Publikationsserver der Universitätsbibliothek Marburg
Titel:Identifikation neuer Komponenten der dritten Plastidenmembran und Subkompartimentierung des endoplasmatischen Retikulums in Phaeodactylum tricornutum
Autor:Gentil, Jonny
Weitere Beteiligte: Maier, Uwe (Prof. Dr.)
Veröffentlicht:2017
URI:https://archiv.ub.uni-marburg.de/diss/z2018/0045
DOI: https://doi.org/10.17192/z2018.0045
URN: urn:nbn:de:hebis:04-z2018-00457
DDC: Biowissenschaften, Biologie
Titel (trans.):Identification of new components of the third plastidal membrane and subcompartmentalization of the endoplasmic reticulum of Phaeodactylum tricornutum
Publikationsdatum:2018-01-08
Lizenz:https://rightsstatements.org/vocab/InC-NC/1.0/

Dokument

Schlagwörter:
cER, cER, Plastidenevolution, Phaeodactylum tricornutum, Diatomeen, β-barrel proteins, sekundäre Endosymbiose, hER, Phaeodactylum tricornutum, komplexe Plastiden, BAM, hER, diatoms, BAM, complex plastids, endoplasmatisches Retikulum, β-barrel Proteine, Subkompartimentierung, endoplasmic reticulum

Zusammenfassung:
Durch einen Prozess, der als sekundäre Endosymbiose bezeichnet wird, wurde eine Rotalge als Endosymbiont aufgenommen. Dies führte zur Entstehung der komplexen Plastiden von Cryptophyten, Haptophyten, Heterokontophyten und Apicomplexa. Das Genom dieser ehemaligen Rotalge wurde im Laufe der Evolution dramatisch reduziert und zum größten Teil in den Wirtskern transferiert. Dies führte dazu, dass die meisten plastidären Proteine nun im Zellkern des Wirtes kodiert sind und aus dem Cytosol in die Plastide importiert werden müssen. Es mussten entsprechende Translokationsmechanismen entwickelt werden. Im Rahmen dieser Arbeit wurde versucht neue Komponenten der dritten Plastidenmembran zu identifizieren, welche auf die äußere Chloroplastenmembran primärer Plastiden zurückgeht. Diese Membran unterscheidet sich von anderen plastidären Membranen durch die Präsenz von β-barrel Proteinen, die für die äußeren Membranen von Gram-negativen Bakterien, Mitochondrien und Chloroplasten charakteristisch sind. Mit Hilfe verschiedener Algorithmen wurden putative plastidäre β-barrel Proteine vorhergesagt und als Fusionsproteine in P. tricornutum lokalisiert. Es wurden von 23 Proteinen, vier in der Plasmamembran, vier im Cytosol, fünf im ER, fünf außerhalb der Plastide und fünf in der Plastide lokalisiert. Es konnte kein Protein in der dritten Plastidenmembran identifiziert werden. Die Vorhersagealgorithmen sind nicht dafür geeignet eukaryote Proteome auf β-barrel Proteine hin zu analysieren. Des Weiteren lag ein anderes Problem in der Beschaffenheit der Genmodelle, welche die Basis der Vorhersage bildeten. In einem zweiten Projekt wurde die Subkompartimentierung des ERs in P. tricornutum untersucht. Basierend auf der Erkenntnis, dass das ER in ein hostER, die Kernhülle (NE) und das cER eingeteilt werden kann, wurde untersucht, ob sich hER und cER in ihrer Funktion unterscheiden. Basierend auf der Annahme, dass hER und cER durch den Tag-Nacht-Zyklus der Photosynthese unterschiedlichen physiologischen Bedingungen ausgesetzt sind, wurde gefolgert, dass einige Funktionen wie zum Beispiel die Proteinqualitätskontrolle und -faltung auf das hER beschränkt sein könnten. Daher wurden Faktoren der UPR in P. tricornutum untersucht. Überraschenderweise konnten IRE1 und PERK in Heterokontophyten und Haptophyten identifiziert werden. Lokalisationsstudien der UPR-Faktoren zeigten, dass diese hauptsächlich auf das hER und den NE beschränkt sind, wohingegen hDer1-2 als Beispiel für Proteindegradation im gesamten ER und Transporterproteine wie Tpt1 hauptsächlich im cER vorhanden sind. Die Abwesenheit der UPR im cER lässt sich durch die Physiologie begründen. Außerdem wirft die Präsenz von PERK und IRE1 in Protisten ein neues Licht auf die Sichtweise der Evolution der UPR. So ist eine alternative Entstehungsgeschichte der UPR denkbar.

Bibliographie / References

  1. Richter, S.; Lamppa, G. K. (1998): A chloroplast processing enzyme functions as the general stromal processing peptidase. In: Proceedings of the National Academy of Sciences of the United States of America 95 (13), S. 7463-7468.
  2. Taniura, H.; Glass, C.; Gerace, L. (1995): A chromatin binding site in the tail domain of nuclear lamins that interacts with core histones. In: The Journal of cell biology 131 (1), S. 33-44.
  3. Käll, L.; Krogh, A.; Sonnhammer, E. L. L. (2004): A combined transmembrane topology and signal peptide prediction method. In: Journal of molecular biology 338 (5), S. 1027-1036.
  4. Janouskovec, J.; Horák, A.; Oborník, M.; Lukes, J.; Keeling, P. J. (2010): A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids. In: Proceedings of the National Academy of Sciences of the United States of America 107 (24), S. 10949-10954.
  5. Lahiri, S.; Chao, J. T.; Tavassoli, S.; Wong, A. K. O.; Choudhary, V.; Young, B. P. et al. (2014): A conserved endoplasmic reticulum membrane protein complex (EMC) facilitates phospholipid transfer from the ER to mitochondria. In: PLoS biology 12 (10), e1001969.
  6. Iwata, Y.; Ashida, M.; Hasegawa, C.; Tabara, K.; Mishiba, K.-I.; Koizumi, N. (2017): Activation of the Arabidopsis membrane-bound transcription factor bZIP28 is mediated by site-2 protease, but not site-1 protease. In: The Plant journal : for cell and molecular biology 91 (3), S. 408-415.
  7. Kobylewski, S. E.; Henderson, K. A.; Yamada, K. E.; Eckhert, C. D. (2017): Activation of the EIF2α/ATF4 and ATF6 Pathways in DU-145 Cells by Boric Acid at the Concentration Reported in Men at the US Mean Boron Intake. In: Biological trace element research 176 (2), S. 278-293.
  8. Liu, X.; Hempel, F.; Stork, S.; Bolte, K.; Moog, D.; Heimerl, T. et al. (2016): Addressing various compartments of the diatom model organism Phaeodactylum tricornutum via sub-cellular marker proteins. In: Algal Research 20, S. 249-257.
  9. Käll, L.; Krogh, A.; Sonnhammer, E. L. L. (2007): Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server. In: Nucleic acids research 35 (Web Server issue), W429-432.
  10. Joshi, A. S.; Huang, X.; Choudhary, V.; Levine, T. P.; Hu, J.; Prinz, W. A. (2016): A family of membrane-shaping proteins at ER subdomains regulates pre-peroxisomal vesicle biogenesis. In: The Journal of cell biology 215 (4), S. 515-529.
  11. Bae, W.; Lee, Y. J.; Kim, D. H.; Lee, J.; Kim, S.; Sohn, E. J.; Hwang, I. (2008): AKR2A-mediated import of chloroplast outer membrane proteins is essential for chloroplast biogenesis. In: Nature cell biology 10 (2), S. 220-227.
  12. Curtis, B. A.; Tanifuji, G.; Burki, F.; Gruber, A.; Irimia, M.; Maruyama, S. et al. (2012): Algal genomes reveal evolutionary mosaicism and the fate of nucleomorphs. In: Nature 492 (7427), S. 59-65.
  13. Yoon, H. S.; Hackett, J. D.; Ciniglia, C.; Pinto, G.; Bhattacharya, D. (2004): A molecular timeline for the origin of photosynthetic eukaryotes. In: Molecular biology and evolution 21 (5), S. 809-818.
  14. Kim, D. H.; Park, M.-J.; Gwon, G. H.; Silkov, A.; Xu, Z.-Y.; Yang, E. C. et al. (2014): An ankyrin repeat domain of AKR2 drives chloroplast targeting through coincident binding of two chloroplast lipids. In: Developmental cell 30 (5), S. 598-609.
  15. Liu, J.-X.; Srivastava, R.; Che, P.; Howell, S. H. (2007): An endoplasmic reticulum stress response in Arabidopsis is mediated by proteolytic processing and nuclear relocation of a membrane- associated transcription factor, bZIP28. In: The Plant cell 19 (12), S. 4111-4119.
  16. Spycher, C.; Herman, E. K.; Morf, L.; Qi, W.; Rehrauer, H.; Aquino Fournier, C. et al. (2013): An ER- directed transcriptional response to unfolded protein stress in the absence of conserved sensor- transducer proteins in Giardia lamblia. In: Molecular microbiology 88 (4), S. 754-771.
