Spatial expression of the genome: the signal hypothesis at forty

PERSPECTIVES
TIMELINE
Spatial expression of the genome:
the signal hypothesis at forty
Karl S. Matlin
Abstract | The signal hypothesis, formulated by Günter Blobel and David Sabatini
in 1971, and elaborated by Blobel and his colleagues between 1975 and 1980,
fundamentally expanded our view of cells by introducing the concept of topogenic
signals. Cells were no longer just morphological entities with compartmentalized
biochemical functions; they were now active participants in the creation and
perpetuation of their own form and identity, the decoders of linear genetic
information into three dimensions.
In the 1970s, Günter Blobel and David
Sabatini postulated the existence of a
“commo­n sequence of amino acids near
the N‑terminal of the nascent chain” (REF. 1)
to explain how ribosomes synthesizing
secretory proteins are specifically targeted
to the endoplasmic reticulum (ER)1. This
formed the basis for the signal hypothesis,
which states that a unique peptide sequence
is encoded by mRNA specific for proteins
destined for translocation across the ER
membrane2. This peptide signal directs the
active ribosome to the membrane surface
and creates the conditions for transfer of the
nascent polypeptide across the membrane2.
Although this idea explained for the first
time how proteins are targeted for secre‑
tion, the generalization of the hypothesis
to include signals for every organelle and
location within the cell had an impact far
beyond illuminating part of the secretory
mechanism, as it introduced the con‑
cept of ‘topogenic’ signals1–11 (TIMELINE).
Before the signal hypothesis, it was almost
in­conceivable that information encoded in
the polypeptide chain could determine the
localization of proteins in the cell5. Indeed,
a search in PubMed using terms such as
‘sorting signal’, ‘signal sequence’ or ‘target‑
ing signal’ returns almost 12,000 ref­erences,
but nothing before 1971.
Today, the concepts of sorting signals and
spatial differentiation are commonplace.
Even DNA is recognized as having ‘zip codes’
dictating the location of genes in the nucleus,
with that location in part regulating expres‑
sion of those genes12. Deciphering these
spatial signals and understanding the impact
of cellular location on function is the key to
penetrating cellular complexity.
On the fortieth anniversary of the signal
hypothesis, this Timeline article reviews
the long history of discoveries leading to its
formulation, the experiments that proved it
to be true, and its generalization into the con‑
cept of topogenic sequences that explain how
three-dimensional information is extracted
from the linear genome. Quotations that
are not attributed to a specific citation used
in this Timeline article are taken from
interview­s conducted by the author.
The signal hypothesis ...
fundamentally expanded our
view of cells by introducing the
concept of topogenic signals.
The foundation of the signal hypothesis
A remarkable aspect of the work that estab‑
lished the signal hypothesis was its continuity
with previous studies carried out in the same
Laboratory of Cell Biology at the Rockefeller
Institute (later University) in New York
City, USA13. Although the term ‘cell biology’
was first used in the nineteenth century 14,
the discipline of cell biology was created
NATURE REVIEWS | MOLECULAR CELL BIOLOGY
at Rockefeller in the late 1940s and 1950s
through the work of Albert Claude, Keith
Porter and George Palade13. Claude employed
and further developed differential centri­
fugation as a means to separate sub­cellular
particles. By contrast, Porter was largely
responsible for devising techniques that
allowed electron microscopy to be applied
to biological specimens. Palade, who joined
Claude and Porter later, effectively integrated
these techniques and added biochemical
analysis to create an approach to the study
of cells that relied on parallel examination of
the whole cell and its parts to discover cell­
ular mechanisms13. This fusion of traditional
cytology and biochemistry with the sophis‑
ticated new methods of differential centri­
fugation and electron microscopy led to the
birth of what we now know as cell biology.
