Abstract
The review characterizes the main enzymatic systems of selective proteolysis responsible for maintenance of intracellular proteome in prokaryotes, eukaryotes and archaea. The features of proteolytic components of the ATP-dependent proteases as well as similarity and diversity of their regulatory components belonging to AAA+ ATPases are discussed.
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Goldberg, A.L., Eur. J. Biochem., 1992, vol. 203, pp. 9–23.
Pahl, H.L. and Baeuerle, P.A., Curr. Opin. Cell Biol., 1996, vol. 8, pp. 340–347.
Martoglio, B., Protoplasma, 1999, vol. 207, pp. 141–146.
Gottesman, S., Annu. Rev. Cell Dev. Biol., 2003, vol. 19, pp. 565–587.
King, R.W., Deshaies, R.J., Peters, J.M., and Kirschner, M.W., Science, 1996, vol. 274, pp. 1652–1659.
Neuwald, A.F., Aravind, L., Spouge, J.L., and Koonin, E.V., Genome Res., 1999, vol. 9, pp. 27–43.
Swamy, K.S. and Goldberg, A.L., Nature, 1981, vol. 292, pp. 652–654.
Coux, O., Tanaka, K., and Goldberg, A.L., Ann. Rev. Biochem., 1996, vol. 65, pp. 801–847.
Maupin-Furlow, J.A., Wilson, H.L., Kaczowka, S.J., and Ou, M.S., Front. Biosci., 2000, vol. 5, pp. D837–D865.
Erdmann, R., Wiebel, F.F., Flessau, A., Rytka, J., Beyer, A., Frohlich, K.U., and Kunau, W.H., Cell, 1991, vol. 64, pp. 499–510.
Iyer, L.M., Leipe, D.D., Koonin, E.V., and Aravind, L., J. Struct. Biol., 2004, vol. 146, pp. 11–31.
Hanson, Ph.I. and Whiteheart, S.W., Mol. Cell Biol., 2005, vol. 6, pp. 519–529.
Lupas, A.N. and Martin, J., Curr. Opin. Struct. Biol., 2002, vol. 12, pp. 746–753.
Frickey, T. and Lupas, A.N., J. Struct. Biol., 2004, vol. 146, pp. 2–10.
Schirmer, E.C., Glover, J.R., Singer, M.A., and Lindquist, S., Trends Biochem. Sci., 1996, vol. 21, pp. 289–296.
Erzberger, J.P. and Berger, J.M., Ann. Rev. Biophys. Biomol. Struct., 2006, vol. 35, pp. 93–114.
Tucker, P.A. and Sallai, L., Curr. Opin. Struct. Biol., 2007, vol. 17, pp. 641–652.
Singh, S.K., Rozycki, J., Ortega, J., Ishikawa, T., Lo, J., Steven, A.C., and Maurizi, M.R., J. Biol. Chem., 2001, vol. 276, pp. 29420–29429.
Dougan, D.A., Mogk, A., Zeth, K., Turgay, K., and Bukau, B., FEBS Lett., 2002, vol. 529, pp. 6–10.
Tomoyasu, T., Mogk, A., Langen, H., Goloubinoff, P., and Bukau, B., Mol. Microbiol., 2001, vol. 40, pp. 397–413.
Keiler, K.C., Waller, P.R., and Sauer, R.T., Science, 1996, vol. 271, pp. 990–993.
Martin, J., Gruber, M., and Lupas, A.N., Trends Biochem. Sci., 2004, vol. 29, pp. 455–458.
Rouiller, I., DeLaBarre, B., May, A.P., Weis, W.I., Brunger, A.T., Milligan, R.A., and Wilson-Kubalek, E.M., Nat. Struct. Biol., 2002, vol. 9, pp. 950–957.
Vale, R.D., J. Cell Biol., 2000, vol. 150, pp. F13–F19.
Singh, S.K., Grimaud, R., Hoskins, J.R., Wickner, S., and Maurizi, M.R., Proc. Natl. Acad. Sci. USA, 2000, vol. 97, pp. 8898–8903.
Seol, J.H., Yoo, S.J., Shin, D.H., Shim, Y.K., Kang, M.S., Goldberg, A.L., and Chung, C.H., Eur. J. Biochem., 1997, vol. 247, pp. 1143–1150.
Mogk, A., Dougan, D., Weibezahn, J., Schlieker, C., Turgay, K., and Bukau, B., J. Struct. Biol., 2004, vol. 146, pp. 90–98.
Hinnerwisch, J., Reid, B.G., Fenton, W.A., and Horwich, A.L., J. Biol. Chem., 2005, vol. 280, pp. 40838–40844.
