Towards the discovery of novel molecular clocks in Prokaryotes

Géron, Augustin; Werner, Johannes; Wattiez, Ruddy; Matallana-Surget, Sabine

doi:10.1080/1040841x.2023.2220789

Cited by 7 publications

(3 citation statements)

References 98 publications

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“…A new methodology has been proposed to identify the initiating molecular events when model cell lines are exposed to toxic substances, starting with the demonstration of altered solubility of the integral proteome of HepG2 cells exposed to tetrachlorinated dioxins. Proteomics has also identified a circadian clock in cyanobacteria, a key biological mechanism in new prokaryotic models . Proteogenomics can identify and characterize the structure of new coding sequences to better define their function through short open reading frames and their possible PTMs .…”

Section: Biology and Disease-driven Hppmentioning

confidence: 99%

“…Proteomics has also identified a circadian clock in cyanobacteria, a key biological mechanism in new prokaryotic models. 41 Proteogenomics can identify and characterize the structure of new coding sequences to better define their function through short open reading frames and their possible PTMs. 42 New methodologies may improve the functional characterization of protein−protein interactomes.…”

Section: Initiative For Model Organism Proteomics (Imop)mentioning

confidence: 99%

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The 2023 Report on the Proteome from the HUPO Human Proteome Project

Omenn,

Lane,

Overall

et al. 2024

J. Proteome Res.

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Since 2010, the Human Proteome Project (HPP), the flagship initiative of the Human Proteome Organization (HUPO), has pursued two goals: (1) to credibly identify the protein parts list and (2) to make proteomics an integral part of multiomics studies of human health and disease. The HPP relies on international collaboration, data sharing, standardized reanalysis of MS data sets by PeptideAtlas and MassIVE-KB using HPP Guidelines for quality assurance, integration and curation of MS and non-MS protein data by neXtProt, plus extensive use of antibody profiling carried out by the Human Protein Atlas. According to the neXtProt release 2023-04-18, protein expression has now been credibly detected (PE1) for 18,397 of the 19,778 neXtProt predicted proteins coded in the human genome (93%). Of these PE1 proteins, 17,453 were detected with mass spectrometry (MS) in accordance with HPP Guidelines and 944 by a variety of non-MS methods. The number of neXtProt PE2, PE3, and PE4 missing proteins now stands at 1381. Achieving the unambiguous identification of 93% of predicted proteins encoded from across all chromosomes represents remarkable experimental progress on the Human Proteome parts list. Meanwhile, there are several categories of predicted proteins that have proved resistant to detection regardless of protein-based methods used. Additionally there are some PE1–4 proteins that probably should be reclassified to PE5, specifically 21 LINC entries and ∼30 HERV entries; these are being addressed in the present year. Applying proteomics in a wide array of biological and clinical studies ensures integration with other omics platforms as reported by the Biology and Disease-driven HPP teams and the antibody and pathology resource pillars. Current progress has positioned the HPP to transition to its Grand Challenge Project focused on determining the primary function(s) of every protein itself and in networks and pathways within the context of human health and disease.

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Section: Biology and Disease-driven Hppmentioning

confidence: 99%

Section: Initiative For Model Organism Proteomics (Imop)mentioning

confidence: 99%

The 2023 Report on the Proteome from the HUPO Human Proteome Project

Omenn,

Lane,

Overall

et al. 2024

J. Proteome Res.

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“…Bioinformatic analyses have revealed that homologs of Kai proteins are widespread in Prokaryotes and present in purple bacteria [ 9 , 15 , 16 ]. A recent comprehensive review emphasizes the importance of circadian clocks in Prokaryotes and their potential applications in various fields, including medical research, environmental sciences, and biotechnology [ 17 ].…”

Section: Introductionmentioning

confidence: 99%

Diel Cycle Proteomics: Illuminating Molecular Dynamics in Purple Bacteria for Optimized Biotechnological Applications

Matallana-Surget,

Geron,

Decroo

et al. 2024

IJMS

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Circadian rhythms, characterized by approximately 24 h cycles, play a pivotal role in enabling various organisms to synchronize their biological activities with daily variations. While ubiquitous in Eukaryotes, circadian clocks remain exclusively characterized in Cyanobacteria among Prokaryotes. These rhythms are regulated by a core oscillator, which is controlled by a cluster of three genes: kaiA, kaiB, and kaiC. Interestingly, recent studies revealed rhythmic activities, potentially tied to a circadian clock, in other Prokaryotes, including purple bacteria such as Rhodospirillum rubrum, known for its applications in fuel and plastic bioproduction. However, the pivotal question of how light and dark cycles influence protein dynamics and the expression of putative circadian clock genes remains unexplored in purple non-sulfur bacteria. Unraveling the regulation of these molecular clocks holds the key to unlocking optimal conditions for harnessing the biotechnological potential of R. rubrum. Understanding how its proteome responds to different light regimes—whether under continuous light or alternating light and dark cycles—could pave the way for precisely fine-tuning bioproduction processes. Here, we report for the first time the expressed proteome of R. rubrum grown under continuous light versus light and dark cycle conditions using a shotgun proteomic analysis. In addition, we measured the impact of light regimes on the expression of four putative circadian clock genes (kaiB1, kaiB2, kaiC1, kaiC2) at the transcriptional and translational levels using RT-qPCR and targeted proteomic (MRM-MS), respectively. The data revealed significant effects of light conditions on the overall differential regulation of the proteome, particularly during the early growth stages. Notably, several proteins were found to be differentially regulated during the light or dark period, thus impacting crucial biological processes such as energy conversion pathways and the general stress response. Furthermore, our study unveiled distinct regulation of the four kai genes at both the mRNA and protein levels in response to varying light conditions. Deciphering the impact of the diel cycle on purple bacteria not only enhances our understanding of their ecology but also holds promise for optimizing their applications in biotechnology, providing valuable insights into the origin and evolution of prokaryotic clock mechanisms.

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