1
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Tufail MA, Jordan B, Hadjeras L, Gelhausen R, Cassidy L, Habenicht T, Gutt M, Hellwig L, Backofen R, Tholey A, Sharma CM, Schmitz RA. Uncovering the small proteome of Methanosarcina mazei using Ribo-seq and peptidomics under different nitrogen conditions. Nat Commun 2024; 15:8659. [PMID: 39370430 PMCID: PMC11456600 DOI: 10.1038/s41467-024-53008-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 09/25/2024] [Indexed: 10/08/2024] Open
Abstract
The mesophilic methanogenic archaeal model organism Methanosarcina mazei strain Gö1 is crucial for climate and environmental research due to its ability to produce methane. Here, we establish a Ribo-seq protocol for M. mazei strain Gö1 under two growth conditions (nitrogen sufficiency and limitation). The translation of 93 previously annotated and 314 unannotated small ORFs, coding for proteins ≤ 70 amino acids, is predicted with high confidence based on Ribo-seq data. LC-MS analysis validates the translation for 62 annotated small ORFs and 26 unannotated small ORFs. Epitope tagging followed by immunoblotting analysis confirms the translation of 13 out of 16 selected unannotated small ORFs. A comprehensive differential transcription and translation analysis reveals that 29 of 314 unannotated small ORFs are differentially regulated in response to nitrogen availability at the transcriptional and 49 at the translational level. A high number of reported small RNAs are emerging as dual-function RNAs, including sRNA154, the central regulatory small RNA of nitrogen metabolism. Several unannotated small ORFs are conserved in Methanosarcina species and overproducing several (small ORF encoded) small proteins suggests key physiological functions. Overall, the comprehensive analysis opens an avenue to elucidate the function(s) of multitudinous small proteins and dual-function RNAs in M. mazei.
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Affiliation(s)
| | - Britta Jordan
- Institute for General Microbiology, Kiel University, 24118, Kiel, Germany
| | - Lydia Hadjeras
- Institute of Molecular Infection Biology, University of Würzburg, 97080, Würzburg, Germany
| | - Rick Gelhausen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110, Freiburg, Germany
| | - Liam Cassidy
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Kiel University, 24105, Kiel, Germany
| | - Tim Habenicht
- Institute for General Microbiology, Kiel University, 24118, Kiel, Germany
| | - Miriam Gutt
- Institute for General Microbiology, Kiel University, 24118, Kiel, Germany
| | - Lisa Hellwig
- Institute for General Microbiology, Kiel University, 24118, Kiel, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110, Freiburg, Germany
| | - Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Kiel University, 24105, Kiel, Germany
| | - Cynthia M Sharma
- Institute of Molecular Infection Biology, University of Würzburg, 97080, Würzburg, Germany
| | - Ruth A Schmitz
- Institute for General Microbiology, Kiel University, 24118, Kiel, Germany.
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2
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Müller MC, Lemaire ON, Kurth JM, Welte CU, Wagner T. Differences in regulation mechanisms of glutamine synthetases from methanogenic archaea unveiled by structural investigations. Commun Biol 2024; 7:111. [PMID: 38243071 PMCID: PMC10799026 DOI: 10.1038/s42003-023-05726-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 12/19/2023] [Indexed: 01/21/2024] Open
Abstract
Glutamine synthetases (GS) catalyze the ATP-dependent ammonium assimilation, the initial step of nitrogen acquisition that must be under tight control to fit cellular needs. While their catalytic mechanisms and regulations are well-characterized in bacteria and eukaryotes, only limited knowledge exists in archaea. Here, we solved two archaeal GS structures and unveiled unexpected differences in their regulatory mechanisms. GS from Methanothermococcus thermolithotrophicus is inactive in its resting state and switched on by 2-oxoglutarate, a sensor of cellular nitrogen deficiency. The enzyme activation overlays remarkably well with the reported cellular concentration for 2-oxoglutarate. Its binding to an allosteric pocket reconfigures the active site through long-range conformational changes. The homolog from Methermicoccus shengliensis does not harbor the 2-oxoglutarate binding motif and, consequently, is 2-oxoglutarate insensitive. Instead, it is directly feedback-inhibited through glutamine recognition by the catalytic Asp50'-loop, a mechanism common to bacterial homologs, but absent in M. thermolithotrophicus due to residue substitution. Analyses of residue conservation in archaeal GS suggest that both regulations are widespread and not mutually exclusive. While the effectors and their binding sites are surprisingly different, the molecular mechanisms underlying their mode of action on GS activity operate on the same molecular determinants in the active site.
