Evolutionary grouping of the RAS-protein family

Vol.

176,

No.

May

15, 1991

BIOCHEMICAL

3, 1991

AND

RESEARCH

COMMUNICATIONS Pages

EVOLUTIONARY George

T.

GROUPING

Drivas,

OF

Stephen and

February

28,

RAS-PROTEIN

Palmieri, G.

of

FAMILY

Peter

D'Eustachio

Rush

School

York,

1130-1135

Biochemistry,

University New

THE

Mark

Department York

New

Received

BIOPHYSICAL

New

of

York,

Medicine,

10016

1991

Over 50 proteins related to the mammalian H-, K-, and N-RAS GTP binding and hydrolyzing proteins are known. These relatively low molecular weight proteins are usually grouped into four subfamilies, termed true RAS, RAS-like, RHO, and RAB/YPT, based on the presence of shared amino acid sequence motifs in addition to those involved in guanine nucleotide binding. Here, we apply parsimony analysis to the overall amino acid sequences of these proteins to infer possible phylogenetic relationships among them. 0 1991 Academic Press, Inc.

The

RAS

overall ancestral both

true

1,3).

RAS), we

relationships

AND

I

reported)

were

and

devised

by be

trees proteins,

accumulation

Gene

Analysis true to

of

these

include of and

domains four

RHO

true

could

conversion

of into

RAS),

homology

have

generated and

to

of

conserved

subfamilies (about

RAS) to

termed

35%

(for

proteins

in

required

RAS

more 15

than

homology

reviews,

see

analyze

0006-291X/91 $1.50 Copyright 0 1991 by Academic Press. Inc. All rights of reproduction in any form reserved.

the

program

one

change

were

with

the

that

proteins respectively.

was Figures

then l-3

considered

of

amino

those acid

optimized PROTPARS

any

program

changes

of

amino

only nucleotide Thus if two proteins

recognizes at

seguencee and

75%

subfamily,

and considers substitutions.

shown),

1130

(about

(5)

insists

subfamily.

RAS-like

proteins,

analysis

representative

not each

and

acid

position,

each

program

program code,

amino

(data

RAB/YPT

parsimony

membere

For

GAP

genetic

acid

family

study. the

This

the

within for

fx

this

with

classified

sequences

RAS

in

result

subfamilies of

family

the

whose a common

subfamilies.

(6).

amino

reliably

recognized number

analyzed

with

given

a

may

program

the

subjected

that

difference

30%

representative

Felsenstein

consistent

at

of

the

as

well

family

to

sequences

generated

then

J.

substitutions differ

77

alignments

manually,

(about

all

lists

that

sequence

homology

entire

of

as

insertions. the

kd) from

history

possible. of

(20-30

evolution

DISCUSSION

Table

acids

the

within

RESULTS

50%

RAB/YPT

use

also

GTPases

suggest

and

division

(about

and

Here,

are allows

RAS-like

small

duplications, deletions,

sequence

RAS,

various sequences

evolutionary

recent

transmission

acid

for

acid

The

more

substitutions,

interspecies amino

codes amino

(1,2,3,4). and

nucleotide

to

family and

gene ancient

true

gene

structures

the

that

this

nucleotide into

used

to

show as

level.

the the

The

four

analyze

a larger

parsimony

a group,

for

RliO

Vol.

176,

No.

BIOCHEMICAL

3, 1991

AND

BIOPHYSICAL

Table

RESEARCH

COMMUNICATIONS

I

RAS GENE FAMILY I.

&B

subfamily

As-rae Dm-raal Xl-ram Fi-r-as II.

(9) 1::;

Rag-like

(20) (21) (22) (23) (20)

Bo-smg2la

Hu-raplb Bo-smg2lb Hu-rap2a Rho

Hu-ralB Dm-ras2 Mu-Rras Hu-Rrae Hu-TC21

(28) (29) (30) (30) (31)

Ca-rho1 Hu-rhoA Hu-rhoB Hu-rhoC

(33) (39) (40) (40)

Ca-rabl0 Ca-rab8 SP-YPt2 Dd-sasl Dd-sas2 SC-SEC4 Bo-smg25C(56) Bo-•mg25B(56) Hu-rab3b Bo-•mg25A(56) Ra-rab3 Hu-rab3a

(33) (33) (53) (54) (54) (55)

y;

-

Hu-rap2b Dm-ras3 ;z;-';'

(24) (25)

(26)

(27) (28)

Hu-ralA

subfamily

Hu-racl Ca-racl Hu-rac2 Hu-en7 Hu-TClO IV.

(17) (18)

subfamily

Hu-rapla

III.