  17. Tranel, P. J.; Keegstra, K. (1996): A novel, bipartite transit peptide targets OEP75 to the outer membrane of the chloroplastic envelope. In: The Plant cell 8 (11), S. 2093-2104.
  18. Li, H. m.; Chen, L. J. (1997): A novel chloroplastic outer membrane-targeting signal that functions at both termini of passenger polypeptides. In: The Journal of biological chemistry 272 (16), S. 10968-10974.
  19. Kamhi-Nesher, S.; Shenkman, M.; Tolchinsky, S.; Fromm, S. V.; Ehrlich, R.; Lederkremer, G. Z. (2001): A novel quality control compartment derived from the endoplasmic reticulum. In: Molecular biology of the cell 12 (6), S. 1711-1723.
  20. Lee, Y.-Y.; Cevallos, R. C.; Jan, E. (2009): An upstream open reading frame regulates translation of GADD34 during cellular stresses that induce eIF2alpha phosphorylation. In: The Journal of biological chemistry 284 (11), S. 6661-6673.
  21. Marin, B.; Nowack, E. C. M.; Melkonian, M. (2005): A plastid in the making: evidence for a second primary endosymbiosis. In: Protist 156 (4), S. 425-432.
  22. Inoue, K.; Keegstra, K. (2003): A polyglycine stretch is necessary for proper targeting of the protein translocation channel precursor to the outer envelope membrane of chloroplasts. In: The Plant journal : for cell and molecular biology 34 (5), S. 661-669.
  23. Karnik, S. K.; Trelease, R. N. (2005): Arabidopsis peroxin 16 coexists at steady state in peroxisomes and endoplasmic reticulum. In: Plant physiology 138 (4), S. 1967-1981.
  24. Karnik, S. K.; Trelease, R. N. (2007): Arabidopsis peroxin 16 trafficks through the ER and an intermediate compartment to pre-existing peroxisomes via overlapping molecular targeting signals. In: Journal of experimental botany 58 (7), S. 1677-1693.
  25. Birnboim, H. C.; Doly, J. (1979): A rapid alkaline extraction procedure for screening recombinant plasmid DNA. In: Nucleic acids research 7 (6), S. 1513-1523.
  26. Schaffner, W.; Weissmann, C. (1973): A rapid, sensitive, and specific method for the determination of protein in dilute solution. In: Analytical biochemistry 56 (2), S. 502-514.
  27. Doyle, J.J., Doyle, J.L. (1990): A rapid total DNA preparation procedure for fresh plant tissue. In: Focus (12), S. 13-15.
  28. Misra, R. (2012): Assembly of the beta-Barrel Outer Membrane Proteins in Gram-Negative Bacteria, Mitochondria, and Chloroplasts. In: ISRN molecular biology 2012, 708203.
  29. Habib, S. J.; Waizenegger, T.; Lech, M.; Neupert, W.; Rapaport, D. (2005): Assembly of the TOB complex of mitochondria. In: The Journal of biological chemistry 280 (8), S. 6434-6440.
  30. Wang, Y.; Wang, R.; Jin, F.; Liu, Y.; Yu, J.; Fu, X.; Chang, Z. (2016): A Supercomplex Spanning the Inner and Outer Membranes Mediates the Biogenesis of beta-Barrel Outer Membrane Proteins in Bacteria. In: The Journal of biological chemistry 291 (32), S. 16720-16729.
  31. Yoshida, H.; Okada, T.; Haze, K.; Yanagi, H.; Yura, T.; Negishi, M.; Mori, K. (2000): ATF6 activated by proteolysis binds in the presence of NF-Y (CBF) directly to the cis-acting element responsible for the mammalian unfolded protein response. In: Molecular and cellular biology 20 (18), S. 6755- 6767.
  32. Inaba, T.; Li, M.; Alvarez-Huerta, M.; Kessler, F.; Schnell, D. J. (2003): atTic110 functions as a scaffold for coordinating the stromal events of protein import into chloroplasts. In: The Journal of biological chemistry 278 (40), S. 38617-38627.
  33. Xie, W.; Chojnowski, A.; Boudier, T.; Lim, J. S. Y.; Ahmed, S.; Ser, Z. et al. (2016): A-type Lamins Form Distinct Filamentous Networks with Differential Nuclear Pore Complex Associations. In: Current biology : CB 26 (19), S. 2651-2658.
  34. Heuck, A.; Schleiffer, A.; Clausen, T. (2011): Augmenting β-augmentation. Structural basis of how BamB binds BamA and may support folding of outer membrane proteins. In: Journal of molecular biology 406 (5), S. 659-666.
  35. Endo, T.; Kawano, S.; Yamano, K. (2011): BamE structure. The assembly of β-barrel proteins in the outer membranes of bacteria and mitochondria. In: EMBO reports 12 (2), S. 94-95.
  36. Srivastava, R.; Deng, Y.; Shah, S.; Rao, A. G.; Howell, S. H. (2013): BINDING PROTEIN is a master regulator of the endoplasmic reticulum stress sensor/transducer bZIP28 in Arabidopsis. In: The Plant cell 25 (4), S. 1416-1429.
  37. Becker, T.; Wenz, L.-S.; Thornton, N.; Stroud, D.; Meisinger, C.; Wiedemann, N.; Pfanner, N. (2011): Biogenesis of mitochondria: dual role of Tom7 in modulating assembly of the preprotein translocase of the outer membrane. In: Journal of molecular biology 405 (1), S. 113-124.
  38. Stroud, D. A.; Becker, T.; Qiu, J.; Stojanovski, D.; Pfannschmidt, S.; Wirth, C. et al. (2011): Biogenesis of mitochondrial beta-barrel proteins: the POTRA domain is involved in precursor release from the SAM complex. In: Molecular biology of the cell 22 (16), S. 2823-2833.
  39. Pincus, D.; Chevalier, M. W.; Aragón, T.; van Anken, E.; Vidal, S. E.; El-Samad, H.; Walter, P. (2010): BiP binding to the ER-stress sensor Ire1 tunes the homeostatic behavior of the unfolded protein response. In: PLoS biology 8 (7), e1000415.
  40. Ishiwata-Kimata, Y.; Promlek, T.; Kohno, K.; Kimata, Y. (2013): BiP-bound and nonclustered mode of Ire1 evokes a weak but sustained unfolded protein response. In: Genes to cells : devoted to molecular & cellular mechanisms 18 (4), S. 288-301.
  41. Hayat, S.; Elofsson, A. (2012): BOCTOPUS: improved topology prediction of transmembrane beta barrel proteins. In: Bioinformatics (Oxford, England) 28 (4), S. 516-522.
  42. Berven, F. S.; Flikka, K.; Jensen, H. B.; Eidhammer, I. (2004): BOMP: a program to predict integral beta-barrel outer membrane proteins encoded within genomes of Gram-negative bacteria. In: Nucleic acids research 32 (Web Server issue), S. W394-399.
  43. Liu, J.-X.; Howell, S. H. (2010): bZIP28 and NF-Y transcription factors are activated by ER stress and assemble into a transcriptional complex to regulate stress response genes in Arabidopsis. In: The Plant cell 22 (3), S. 782-796.
  44. Struyvé, M.; Moons, M.; Tommassen, J. (1991): Carboxy-terminal phenylalanine is essential for the correct assembly of a bacterial outer membrane protein. In: Journal of molecular biology 218 (1), S. 141-148.
  45. Wieckowski, M. R.; Cavagna, D. et al. (2006): Chaperone-mediated coupling of endoplasmic reticulum and mitochondrial Ca2+ channels. In: The Journal of cell biology 175 (6), S. 901-911.
  46. Courjol, F.; Mouveaux, T.; Lesage, K.; Saliou, J.-M.; Werkmeister, E.; Bonabaud, M. et al. (2017): Characterization of a nuclear pore protein sheds light on the roles and composition of the Toxoplasma gondii nuclear pore complex. In: Cellular and molecular life sciences : CMLS 74 (11), S. 2107-2125.
  47. Gibson, D. G.; Smith, H. O.; Hutchison, C. A. 3.; Venter, J. C.; Merryman, C. (2010): Chemical synthesis of the mouse mitochondrial genome. In: Nature methods 7 (11), S. 901-903.
  48. Ulrich, T.; Gross, L. E.; Sommer, M. S.; Schleiff, E.; Rapaport, D. (2012): Chloroplast beta-barrel proteins are assembled into the mitochondrial outer membrane in a process that depends on the TOM and TOB complexes. In: The Journal of biological chemistry 287 (33), S. 27467-27479.
  49. Sommer, M. S.; Daum, B.; Gross, L. E.; Weis, B. L. M.; Mirus, O.; Abram, L. et al. (2011): Chloroplast Omp85 proteins change orientation during evolution. In: Proceedings of the National Academy of Sciences of the United States of America 108 (33), S. 13841-13846.
  50. Bodyl, A.; Stiller, J. W.; Mackiewicz, P. (2009): Chromalveolate plastids: direct descent or multiple endosymbioses? In: Trends in ecology & evolution 24 (3), S. 119-121.