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Affiliation(s)
- Marie-Caroline Müller
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Olivier N Lemaire
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Julia M Kurth
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
- Microcosm Earth Center, Philipps-University Marburg and Max Planck Institute for Terrestrial Microbiology, Hans-Meerwein-Str. 4, 35032, Marburg, Germany
| | - Cornelia U Welte
- Department of Microbiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Tristan Wagner
- Microbial Metabolism Research Group, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.
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3
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Habenicht T, Weidenbach K, Velazquez-Campoy A, Buey RM, Balsera M, Schmitz RA. Small protein mediates inhibition of ammonium transport in Methanosarcina mazei-an ancient mechanism? Microbiol Spectr 2023; 11:e0281123. [PMID: 37909787 PMCID: PMC10714827 DOI: 10.1128/spectrum.02811-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023] Open
Abstract
IMPORTANCE Small proteins containing fewer than 70 amino acids, which were previously disregarded due to computational prediction and biochemical detection challenges, have gained increased attention in the scientific community in recent years. However, the number of functionally characterized small proteins, especially in archaea, is still limited. Here, by using biochemical and genetic approaches, we demonstrate a crucial role of the small protein sP36 in the nitrogen metabolism of M. mazei, which modulates the ammonium transporter AmtB1 according to nitrogen availability. This modulation might represent an ancient archaeal mechanism of AmtB1 inhibition, in contrast to the well-studied uridylylation-dependent regulation in bacteria.
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Affiliation(s)
- Tim Habenicht
- Institut für allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Katrin Weidenbach
- Institut für allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Universidad de Zaragoza, Zaragoza, Spain
- Departamento de Bioquímica y Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Investigaciones Sanitarias de Aragón (IIS Aragón), Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Madrid, Spain
| | - Ruben M. Buey
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
| | - Monica Balsera
- Instituto de Recursos Naturales y Agrobiología de Salamanca, Spanish National Research Council (IRNASA-CSIC), Salamanca, Spain
| | - Ruth A. Schmitz
- Institut für allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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4
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Jordan B, Weidenbach K, Schmitz RA. The power of the small: the underestimated role of small proteins in bacterial and archaeal physiology. Curr Opin Microbiol 2023; 76:102384. [PMID: 37776678 DOI: 10.1016/j.mib.2023.102384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/04/2023] [Accepted: 09/04/2023] [Indexed: 10/02/2023]
Abstract
Small proteins encoded by small open-reading frames (sORFs) (≤70 aa) were overlooked for decades due to methodological reasons and are thus often missing in genome annotations. Novel detection methods such as ribosome profiling (Ribo-Seq) and mass spectrometry optimized for small proteins (peptidomics) have opened up a new field of interest and several catalogs of small proteins in bacteria and archaea have been recently reported. Many translated sORFs have been discovered in genomic locations previously thought to be noncoding, such as 5' or 3' untranslated regions or well-studied regulatory small RNAs (sRNAs). Even within longer ORFs, additional functional sORFs have been detected. Today, only a small proportion is characterized, but those small proteins indicate important and diverse functions in cellular physiology. Here, we summarize recently characterized small proteins involved in microbial metabolism.
