Direct Iterative Protein Profiling (DIPP) - an Innovative Method for Large-scale Protein Detection Applied to Budding Yeast Mitosis

Lavigne, Rob; Becker, E.; Liu, Yuchen; Evrard, Bertrand; Lardenois, Aurélie; Primig, Michael; Pineau, Charles

doi:10.1074/mcp.m111.012682

Cited by 22 publications

(29 citation statements)

References 48 publications

(60 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To determine the proteome in the presence of glucose or acetate we combined previously published DIPP data on rapid growth in rich medium with glucose (YPD) [34], with a new dataset from cells cultured in a medium where glucose was replaced by acetate (YPA). We included published RNA profiling data from YPD and YPA samples that were analyzed with tiling arrays (Sc_tlg) [36].…”

Section: Resultsmentioning

confidence: 99%

“…Samples from YPD (yeast extract, peptone and dextrose) were cultured as published [34]. In addition, cells grown in YPD were transferred into 100 ml YPA (rich medium with acetate) pre-warmed to 30 °C at a cell density of 2 × 10 6 cells/ml and cultured until they reached 3 × 10 7 cells/ml, before they were harvested in two 50 ml aliquots and washed with sterile water.…”

Section: Methodsmentioning

confidence: 99%

“…Duplicate samples from YPA were pre-fractionated, and the samples were analyzed using DIPP as published [34]. Data were analyzed using the Proteome Discoverer 1.2 software in conjunction with Mascot (Matrixscience) and SEQUEST database search engines to identify peptides and proteins.…”

Section: Methodsmentioning

confidence: 99%

“…Phosphorylated site predictions were extracted from [46]. Genome annotation data for haploid S288c and SK1 strains were used as published [34]. …”

Section: Methodsmentioning

confidence: 99%

“…In earlier work we have developed Direct Iterative Protein Profiling (DIPP) to comprehensively analyze the proteome of fermenting diploid yeast cells in a cost-effective manner by widely available standard mass spectrometry [34]. In the present study we report the changes in the proteome of diploid MAT a /α yeast cells undergoing logarithmic growth in rich medium with fermentable glucose (YPD) or non-fermentable acetate (YPA) in the context of corresponding RNA-profiling data from wild-type cells and a ume6 mutant strain.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Integrated RNA- and protein profiling of fermentation and respiration in diploid budding yeast provides insight into nutrient control of cell growth and development

Becker

Liu

Lardenois

et al. 2015

Journal of Proteomics

Self Cite

View full text Add to dashboard Cite

Diploid budding yeast undergoes rapid mitosis when it ferments glucose, and in the presence of a non-fermentable carbon source and the absence of a nitrogen source it triggers sporulation. Rich medium with acetate is a commonly used pre-sporulation medium, but our understanding of the molecular events underlying the acetate-driven transition from mitosis to meiosis is still incomplete. We identified 263 proteins for which mRNA and protein synthesis are linked or uncoupled in fermenting and respiring cells. Using motif predictions, interaction data and RNA profiling we find among them 28 likely targets for Ume6, a subunit of the conserved Rpd3/Sin3 histone deacetylase-complex regulating genes involved in metabolism, stress response and meiosis. Finally, we identify 14 genes for which both RNA and proteins are detected exclusively in respiring cells but not in fermenting cells in our sample set, including CSM4, SPR1, SPS4 and RIM4, which were thought to be meiosis-specific. Our work reveals intertwined transcriptional and post-transcriptional control mechanisms acting when a MATa/α strain responds to nutritional signals, and provides molecular clues how the carbon source primes yeast cells for entering meiosis. Biological significance Our integrated genomics study provides insight into the interplay between the transcriptome and the proteome in diploid yeast cells undergoing vegetative growth in the presence of glucose (fermentation) or acetate (respiration). Furthermore, it reveals novel target genes involved in these processes for Ume6, the DNA binding subunit of the conserved histone deacetylase Rpd3 and the co-repressor Sin3. We have combined data from an RNA profiling experiment using tiling arrays that cover the entire yeast genome, and a large-scale protein detection analysis based on mass spectrometry in diploid MATa/α cells. This distinguishes our study from most others in the field—which investigate haploid yeast strains—because only diploid cells can undergo meiotic development in the simultaneous absence of a non-fermentable carbon source and nitrogen. Indeed, we report molecular clues how respiration of acetate might prime diploid cells for efficient spore formation, a phenomenon that is well known but poorly understood.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

“…Phosphorylated site predictions were extracted from [46]. Genome annotation data for haploid S288c and SK1 strains were used as published [34]. …”

