System wide analyses have underestimated protein abundances and the importance of transcription in mammals

Large scale surveys in mammalian tissue culture cells suggest that the protein expressed at the median abundance is present at 8,000–16,000 molecules per cell and that differences in mRNA expression between genes explain only 10–40% of the differences in protein levels. We find, however, that these surveys have significantly underestimated protein abundances and the relative importance of transcription. Using individual measurements for 61 housekeeping proteins to rescale whole proteome data from Schwanhausser et al. (2011), we find that the median protein detected is expressed at 170,000 molecules per cell and that our corrected protein abundance estimates show a higher correlation with mRNA abundances than do the uncorrected protein data. In addition, we estimated the impact of further errors in mRNA and protein abundances using direct experimental measurements of these errors. The resulting analysis suggests that mRNA levels explain at least 56% of the differences in protein abundance for the 4,212 genes detected by Schwanhausser et al. (2011), though because one major source of error could not be estimated the true percent contribution should be higher. We also employed a second, independent strategy to determine the contribution of mRNA levels to protein expression. We show that the variance in translation rates directly measured by ribosome profiling is only 9% of that inferred by Schwanhausser et al. (2011), and that the measured and inferred translation rates correlate poorly (R2 = 0.14). Based on this, our second strategy suggests that mRNA levels explain ∼84% of the variance in protein levels. We also determined the percent contributions of transcription, RNA degradation, translation and protein degradation to the variance in protein abundances using both of our strategies. While the magnitudes of the two estimates vary, they both suggest that transcription plays a more important role than the earlier studies implied and translation a much smaller role. Finally, the above estimates apply to those genes whose mRNA and protein expression was detected. Based on a detailed analysis by Hebenstreit et al. (2012), we estimate that approximately 40% of genes in a given cell within a population express no mRNA. Since there can be no translation in the absence of mRNA, we argue that differences in translation rates can play no role in determining the expression levels for the ∼40% of genes that are non-expressed

EDEN Survey: Small Transiting Planet Detection Limits and Constraints on the Occurrence Rates for Late M Dwarfs within 15 pc

Earth-sized exoplanets that transit nearby, late spectral type red dwarfs will be prime targets for atmospheric characterization in the coming decade. Such systems, however, are difficult to find via wide-field transit surveys like Kepler or TESS. Consequently, the presence of such transiting planets is unexplored and the occurrence rates of short-period Earth-sized planets around late M dwarfs remain poorly constrained. Here, we present the deepest photometric monitoring campaign of 22 nearby late M dwarf stars, using data from over 500 nights on seven 1-2 meter class telescopes. Our survey includes all known single quiescent northern late M dwarfs within 15 pc. We use transit-injection-and-recovery tests to quantify the completeness of our survey, successfully identify most ($>80\%$) transiting short-period (0.5-1 d) super-Earths ($R > 1.9 R_\oplus$), and are sensitive ($\sim50\%$) to transiting Earth-sized planets ($1.0-1.2 R_\oplus$). Our high sensitivity to transits with a near-zero false positive rate demonstrates an efficient survey strategy. Our survey does not yield a transiting planet detection, yet it provides the most sensitive upper limits on transiting planets orbiting our target stars. Finally, we explore multiple hypotheses about the occurrence rates of short-period planets (from Earth-sized planets to giant planets) around late M dwarfs. We show, for example, that giant planets at short periods ($<1$ day) are uncommon around our target stars. Our dataset provides some insight into occurrence rates of short-period planets around TRAPPIST-1-like stars, and our results can help test planetary formation and system evolution models, as well as guide future observations of nearby late M dwarfs.Comment: 27 pages, 11 figure

Time, space, and disorder in the expanding proteome universe

Proteins are highly dynamic entities. Their myriad functions require specific structures, but proteins’ dynamic nature ranges all the way from the local mobility of their amino acid constituents to mobility within and well beyond single cells. A truly comprehensive view of the dynamic structural proteome includes: (i) alternative sequences, (ii) alternative conformations, (iii) alternative interactions with a range of biomolecules, (iv) cellular localizations, (v) alternative behaviors in different cell types. While these aspects have traditionally been explored one protein at a time, we highlight recently emerging global approaches that accelerate comprehensive insights into these facets of the dynamic nature of protein structure. Computational tools that integrate and expand on multiple orthogonal data types promise to enable the transition from a disjointed list of static snapshots to a structurally explicit understanding of the dynamics of cellular mechanisms.D.P.M. is funded by BBSRC grant BB/N010493/1

Cytokinin-induced promotion of root meristem size in the fern Azolla supports a shoot-like origin of euphyllophyte roots

de Vries J, Fischer AM, Roettger M, et al. Cytokinin-induced promotion of root meristem size in the fern Azolla supports a shoot-like origin of euphyllophyte roots. New Phytologist. 2016;209(2):705-720.The phytohormones cytokinin and auxin orchestrate the root meristem development in angiosperms by determining embryonic bipolarity. Ferns, having the most basal euphyllophyte root, form neither bipolar embryos nor permanent embryonic primary roots but rather an adventitious root system. This raises the questions of how auxin and cytokinin govern fern root system architecture and whether this can tell us something about the origin of that root. Using Azolla filiculoides, we characterized the influence of IAA and zeatin on adventitious fern root meristems and vasculature by Nomarski microscopy. Simultaneously, RNAseq analyses, yielding 36 091 contigs, were used to uncover how the phytohormones affect root tip gene expression. We show that auxin restricts Azolla root meristem development, while cytokinin promotes it; it is the opposite effect of what is observed in Arabidopsis. Global gene expression profiling uncovered 145 genes significantly regulated by cytokinin or auxin, including cell wall modulators, cell division regulators and lateral root formation coordinators. Our data illuminate both evolution and development of fern roots. Promotion of meristem size through cytokinin supports the idea that root meristems of euphyllophytes evolved from shoot meristems. The foundation of these roots was laid in a postembryonically branching shoot system