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Schulze S, Pohlschroder M. Proteomic Sample Preparation and Data Analysis in Line with the Archaeal Proteome Project. Methods Mol Biol 2022; 2522:287-300. [PMID: 36125757 DOI: 10.1007/978-1-0716-2445-6_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Despite the ecological, evolutionary and economical significance of archaea, key aspects of their cell biology, metabolic pathways, and adaptations to a wide spectrum of environmental conditions, remain to be elucidated. Proteomics allows for the system-wide analysis of proteins, their changes in abundance between different conditions, as well as their post-translational modifications, providing detailed insights into the function of proteins and archaeal cell biology. In this chapter, we describe a sample preparation and mass spectrometric analysis workflow that has been designed for Haloferax volcanii but can be applied to a broad range of archaeal species. Furthermore, proteomics experiments provide a wealth of data that is invaluable to various disciplines. Therefore, we previously initiated the Archaeal Proteome Project (ArcPP), a community project that combines the analysis of multiple datasets with expert knowledge in various fields of archaeal research. The corresponding bioinformatic analysis, allowing for the integration of new proteomics data into the ArcPP, as well as the interactive exploration of ArcPP results is also presented here. In combination, these protocols facilitate an optimized, detailed and collaborative approach to archaeal proteomics.
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Affiliation(s)
- Stefan Schulze
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA.
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The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics. Nat Commun 2020; 11:3145. [PMID: 32561711 PMCID: PMC7305310 DOI: 10.1038/s41467-020-16784-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 05/18/2020] [Indexed: 11/08/2022] Open
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.
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Cao J, Wang Q, Liu T, Peng N, Huang L. Insights into the post-translational modifications of archaeal Sis10b (Alba): lysine-16 is methylated, not acetylated, and this does not regulate transcription or growth. Mol Microbiol 2018; 109:192-208. [PMID: 29679495 DOI: 10.1111/mmi.13973] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2018] [Indexed: 12/26/2022]
Abstract
Nucleic acid-binding proteins of the Sac10b family, also referred to as Alba (for acetylation lowers binding affinity), are highly conserved in Archaea. It was reported that Sso10b, a Sac10b homologue from Sulfolobus solfataricus, was acetylated at the ɛ-amino group of K16 and the α-amino group of the N-terminal residue. Notably, acetylation of K16 reduced the affinity of Sso10b for DNA and de-repressed transcription in vitro. Here, we show that Sis10b, a Sac10b homologue from Sulfolobus islandicus, underwent a range of post-translational modifications (PTMs). K16 in Sis10b as well as Sso10b was not acetylated. Substitution of K16 for R16, which resulted in the loss of the PTMs at the site, showed little effect on the growth of the cell and resulted in only a slight change in the expression of a very small fraction of the genes. The N-terminus of Sis10b was nearly completely Nα -acetylated. The reduction or loss of the terminal acetylation led to a significant increase in the cellular concentration of Sis10b, suggesting the involvement of the modification in the control of the turnover of the protein. These results have clarified the PTMs of Sac10b homologues and shed light on the proposed roles of acetylation of the protein.