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Integrated RNA- and protein profiling of fermentation and respiration in diploid budding yeast provides insight into nutrient control of cell growth and development

Becker

Liu

Lardenois

et al. 2015

Journal of Proteomics

Self Cite

View full text Add to dashboard Cite

show abstract

hnRNP‐A1 binds to the IRES of MELOE‐1 antigen to promote MELOE‐1 translation in stressed melanoma cells

et al. 2021

Self Cite

View full text Add to dashboard Cite

The major challenge in antigen-specific immunotherapy of cancer is to select the most relevant tumor antigens to target. To this aim, understanding their mode of expression by tumor cells is critical. We previously identified a melanoma-specific antigen, melanoma-overexpressed antigen 1 (MELOE-1) -coded for by a long non-coding RNA -whose internal ribosomal entry sequence (IRES)-dependent translation is restricted to tumor cells. This restricted expression is associated with the presence of a broad specific T cell repertoire that is involved in tumor immunosurveillance in melanoma patients. In the present work, we explored the translation control of MELOE-1 and provide evidence that heterogeneous nuclear ribonucleoprotein A1 (hnRNP-A1) binds to the MELOE-1 IRES and acts as an IRES trans-activating factor (ITAF) to promote the translation of MELOE-1 in melanoma cells. In addition, we showed that endoplasmic reticulum (ER) stress induced by thapsigargin, which promotes hnRNP-A1 cytoplasmic translocation, enhances MELOE-1 translation and recognition of melanoma cells by a MELOE-1specific T cell clone. These findings suggest that pharmacological stimulation of stress pathways may enhance the efficacy of immunotherapies targeting stress-induced tumor antigens such as MELOE-1.

show abstract

Genome editing reveals reproductive and developmental dependencies on specific types of vitellogenin in zebrafish (Danio rerio)

Yilmaz

Patinote

Nguyen

et al. 2019

Molecular Reproduction Devel

Self Cite

View full text Add to dashboard Cite

Oviparous vertebrates produce multiple forms of vitellogenin (Vtg), the major source of yolk nutrients, but little is known about their individual contributions to reproduction and development. This study utilized clustered regularly interspaced short palindromic repeats/CRISPR‐associated protein 9 (CRISPR/Cas9) genome editing to assess essentiality and functionality of zebrafish (Danio rerio) type‐I and type‐III Vtgs. A multiple CRISPR approach was employed to knockout (KO) all genes encoding type‐I vtgs (vtg1, 4, 5, 6, and 7) simultaneously (vtg1‐KO), and the type‐III vtg (vtg3) individually (vtg3‐KO). Results of polymerase chain reaction (PCR) genotyping and sequencing, quantitative PCR, liquid chromatography‐tandem mass spectrometry, and Western blot analysis showed that only vtg6 and vtg7 escaped Cas9 editing. In fish whose remaining type‐I vtgs were incapacitated (vtg1‐KO), and in vtg3‐KO fish, significant increases in Vtg7 transcript and protein levels occurred in liver and eggs, revealing a heretofore‐unknown mechanism of genetic compensation regulating Vtg homeostasis. Egg numbers per spawn were elevated more than 2‐fold in vtg1‐KO females, and egg fertility was approximately halved in vtg3‐KO females. Substantial mortality was evident in vtg3‐KO eggs/embryos after only 8 hr of incubation and in vtg1‐KO embryos after 5 days. Hatching rate and timing were markedly impaired in embryos from vtg mutant mothers and pericardial and yolk sac/abdominal edema and spinal lordosis were evident in the larvae, with feeding and motor activities also being absent in vtg1‐KO larvae. By late larval stages, vtg mutations were either completely lethal (vtg1‐KO) or nearly so (vtg3‐KO). These novel findings offer the first experimental evidence that different types of vertebrate Vtg are essential and have disparate requisite functions at different times during both reproduction and development.

show abstract

Direct Iterative Protein Profiling (DIPP) - an Innovative Method for Large-scale Protein Detection Applied to Budding Yeast Mitosis

Cited by 22 publications

References 48 publications

Integrated RNA- and protein profiling of fermentation and respiration in diploid budding yeast provides insight into nutrient control of cell growth and development

Integrated RNA- and protein profiling of fermentation and respiration in diploid budding yeast provides insight into nutrient control of cell growth and development

hnRNP‐A1 binds to the IRES of MELOE‐1 antigen to promote MELOE‐1 translation in stressed melanoma cells

Genome editing reveals reproductive and developmental dependencies on specific types of vitellogenin in zebrafish (Danio rerio)

Contact Info

Product

Resources

About