  51. Laemmli, U. K. (1970): Cleavage of structural proteins during the assembly of the head of bacteriophage T4. In: Nature 227 (5259), S. 680-685.
  52. Saito, K.; Yamashiro, K.; Shimazu, N.; Tanabe, T.; Kontani, K.; Katada, T. (2014): Concentration of Sec12 at ER exit sites via interaction with cTAGE5 is required for collagen export. In: The Journal of cell biology 206 (6), S. 751-762.
  53. Hooks, K. B.; Griffiths-Jones, S. (2011): Conserved RNA structures in the non-canonical Hac1/Xbp1 intron. In: RNA biology 8 (4), S. 552-556.
  54. Hoepfner, D.; Schildknegt, D.; Braakman, I.; Philippsen, P.; Tabak, H. F. (2005): Contribution of the endoplasmic reticulum to peroxisome formation. In: Cell 122 (1), S. 85-95.
  55. Kakoi, S.; Yorimitsu, T.; Sato, K. (2013): COPII machinery cooperates with ER-localized Hsp40 to sequester misfolded membrane proteins into ER-associated compartments. In: Molecular biology of the cell 24 (5), S. 633-642.
  56. Urano, F.; Wang, X.; Bertolotti, A.; Zhang, Y.; Chung, P.; Harding, H. P.; Ron, D. (2000): Coupling of stress in the ER to activation of JNK protein kinases by transmembrane protein kinase IRE1. In: Science (New York, N.Y.) 287 (5453), S. 664-666.
  57. Kim, K. H.; Aulakh, S.; Tan, W.; Paetzel, M. (2011b): Crystallographic analysis of the C-terminal domain of the Escherichia coli lipoprotein BamC. In: Acta crystallographica. Section F, Structural biology and crystallization communications 67 (Pt 11), S. 1350-1358.
  58. Sandoval, C. M.; Baker, S. L.; Jansen, K.; Metzner, S. I.; Sousa, M. C. (2011): Crystal structure of BamD. An essential component of the β-Barrel assembly machinery of gram-negative bacteria. In: Journal of molecular biology 409 (3), S. 348-357.
  59. Kim, K. H.; Aulakh, S.; Paetzel, M. (2011a): Crystal structure of β-barrel assembly machinery BamCD protein complex. In: The Journal of biological chemistry 286 (45), S. 39116-39121.
  60. Kim, K. H.; Paetzel, M. (2011): Crystal structure of Escherichia coli BamB, a lipoprotein component of the β-barrel assembly machinery complex. In: Journal of molecular biology 406 (5), S. 667-678.
  61. AhYoung, A. P.; Lu, B.; Cascio, D.; Egea, P. F. (2017): Crystal structure of Mdm12 and combinatorial reconstitution of Mdm12/Mmm1 ERMES complexes for structural studies. In: Biochemical and biophysical research communications 488 (1), S. 129-135.
  62. Lehr, U.; Schütz, M.; Oberhettinger, P.; Ruiz-Perez, F.; Donald, J. W.; Palmer, T. et al. (2010): C- terminal amino acid residues of the trimeric autotransporter adhesin YadA of Yersinia enterocolitica are decisive for its recognition and assembly by BamA. In: Molecular microbiology 78 (4), S. 932-946.
  63. Fellerer, C.; Schweiger, R.; Schongruber, K.; Soll, J.; Schwenkert, S. (2011): Cytosolic HSP90 cochaperones HOP and FKBP interact with freshly synthesized chloroplast preproteins of Arabidopsis. In: Molecular plant 4 (6), S. 1133-1145.
  64. Kim, D. H.; Lee, J.-E.; Xu, Z.-Y.; Geem, K. R.; Kwon, Y.; Park, J. W.; Hwang, I. (2015): Cytosolic targeting factor AKR2A captures chloroplast outer membrane-localized client proteins at the ribosome during translation. In: Nature communications 6, S. 6843.
  65. Guo, J.; Polymenis, M. (2006): Dcr2 targets Ire1 and downregulates the unfolded protein response in Saccharomyces cerevisiae. In: EMBO reports 7 (11), S. 1124-1127.
  66. Hollien, J.; Weissman, J. S. (2006): Decay of endoplasmic reticulum-localized mRNAs during the unfolded protein response. In: Science (New York, N.Y.) 313 (5783), S. 104-107.
  67. Simm, S.; Papasotiriou, D. G.; Ibrahim, M.; Leisegang, M. S.; Müller, B.; Schorge, T. et al. (2013): Defining the core proteome of the chloroplast envelope membranes. In: Frontiers in plant science 4.
  68. Sklar, J. G.; Wu, T.; Kahne, D.; Silhavy, T. J. (2007): Defining the roles of the periplasmic chaperones SurA, Skp, and DegP in Escherichia coli. In: Genes & development 21 (19), S. 2473- 2484.
  69. Sommer, M. S.; Gould, S. B.; Lehmann, P.; Gruber, A.; Przyborski, J. M.; Maier, U.-G. (2007): Der1- mediated preprotein import into the periplastid compartment of chromalveolates? In: Molecular biology and evolution 24 (4), S. 918-928.
  70. angeregt. Die Fluoreszenz wurde mit Photomultiplier auf verschiedenen Kanälen detektiert. eGFP wurde bei 500 -525 nm, der MitoTracker bei 560 -590 nm, mRFP bei 580 -600 nm und die Chlorophyll Autofluoreszenz bei 625 -720 nm detektiert.
  71. Foth, B. J.; Ralph, S. A.; Tonkin, C. J.; Struck, N. S.; Fraunholz, M.; Roos, D. S. et al. (2003): Dissecting apicoplast targeting in the malaria parasite Plasmodium falciparum. In: Science (New York, N.Y.) 299 (5607), S. 705-708.
  72. Kutik, S.; Stojanovski, D.; Becker, L.; Becker, T.; Meinecke, M.; Krüger, V. et al. (2008): Dissecting membrane insertion of mitochondrial beta-barrel proteins. In: Cell 132 (6), S. 1011-1024.
  73. McMorran, L. M.; Bartlett, A. I.; Huysmans, G. H. M.; Radford, S. E.; Brockwell, D. J. (2013): Dissecting the effects of periplasmic chaperones on the in vitro folding of the outer membrane protein PagP. In: Journal of molecular biology 425 (17), S. 3178-3191.
  74. Maeda, M.; Saito, K.; Katada, T. (2016): Distinct isoform-specific complexes of TANGO1 cooperatively facilitate collagen secretion from the endoplasmic reticulum. In: Molecular biology of the cell 27 (17), S. 2688-2696.
  75. Dhanoa, P. K.; Richardson, L. G. L.; Smith, M. D.; Gidda, S. K.; Henderson, M. P. A.; Andrews, D. W.; Mullen, R. T. (2010): Distinct pathways mediate the sorting of tail-anchored proteins to the plastid outer envelope. In: PloS one 5 (4), e10098.
  76. Agrawal, G.; Fassas, S. N.; Xia, Z.-J.; Subramani, S. (2016): Distinct requirements for intra-ER sorting and budding of peroxisomal membrane proteins from the ER. In: The Journal of cell biology 212 (3), S. 335-348.
  77. Stork, S.; Moog, D.; Przyborski, J. M.; Wilhelmi, I.; Zauner, S.; Maier, U. G. (2012): Distribution of the SELMA translocon in secondary plastids of red algal origin and predicted uncoupling of ubiquitin-dependent translocation from degradation. In: Eukaryotic cell 11 (12), S. 1472-1481.
  78. Dorrell, R. G.; Smith, A. G. (2011): Do red and green make brown?: perspectives on plastid acquisitions within chromalveolates. In: Eukaryotic cell 10 (7), S. 856-868.
  79. Bertolotti, A.; Zhang, Y.; Hendershot, L. M.; Harding, H. P.; Ron, D. (2000): Dynamic interaction of BiP and ER stress transducers in the unfolded-protein response. In: Nature cell biology 2 (6), S. 326-332.
  80. Towbin, H.; Staehelin, T.; Gordon, J. (1979): Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: procedure and some applications. In: Proceedings of the National Academy of Sciences of the United States of America 76 (9), S. 4350-4354.
  81. Santi-Rocca, J.; Smith, S.; Weber, C.; Pineda, E.; Hon, C.-C.; Saavedra, E. et al. (2012): Endoplasmic reticulum stress-sensing mechanism is activated in Entamoeba histolytica upon treatment with nitric oxide. In: PloS one 7 (2), e31777.
  82. Nowack, E. C. M.; Vogel, H.; Groth, M.; Grossman, A. R.; Melkonian, M.; Glockner, G. (2011): Endosymbiotic gene transfer and transcriptional regulation of transferred genes in Paulinella chromatophora. In: Molecular biology and evolution 28 (1), S. 407-422.
  83. Burki, F.; Imanian, B.; Hehenberger, E.; Hirakawa, Y.; Maruyama, S.; Keeling, P. J. (2014): Endosymbiotic gene transfer in tertiary plastid-containing dinoflagellates. In: Eukaryotic cell 13 (2), S. 246-255.