Porter’s first electron micrograph of a cell
was published in 1945, and in this paper he
reported a “lace-like reticulum” (REF. 15) in the
so-called ground substance (later termed
the cytoplasm). The ER, as it was renamed,
soon became an object of intense study by
both Porter and Palade. By 1954 it seemed
clear that the ER was more prominent in
cells making large amounts of protein,
suggestin­g a possible role for the ER in the
secretory process16,17. Further observations
by Palade described “a particulate compo‑
nent of the cytoplasm” (REF. 18), later known
as the ribosome, and noted that “endo­
plasmic reticulum of the rough surfaced
variety” (REF. 17), which was covered with
these particles, was the predominant type
of ER found in secretory cells.
While morphological characterization
of the ER and ribosomes was proceeding at
Rockefeller, Paul Zamecnik was also makin­g
progress on the biochemical mechanism
of protein synthesis at the Massachusetts
General Hospital in Boston, USA19. Zamecnik
took advantage of the availability of radio­
active amino acids after the Second World
War to develop the first cell-free system from
rat liver homogenates capable of de novo pro‑
tein synthesis. Activity was concentrated in
‘microsomes’, a term that originally referred
to the ill-defined non-nuclear membrane
pellet isolated by centrifugation using
techniques developed in part by Claude
at Rockefeller 19.
VOLUME 12 | MAY 2011 | 1
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PERSPECTIVES
Timeline | The development and generalization of the signal hypothesis
The first bacterial precursor protein is characterized67, and gene-fusion techniques
to study protein localization to the outer membrane of Escherichia coli are reported68
Description of post-translational translocation of newly made proteins into mitochondria47
The first signal sequence for transport of proteins into chloroplasts is identified6
Description of a “lace-like reticulum” in
the first electron micrograph of a cell15
A larger form of the immunoglobulin light chain that is
synthesized in a cell-free translation system is observed
and suggested to have an amino-terminal “signal” to
achieve segregation of the protein in microsomes27
Secretory proteins are found to be made on the
rough endoplasmic reticulum (ER) and rough
microsomes to be fragments of the rough ER20
Nascent polypeptides shown to
be protected from proteolysis by
the microsomal membrane28,29
Vesicular stomatitis virus G protein is
found to use the same mechanism as
secretory proteins to cross and integrate
into the microsomal membrane8
Fish proinsulin is found to use the same
signalling mechanism to reach the ER as
mammalian secretory proteins31
The concept of
‘topogenic’
sequences is
introduced, and the
existence of sorting
signals for post-ER
protein localization
is predicted5
A 7S RNA that is part
of SRP is discovered;
SRP is renamed
signal recognition
particle42
The SRP receptor is
discovered38-41
1945195519601966197019711972197519771979198019811982
Description of “a small particulate component
of the cytoplasm” (the ribosome) and
“endoplasmic reticulum of the rough surfaced
variety” (REFS 17,18)
Report of “vectorial discharge” of
polypeptides terminated by puromycin inside
microsomes and prediction that the nascent
polypeptide may make ribosomes “stick to
the [microsomal] membrane” (REFS 23,24)
The signal hypothesis is proposed1
Reconstitution of the synthesis, segregation into microsomes
and proteolytic processing of the immunoglobulin light chain
in a cell-free system with defined components; an updated
version of the signal hypothesis is proposed2,3
Signal sequences from pancreatic secretory proteins are
shown to be hydrophobic and to resemble the signal
sequence of the immunoglobulin light chain4
Philip Siekevitz was the first person in
Zamecnik’s laboratory to achieve incorpora‑
tion of radioactive amino acids into protein
in a cell-free system19. Recognizing the need
for a biochemist with knowledge of pro‑
tein synthesis, Palade brought Siekevitz to
New York in 1954 to help determine whether
the rough ER was indeed involved in protein
synthesis. Over the next few years, Siekevitz
and Palade were able to link the morphol‑
ogy and biochemical activities of isolated cell
fractions to organelles identified in whole
cells by electron microscopy 13. From these
observations, they concluded that rough
microsomes corresponded to fragments of
the rough ER and were the site of synthe‑
sis for secretory proteins20. The molecular
mechanism by which ribosomes attached to
the ER membrane remained a mystery.
transfer the secretory enzyme amylase across
the microsoma­l membrane into the lumen.