Wojtyra, U.A., Thibault, G., Tuite, A., and Houry, W.A., J. Biol. Chem., 2003, vol. 278, pp. 48981–48990.
Flynn, J.M., Neher, S.B., Kim, Y.I., Sauer, R.T., and Baker, T.A., Mol. Cell, 2003, vol. 11, pp. 671–683.
Guo, F., Maurizi, M.R., Esser, L., and Xia, D., J. Biol. Chem., 2002, vol. 277, pp. 46743–46752.
Kim, D.Y. and Kim, K.K., J. Biol. Chem., 2003, vol. 278, pp. 50664–50670.
Sousa, M.C., Trame, C.B., Tsuruta, H., Wilbanks, S.M., Reddy, V.S., and McKay, D.B., Cell, 2000, vol. 103, pp. 633–643.
Bochtler, M., Hartmann, C., Song, H.K., Bourenkov, G.P., Bartunik, H.D., and Huber, R., Nature, 2000, vol. 403, pp. 800–805.
Wang, J., Song, J.J., Franklin, M.C., Kamtekar, S., Im, Y.J., Rho, S.H., Seong, I.S., Lee, C.S., Chung, C.H., and Eom, S.H., Structure (Camb), 2001, vol. 9, pp. 177–184.
Krzywda, S., Brzozowski, A.M., Verma, C., Karata, K., Ogura, T., and Wilkinson, A.J., Structure (Camb), 2002, vol. 10, pp. 1073–1083.
Niwa, H., Tsuchiya, D., Makyio, H., Yoshida, M., and Morikawa, K., Structure (Camb), 2002, vol. 10, pp. 1415–1423.
Bieniossek, C, Schalch, T, Bumann, M, Meister, M, Meier, R, and Baumann, U., Proc. Natl. Acad. Sci. USA, 2006, vol. 103, pp. 3066–3071.
Suno, R., Niwa, H., Tsuchiya, D., Zhang, X., Yoshida, M., and Morikawa, K., Mol. Cell, 2006, vol. 22, pp. 575–585.
Barrett, A.J., Rawlings, N.D., and O’Brien, E.A., J. Struct. Biol., 2001, vol. 134, pp. 95–102.
Chung, C.H. and Goldberg, A.L., Proc. Natl. Acad. Sci. USA, 1981, vol. 78, pp. 4931–4935.
Charette, M.F., Henderson, G.W., and Markovitz, A., Proc. Natl. Acad. Sci. USA, 1981, vol. 78, pp. 4728–4732.
Amerik, A.Yu., Chistyakova, L.G., Ostroumova, N.I., Gurevich, A.I., and Antonov, V.K., Bioorgan. Khimiya, 1988, vol. 14, pp. 408–411.
Amerik, A.Yu., Antonov, V.K., Ostroumova, N.I., Rotanova, T.V., and Chistyakova, L.G., Bioorgan. Khimiya, 1990, vol. 16, pp. 869–880.
Amerik, A.Yu., Antonov, V.K., Gorbalenya, A.E., Kotova, S.A., Rotanova, T.V., and Shimbarevich, E.V., FEBS Lett., 1991, vol. 287, pp. 211–214.
Rotanova. T.V., Vopr. Med. Khim., 2002, vol. 48, pp. 541–552.
Rotanova, T.V., Mel’nikov, E.E., and Tsirul’nikov, K.B., Bioorgan. Khimiya, 2003, vol. 29, pp. 97–99.
Botos, I., Melnikov, E.E., Cherry, S., Tropea, J., Khalatova, A.G., Rasulova, F.S., Dauter, Z., Maurizi, M.R., Rotanova, T.V., Wlodawer, A., and Gustchina, A., J. Biol. Chem., 2004, vol. 279, pp. 8140–8148.
Rotanova, T.V., Melnikov, E.E., Khalatova, A.G., Makhovskaya, O.V., Botos, I., Wlodawer, A., and Gustchina, A., Eur. J. Biochem., 2004, vol. 271, pp. 4865–4871.
Botos, I., Melnikov, E.E., Cherry, S., Kozlov, S., Makhovskaya, O.V., Tropea, J., Gustchina, A., Rotanova, T.V., and Wlodawer, A., J. Mol. Biol., 2005, vol. 351, pp. 144–157.
Chung, C.H. and Goldberg, A.L., Handbook of Proteolytic Enzymes, Barrett A.J., Rawlings N.D., Woessner J.F., Eds., 2004, pp. 1998–2002.
Nishii, W., Maruyama, T., Matsuoka, R., Muramatsu, T., and Takahashi, K., Eur. J. Biochem., 2002, vol. 269, pp. 451–457.