  84. Zimorski, V.; Ku, C.; Martin, W. F.; Gould, S. B. (2014): Endosymbiotic theory for organelle origins. In: Current opinion in microbiology 22, S. 38-48.
  85. Gibson, D. G.; Young, L.; Chuang, R.-Y.; Venter, J. C.; Hutchison, C. A. 3.; Smith, H. O. (2009): Enzymatic assembly of DNA molecules up to several hundred kilobases. In: Nature methods 6 (5), S. 343-345.
  86. Felsner, G.; Sommer, M. S.; Gruenheit, N.; Hempel, F.; Moog, D.; Zauner, S. et al. (2011): ERAD components in organisms with complex red plastids suggest recruitment of a preexisting protein transport pathway for the periplastid membrane. In: Genome biology and evolution 3, S. 140-150.
  87. Hempel, F.; Bullmann, L.; Lau, J.; Zauner, S.; Maier, U. G. (2009): ERAD-derived preprotein transport across the second outermost plastid membrane of diatoms. In: Molecular biology and evolution 26 (8), S. 1781-1790.
  88. Ye, J.; Rawson, R. B.; Komuro, R.; Chen, X.; Davé, U. P.; Prywes, R. et al. (2000): ER stress induces cleavage of membrane-bound ATF6 by the same proteases that process SREBPs. In: Molecular cell 6 (6), S. 1355-1364.
  89. Shen, J.; Chen, X.; Hendershot, L.; Prywes, R. (2002): ER stress regulation of ATF6 localization by dissociation of BiP/GRP78 binding and unmasking of Golgi localization signals. In: Developmental cell 3 (1), S. 99-111.
  90. Villarejo, A.; Buren, S.; Larsson, S.; Dejardin, A.; Monne, M.; Rudhe, C. et al. (2005): Evidence for a protein transported through the secretory pathway en route to the higher plant chloroplast. In: Nature cell biology 7 (12), S. 1224-1231.
  91. Hehenberger, E.; Imanian, B.; Burki, F.; Keeling, P. J. (2014): Evidence for the retention of two evolutionary distinct plastids in dinoflagellates with diatom endosymbionts. In: Genome biology and evolution 6 (9), S. 2321-2334.
  92. Day, P. M.; Potter, D.; Inoue, K. (2014): Evolution and targeting of Omp85 homologs in the chloroplast outer envelope membrane. In: Frontiers in plant science 5, 535.
  93. Ulrich, T.; Oberhettinger, P.; Schutz, M.; Holzer, K.; Ramms, A. S.; Linke, D. et al. (2014): Evolutionary conservation in biogenesis of beta-barrel proteins allows mitochondria to assemble a functional bacterial trimeric autotransporter protein. In: The Journal of biological chemistry 289 (43), S. 29457-29470.
  94. Hollien, J. (2013): Evolution of the unfolded protein response. In: Biochimica et biophysica acta 1833 (11), S. 2458-2463.
  95. Novoa, I.; Zeng, H.; Harding, H. P.; Ron, D. (2001): Feedback inhibition of the unfolded protein response by GADD34-mediated dephosphorylation of eIF2alpha. In: The Journal of cell biology 153 (5), S. 1011-1022.
  96. Bullmann, L.; Haarmann, R.; Mirus, O.; Bredemeier, R.; Hempel, F.; Maier, U. G.; Schleiff, E. (2010): Filling the gap, evolutionarily conserved Omp85 in plastids of chromalveolates. In: The Journal of biological chemistry 285 (9), S. 6848-6856.
  97. Bagos, P. G.; Liakopoulos, T. D.; Hamodrakas, S. J. (2004a): Finding beta-barrel outer membrane proteins with a markov chain model. In: WSEAS Transactions on Biology and Biomedicine 2004 (2), S. 186-189.
  98. Knowles, T. J.; Jeeves, M.; Bobat, S.; Dancea, F.; McClelland, D.; Palmer, T. et al. (2008): Fold and function of polypeptide transport-associated domains responsible for delivering unfolded proteins to membranes. In: Molecular microbiology 68 (5), S. 1216-1227.
  99. Frost, A.; Elgort, M. G.; Brandman, O.; Ives, C.; Collins, S. R.; Miller-Vedam, L. et al. (2012): Functional repurposing revealed by comparing S. pombe and S. cerevisiae genetic interactions. In: Cell 149 (6), S. 1339-1352.
  100. Bos, M. P.; Robert, V.; Tommassen, J. (2007): Functioning of outer membrane protein assembly factor Omp85 requires a single POTRA domain. In: EMBO reports 8 (12), S. 1149-1154.
  101. Herrmann (1998): Gene transfer from organelles to the nucleus: how much, what happens, and Why? In: Plant physiology 118 (1), S. 9-17.
  102. Moustafa, A.; Beszteri, B.; Maier, U. G.; Bowler, C.; Valentin, K.; Bhattacharya, D. (2009): Genomic footprints of a cryptic plastid endosymbiosis in diatoms. In: Science (New York, N.Y.) 324 (5935), S. 1724-1726.
  103. Archibald, J. M. (2015): Genomic perspectives on the birth and spread of plastids. In: Proceedings of the National Academy of Sciences of the United States of America 112 (33), S. 10147-10153.
  104. Cavalier-Smith, T. (2003): Genomic reduction and evolution of novel genetic membranes and protein-targeting machinery in eukaryote-eukaryote chimaeras (meta-algae). In: Philosophical transactions of the Royal Society of London. Series B, Biological sciences 358 (1429), 109-134.
  105. Cheng, G.; Feng, Z.; He, B. (2005): Herpes simplex virus 1 infection activates the endoplasmic reticulum resident kinase PERK and mediates eIF-2alpha dephosphorylation by the gamma(1)34.5 protein. In: Journal of virology 79 (3), S. 1379-1388.
  106. Mayerhofer, P. U.; Bañó-Polo, M.; Mingarro, I.; Johnson, A. E. (2016): Human Peroxin PEX3 Is Co- translationally Integrated into the ER and Exits the ER in Budding Vesicles. In: Traffic (Copenhagen, Denmark) 17 (2), S. 117-130.
  107. Kilian, O.; Kroth, P. G. (2005): Identification and characterization of a new conserved motif within the presequence of proteins targeted into complex diatom plastids. In: The Plant journal : for cell and molecular biology 41 (2), S. 175-183.
  108. Hayashi, S.; Takahashi, H.; Wakasa, Y.; Kawakatsu, T.; Takaiwa, F. (2013): Identification of a cis- element that mediates multiple pathways of the endoplasmic reticulum stress response in rice. In: The Plant journal : for cell and molecular biology 74 (2), S. 248-257.
  109. Lee, Y. J.; Kim, D. H.; Kim, Y. W.; Hwang, I. (2001): Identification of a signal that distinguishes between the chloroplast outer envelope membrane and the endomembrane system in vivo. In: The Plant cell 13 (10), S. 2175-2190.
  110. Akita, M.; Nielsen, E.; Keegstra, K. (1997): Identification of protein transport complexes in the chloroplastic envelope membranes via chemical cross-linking. In: The Journal of cell biology 136 (5), S. 983-994.
  111. Kessler, F.; Blobel, G.; Patel, H. A.; Schnell, D. J. (1994): Identification of two GTP-binding proteins in the chloroplast protein import machinery. In: Science (New York, N.Y.) 266 (5187), S. 1035- 1039.
  112. Tu, S.-L.; Chen, L.-J.; Smith, M. D.; Su, Y.-s.; Schnell, D. J.; Li, H.-M. (2004): Import pathways of chloroplast interior proteins and the outer-membrane protein OEP14 converge at Toc75. In: The Plant cell 16 (8), S. 2078-2088.
  113. Bendtsen, J. D.; Nielsen, H.; Heijne, G. von; Brunak, S. (2004): Improved prediction of signal peptides. SignalP 3.0. In: Journal of molecular biology 340 (4), S. 783-795.
  114. Hayat, S.; Peters, C.; Shu, N.; Tsirigos, K. D.; Elofsson, A. (2016): Inclusion of dyad-repeat pattern improves topology prediction of transmembrane beta-barrel proteins. In: Bioinformatics (Oxford, England) 32 (10), S. 1571-1573.
  115. Yorimitsu, T.; Sato, K. (2012): Insights into structural and regulatory roles of Sec16 in COPII vesicle formation at ER exit sites. In: Molecular biology of the cell 23 (15), S. 2930-2942.
  116. Fricker, M.; Hollinshead, M.; White, N.; Vaux, D. (1997): Interphase nuclei of many mammalian cell types contain deep, dynamic, tubular membrane-bound invaginations of the nuclear envelope. In: The Journal of cell biology 136 (3), S. 531-544.
  117. Gosline, S. J. C.; Nascimento, M.; McCall, L.-I.; Zilberstein, D.; Thomas, D. Y.; Matlashewski, G.; Hallett, M. (2011): Intracellular eukaryotic parasites have a distinct unfolded protein response. In: PloS one 6 (4), e19118.