Redman, now joined by newcomer David
Sabatini, subsequently found that, when
polypeptide synthesis was pre­maturely term­
inated by treatment with the antibiotic puro‑
mycin, the unfinished polypeptides were still
transferred to the interior of microsomal ves‑
icles. This suggested that their transfer across
the membrane, which Redman and Sabatini
termed “vectorial discharge” (REF. 23), was
initiated during polypeptide synthesis.
Independently, Sabatini began to character­ize
the mechan­ism by which ribosomes attached
to the membrane, concluding that the attach‑
ment was mediated by the large ribosomal
subunit and speculating that the nascent
poly­peptide itself is “what makes them stick
to the membran­e” (REF. 24).
Development of the signal hypothesis
In 1966 Colvin Redman, a postdoctoral
fell­ow with Siekevitz and Palade, reported
that microsomes isolated from pigeon
pancrea­s (chosen because of high levels
of protein synthesis but low levels of ribo­
nuclease21) could incorporate amino acids
into protein, and that most of the synthe‑
sized protein remained associated with the
microsomes unless they were disrupted
by detergen­t22. From these observations,
Redman conclu­ded that rough microsomes
could synthesize and unidirectionally
The ‘X’ drawn at the amino
terminus ... was ... responsible
for directing active ribosomes to
the membrane
Günter Blobel arrived at Rockefeller as a
postdoctoral fellow in the Siekevitz laboratory
in late 1966. He had just completed his doc‑
toral studies on free and membrane-bound
ribosomes, and before long these interests
led him to Sabatini, who was by that point an
2 | MAY 2011 | VOLUME 12
The signal hypothesis is
extended to lysosomal proteins10
(1979–1981) The M13 phage coat
protein is found to be posttranslationall­y inserted into the
E. coli bacterial membrane51,52
The signal recognition
protein (SRP) is
discovered35-37
Suppressor mutations in
E. coli that affect protein
localization to a locus (later
shown to be the bacterial
protein translocation pore
SecY) are mapped69
assistant professor. The Blobel and Sabatini
partnership was particularly creative, no
doubt as a consequence of their distinctive
personalities and approaches, and resulted in
many new ideas generated through intensive
arguments and discussions25 (Sabatini and
others have pointed to a blackboard in his
laboratory as the site of these vigorous but
fruitful exchanges25). Eventually Blobel, who
wanted to establish his identity and independ‑
ence, sought out opportunities to present
their work and ideas in public. Such an
opportunity arose at a meeting on bio­logical
membranes held in Gatlinburg, Tennessee,
USA, in April of 1971. Despite its remote
location, the meeting was anything but
obscure, with many leading membrane inves‑
tigators in attendance. Blobel’s presentation
was brief, and the write-up, which was pub‑
lished in its original typescript form the same
year, was only three pages long. Although the
presentation was blandly titled “Ribosomemembrane interaction in eukaryotic cells”,
the single figure contained a revolutionary
proposal1. The ‘X’ drawn at the amino ter‑
minus of nascent polypeptides emerging
from actively synthesizing ribosomes was
described as the primary element responsible
for directing active ribosomes to the mem‑
brane (FIG. 1a). At the time, this proposal was
not supported by any direct data and was later
described by Blobel as a “fantasy”. The writeup itself, which did not seem to cause much of
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The insertion of the polytopic
membrane protein opsin into the
microsomal membrane using multiple
signal sequences is reported71
A mammalian homologue of the yeast
protein Sec61 is reported to be part of
the translocation apparatus57
The protein-conducting
channel is shown to be
an aqueous, gated pore58
The first peroxisome-targeting
signal is discovered73
Günter Blobel wins the
Nobel Prize in Physiology
or Medicine for his work
on protein targeting
The first X-ray structure
of the protein-conducting
channel is reported77
DNA ‘zip codes’ for
targeting genes to
specific sites in the
nucleus are described12
19841985198719891991199219931994199719992000200420092010
The first nuclear
localization signal for
targeting proteins to the
nucleus is characterized70
The sec61 yeast mutant, which is
defective in secretory protein
transport into the ER, is described55
A protein-conducting channel in
rough microsomes fused to planar
lipid bilayers is identified56
An autonomous sorting signal for
the basolateral plasma membrane
of polarized epithelial cells is
described74
The first three-dimensional structure of the
ribosome protein-conducting channel is
reported75
Reconstitution of protein transport
across, and integration into, phospholipid
vesicles reconstituted with the SRP
receptor and the Sec61 complex 59
The structure of a ribosome protein-conducting
channel complex during co-translational
protein translocation is described78
Biophysical and biochemical
characterization of signal sequences leads to
efforts to predict the subcellular localization
of proteins by sequence analysis60,76
Components of the translocation apparatus contacted by signal sequences are identified72
a stir in the scientific community, was kindly
but derisively referred to as “the blurb” by
other members of the laboratory.