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Affiliation(s)
- Britta Jordan
- Institute for General Microbiology, Christian-Albrechts-University, 24118 Kiel, Germany
| | - Katrin Weidenbach
- Institute for General Microbiology, Christian-Albrechts-University, 24118 Kiel, Germany
| | - Ruth A Schmitz
- Institute for General Microbiology, Christian-Albrechts-University, 24118 Kiel, Germany.
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5
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Schumacher MA, Salinas R, Travis BA, Singh RR, Lent N. M. mazei glutamine synthetase and glutamine synthetase-GlnK1 structures reveal enzyme regulation by oligomer modulation. Nat Commun 2023; 14:7375. [PMID: 37968329 PMCID: PMC10651883 DOI: 10.1038/s41467-023-43243-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/03/2023] [Indexed: 11/17/2023] Open
Abstract
Glutamine synthetases (GS) play central roles in cellular nitrogen assimilation. Although GS active-site formation requires the oligomerization of just two GS subunits, all GS form large, multi-oligomeric machines. Here we describe a structural dissection of the archaeal Methanosarcina mazei (Mm) GS and its regulation. We show that Mm GS forms unstable dodecamers. Strikingly, we show this Mm GS oligomerization property is leveraged for a unique mode of regulation whereby labile Mm GS hexamers are stabilized by binding the nitrogen regulatory protein, GlnK1. Our GS-GlnK1 structure shows that GlnK1 functions as molecular glue to affix GS hexamers together, stabilizing formation of GS active-sites. These data, therefore, reveal the structural basis for a unique form of enzyme regulation by oligomer modulation.
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Affiliation(s)
- Maria A Schumacher
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA.
| | - Raul Salinas
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA
| | - Brady A Travis
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA
| | - Rajiv Ranjan Singh
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA
| | - Nicholas Lent
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA
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6
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Hadjeras L, Bartel J, Maier LK, Maaß S, Vogel V, Svensson SL, Eggenhofer F, Gelhausen R, Müller T, Alkhnbashi OS, Backofen R, Becher D, Sharma CM, Marchfelder A. Revealing the small proteome of Haloferax volcanii by combining ribosome profiling and small-protein optimized mass spectrometry. MICROLIFE 2023; 4:uqad001. [PMID: 37223747 PMCID: PMC10117724 DOI: 10.1093/femsml/uqad001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/29/2022] [Accepted: 01/13/2023] [Indexed: 05/25/2023]
Abstract
In contrast to extensively studied prokaryotic 'small' transcriptomes (encompassing all small noncoding RNAs), small proteomes (here defined as including proteins ≤70 aa) are only now entering the limelight. The absence of a complete small protein catalogue in most prokaryotes precludes our understanding of how these molecules affect physiology. So far, archaeal genomes have not yet been analyzed broadly with a dedicated focus on small proteins. Here, we present a combinatorial approach, integrating experimental data from small protein-optimized mass spectrometry (MS) and ribosome profiling (Ribo-seq), to generate a high confidence inventory of small proteins in the model archaeon Haloferax volcanii. We demonstrate by MS and Ribo-seq that 67% of the 317 annotated small open reading frames (sORFs) are translated under standard growth conditions. Furthermore, annotation-independent analysis of Ribo-seq data showed ribosomal engagement for 47 novel sORFs in intergenic regions. A total of seven of these were also detected by proteomics, in addition to an eighth novel small protein solely identified by MS. We also provide independent experimental evidence in vivo for the translation of 12 sORFs (annotated and novel) using epitope tagging and western blotting, underlining the validity of our identification scheme. Several novel sORFs are conserved in Haloferax species and might have important functions. Based on our findings, we conclude that the small proteome of H. volcanii is larger than previously appreciated, and that combining MS with Ribo-seq is a powerful approach for the discovery of novel small protein coding genes in archaea.