  118. Chen, X.; Smith, M. D.; Fitzpatrick, L.; Schnell, D. J. (2002b): In vivo analysis of the role of atTic20 in protein import into chloroplasts. In: The Plant cell 14 (3), S. 641-654.
  119. Chen, Y.; Brandizzi, F. (2013): IRE1: ER stress sensor and cell fate executor. In: Trends in cell biology 23 (11), S. 547-555.
  120. Moore, K.; Hollien, J. (2015): Ire1-mediated decay in mammalian cells relies on mRNA sequence, structure, and translational status. In: Molecular biology of the cell 26 (16), S. 2873-2884.
  121. Cavalier-Smith, T. (2010): Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree. In: Biology letters 6 (3), S. 342-345.
  122. Ulitzur, N.; Harel, A.; Feinstein, N.; Gruenbaum, Y. (1992): Lamin activity is essential for nuclear envelope assembly in a Drosophila embryo cell-free extract. In: The Journal of cell biology 119 (1), S. 17-25.
  123. Noinaj, N.; Kuszak, A. J.; Balusek, C.; Gumbart, J. C.; Buchanan, S. K. (2014): Lateral opening and exit pore formation are required for BamA function. In: Structure (London, England : 1993) 22 (7), S. 1055-1062.
  124. Pineau, L.; Colas, J.; Dupont, S.; Beney, L.; Fleurat-Lessard, P.; Berjeaud, J.-M. et al. (2009): Lipid- induced ER stress: synergistic effects of sterols and saturated fatty acids. In: Traffic (Copenhagen, Denmark) 10 (6), S. 673-690.
  125. Moog, D.; Rensing, S. A.; Archibald, J. M.; Maier, U. G.; Ullrich, K. K. (2015): Localization and Evolution of Putative Triose Phosphate Translocators in the Diatom Phaeodactylum tricornutum. In: Genome biology and evolution 7 (11), S. 2955-2969.
  126. Sato, Y.; Nadanaka, S.; Okada, T.; Okawa, K.; Mori, K. (2011): Luminal domain of ATF6 alone is sufficient for sensing endoplasmic reticulum stress and subsequent transport to the Golgi apparatus. In: Cell structure and function 36 (1), S. 35-47.
  127. Flinner, N.; Ellenrieder, L.; Stiller, S. B.; Becker, T.; Schleiff, E.; Mirus, O. (2013): Mdm10 is an ancient eukaryotic porin co-occurring with the ERMES complex. In: Biochimica et biophysica acta 1833 (12), S. 3314-3325.
  128. Dewez, D.; Park, S.; García-Cerdán, J. G.; Lindberg, P.; Melis, A. (2009): Mechanism of REP27 protein action in the D1 protein turnover and photosystem II repair from photodamage. In: Plant physiology 151 (1), S. 88-99.
  129. Promlek, T.; Ishiwata-Kimata, Y.; Shido, M.; Sakuramoto, M.; Kohno, K.; Kimata, Y. (2011): Membrane aberrancy and unfolded proteins activate the endoplasmic reticulum stress sensor Ire1 in different ways. In: Molecular biology of the cell 22 (18), S. 3520-3532.
  130. Cavalier-Smith, T. (2000): Membrane heredity and early chloroplast evolution. In: Trends in plant science 5 (4), S. 174-182.
  131. Meisinger, C.; Wiedemann, N.; Rissler, M.; Strub, A.; Milenkovic, D.; Schönfisch, B. et al. (2006): Mitochondrial protein sorting. Differentiation of beta-barrel assembly by Tom7-mediated segregation of Mdm10. In: The Journal of biological chemistry 281 (32), S. 22819-22826.
  132. Deguil, J.; Pineau, L.; Rowland Snyder, E. C.; Dupont, S.; Beney, L.; Gil, A. et al. (2011): Modulation of lipid-induced ER stress by fatty acid shape. In: Traffic (Copenhagen, Denmark) 12 (3), S. 349- 362.
  133. Sambrook, J., Fritsch, E., Maniatis, T. (Hg.) (1989): Molecular cloning: A laboratory manual. New York.: Cold Spring Harbor Laboratory Press.
  134. Chiribau, C.-B.; Gaccioli, F.; Huang, C. C.; Yuan, C. L.; Hatzoglou, M. (2010): Molecular symbiosis of CHOP and C/EBP beta isoform LIP contributes to endoplasmic reticulum stress-induced apoptosis. In: Molecular and cellular biology 30 (14), S. 3722-3731.
  135. Wakasa, Y.; Hayashi, S.; Ozawa, K.; Takaiwa, F. (2012): Multiple roles of the ER stress sensor IRE1 demonstrated by gene targeting in rice. In: Scientific reports 2, 944.
  136. Paila, Y. D.; Richardson, L. G. L.; Schnell, D. J. (2015): New insights into the mechanism of chloroplast protein import and its integration with protein quality control, organelle biogenesis and development. In: Journal of molecular biology 427 (5), S. 1038-1060.
  137. Moraes, M. C. S.; Jesus, T. C. L.; Hashimoto, N. N.; Dey, M.; Schwartz, K. J.; Alves, V. S. et al. (2007): Novel membrane-bound eIF2alpha kinase in the flagellar pocket of Trypanosoma brucei. In: Eukaryotic cell 6 (11), S. 1979-1991.
  138. Cullinan, S. B.; Zhang, D.; Hannink, M.; Arvisais, E.; Kaufman, R. J.; Diehl, J. A. (2003): Nrf2 is a direct PERK substrate and effector of PERK-dependent cell survival. In: Molecular and cellular biology 23 (20), S. 7198-7209.
  139. Lau, J. B.; Stork, S.; Moog, D.; Sommer, M. S.; Maier, U. G. (2015): N-terminal lysines are essential for protein translocation via a modified ERAD system in complex plastids. In: Molecular microbiology 96 (3), S. 609-620.
  140. Ulitzur, N.; Gruenbaum, Y. (1989): Nuclear envelope assembly around sperm chromatin in cell- free preparations from Drosophila embryos. In: FEBS letters 259 (1), S. 113-116.
  141. Denais, C. M.; Gilbert, R. M.; Isermann, P.; McGregor, A. L.; te Lindert, M.; Weigelin, B. et al. (2016): Nuclear envelope rupture and repair during cancer cell migration. In: Science (New York, N.Y.) 352 (6283), S. 353-358.
  142. Ulitzur, N.; Harel, A.; Goldberg, M.; Feinstein, N.; Gruenbaum, Y. (1997): Nuclear membrane vesicle targeting to chromatin in a Drosophila embryo cell-free system. In: Molecular biology of the cell 8 (8), S. 1439-1448.
  143. Peyro, M.; Soheilypour, M.; Ghavami, A.; Mofrad, M. R. K. (2015): Nucleoporin's Like Charge Regions Are Major Regulators of FG Coverage and Dynamics Inside the Nuclear Pore Complex. In: PloS one 10 (12), e0143745.
  144. Harper, J. T.; Keeling, P. J. (2003): Nucleus-encoded, plastid-targeted glyceraldehyde-3-phosphate dehydrogenase (GAPDH) indicates a single origin for chromalveolate plastids. In: Molecular biology and evolution 20 (10), S. 1730-1735.
  145. Gould, S. B.; Sommer, M. S.; Kroth, P. G.; Gile, G. H.; Keeling, P. J.; Maier, U.-G. (2006): Nucleus-to- nucleus gene transfer and protein retargeting into a remnant cytoplasm of cryptophytes and diatoms. In: Molecular biology and evolution 23 (12), S. 2413-2422.
  146. Kriechbaumer, V.; Ewan, R. A.; Jonczyk, R.; Lehmann, S.; Young, J. C.; Abell, B. M. (2011): OEP61 is a chaperone receptor at the plastid outer envelope. In: The Biochemical journal 438 (1), S. 143-153.
  147. Arnold, T.; Zeth, K.; Linke, D. (2010): Omp85 from the thermophilic cyanobacterium Thermosynechococcus elongatus differs from proteobacterial Omp85 in structure and domain composition. In: The Journal of biological chemistry 285 (23), S. 18003-18015.
  148. Stoebe, B.; Maier, U.-G. (2002): One, two, three: nature's tool box for building plastids. In: Protoplasma 219 (3-4), S. 123-130.
  149. Credle, J. J.; Finer-Moore, J. S.; Papa, F. R.; Stroud, R. M.; Walter, P. (2005): On the mechanism of sensing unfolded protein in the endoplasmic reticulum. In: Proceedings of the National Academy of Sciences of the United States of America 102 (52), S. 18773-18784.
  150. Harper, J. T.; Waanders, E.; Keeling, P. J. (2005): On the monophyly of chromalveolates using a six- protein phylogeny of eukaryotes. In: International journal of systematic and evolutionary microbiology 55 (Pt 1), S. 487-496.
