(5'-GCTGAACCTTCATCCTC-3')
and
His2W2,
and
HisAF
(5'-TGACAACCCAGCCATGACCC-
3')
and
His6W12
(5'-TGCGAGTCTGAATGGCG-3').
The
i s
wo
se s
o
p ime s
we e
used
o
ampli y
he
5'
end
o
he
gene
whe eas
he
las
se
was
used
o
ampli y
he
3'
end.
The
ampli ied
DNA
was
cloned
and
sequenced
by
he
chain-
Abb e ia ions:
HisRS,
his idyl- RNA
syn he ase;
GluP oRS,
glu-
amyl-p olyl- RNA
syn he ase;
T pRS,
yp ophanyl- RNA
syn-
he ase;
GlyRS,
glycyl- RNA
syn he ase.
Da a
deposi ion:
The
sequence
epo ed
in
his
pape
has
been
deposi ed
in
he
GenBank
da a
base
(accession
no.
Z54243)
*To
whom
ep in
eques s
should
be
sen
a
he
p esen
add ess:
King's
College,
Camb idge
CB2
1ST,
Uni ed
Kingdom.
P esen
add ess:
Depa amen o
de
Gene ica,
Uni e sidad
de
Se illa,
Apa ado
1095,
E-41080
Se illa,
Spain.
8485
The
publica ion
cos s
o
his
a icle
we e
de ayed
in
pa
by
page
cha ge
paymen .
This
a icle
mus
he e o e
be
he eby
ma ked
"ad e isemen "
in
acco dance
wi h
18
U.S.C.
§1734
solely
o
indica e
his
ac .
8486
E olu ion:
B enne
and
Co ochano
e mina ion
me hod
(18)
by
using
syn he ic
oligonucleo ides
as
p ime s.
RESULTS
The
simila i y
be ween
human
and
Fugu
HisRS
allowed
he
iden i ica ion
o
coding
sequences
and
in ons
in
he
hisS
gene
sequence.
The
posi ion
o
in ons
was
u he
con i med
by
sequencing
h ee
o e lapping
clones
con aining
a
Fugu
hisS
cDNA
om
407
bp
ups eam
o
he
pu a i e
ini ia o
me hi-
onine
o
65
bp
downs eam
o
he
s op
codon.
The
cDNA
clones
con ained
se e al
in- ame
s op
codons
ups eam
o
he
i s
me hionine,
and
he
s op
codon
in
he
las
exon,
con i m-
ing
he
coding
sequence
p edic ed
by
simila i ies
wi h
human
and
hams e
HisRS
(13,
16).
The
hisS
gene
comp ises
13
exons
and
12
in ons
in
abou
3.5
kbp
(Table
1).
The
coding
sequence
has
a
G+C
con en
o
48.9%,
and
he
in onic
DNA
has
a
G+C
o
36.5%.
In ons
in
he
Fugu
hisS
gene
ollow
he
GT/AG
ule.
All
in ons
a e
in
posi ion
0
(be ween
codons)
excep
in on
8,
which
is
in
posi ion
1,
a e
he
i s
nucleo ide
o
he
codon.
The
a e age
in on
size
is
172
bp,
bu
mos
in ons
a e
abou
100
bp
in
leng h
(Table
1).
The
Fugu
hisS
gene
encodes
a
pu a i e
p o ein
o
519
amino
acids
wi h
he
h ee mo i s
iden i ied
as
signa u es
o
class
2
aminoacyl- RNA
syn he ases
( esul
no
shown).
As
in
he
hams e
gene,
he
posi ion
o
in ons
in
he
Fugu
hisS
gene
a e
loca ed
close
o
known
unc ional
and
s uc u al
domains.
The
Fugu
HisRS
is
e y
simila
o
i s
human
coun e pa :
83.5%
o
he
esidues
a e
simila
and
72.3%
a e
iden ical.
The
simila -
i ies
ex end
h oughou
he
whole
p o ein,
bu
he
amino
end
is
ma kedly
di e en
be ween
he
wo
enzymes.
In e es ingly,
an
in on
is
p esen
be ween
he
segmen
o
low
simila i y
and
he
es
o
he
gene,
sugges ing
ha
he
i s
exon
and
he
es
o
he
gene
migh
ha e
di e en
e olu iona y
o igins
(Fig.
