Cell, Vol.
64, 13-15, January 11, 1991, Copyright 0 1991 by Cell Press
Naming a Targeting Signal
A staggering variety of potential fates awaits a protein
emerging from a ribosome. The presence (or absence) of
certain amino acid sequences in a nascent protein con-
strains the set of metabolic fates that actually befall it by
making some fates more probable than others. These se-
quences, known as targeting signals, can determine the
spatial destination of a protein, its folding, posttransla-
tional modifications, and metabolic stability. The under-
standing of targeting signals has grown enormously over
the last fifteen years (reviewed by Blobel, 1980; Wold,
1981; Creighton, 1984; Walter and Lingappa, 1987; Ran-
dall et al., 1987; Pfeffer and Rothman, 1987; Burgess and
Kelly, 1987; Verner and Schatz, 1988; Gierasch, 1989;
Hart1 and Neupert, 1990). Unfortunately, these advances
have not been accompanied by a clarification and simplifi-
cation of terminology. For instance, signals that enable a
protein to translocate across the plane of a membrane are
called signal sequences, topogenic sequences, targeting
sequences, transit sequences, presequences, transloca-
tion sequences, or leader sequences. Ad hoc, often
semantically cumbersome terms are also used to denote
other targeting signals. Yet most of the transformations
that proteins undergo can be grouped into five distinct
classes of transitions:
l Translocation of a protein across the plane of a mem-
brane separating two compartments.
l Transfer of a protein between compartments without
crossing the plane of a membrane (vesicle-mediated
transport).
l Hydrolysis of some or all of the peptide bonds in a pro-
tein.
l Chemical modifications of a protein that do not involve
hydrolysis of peptide bonds.
l Conformational modifications of a protein, including its
folding and oligomerization.
I propose the terms transferon, comperfon, degron, and
modon for signals that specify each of the first four fates,
respectively (Table 1). Examples of the new terminology
are presented in Table 2. The distinction between trans-
ferons and compartons is illustrated in the figure. (Termi-
nology for the fifth class of transitions has been left for
braver people to deal with.)
The known complexities of targeting signals are many
and continue to accrue. For instance, the distinction be-
tween transferons (Table 1) and stop-transfer signals that
halt the translocation process is ambiguous for those
stop-transfer signals that can act as transferons when
positioned within other sequence contexts (Saier et al.,
1989). A transferon may or may not be accompanied by
a distinct degron that specifies removal of the transferon
by a membrane-attached protease. Nonremovable trans-
ferons can serve as membrane anchors, sharing this func-
Letter to the Editor
tion with stop-transfer signals (von Heijne, 1988). Transi-
tions of one class often immediately precede, follow, or
depend on transitions of another class in the same pro-
tein. Amino acid sequences specifying a targeting signal
are not always contiguous, are often highly degenerate
(Kaiser and Botstein, 1990; Bachmair and Varshavsky,
1989) and may even reside within different subunits of an
oligomeric protein (Johnson et al., 1990).
The new terminology can accomodate these and other
complexities of targeting signals because the proposed
terms denote fundamental distinctions and are functional
rather than sequence-, structure-, or mechanism-based
terms. For example, an X-comparton (Table 1) is defined
as a signal that confers retention of a protein in a compart-
ment X, irrespective of whether the retention is achieved
Table 1, Definitions of Targeting Signals
Class Property Conferred on a Protein
Traneferon Translocation from a compartment X to a
compartment Y (X/Y-transferon) across the
real or “virtual” plane of a membranes
Cornpatton Retention in a compartment X (X-comparton)
or transfer from a compartment X to a com-
partment Y (WY-comparton)without crossing
the plane of a membrane
Degron Metabolic instability of some or all of the
peptide bonds in a protein
Modon Chemical modification other than proteolvsis
B When the first compartment is cytoeol, a shorter name (Y-transferon)
can be used. The inclusion of a virtual plane expands the definition
of transferon to include cases such as nuclear pore-mediated trans-
fer, in which a protein is transported through an aqueous channel
across a plane defined by two or more juxtaposed but noncontiguous
membranes (Figure 16).
The Distinction between Transferons and Compartons
(A and B) Transferons confer on a protein (wavy lines) the ability to
translocate through a distinct aqueous channel across the real (A) or
“virtual” (8) plane of a membrane (thick lines). Proteinaceous aqueous
channels (rectangles) either directly span a membrane (A) or are em-
bedded at points of convergence between juxtaposed but noncontigu-
ous membranes (B). Translocation from and into the nucleus through
the nuclear pores is an example of the latter kind. (C) Compartons
specify vesicle-mediated transitions in which proteins (dots) move be-
tween compartments without crossing the plane of a membrane.
Cell
14

Table 2. Examples of Proposed and Current Terminologies

Proposed Name
of a Signal Some Names Currently in Use Function
ER-transferon Signal sequence, leader Translocation from cytosol into endoplasmic reticulum
sequence
M-transferon Matrix targeting sequence, Translocation from cytosol into mitochondrial matrix (compartment
mitochondrial presequence enclosed by the inner membrane). See footnote to Table 1
MAIMS-transferon Intermembrane space targeting Translocation from mitochondrial matrix (M) into intermembrane space
sequence (IMS) between the inner and outer membranes. Proteins destined to
reside in IMS contain both an M-transferon and an MIIMS-transferon,
which act sequentially (Hart1 and Neupert, 1990)
Nu-transferon Nuclear targeting sequence, Translocation from cytosol into nucleus. See Figure 1B and footnote to
nuclear translocation signal Table 1
Eflcomparton ER retention signal Retention in endoplasmic reticulum (Pelham, 1969)
GIL-comparton Lysosome transfer signal Transfer from trens-Golgi to lysosomes (see text)
Xa-degron Factor Xa recognition sequence Conversion of prothrombin into thrombin by Factor Xa, one of the
proteases in the blood clotting cascade (Nagai and Thbgersen, 1967)
N-degron Amino-terminal degradation N-degron is manifested as the N-end rule, which relates the metabolic
signal stability of a protein to the identity of its amino-terminal residue (Johnson
et al., 1990)
Nlaa-modon Signal for conjugation of an Generation of N-degron (see text)
amino acid to the amino
terminus of a protein
ManGP-modon Golgi-mediated generation of Man6P residues on a protein (see text)

