title: Daily rhythms in the cyanobacterium synechococcus elongatus probed by high-resolution mass spectrometry-based proteomics reveals a small defined set of cyclic proteins.
abstract: Circadian rhythms are self-sustained and adjustable cycles, typically entrained with light/dark and/or temperature cycles. These rhythms are present in animals, plants, fungi, and several bacteria. The central mechanism behind these "pacemakers" and the connection to the circadian regulated pathways are still poorly understood. The circadian rhythm of the cyanobacterium Synechococcus elongatus PCC 7942 (S. elongatus) is highly robust and controlled by only three proteins, KaiA, KaiB, and KaiC. This central clock system has been extensively studied functionally and structurally and can be reconstituted in vitro. These characteristics, together with a relatively small genome (2.7 Mbp), make S. elongatus an ideal model system for the study of circadian rhythms. Different approaches have been used to reveal the influence of the central S. elongatus clock on rhythmic gene expression, rhythmic mRNA abundance, rhythmic DNA topology changes, and cell division. However, a global analysis of its proteome dynamics has not been reported yet. To uncover the variation in protein abundances during 48 h under light and dark cycles (12:12 h), we used quantitative proteomics, with TMT 6-plex isobaric labeling. We queried the S. elongatus proteome at 10 different time points spanning a single 24-h period, leading to 20 time points over the full 48-h period. Employing multidimensional separation and high-resolution mass spectrometry, we were able to find evidence for a total of 82% of the S. elongatus proteome. Of the 1537 proteins quantified over the time course of the experiment, only 77 underwent significant cyclic variations. Interestingly, our data provide evidence for in- and out-of-phase correlation between mRNA and protein levels for a set of specific genes and proteins. As a range of cyclic proteins are functionally not well annotated, this work provides a resource for further studies to explore the role of these proteins in the cyanobacterial circadian rhythm.
authors.affiliation: From the ‡Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands;
authors.forename: Ana C L
authors.initials: AC
authors.lastname: Guerreiro
authors.affiliation: From the ‡Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands;
authors.forename: Marco
authors.initials: M
authors.lastname: Benevento
authors.affiliation: ¶Institute for Theoretical Biology (ITB), Humboldt-Universitaet zu Berlin, Invalidenstrasse 43, D-10115 Berlin, Germany;
authors.forename: Robert
authors.initials: R
authors.lastname: Lehmann
authors.affiliation: From the ‡Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands;
authors.forename: Bas
authors.initials: B
authors.lastname: van Breukelen
authors.affiliation: From the ‡Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands;
authors.forename: Harm
authors.initials: H
authors.lastname: Post
authors.affiliation: From the ‡Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands;
authors.forename: Piero
authors.initials: P
authors.lastname: Giansanti
authors.affiliation: From the ‡Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands; a.j.r.heck@uu.nl ilka.axmann@hhu.de m.altelaar@uu.nl.
authors.forename: A F
authors.initials: AF
authors.lastname: Maarten Altelaar
authors.affiliation: ¶Institute for Theoretical Biology (ITB), Humboldt-Universitaet zu Berlin, Invalidenstrasse 43, D-10115 Berlin, Germany; **Institute for Synthetic Microbiology, Heinrich-Heine-Universitaet Duesseldorf, Universitaetsstrasse 1, D-40225 Duesseldorf, Germany a.j.r.heck@uu.nl ilka.axmann@hhu.de m.altelaar@uu.nl.
authors.forename: Ilka M
authors.initials: IM
authors.lastname: Axmann
authors.affiliation: From the ‡Biomolecular Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands; §Netherlands Proteomics Centre, Padualaan 8, 3584 CH Utrecht, The Netherlands; a.j.r.heck@uu.nl ilka.axmann@hhu.de m.altelaar@uu.nl.
authors.forename: Albert J R
authors.initials: AJ
authors.lastname: Heck
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000302:isolation & purification*; D002940:Circadian Rhythm; D056925:Circadian Rhythm Signaling Peptides and Proteins / Q000235:genetics / Q000302:isolation & purification; D015964:Gene Expression Regulation, Bacterial; D013058:Mass Spectrometry / Q000379:methods; D040901:Proteomics / Q000379:methods*; D046940:Synechococcus / Q000502:physiology*
chemical_list: D001426:Bacterial Proteins; D056925:Circadian Rhythm Signaling Peptides and Proteins