1).
We
could
no
ind
any
signi ican
simila i y
be ween
he
amino
acid
sequence
o
he
i s
exon
o
Fugu
HisRS
and
any
o he
p o ein
in
he
P o ein
Iden i ica ion
Resou ce
and
SwissP o
da a
bases.
DISCUSSION
I
we
de ine
he
leng h
o
a
gene
om
he
ini ia o
codon
o
he
s op
codon,
hen
he
Fugu
hisS
gene
is
3.5
kbp
long
as
compa ed
wi h
he
hams e
gene
which
is
18
kbp
in
leng h
(13).
Bo h
genes
con ain
12
in ons
and
13
exons.
As
shown
in
Table
1,
he
leng hs
o
he
coding
sequence
a e
simila ,
abou
1.5
kbp;
hus
he e
is
an
eigh - old
expansion
o
in on
leng hs
in
he
hams e
gene.
Mos
o
he
in ons
in
he
Fugu
gene
a e
small;
10
a e
150
bp
o
less.
O he
Fugu
genes
con ain
simila ly
small
P oRS-Human
P oRS-D osophila
T pRS-Human
GlyRS-Human
GlyRS-Bombyx
HisRS-Human
HisRS-Hams e
HisRS-Fugu
H03-Human
Table
1.
Size
o
exons
and
in ons
in
he
HisRS
encoding
gene
o
Fugu
and
hams e
Exon
size,
bp*
In on
size,
bp
No.
Fugu
Hams e
Fugu Hams e
1
2
3
4
5
6
7
8
9
10
11
12
13
To al
105
90
120
96
126
108
99
94
128
273
117
147
57
1560
90
90
120
96
125
109
99
99
122
240
117
145
72
1524
120
240
150
7,500
105
1,800
665
1,100
102
1,000
72
120
128
350
120
2,900
80
100
129
180
86
300
306
900
2063
16,500
Hams e
da a
ha e
been
aken
om
Tsui
and
Simino i ch
(13).
*The
limi s
o
he
i s
and
he
las
exons
co espond
o
he
p edic ed
coding
sequences.
The
size
o
he
las
in on
in
hams e
has
been
es ima ed
om
he
o al
leng h
o
he
HisRS
encoding
gene
(13).
in ons
(14,
21-23).
The
di e ence
in
he
leng h
o
in ons
can
accoun
o
a
majo
pa
o
he
o e all
educ ion
o
genome
size
o
Fugu.
All
he
in ons
in
he
Fugu
hisS
gene
a e
in
he
same
posi ion
as
in
he
published
hams e
sequence
(13),
excep
o
in on
8
which
is
shi ed
5
bp
ela i e
o
he
hams e
in on.
The
sequence
a ound
he
5'-splicing
si e
o
in on
8
in
Fugu
is
he
same
as
he
3'
end
o
hams e
exon
7
(Fig.
2).
We
sugges
ha
he
shi ing
o
in on
8
can
be
explained
by
he
ollowing
plausible
sequence
o
e en s.
The
Fugu
sequence
is
aken
o
be
he
ances al
o m.
A
c yp ic
mu a ion
in
he
in on
c ea ing
an
al e na i e
dono
(GT)
splicing
si e
could
be
hen
ollowed
by
an
inse ion
mu a ion
in-
he
exon
c ea ing
a
new
ac i e
"AG"
accep o
si e.
I
has
been
cus oma y,
in
he
compa ison
o
in on
posi ions,
o
assume
ha
in ons
in
di e en
homol-
ogous
genes
ha
occupy
posi ions
close
o
each
o he ,
ega d-
less
o
phase,
ep esen
he
same
o iginal
in on,
one
ep e-
sen a i e
ha ing
mo ed
by
an
unde ined
p ocess
o
in on
sliding.
This
has
been
igh ly
c i icized,
and
hese
cases
ha e
been
used
as
e idence
o
independen
inse ions
(24-26).
We
a e
o una e
he e
o
be
able
o
p o ide
a
plausible
basis
o
an
in on
shi
which
has
occu ed
ela i ely
ecen ly.
