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Background: Sequestration of transcription factors in the membrane is emerging as an importantmechanism for the regulation of gene expression. A handful of membrane-spanning transcriptionfactors has been previously identified whose access to the nucleus is regulated by proteolyticcleavage from the membrane. To investigate the existence of other transmembrane transcriptionfactors, we analyzed computationally all proteins in SWISS-PROT/TrEMBL for the combinedpresence of a DNA-binding domain and a transmembrane segment.
Results: Using Pfam hidden Markov models and four transmembrane-prediction programs, weidentified with high confidence 76 membrane-spanning transcription factors in SWISS-PROT/TrEMBL.Analysis of the distribution of two proteins predicted by our method, MTJ1 and DMRT2,confirmed their localization to intracellular membrane compartments. Furthermore, elimination ofthe predicted transmembrane segment led to nuclear localization for each of these proteins.
Conclusions: Our analysis uncovered a wealth of predicted membrane-spanning transcription factorsthat are structurally and taxonomically diverse, 56 of which lack experimental annotation. Seventy-fiveof the proteins are modular in structure, suggesting that a single proteolysis may be sufficient toliberate a DNA-binding domain from the membrane. This study provides grounds for investigationsinto the stimuli and mechanisms that release this intriguing class of transcription factors frommembranes.
Published: 14 November 2001
Genome Biology 2001, 2(12):research0050.1–0050.6
The electronic version of this article is the complete one and can befound online at http://genomebiology.com/2001/2/12/research/0050
Results and discussionComputational analysis of protein databases reveals alarge number of predicted transmembranetranscription factors��� ����� - ��� 5/?6� ������ !������ ������� ��� @+� �B�*
Figure 1 (see the figure on the next page)The domain structure of predicted TMTFs is shown. Pfam-predicted DNA-binding domains, transmembrane segments andbipartite nuclear localization signals are shown for linear protein models and identified by SWISS-PROT/TrEMBL accessionnumber. The total number of proteins predicted for each species is given. Colored icons represent various DNA-bindingdomains. Predicted transmembrane segments for each program are represented by a filled box. Protein lengths are drawnapproximately to scale; positions of domains are approximate. Arrows in MTJ1 and DMRT2 indicate sites for truncatedprotein localization experiments shown in Figure 2. The scale of proteins O80659 and Q9SGP0 is reduced by half. Orthologsof predicted TMTFs not shown are: Luman (Q9UE77 Homo sapiens), SREBP-1 (Q60416 Cricetulus griseus, Q9WTN3 Musmusculus, P56720 Rattus norvegicus, Q9XX00 Caenorhabditis elegans), SREBP-2 (Q9UH04 H. sapiens, Q60429 C. griseus), andAFLR Reg (P43651 Aspergillus parasiticus). Open reading frames (ORFs) for O65420, O43989, Q17928 were extended usingadditional nucleotide sequence available in the NCBI database (indicated by stippled rectangles).
Figure 2Subcellular localizations of predicted and truncated TMTFsin COS-7 cells were detected using anti-Myc antibodies. Full-length proteins are localized to intracellular membranecompartments, but truncated forms (∆∆) lacking predictedtransmembrane segments accumulate in the nucleus. Nucleiare stained with Hoechst. (a) mouse MTJ1; (b) humanDMRT2.
AcknowledgementsWe thank J. Rine and O. Kelly for critical comments on the manuscript,and D. He for assembling overlapping domains. This work was supportedby the NIH (S.E.B. and W.C.S.). S.E.B. and W.C.S. are Searle Scholars.
References1. Kaffman A, O’Shea EK: Regulation of nuclear localization: a key
to a door. Annu Rev Cell Dev Biol 1999, 15:291-339.2. Brown MS, Ye J, Rawson RB, Goldstein JL: Regulated intramem-
brane proteolysis: a control mechanism conserved frombacteria to humans. Cell 2000, 100:391-398.
3. Haze K, Yoshida H, Yanagi H, Yura T, Mori K: Mammalian tran-scription factor ATF6 is synthesized as a transmembraneprotein and activated by proteolysis in response to endo-plasmic reticulum stress. Mol Biol Cell 1999, 10:3787-3799.
4. Haze K, Okada T, Yoshida H, Yanagi H, Yura T, Negishi M, Mori K:Identification of the G13 (cAMP-response-element-bindingprotein-related protein) gene product related to activatingtranscription factor 6 as a transcriptional activator of themammalian unfolded protein response. Biochem J 2001,355:19-28.
