The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics

Schulze, Stefan; Adams, Zachary; Cerletti, Micaela; De Castro, Rosana; Ferreira-Cerca, Sébastien; Fufezan, Christian; Giménez, María Inés; Hippler, Michael; Jevtic, Zivojin; Knüppel, Robert; Legerme, Georgio; Lenz, Christof; Marchfelder, Anita; Maupin-Furlow, Julie; Paggi, Roberto A.; Pfeiffer, Friedhelm; Poetsch, Ansgar; Urlaub, Henning; Pohlschroder, Mechthild

doi:10.1038/s41467-020-16784-7

The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics

Journal Article · Fri Jun 19 00:00:00 EDT 2020 · Nature Communications

DOI:https://doi.org/10.1038/s41467-020-16784-7· OSTI ID:1633928

; ; Cerletti, Micaela; ; ; Fufezan, Christian; Giménez, María Inés; ; Jevtic, Zivojin; Knüppel, Robert; Legerme, Georgio; ; ; ; Paggi, Roberto A.; ; Poetsch, Ansgar; Urlaub, Henning;

Abstract

While many aspects of archaeal cell biology remain relatively unexplored, systems biology approaches like mass spectrometry (MS) based proteomics offer an opportunity for rapid advances. Unfortunately, the enormous amount of MS data generated often remains incompletely analyzed due to a lack of sophisticated bioinformatic tools and field-specific biological expertise for data interpretation. Here we present the initiation of the Archaeal Proteome Project (ArcPP), a community-based effort to comprehensively analyze archaeal proteomes. Starting with the model archaeon Haloferax volcanii , we reanalyze MS datasets from various strains and culture conditions. Optimized peptide spectrum matching, with strict control of false discovery rates, facilitates identifying > 72% of the reference proteome, with a median protein sequence coverage of 51%. These analyses, together with expert knowledge in diverse aspects of cell biology, provide meaningful insights into processes such as N-terminal protein maturation, N -glycosylation, and metabolism. Altogether, ArcPP serves as an invaluable blueprint for comprehensive prokaryotic proteomics.

View Journal Article

Sponsoring Organization:: USDOE

OSTI ID:: 1633928

Alternate ID(s):: OSTI ID: 1646997

Journal Information:: Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 11; ISSN 2041-1723

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (110)

Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions Bjellqvist, Bengt; Basse, Bodil; Olsen, Eydfinnur Electrophoresis, Vol. 15, Issue 1 https://doi.org/10.1002/elps.1150150171	journal	January 1994
Comparative proteomic analysis of Methanothermobacter thermautotrophicus reveals methane formation from H ₂ and CO ₂ under different temperature conditions Liu, Cong; Mao, Lihui; Zheng, Xiongmin MicrobiologyOpen, Vol. 8, Issue 5 https://doi.org/10.1002/mbo3.715	journal	September 2018
The membrane proteome ofHalobacterium salinarum Klein, Christian; Garcia-Rizo, Carolina; Bisle, Birgit PROTEOMICS, Vol. 5, Issue 1 https://doi.org/10.1002/pmic.200400943	journal	January 2005
Improving sensitivity in proteome studies by analysis of false discovery rates for multiple search engines Jones, Andrew R.; Siepen, Jennifer A.; Hubbard, Simon J. PROTEOMICS, Vol. 9, Issue 5 https://doi.org/10.1002/pmic.200800473	journal	March 2009
A peptide resource for the analysis of Staphylococcus aureus in host-pathogen interaction studies Depke, Maren; Michalik, Stephan; Rabe, Alexander PROTEOMICS, Vol. 15, Issue 21 https://doi.org/10.1002/pmic.201500091	journal	September 2015
Identifying New Small Proteins in Escherichia coli VanOrsdel, Caitlin E.; Kelly, John P.; Burke, Brittany N. PROTEOMICS, Vol. 18, Issue 10 https://doi.org/10.1002/pmic.201700064	journal	May 2018
Proteomic Study of the Exponential-Stationary Growth Phase Transition in the Haloarchaea Natrialba magadii and Haloferax volcanii Cerletti, Micaela; Giménez, María Ines; Tröetschel, Christian PROTEOMICS, Vol. 18, Issue 14 https://doi.org/10.1002/pmic.201800116	journal	June 2018
The Response of Haloferax volcanii to Salt and Temperature Stress: A Proteome Study by Label‐Free Mass Spectrometry Jevtić, Živojin; Stoll, Britta; Pfeiffer, Friedhelm PROTEOMICS, Vol. 19, Issue 20 https://doi.org/10.1002/pmic.201800491	journal	September 2019
Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen Krogh, Anders; Larsson, Björn; von Heijne, Gunnar Journal of Molecular Biology, Vol. 305, Issue 3 https://doi.org/10.1006/jmbi.2000.4315	journal	January 2001
Genome information management and integrated data analysis with HaloLex Pfeiffer, Friedhelm; Broicher, Alexander; Gillich, Thomas Archives of Microbiology, Vol. 190, Issue 3 https://doi.org/10.1007/s00203-008-0389-z	journal	July 2008
Fast and Accurate Protein False Discovery Rates on Large-Scale Proteomics Data Sets with Percolator 3.0 The, Matthew; MacCoss, Michael J.; Noble, William S. Journal of The American Society for Mass Spectrometry, Vol. 27, Issue 11 https://doi.org/10.1007/s13361-016-1460-7	journal	August 2016
A simple method for displaying the hydropathic character of a protein Kyte, Jack; Doolittle, Russell F. Journal of Molecular Biology, Vol. 157, Issue 1, p. 105-132 https://doi.org/10.1016/0022-2836(82)90515-0	journal	May 1982
Assembling the Community-Scale Discoverable Human Proteome Wang, Mingxun; Wang, Jian; Carver, Jeremy Cell Systems, Vol. 7, Issue 4 https://doi.org/10.1016/j.cels.2018.08.004	journal	October 2018
The Mtb Proteome Library: A Resource of Assays to Quantify the Complete Proteome of Mycobacterium tuberculosis Schubert, Olga T.; Mouritsen, Jeppe; Ludwig, Christina Cell Host & Microbe, Vol. 13, Issue 5 https://doi.org/10.1016/j.chom.2013.04.008	journal	May 2013
Archaeal N-terminal Protein Maturation Commonly Involves N-terminal Acetylation: A Large-scale Proteomics Survey Falb, Michaela; Aivaliotis, Michalis; Garcia-Rizo, Carolina Journal of Molecular Biology, Vol. 362, Issue 5 https://doi.org/10.1016/j.jmb.2006.07.086	journal	October 2006
Exploring the membrane proteome—Challenges and analytical strategies Helbig, Andreas O.; Heck, Albert J. R.; Slijper, Monique Journal of Proteomics, Vol. 73, Issue 5 https://doi.org/10.1016/j.jprot.2010.01.005	journal	March 2010