The
i s
wo
exons
o
he
human
HisRS
gene
encode
a
32-amino
acid
epea
sequence
ha
is
also
p esen
a
he
N- e minal
ends
o
euka yo ic
HisRS,
T pRS,
and
glycyl-
--
__-----------
epea
--------------
*
*
*
**
*
**
*
**
*
*
.~~~~~~~~~~.
. .
.
.
...
.
.
. .
....... ....
672-CTTSEDSLVLYNRVAVQGDV.VRELKAKKAPK
ED
VDAA
VKQLLSLKAEYKEKTGQEYKPGNPPA
EIGQNISSNSSASIL
ESKSLYDEVAAQGEV.VRKLKAEKSPK=AK
INEA
VECLLSLKAQYKEKTGKEYIPGQPPL
SQSSDSSPTRNSEPAGLETP
EAKVLFDKVASQGEV.VRKLKTEKAPK=DQ
VDIA
VQELLQLKAQYKSLIGVEYKPVSATG
AEDKDKKKKEKENKSEKQNK
1118-AKDELTQEINAQGEK.VRAAKGNKAAK
EV
IDAE
VAKLLALKAKYKEVTGTDF.PVAGRG
GGGGGGSAKKAPKEAQPKPA
1-MPNSEPASLLELFNSIATQGEL.VRSLKAGNASK=DE
IDSA
VKMLVSLKMSYKAAACEDYKADCPPG
NPAPTSNHGPDATEAEEDFV
1-MDGAGAEEVLAPLRLAVRQQGDL.VRKLKEDKAPQ
VD
VDKA
VAELKARKRVLEAKELALQPKDDIVD
RAKMEDTLKRRFFYDQAFAI
1-MADPKIEEILAPLRANVKEQGDL.VRKLKEEKAPE
ID
IKKA
VAELKTRKKILEDKELSLAPAEDLFD
RAKMEDLIKRRFFYDQSFSM
1-MAERAALEELVKLQGER.VRGLKQQKASA
EL
IEEE
VAKLLKLKAQLGPDESKQKFVLKTPK
GTRDYSPRQMAVREKVFDVI
1-MASPA.LEELVLNSRHRLVRGLKQQKASA
DQ=IEEE
VAKLLKLKAQLGHDESKQKFVLKTPK=GTRDYSPRQMAVREKVFDVI
1-MLAMHCARVCSVLMGCRTTTRALSIRSFPGVTL
AQ=IDEE
VAKLLELKAHLGGDDGKHQFVLKTAK=GTRDYNPKQMAIREKVFNTI
1-MPLLGLLPRRAWASLLSQLLRPPCASCTGAVRCQ
SQ=VAEA
V.....
LTSQLKAHQEKPNFIIKTPK
GTRDLSPQHMVVREKILDLV
-
-----------
epea ---------------
FIG.
1.
A
epea
in
se e al
aminoacyl- RNA
syn he ases.
The
symbol
"*"
indica es
a
conse ed
amino
acid,
and
he
symbol
"
"
indica es
ha
mos
o
he
amino
acids
in
ha
posi ion
a e
conse ed
among
P oRS
and
T pRS.
In ons
a e
ma ked
by
he
symbol
"="
and
a
gap
in
he
amino
acid
sequence
is
shown
wi h
a
do .
The
posi ion
o
he
in on
in
he
hams e
HisRS
gene
comes
om
Tsui
and
Simino i ch
(13);
he
in on
posi ions
in
he
human
genes
encoding
T pRS,
and
GluP oRS
om
F olo a
e
al.
(11)
and
Kaise
e
al.
(10)
espec i ely,
and
posi ion
o
he
H03
in on
was
ob ained
om
GenBank
(accession
no.
U18936).
Only
he
las
epea
om
he
GluP oRS
o
D osophila
is
shown.
P oc.
Na l.
Acad.
Sci.
USA
93
(1996)
P oc.
Na l.
Acad.
Sci.
