Reiter L et al. (2009) Mol Cell Proteomics "Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry."

Jovanovic M, Buhmann JM, Schrimpf SP, Reiter L, Claassen M, Schmidt A, Hengartner MO, Aebersold R

[Mol Cell Proteomics, 2009]

Comprehensive characterization of a proteome is a fundamental goal in proteomics. To achieve saturation coverage of a proteome or specific subproteome via tandem mass spectrometric identification of tryptic protein sample digests, proteomics data sets are growing dramatically in size and heterogeneity. The trend toward very large integrated data sets poses so far unsolved challenges to control the uncertainty of protein identifications going beyond well established confidence measures for peptide-spectrum matches. We present MAYU, a novel strategy that reliably estimates false discovery rates for protein identifications in large scale data sets. We validated and applied MAYU using various large proteomics data sets. The data show that the size of the data set has an important and previously underestimated impact on the reliability of protein identifications. We particularly found that protein false discovery rates are significantly elevated compared with those of peptide-spectrum matches. The function provided by MAYU is critical to control the quality of proteome data repositories and thereby to enhance any study relying on these data sources. The MAYU software is available as standalone software and also integrated into the Trans-Proteomic Pipeline.

Matsumoto, Shinya et al. (2015) International Worm Meeting "Analysis of intergenerational effects of starvation."

Matsumura, Yasuki, Matsumoto, Shinya, Morishita, Mayu, Sei, Megumi, Ogai, Midori, Kato, Kosuke, Saito, Haruka, Nishida, Ayano, Sawanaga, Akari, Okada, Sawako, Sakagami, Midori

[International Worm Meeting, 2015]

According to the DOHaD (Developmental Origins of Health and Disease) concept, poor nutritional environment during early life (including conception, embryogenesis, infancy and early childhood) induces changes in development that increase the disease risk in adult stage. The DOHaD is attracting many attention because not only it could change our view toward health and diseases, but also it causes concern about the health of our future generation. Generally, the three molecular events, DNA methylation, histone modifications, and non-coding RNAs are considered to be involved in DOHaD process in vertebrates, but the precise mechanism is not well defined. To gain information concerning the molecular mechanism of DOHaD, starvation was introduced to the parent worms, and the offsprings were analyzed for their fecundity, life span, mobility and fat accumulation. There were no difference observed in fecundity, life span and mobility between the offsprings derived from starvation-experienced and fed-parent worms. However, Nile Red staining showed that fat content was significantly increased in the offsprings derived from starvation-experienced worms compared with that of control offsprings. Fat accumulation was further indicated by gas chromatography analysis. DNA microarray is now being conducted to analyse the gene expression pattern.The data is in line with DOHaD concept, which may indicate that C.elegans can be used in DOHaD model animal.

Jha, Sweta et al. (2021) International Worm Meeting "UPS modulation and autophagy."

Jha, Sweta, Holmberg, Carina

[International Worm Meeting, 2021]

The ubiquitin-proteasome system (UPS) and the autophagy-lysosomal pathway (ALP) are the two main eukaryotic intracellular proteolytic systems involved in maintaining proteostasis. Autophagy is responsible for degrading defective cellular organelles and long-lived proteins in the cytosol and is involved in cell growth, survival, development and death. UPS mostly degrades soluble and short-lived proteins in the nucleus and cytosol and affects various cellular processes. These two proteolytic systems are essential components of the cellular protein quality control system. Several studies have reported an interplay between the UPS and ALP, however it still remains largely unknown how these systems communicate in a multicellular organism. We have recently shown that downregulation of autophagy genes elicits tissue-specific effects on UPS function in C. elegans1. Here, we address how genetic or pharmacological modulation of the proteasome and the proteasome-associated DUBs affects autophagy. We use transgenic C. elegans expressing the autophagy reporters GFP::LGG-12 or mCherry::GFP::LGG-13 and analyze the accumulation of LGG-1 puncta and autophagic flux. Our preliminary data show that downregulation of the proteasome-associated DUBs ubh-4, usp-14 and rpn-11 as well as some proteasomal subunits affect the number of puncta positive for autophagosomes in hypodermal seam cells, intestinal cells as well as in pharynx. To nvestigate a conserved function of the UPS on autophagy in human cells, we are utilizing a HeLa cell line expressing the fluorescence probe GFP::LC3::RFP::LC3G4. A better understanding of the multilayered crosstalk between UPS and ALP in vivo may facilitate development of therapeutic options for various disorders linked to dysfunction in proteostasis. References Jha, S., Holmberg, C.I. Tissue-Specific Impact of Autophagy Genes on the Ubiquitin-Proteasome System in C. elegans. Cells 2020, 9, 1858. Melendez A, Talloczy Z, Seaman M, Eskelinen E-L, Hall DH, Levine B. Autophagy genes are essential for dauer develop-ment and life-span extension in C. elegans. Science 2003. 301:1387-91 Chang J.T., Kumsta C., Hellman A.B., Adams L.M., Hansen M. (2017). Spatiotemporal regulation of autophagy during caenorhabditis elegans aging. Elife. pii: e18459 Kaizuka T., Morishita H., Hama Y., Tsukamoto S., Matsui T., Toyota Y., Kodama A., Ishihara T., Mizushima T., Mizushima N. (2016). An autophagic flux probe that releases an internal control. Mol Cell. 64(4):835-849.