Global role of the membrane protease LonB in Archaea: Potential protease targets revealed by quantitative proteome analysis of a lonB mutant in Haloferax volcanii Cerletti, Micaela; Paggi, Roberto A.; Guevara, Carina Ramallo Journal of Proteomics, Vol. 121 https://doi.org/10.1016/j.jprot.2015.03.016	journal	May 2015
Global effect of the lack of inorganic polyphosphate in the extremophilic archaeon Sulfolobus solfataricus: A proteomic approach Soto, Daniela F.; Recalde, Alejandra; Orell, Alvaro Journal of Proteomics, Vol. 191 https://doi.org/10.1016/j.jprot.2018.02.024	journal	January 2019
The LonB protease modulates the degradation of CetZ1 involved in rod-shape determination in Haloferax volcanii Ferrari, María C.; Cerletti, Micaela; Paggi, Roberto A. Journal of Proteomics, Vol. 211 https://doi.org/10.1016/j.jprot.2019.103546	journal	January 2020
Extreme challenges and advances in archaeal proteomics Maupin-Furlow, Julie A.; Humbard, Matthew A.; Kirkland, Phillip Aaron Current Opinion in Microbiology, Vol. 15, Issue 3 https://doi.org/10.1016/j.mib.2012.02.002	journal	June 2012
Haloferax volcanii Pohlschroder, Mechthild; Schulze, Stefan Trends in Microbiology, Vol. 27, Issue 1 https://doi.org/10.1016/j.tim.2018.10.004	journal	January 2019
Phenol-hypochlorite reaction for determination of ammonia Weatherburn, M. W. Analytical Chemistry, Vol. 39, Issue 8 https://doi.org/10.1021/ac60252a045	journal	July 1967
Ursgal, Universal Python Module Combining Common Bottom-Up Proteomics Tools for Large-Scale Analysis Kremer, Lukas P. M.; Leufken, Johannes; Oyunchimeg, Purevdulam Journal of Proteome Research, Vol. 15, Issue 3 https://doi.org/10.1021/acs.jproteome.5b00860	journal	January 2016
Haloferax volcanii Proteome Response to Deletion of a Rhomboid Protease Gene Costa, Mariana I.; Cerletti, Micaela; Paggi, Roberto A. Journal of Proteome Research, Vol. 17, Issue 3 https://doi.org/10.1021/acs.jproteome.7b00530	journal	February 2018
Proteomic Landscape of Patient-Derived CD4+ T Cells in Recent-Onset Type 1 Diabetes Lepper, Marlen F.; Ohmayer, Uli; von Toerne, Christine Journal of Proteome Research, Vol. 17, Issue 1 https://doi.org/10.1021/acs.jproteome.7b00712	journal	November 2017
LonB Protease Is a Novel Regulator of Carotenogenesis Controlling Degradation of Phytoene Synthase in Haloferax volcanii Cerletti, Micaela; Paggi, Roberto; Troetschel, Christian Journal of Proteome Research, Vol. 17, Issue 3 https://doi.org/10.1021/acs.jproteome.7b00809	journal	February 2018
ProteinExplorer: A Repository-Scale Resource for Exploration of Protein Detection in Public Mass Spectrometry Data Sets Pullman, Benjamin S.; Wertz, Julie; Carver, Jeremy Journal of Proteome Research, Vol. 17, Issue 12 https://doi.org/10.1021/acs.jproteome.8b00496	journal	August 2018
ThermoRawFileParser: Modular, Scalable, and Cross-Platform RAW File Conversion Hulstaert, Niels; Shofstahl, Jim; Sachsenberg, Timo Journal of Proteome Research, Vol. 19, Issue 1 https://doi.org/10.1021/acs.jproteome.9b00328	journal	November 2019
Progress on Identifying and Characterizing the Human Proteome: 2019 Metrics from the HUPO Human Proteome Project Omenn, Gilbert S.; Lane, Lydie; Overall, Christopher M. Journal of Proteome Research, Vol. 18, Issue 12 https://doi.org/10.1021/acs.jproteome.9b00434	journal	August 2019
The Low Molecular Weight Proteome of Halobacterium salinarum Klein, Christian; Aivaliotis, Michalis; Olsen, Jesper V. Journal of Proteome Research, Vol. 6, Issue 4 https://doi.org/10.1021/pr060634q	journal	April 2007
MS Amanda, a Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra Dorfer, Viktoria; Pichler, Peter; Stranzl, Thomas Journal of Proteome Research, Vol. 13, Issue 8 https://doi.org/10.1021/pr500202e	journal	June 2014
Tandem Mass Spectrum Identification via Cascaded Search Kertesz-Farkas, Attila; Keich, Uri; Noble, William Stafford Journal of Proteome Research, Vol. 14, Issue 8 https://doi.org/10.1021/pr501173s	journal	June 2015
