Translation from the 5′ untranslated region shapes the integrated stress response
How cells keep going in the face of adversity
When cells experience stresses that affect their ability to process newly synthesized proteins, they turn down their rates of translation to help them survive the stress. They also turn on the translation of proteins that will help them cope with the misfolded proteins generated during stress. How do they turn down translation in general, but maintain or increase translation of specific proteins? Starck et al. developed an approach that allowed them to look at the translation of specific messenger RNAs that were not down-regulated by stress. They identified a motif that helped keep chaperone protein synthesis going.
Science, this issue p. 10.1126/science.aad3867
Structured Abstract
INTRODUCTION
Protein synthesis is controlled by a plethora of developmental and environmental conditions. One intracellular signaling network, the integrated stress response (ISR), activates one of four kinases in response to a variety of distinct stress stimuli: the endoplasmic reticulum (ER)–resident kinase (PERK), the interferon-induced double-stranded RNA–dependent eIF2α kinase (PKR), the general control nonderepressible 2 (GCN2), or the heme-regulated inhibitor kinase (HRI). These four kinases recognize a central target and phosphorylate a single residue, Ser51, on the α subunit of the eukaryotic initiation factor 2 (eIF2α), which is a component of the trimeric initiation factor eIF2 that catalyzes translation initiation at AUG start codons. Phosphorylation of eIF2α down-regulates eIF2-dependent protein synthesis, which is important in development and immunity but also is implicated in neurodegeneration, cancer, and autoimmunity. However, protein synthesis does not cease on all mRNAs during the ISR. Rather, eIF2α phosphorylation is required for expression of select mRNAs, such as ATF4 and CHOP, that harbor small upstream open reading frames (uORFs) in their 5′ untranslated regions (5′ UTRs). Still other mRNAs sustain translation despite ISR activation. We developed tracing translation by T cells (3T) as an exquisitely sensitive technique to probe the translational dynamics of uORFs directly during the ISR. With 3T, we measured the peptide products of uORFs present in the 5′ UTR of the essential ER-resident chaperone, binding immunoglobulin protein (BiP), also known as heat shock protein family A member 5 (HSPA5), and characterized their requirement for BiP expression during the ISR.
RATIONALE
We repurposed the sensitivity and specificity of T cells to interrogate the translational capacity of RNA outside of annotated protein coding sequences (CDSs). 3T relies on insertion of a tracer peptide coding sequence into a candidate DNA sequence. The resulting mRNAs harboring the nested tracer peptide coding sequence are translated to produce tracer peptides. These translation products are processed and loaded onto major histocompatibility complex class I (MHC I) molecules in the ER and transit to the cell surface, where they can be detected by specific T cell hybridomas that are activated and quantified using a colorimetric reagent. 3T provides an approach to interrogate the thousands of predicted uORFs in mammalian genomes, characterize the importance of uORF biology for regulation, and generate fundamental insights into uORF mutation-based diseases.
RESULTS
3T proved to be a sensitive and robust indicator of uORF expression. We measured uORF expression in the 5′ UTR of mRNAs at multiple distinct regions, while simultaneously detecting expression of the CDS. We directly measured uORF peptide expression from ATF4 mRNA and showed that its translation persisted during the ISR. We applied 3T to study BiP expression, an ER chaperone stably synthesized during the ISR. We showed that the BiP 5′ UTR harbors uORFs that are exclusively initiated by UUG and CUG start codons. BiP uORF expression bypassed a requirement for eIF2 and was dependent on the alternative initiation factor eIF2A. Both translation of the UUG-initiated uORF and eIF2A were necessary for BiP expression during the ISR. Unexpectedly, the products of uORF translation are predicted to generate MHC I peptides active in adaptive immunity. We propose that this phenomenon presents an extracellular signature during the ISR.
CONCLUSION
Our findings introduce the notion that cells harbor a distinct translation initiation pathway to respond to a variety of environmental conditions and cellular dysfunction. We showed that cells utilize a distinct, eIF2A-mediated initiation pathway, which includes uORF translation, to sustain expression of particular proteins during the ISR. 3T offers a valuable method to characterize the thousands of predicted translation events in 5′ UTRs and other noncoding RNAs and, expanded to a genome-wide scale, can complement ribosome profiling and mass spectrometry in uORF and short ORF discovery. Our observations underscore the importance of translation outside of annotated CDSs and challenge the very definition of the U in 5′ UTR.
