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Nalpas N, Hoyles L, Anselm V, Ganief T, Martinez-Gili L, Grau C, Droste-Borel I, Davidovic L, Altafaj X, Dumas ME, Macek B. An integrated workflow for enhanced taxonomic and functional coverage of the mouse fecal metaproteome. Gut Microbes 2022; 13:1994836. [PMID: 34763597 PMCID: PMC8726736 DOI: 10.1080/19490976.2021.1994836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Intestinal microbiota plays a key role in shaping host homeostasis by regulating metabolism, immune responses and behavior. Its dysregulation has been associated with metabolic, immune and neuropsychiatric disorders and is accompanied by changes in bacterial metabolic regulation. Although proteomics is well suited for analysis of individual microbes, metaproteomics of fecal samples is challenging due to the physical structure of the sample, presence of contaminating host proteins and coexistence of hundreds of taxa. Furthermore, there is a lack of consensus regarding preparation of fecal samples, as well as downstream bioinformatic analyses following metaproteomics data acquisition. Here we assess sample preparation and data analysis strategies applied to mouse feces in a typical mass spectrometry-based metaproteomic experiment. We show that subtle changes in sample preparation protocols may influence interpretation of biological findings. Two-step database search strategies led to significant underestimation of false positive protein identifications. Unipept software provided the highest sensitivity and specificity in taxonomic annotation of the identified peptides of unknown origin. Comparison of matching metaproteome and metagenome data revealed a positive correlation between protein and gene abundances. Notably, nearly all functional categories of detected protein groups were differentially abundant in the metaproteome compared to what would be expected from the metagenome, highlighting the need to perform metaproteomics when studying complex microbiome samples.
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Affiliation(s)
- Nicolas Nalpas
- Proteome Center Tuebingen, University of Tuebingen, Tuebingen, Germany
| | - Lesley Hoyles
- Biomolecular Medicine Section, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK,Department of Biosciences, Nottingham Trent University, Nottingham, UK
| | - Viktoria Anselm
- Proteome Center Tuebingen, University of Tuebingen, Tuebingen, Germany
| | - Tariq Ganief
- Proteome Center Tuebingen, University of Tuebingen, Tuebingen, Germany
| | - Laura Martinez-Gili
- Biomolecular Medicine Section, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Cristina Grau
- Pharmacology unit, Bellvitge Biomedical Research Institute, University of Barcelona, Barcelona, Spain
| | | | | | - Xavier Altafaj
- Pharmacology unit, Bellvitge Biomedical Research Institute, University of Barcelona, Barcelona, Spain,Neurophysiology Unit, University of Barcelona – Idibaps, Barcelona, Spain
| | - Marc-Emmanuel Dumas
- Biomolecular Medicine Section, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK,Genomic and Environmental Medicine, National Heart & Lung Institute, Faculty of Medicine, Imperial College London, London, UK,European Genomic Institute for Diabetes, Inserm Umr 1283, Cnrs Umr 8199, Institut Pasteur De Lille, Lille University Hospital, University of Lille, Lille, France
| | - Boris Macek
- Proteome Center Tuebingen, University of Tuebingen, Tuebingen, Germany,CONTACT Boris Macek Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, Auf Der Morgenstelle 15, Tuebingen72076, Germany
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de Francisco Amorim M, Willing EM, Szabo EX, Francisco-Mangilet AG, Droste-Borel I, Maček B, Schneeberger K, Laubinger S. The U1 snRNP Subunit LUC7 Modulates Plant Development and Stress Responses via Regulation of Alternative Splicing. Plant Cell 2018; 30:2838-2854. [PMID: 30309899 PMCID: PMC6305971 DOI: 10.1105/tpc.18.00244] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 09/11/2018] [Accepted: 10/05/2018] [Indexed: 05/21/2023]
Abstract
Introns are removed by the spliceosome, a large macromolecular complex composed of five ribonucleoprotein subcomplexes (U snRNPs). The U1 snRNP, which binds to 5' splice sites, plays an essential role in early steps of the splicing reaction. Here, we show that Arabidopsis thaliana LETHAL UNLESS CBC7 (LUC7) proteins, which are encoded by a three-member gene family in Arabidopsis, are important for plant development and stress resistance. We show that LUC7 is a U1 snRNP accessory protein by RNA immunoprecipitation experiments and LUC7 protein complex purifications. Transcriptome analyses revealed that LUC7 proteins are not only important for constitutive splicing, but also affect hundreds of alternative splicing events. Interestingly, LUC7 proteins specifically promote splicing of a subset of terminal introns. Splicing of LUC7-dependent introns is a prerequisite for nuclear export, and some splicing events are modulated by stress in a LUC7-dependent manner. Taken together, our results highlight the importance of the U1 snRNP component LUC7 in splicing regulation and suggest a previously unrecognized role of a U1 snRNP accessory factor in terminal intron splicing.
