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Posttranslational Modification and Degradation Archaea Archaeal Protein Biogenesis: Posttranslational Modification and Degradation Guest Editors: Jerry Eichler, Julie Maupin-Furlow, and Joerg Soppa Archaeal Protein Biogenesis: Posttranslational Modification and Degradation Archaea Archaeal Protein Biogenesis: Posttranslational Modification and Degradation Guest Editors: Jerry Eichler, Julie Maupin-Furlow, and Joerg Soppa Copyright © 2010 Hindawi Publishing Corporation. All rights reserved. This is a special issue published in volume 2010 of “Archaea.” All articles are open access articles distributed under the Creative Com- mons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Archaea Editorial Board Maqsudul Alam, USA Dennis W. Grogan, USA Francesca M. Pisani, Italy Sonja Verena Albers, Germany Robert P. Gunsalus, USA Marina Porcelli, Italy Ricardo Amils, Spain Reinhard Hensel, Germany David Prangishvili, France Haruyuki Atomi, Japan Li Huang, China Reinhard Rachel, Germany Nils-Kare˚ Birkeland, Norway Michael Ibba, USA Anna-Louise Reysenbach, USA Paul H. Blum, USA Y. Ishino, Japan Frank T. Robb, USA E. A. Bonch-Osmolovskaya, Russia Toshio Iwasaki, Japan Francisco Rodriguez-Valera, Spain MariaJ.Bonete,Spain Zvi Kelman, USA Roberto Scandurra, Italy Giovanna Cacciapuoti, Italy S. W. M. Kengen, The Netherlands Kevin R. Sowers, USA IsaacK.O.Cann,USA Hans-Peter Klenk, Germany Stefan Spring, Germany Daniel¨ Charlier, Belgium Paola Londei, Italy Michael Thomm, Germany Antoine Danchin, France Peter A. Lund, UK Herman van Tilbeurgh, France Uwe Deppenmeier, Germany Giuseppe Manco, Italy Antonio Ventosa, Spain Nejat Duzg¨ unes,¨ USA William W. Metcalf, USA William B. Whitman, USA Jerry Eichler, Israel Marco Moracci, Italy Masafumi Yohda, Japan Harald Engelhardt, Germany Masaaki Morikawa, Japan Chuanlun Zhang, USA Michael W. Friedrich, Germany Volker Mueller, Germany ChristianW.Zwieb,USA Toshiaki Fukui, Japan Katsuhiko Murakami, USA Roger Garrett, Denmark Alla Nozhevnikova, Russia Contents Archaeal Protein Biogenesis: Posttranslational Modification and Degradation, Jerry Eichler, Julie Maupin-Furlow, and Joerg Soppa Volume 2010, Article ID 643046, 2 pages Fidelity in Archaeal Information Processing, Bart de Koning, Fabian Blombach, Stan J. J. Brouns, and John van der Oost Volume 2010, Article ID 960298, 15 pages Selenocysteine, Pyrrolysine, and the Unique Energy Metabolism of Methanogenic Archaea, Michael Rother and Joseph A. Krzycki Volume 2010, Article ID 453642, 14 pages Protein Acetylation in Archaea, Bacteria, and Eukaryotes,Jorg¨ Soppa Volume 2010, Article ID 820681, 9 pages Extensive Lysine Methylation in Hyperthermophilic Crenarchaea: Potential Implications for Protein Stability and Recombinant Enzymes, Catherine H. Botting, Paul Talbot, Sonia Paytubi, and Malcolm F. White Volume 2010, Article ID 106341, 6 pages Iron-Sulfur World in Aerobic and Hyperthermoacidophilic Archaea Sulfolobus, Toshio Iwasaki Volume 2010, Article ID 842639, 14 pages Archaeal Ubiquitin-Like Proteins: Functional Versatility and Putative Ancestral Involvement in tRNA Modification Revealed by Comparative Genomic Analysis, Kira S. Makarova and Eugene V. Koonin Volume 2010, Article ID 710303, 10 pages Phosphorylation and Methylation of Proteasomal Proteins of the Haloarcheon Haloferax volcanii, Matthew A. Humbard, Christopher J. Reuter, Kheir Zuobi-Hasona, Guangyin Zhou, and Julie A. Maupin-Furlow Volume 2010, Article ID 481725, 10 pages Archaea Signal Recognition Particle Shows the Way, Christian Zwieb and Shakhawat Bhuiyan Volume 2010, Article ID 485051, 11 pages Mutational and Bioinformatic Analysis of Haloarchaeal Lipobox-Containing Proteins, Stefanie Storf, Friedhelm Pfeiffer, Kieran Dilks, Zhong Qiang Chen, Saheed Imam, and Mechthild Pohlschroder¨ Volume 2010, Article ID 410975, 11 pages Shaping the Archaeal Cell Envelope, Albert F. Ellen, Behnam Zolghadr, Arnold M. J. Driessen, and Sonja-Verena Albers Volume 2010, Article ID 608243, 13 pages S-Layer Glycoproteins and Flagellins: Reporters of Archaeal Posttranslational Modifications, Ken F. Jarrell, Gareth M. Jones, Lina Kandiba, Divya B. Nair, and Jerry Eichler Volume 2010, Article ID 612948, 13 pages The S-Layer Glycoprotein of the Crenarchaeote Sulfolobus acidocaldarius Is Glycosylated at Multiple Sites with Chitobiose-Linked N-Glycans, Elham Peyfoon, Benjamin Meyer, Paul G. Hitchen, Maria Panico, Howard R. Morris, Stuart M. Haslam, Sonja-Verena Albers, and Anne Dell Volume 2010, Article ID 754101, 10 pages Identification of Residues Important for the Activity of Haloferax volcanii AglD, a Component of the Archaeal N-Glycosylation Pathway, Lina