3T reveals the translational landscape of the genome outside of annotated coding sequences.
Tracer peptide coding sequences are inserted into regions outside the annotated CDS, such as uORFs. When translated, they generate peptides that are transported into the ER, loaded onto MHC I, and transit to the cell surface. T cell hybridomas that recognize the specific tracer peptide–MHC I complex become activated, which is detected using a colorimetric substrate.
Abstract
Translated regions distinct from annotated coding sequences have emerged as essential elements of the proteome. This includes upstream open reading frames (uORFs) present in mRNAs controlled by the integrated stress response (ISR) that show “privileged” translation despite inhibited eukaryotic initiation factor 2–guanosine triphosphate–initiator methionyl transfer RNA (eIF2·GTP·Met-tRNAiMet). We developed tracing translation by T cells to directly measure the translation products of uORFs during the ISR. We identified signature translation events from uORFs in the 5′ untranslated region of binding immunoglobulin protein (BiP) mRNA (also called heat shock 70-kilodalton protein 5 mRNA) that were not initiated at the start codon AUG. BiP expression during the ISR required both the alternative initiation factor eIF2A and non–AUG-initiated uORFs. We propose that persistent uORF translation, for a variety of chaperones, shelters select mRNAs from the ISR, while simultaneously generating peptides that could serve as major histocompatibility complex class I ligands, marking cells for recognition by the adaptive immune system.
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Supplementary Material
Summary
Material and Methods
Figs. S1 to S15
Resources
File (aad3867_starck_sm.pdf)
References and Notes
1
Walter P. and Ron D., The unfolded protein response: From stress pathway to homeostatic regulation. Science 334, 1081–1086 (2011).
2
Shi Y., Vattem K. M., Sood R., An J., Liang J., Stramm L., and Wek R. C., Identification and characterization of pancreatic eukaryotic initiation factor 2 alpha-subunit kinase, PEK, involved in translational control. Mol. Cell. Biol. 18, 7499–7509 (1998).
3
Harding H. P., Zhang Y., and Ron D., Protein translation and folding are coupled by an endoplasmic-reticulum-resident kinase. Nature 397, 271–274 (1999).
4
Galabru J., Katze M. G., Robert N., and Hovanessian A. G., The binding of double-stranded RNA and adenovirus VAI RNA to the interferon-induced protein kinase. Eur. J. Biochem. 178, 581–589 (1989).
5
Meurs E., Chong K., Galabru J., Thomas N. S., Kerr I. M., Williams B. R., and Hovanessian A. G., Molecular cloning and characterization of the human double-stranded RNA-activated protein kinase induced by interferon. Cell 62, 379–390 (1990).
6
Berlanga J. J., Santoyo J., and De Haro C., Characterization of a mammalian homolog of the GCN2 eukaryotic initiation factor 2alpha kinase. Eur. J. Biochem. 265, 754–762 (1999).
7
Lu L., Han A. P., and Chen J. J., Translation initiation control by heme-regulated eukaryotic initiation factor 2alpha kinase in erythroid cells under cytoplasmic stresses. Mol. Cell. Biol. 21, 7971–7980 (2001).
8
Jackson R. J., Hellen C. U., and Pestova T. V., The mechanism of eukaryotic translation initiation and principles of its regulation. Nat. Rev. Mol. Cell Biol. 11, 113–127 (2010).
9
Hai T. W., Liu F., Coukos W. J., and Green M. R., Transcription factor ATF cDNA clones: An extensive family of leucine zipper proteins able to selectively form DNA-binding heterodimers. Genes Dev. 3 (12B), 2083–2090 (1989).
10
Lu P. D., Harding H. P., and Ron D., Translation reinitiation at alternative open reading frames regulates gene expression in an integrated stress response. J. Cell Biol. 167, 27–33 (2004).
11
Vattem K. M. and Wek R. C., Reinitiation involving upstream ORFs regulates ATF4 mRNA translation in mammalian cells. Proc. Natl. Acad. Sci. U.S.A. 101, 11269–11274 (2004).
12
Fornace A. J. Jr., Alamo I. Jr., and Hollander M. C., DNA damage-inducible transcripts in mammalian cells. Proc. Natl. Acad. Sci. U.S.A. 85, 8800–8804 (1988).