Clues from abroad
While Blobel and Sabatini were developing
their model, Timothy Harrison was con‑
ducting his doctoral research with George
Brownlee in the Laboratory of Molecular
Biology (LMB) in Cambridge, UK26 (FIG. 2a).
Brownlee was an expert in RNA sequencing
and assigned Harrison, in collaboration with
Cesar Milstein, a project to purify the mRNA
of immunoglobulin light chains. At the time,
it was exceedingly challenging to isolate
mRNAs. Even though the plasma­cytoma
and myeloma cells that Harrison used as
starting material produced large amounts
of immuno­globulins, mRNA specific for
the light chains was only a small fraction
of the total RNA in the cell. To overcome this
obstacle, Harrison enriched for light chain
mRNA by isolating polyribosomes (clusters
of actively synthesizing ribosomes linked by
the mRNA) from microsomes, reasoning
that, as secretory proteins, immunoglobulins
would be made by ribosomes attached to the
rough ER. Putative mRNA-containing frac‑
tions were then separated by sucrose density
gradient centrifugation.
Because at the time there was no direct
assay for specific mRNAs, Harrison used
the synthesis of the light chain in an in vitro
translation system derived from a mouse
ascites tumour to determine where the
light chain mRNA migrated on the sucrose
gradient. Harrison incubated his various
fractions in this system and then examined
possible translation products by SDS-gel
electrophoresis. In the first experiment,
Harrison noticed that there were two trans‑
lation products migrating on the SDS gel
at molecular weights similar to that of the
secreted light chain polypeptide; one was
exactly the same size as authentic light chain,
whereas the other was ~1.5 kDa larger.
In additional experiments, Harrison linked
the correctly sized product to the presence
of microsomal membranes in the trans­
lation system, and he noted that the larger
polypeptide was synthesized exclusively in
membrane-free preparations. To determine
whether both products were indeed related
to the light chain, Harrison and Milstein
peptide-mapped them. In addition to iden‑
tifying them both as light chains, the map‑
ping showed that they differed only in the
N term­inus, with the initiator Met residue
only being present in the larger product.
Overall, the results suggested that the larger
form might be a precursor of the smaller
one and that generation of a light chain that
matched that of the authentic light chain
depended on microsomal membranes.
Drawing on Harrison’s knowledge of the
published literature on rough microsomes
NATURE REVIEWS | MOLECULAR CELL BIOLOGY
and secretion, Milstein, Brownlee and
Harrison postulated that the original N ter‑
minus of the light chain, which seemed to
be removed when the microsomal mem‑
brane was encountered, might in fact be a
“signal” (REF. 27) directing polyribosomes
to the membrane. In their ensuing Nature
New Biology paper, published in September
1972 (REF. 27), neither Blobel nor Sabatini
was mentioned because the authors were
unaware of the Gatlinburg meeting report
published a year earlier (although Harrison’s
thesis, submitted in December 1972, fully
cited all of the work from the Rockefeller
group26). After the Nature New Biology paper
was in press, Mike Matthews (a co-author of
the paper) presented the work at a Gordon
conference also attended by Blobel, and at
that point learned of Blobel’s “fantasy”.