  151. Soo, R. M.; Hemp, J.; Parks, D. H.; Fischer, W. W.; Hugenholtz, P. (2017): On the origins of oxygenic photosynthesis and aerobic respiration in Cyanobacteria. In: Science (New York, N.Y.) 355 (6332), S. 1436-1440.
  152. Margulis, Lynn (1970): Origin of eucaryotic cells. New Haven: Yale university press.
  153. Harding, H. P.; Zhang, Y.; Bertolotti, A.; Zeng, H.; Ron, D. (2000b): Perk is essential for translational regulation and cell survival during the unfolded protein response. In: Molecular cell 5 (5), S. 897- 904.
  154. Verfaillie, T.; Rubio, N.; Garg, A. D.; Bultynck, G.; Rizzuto, R.; Decuypere, J.-P. et al. (2012): PERK is required at the ER-mitochondrial contact sites to convey apoptosis after ROS-based ER stress. In: Cell death and differentiation 19 (11), S. 1880-1891.
  155. Gupta, A.; Hossain, M. M.; Read, D. E.; Hetz, C.; Samali, A.; Gupta, S. (2015): PERK regulated miR- 424(322)-503 cluster fine-tunes activation of IRE1 and ATF6 during Unfolded Protein Response. In: Scientific reports 5, 18304.
  156. Mullen, R. T.; Lisenbee, C. S.; Miernyk, J. A.; Trelease, R. N. (1999): Peroxisomal membrane ascorbate peroxidase is sorted to a membranous network that resembles a subdomain of the endoplasmic reticulum. In: The Plant cell 11 (11), S. 2167-2185.
  157. Goldshmidt, H.; Matas, D.; Kabi, A.; Carmi, S.; Hope, R.; Michaeli, S. (2010): Persistent ER stress induces the spliced leader RNA silencing pathway (SLS), leading to programmed cell death in Trypanosoma brucei. In: PLoS pathogens 6 (1), e1000731.
  158. Stone, S. J.; Vance, J. E. (2000): Phosphatidylserine synthase-1 and -2 are localized to mitochondria-associated membranes. In: The Journal of biological chemistry 275 (44), S. 34534- 34540.
  159. Kannan, M.; Lahiri, S.; Liu, L.-K.; Choudhary, V.; Prinz, W. A. (2017): Phosphatidylserine synthesis at membrane contact sites promotes its transport out of the ER. In: Journal of lipid research 58 (3), S. 553-562.
  160. Aarti, I.; Rajesh, K.; Ramaiah, K. V. A. (2010): Phosphorylation of eIF2 alpha in Sf9 cells: a stress, survival and suicidal signal. In: Apoptosis : an international journal on programmed cell death 15 (6), S. 679-692.
  161. DuRose, J. B.; Scheuner, D.; Kaufman, R. J.; Rothblum, L. I.; Niwa, M. (2009): Phosphorylation of eukaryotic translation initiation factor 2alpha coordinates rRNA transcription and translation inhibition during endoplasmic reticulum stress. In: Molecular and cellular biology 29 (15), S. 4295- 4307.
  162. Hackett, J. D.; Yoon, H. S.; Li, S.; Reyes-Prieto, A.; Rümmele, S. E.; Bhattacharya, D. (2007): Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates. In: Molecular biology and evolution 24 (8), S. 1702- 1713.
  163. Baurain, D.; Brinkmann, H.; Petersen, J.; Rodriguez-Ezpeleta, N.; Stechmann, A.; Demoulin, V. et al. (2010): Phylogenomic evidence for separate acquisition of plastids in cryptophytes, haptophytes, and stramenopiles. In: Molecular biology and evolution 27 (7), S. 1698-1709.
  164. Gould, S. B.; Waller, R. F.; McFadden, G. I. (2008): Plastid evolution. In: Annual review of plant biology 59, S. 491-517.
  165. Gruber, A.; Rocap, G.; Kroth, P. G.; Armbrust, E. V.; Mock, T. (2015): Plastid proteome prediction for diatoms and other algae with secondary plastids of the red lineage. In: The Plant journal : for cell and molecular biology 81 (3), S. 519-528.
  166. Roy Choudhury, A.; Novic, M. (2015): PredbetaTM: A Novel beta-Transmembrane Region Prediction Algorithm. In: PloS one 10 (12), e0145564.
  167. Emanuelsson, O.; Nielsen, H.; Brunak, S.; Heijne, G. von (2000): Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. In: Journal of molecular biology 300 (4), S. 1005-1016.
  168. Bernsel, A.; Viklund, H.; Falk, J.; Lindahl, E.; Heijne, G. von; Elofsson, A. (2008): Prediction of membrane-protein topology from first principles. In: Proceedings of the National Academy of Sciences of the United States of America 105 (20), S. 7177-7181.
  169. Tsirigos, K. D.; Elofsson, A.; Bagos, P. G. (2016): PRED-TMBB2: improved topology prediction and detection of beta-barrel outer membrane proteins. In: Bioinformatics (Oxford, England) 32 (17), i665-i671.
  170. Bagos, P. G.; Liakopoulos, T. D.; Spyropoulos, I. C.; Hamodrakas, S. J. (2004b): PRED-TMBB: a web server for predicting the topology of beta-barrel outer membrane proteins. In: Nucleic acids research 32 (Web Server issue), W400-404.
  171. Becker, T.; Jelic, M.; Vojta, A.; Radunz, A.; Soll, J.; Schleiff, E. (2004): Preprotein recognition by the Toc complex. In: The EMBO journal 23 (3), S. 520-530.
  172. Cavalier-Smith, T. (1999): Principles of protein and lipid targeting in secondary symbiogenesis: euglenoid, dinoflagellate, and sporozoan plastid origins and the eukaryote family tree. In: The Journal of eukaryotic microbiology 46 (4), S. 347-366.
  173. Gould, S. B.; Maier, U.-G.; Martin, W. F. (2015): Protein import and the origin of red complex plastids. In: Current biology : CB 25 (12), R515-521.
  174. May, T.; Soll, J. (2000): 14-3-3 proteins form a guidance complex with chloroplast precursor proteins in plants. In: The Plant cell 12 (1), S. 53-64.
  175. Sheiner, L.; Striepen, B. (2013): Protein sorting in complex plastids. In: Biochimica et biophysica acta 1833 (2), S. 352-359.
  176. Li, H. m.; Chen, L. J. (1996): Protein targeting and integration signal for the chloroplastic outer envelope membrane. In: The Plant cell 8 (11), S. 2117-2126.
  177. Heiny, S. R.; Pautz, S.; Recker, M.; Przyborski, J. M. (2014): Protein Traffic to the Plasmodium falciparum apicoplast: evidence for a sorting branch point at the Golgi. In: Traffic (Copenhagen, Denmark) 15 (12), S. 1290-1304.
  178. Harding, H. P.; Zhang, Y.; Ron, D. (1999): Protein translation and folding are coupled by an endoplasmic-reticulum-resident kinase. In: Nature 397 (6716), S. 271-274.
  179. Lang, M.; Apt, K. E.; Kroth, P. G. (1998): Protein transport into "complex" diatom plastids utilizes two different targeting signals. In: The Journal of biological chemistry 273 (47), S. 30973-30978.
  180. Huesgen, P. F.; Alami, M.; Lange, P. F.; Foster, L. J.; Schroder, W. P.; Overall, C. M.; Green, B. R. (2013): Proteomic amino-termini profiling reveals targeting information for protein import into complex plastids. In: PloS one 8 (9), e74483.
  181. Yu, N. Y.; Wagner, J. R.; Laird, M. R.; Melli, G.; Rey, S.; Lo, R. et al. (2010): PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. In: Bioinformatics (Oxford, England) 26 (13), S. 1608-1615.
  182. Woehle, C.; Dagan, T.; Martin, W. F.; Gould, S. B. (2011): Red and problematic green phylogenetic signals among thousands of nuclear genes from the photosynthetic and apicomplexa-related Chromera velia. In: Genome biology and evolution 3, S. 1220-1230.
  183. Deschamps, P.; Moreira, D. (2012): Reevaluating the green contribution to diatom genomes. In: Genome biology and evolution 4 (7), S. 683-688.
  184. Burki, F.; Flegontov, P.; Obornik, M.; Cihlar, J.; Pain, A.; Lukes, J.; Keeling, P. J. (2012a): Re- evaluating the green versus red signal in eukaryotes with secondary plastid of red algal origin. In: Genome biology and evolution 4 (6), S. 626-635.
  185. Hollien, J.; Lin, J. H.; Li, H.; Stevens, N.; Walter, P.; Weissman, J. S. (2009): Regulated Ire1- dependent decay of messenger RNAs in mammalian cells. In: The Journal of cell biology 186 (3), S. 323-331.
  186. Harding, H. P.; Novoa, I.; Zhang, Y.; Zeng, H.; Wek, R.; Schapira, M.; Ron, D. (2000a): Regulated translation initiation controls stress-induced gene expression in mammalian cells. In: Molecular cell 6 (5), S. 1099-1108.