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Affiliation(s)
- Jingjing Cao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.,College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Qian Wang
- Core Facility of Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
| | - Tao Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Nan Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China.,College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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Losensky G, Jung K, Urlaub H, Pfeifer F, Fröls S, Lenz C. Shedding light on biofilm formation ofHalobacterium salinarumR1 by SWATH-LC/MS/MS analysis of planktonic and sessile cells. Proteomics 2016; 17. [DOI: 10.1002/pmic.201600111] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 07/30/2016] [Accepted: 09/05/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Gerald Losensky
- Microbiology and Archaea; Department of Biology; Technische Universität Darmstadt; Darmstadt Germany
| | - Klaus Jung
- Institute for Animal Breeding and Genetics; University of Veterinary Medicine Foundation; Hannover Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group; Max Planck Institute for Biophysical Chemistry; Göttingen Germany
- Institute of Clinical Chemistry; Bioanalytics; University Medical Center Göttingen; Göttingen Germany
| | - Felicitas Pfeifer
- Microbiology and Archaea; Department of Biology; Technische Universität Darmstadt; Darmstadt Germany
| | - Sabrina Fröls
- Microbiology and Archaea; Department of Biology; Technische Universität Darmstadt; Darmstadt Germany
| | - Christof Lenz
- Bioanalytical Mass Spectrometry Group; Max Planck Institute for Biophysical Chemistry; Göttingen Germany
- Institute of Clinical Chemistry; Bioanalytics; University Medical Center Göttingen; Göttingen Germany
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Walsh G. Proteins and Proteomics. Proteins 2015. [DOI: 10.1002/9781119117599.ch1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Makhalanyane TP, Valverde A, Gunnigle E, Frossard A, Ramond JB, Cowan DA. Microbial ecology of hot desert edaphic systems. FEMS Microbiol Rev 2015; 39:203-21. [DOI: 10.1093/femsre/fuu011] [Citation(s) in RCA: 223] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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Paggi RA, Giménez MI, De Castro RE, Cesari A. A simple technique to improve the resolution of membrane acidic proteins of the haloarchaeon Haloferax volcanii by 2D electrophoresis. Electrophoresis 2014; 35:3518-22. [PMID: 25224925 DOI: 10.1002/elps.201400407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 08/27/2014] [Accepted: 08/29/2014] [Indexed: 11/06/2022]
Abstract
Proteins present in the archaeal cell envelope play key roles in a variety of processes necessary for survival in extreme environments. The haloarchaeon Haloferax volcanii is a good model for membrane proteomic studies because its genome sequence is known, it can be genetically manipulated, and a number of studies at the "omics" level have been performed in this organism. This work reports an easy strategy to improve the resolution of acidic membrane proteins from H. volcanii by 2DE. The method is based on the solubilization, delipidation, and salt removal from membrane proteins. Due to the abundance of the S-layer glycoprotein (SLG) in membrane protein extracts, other proteins from the envelope are consequently underrepresented. Thus, a protocol to reduce the amount of the SLG by EDTA treatment was applied and 11 cm narrow range pH (3.9-5.1) IPG strips were used to fractionate the remaining proteins. Using this method, horizontal streaking was substantially decreased and at least 75 defined spots (20% of the predicted membrane proteome within this pI/Mw range) were reproducibly detected. Two of these spots were identified as thermosome subunit 1 and NADH dehydrogenase from H. volcanii, confirming that proteins from the membrane fraction were enriched. Removal of the SLG from membrane protein extracts can be applied to increase protein load for 2DE as well as for other proteomic methods.
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Affiliation(s)
- Roberto A Paggi
- Instituto de Investigaciones Biológicas, UNMdP-CONICET, Mar del Plata, Argentina
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Kort JC, Esser D, Pham TK, Noirel J, Wright PC, Siebers B. A cool tool for hot and sour Archaea: Proteomics of Sulfolobus solfataricus. Proteomics 2013; 13:2831-50. [DOI: 10.1002/pmic.201300088] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/23/2013] [Accepted: 05/03/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Julia Christin Kort
- Molecular Enzyme Technology and Biochemistry; Biofilm Centre, Faculty of Chemistry, University of Duisburg-Essen; Essen Germany
| | - Dominik Esser
- Molecular Enzyme Technology and Biochemistry; Biofilm Centre, Faculty of Chemistry, University of Duisburg-Essen; Essen Germany
| | - Trong Khoa Pham
- Department of Chemical and Biological Engineering; ChELSI Institute, The University of Sheffield; Sheffield UK
| | - Josselin Noirel
- Department of Chemical and Biological Engineering; ChELSI Institute, The University of Sheffield; Sheffield UK
| | - Phillip C. Wright
- Department of Chemical and Biological Engineering; ChELSI Institute, The University of Sheffield; Sheffield UK
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry; Biofilm Centre, Faculty of Chemistry, University of Duisburg-Essen; Essen Germany
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Affiliation(s)
- Finn Werner
- RNAP Laboratory, Institute for Structural and Molecular Biology, Division of Biosciences, University College London , Darwin Building, Gower Street, London WC1E 6BT, U.K
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Angel R, Pasternak Z, Soares MIM, Conrad R, Gillor O. Active and total prokaryotic communities in dryland soils. FEMS Microbiol Ecol 2013; 86:130-8. [PMID: 23730745 DOI: 10.1111/1574-6941.12155] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 05/24/2013] [Accepted: 05/24/2013] [Indexed: 11/30/2022] Open
Abstract
The relationship between total and metabolically active soil microbial communities can change drastically with environment. In dry lands, water availability is a key factor limiting cells' activity. We surveyed the diversity of total and active Archaea and Bacteria in soils ranging from arid desert to Mediterranean forests. Thirty composited soil samples were retrieved from five sites along a precipitation gradient, collected from patches located between and under the dominant perennial plant at each site. Molecular fingerprinting was used to site-sort the communities according of their 16S rRNA genes (total community) and their rRNA (active community) amplified by PCR or RT-PCR from directly extracted soil nucleic acids. The differences between soil samples were much higher in total rather than active microbial communities: differences in DNA fingerprints between sites were 1.2 and 2.5 times higher than RNA differences (for Archaea and Bacteria, respectively). Patch-type discrepancies between DNA fingerprints were on average 2.7-19.7 times greater than RNA differences. Moreover, RNA-based community patterns were highly correlated with soil moisture but did not necessarily follow spatial distribution pattern. Our results suggest that in water-limited environments, the spatial patterns obtained by the analysis of active communities are not as robust as those drawn from total communities.
