Reconstruction of protein networks from an atlas of maize seed proteotypes.

A comprehensive knowledge of proteomic states is essential for understanding biological systems. Using mass spectrometry, we mapped an atlas of developing maize seed proteotypes comprising 14,165 proteins and 18,405 phosphopeptides (from 4,511 proteins), quantified across eight tissues. We found that many of the most abundant proteins are not associated with detectable levels of their mRNAs, and we provide evidence for three potential explanations: transport of proteins between tissues; diurnal, out-of-phase accumulation of mRNAs and cognate proteins; and differential lifetimes of mRNAs compared with proteins. Likewise, many of the most abundant mRNAs were not associated with detectable levels of their proteins. Across the entire dataset, protein abundance was poorly correlated with mRNA levels and was largely independent of phosphorylation status. Comparisons between proteotypes revealed the quantitative contribution of specific proteins and phosphorylation events to the spatially and temporally regulated starch and oil biosynthetic pathways. Reconstruction of signaling networks established associations of proteins and phosphoproteins with distinct biological processes acting during seed development. Additionally, a protein kinase substrate network was reconstructed, enabling the identification of 762 potential substrates of specific protein kinases. Finally, examination of 694 transcription factors revealed remarkable constraints on patterns of expression and phosphorylation within transcription factor families. These results provide a resource for understanding seed development in a crop that is the foundation of modern agriculture.

Water depth influences survival and predator-specific patterns of nest loss in three secretive marsh bird species.

Wetlands have become increasingly rare in the United States, negatively influencing wetland-dependent birds, and many remaining wetlands are intensively managed through seasonal dewatering mimicking historic flood pulses during spring and summer. However, water around nests may provide protection from terrestrial predators, and lowering water levels during the breeding season of wetland birds may increase predation risk and exacerbate marsh bird population declines. Understanding interactions between water depth, nesting marsh birds, and nest predators is critical to aid managers in developing a multi-species management approach in emergent wetlands. During the 2020 and 2021 breeding seasons, we examined nest survival of 148 marsh bird nests (American Coot, Fulica americana, n = 1; Common Gallinule, Gallinula galeata, n = 64; and Least Bittern; Ixobrychus exilis, n = 83) and installed cameras at 78 nests to identify predators at a large, restored floodplain wetland in Illinois where the primary management technique is seasonal water removal to stimulate germination of moist soil plants. We found nest predation of, and abandonment by, Least Bittern and Common Gallinule were related to shallower water, and early season, high volume dewatering. Least Bitterns nested more commonly along wetland edges and nests farther from the shore were more likely to survive. Similarly, we found mammalian depredation of nests and nest abandonment decreased when deeper water was present around nests. Alternatively, snake predation was observed earlier in the year prior to water removal from inundated emergent vegetation. Our results demonstrate water depth may be an important deterrent of nest predators, especially mammals, during the breeding season. Further, we recommend managers delay dewatering until after the nesting season at sites where management for conservation-priority marsh birds is a focus.

Extensive chromosomal instability in Rad51d-deficient mouse cells.

Homologous recombination is a double-strand break repair pathway required for resistance to DNA damage and maintaining genomic integrity. In mitotically dividing vertebrate cells, the primary proteins involved in homologous recombination repair are RAD51 and the five RAD51 paralogs, RAD51B, RAD51C, RAD51D, XRCC2, and XRCC3. In the absence of Rad51d, human and mouse cells fail to proliferate, and mice defective for Rad51d die before birth, likely as a result of genomic instability and p53 activation. Here, we report that a p53 deletion is sufficient to extend the life span of Rad51d-deficient embryos by up to 6 days and rescue the cell lethal phenotype. The Rad51d-/- Trp53-/- mouse embryo-derived fibroblasts were sensitive to DNA-damaging agents, particularly interstrand cross-links, and exhibited extensive chromosome instability including aneuploidy, chromosome fragments, deletions, and complex rearrangements. Additionally, loss of Rad51d resulted in increased centrosome fragmentation and reduced levels of radiation-induced RAD51-focus formation. Spontaneous frequencies of sister chromatid exchange were not affected by the absence of Rad51d, but sister chromatid exchange frequencies did fail to be induced upon challenge with the DNA cross-linking agent mitomycin C. These findings support a crucial role for mammalian RAD51D in normal development, recombination, and maintaining mammalian genome stability.