  187. Echevarría, W.; Leite, M. F.; Guerra, M. T.; Zipfel, W. R.; Nathanson, M. H. (2003): Regulation of calcium signals in the nucleus by a nucleoplasmic reticulum. In: Nature cell biology 5 (5), S. 440- 446.
  188. Imagawa, Y.; Hosoda, A.; Sasaka, S.-I.; Tsuru, A.; Kohno, K. (2008): RNase domains determine the functional difference between IRE1alpha and IRE1beta. In: FEBS letters 582 (5), S. 656-660.
  189. Volokhina, E. B.; Grijpstra, J.; Stork, M.; Schilders, I.; Tommassen, J.; Bos, M. P. (2011): Role of the periplasmic chaperones Skp, SurA, and DegQ in outer membrane protein biogenesis in Neisseria meningitidis. In: Journal of bacteriology 193 (7), S. 1612-1621.
  190. Ellenrieder, L.; Opaliński, Ł.; Becker, L.; Krüger, V.; Mirus, O.; Straub, S. P. et al. (2016): Separating mitochondrial protein assembly and endoplasmic reticulum tethering by selective coupling of Mdm10. In: Nature communications 7, 13021.
  191. Mori, K. (2009): Signalling pathways in the unfolded protein response: development from yeast to mammals. In: Journal of biochemistry 146 (6), S. 743-750.
  192. Petersen, T. N.; Brunak, S.; Heijne, G. von; Nielsen, H. (2011): SignalP 4.0. Discriminating signal peptides from transmembrane regions. In: Nature methods 8 (10), S. 785-786.
  193. Hayashi, S.; Wakasa, Y.; Takahashi, H.; Kawakatsu, T.; Takaiwa, F. (2012): Signal transduction by IRE1-mediated splicing of bZIP50 and other stress sensors in the endoplasmic reticulum stress response of rice. In: The Plant journal : for cell and molecular biology 69 (6), S. 946-956.
  194. Barton, K.; Mathur, N.; Mathur, J. (2013): Simultaneous live-imaging of peroxisomes and the ER in plant cells suggests contiguity but no luminal continuity between the two organelles. In: Frontiers in physiology 4, 196.
  195. Elias, M.; Archibald, J. M. (2009): Sizing up the genomic footprint of endosymbiosis. In: BioEssays : news and reviews in molecular, cellular and developmental biology 31 (12), S. 1273-1279.
  196. Shang, W.; Feierabend, J. (1998): Slow turnover of the D1 reaction center protein of photosystem II in leaves of high mountain plants. In: FEBS letters 425 (1), S. 97-100.
  197. Mullis, K.; Faloona, F.; Scharf, S.; Saiki, R.; Horn, G.; Erlich, H. (1986): Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. In: Cold Spring Harbor symposia on quantitative biology 51 Pt 1, S. 263-273.
  198. Apt, K. E.; Kroth-Pancic, P. G.; Grossman, A. R. (1996): Stable nuclear transformation of the diatom Phaeodactylum tricornutum. In: Molecular & general genetics : MGG 252 (5), S. 572-579.
  199. Chou, M.-L.; Chu, C.-C.; Chen, L.-J.; Akita, M.; Li, H.-M. (2006): Stimulation of transit-peptide release and ATP hydrolysis by a cochaperone during protein import into chloroplasts. In: The Journal of cell biology 175 (6), S. 893-900.
  200. Novoa, I.; Zhang, Y.; Zeng, H.; Jungreis, R.; Harding, H. P.; Ron, D. (2003): Stress-induced gene expression requires programmed recovery from translational repression. In: The EMBO journal 22 (5), S. 1180-1187.
  201. Gu, Y.; Li, H.; Dong, H.; Zeng, Y.; Zhang, Z.; Paterson, N. G. et al. (2016): Structural basis of outer membrane protein insertion by the BAM complex. In: Nature 531 (7592), S. 64-69.
  202. Kim, S.; Malinverni, J. C.; Sliz, P.; Silhavy, T. J.; Harrison, S. C.; Kahne, D. (2007): Structure and function of an essential component of the outer membrane protein assembly machine. In: Science (New York, N.Y.) 317 (5840), S. 961-964.
  203. Lee, K. P. K.; Dey, M.; Neculai, D.; Cao, C.; Dever, T. E.; Sicheri, F. (2008): Structure of the dual enzyme Ire1 reveals the basis for catalysis and regulation in nonconventional RNA splicing. In: Cell 132 (1), S. 89-100.
  204. Saito, K.; Chen, M.; Bard, F.; Chen, S.; Zhou, H.; Woodley, D. et al. (2009): TANGO1 facilitates cargo loading at endoplasmic reticulum exit sites. In: Cell 136 (5), S. 891-902.
  205. Maeda, M.; Katada, T.; Saito, K. (2017): TANGO1 recruits Sec16 to coordinately organize ER exit sites for efficient secretion. In: The Journal of cell biology 216 (6), S. 1731-1743.
  206. Liu, M.; Feng, Z.; Ke, H.; Liu, Y.; Sun, T.; Dai, J. et al. (2017): Tango1 spatially organizes ER exit sites to control ER export. In: The Journal of cell biology 216 (4), S. 1035-1049.
  207. Mayerhofer, P. U. (2016): Targeting and insertion of peroxisomal membrane proteins. ER trafficking versus direct delivery to peroxisomes. In: Biochimica et biophysica acta 1863 (5), S. 870-880.
  208. Rolls, M. M.; Hall, D. H.; Victor, M.; Stelzer, E. H. K.; Rapoport, T. A. (2002): Targeting of rough endoplasmic reticulum membrane proteins and ribosomes in invertebrate neurons. In: Molecular biology of the cell 13 (5), S. 1778-1791.
  209. Ye, C.-M.; Chen, S.; Payton, M.; Dickman, M. B.; Verchot, J. (2013): TGBp3 triggers the unfolded protein response and SKP1-dependent programmed cell death. In: Molecular plant pathology 14 (3), S. 241-255.
  210. Kim, K. H.; Aulakh, S.; Paetzel, M. (2012): The bacterial outer membrane beta-barrel assembly machinery. In: Protein science : a publication of the Protein Society 21 (6), S. 751-768.
  211. Noinaj, N.; Gumbart, J. C.; Buchanan, S. K. (2017): The beta-barrel assembly machinery in motion. In: Nature reviews. Microbiology 15 (4), S. 197-204.
  212. Inoue, K.; Potter, D. (2004): The chloroplastic protein translocation channel Toc75 and its paralog OEP80 represent two distinct protein families and are targeted to the chloroplastic outer envelope by different mechanisms. In: The Plant journal : for cell and molecular biology 39 (3), S. 354-365.
  213. Rogers, M. B.; Gilson, P. R.; Su, V.; McFadden, G. I.; Keeling, P. J. (2007): The complete chloroplast genome of the chlorarachniophyte Bigelowiella natans. Evidence for independent origins of chlorarachniophyte and euglenid secondary endosymbionts. In: Molecular biology and evolution 24 (1), S. 54-62.
  214. Teske, B. F.; Wek, S. A.; Bunpo, P.; Cundiff, J. K.; McClintick, J. N.; Anthony, T. G.; Wek, R. C. (2011): The eIF2 kinase PERK and the integrated stress response facilitate activation of ATF6 during endoplasmic reticulum stress. In: Molecular biology of the cell 22 (22), S. 4390-4405.
  215. van Vliet, A. R.; Giordano, F.; Gerlo, S.; Segura, I.; van Eygen, S.; Molenberghs, G. et al. (2017): The ER Stress Sensor PERK Coordinates ER-Plasma Membrane Contact Site Formation through Interaction with Filamin-A and F-Actin Remodeling. In: Molecular cell 65 (5), 885-899.
  216. Burki, F.; Okamoto, N.; Pombert, J.-F.; Keeling, P. J. (2012b): The evolutionary history of haptophytes and cryptophytes: phylogenomic evidence for separate origins. In: Proceedings. Biological sciences 279 (1736), S. 2246-2254.
  217. Stiller, J. W.; Schreiber, J.; Yue, J.; Guo, H.; Ding, Q.; Huang, J. (2014): The evolution of photosynthesis in chromist algae through serial endosymbioses. In: Nature communications 5, 5:5764.
  218. Lu, S.-J.; Zhang, S.-S.; Zhou, S.-F.; Sun, L.; Liu, J.-X. (2013): The lumen-facing domain is important for the biological function and organelle-to-organelle movement of bZIP28 during ER stress in Arabidopsis. In: Molecular plant 6 (5), S. 1605-1615.
  219. Chen, X.; Shen, J.; Prywes, R. (2002a): The luminal domain of ATF6 senses endoplasmic reticulum (ER) stress and causes translocation of ATF6 from the ER to the Golgi. In: The Journal of biological chemistry 277 (15), S. 13045-13052.
  220. Meisinger, C.; Rissler, M.; Chacinska, A.; Szklarz, L. K. S.; Milenkovic, D.; Kozjak, V. et al. (2004): The mitochondrial morphology protein Mdm10 functions in assembly of the preprotein translocase of the outer membrane. In: Developmental cell 7 (1), S. 61-71.