13
Ron D. and Habener J. F., CHOP, a novel developmentally regulated nuclear protein that dimerizes with transcription factors C/EBP and LAP and functions as a dominant-negative inhibitor of gene transcription. Genes Dev. 6, 439–453 (1992).
14
Han J., Back S. H., Hur J., Lin Y. H., Gildersleeve R., Shan J., Yuan C. L., Krokowski D., Wang S., Hatzoglou M., Kilberg M. S., Sartor M. A., and Kaufman R. J., ER-stress-induced transcriptional regulation increases protein synthesis leading to cell death. Nat. Cell Biol. 15, 481–490 (2013).
15
Hinnebusch A. G., The scanning mechanism of eukaryotic translation initiation. Annu. Rev. Biochem. 83, 779–812 (2014).
16
Joslin G., Hafeez W., and Perlmutter D. H., Expression of stress proteins in human mononuclear phagocytes. J. Immunol. 147, 1614–1620 (1991).
17
Panniers R., Translational control during heat shock. Biochimie 76, 737–747 (1994).
18
Richter K., Haslbeck M., and Buchner J., The heat shock response: Life on the verge of death. Mol. Cell 40, 253–266 (2010).
19
Der S. D. and Lau A. S., Involvement of the double-stranded-RNA-dependent kinase PKR in interferon expression and interferon-mediated antiviral activity. Proc. Natl. Acad. Sci. U.S.A. 92, 8841–8845 (1995).
20
Gilfoy F. D. and Mason P. W., West Nile virus-induced interferon production is mediated by the double-stranded RNA-dependent protein kinase PKR. J. Virol. 81, 11148–11158 (2007).
21
Hsu L.-C., Park J. M., Zhang K., Luo J.-L., Maeda S., Kaufman R. J., Eckmann L., Guiney D. G., and Karin M., The protein kinase PKR is required for macrophage apoptosis after activation of Toll-like receptor 4. Nature 428, 341–345 (2004).
22
Shiu R. P., Pouyssegur J., and Pastan I., Glucose depletion accounts for the induction of two transformation-sensitive membrane proteins[ ]in Rous sarcoma virus-transformed chick embryo fibroblasts. Proc. Natl. Acad. Sci. U.S.A. 74, 3840–3844 (1977).
23
Haas I. G. and Wabl M., Immunoglobulin heavy chain binding protein. Nature 306, 387–389 (1983).
24
Munro S. and Pelham H. R., An Hsp70-like protein in the ER: Identity with the 78 kd glucose-regulated protein and immunoglobulin heavy chain binding protein. Cell 46, 291–300 (1986).
25
Li J. and Lee A. S., Stress induction of GRP78/BiP and its role in cancer. Curr. Mol. Med. 6, 45–54 (2006).
26
Gorbatyuk M. S. and Gorbatyuk O. S., The molecular chaperone GRP78/BiP as a therapeutic target for neurodegenerative disorders: A mini review. J. Genet. Syndr. Gene Ther. 4, 128 (2013).
27
Booth L., Roberts J. L., Cash D. R., Tavallai S., Jean S., Fidanza A., Cruz-Luna T., Siembiba P., Cycon K. A., Cornelissen C. N., and Dent P., GRP78/BiP/HSPA5/Dna K is a universal therapeutic target for human disease. J. Cell. Physiol. 230, 1661–1676 (2015).
28
Hellen C. U. and Sarnow P., Internal ribosome entry sites in eukaryotic mRNA molecules. Genes Dev. 15, 1593–1612 (2001).
29
Zhou J., Wan J., Gao X., Zhang X., Jaffrey S. R., and Qian S. B., Dynamic m(6)A mRNA methylation directs translational control of heat shock response. Nature 526, 591–594 (2015).
30
Calvo S. E., Pagliarini D. J., and Mootha V. K., Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans. Proc. Natl. Acad. Sci. U.S.A. 106, 7507–7512 (2009).
31
Resch A. M., Ogurtsov A. Y., Rogozin I. B., Shabalina S. A., and Koonin E. V., Evolution of alternative and constitutive regions of mammalian 5′UTRs. BMC Genomics 10, 162 (2009).
32
Ingolia N. T., Lareau L. F., and Weissman J. S., Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147, 789–802 (2011).