USA
93
(1996)
8487
DNA
sequence
a ound
in on
8
o
he
his idyl- RNA
syn he ase
gene
HisRS-Fugu
HisRS-Hams e
HisRS-Human
B
TATGTTGGTATGCAAGg gaa --- c g agGTGGAATGGATTTGGCTGAACGT
TATGTCCAGCAGCACGG1G3g aaa-----gc ccccagGTGTGTCTGGTAGAGCAG
TATGTCCAGCAACATG4GSG
GTATCCCTGGTGGAACAG
Model
o
he
shi
o
in on
8
Taking
he
Fugu
in on
as
he
ances al,
an
A
o
G
change
c ea es
a
c yp ic
splicing
si e
Y
V
G
M
Q
G
G
M
D
L
A
E
R
TATGTTGGTATGCAAGg gaga --- c g agGTGGAATGGATTTGGCTGAACGT
TATGTTGGTATGCAAGg gagg --- c g agGTGGAATGGATTTGGCTGAACGT
An
inse ion
o
a
G
c ea es
a
ameshi
( op)
which
would
be
le hal
unless
he
c yp ic
splicing
si e
becomes
unc ional
(bo om).
Y
V
G
M
Q
G
G
D
G
F
G
STOP
TATGTTGGTATGCAAGg gagg --- c g agGTGGAGATGGATTTGGCTGAACGT
TATGTTGGTATGCAAGGTGAGg --- c g agg ggagATGGATTTGGCTGAACGT
Y
V
G
M
Q
G
E
M
D
L
A
E
R
The
esul
is
a
5
nucleo ide
shi
in
he
posi ion
o
he
in on
bu
only
a
G
o
E
mu a ion
in
he
amino
acid
sequence
old
Y
V
G
M
Q
G
G
M
D
L
A
E
R
new
Y
V
G
M
Q
G
E
M
D
L
A
E
R
FIG.
2.
In on
shi
in
he
hisS
gene.
(A)
Compa ison
o
he
sequence
a ound
in on
8
in
Fugu,
human,
and
hams e
HisRS
encoding
genes
is
shown.
Lowe case
le e s
deno e
in on
sequence,
and
uppe case,
exon
sequence.
The
segmen
o
he
Fugu
in on
8
iden ical
o
hams e
exon
sequence
is
in
bold ace
ype.
The
human
and
hams e
sequences
we e
ob ained
om
Tsui
and
Simino i ch
(13).
(B)
A
model
o
he
shi
o
in on
8.
A
c yp ic
splicing
si e
is
c ea ed
by
an
A
o
G
mu a ion,
and
an
inse ion
o
a
G
c ea es
a
ameshi
ha
would
be
le hal
unless
he
c yp ic
splicing
si es
becomes
unc ional,
esul ing
in
an
in on
shi .
Nucleo ide
changes
a e
in
bold ace
ype
and
ma ked
by
a ows.
RNA
syn he ase
(GlyRS),
bu
absen
in
hei
bac e ial
coun-
e pa s
( e s.
16,
27,
and
28;
Fig.
1).
Se e al
copies
o
he
same
epea
a e
also
p esen
a
he
N- e minal
end
o
he
P oRS
coding
egion
o
he
GluP oRS
o
human
and
D osophila
(29,
30).
The
p esence
o
a
conse ed
sequence
in
di e en
ami-
noacyl- RNA
syn he ases
sugges s
ha
hey
had
a
common
o igin
(8,
28,
31).
The
DNA
sequence
encoding
he
epea
is
spli
by
an
in on
in
he
genes
encoding
hams e
HisRS
and
human
T pRS,
and
in
wo
o
he h ee
epea s
o
he
human
GluP oRS
(Fig.
1).
Al hough
he
posi ion
o
his
in on
di e s
by
wo
codons
in
he
P oRS
and
HisRS
genes,
we
will
ea
i
as
he
same
in on.
I
is
emp ing
o
specula e
ha
his
in on
migh
also
be
p esen
in
a
simila
loca ion
in
he
e eb a e
genes
encoding
GlyRS.
The
unc ion
o
he
epea
is
no
known,
bu
he
i s
wo
exons
o
he
gene
encoding
human
HisRS,
including
he
epea ,
a e
necessa y
o
enzyma ic
ac i i y
(28).
Howe e ,
in
he
case
o
he
human
T pRS
gene,
al e na i e
splicing
elimina es
he
exon
encoding
he
i s
hal
o
he
epea
wi hou
loss
o
unc ion
(32).
The
p esence
o
he
epea
as
well
as
he
in on
in
he
gene
encoding
T pRS,
a
class
1
enzyme,
sugges s
ha
his
sequence
sha es
a
common
o igin
wi h
he
same
wo
exons
o
he
genes
encoding
human
P oRS,
and
HisRS
class
2
enzymes.
