Daphnia pulex is a keystone species for aquatic habitats and an ecological/evolution model organism. Although significant progress has been made on characterizing its genome, the D. pulex proteome remains largely uncharacterized partially due to abnormally high protein degradation during homogenization and emphasis on genomic analysis. In this study, various sample preparation and mass spectrometry acquisition methods are performed for the purpose of improving D. pulex proteome exploration. Benefits for employing both in-gel and in-solution methods of trypsin digestion are observed. Furthermore, acquisition methods employing ion mobility separation greatly increase peptide identification and more than doubled the proteome coverage. Bioinformatic analysis suggests that mitochondrial and hydrolytic activities are enriched in D. pulex compared to closely related invertebrates or Homo sapiens. Also, novel D. pulex proteins possessing putative genome modifying functional domains are identified. Data are available via ProteomeXchange with identifier PXD008455.
Spinal muscular atrophy
(SMA) is a human genetic disorder characterized
by muscle weakness, muscle atrophy, and death of motor neurons. SMA
is caused by mutations or deletions in a gene called survival
motor neuron 1 (SMN1). SMN1 is a housekeeping gene, but the most prominent pathologies in SMA
are atrophy of myofibers and death of motor neurons. Further, degeneration
of neuromuscular junctions, of synapses, and of axonal regions are
features of SMA disease. Here, we have investigated the proteome dynamics
of central synapses in P14 Smn
2B/–
mice, a model of SMA. Label-free quantitative proteomics on
isolated synaptosomes from spinal cords of these animals identified
2030 protein groups. Statistical data analysis revealed 65 specific
alterations in the proteome of the central synapses at the early onset
stage of disease. Functional analysis of the dysregulated proteins
indicated a significant enrichment of proteins associated with mitochondrial
dynamics, cholesterol biogenesis, and protein clearance. These pathways
represent potential targets for therapy development with the goal
of providing stability to the central synapses, thereby preserving
neuronal integrity in the context of SMA disease. Data are available
via ProteomeXchange with identifier PXD012850.
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