title: First description of small proteins encoded by spRNAs in Methanosarcina mazei strain Gö1.
abstract: In Methanosarcina mazei several small RNAs have been identified containing a small putative open reading frame (sORF) and thus classified as spRNAs. Here, we report on the first detection of three small proteins in M. mazei encoded by spRNAs using LC-MS/MS analysis of total protein extracts of cells grown under various stress conditions. Each spRNA shows high conservation in Methanosarcina species with regard to the sORF and the flanking non-coding RNA regions, moreover the predicted RNA structures are as well highly conserved. Characterizing the respective transcript levels in response to several stress conditions by northern blots demonstrated an enormous decrease of spRNA36 and spRNA44 during stationary growth (to less than 5%), and a significant increase of spRNA36 (2.5-fold) in response to nitrogen limitation. spRNA41, however, was only detected by RNA-Seq approaches. Quantification of the small proteins by LC-MS/MS using synthetic stable isotope labeled oligopeptides as standards indicated that the concentration of oligopetide36 and 41 in mid exponential phase is induced under nitrogen limitation, which in case of oligopeptide36 is in accordance with its transcript level. The relative amount of the three oligopeptides did not change upon entering stationary growth phase, even though the transcript levels decreased dramatically. Additional production of the oligopeptides in M. mazei did not result in any evident phenotype under standard or nitrogen limiting growth conditions. However, overall the transcript levels of several genes involved in carbon metabolism or in heat shock response were reduced 2-3 fold due to the overproduction, though no sORF specific change was observed. Based on our findings we hypothesize that oligopeptide36 might have a regulatory function in nitrogen metabolism by modulating the activity of a yet unknown target protein involved in the central nitrogen metabolism.
authors.affiliation: Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, 24118 Kiel, Germany.
authors.forename: Daniela
authors.initials: D
authors.lastname: Prasse
authors.affiliation: Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, 24118 Kiel, Germany.
authors.forename: Jens
authors.initials: J
authors.lastname: Thomsen
authors.affiliation: Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, 24118 Kiel, Germany.
authors.forename: Rebecca
authors.initials: R
authors.lastname: De Santis
authors.affiliation: Department of Microbial Physiology, Institute for Microbiology, Ernst-Moritz-Arndt-University, F.-L.-Jahn-Str. 15, 17489 Greifswald, Germany.
authors.forename: Jan
authors.initials: J
authors.lastname: Muntel
authors.affiliation: Department of Microbial Physiology, Institute for Microbiology, Ernst-Moritz-Arndt-University, F.-L.-Jahn-Str. 15, 17489 Greifswald, Germany.
authors.forename: Dörte
authors.initials: D
authors.lastname: Becher
authors.affiliation: Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität zu Kiel, Am Botanischen Garten 1-9, 24118 Kiel, Germany. Electronic address: rschmitz@ifam.uni-kiel.de.
authors.forename: Ruth A
authors.initials: RA
authors.lastname: Schmitz
mesh_terms: D000595:Amino Acid Sequence; D000693:Anaerobiosis; D019843:Archaeal Proteins / Q000235:genetics* / Q000378:metabolism; D015152:Blotting, Northern; D002853:Chromatography, Liquid; D020869:Gene Expression Profiling / Q000379:methods; D019848:Gene Expression Regulation, Archaeal / Q000187:drug effects; D018507:Gene Expression Regulation, Developmental / Q000187:drug effects; D020745:Genome, Archaeal / Q000235:genetics; D017020:Methanosarcina / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009842:Oligopeptides / Q000235:genetics / Q000378:metabolism; D016366:Open Reading Frames / Q000235:genetics*; D019642:RNA, Archaeal / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D022661:RNA, Untranslated / Q000235:genetics; D012965:Sodium Chloride / Q000494:pharmacology; D053719:Tandem Mass Spectrometry; D013696:Temperature
chemical_list: D019843:Archaeal Proteins; D009842:Oligopeptides; D019642:RNA, Archaeal; D022661:RNA, Untranslated; D012965:Sodium Chloride
keywords: Archaea; Methanosarcina mazei; Small proteins; sORFs; spRNAs