Waxman, L. and Goldberg, A.L., J. Biol. Chem., 1985, vol. 260, pp. 12022–12028.
Thomas-Wohlever, J. and Lee, I., Biochemistry, 2002, vol. 41, pp. 9418–9425.
Hilliard, J.J., Simon, L.D., Van Melderen, L., and Maurizi, M.R., J. Biol. Chem., 1998, vol. 273, pp. 524–527.
Tomoyasu, T., Yuki, T., Morimura, S., Mori, H., Yamanaka, K., Niki, H., Hiraga, S., and Ogura, T., J. Bacteriol., 1993, vol. 175, pp. 1344–1351.
Ito, K. and Akiyama, Y., Ann. Rev. Microbiol., 2005, vol. 59, pp. 211–231.
Akiyama, Y., Yoshihisa, T., and Ito, K., J. Biol. Chem., 1995, vol. 270, pp. 23485–23490.
Herman, C., Lecat, S., D’Ari, R., and Bouloc, P., Mol. Microbiol., 1995, vol. 18, pp. 247–255.
Tomoyasu, T., Gamer, J., Bukau, B., Kanemori, M., Mori, H., Rutman, A.J., Oppenheim, A.B., Yura, T., Yamanaka, K., Niki, H., Hiraga, S., and Ogura, T., EMBO J., 1995, vol. 14, pp. 2551–2560.
Saikawa, N., Ito, K., and Akiyama, Y., Biochemistry, 2002, vol. 41, pp. 1861–1868.
Shotland, Y., Teff, D., Koby, S., Kobiler, O., and Oppenheim, A.B., J. Mol. Biol., 2000, vol. 299, pp. 953–964.
Akiyama, Y., Kihara, A., Tokuda, H., and Ito, K., J. Biol. Chem., 1996, vol. 271, pp. 31196–31201.
Tomoyasu, T., Yamanaka, K., Murata, K., Suzaki, T., Bouloc, P., Kato, A., Niki, H., Hiraga, S., and Ogura, T., J. Bacteriol., 1993, vol. 175, pp. 1352–1357.
Kihara, A., Akiyama, Y., and Ito, K., EMBO J., 1999, vol. 18, pp. 2970–2981.
Chiba, S., Akiyama, Y., and Ito, K., J. Bacteriol., 2002, vol. 184, pp. 4775–4782.
Kanemori, M., Yanagi, H., and Yura, T., J. Biol. Chem., 1999, vol. 274, pp. 22002–22007.
Rist, W., Jorgensen, T.J., Roepstorff, P., Bukau, B., and Mayer, M.P., J. Biol. Chem., 2003, vol. 278, pp. 51415–51421.
Okuno, T., Yamada-Inagawa, T., Karata, K., Yamanaka, K., and Ogura, T., J. Struct. Biol., 2004, vol. 146, pp. 148–154.
Herman, C., Thevenet, D., D’Ari, R., and Bouloc, P., J. Bacteriol., 1997, vol. 179, pp. 358–363.
Prajapati, R.S., Ogura, T., and Cutting, S.M., Biochim. Biophys. Acta, 2000, vol. 1475, pp. 353–359.
Saikawa, N., Akiyama, Y., and Ito, K., J. Struct. Biol., 2004, vol. 146, pp. 123–129.
Hwang, B.J., Woo, K.M., Goldberg, A.L., and Chung, C.H., J. Biol. Chem., 1988, vol. 263, pp. 8727–8734.
Gottesman, S., Clark, W.P., de Crecy-Lagard, V., and Maurizi, M.R., J. Biol. Chem., 1993, vol. 268, pp. 22618–22626.
Maurizi, M.R., Clark, W.P., Kim, S.H., and Gottesman, S., J. Biol. Chem., 1990, vol. 265, pp. 12546–12552.
Wang, J., Hartling, J.A., and Flanagan, J.M., J. Struct. Biol., 1998, vol. 124, pp. 151–163.
Maurizi, M.R., Thompson, M.W., Singh, S.K., and Kim, S.H., Meth. Enzymol., 1994, vol. 244, pp. 314–331.
Lupas, A., Flanagan, J.M., Tamura, T., and Baumeister, W., Trends Biochem. Sci., 1997, vol. 22, pp. 399–404.
Beuron, F., Maurizi, M.R., Belnap, D.M., Kocsis, E., Booy, F.P., Kessel, M., and Steven, A.C., J. Struct. Biol., 1998, vol. 123, pp. 248–259.