5. Dell CL, Neely MN, Olson ER: Altered pH and lysine signallingmutants of cadC, a gene encoding a membrane-bound tran-scriptional activator of the Escherichia coli cadBA operon.Mol Microbiol 1994, 14:7-16.
6. Krukonis ES, Yu RR, Dirita VJ: The Vibrio cholerae ToxR/TcpP/ToxT virulence cascade: distinct roles for two mem-brane-localized transcriptional activators on a single pro-moter. Mol Microbiol 2000, 38:67-84.
7. Lu R, Misra V: Potential role for luman, the cellular homo-logue of herpes simplex virus VP16 (alpha gene trans-induc-ing factor), in herpesvirus latency. J Virol 2000, 74:934-943.
8. Blaumueller CM, Qi H, Zagouras P, Artavanis-Tsakonas S: Intracel-lular cleavage of Notch leads to a heterodimeric receptoron the plasma membrane. Cell 1997, 90:281-291.
9. Hoppe T, Matuschewski K, Rape M, Schlenker S, Ulrich HD, JentschS: Activation of a membrane-bound transcription factor byregulated ubiquitin/proteasome-dependent processing. Cell2000, 102:577-586.
10. Ye J, Rawson RB, Komuro R, Chen X, Dave UP, Prywes R, BrownMS, Goldstein JL: ER stress induces cleavage of membrane-bound ATF6 by the same proteases that process SREBPs.Mol Cell 2000, 6:1355-1364.
11. Artavanis-Tsakonas S, Rand MD, Lake RJ: Notch signaling: cellfate control and signal integration in development. Science1999, 284:770-776.
12. Weinmaster G: Notch signal transduction: a real rip andmore. Curr Opin Genet Dev 2000, 10:363-369.
13. Wang X, Sato R, Brown MS, Hua X, Goldstein JL: SREBP-1, amembrane-bound transcription factor released by sterol-regulated proteolysis. Cell 1994, 77:53-62.
14. Skeiky YA, Drevet JR, Swevers L, Iatrou K: Protein phosphoryla-tion and control of chorion gene activation through tempo-ral mobilization of a promoter DNA binding factor from thecytoplasm into the nucleus. J Biol Chem 1994, 269:12196-12203.
15. Brightman SE, Blatch GL, Zetter BR: Isolation of a mouse cDNAencoding MTJ1, a new murine member of the DnaJ family ofproteins. Gene 1995, 153:249-254.
16. Bateman A, Birney E, Durbin R, Eddy SR, Howe KL, Sonnhammer EL:The Pfam protein families database. Nucleic Acids Res 2000,28:263-266.
17. Bairoch A, Apweiler R: The SWISS-PROT protein sequencedatabase and its supplement TrEMBL in 2000. Nucleic AcidsRes 2000, 28:45-48.
18. Rost B, Fariselli P, Casadio R: Topology prediction for helicaltransmembrane proteins at 86% accuracy. Protein Sci 1996,5:1704-1718.
19. Sonnhammer EL, von Heijne G, Krogh A: A hidden Markovmodel for predicting transmembrane helices in proteinsequences. Proc Int Conf Intell Syst Mol Biol 1998, 6:175-182.
20. Tusnady GE, Simon I: Principles governing amino acid compo-sition of integral membrane proteins: application to topol-ogy prediction. J Mol Biol 1998, 283:489-506.
21. Nakai K, Horton P: PSORT: a program for detecting sortingsignals in proteins and predicting their subcellular localiza-tion. Trends Biochem Sci 1999, 24:34-36.
22. Raymond CS, Shamu CE, Shen MM, Seifert KJ, Hirsch B, Hodgkin J,Zarkower D: Evidence for evolutionary conservation of sex-determining genes. Nature 1998, 391:691-695.
23. Raymond CS, Parker ED, Kettlewell JR, Brown LG, Page DC, Kusz K,Jaruzelska J, Reinberg Y, Flejter WL, Bardwell VJ, et al.: A region ofhuman chromosome 9p required for testis developmentcontains two genes related to known sexual regulators. HumMol Genet 1999, 8:989-996.
24. Lum DH, Kuwabara PE, Zarkower D, Spence AM: Direct protein-protein interaction between the intracellular domain ofTRA-2 and the transcription factor TRA-1A modulates fem-inizing activity in C. elegans. Genes Dev 2000, 14:3153-3165.
25. Yi W, Ross JM, Zarkower D: mab-3 is a direct tra-1 target generegulating diverse aspects of C. elegans male sexual develop-ment and behavior. Development 2000, 127:4469-4480.
26. Ausubel FM: Current Protocols in Molecular Biology. New York: GreenePublishing. Associates/Wiley-Interscience; 1988.