Kaminski and Jerry Eichler Volume 2010, Article ID 315108, 9 pages Hindawi Publishing Corporation Archaea Volume 2010, Article ID 643046, 2 pages doi:10.1155/2010/643046 Editorial Archaeal Protein Biogenesis: Posttranslational Modification and Degradation Jerry Eichler,1 Julie Maupin-Furlow,2 and Joerg Soppa3 1 Department of Life Sciences, Ben-Gurion University of the Negev, Beersheva, Israel 2 Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA 3 Institute for Molecular Biosciences, Frankfurt University, 60325 Frankfurt, Germany Correspondence should be addressed to Jerry Eichler, [email protected] Received 1 August 2010; Accepted 1 August 2010 Copyright © 2010 Jerry Eichler et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The study of Archaea at the DNA and RNA levels has Protein degradation is the focus of two articles in this provided considerable insight into replication, transcription, special issue. Makarova and Koonin rely on comparative and other information-associated events which are either genomic analysis to reveal functional versatility of archaeal unique to this remarkable group of organisms or which ubiquitin-like proteins, while Humbard et al. report on were later found to also occur in Bacteria and/or Eukarya. the phosphorylation and methylation of Haloferax volcanii In contrast, largely due to a lack of suitable model systems proteasomal proteins. and a limited number of appropriate molecular tools, Archaeal cell surface proteins undergo a variety of post- considerably less was known about archaeal proteins in terms translational modifications. However, such proteins must of their biogenesis, modification, trafficking, or degradation. first be targeted to and traverse the plasma membrane. In recent years, however, we have witnessed major advances Accordingly, Zwieb and Bhuiyan discuss the latest findings in proteomics, successful in vitro reconstitutions, and the on the archaeal signal recognition particle targeting system. development of reporter systems compatible with extreme Storf et al. address questions related to the biogenesis of conditions. Relying on such tools, insight into different stages one class of membrane proteins, namely, lipoproteins. An in the life of archaeal proteins has begun to accumulate. article by Ellen et al. considers archaeal protein export and In this special issue of Archaea, we present a series of describes different cell surface structures, while a report articles addressing the current state of understanding of by Jarrell et al. focuses on the S-layer glycoprotein and selected facets of archaeal protein biogenesis and process- flagella as reporters of choice of different protein processing ing. events. With this in mind, Peyfoon and colleagues describe An article by De Koning et al. discussing how fidelity the N-linked glycan decorating the S-layer glycoprotein in archaeal information processing at the DNA, RNA, and of Sulfolobus acidocaldarius. Finally, Kaminski and Eichler protein levels is achieved begins this special issue. Rother consider the workings of AglD, one of the enzymes which and Krzycki then address proteins containing the unusual is involved in Haloferax volcanii S-layer glycoprotein N- animo acids, selenocysteine, and pyrrolysine, as related to the glycosylation. unique energy metabolism of methanogenic archaea. Soppa In this, the first special issue of Archaea dedicated to compares one specific posttranslational modification, acety- archaeal protein biogenesis, we have tried to give the reader lation, across evolutionary lines, while Botting et al. discuss a sampling of the current research scene. It is our sincere the importance of lysine methylation in hyperthermophilic hope that the community will find interest in the articles crenarchaeota. Questions related to protein assembly are included here. More importantly, it is our intention that the considered when Iwasaki addresses the iron-sulfur world in work presented will stimulate other laboratories to begin hyperthermoacidophilic archaea. studying questions related to archaeal protein biogenesis, 2 Archaea hopefully in time for the next installment of this special issue. Jerry Eichler Julie Maupin-Furlow Joerg Soppa Hindawi Publishing Corporation Archaea Volume 2010, Article ID 960298, 15 pages doi:10.1155/2010/960298 Review Article Fidelity in Archaeal Information Processing Bart de Koning, Fabian Blombach, Stan J. J. Brouns, and John van der Oost Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands Correspondence should be addressed to Bart de Koning, [email protected] Received 15 May 2010; Accepted 12 July 2010 Academic Editor:
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