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Affiliation(s)
- Roey Angel
- Max-Planck-Institute for Terrestrial Microbiology, Marburg, Germany
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Eichler J, Maupin-Furlow J. Post-translation modification in Archaea: lessons from Haloferax volcanii and other haloarchaea. FEMS Microbiol Rev 2012; 37:583-606. [PMID: 23167813 DOI: 10.1111/1574-6976.12012] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 11/13/2012] [Accepted: 11/13/2012] [Indexed: 01/11/2023] Open
Abstract
As an ever-growing number of genome sequences appear, it is becoming increasingly clear that factors other than genome sequence impart complexity to the proteome. Of the various sources of proteomic variability, post-translational modifications (PTMs) most greatly serve to expand the variety of proteins found in the cell. Likewise, modulating the rates at which different proteins are degraded also results in a constantly changing cellular protein profile. While both strategies for generating proteomic diversity are adopted by organisms across evolution, the responsible pathways and enzymes in Archaea are often less well described than are their eukaryotic and bacterial counterparts. Studies on halophilic archaea, in particular Haloferax volcanii, originally isolated from the Dead Sea, are helping to fill the void. In this review, recent developments concerning PTMs and protein degradation in the haloarchaea are discussed.
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Affiliation(s)
- Jerry Eichler
- Department of Life Sciences, Ben Gurion University, Beersheva, Israel.
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Abstract
High-throughput identification of proteins with the latest generation of hybrid high-resolution mass spectrometers is opening new perspectives in microbiology. I present, here, an overview of tandem mass spectrometry technology and bioinformatics for shotgun proteomics that make 2D-PAGE approaches obsolete. Non-labelling quantitative approaches have become more popular than labelling techniques on most proteomic platforms because they are easier to carry out while their quantitative outcome is rather robust. Parameters for recording mass spectrometry data, however, need to be chosen carefully and statistics to assess the confidence of the results should not be neglected. Interestingly, next-generation sequencing methodologies make any microbial model quickly amenable to proteomics, leading to the documentation of a wide range of organisms from diverse environments. Some recent discoveries made using microbial proteomics have challenged some biological dogma, such as: (i) initiation of the translation does not occur predominantly from ATG codons in some microorganisms, (ii) non-canonical initiation codons are used to regulate the production of specific but important proteins and (iii) a gene may code for multiple polypeptide species, heterogeneous in terms of sequences. Microbial diversity and microbial physiology can now be revisited by means of exhaustive comparative proteomic surveys where thousands of proteins are detected and quantified. Proteogenomics, consisting of better annotating of genomes with the help of proteomic evidence, is paving the way for integrated multi-omic approaches in microbiology. Finally, meta-proteomic tools and approaches are emerging for tackling the high complexity of the microbial world as a whole, opening new perspectives for assessing how microbial communities function.
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Affiliation(s)
- Jean Armengaud
- CEA, DSV, IBEB, Lab Biochim System Perturb, F-30207 Bagnols-sur-Cèze, France.
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