Posterior Error Probabilities and False Discovery Rates: Two Sides of the Same Coin Käll, Lukas; Storey, John D.; MacCoss, Michael J. Journal of Proteome Research, Vol. 7, Issue 1 https://doi.org/10.1021/pr700739d	journal	January 2008
Halobacterium salinarum NRC-1 PeptideAtlas: Toward Strategies for Targeted Proteomics and Improved Proteome Coverage Van, Phu T.; Schmid, Amy K.; King, Nichole L. Journal of Proteome Research, Vol. 7, Issue 9 https://doi.org/10.1021/pr800031f	journal	September 2008
Shotgun Proteomics of the Haloarchaeon Haloferax volcanii Kirkland, P. Aaron; Humbard, Matthew A.; Daniels, Charles J. Journal of Proteome Research, Vol. 7, Issue 11 https://doi.org/10.1021/pr800517a	journal	November 2008
False Discovery Rates of Protein Identifications: A Strike against the Two-Peptide Rule Gupta, Nitin; Pevzner, Pavel A. Journal of Proteome Research, Vol. 8, Issue 9 https://doi.org/10.1021/pr9004794	journal	September 2009
Quantitative Proteomic Analysis of Sulfolobus solfataricus Membrane Proteins Pham, Trong Khoa; Sierocinski, Pawel; van der Oost, John Journal of Proteome Research, Vol. 9, Issue 2 https://doi.org/10.1021/pr9007688	journal	February 2010
Value of Using Multiple Proteases for Large-Scale Mass Spectrometry-Based Proteomics Swaney, Danielle L.; Wenger, Craig D.; Coon, Joshua J. Journal of Proteome Research, Vol. 9, Issue 3 https://doi.org/10.1021/pr900863u	journal	March 2010
Microbial ecology of an Antarctic hypersaline lake: genomic assessment of ecophysiology among dominant haloarchaea Williams, Timothy J.; Allen, Michelle A.; DeMaere, Matthew Z. The ISME Journal, Vol. 8, Issue 8 https://doi.org/10.1038/ismej.2014.18	journal	February 2014
The growing tree of Archaea: new perspectives on their diversity, evolution and ecology Adam, Panagiotis S.; Borrel, Guillaume; Brochier-Armanet, Céline The ISME Journal, Vol. 11, Issue 11 https://doi.org/10.1038/ismej.2017.122	journal	August 2017
Ubiquitin-like small archaeal modifier proteins (SAMPs) in Haloferax volcanii Humbard, Matthew A.; Miranda, Hugo V.; Lim, Jae-Min Nature, Vol. 463, Issue 7277 https://doi.org/10.1038/nature08659	journal	January 2010
Mass-spectrometry-based draft of the human proteome Wilhelm, Mathias; Schlegl, Judith; Hahne, Hannes Nature, Vol. 509, Issue 7502 https://doi.org/10.1038/nature13319	journal	May 2014
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification Cox, Jürgen; Mann, Matthias Nature Biotechnology, Vol. 26, Issue 12 https://doi.org/10.1038/nbt.1511	journal	November 2008
The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome Paik, Young-Ki; Jeong, Seul-Ki; Omenn, Gilbert S. Nature Biotechnology, Vol. 30, Issue 3 https://doi.org/10.1038/nbt.2152	journal	March 2012
A cross-platform toolkit for mass spectrometry and proteomics Chambers, Matthew C.; Maclean, Brendan; Burke, Robert Nature Biotechnology, Vol. 30, Issue 10 https://doi.org/10.1038/nbt.2377	journal	October 2012
The quantitative and condition-dependent Escherichia coli proteome Schmidt, Alexander; Kochanowski, Karl; Vedelaar, Silke Nature Biotechnology, Vol. 34, Issue 1 https://doi.org/10.1038/nbt.3418	journal	December 2015
Universal sample preparation method for proteome analysis Wiśniewski, Jacek R.; Zougman, Alexandre; Nagaraj, Nagarjuna Nature Methods, Vol. 6, Issue 5 https://doi.org/10.1038/nmeth.1322	journal	April 2009
MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry–based proteomics Kong, Andy T.; Leprevost, Felipe V.; Avtonomov, Dmitry M. Nature Methods, Vol. 14, Issue 5 https://doi.org/10.1038/nmeth.4256	journal	April 2017
Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry Elias, Joshua E.; Gygi, Steven P. Nature Methods, Vol. 4, Issue 3 https://doi.org/10.1038/nmeth1019	journal	February 2007
The essential genome of the crenarchaeal model Sulfolobus islandicus Zhang, Changyi; Phillips, Alex P. R.; Wipfler, Rebecca L. Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-07379-4	journal	November 2018
