Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe
Open accessAbstract
The fission yeast Schizosaccharomyces pombe is a widely used model organism to study basic mechanisms of eukaryotic biology, but unlike other model organisms, its proteome remains largely uncharacterized. Using a shotgun proteomics approach based on multidimensional prefractionation and tandem mass spectrometry, we have detected approximately 30% of the theoretical fission yeast proteome. Applying statistical modelling to normalize spectral counts to the number of predicted tryptic peptides, we have performed label-free quantification of 1465 proteins. The fission yeast protein data showed considerable correlations with mRNA levels and with the abundance of orthologous proteins in budding yeast. Functional pathway analysis indicated that the mRNA-protein correlation is strong for proteins involved in signalling and metabolic processes, but increasingly discordant for components of protein complexes, which clustered in groups with similar mRNA-protein ratios. Self-organizing map clustering of large-scale protein and mRNA data from fission and budding yeast revealed coordinate but not always concordant expression of components of functional pathways and protein complexes. This finding reaffirms at the protein level the considerable divergence in gene expression patterns of the two model organisms that was noticed in previous transcriptomic studies.
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The lack of concordance between mRNA and protein concentrations is particularly true for mRNAs specifying proteins that are part of multifunction protein complexes.
“which is particularly true for mRNAs that specify proteins that are part of multifunction protein complexes (37 ).”
From The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments (2009) · cites this paper as [37]
The Functional pathway analysis reports very low or negative protein–mRNA correlations for most multisubunit protein complexes, supporting the claim of poor concordance for their subunits. It does not establish that these complexes are multifunctional; that qualifier differs from the paper’s “multisubunit.” (LLM, conf=0.82)
Experimental — accuracy not yet measuredRibosomal proteins rely more on mRNA levels than on translation for their high abundance.
“This observation, and related data from Schmidt et al. (2007), suggests that ribosomal proteins rely more on mRNA levels than on translation for their high abundance.”
From Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells (2012) · cites this paper as Schmidt et al. (2007)
The consensus across studies holds that, in a wide array of organisms, transcriptional regulation explains 30-50% of the variation in steady-state protein levels, leaving half or more to be explained by post-transcriptional regulatory processes.
“The consensus across these studies holds that, in a wide array of organisms, transcriptional regulation explains 30–50% of the variation in steady-state protein levels, leaving half or more to be explained by post-transcriptional regulatory processes [3, 7, 9–16].”
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- Authors
- Schmidt, M. W., Houseman, A., Ivanov, A. R., & Wolf, D. A.
- Affiliations
- University of Stuttgart (DE)
- Harvard University (US)
- Corresponding author
- Ivanov, Alexander R
- Wolf, Dieter A
- Venue
- Molecular Systems Biology
- Published
- 2007-02-13
- Volume
- 3
- Issue
- 1
- Pages
- 79-79
- ISSN
- 1744-4292 (ISSN-L)
- PMC
- PMC1828747
- OpenAlex
- W2148598563
- Cited by
- 114
- References
- 45
- Citations by year
- 2025: 1 · 2024: 3 · 2023: 1 · 2022: 2 · 2021: 1 · 2020: 1 · 2019: 2 · 2018: 4 · 2016: 4 · 2015: 2 · 2014: 12 · 2013: 7 · 2012: 10
- FWCI
- 8.03
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Molecular Systems Biology (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- Funders
- Universität Stuttgart
- National Institutes of Health (00002, ES-00002)
- National Institute of General Medical Sciences (R01GM059780, GM 59780)
- National Institute of Environmental Health Sciences (P30ES000002, ES 00002, 00002)
- National Center for Research Resources (S10RR019028)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Keywords
- Schizosaccharomyces pombe, proteomic profiling, mRNA-protein correlation, label-free quantification, orthologous proteins, protein complexes, functional pathway analysis, self-organizing map clustering, gene expression divergence
- MeSH terms
- Metabolism, Proteins, RNA, Messenger, Schizosaccharomyces, Models, Statistical, Signal Transduction, Cluster Analysis, Gene Expression Profiling, Schizosaccharomyces pombe Proteins, Proteomics, Multiprotein Complexes, Tandem Mass Spectrometry
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