Fig.
1
also
e eals
ha
he
simila i ies
be ween
human
P oRS
and
T pRS
ex end
beyond
he
epea
and
end
a
a
posi ion
whe e
ano he
in on
is
p esen
in
he
human
HisRS
gene.
We
can
bes
explain
hese
esul s
by
assuming
ha
he
wo-exon
epea
was
p esen
in
he
ances o
gene
ha
ga e
ise
o
a
leas
some,
i
no
all,
o
he
class
2
enzymes,
and
ha
he
T pRS
gene
acqui ed
his
sequence
by
ansloca ion
in o
he
second
in on
o
a
duplica ed
class
2
enzyme
gene
(Fig.
3).
We
ha e
o
explain
he
absence
o
his
in on
om
he
T pRS
gene
by
i s
subse-
quen
loss,
which
is
mo e
plausible
han
an
accu a e
usion
be ween
wo
coding
sequences.
We
hink
hese
e en s
ook
place
a
long
ime
ago,
a
leas
be o e
he
di e gence
o
insec s
and
mammals
as
deduced
om
he
simila i y
o
he
s uc u es
o
P oRS
and
GlyRS.
The
amino
end
o
he
Fugu
HisRS
is
e y
di e en
om
he
human
HisRS,
and
i
only
has
he
second
hal
o
he
32-amino
acid
epea
(Fig.
1).
We
no e
ha
he
i s
in on
clea ly
sepa a es
he
egion
o
low
simila i y
om
he
es
o
he
p o ein,
sugges ing
ha
he
i s
exon
in
he
human
and
Fugu
hisS
genes
had
di e en
e olu iona y
o igins.
We
p opose
ha
he
Fugu
gene
has
been
ansloca ed
h ough
he
i s
in on
om
i s
o iginal
posi ion
in o
a
new
loca ion,
cap u ing
an
exon
and
acqui ing
a
new
sequence
a
i s
amino
end
(Fig.
3).
This
is
suppo ed
by
he
ac
ha
we
could
no
de ec
any
simila i y
be ween
he
5'
ups eam
egions
o
he
human
and
Fugu
hisS
genes.
Such
ansloca ions
may
be
impo an
in
e olu ion,
allowing
coding
sequences
o
acqui e
no el
egula o y
p op-
e ies,
bu
hey
could
also
be
g a ui ous.
In
any
e en ,
we
can
p edic
ha
he
genes
would
occupy
di e en
posi ions
in
he
human
and
ish
genomes.
An
analogous
ansloca ion
seems
o
ha e
occu ed
in
a
sequence
homologous
o
he
human
HisRS
gene,
designa ed
H03
in
Fig.
1,
which
is
ound
jus
ups eam
o
he
gene
bu
in
he
opposi e
o ien a ion
(33).
This
homolog
has
an
amino
end
e y
di e en
om
he
o he
human
and
hams e
HisRS,
wi h
an
in on
sepa a ing
egions
o
high
and
low
simila i y.
Like
Fugu
HisRS,
H03
has
mos
likely
los
he
amino
end
o
he
epea
by
ansloca ion
o
an
in e ed
duplica ion
h ough
he
i s
in on
(Fig.
3).
Since
such
a
sequence
was
no
ound
in
Fugu,
his
is
also
a
compa a i ely
ecen
e en .
Exon
shu ling
has
been
p oposed
as
a
majo
mode
o
he
e olu ion
o
p o ein
di e si y.
I
his
happened
a
a
e y
ea ly
s age
o
p o ein
e olu ion,
hen
he e
needs
o
be
some
co espondence
be ween
p imi i e
exons
and
seconda y
es-
uc u e
elemen s
o
else
mos
o
he
combina ions
would
be
A
E olu ion:
B enne
and
Co ochano
8488
E olu ion:
B enne
and
Co ochano
hypo e ical
ansloca ion
e en s
in
he
e olu ion
o
aminoacyl- RNA
syn he ases
32-aa
epea
exons
es
o
he
gene
in on
loss
ances al
class
2
P olyl- RNA
syn he ase
gene
aminoacyl- RNA
syn he ase
gene
in e ed
duplica ion
and
ansloca ion
&
I
1
/
~~~~H03
I
p
His idyl- RNA
syn he ase
gene
ansloca ion
h oug
L 1 L
IF
he
i s
inl on
E
His idyl- RNA
syn he ase
gene
Luman
Fugu
His idyl- RNA
syn he ase
gene
class
2
aminoacyl- RNA
syn he ase
gene
LIJEx.
ansloca ion
h ough
he
second
in on
in on
loss
T yp ophanyl- RNA
syn he ase
gene
T yp ophanyl- RNA
syn he ase
gene
FIG.