SignalP 5.0 improves signal peptide predictions using deep neural networks Almagro Armenteros, José Juan; Tsirigos, Konstantinos D.; Sønderby, Casper Kaae Nature Biotechnology, Vol. 37, Issue 4 https://doi.org/10.1038/s41587-019-0036-z	journal	February 2019
A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host-pathogen interactions Michalik, Stephan; Depke, Maren; Murr, Annette Scientific Reports, Vol. 7, Issue 1 https://doi.org/10.1038/s41598-017-10059-w	journal	September 2017
The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity Payne, Samuel H.; Monroe, Matthew E.; Overall, Christopher C. Scientific Data, Vol. 2, Issue 1 https://doi.org/10.1038/sdata.2015.41	journal	August 2015
Structural Basis for Substrate-specific Acetylation of Nα-acetyltransferase Ard1 from Sulfolobus solfataricus Chang, Yu-Yung; Hsu, Chun-Hua Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep08673	journal	March 2015
Morphological and proteomic analysis of biofilms from the Antarctic archaeon, Halorubrum lacusprofundi Liao, Y.; Williams, T. J.; Ye, J. Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep37454	journal	November 2016
Towards functional characterization of archaeal genomic dark matter Makarova, Kira S.; Wolf, Yuri I.; Koonin, Eugene V. Biochemical Society Transactions, Vol. 47, Issue 1 https://doi.org/10.1042/BST20180560	journal	February 2019
Adaptation of protein secretion to extremely high-salt conditions by extensive use of the twin-arginine translocation pathway Rose, R. Wesley; Bruser, Thomas; Kissinger, Jessica C. Molecular Microbiology, Vol. 45, Issue 4 https://doi.org/10.1046/j.1365-2958.2002.03090.x	journal	August 2002
E1- and ubiquitin-like proteins provide a direct link between protein conjugation and sulfur transfer in archaea Miranda, H. V.; Nembhard, N.; Su, D. Proceedings of the National Academy of Sciences, Vol. 108, Issue 11 https://doi.org/10.1073/pnas.1018151108	journal	February 2011
Role for urea in nitrification by polar marine Archaea Alonso-Saez, L.; Waller, A. S.; Mende, D. R. Proceedings of the National Academy of Sciences, Vol. 109, Issue 44 https://doi.org/10.1073/pnas.1201914109	journal	October 2012
A Rhomboid Protease Gene Deletion Affects a Novel Oligosaccharide N -Linked to the S-layer Glycoprotein of Haloferax volcanii Parente, Juliana; Casabuono, Adriana; Ferrari, María Celeste Journal of Biological Chemistry, Vol. 289, Issue 16 https://doi.org/10.1074/jbc.M113.546531	journal	March 2014
Identification of Haloferax volcanii Pilin N -Glycans with Diverse Roles in Pilus Biosynthesis, Adhesion, and Microcolony Formation Esquivel, Rianne N.; Schulze, Stefan; Xu, Rachel Journal of Biological Chemistry, Vol. 291, Issue 20 https://doi.org/10.1074/jbc.M115.693556	journal	March 2016
The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search Kim, Sangtae; Mischerikow, Nikolai; Bandeira, Nuno Molecular & Cellular Proteomics, Vol. 9, Issue 12 https://doi.org/10.1074/mcp.M110.003731	journal	September 2010
Archaeal Ubiquitin-like SAMP3 is Isopeptide-linked to Proteins via a UbaA-dependent Mechanism Miranda, Hugo V.; Antelmann, Haike; Hepowit, Nathaniel Molecular & Cellular Proteomics, Vol. 13, Issue 1 https://doi.org/10.1074/mcp.M113.029652	journal	October 2013
A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets Savitski, Mikhail M.; Wilhelm, Mathias; Hahne, Hannes Molecular & Cellular Proteomics, Vol. 14, Issue 9 https://doi.org/10.1074/mcp.M114.046995	journal	May 2015
mzML—a Community Standard for Mass Spectrometry Data Martens, Lennart; Chambers, Matthew; Sturm, Marc Molecular & Cellular Proteomics, Vol. 10, Issue 1 https://doi.org/10.1074/mcp.R110.000133	journal	August 2010
PROTEOFORMER 2.0: Further Developments in the Ribosome Profiling-assisted Proteogenomic Hunt for New Proteoforms Verbruggen, Steven; Ndah, Elvis; Van Criekinge, Wim Molecular & Cellular Proteomics, Vol. 18, Issue 8 suppl 1 https://doi.org/10.1074/mcp.RA118.001218	journal	April 2019