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Affiliation(s)
- Lydia Hadjeras
- Department of Molecular Infection Biology II, Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Straße 2 / D15, 97080 Würzburg, Germany
| | - Jürgen Bartel
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany
| | | | - Sandra Maaß
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany
| | - Verena Vogel
- Biology II, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Sarah L Svensson
- Department of Molecular Infection Biology II, Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Straße 2 / D15, 97080 Würzburg, Germany
| | - Florian Eggenhofer
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Rick Gelhausen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Teresa Müller
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Omer S Alkhnbashi
- Information and Computer Science Department, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany
| | - Dörte Becher
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany
| | - Cynthia M Sharma
- Department of Molecular Infection Biology II, Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Straße 2 / D15, 97080 Würzburg, Germany
| | - Anita Marchfelder
- Biology II, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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7
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Thomsen J, Schmitz RA. Generating a Small Shuttle Vector for Effective Genetic Engineering of Methanosarcina mazei Allowed First Insights in Plasmid Replication Mechanism in the Methanoarchaeon. Int J Mol Sci 2022; 23:ijms231911910. [PMID: 36233214 PMCID: PMC9569500 DOI: 10.3390/ijms231911910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/16/2022] Open
Abstract
Due to their role in methane production, methanoarchaea are of high ecological relevance and genetic systems have been ever more established in the last two decades. The system for protein expression in Methanosarcina using a comprehensive shuttle vector is established; however, details about its replication mechanism in methanoarchaea remain unknown. Here, we report on a significant optimisation of the rather large shuttle vector pWM321 (8.9 kbp) generated by Metcalf through a decrease in its size by about 35% by means of the deletion of several non-coding regions and the ssrA gene. The resulting plasmid (pRS1595) still stably replicates in M. mazei and—most likely due to its reduced size—shows a significantly higher transformation efficiency compared to pWM321. In addition, we investigate the essential gene repA, coding for a rep type protein. RepA was heterologously expressed in Escherichia coli, purified and characterised, demonstrating the significant binding and nicking activity of supercoiled plasmid DNA. Based on our findings we propose that the optimised shuttle vector replicates via a rolling circle mechanism with RepA as the initial replication protein in Methanosarcina. On the basis of bioinformatic comparisons, we propose the presence and location of a double-strand and a single-strand origin, which need to be further verified.
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8
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Travis BA, Peck JV, Salinas R, Dopkins B, Lent N, Nguyen VD, Borgnia MJ, Brennan RG, Schumacher MA. Molecular dissection of the glutamine synthetase-GlnR nitrogen regulatory circuitry in Gram-positive bacteria. Nat Commun 2022; 13:3793. [PMID: 35778410 PMCID: PMC9249791 DOI: 10.1038/s41467-022-31573-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 06/21/2022] [Indexed: 11/23/2022] Open
Abstract
How bacteria sense and respond to nitrogen levels are central questions in microbial physiology. In Gram-positive bacteria, nitrogen homeostasis is controlled by an operon encoding glutamine synthetase (GS), a dodecameric machine that assimilates ammonium into glutamine, and the GlnR repressor. GlnR detects nitrogen excess indirectly by binding glutamine-feedback-inhibited-GS (FBI-GS), which activates its transcription-repression function. The molecular mechanisms behind this regulatory circuitry, however, are unknown. Here we describe biochemical and structural analyses of GS and FBI-GS-GlnR complexes from pathogenic and non-pathogenic Gram-positive bacteria. The structures show FBI-GS binds the GlnR C-terminal domain within its active-site cavity, juxtaposing two GlnR monomers to form a DNA-binding-competent GlnR dimer. The FBI-GS-GlnR interaction stabilizes the inactive GS conformation. Strikingly, this interaction also favors a remarkable dodecamer to tetradecamer transition in some GS, breaking the paradigm that all bacterial GS are dodecamers. These data thus unveil unique structural mechanisms of transcription and enzymatic regulation.