Proof through reconstitution
At Rockefeller, the findings of Harrison,
Milstein and colleagues were greeted
with great excitement because Blobel and
Sabatini realized that the hypothetical
scheme invoking an N‑terminal extension
might, in fact, be true. Although very sug‑
gestive, the Nature New Biology paper only
proposed a precursor–product relationship
between the larger and smaller forms of the
light chain synthesized in vitro but did not
demonstrate it 27. Now this had to be proven
definitively.
VOLUME 12 | MAY 2011 | 3
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PERSPECTIVES
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Figure 1 | Genealogy of the signal hypothesis. a | The signal hypothesis as it was originally proposed
0CVWTG4GXKGYU^/QNGEWNCT%GNN$KQNQI[
by Günter Blobel and David Sabatini in 1971 (REF.1). b | The revised signal hypothesis from 1975, now
2
including proteolytic processing of signal peptides . c | The modern version of the signal hypothesis,
incorporating known major components. As the nascent chain emerges from the ribosome tunnel during translation, it is bound by the signal recognition particle (SRP). When the entire translating complex
reaches the membrane, SRP interacts with its receptor, and the ribosome and nascent chain are transferred to the protein-conducting channel (the Sec61 complex). The signal peptide inserts in an inverted
orientation, and translocation proceeds. In many cases, signal peptidase cleaves the amino-terminal
signal. For secretory proteins, this releases the protein into the endoplasmic reticulum (ER) lumen. For
membrane proteins, translocation stops when the transmembrane domain (stop transfer peptide) is
reached and the polypeptide, now integrated in the lipid bilayer, moves laterally out of the proteinconducting channel. Variations on this mechanism result in membrane proteins with an inverted orientation; an alternating series of signal sequences (start transfer) and transmembrane sequences (stop
transfer) can result in a protein spanning the membrane multiple times (polytopic). d | A posttranslationa­l translocation mechanism using some of the same machinery also exists in the ER46. The
Sec61 complex is now joined by Sec62–Sec63. Completed polypeptides in the cytoplasm are maintained in a translocatio­n-competent conformation by association with chaperones. After translocation
begins and the translocating polypeptide is exposed in the lumen of the ER, other chaperones, such as
BIP, associate with it, trapping and essentially pulling it through the channel. Figure in part a is reproduced, with permission, from REF. 1 © (1971) Springer. Figure in part b is reproduced, with permission,
from REF. 2 © (1975) The Rockefeller University Press. Figures in parts c and d are modifie­d, with
permissio­n, from REF. 79 © (2007) Macmillan Publishers Ltd. All rights reserved.
In 1972, the Blobel–Sabatini partnership
dissolved when Sabatini left Rockefeller to
become Chairman of Cell Biology at New
York University Medical School, USA.
Blobel, encouraged by Palade and drawing
on his training as a biochemist, decided to
create a completely reconstituted system
that could replicate and extend the results of
the Cambridge group. After a pain­staking
process that required the purification
4 | MAY 2011 | VOLUME 12
and character­ization of each component,
Blobel finally achieved his first success on
Christmas Day 1974.
Blobel and his postdoctoral fellow
Bernhard Dobberstein used an in vitro pro‑
tein synthesis system to prove a precursor–
product relationship between the two
forms of the immunoglobulin light chain.
Specifically, this system could complete the
synthesis of polypeptides begun on poly­
ribosomes that had been detergent-extracted
from microsomes, but could not initiate new
polypeptide synthesis. Using this “read-out”
(REF. 2) system, they showed in a crucial
experiment that light chains synthesized
with short incubation times had the same
molecular weight as the authentic, mature
light chain2 (FIG. 3). As readout progressed,
however, more and more light chains with
the higher molecular weight of the putative
precursor appeared. Apparently, those light
chains the synthesis of which had progressed
to some extent while the polyribosomes were
still bound to the microsomal membrane
in vivo had already been processed to the
right size by the membrane. By contrast,
those light chains that had started being
synthesized at the time the membrane
was dissolved were not processed.