Levchenko, I., Smith, C.K., Walsh, N.P., Sauer, R.T., and Baker, T.A., Cell, 1997, vol. 91, pp. 939–947.
Ortega, J., Singh, S.K., Ishikawa, T., Maurizi, M.R., and Steven, A.C., Mol. Cell, 2000, vol. 6, pp. 1515–1521.
Lee, C., Schwartz, M.P., Prakash, S., Iwakura, M., and Matouschek, A., Mol. Cell, 2001, vol. 7, pp. 627–637.
Reid, B.G., Fenton, W.A., Homwich, A.L., and Weber-Ban, E.U., Proc. Natl. Acad. Sci. USA, 2001, vol. 98, pp. 3768–3772.
Thompson, M.W., Maurizi, M.R., J. Biol. Chem., 1994, vol. 269, pp. 18201–18208.
Arribas, J. and Castano, J.G., J. Biol. Chem., 1993, vol. 268, pp. 21165–21171.
Halperin, T., Ostersetzer, O., and Adam, Z., Planta, 1999, vol. 213, pp. 614–619.
Rohrwild, M., Coux, O., Huang, H.C., Moerschell, R.P., Yoo, S.J., Seol, J.H., Chung, C.H., and Goldberg, A.L., Proc. Natl. Acad. Sci. USA, 1996, vol. 93, pp. 5808–5813.
Kang, M.S., Lim, B.K., Seong, I.S., Seol, J.H., Tanahashi, N., Tanaka, K., and Chung, C.H., EMBO J., 2001, vol. 20, pp. 734–742.
Kang, M.S., Kim, S.R., Kwack, P., Lim, B.K., Ahn, S.W., Rho, Y.M., Seong, I.S., Park, S.C., Eom, S.H., Cheong, G.W., and Chung, C.H., EMBO J., 2003, vol. 22, pp. 2893–2902.
Yoo, S.J., Shim, Y.K., Seong, I.S., Seol, J.H., Kang, M.S., and Chung, C.H., FEBS Lett., 1997, vol. 412, pp. 57–60.
Rohrwild, M., Pfeifer, G., Santarius, U., Muller, S.A., Huang, H.C., Engel, A., Baumeister, W., and Goldberg, A.L., Nat. Struct. Biol., 1997, vol. 4, pp. 133–139.
Yoo, S.J., Seol, J.H., Seong, I.S., Kang, M.S., and Chung, C.H., Biochem. Biophys. Res. Commun., 1997, vol. 238, pp. 581–585.
Sousa, M.C., Kessler, B.M., Overkleeft, H.S., and McKay, D.B., J. Mol. Biol., 2002, vol. 318, pp. 779–785.
Lowe, J., Stock, D., Jap, B., Zwickl, P., Baumeister, W., and Huber, R., Science, 1995, vol. 268, pp. 533–539.
Groll, M., Brandstetter, H., Bartunik, H., Bourenkow, G., and Huber, R., J. Mol. Biol., 2003, vol. 327, pp. 75–83.
Pickart, C.M., FASEB J., 1997, vol. 11, pp. 1055–1066.
Grziwa, A., Baumeister, W., Dahlmann, B., and Kopp, F., FEBS Lett., 1991, vol. 290, pp. 186–190.
Seemüller, E., Lupas, A., Stock, D., Löwe, J., Huber, R., and Baumeister, W., Science, 1995, vol. 268, pp. 579–582.
Groll, M. and Huber, R., Int. J. Biochem. Cell Biol., 2003, vol. 35, pp. 606–616.
Maupin-Furlow, J.A., Gil, M.A., Karadzic, I.M., Kirkland, P.A., and Reuter, C.J., Front. Biosci., 2004, vol. 9, pp. 1743–1758.
Kisselev, A.F., Songyang, Z., and Goldberg, A.L., J. Biol. Chem., 2000, vol. 275, pp. 14831–14837.
Zwickl, P., Seemuller, E., Kapelari, B., and Baumeister, W., Adv. Protein Chem., 2001, vol. 59, pp. 187–222.
Claverol, S., Burlet-Schiltz, O., Girbal-Neuhauser, E., Gairin, J.E., and Monsarrat, B., Mol. Cell. Proteomics, 2002, vol. 1, pp. 567–578.
Groll, M., Ditzel, L., Lowe, J., Stock, D., Bochtler, M., Bartunik, H.D., and Huber, R., Nature, 1997, vol. 386, pp. 463–471.
Orlowski, M., Biochemistry, 1990, vol. 29, pp. 10289–10297.
Heinemeyer, W., Fischer, M., Krimmer, T., Stachon, U., and Wolf, D.H., J. Biol. Chem., 1997, vol. 272, pp. 25200–25209.
