An Optimized Proteomics Approach Reveals Novel Alternative Proteins in Mouse Liver Development

Alternative ORFs (AltORFs) are unannotated sequences in genome that encode novel peptides or proteins named alternative proteins (AltProts). Although ribosome profiling and bioinformatics predict a large number of AltProts, mass spectrometry as the only direct way of identification is hampered by the short lengths and relative low abundance of AltProts. There is an urgent need for improvement of mass spectrometry methodologies for AltProt identification. Here, we report an approach based on size-exclusion chromatography for simultaneous enrichment and fractionation of AltProts from complex proteome. This method greatly simplifies the variance of AltProts discovery by enriching small proteins smaller than 40 kDa. In a systematic comparison between 10 methods, the approach we reported enabled the discovery of more AltProts with overall higher intensities, with less cost of time and effort compared to other workflows. We applied this approach to identify 89 novel AltProts from mouse liver, 39 of which were differentially expressed between embryonic and adult mice. During embryonic development, the upregulated AltProts were mainly involved in biological pathways on RNA splicing and processing, whereas the AltProts involved in metabolisms were more active in adult livers. Our study not only provides an effective approach for identifying AltProts but also novel AltProts that are potentially important in developmental biology.     

Ribosome ADP-ribosylation inhibits translation and maintains proteostasis in cancers

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Bifidobacteria-mediated immune system imprinting early in life

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Cell-type-specific Hox regulatory strategies orchestrate tissue identity

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Sexual dimorphism and gonadal development of the Australian longfinned river eel

The sex and stage of gonadal development of longfinned river eels Anguilla reinhardtii , captured from nine river catchments in New South Wales, Australia, between 1999 and 2001, were determined macroscopically. Sex was verified by histology. Histology was also necessary, however, to accurately define stages of gonadal development, particularly in individuals <600 mm in total body length. Anguilla reinhardtii displayed asynchronous gamete development. The most advanced cells present in migrating male and female A. reinhardtii were spermatocytes and pre-vitellogenic oocytes, respectively. Gonadal development stages were positively correlated with body size in both sexes. Females, however, were significantly larger than males and their gonads matured over a broader size range. Size at sexual differentiation (42–60 cm for males and 50–76 cm for females) was much larger than for most other anguillids that have been studied, with the exception of the New Zealand longfinned eel Anguilla dieffenbachii . Corresponding with its large range in size at sexual differentiation was a relatively large range in size at migration for both males (44–62 cm) and females (74–142 cm).