Thus, by demonstrating that light chain
synthesis on polyribosomes occurring later
produced polypeptides larger than those
synthesized earlier, Blobel established a
precursor–produc­t relationshi­p2 (FIG. 3).
Next, Blobel and Dobberstein set out
to demonstrate that a cell-free system
reconstituted from individual purified
components was capable of processing light
chain polypeptides that were completely
synthesized in vitro from initiation to ter­
m­ination. To construct this, they isolated
rough microsomes from dog pancreas
(which, like pigeon pancreas, has low levels
of ribo­nuclease21) and treated them with
chelating agents to remove any attached
poly­ribosomes without damaging the
membrane. They then incubated purified
light chain mRNA with isolated ribosomal
subunits and other components needed
for protein synthesis in either the presence
or absence of the stripped microsomes. As
hoped, only the sample that contained the
membranes produced the processed light
chain. Drawing on Blobel’s prior work
with Sabatini28,29, Blobel and Dobberstein
then digested the incubation mixtures
with proteolytic enzymes and saw that only
the processed product was protected from
proteolysis, indicating that it was inside the
microsomal vesicles. When the cytoplasmic
protein globin was synthesized in the same
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C
the ER membrane33–42,44. Furthermore, the
enzyme that cleaves the signals as they are
exposed in the ER lumen, signal peptidase,
was purified45. Gradually, elements of the
translocation machinery in bacteria and
in the mitochondria and chloroplasts of
eukaryotic cells were elucidated46.
As the concepts of the signal hypothesis
were extended beyond the ER, evidence
began accumulating which suggested that the
co-translational translocation mechanism
(FIG. 1c) was not the only way in which newly
synthesized proteins either crossed or inte‑
grated into membranes47–53. In the same year
that the first chloroplast protein precursor
was discovered6, Walter Neupert and col‑
leagues showed that mitochondrial proteins
could enter mitochondria after their synthesis
in the cytoplasm was complete47. In the next
year, transport of proteins into the chloroplast
was also shown to be post-translational48,49.
In addition, post-translational translocation
or membrane insertion was shown to occur
in bacteria, primarily Escherichia coli, and
to coexist with co-translational transloca‑
tion50,51,53,54. Finally, after experiments in yeast
demonstrated post-translational transloca‑
tion in the ER, it became accepted that both
mechanisms operate in both bacteria and
eukaryotes46 (FIG. 1d).
D
Figure 2 | The key players. a | Top to bottom: Timothy Harrison (circa 1969), Cesar Milstein (circa 1975)
and George Brownlee (circa 1975). b | Günter Blobel (left) and
Anne Devillers-Thiéry (right) in 1975.
0CVWTG4GXKGYU^/QNGEWNCT%GNN$KQNQI[
Devillers-Thiéry first sequenced the signal peptides for pancreatic proteins in the Blobel laboratory4.
Photographs in part a are courtesy of the Laboratory of Molecular Biology, University of Cambridge, UK.
Photograph in part b is courtesy of N. Dwyer, US National Institutes of Health, Bethesda, Maryland, USA.
system from mRNA, it was neither pro­
cessed to a different size nor protected from
proteolysis in the presence of microsomes.
Thus, the reconstituted system was capa‑
ble of completely synthesizing a secretory
protein, translocating it into the interior
of microsomal vesicles, and proteolytically
processing it to its authentic size3.
By May 1975, Blobel and his laborator­y
(FIG. 2b) completed the studies with the
reconstituted systems and, by the end of the
summer, had also determined the amino acid
sequence of signal peptides from several pre‑
cursors4. After favourable reviews and some
mild arm-twisting, The Journal of Cell Biology
published two back-to-back papers describ‑
ing the major experiments and a new, more
complete model of the signal hypothesi­s in
December 1975 (REFS 2,3) (FIG. 1b).
Elaborating the hypothesis
Over the next several years, Blobel’s labo‑
ratory extended the signal hypothesis to
integral membrane proteins (with Flora Katz
and Harvey Lodish)8 and a series of other
secretory and lysosomal proteins10,30,31,32.