33
Lee S., Liu B., Lee S., Huang S. X., Shen B., and Qian S. B., Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution. Proc. Natl. Acad. Sci. U.S.A. 109, E2424–E2432 (2012).
34
Ingolia N. T., Brar G. A., Stern-Ginossar N., Harris M. S., Talhouarne G. J., Jackson S. E., Wills M. R., and Weissman J. S., Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes. Cell Reports 8, 1365–1379 (2014).
35
Cazzola M. and Skoda R. C., Translational pathophysiology: A novel molecular mechanism of human disease. Blood 95, 3280–3288 (2000).
36
Kondo T., Okabe M., Sanada M., Kurosawa M., Suzuki S., Kobayashi M., Hosokawa M., and Asaka M., Familial essential thrombocythemia associated with one-base deletion in the 5′-untranslated region of the thrombopoietin gene. Blood 92, 1091–1096 (1998).
37
Wiestner A., Schlemper R. J., van der Maas A. P., and Skoda R. C., An activating splice donor mutation in the thrombopoietin gene causes hereditary thrombocythaemia. Nat. Genet. 18, 49–52 (1998).
38
Ghilardi N. and Skoda R. C., A single-base deletion in the thrombopoietin (TPO) gene causes familial essential thrombocythemia through a mechanism of more efficient translation of TPO mRNA. Blood 94, 1480–1482 (1999).
39
Slavoff S. A., Mitchell A. J., Schwaid A. G., Cabili M. N., Ma J., Levin J. Z., Karger A. D., Budnik B. A., Rinn J. L., and Saghatelian A., Peptidomic discovery of short open reading frame-encoded peptides in human cells. Nat. Chem. Biol. 9, 59–64 (2013).
40
Andrews S. J. and Rothnagel J. A., Emerging evidence for functional peptides encoded by short open reading frames. Nat. Rev. Genet. 15, 193–204 (2014).
41
Olexiouk V., Crappé J., Verbruggen S., Verhegen K., Martens L., and Menschaert G., sORFs.org: A repository of small ORFs identified by ribosome profiling. Nucleic Acids Res. gkv1175 (2015).
42
Pauli A., Norris M. L., Valen E., Chew G. L., Gagnon J. A., Zimmerman S., Mitchell A., Ma J., Dubrulle J., Reyon D., Tsai S. Q., Joung J. K., Saghatelian A., and Schier A. F., Toddler: An embryonic signal that promotes cell movement via Apelin receptors. Science 343, 1248636 (2014).
43
Andreev D. E., O’Connor P. B., Fahey C., Kenny E. M., Terenin I. M., Dmitriev S. E., Cormican P., Morris D. W., Shatsky I. N., and Baranov P. V., Translation of 5′ leaders is pervasive in genes resistant to eIF2 repression. eLife 4, e03971 (2015).
44
Sidrauski C., McGeachy A. M., Ingolia N. T., and Walter P., The small molecule ISRIB reverses the effects of eIF2α phosphorylation on translation and stress granule assembly. eLife 4, (2015).
45
Somers J., Pöyry T., and Willis A. E., A perspective on mammalian upstream open reading frame function. Int. J. Biochem. Cell Biol. 45, 1690–1700 (2013).
46
Karttunen J., Sanderson S., and Shastri N., Detection of rare antigen-presenting cells by the lacZ T-cell activation assay suggests an expression cloning strategy for T-cell antigens. Proc. Natl. Acad. Sci. U.S.A. 89, 6020–6024 (1992).
47
Materials and methods are available as supplementary materials on Science Online.
48
Harding H. P., Zhang Y., Zeng H., Novoa I., Lu P. D., Calfon M., Sadri N., Yun C., Popko B., Paules R., Stojdl D. F., Bell J. C., Hettmann T., Leiden J. M., and Ron D., An integrated stress response regulates amino acid metabolism and resistance to oxidative stress. Mol. Cell 11, 619–633 (2003).
49
Mielnicki L. M., Hughes R. G., Chevray P. M., and Pruitt S. C., Mutated Atf4 suppresses c-Ha-ras oncogene transcript levels and cellular transformation in NIH3T3 fibroblasts. Biochem. Biophys. Res. Commun. 228, 586–595 (1996).
50
Paton A. W., Beddoe T., Thorpe C. M., Whisstock J. C., Wilce M. C., Rossjohn J., Talbot U. M., and Paton J. C., AB5 subtilase cytotoxin inactivates the endoplasmic reticulum chaperone BiP. Nature 443, 548–552 (2006).