Functional Insights Into Protein Acetylation in the Hyperthermophilic Archaeon Sulfolobus islandicus Cao, Jingjing; Wang, Tongkun; Wang, Qian Molecular & Cellular Proteomics, Vol. 18, Issue 8 https://doi.org/10.1074/mcp.RA119.001312	journal	June 2019
TANDEM: matching proteins with tandem mass spectra Craig, R.; Beavis, R. C. Bioinformatics, Vol. 20, Issue 9 https://doi.org/10.1093/bioinformatics/bth092	journal	February 2004
Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows Specht, Michael; Kuhlgert, Sebastian; Fufezan, Christian Bioinformatics, Vol. 27, Issue 8 https://doi.org/10.1093/bioinformatics/btr081	journal	February 2011
Structural characterization of the N-linked pentasaccharide decorating glycoproteins of the halophilic archaeon Haloferax volcanii Kandiba, Lina; Lin, Chia-Wei; Aebi, Markus Glycobiology, Vol. 26, Issue 7 https://doi.org/10.1093/glycob/cww014	journal	February 2016
PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies Akhter, Sajia; Aziz, Ramy K.; Edwards, Robert A. Nucleic Acids Research, Vol. 40, Issue 16 https://doi.org/10.1093/nar/gks406	journal	May 2012
The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition Deutsch, Eric W.; Csordas, Attila; Sun, Zhi Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw936	journal	October 2016
The PRIDE database and related tools and resources in 2019: improving support for quantification data Perez-Riverol, Yasset; Csordas, Attila; Bai, Jingwen Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky1106	journal	November 2018
The jPOST environment: an integrated proteomics data repository and database Moriya, Yuki; Kawano, Shin; Okuda, Shujiro Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky899	journal	October 2018
Haloferax volcanii cells lacking the flagellin FlgA2 are hypermotile Tripepi, Manuela; Esquivel, Rianne N.; Wirth, Reinhard Microbiology, Vol. 159, Issue Pt_11 https://doi.org/10.1099/mic.0.069617-0	journal	November 2013
An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics Omasits, Ulrich; Varadarajan, Adithi R.; Schmid, Michael Genome Research, Vol. 27, Issue 12 https://doi.org/10.1101/gr.218255.116	journal	November 2017
Prediction of lipoprotein signal peptides in Gram-negative bacteria Juncker, Agnieszka S.; Willenbrock, Hanni; von Heijne, Gunnar Protein Science, Vol. 12, Issue 8 https://doi.org/10.1110/ps.0303703	journal	August 2003
The LonB protease controls membrane lipids composition and is essential for viability in the extremophilic haloarchaeon H aloferax volcanii: Characterization of lonB mutants in Haloferax volcanii Cerletti, Micaela; Martínez, María J.; Giménez, María I. Environmental Microbiology, Vol. 16, Issue 6 https://doi.org/10.1111/1462-2920.12385	journal	February 2014
Oxidation of urea-derived nitrogen by thaumarchaeota-dominated marine nitrifying communities: Oxidation of urea-derived nitrogen in the sea Tolar, Bradley B.; Wallsgrove, Natalie J.; Popp, Brian N. Environmental Microbiology, Vol. 19, Issue 12 https://doi.org/10.1111/1462-2920.13457	journal	August 2016
Multiplex quantitative SILAC for analysis of archaeal proteomes: a case study of oxidative stress responses: Multiplex SILAC for archaeal proteomics McMillan, Lana J.; Hwang, Sungmin; Farah, Rawan E. Environmental Microbiology, Vol. 20, Issue 1 https://doi.org/10.1111/1462-2920.14014	journal	December 2017
Post-translation modification in Archaea: lessons from Haloferax volcanii and other haloarchaea Eichler, Jerry; Maupin-Furlow, Julie FEMS Microbiology Reviews, Vol. 37, Issue 4 https://doi.org/10.1111/1574-6976.12012	journal	July 2013
All three chaperonin genes in the archaeon Haloferax volcanii are individually dispensable Kapatai, Georgia; Large, Andrew; Benesch, Justin L. P. Molecular Microbiology, Vol. 61, Issue 6 https://doi.org/10.1111/j.1365-2958.2006.05324.x	journal	September 2006
