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 © 2011 Macmillan Publishers Limited. All rights reserved 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 www.nature.com/reviews/molcellbio © 2011 Macmillan Publishers Limited. All rights reserved PERSPECTIVES 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 © 2011 Macmillan Publishers Limited. All rights reserved PERSPECTIVES C D E 4KDQUQOG 542 2GRVKFG 5KIPCN UGSWGPEG %[VQRNCUO 542 TGEGRVQT F 5GE EQORNGZ '4 5KIPCN RGRVKFCUG 5GETGVQT[ QT RTQVGKP %[VQUQNKE EJCRGTQPGU 5KIPCN UGSWGPEG /GODTCPG RTQVGKP 5GEs5GE %[VQRNCUO 5GE EQORNGZ $+2 ATP $+2 ADP $+2 ADP $+2 ADP ADP $+2 $+2 ADP $+2 ADP ATP $+2 '4 $+2 ATP $+2 ATP Figure 1 | Genealogy of the signal hypothesis. a | The signal hypothesis as it was originally proposed 0CVWTG4GXKGYU^/QNGEWNCT%GNN$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 www.nature.com/reviews/molcellbio © 2011 Macmillan Publishers Limited. All rights reserved PERSPECTIVES 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 C6KOGQHKPEWDCVKQP OKP # 5 D6JGTGCFQWVGZRGTKOGPV ′ #7 ) 4KDQUQOG 2GRVKFG 5KIPCNUGSWGPEG 2GRVKFGYKVJENGCXGF UKIPCNUGSWGPEG ′ ′ O40# /KETQUQOCNOGODTCPG &GVGTIGPVGZVTCEVKQP ′ #7 ) %QPVKPWGFKPXKVTQ VTCPUNCVKQP TGCFQWV /CVWTG 2TGEWTUQT RQN[RGRVKFG RQN[RGRVKFG 2TGEWTUQTRQN[RGRVKFGU YKVJUKIPCNUGSWGPEGU /CVWTG RQN[RGRVKFGU 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. NATURE REVIEWS | MOLECULAR CELL BIOLOGY VOLUME 12 | MAY 2011 | 5 © 2011 Macmillan Publishers Limited. All rights reserved PERSPECTIVES 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. #RKECNVCTIGVKPIUKIPCN .[UQUQOCN VCTIGVKPIUKIPCNU 'PFQE[VQUKUUKIPCN .[UQUQOG 6TCPU)QNIKPGVYQTM NQECNK\CVKQPUKIPCN 6TCPU)QNIK PGVYQTM 'CTN[ GPFQUQOG $CUQNCVGTCN VCTIGVKPIUKIPCN '4TGVGPVKQP UKIPCN ER '4VTCPUNQECVKQP UKIPCN 0WENGWU &0#\KREQFGU 0WENGCTRQTG EQORNGZ /KVQEJQPFTKCN VCTIGVKPIUKIPCN 2GTQZKUQOCN VCTIGVKPIUKIPCN /KVQEJQPFTKQP 2GTQZKUQOG 0WENGCTKORQTVCPF GZRQTVUKIPCN 6 | MAY 2011 | VOLUME 12 0CVWTG4GXKGYU^/QNGEWNCT%GNN$KQNQI[ © 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 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. Blobel, G. & Sabatini, D. D. in Biomembranes Vol. 2 (ed. Manson, L. A.) 193–195 (Plenum Publishing Corporation, New York, 1971). Blobel, G. & Dobberstein, B. 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Protein translocation across the eukaryotic endoplasmic reticulum and bacterial plasma membrane. Nature 450, 663–669 (2007). 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 ALL LINKS ARE ACTIVE IN THE ONLINE PDF www.nature.com/reviews/molcellbio © 2011 Macmillan Publishers Limited. All rights reserved