51
Sidrauski C., Acosta-Alvear D., Khoutorsky A., Vedantham P., Hearn B. R., Li H., Gamache K., Gallagher C. M., Ang K. K., Wilson C., Okreglak V., Ashkenazi A., Hann B., Nader K., Arkin M. R., Renslo A. R., Sonenberg N., and Walter P., Pharmacological brake-release of mRNA translation enhances cognitive memory. eLife 2, e00498 (2013).
52
Sidrauski C., Tsai J. C., Kampmann M., Hearn B. R., Vedantham P., Jaishankar P., Sokabe M., Mendez A. S., Newton B. W., Tang E. L., Verschueren E., Johnson J. R., Krogan N. J., Fraser C. S., Weissman J. S., Renslo A. R., and Walter P., Pharmacological dimerization and activation of the exchange factor eIF2B antagonizes the integrated stress response. eLife 4, e07314 (2015).
53
Sekine Y., Zyryanova A., Crespillo-Casado A., Fischer P. M., Harding H. P., and Ron D., Mutations in a translation initiation factor identify the target of a memory-enhancing compound. Science 348, 1027–1030 (2015).
54
Zhan K., Vattem K. M., Bauer B. N., Dever T. E., Chen J. J., and Wek R. C., Phosphorylation of eukaryotic initiation factor 2 by heme-regulated inhibitor kinase-related protein kinases in Schizosaccharomyces pombe is important for resistance to environmental stresses. Mol. Cell. Biol. 22, 7134–7146 (2002).
55
Abastado J. P., Miller P. F., Jackson B. M., and Hinnebusch A. G., Suppression of ribosomal reinitiation at upstream open reading frames in amino acid-starved cells forms the basis for GCN4 translational control. Mol. Cell. Biol. 11, 486–496 (1991).
56
Gülow K., Bienert D., and Haas I. G., BiP is feed-back regulated by control of protein translation efficiency. J. Cell Sci. 115, 2443–2452 (2002).
57
Schwab S. R., Shugart J. A., Horng T., Malarkannan S., and Shastri N., Unanticipated antigens: Translation initiation at CUG with leucine. PLOS Biol. 2, e366 (2004).
58
Starck S. R., Jiang V., Pavon-Eternod M., Prasad S., McCarthy B., Pan T., and Shastri N., Leucine-tRNA initiates at CUG start codons for protein synthesis and presentation by MHC class I. Science 336, 1719–1723 (2012).
59
Liang H., He S., Yang J., Jia X., Wang P., Chen X., Zhang Z., Zou X., McNutt M. A., Shen W. H., and Yin Y., PTENα, a PTEN isoform translated through alternative initiation, regulates mitochondrial function and energy metabolism. Cell Metab. 19, 836–848 (2014).
60
Robert F., Kapp L. D., Khan S. N., Acker M. G., Kolitz S., Kazemi S., Kaufman R. J., Merrick W. C., Koromilas A. E., Lorsch J. R., and Pelletier J., Initiation of protein synthesis by hepatitis C virus is refractory to reduced eIF2·GTP·Met-tRNAiMet ternary complex availability. Mol. Biol. Cell 17, 4632–4644 (2006).
61
Rammensee H., Bachmann J., Emmerich N. P., Bachor O. A., and Stevanović S., SYFPEITHI: Database for MHC ligands and peptide motifs. Immunogenetics 50, 213–219 (1999).
62
Reits E. A., Vos J. C., Grommé M., and Neefjes J., The major substrates for TAP in vivo are derived from newly synthesized proteins. Nature 404, 774–778 (2000).
63
Androlewicz M. J. and Cresswell P., How selective is the transporter associated with antigen processing? Immunity 5, 1–5 (1996).
64
Hammer G. E., Kanaseki T., and Shastri N., The final touches make perfect the peptide-MHC class I repertoire. Immunity 26, 397–406 (2007).
65
Brandvold K. R. and Morimoto R. I., The chemical biology of molecular chaperones—Implications for modulation of proteostasis. J. Mol. Biol. 427, 2931–2947 (2015).
66
Wu B., Hunt C., and Morimoto R., Structure and expression of the human gene encoding major heat shock protein HSP70. Mol. Cell. Biol. 5, 330–341 (1985).