by preventing the protein’s transfer or by a compartment-
specific return of the transferred protein (Pelham, 1989;
Warren, 1990). This terminology is therefore inherently
flexible. Its other advantages are brevity, logical con-
sistency, and uniformity of designations within a class of
transitions. The proposed terms can also be used with
other biopolymers; for instance, degrons and modons oc-
cur in both RNA and DNA.
When applied to proteins, the signals of Table 1 are
specified exclusively by amino acid sequences. This con-
straint bypasses the difficulty of deciding, for example,
whether a comparton is defined by amino acid residues
of a comparton-bearing protein or by the protein’s carbo-
hydrate moieties as well. More generally, if an amino acid
sequence specifies a modon, and the resultant chemical
modification of a protein is required for the function of its
other signals, one still defines these signals exclusively in
terms of amino acid sequences-by including sequences
that specify the relevant modon as well. (Amino acid se-
quences that specify a modon encompass both the
modification site(s] in a protein and sequences required
for the modon’s recognition.)
Example: upon arrival from the endoplasmic reticulum
(ER) to a compartment close to but apparently distinct
from the cis-Golgi, future lysosomal enzymes bearing the
mannose-bphosphate (ManGP)-modon (Table 2) are rec-
ognized by a transferase that adds N-acetylglucosaminyl
phosphate (GlcNAc-P) to a-1,24inked mannose residues
present on the N-linked oligosaccharides that have been
added to these proteins in the ER. Later, in the Golgi, an-
other enzyme converts the modified mannose residues
into the Man8P residues. Since the presence of sterically
accessible Man8P residues in a Golgi-located protein is
apparently sufficient for its delivery to lysosomes (Korn-,
feld and Mellman, 1989), amino acid sequences compris-
ing this type of a G/L-comparton (Table 2) may be identical
to those specifying the ManGP-modon. As with other
“downstream“ signals, implementation of the GIL-corn-
parton is conditional upon the completion of several pre-
ceding transitions involving the same protein, in particular
those that require the ER-transferon (Table 2) and modons
for ER-specific glycosylation.
In the absence of additional instructions, the default
secretory pathway transports a protein that has entered
the ER to the outside of the cell. A default secretion signal
is therefore simply the ER-transferon (Table 2). To avoid
secretion by the default pathway, a protein that bears the
ER-transferon should also contain a comparton, for exam-
ple, the ERcomparton, the GIL-comparton (Table 2) or a
comparton that causes transfer of the protein to storage
vesicles of a regulated secretory pathway (Burgess and
Kelly, 1987). Proteins recognized as abnormal (misfolded
or misassembled) after their translocation into the ER also
fail to be secreted by the default pathway. Such proteins
are selectively degraded either in the ER or after their
diversion (via the Golgi) into lysosomes; they may also be
spared but retained in the ER through an associatioa with
a resident ER protein such as BiP that bears the ER-
comparton (Table 2) (Hurtley and Helenius, 1989; Klaus-
ner and Sitia, 1990).
A targeting signal may function either differently or not
at all in a different in vivo setting. For instance, the N/Arg-
modon, which causes the conjugation of arginine to the
amino terminus of a protein (Table 2) is a single amino-
terminal residue, Asp or Glu (and Cys in some cells)
(Gonda et al., 1989). Implementation of the N/Arg-modon
Letter to the Editor
15

is required to generate a specific degradation signal in a von Heijne. G. (1966). Biochim. Biophys. Acta 947: 307-333.
modon-bearing protein. This signal (N-degron; Table 2) is Walter, P, and Lingappa, V. R. (1967). Annu. Rev. Cell Biol. 2,499-516.
manifested as the N-end rule, which relates the metabolic Warren, G. (1990). Cell 62, l-2.
stability of a protein to the identity of its amino-terminal Weld, F. (1961). Annu. Rev. B&hem. 50, 763-614.
residue (Johnson et al., 1990). The NIArg-modon is active
in eukaryotes, which contain Arg-tRNA-protein transfer-
ase, but inactive in bacteria, which lack this enzyme. A
different, N/Phe,Leu-modon, is active in bacteria. This
modon causes the conjugation of either Phe or Leu to the
amino terminus of a modon-bearing protein @offer, 1980).
Thus, specification of a targeting signal implies a refer-
ence to an appropriate in vivo environment, and to a rele-
vant genetic background as well.
In a discourse that employs the new terms, one could
start by introducing the full name of a signal, for instance,
the mitochrondrial matrix transferon, then specify and use
its acronym, M-transferon (Table 2). When the names for
different signals share first letters, one could assign a sin-
gle-letter acronym to some of these signals (e.g., N-deg-
ron) and use multiple-letter acronyms for the other signals
(e.g., Nu-transferon). Table 2 lists nonoverlapping acro-
nyms for some of the targeting signals; other such acro-
nyms could evolve gradually, by consensus.
I thank R. Baker, B. Bartel, L. Gierasch, G. von Heijne,
M. Hochstrasser, K. Lewis, H. Pelham, T. Shrader, and one
of the reviewers for comments, and B. Doran for secre-
tarial assistance.

Alexander Varehaveky
Department of Biology
Massachusetts Institute of Technology
Cambridge, Massachusetts 02139

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