  221. Qbadou, S.; Becker, T.; Mirus, O.; Tews, I.; Soll, J.; Schleiff, E. (2006): The molecular chaperone Hsp90 delivers precursor proteins to the chloroplast import receptor Toc64. In: The EMBO journal 25 (9), S. 1836-1847.
  222. Adl, S. M.; Simpson, A. G. B.; Farmer, M. A.; Andersen, R. A.; Anderson, O. R.; Barta, J. R. et al. (2005): The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. In: The Journal of eukaryotic microbiology 52 (5), S. 399-451.
  223. Habib, S. J.; Waizenegger, T.; Niewienda, A.; Paschen, S. A.; Neupert, W.; Rapaport, D. (2007): The N-terminal domain of Tob55 has a receptor-like function in the biogenesis of mitochondrial beta- barrel proteins. In: The Journal of cell biology 176 (1), S. 77-88.
  224. Aebi, U.; Cohn, J.; Buhle, L.; Gerace, L. (1986): The nuclear lamina is a meshwork of intermediate- type filaments. In: Nature 323 (6088), S. 560-564.
  225. Malhas, A.; Goulbourne, C.; Vaux, D. J. (2011): The nucleoplasmic reticulum: form and function. In: Trends in cell biology 21 (6), S. 362-373.
  226. Bannykh, S. I.; Rowe, T.; Balch, W. E. (1996): The organization of endoplasmic reticulum export complexes. In: The Journal of cell biology 135 (1), S. 19-35.
  227. Kim, P. K.; Mullen, R. T.; Schumann, U.; Lippincott-Schwartz, J. (2006): The origin and maintenance of mammalian peroxisomes involves a de novo PEX16-dependent pathway from the ER. In: The Journal of cell biology 173 (4), S. 521-532.
  228. Schopf, W. J. (2011): The paleobiological record of photosynthesis. In: Photosynthesis research 107 (1), S. 87-101.
  229. Felsner, G.; Sommer, M. S.; Maier, U. G. (2010): The physical and functional borders of transit peptide-like sequences in secondary endosymbionts. In: BMC plant biology 10, 223.
  230. Archibald, J. M. (2009): The puzzle of plastid evolution. In: Current biology : CB 19 (2), R81-88.
  231. Lyons, T. W.; Reinhard, C. T.; Planavsky, N. J. (2014): The rise of oxygen in Earth's early ocean and atmosphere. In: Nature 506 (7488), S. 307-315.
  232. Gibbs, S. P. (1979): The route of entry of cytoplasmically synthesized proteins into chloroplasts of algae possessing chloroplast ER. In: Journal of cell science 35, S. 253-266.
  233. McMahon, C.; Studer, S. M.; Clendinen, C.; Dann, G. P.; Jeffrey, P. D.; Hughson, F. M. (2012): The structure of Sec12 implicates potassium ion coordination in Sar1 activation. In: The Journal of biological chemistry 287 (52), S. 43599-43606.
  234. Cui, W.; Li, J.; Ron, D.; Sha, B. (2011): The structure of the PERK kinase domain suggests the mechanism for its activation. In: Acta crystallographica. Section D, Biological crystallography 67 (Pt 5), S. 423-428.
  235. Tsirigos, K. D.; Peters, C.; Shu, N.; Käll, L.; Elofsson, A. (2015): The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides. In: Nucleic acids research 43 (W1), W401-407.
  236. Lee, Y. J.; Sohn, E. J.; Lee, K. H.; Lee, D. W.; Hwang, I. (2004): The transmembrane domain of AtToc64 and its C-terminal lysine-rich flanking region are targeting signals to the chloroplast outer envelope membrane correction. In: Molecules and cells 17 (2), S. 281-291.
  237. Kimmig, P.; Diaz, M.; Zheng, J.; Williams, C. C.; Lang, A.; Aragón, T. et al. (2012): The unfolded protein response in fission yeast modulates stability of select mRNAs to maintain protein homeostasis. In: eLife 1, e00048.
  238. Zhang, L.; Chen, H.; Brandizzi, F.; Verchot, J.; Wang, A. (2015): The UPR branch IRE1-bZIP60 in plants plays an essential role in viral infection and is complementary to the only UPR pathway in yeast. In: PLoS genetics 11 (4), e1005164.
  239. Teng, Y.-S.; Su, Y.-s.; Chen, L.-J.; Lee, Y. J.; Hwang, I.; Li, H.-M. (2006): Tic21 is an essential translocon component for protein translocation across the chloroplast inner envelope membrane. In: The Plant cell 18 (9), S. 2247-2257.
  240. Glaser, S.; van Dooren, G. G.; Agrawal, S.; Brooks, C. F.; McFadden, G. I.; Striepen, B.; Higgins, M. K. (2012): Tic22 is an essential chaperone required for protein import into the apicoplast. In: The Journal of biological chemistry 287 (47), S. 39505-39512.
  241. Ou, Y.-Y.; Gromiha, M. M.; Chen, S.-A.; Suwa, M. (2008): TMBETADISC-RBF: Discrimination of beta- barrel membrane proteins using RBF networks and PSSM profiles. In: Computational biology and chemistry 32 (3), S. 227-231.
  242. Gromiha, M. M.; Ahmad, S.; Suwa, M. (2005): TMBETA-NET: discrimination and prediction of membrane spanning beta-strands in outer membrane proteins. In: Nucleic acids research 33 (Web Server issue), W164-167.
  243. Randall, A.; Cheng, J.; Sweredoski, M.; Baldi, P. (2008): TMBpro. Secondary structure, beta-contact and tertiary structure prediction of transmembrane beta-barrel proteins. In: Bioinformatics (Oxford, England) 24 (4), S. 513-520.
  244. van Dooren, G. G.; Tomova, C.; Agrawal, S.; Humbel, B. M.; Striepen, B. (2008): Toxoplasma gondii Tic20 is essential for apicoplast protein import. In: Proceedings of the National Academy of Sciences of the United States of America 105 (36), S. 13574-13579.
  245. Nowack, E. C. M.; Grossman, A. R. (2012): Trafficking of protein into the recently established photosynthetic organelles of Paulinella chromatophora. In: Proceedings of the National Academy of Sciences of the United States of America 109 (14), S. 5340-5345.
  246. Zaslavskaia, L. A.; Lippmeier, J. C.; Kroth, P. G.; Grossman, A. R.; Apt, K. E. (2000): Transformation of the diatom Phaeodactylum tricornutum (Bacillariophyceae) with a variety of selectable marker and reporter genes. In: Journal of phycology 36 (2), S. 379-386.
  247. Patron, N. J.; Waller, R. F. (2007): Transit peptide diversity and divergence: A global analysis of plastid targeting signals. In: BioEssays : news and reviews in molecular, cellular and developmental biology 29 (10), S. 1048-1058.
  248. Narasimhan, J.; Joyce, B. R.; Naguleswaran, A.; Smith, A. T.; Livingston, M. R.; Dixon, S. E. et al. (2008): Translation regulation by eukaryotic initiation factor-2 kinases in the development of latent cysts in Toxoplasma gondii. In: The Journal of biological chemistry 283 (24), S. 16591- 16601.
  249. Reynolds, S. M.; Käll, L.; Riffle, M. E.; Bilmes, J. A.; Noble, W. S. (2008): Transmembrane topology and signal peptide prediction using dynamic bayesian networks. In: PLoS computational biology 4 (11), e1000213.
  250. Kikuchi, S.; Bedard, J.; Hirano, M.; Hirabayashi, Y.; Oishi, M.; Imai, M. et al. (2013): Uncovering the protein translocon at the chloroplast inner envelope membrane. In: Science (New York, N.Y.) 339 (6119), S. 571-574.
  251. Gardner, B. M.; Walter, P. (2011): Unfolded proteins are Ire1-activating ligands that directly induce the unfolded protein response. In: Science (New York, N.Y.) 333 (6051), S. 1891-1894.
  252. Burki, F.; Kaplan, M.; Tikhonenkov, D. V.; Zlatogursky, V.; Minh, B. Q.; Radaykina, L. V. et al. (2016): Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta and Cryptista. In: Proceedings. Biological sciences 283 (1823), 20152802.
  253. D'Arcangelo, J. G.; Stahmer, K. R.; Miller, E. A. (2013): Vesicle-mediated export from the ER: COPII coat function and regulation. In: Biochimica et biophysica acta 1833 (11), S. 2464-2472.
  254. Acosta-Alvear, D.; Zhou, Y.; Blais, A.; Tsikitis, M.; Lents, N. H.; Arias, C. et al. (2007): XBP1 controls diverse cell type-and condition-specific transcriptional regulatory networks. In: Molecular cell 27 (1), S. 53-66.
  255. Kimata, Y.; Ishiwata-Kimata, Y.; Yamada, S.; Kohno, K. (2006): Yeast unfolded protein response pathway regulates expression of genes for anti-oxidative stress and for cell surface proteins. In: Genes to cells : devoted to molecular & cellular mechanisms 11 (1), S. 59-69.

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