67
Zhang X., Gao X., Coots R. A., Conn C. S., Liu B., and Qian S. B., Translational control of the cytosolic stress response by mitochondrial ribosomal protein L18. Nat. Struct. Mol. Biol. 22, 404–410 (2015).
68
Zoll W. L., Horton L. E., Komar A. A., Hensold J. O., and Merrick W. C., Characterization of mammalian eIF2A and identification of the yeast homolog. J. Biol. Chem. 277, 37079–37087 (2002).
69
Kim J. H., Park S. M., Park J. H., Keum S. J., and Jang S. K., eIF2A mediates translation of hepatitis C viral mRNA under stress conditions. EMBO J. 30, 2454–2464 (2011).
70
Ventoso I., Sanz M. A., Molina S., Berlanga J. J., Carrasco L., and Esteban M., Translational resistance of late alphavirus mRNA to eIF2alpha phosphorylation: A strategy to overcome the antiviral effect of protein kinase PKR. Genes Dev. 20, 87–100 (2006).
71
Macejak D. G. and Sarnow P., Internal initiation of translation mediated by the 5′ leader of a cellular mRNA. Nature 353, 90–94 (1991).
72
Kim Y. K. and Jang S. K., Continuous heat shock enhances translational initiation directed by internal ribosomal entry site. Biochem. Biophys. Res. Commun. 297, 224–231 (2002).
73
Lai M. C., Lee Y. H., and Tarn W. Y., The DEAD-box RNA helicase DDX3 associates with export messenger ribonucleoproteins as well as tip-associated protein and participates in translational control. Mol. Biol. Cell 19, 3847–3858 (2008).
74
Pisareva V. P., Pisarev A. V., Komar A. A., Hellen C. U., and Pestova T. V., Translation initiation on mammalian mRNAs with structured 5′UTRs requires DExH-box protein DHX29. Cell 135, 1237–1250 (2008).
75
Skabkin M. A., Skabkina O. V., Dhote V., Komar A. A., Hellen C. U., and Pestova T. V., Activities of Ligatin and MCT-1/DENR in eukaryotic translation initiation and ribosomal recycling. Genes Dev. 24, 1787–1801 (2010).
76
Oyama M., Itagaki C., Hata H., Suzuki Y., Izumi T., Natsume T., Isobe T., and Sugano S., Analysis of small human proteins reveals the translation of upstream open reading frames of mRNAs. Genome Res. 14 (10B), 2048–2052 (2004).
77
Purbhoo M. A., Irvine D. J., Huppa J. B., and Davis M. M., T cell killing does not require the formation of a stable mature immunological synapse. Nat. Immunol. 5, 524–530 (2004).
78
Hunt D. F., Henderson R. A., Shabanowitz J., Sakaguchi K., Michel H., Sevilir N., Cox A. L., Appella E., and Engelhard V. H., Characterization of peptides bound to the class I MHC molecule HLA-A2.1 by mass spectrometry. Science 255, 1261–1263 (1992).
79
Escobar H., Crockett D. K., Reyes-Vargas E., Baena A., Rockwood A. L., Jensen P. E., and Delgado J. C., Large scale mass spectrometric profiling of peptides eluted from HLA molecules reveals N-terminal-extended peptide motifs. J. Immunol. 181, 4874–4882 (2008).
80
Engelhard V. H., The contributions of mass spectrometry to understanding of immune recognition by T lymphocytes. Int. J. Mass Spectrom. 259, 32–39 (2007).
81
Vanderperre B., Lucier J. F., Bissonnette C., Motard J., Tremblay G., Vanderperre S., Wisztorski M., Salzet M., Boisvert F. M., and Roucou X., Direct detection of alternative open reading frames translation products in human significantly expands the proteome. PLOS ONE 8, e70698 (2013).
82
Crotzer V. L., Christian R. E., Brooks J. M., Shabanowitz J., Settlage R. E., Marto J. A., White F. M., Rickinson A. B., Hunt D. F., and Engelhard V. H., Immunodominance among EBV-derived epitopes restricted by HLA-B27 does not correlate with epitope abundance in EBV-transformed B-lymphoblastoid cell lines. J. Immunol. 164, 6120–6129 (2000).
83
Lubec G. and Afjehi-Sadat L., Limitations and pitfalls in protein identification by mass spectrometry. Chem. Rev. 107, 3568–3584 (2007).