3.
Hypo he ical
ansloca ion
e en s
in
he
e olu ion
o
aminoacyl- RNA
syn he ases.
The
wo
exons
encoding
he
32-amino
acid
epea
and
he
es
o
he
gene
a e
shown
by
g ey
and
ha ched
boxes,
espec i ely.
An
ances al
class
2
aminoacyl- RNA
syn he ase
gene
con aining
he
wo
exons
encoding
he
32-amino
acid
epea
ga e
ise
o
he
genes
encoding
a
leas
P oRS
and
HisRS.
P esen -day
P oRS
in
animals
con ain
se e al
copies
o
he
epea
and
is
used
o
he
gene
encoding
GluRS
(no
shown).
The
gene
encoding
HisRS
su e ed
an
in e ed
duplica ion
and
a
ansloca ion
in
he
human
lineage
esul ing
in
wo
genes
in
opposi e
o ien a ion.
The
ansloca ion
migh
ha e
occu ed
h ough
he
i s
in on
esul ing
in
he
cap u ing
o
a
new
exon
in
he
H03
gene
(HisRS
homolog).
In
he
ish
lineage,
a
ansloca ion
h ough
he
i s
in on
allowed
he
cap u ing
o
a
new
exon
in
he
Fugu
HisRS
gene.
The
human
T pRS
gene
(a
class
1
enzyme)
has
cap u ed
he
wo
exons
epea
by
ansloca ion
in o
a
class
2
gene.
A
u he in on
loss
esul ed
in
he
p esen -day
s uc u e
o
he
human
T pRS
gene.
useless.
Whe he
a
esidue
o
his
is
s ill
p esen
in
con em-
po a y
genes
is
s ill
a
ma e
o
deba e
(25,
26,
34-37).
Howe e ,
usion
o
la ge
p o ein
domains
would
also
be
acili a ed
by
exchanges
h ough
in ons,
which
is
less
demand-
ing
han
he
ecombina ion
o
coding
sequences.
The e
a e
many
examples
o
his
in
he
s uc u e
o
complex
genes,
and
in
many
ins ances
an
in on
can
be
ound
o
ma k
he
bounda y
be ween
wo
di e en
la ge
domains
(38).
We
p e e
o
call
hese
e en s
ansloca ions,
a he
han
using
he
loose
e m
o
exon
shu ling,
since
we
wan
o
emphasize
ha
his
is
a
ecombina ion
p ocess
which
mus
lead
o
a
change
in
he
posi ion
o
a
gene
in
he
genome.
We
also
belie e
ha
such
a
ansloca ion
will
p o e
o
be
he
majo
sou ce
o
e olu iona y
di e si y
in
he
e olu ion
o
complex
o ganisms.
Th ough
i ,
no el
pa hs
o
gene
egula ion
can
be
explo ed.
Since
many
genes
con ain
in ons
in
hei
5'
un ansla ed
sequences,
ansloca ion
h ough
hese
in ons
would
be
he
bes
way
o
achie e
such
ansloca ions,
because
he
exchange
p ocess
need
no
depend
on
he
phases
o
he
ecombining
in ons.
Since
he
posi ion
o
a
gene
in
a
genome
changes
as
a
consequence
o
ansloca ion,
he
compa a i e
s udy
o
genome
s uc u es
migh
con ain
impo an
clues
o
he
e olu ion
o
complex
unc ions,
e en
hough
many
o
hese
ansloca ion
e en s
may
no
be
p oduc i e
bu
g a ui ous.
Aminoacyl- RNA
syn he ases
a e
old
p o eins
and
a e
com-
posed
o
se e al
s uc u al
and
unc ional
mo i s
(8).