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Affiliation(s)
- Brady A Travis
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA
| | - Jared V Peck
- Cryo-EM core, Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Raul Salinas
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA
| | - Brandon Dopkins
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA
| | - Nicholas Lent
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA
| | - Viet D Nguyen
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Richard G Brennan
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA
| | - Maria A Schumacher
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC, 27710, USA.
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9
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Weidenbach K, Gutt M, Cassidy L, Chibani C, Schmitz RA. Small Proteins in Archaea, a Mainly Unexplored World. J Bacteriol 2022; 204:e0031321. [PMID: 34543104 PMCID: PMC8765429 DOI: 10.1128/jb.00313-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In recent years, increasing numbers of small proteins have moved into the focus of science. Small proteins have been identified and characterized in all three domains of life, but the majority remains functionally uncharacterized, lack secondary structure, and exhibit limited evolutionary conservation. While quite a few have already been described for bacteria and eukaryotic organisms, the amount of known and functionally analyzed archaeal small proteins is still very limited. In this review, we compile the current state of research, show strategies for systematic approaches for global identification of small archaeal proteins, and address selected functionally characterized examples. Besides, we document exemplarily for one archaeon the tool development and optimization to identify small proteins using genome-wide approaches.
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Affiliation(s)
- Katrin Weidenbach
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
| | - Miriam Gutt
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
| | - Liam Cassidy
- AG Proteomics & Bioanalytics, Institute for Experimental Medicine, Christian Albrechts University, Kiel, Germany
| | - Cynthia Chibani
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
| | - Ruth A. Schmitz
- Institute for General Microbiology, Christian Albrechts University, Kiel, Germany
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10
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Abstract
In recent years, there has been increased appreciation that a whole category of proteins, small proteins of around 50 amino acids or fewer in length, has been missed by annotation as well as by genetic and biochemical assays. With the increased recognition that small proteins are stable within cells and have regulatory functions, there has been intensified study of these proteins. As a result, important questions about small proteins in bacteria and archaea are coming to the fore. Here, we give an overview of these questions, the initial answers, and the approaches needed to address these questions more fully. More detailed discussions of how small proteins can be identified by ribosome profiling and mass spectrometry approaches are provided by two accompanying reviews (N. Vazquez-Laslop, C. M. Sharma, A. S. Mankin, and A. R. Buskirk, J Bacteriol 204:e00294-21, 2022, https://doi.org/10.1128/JB.00294-21; C. H. Ahrens, J. T. Wade, M. M. Champion, and J. D. Langer, J Bacteriol 204:e00353-21, 2022, https://doi.org/10.1128/JB.00353-21). We are excited by the prospects of new insights and possible therapeutic approaches coming from this emerging field.
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Affiliation(s)
- Todd Gray
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
- Department of Biomedical Sciences, University at Albany, Albany, New York, USA
| | - Gisela Storz
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland, USA
| | - Kai Papenfort
- Institute of Microbiology, Friedrich Schiller University, Jena, Germany
- Microverse Cluster, Friedrich Schiller University, Jena, Germany
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11
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Miyakoshi M, Morita T, Kobayashi A, Berger A, Takahashi H, Gotoh Y, Hayashi T, Tanaka K. Glutamine synthetase mRNA releases sRNA from its 3'UTR to regulate carbon/nitrogen metabolic balance in Enterobacteriaceae. eLife 2022; 11:82411. [PMID: 36440827 PMCID: PMC9731577 DOI: 10.7554/elife.82411] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/27/2022] [Indexed: 11/29/2022] Open
Abstract
Glutamine synthetase (GS) is the key enzyme of nitrogen assimilation induced under nitrogen limiting conditions. The carbon skeleton of glutamate and glutamine, 2-oxoglutarate, is supplied from the TCA cycle, but how this metabolic flow is controlled in response to nitrogen availability remains unknown. We show that the expression of the E1o component of 2-oxoglutarate dehydrogenase, SucA, is repressed under nitrogen limitation in Salmonella enterica and Escherichia coli. The repression is exerted at the post-transcriptional level by an Hfq-dependent sRNA GlnZ generated from the 3'UTR of the GS-encoding glnA mRNA. Enterobacterial GlnZ variants contain a conserved seed sequence and primarily regulate sucA through base-pairing far upstream of the translation initiation region. During growth on glutamine as the nitrogen source, the glnA 3'UTR deletion mutants expressed SucA at higher levels than the S. enterica and E. coli wild-type strains, respectively. In E. coli, the transcriptional regulator Nac also participates in the repression of sucA. Lastly, this study clarifies that the release of GlnZ from the glnA mRNA by RNase E is essential for the post-transcriptional regulation of sucA. Thus, the mRNA coordinates the two independent functions to balance the supply and demand of the fundamental metabolites.