84
Starck S. R. and Shastri N., Non-conventional sources of peptides presented by MHC class I. Cell. Mol. Life Sci. 68, 1471–1479 (2011).
85
Kowalewski D. J., Schuster H., Backert L., Berlin C., Kahn S., Kanz L., Salih H. R., Rammensee H. G., Stevanovic S., and Stickel J. S., HLA ligandome analysis identifies the underlying specificities of spontaneous antileukemia immune responses in chronic lymphocytic leukemia (CLL). Proc. Natl. Acad. Sci. U.S.A. 112, E166–E175 (2015).
86
Law G. L., Raney A., Heusner C., and Morris D. R., Polyamine regulation of ribosome pausing at the upstream open reading frame of S-adenosylmethionine decarboxylase. J. Biol. Chem. 276, 38036–38043 (2001).
87
Ventura A., Meissner A., Dillon C. P., McManus M., Sharp P. A., Van Parijs L., Jaenisch R., and Jacks T., Cre-lox-regulated conditional RNA interference from transgenes. Proc. Natl. Acad. Sci. U.S.A. 101, 10380–10385 (2004).
88
Morinaga N., Yahiro K., Matsuura G., Watanabe M., Nomura F., Moss J., and Noda M., Two distinct cytotoxic activities of subtilase cytotoxin produced by shiga-toxigenic Escherichia coli. Infect. Immun. 75, 488–496 (2007).
89
Sanderson S. and Shastri N., LacZ inducible, antigen/MHC-specific T cell hybrids. Int. Immunol. 6, 369–376 (1994).
90
Kunisawa J. and Shastri N., The group II chaperonin TRiC protects proteolytic intermediates from degradation in the MHC class I antigen processing pathway. Mol. Cell 12, 565–576 (2003).
91
Malarkannan S., Shih P. P., Eden P. A., Horng T., Zuberi A. R., Christianson G., Roopenian D., and Shastri N., The molecular and functional characterization of a dominant minor H antigen, H60. J. Immunol. 161, 3501–3509 (1998).
92
Malarkannan S., Mendoza L. M., and Shastri N., Generation of antigen-specific, lacZ-inducible T-cell hybrids. Methods Mol. Biol. 156, 265–272 (2001).
93
Cardinaud S., Starck S. R., Chandra P., and Shastri N., The synthesis of truncated polypeptides for immune surveillance and viral evasion. PLOS ONE 5, e8692 (2010).
94
Kim Y., Ponomarenko J., Zhu Z., Tamang D., Wang P., Greenbaum J., Lundegaard C., Sette A., Lund O., Bourne P. E., Nielsen M., and Peters B., Immune epitope database analysis resource. Nucleic Acids Res. 40 (W1), W525–W530 (2012).
95
Nielsen M., Lundegaard C., Worning P., Lauemøller S. L., Lamberth K., Buus S., Brunak S., and Lund O., Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci. 12, 1007–1017 (2003).
96
Lundegaard C., Lamberth K., Harndahl M., Buus S., Lund O., and Nielsen M., NetMHC-3.0: Accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8-11. Nucleic Acids Res. 36 (Web Server), W509–W512 (2008).
97
Peters B. and Sette A., Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. BMC Bioinformatics 6, 132 (2005).
98
Sidney J., Assarsson E., Moore C., Ngo S., Pinilla C., Sette A., and Peters B., Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries. Immunome Res. 4, 2 (2008).
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Published In
Science
Volume 351 | Issue 6272
29 January 2016
29 January 2016
Copyright
Copyright © 2016, American Association for the Advancement of Science.
Submission history
Received: 5 September 2015
Accepted: 3 December 2015
Published in print: 29 January 2016
Acknowledgments
We are grateful for technical help from K. Banta and S. J. Yang (University of California, Berkeley) and K. Crotty (University of California, San Francisco). We thank M. Elvekrog, E. Costa, M. Lam, and W. Merrick for critical reading of the manuscript and C. Sidrauski, S. Ramundo, H. Tran, N. Ingolia, and J. Weissman for helpful discussions and advice. The human retinal pigment epithelial cell line (RPE-19) was a gift from X. Gong (School of Optometry, University of California, Berkeley). This research was supported by grants from the NIH to N.S. and P.W. P.W. is an Investigator of the Howard Hughes Medical Institute.
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