;y;s

(12)

Dd-rasG sc-RASl

Hu-G25 SC-CDC42 sc-RHO2 SC-RHO1 Ap-rho

I::; Ii:; (31)

RablYPT

subfamily

Sc-Sarl Hu-TC4 Ca-rabl Ra-BRLras Sp-ryhl Hu-rab6 Ca-rab5 Hu-rab5 At-ara SP-YPt3 Ca-rabll Hu-YL8

Ca-rab4b

(33)

;:I;:;; Ra-rab2 Ca-tab2 Hu-tab2 SC-YPTl SP-YPtl Ra-rablb Mu-Yptl Ra-rabla Hu-rabl

;g ; (49) (42) (45) (50) (47) (51) (52) (49) (45)

(45) (49) (45)

1 to 3. References to aeguences are RAS-proteins analyzed in Figs. in parentheses. The first two letters of each family member indicate the source of the protein. Hu, human; Bo, bovine; Dm, Drosophila melanogaster; Saccharomyces cerevisiae (yeast); So, Saguinus Oedipus (simian); As, Artemia salina (shrimp); Xl, Xenopus laevis (toad); Fi, fish; Dd, Dictyostelium discodium (slime mold); Sp, Schizosaccharomyces pombe, (yeast); Mu, murine; (mollusc); Ca, canine; Ra, rat; At, Arabidopsis thaliana (plant). AP, Aplysia

It

is

important

proportional

to

parsimony in

program

which

and/or

the

can

changes

phylogeny, are not

that

the and

branch have

in

some

cases,

the

branch

distance,

and

over

that

the

the

The

species

accurate

analysis.

different

species, need not

be In

such of

timo

change

in

homologous

performing

different

rates.

represent

groupings

with

essence,

which the phylogenetic

overall tree.

topologies

the the

a strong are

same

trees

RAS function

presented

bias close

towards to

1131

those

to

requires

that

a branch

branches assumed

the too

RAS

proteins here

the

great

from be

be

considered

a true

of such

an

two

m evolving

relationships, for

phylogeny for

the

may

should

amino

divergence

within thus

time

the

proteins

phylogenetic expected

few of

of

for

often

and

trees

proportional

in

different

are not This

phylogenetic

are

involved

times

these trees symmetrically.

construct

1 to 3 are in Figs. two highly homologous

addition, two highly

of

a construction

evolutionary

covered In or

to (nodes)

but of

lengths been drawn

points

lengths

rates

different.

biological

species,

time, used,

to

occur

very

note

be

distances

evolutionary

acid

the

to

evolutionary

SC,

at to in

Vol.

176,

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Hu-rap2b

Hu-raplb/Ba-sm,?Zlb

, 68%

87% Fi-ras w

88% 95%

It-

Fia. 1. Comparison of P.&S and MS-like amino acid sequences. The Hu-MB1 sequence is included as an outlying related protein. In those cases where more than one protein is present on a line, they are either identical or exhibit at least 98% sequence identity. The percentages represent either the amino acid identity between two sequences, or the average amino acid identities among Since the parsimony program used to generate this tree more than one sequence. considers the minimum number of nucleotide changes consistent with a given amino acid change, the % amino acid identity alone does not determine the tree topology.

As previously noted, the expected complex evolutionary history of the and conversions) precludes PAS-gene family (involving duplications, mutations, any extensive non-epeculative interpretation of the data shown in Figs. 1 to 3. However, the following three points are worth noting: 1) the overall groupings are generally consistent with those expected on the basis of amino acid sequence homology; 2) certain closely grouped (paired) sequences within the same species such as Hu-rapla/Hu-raplb, Hu-rapZa/Hu-rapZb, Hu-ralA/Hu-ral8 (all in Fig. I), and Hu-racl/Hu-rac2, Hu-rhoA/Hu-rhoC (all in Fig. 2), probably reflect more recent gene duplications; and 3) certain closely grouped sequences between very different species such ae Sp-ypt3/Hu-YL8 and Hurabl/Sc-YPT1 (both in Fig. 3) probably represent interspecfes homologues performing similar if not identical functions. 1132

Vol.

176,

No.

BIOCHEMICAL

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w. included details.

Comparison as an

of outlying

RHO

amino related

AND

BIOPHYSICAL

acid sequences. protein. See

The legend

RESEARCH

Hu-KRAS to Fig.

COMMUNICATIONS

sequence 1 for

is further

HwTC4 Ca-rab7iRa-BRLras I

I

I

I

I

I

I

P

Hu-YLS/Ca-rabll

Ra-rab4/Hu-rab4 Ca-rab2/Hu-rab2iRa-~b2

51% -

Ca-rabl0

8

Grab

.

61%-

6&Z-

5%

-

SC-SEC4

Bo-smgZB/Hu-rab3b

Fia. included details.

3.

Comparison as an outlying

80% -

of

RAE/YPT related

amino protein.

acid

1133

sequences. See legend

to

The Hu-KRAS Fig. 1 for

sequence further

is

Vol.

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1991

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The overall groupings presented in this communication should serve as a framework in which to place, tentatively, newly reported me&era of the family. Most members of the RAS and RAS-like subfamilies are now thought to mediate signal transduction and the regulation of cell growth, and most members of the RAB/YPT subfamily are thought to participate in vesicle sorting A common function of the RHO subfamily remains to (for references, see l-4). be established, but it may be related to the maintenance of cell structure (7,8).

ACKNOWLEDGMENTS We thank Elias Coutavas for many helpful discussions, and Lara Schulman and John Hill of the Research Computing Resource (RCR), Dept. of Cell Biology The RCR is supported by NSF grant for installing the PHYLIP phylogeny package. #DIR-8908095.

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