We
ha e
ound
ha
gene
ansloca ion
appea s
as
he
likely
mechanism
esponsible
o
he
di e gence
in
simila i y
a
he
amino
end
be ween
Fugu
and
human
HisRS.
The
ele ance
o
ansloca-
ions
in
he
e olu ion
o
aminoacyl- RNA
syn he ases
can
only
be
assessed
as
mo e
esul s
a e
ob ained
on
he
genomic
s uc u e
o
he
genes
encoding
hese
p o eins.
We
ha e
shown
ha
he
Fugu
genome,
wi h
small
in ons,
is
an
a ac i e
al e na i e
o
he
ask.
We
hank
D s.
G.
Elga
and
B.
Venka esh
o
he
Fugu
DNA
and
genomic
lib a y,
and
he
Fugu
RNA,
espec i ely.
L.M.C.
was
sup-
po ed
by
a
Wellcome
T us
Pos doc o al
Fellowship.
This
wo k
was
done
in
he
Medical
Resea ch
Council
Molecula
Gene ics
Uni ,
which
was
closed
in
1992.
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P.
(1987)
Annu.
Re .
Biochem.
56,
125-158.
2.
Ca e ,
C.
W.
(1993)
Annu.
Re .
Biochem.
62,
715-748.
3.
E iani,
G.,
Dela ue,
M.,
Poch,
O.,
Ganglo ,
J.
&
Mo as,
D.
(1990)
Na u e
(London)
347,
203-206.
4.
Bu baum,
J. J.
&
Schimmel,
P.
(1991)
J.
Biol.
Chem.
266,
16965-16968.
5.
Mo as,
D.
(1992)
T ends
Biochem.
Sci.
17,
159-164.
6.
E iani,
G.,
Ca a elli,
J.,
Ma in,
F.,
Ado ,
L.,
Rees,
B.,
Thie y,
J.-C.,
Ganglo ,
J.
&
Mo as,
D.
(1995)
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E ol.
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499-508.
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M.
&
Cusack,
S.
(1995)
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Mol.
E ol.
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519-530.
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Dela ue,
M.
&
Mo as,
D.
(1993)
Bioessays
15,
675-687.
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Na l.
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USA
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(1996)
P oc.
Na l.
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USA
93
(1996)
8489
9.
Nagel,
G.
M.
&
Dooli le,
R.
F.
(1995)
J.
Mol.
E oL
40,487-498.
10.
Kaise ,
E.,
Hu,
B.,
Beche ,
S.,
Ebe ha d,
D.,
Sch ay,
B.,
Baack,
M.,
Hameis e ,
H.
&
Knippe s,
R.
(1994)
Genomics
19,
280-
290.
11.
F olo a,
L.
Y.,
G igo ie a,
A.
Y.,
Sudomoina,
M.
A.
&
Kissele ,
L. L.
(1993)
Gene
128,
237-245.
12.
Amaa ,
Y.
G.
&
Baillie,
D.
L.
(1993)
Nucleic
Acids
Res.
21,
4344-4347.
13.
Tsui,
F.
W.
L.
&
Simino i ch,
L.
(1987)
Nucleic
Acids
Res.
15,
3349-3367.
14.
B enne ,
S.,
Elga ,
G.,
Sand o d,
R.,
Mac ae,
A.,
Venka esh,
B.
&
Apa icio,
S.
(1993)
Na u e
(London)
366,
265-268.
15.
Saiki,
R.
KI,
Gel and,
D.
H.,
S o el,
S.,
Scha ,
S.
J.,
Higuchi,
R.,
Ho n,
G.
T.,
Mullis,
K
B.
&
E lich,
H.
A.
(1988)
Science
239,
487-491.
16.
Raben,
N.,
Bo iello,
F.,
Amin,
J.,
Ho wi z,
R.,
F ase ,
D.
&
Plo z,
P.
(1992)
Nucleic
Acids
Res.
20,
1075-1081.
17.
Chu ch,
G.
M.
&
Gilbe ,
W.
(1984)
P oc.
Na l.
Acad.
Sci.
USA
81,
1991-1995.
18.
Sange ,
F.,
Nicklen,
S.
&
Coulson,
A.
R.
(1977)
P oc.
Na l.
Acad.
Sci.
USA
74,
5463-5467.
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E olu ion:
B enne
and
Co ochano