Arendt, C.S. and Hochstrasser, M., Proc. Natl. Acad. Sci. USA, 1997, vol. 94, pp. 7156–7161.
Kisselev, A.F., Akopian, T.N., Woo, K.M., and Goldberg, A.L., J. Biol. Chem., 1999, vol. 274, pp. 3363–3371.
Kisselev, A.F., Akopian, T.N., Castillo, V., and Goldberg, A.L., Mol. Cell, 1999, vol. 4, pp. 395–402.
Zwickl, P., Ng, D., Woo, K.M., Klenk, H.P., and Goldberg, A.L., J. Biol. Chem., 1999, vol. 274, pp. 26008–26014.
Wilson, H.L., Ou, M.S., Aldrich, H.C., and Maupin-Furlow, J., J. Bacteriol., 2000, vol. 182, pp. 1680–1692.
Smith, D.M., Benaroudj, N., and Goldberg, A., J. Struct. Biol., 2006, vol. 156, pp. 72–83.
Mogk, A., Schmidt, R., and Bukau, B., Trends Cell. Biol., 2007, vol. 17, pp. 165–172.
Orino, E., Tanaka, K., Tamura, T., Sone, S., Ogura, T., and Ichihara, A., FEBS Lett., 1991, vol. 284, pp. 206–210.
DeMartino, G.N., Moomaw, C.R., Zagnitko, O.P., Proske, R.J., Chu-Ping, M., Afendis, S.J., Swaffield, J.C., and Slaughter, C.A., J. Biol. Chem., 1994, vol. 269, pp. 20878–20884.
Wollenberg, K. and Swaffield, J.C., Mol. Biol. Evol., 2001, vol. 18, pp. 962–974.
Waxman, L., Fagan, J.M., and Goldberg, A.L., J. Biol. Chem., 1987, vol. 262, pp. 2451–2457.
Hough, R., Pratt, G., and Rechsteiner, M., J. Biol. Chem., 1987, vol. 262, pp. 8303–8313.
Eytan, E., Ganoth, D., Armon, T., and Hershko, A., Proc. Natl. Acad. Sci. USA, 1989, vol. 86, pp. 7751–7755.
Hochstrasser, M., Ann. Rev. Genet., 1996, vol. 30, pp. 405–439.
Gottesman, S., Maurizi, M.R., and Wickner, S., Cell, 1997, vol. 91, pp. 435–438.
Yamada-Inagawa, T., Okuno, T., Karata, K., Yamanaka, K., and Ogura, T., J. Biol. Chem., 2003, vol. 278, pp. 50182–50187.
Hershko, A. and Ciechanover, A., Annu. Rev. Biochem., 1998, vol. 67, pp. 425–479.
Lee, D.H. and Goldberg, A.L., Trends Cell. Biol., 1998, vol. 8, pp. 397–403.
Rotanova, T.V., Abramova, E.B., and Sharova, N.P., Biol. Membrany, 2005, vol. 22, pp. 151–156.
Ciechanover, A., Heller, H., Katz-Etzion, R., and Hershko, A., Proc. Natl. Acad. Sci. USA, 1981, vol. 782, pp. 761–765.
Hershko, A., Ciechanover, A., and Rose, I.A., J. Biol. Chem., 1981, vol. 256, pp. 1525–1528.
Chau, V., Tobias, J.W., Bachmair, A., Marriott, D., Ecker, D.J., Gonda, D.K., and Varshavsky, A., Science, 1989, vol. 243, pp. 1576–1583.
Pickart, C.M., Rose, I.A., J. Biol. Chem., 1985, vol. 260, pp. 1573–1581.
Hadari, T., Warms, J.V., Rose, I.A., and Hershko, A., J. Biol. Chem., 1992, vol. 267, pp. 719–727.
Voges, D., Zwickl, P., and Baumeister, W., Ann. Rev. Biochem., 1999, vol. 68, pp. 1015–1068.
Forster, A., Masters, E.I., Whitby, F.G., Robinson, H., and Hill, C.P., Mol. Cell, 2005, vol. 18, pp. 589–599.
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Original Russian Text © T.V. Rotanova, E.E. Melnikov, 2008, published in Biomeditsinskaya Khimiya.
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Rotanova, T.V., Melnikov, E.E. The ATP-dependent proteases and proteolytic complexes involved into intracellular protein degradation. Biochem. Moscow Suppl. Ser. B 2, 245–257 (2008). https://doi.org/10.1134/S1990750808030049
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DOI: https://doi.org/10.1134/S1990750808030049