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Affiliation(s)
- Masatoshi Miyakoshi
- Department of Infection Biology, Faculty of Medicine, University of TsukubaTsukubaJapan,Transborder Medical Research Center, University of TsukubaTsukubaJapan,International Joint Degree Master’s Program in Agro-Biomedical Science in Food and Health (GIP-TRIAD), University of TsukubaTsukubaJapan
| | - Teppei Morita
- Institute for Advanced Biosciences, Keio UniversityTsuruokaJapan,Graduate School of Media and Governance, Keio UniversityFujisawaJapan
| | - Asaki Kobayashi
- Transborder Medical Research Center, University of TsukubaTsukubaJapan
| | - Anna Berger
- International Joint Degree Master’s Program in Agro-Biomedical Science in Food and Health (GIP-TRIAD), University of TsukubaTsukubaJapan
| | | | - Yasuhiro Gotoh
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu UniversityFukuokaJapan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu UniversityFukuokaJapan
| | - Kan Tanaka
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of TechnologyYokohamaJapan
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12
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New views on PII signaling: from nitrogen sensing to global metabolic control. Trends Microbiol 2022; 30:722-735. [DOI: 10.1016/j.tim.2021.12.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 11/20/2022]
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13
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Steinberg R, Koch HG. The largely unexplored biology of small proteins in pro- and eukaryotes. FEBS J 2021; 288:7002-7024. [PMID: 33780127 DOI: 10.1111/febs.15845] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/11/2021] [Accepted: 03/26/2021] [Indexed: 12/29/2022]
Abstract
The large abundance of small open reading frames (smORFs) in prokaryotic and eukaryotic genomes and the plethora of smORF-encoded small proteins became only apparent with the constant advancements in bioinformatic, genomic, proteomic, and biochemical tools. Small proteins are typically defined as proteins of < 50 amino acids in prokaryotes and of less than 100 amino acids in eukaryotes, and their importance for cell physiology and cellular adaptation is only beginning to emerge. In contrast to antimicrobial peptides, which are secreted by prokaryotic and eukaryotic cells for combatting pathogens and competitors, small proteins act within the producing cell mainly by stabilizing protein assemblies and by modifying the activity of larger proteins. Production of small proteins is frequently linked to stress conditions or environmental changes, and therefore, cells seem to use small proteins as intracellular modifiers for adjusting cell metabolism to different intra- and extracellular cues. However, the size of small proteins imposes a major challenge for the cellular machinery required for protein folding and intracellular trafficking and recent data indicate that small proteins can engage distinct trafficking pathways. In the current review, we describe the diversity of small proteins in prokaryotes and eukaryotes, highlight distinct and common features, and illustrate how they are handled by the protein trafficking machineries in prokaryotic and eukaryotic cells. Finally, we also discuss future topics of research on this fascinating but largely unexplored group of proteins.
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Affiliation(s)
- Ruth Steinberg
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Germany
| | - Hans-Georg Koch
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin (ZMBZ), Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Germany
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