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Affiliation(s)
- Marcella de Francisco Amorim
- Centre for Plant Molecular Biology (ZMBP), University of Tuebingen, 72076 Tuebingen, Germany
- Chemical Genomics Centre of the Max Planck Society, 44227 Dortmund, Germany
- Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany
| | - Eva-Maria Willing
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Emese X Szabo
- Centre for Plant Molecular Biology (ZMBP), University of Tuebingen, 72076 Tuebingen, Germany
- Chemical Genomics Centre of the Max Planck Society, 44227 Dortmund, Germany
- Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany
- Carl von Ossietzky University, 26129 Oldenburg, Germany
| | - Anchilie G Francisco-Mangilet
- Centre for Plant Molecular Biology (ZMBP), University of Tuebingen, 72076 Tuebingen, Germany
- Chemical Genomics Centre of the Max Planck Society, 44227 Dortmund, Germany
- Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany
- Carl von Ossietzky University, 26129 Oldenburg, Germany
| | | | - Boris Maček
- Proteome Centre, University of Tuebingen, 72076 Tuebingen, Germany
| | | | - Sascha Laubinger
- Centre for Plant Molecular Biology (ZMBP), University of Tuebingen, 72076 Tuebingen, Germany
- Chemical Genomics Centre of the Max Planck Society, 44227 Dortmund, Germany
- Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany
- Carl von Ossietzky University, 26129 Oldenburg, Germany
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Speth C, Szabo EX, Martinho C, Collani S, Zur Oven-Krockhaus S, Richter S, Droste-Borel I, Macek B, Stierhof YD, Schmid M, Liu C, Laubinger S. Arabidopsis RNA processing factor SERRATE regulates the transcription of intronless genes. eLife 2018; 7:37078. [PMID: 30152752 PMCID: PMC6135607 DOI: 10.7554/elife.37078] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/22/2018] [Indexed: 01/16/2023] Open
Abstract
Intron splicing increases proteome complexity, promotes RNA stability, and enhances transcription. However, introns and the concomitant need for splicing extend the time required for gene expression and can cause an undesirable delay in the activation of genes. Here, we show that the plant microRNA processing factor SERRATE (SE) plays an unexpected and pivotal role in the regulation of intronless genes. Arabidopsis SE associated with more than 1000, mainly intronless, genes in a transcription-dependent manner. Chromatin-bound SE liaised with paused and elongating polymerase II complexes and promoted their association with intronless target genes. Our results indicate that stress-responsive genes contain no or few introns, which negatively affects their expression strength, but that some genes circumvent this limitation via a novel SE-dependent transcriptional activation mechanism. Transcriptome analysis of a Drosophila mutant defective in ARS2, the metazoan homologue of SE, suggests that SE/ARS2 function in regulating intronless genes might be conserved across kingdoms.
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Affiliation(s)
- Corinna Speth
- Centre for Plant Molecular Biology (ZMBP), University of Tuebingen, Tuebingen, Germany.,Chemical Genomics Centre (CGC) of the Max Planck Society, Dortmund, Germany.,Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Emese Xochitl Szabo
- Centre for Plant Molecular Biology (ZMBP), University of Tuebingen, Tuebingen, Germany.,Chemical Genomics Centre (CGC) of the Max Planck Society, Dortmund, Germany.,Max Planck Institute for Developmental Biology, Tuebingen, Germany.,Institute for Biology and Environmental Science, University of Oldenburg, Oldenburg, Germany
| | - Claudia Martinho
- Centre for Plant Molecular Biology (ZMBP), University of Tuebingen, Tuebingen, Germany.,Chemical Genomics Centre (CGC) of the Max Planck Society, Dortmund, Germany.,Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Silvio Collani
- Department of Plant Physiology, Umea Plant Science Centre, Umeå University, Umea, Sweden
| | | | - Sandra Richter
- Centre for Plant Molecular Biology (ZMBP), University of Tuebingen, Tuebingen, Germany
| | | | - Boris Macek
- Proteome Centre, University of Tuebingen, Tuebingen, Germany
| | - York-Dieter Stierhof
- Centre for Plant Molecular Biology (ZMBP), University of Tuebingen, Tuebingen, Germany
| | - Markus Schmid
- Department of Plant Physiology, Umea Plant Science Centre, Umeå University, Umea, Sweden
| | - Chang Liu
- Centre for Plant Molecular Biology (ZMBP), University of Tuebingen, Tuebingen, Germany
| | - Sascha Laubinger
- Centre for Plant Molecular Biology (ZMBP), University of Tuebingen, Tuebingen, Germany.,Chemical Genomics Centre (CGC) of the Max Planck Society, Dortmund, Germany.,Max Planck Institute for Developmental Biology, Tuebingen, Germany.,Institute for Biology and Environmental Science, University of Oldenburg, Oldenburg, Germany
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Schmidt A, Schäfer E, Rother C, Droste-Borel I, Macek B, Schwarz S. 96 The impact of oxygen limitation on the secretome of Pseudomonas aeruginosa. J Cyst Fibros 2017. [DOI: 10.1016/s1569-1993(17)30460-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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