Importantly, they found that different
N‑terminal signals occurred in nucleusencoded proteins targeted to chloroplasts
(with Dobberstein and Nam-Hai Chua)6
and to mitochondria (with Maria-Luisa
Maccecchini and Gottfried Schatz)11. Great
progress was also made by both Blobel’s
laboratory and others in identifying and
characterizing the targeting, translocation
and processing machinery 33–45. Specifically,
the signal recognition particle (SRP) and its
receptor were discovered and shown to help
transport the ribosome and nascent chain to
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Figure 3 | Demonstrating a precursor–product relationship. a | The original autoradiograph of an SDS 0CVWTG4GXKGYU^/QNGEWNCT%GNN$KQNQI[
gel showing a key readout experiment from the first paper by Günter Blobel and Bernhard Dobberstein
in 1975 (REF. 2). Lane A is a control showing the mobility of the light chain precursor (arrow). The arrow
in lane S shows authentic immunoglobulin light chain secreted from radiolabelled myeloma cells. Lanes
1, 6, 9, 18, 25 and 50 are times in minutes after translation is allowed to resume on detergent-treated,
active polyribosomes in a cell-free system incapable of initiating the translation of new chains. Note
that the first products to appear are polypeptides of the authentic molecular weight (mature polypeptides) because translation of these in vivo, when the polyribosomes were still attached to the microsomal
membrane, had proceeded for long enough to allow the signal sequences to be removed. Later products (precursor polypeptides) had begun translation in vivo, but translation (and, presumably, transport
across the membrane) was insufficiently advanced for the signal peptide to be cleaved. b | Schematic
of the experiment shown in a. In the cell, polyribosomes directed to the endoplasmic reticulum by the
signal recognition particle are likely to remain closely associated with the membrane, often in a circular
or spiral configuration, to facilitate continued initiation and translocatio­n of secretory and membrane
proteins. Figures are modified, with permission, from REF. 2 © (1975) The Rockefeller University Press.
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VOLUME 12 | MAY 2011 | 5
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Box 1 | Simplified topogenic map of the cell
The concept of protein ‘topogenesis’, proposed by Günter Blobel in 1980 (REF. 5), was an outgrowth
of the original signal hypothesis. It states that the localization and disposition of proteins in the
membrane compartments of the cell are determined by topogenic signals (often called sorting
signals) that are encoded in polypeptide chains (see the figure). The cell in which the genes are
expressed deciphers the signals and facilitates their transport to the correct location. Proteins
directed to locations on the secretory pathway (organelles and plasma membrane) have
endoplasmic reticulum (ER) translocation signals and topogenic signals to direct them to their
ultimate destinations once they enter the ER.
Many topogenic signals are short peptides, such as the ER translocation signal, the ER retention
signal, nuclear import and export signals, and mitochondrial targeting signals60. Often signals
directing proteins to the same location are not sequentially conserved but have similar biophysical
properties, such as clustered hydrophobic and charged residues, or shared structures, such as
amphipathic helices60. Others are not only a ‘delivery address’ but also a ‘return address’.
Endocytosis signals, for example, may cause a protein to be internalized but will also cause it to
be recycled back to the same membrane.
Some topogenic signals are modified sugars or lipids. For example, lysosomal hydrolases are
targeted to the lysosome through the recognition of 6‑phosphomannose attached to an Asn-linked
oligosaccharide60. In epithelial cells, the lipid glycosyl phosphotidylinositol attached to proteins
sorts the protein to the apical plasma membrane60. Although such secondary protein modifications
act as sorting signals, the actual topogenic information is encoded in the protein polypeptide chain
that is recognized by the enzymes that add the secondary modifications . Thus, lysosomal
hydrolases are recognized as such early in their transport through the Golgi complex by the
enzyme that adds N‑acetylglucosamine (GlcNAc)-phosphate to mannose. Cleavage of GlcNAc
then exposes 6‑phosphomannose.