An acetylase with relaxed specificity catalyses protein N-terminal acetylation in Sulfolobus solfataricus: Crenarchaeal protein acetylation Mackay, Dale T.; Botting, Catherine H.; Taylor, Garry L. Molecular Microbiology, Vol. 64, Issue 6 https://doi.org/10.1111/j.1365-2958.2007.05752.x	journal	May 2007
Protein glycosylation as an adaptive response in Archaea: growth at different salt concentrations leads to alterations in Haloferax volcanii S-layer glycoprotein N-glycosylation: Salinity modulates Hfx. volcanii N-glycosylation Guan, Ziqiang; Naparstek, Shai; Calo, Doron Environmental Microbiology, Vol. 14, Issue 3 https://doi.org/10.1111/j.1462-2920.2011.02625.x	journal	October 2011
A conserved type IV pilin signal peptide H-domain is critical for the post-translational regulation of flagella-dependent motility: Pili-dependent regulation of swimming motility Esquivel, Rianne N.; Pohlschroder, Mechthild Molecular Microbiology, Vol. 93, Issue 3 https://doi.org/10.1111/mmi.12673	journal	July 2014
Conserved residues are critical for Haloferax volcanii archaeosortase catalytic activity: Implications for convergent evolution of the catalytic mechanisms of non-homologous sortases from archaea and bacteria: Haloferax volcanii archaeosortase catalytic residues Abdul Halim, Mohd Farid; Rodriguez, Ronald; Stoltzfus, Jonathan D. Molecular Microbiology, Vol. 108, Issue 3 https://doi.org/10.1111/mmi.13935	journal	March 2018
The N-Terminal Penultimate Residue of 20S Proteasome 1 Influences its N Acetylation and Protein Levels as Well as Growth Rate and Stress Responses of Haloferax volcanii Humbard, M. A.; Zhou, G.; Maupin-Furlow, J. A. Journal of Bacteriology, Vol. 191, Issue 12 https://doi.org/10.1128/JB.00090-09	journal	April 2009
GlpR Is a Direct Transcriptional Repressor of Fructose Metabolic Genes in Haloferax volcanii Martin, Jonathan H.; Sherwood Rawls, Katherine; Chan, Jou Chin Journal of Bacteriology, Vol. 200, Issue 17 https://doi.org/10.1128/JB.00244-18	journal	June 2018
ArtA-Dependent Processing of a Tat Substrate Containing a Conserved Tripartite Structure That Is Not Localized at the C Terminus Abdul Halim, Mohd Farid; Stoltzfus, Jonathan D.; Schulze, Stefan Journal of Bacteriology, Vol. 199, Issue 7 https://doi.org/10.1128/JB.00802-16	journal	January 2017
Anaerobic Growth of Haloarchaeon Haloferax volcanii by Denitrification Is Controlled by the Transcription Regulator NarO Hattori, Tatsuya; Shiba, Hiromichi; Ashiki, Ken-ichi Journal of Bacteriology, Vol. 198, Issue 7 https://doi.org/10.1128/JB.00833-15	journal	January 2016
Proteasomal Components Required for Cell Growth and Stress Responses in the Haloarchaeon Haloferax volcanii Zhou, G.; Kowalczyk, D.; Humbard, M. A. Journal of Bacteriology, Vol. 190, Issue 24 https://doi.org/10.1128/JB.01180-08	journal	October 2008
Identification of Diverse Archaeal Proteins with Class III Signal Peptides Cleaved by Distinct Archaeal Prepilin Peptidases Szabo, Z.; Stahl, A. O.; Albers, S. -V. Journal of Bacteriology, Vol. 189, Issue 3 https://doi.org/10.1128/JB.01547-06	journal	November 2006
In Vivo Analysis of an Essential Archaeal Signal Recognition Particle in Its Native Host Rose, R. Wesley; Pohlschröder, Mechthild Journal of Bacteriology, Vol. 184, Issue 12 https://doi.org/10.1128/JB.184.12.3260-3267.2002	journal	June 2002
Genetic and Biochemical Analysis of the Twin-Arginine Translocation Pathway in Halophilic Archaea Dilks, Kieran; Giménez, María Inés; Pohlschröder, Mechthild Journal of Bacteriology, Vol. 187, Issue 23 https://doi.org/10.1128/JB.187.23.8104-8113.2005	journal	December 2005
Growth Kinetics of Extremely Halophilic Archaea (Family Halobacteriaceae) as Revealed by Arrhenius Plots Robinson, Jessie L.; Pyzyna, Brandy; Atrasz, Rachelle G. Journal of Bacteriology, Vol. 187, Issue 3 https://doi.org/10.1128/JB.187.3.923-929.2005	journal	February 2005
N-Linked Glycosylation in Archaea: a Structural, Functional, and Genetic Analysis Jarrell, Ken F.; Ding, Yan; Meyer, Benjamin H. Microbiology and Molecular Biology Reviews, Vol. 78, Issue 2 https://doi.org/10.1128/MMBR.00052-13	journal	May 2014
Lipid Anchoring of Archaeosortase Substrates and Midcell Growth in Haloarchaea Abdul-Halim, Mohd Farid; Schulze, Stefan; DiLucido, Anthony mBio, Vol. 11, Issue 2 https://doi.org/10.1128/mBio.00349-20	journal	March 2020
Two Distinct N-Glycosylation Pathways Process the Haloferax volcanii S-Layer Glycoprotein upon Changes in Environmental Salinity Kaminski, L.; Guan, Z.; Yurist-Doutsch, S. mBio, Vol. 4, Issue 6 https://doi.org/10.1128/mBio.00716-13	journal	October 2013
Combination of Proteogenomics with Peptide De Novo Sequencing Identifies New Genes and Hidden Posttranscriptional Modifications Blank-Landeshammer, B.; Teichert, I.; Märker, R. mBio, Vol. 10, Issue 5 https://doi.org/10.1128/mBio.02367-19	journal	October 2019
Mutational and Bioinformatic Analysis of Haloarchaeal Lipobox-Containing Proteins Storf, Stefanie; Pfeiffer, Friedhelm; Dilks, Kieran Archaea, Vol. 2010 https://doi.org/10.1155/2010/410975	journal	January 2010
Phosphorylation and Methylation of Proteasomal Proteins of the Haloarcheon Haloferax volcanii Humbard, Matthew A.; Reuter, Christopher J.; Zuobi-Hasona, Kheir Archaea, Vol. 2010 https://doi.org/10.1155/2010/481725	journal	January 2010
Archaeal Enzymes and Applications in Industrial Biocatalysts Littlechild, Jennifer A. Archaea, Vol. 2015 https://doi.org/10.1155/2015/147671	journal	January 2015
Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq) Babski, Julia; Haas, Karina A.; Näther-Schindler, Daniela BMC Genomics, Vol. 17, Issue 1 https://doi.org/10.1186/s12864-016-2920-y	journal	August 2016
Ureases of Extreme Halophiles of the Genus Haloarcula with a Unique Structure of Gene Cluster Mizuki, Toru; Kamekura, Masahiro; Dassarma, Shiladitya Bioscience, Biotechnology, and Biochemistry, Vol. 68, Issue 2 https://doi.org/10.1271/bbb.68.397	journal	January 2004
The Complete Genome Sequence of Haloferax volcanii DS2, a Model Archaeon Hartman, Amber L.; Norais, Cédric; Badger, Jonathan H. PLoS ONE, Vol. 5, Issue 3 https://doi.org/10.1371/journal.pone.0009605	journal	March 2010
A Comprehensive Analysis of the Importance of Translation Initiation Factors for Haloferax volcanii Applying Deletion and Conditional Depletion Mutants Gäbel, Katrin; Schmitt, Jessica; Schulz, Sebastian PLoS ONE, Vol. 8, Issue 11 https://doi.org/10.1371/journal.pone.0077188	journal	November 2013
Haloferax volcanii N-Glycosylation: Delineating the Pathway of dTDP-rhamnose Biosynthesis Kaminski, Lina; Eichler, Jerry PLoS ONE, Vol. 9, Issue 5 https://doi.org/10.1371/journal.pone.0097441	journal	May 2014
Unraveling the hidden universe of small proteins in bacterial genomes Miravet‐Verde, Samuel; Ferrar, Tony; Espadas‐García, Guadalupe Molecular Systems Biology, Vol. 15, Issue 2 https://doi.org/10.15252/msb.20188290	journal	February 2019
N-glycosylation in Haloferax volcanii: adjusting the sweetness Eichler, Jerry; Arbiv, Adi; Cohen-Rosenzweig, Chen Frontiers in Microbiology, Vol. 4 https://doi.org/10.3389/fmicb.2013.00403	journal	January 2013
Limited Cross-Complementation Between Haloferax volcanii PilB1-C1 and PilB3-C3 Paralogs Legerme, Georgio; Pohlschroder, Mechthild Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00700	journal	April 2019

Similar Records

Multiplex quantitative SILAC for analysis of archaeal proteomes: a case study of oxidative stress responses

Journal Article · Thu Dec 28 23:00:00 EST 2017 · Environmental Microbiology · OSTI ID:1415146

Stabilization of an archaeal DNA-sliding clamp protein, PCNA, by proteasome-activating nucleotidase gene knockout in Haloferax volcanii

Journal Article · Fri May 01 00:00:00 EDT 2009 · FEMS Microbiology Letters · OSTI ID:1625903

The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics

Citation Formats

References (110)

Similar Records

Related Subjects