Recent studies indicate that a DNA sequence can act as a topogenic sequence. These ‘DNA
zip codes’ mediate attachment of specific genes to subunits of the nuclear pore complex, and may
have a role in gene activation12,62. Furthermore, different binding sites on the nuclear pore complex
may hold onto some genes after they are turned off as a way of ‘remembering’ the identities of
genes that were recently expressed.
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© 2011 Macmillan Publishers Limited. All rights reserved
Of the various pieces of the targeting
and translocation machinery postulated in
the first 1975 signal hypothesis paper, the
pore (or, as it was later called, the proteinconducting channel) through the membrane
proved to be the most controversial. Some
believed that N-terminal signal sequences,
which turned out to be hydrophobic, might
be sufficient to direct nascent poly­peptides
through the membrane. However, a pore
with a hydrophilic channel capable of
protein translocation in a signal sequencedependent manner was finally identified
and ultimately characterized after in­genious
biophysical and biochemical experi‑
ments55–58. Ultimately, the demonstration of
translocation across lipid vesicles that had
been reconstituted with the purified channel
complex finally confirmed the importance
of the pore59.
In 1980, Blobel extended the original
hypothesis to include topogenic signals that
directed proteins to intracellular locations
after their translocation or insertion into the
membrane of the ER5. Today, after 30 years,
sorting signals are known for every conceiv‑
able subcompartment of the cell, as Blobel
predicted, and bioinformatic algorithms are
being developed to predict where proteins
are targeted by analysing their sequences60,61
(BOX 1). In the latest development, even genes
have been shown to have DNA zip codes
that target them to specific sites on nuclear
pores, helping to control their expression
and, most strikingly, ‘remember’ that they
were recently active12,62.
Conclusion and perspectives
From the beginning, what distinguished
the hypothesis formulated by Blobel and
Sabatini in 1971 from previous ideas about
the mechanism of ribosome–membrane
interaction was that the proposed “X fac‑
tor” in the model did not only help attach
the translating ribosomes to the membrane
but also provided the information that
specifically targeted them there1,8,63–65. For
membrane proteins, the translocation pro­
cess initiated by the signal sequence also
determined their permanent, asymmetric
disposition in the membrane8,63–65. Thus, sig‑
nal sequences ‘told’ secretory and membrane
proteins where to go to in the cell and how to
orient themselves when they got there.
In essence, topogenic signals mediate
the spatial expression of the genome in the
cell. Because of the signal hypothesis and its
implications, we now realize that bio­logical
information is found not only in DNA
sequences but also in the disposition of the
cell and its membranes in three dimensions.
www.nature.com/reviews/molcellbio
PERSPECTIVES
Just like DNA, cells and their structured
membranes are inherited; indeed, one can
argue that the membranes of our cells can
be traced without interruption to the mem‑
branes of the very first cell. DNA may be the
“code of codes” (REF. 66), but it needs the cell
to decipher it.
Karl S. Matlin is at Department of Surgery,
The University of Chicago,
5841 South Maryland Avenue,
MC 5032, SBRI J557, Chicago,
Illinois 60637‑1470, USA.
e-mail: kmatlin@uchicago.edu
doi:10.1038/nrm3105
Published online 13 April 2011
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8 | MAY 2011 | VOLUME 12
Acknowledgements
The author is grateful for support of this project from the US
National Library of Medicine and the US National Institutes
of Health (NIH), to W. Green, N. Matlin, A. Engelberg and
J. Collier for review of the manuscript, and to members of the
Committee on Conceptual and Historical Studies of Science
at the University of Chicago, Illinois, USA, for stimulating
discussions. Photographs in figure 2 were provided by the
Laboratory of Molecular Biology at the University of
Cambridge, UK, and by N. Dwyer, NIH, USA. The author
thanks the many individuals who have provided information
for this article through interviews.
Competing interests statement
The author declares no competing financial interests.
DATABASES
PubMed: http://www.ncbi.nlm.nih.gov/pubmed
FURTHER INFORMATION
Karl S. Matlin’s homepage:
http://surgicalresearch.bsd.uchicago.edu/faculty/matlin
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