Reinhard, J. | bioRxiv Science

bioRxiv2020

Nested versus independent sampling: Solving the mystery of contradictory species-area relationships

AO_SCPLOWBSTRACTC_SCPLOWSpecies-area relationships (SARs) describe how the number of species increases with the size of the area surveyed, and they usually take the shape of a power law on regional spatial scales. A meta-review of empirical data has shown that the exponent of the power law is on average larger when the areas are sampled in a nested manner, compared to sampling of independent areas such as islands of different sizes. As this is in contrast to ecological reasoning, we performed computer simulations of three qualitatively different models that generate species distributions in space and time by the mechanisms of speciation, dispersal, and extinction. We find that in all cases and over a wide parameter range the SARs obtained by nested sampling have a smaller slope in the regional scale than those obtained by independent sampling. We explain the discrepancy to the empirical data by the different spatial scales on which the two types of empirical investigations were performed.

ecology↗

bioRxiv2019

Systematic cysteine-crosslinking in native membranes establishes the transmembrane architecture in Ire1 clusters

The endoplasmic reticulum (ER) is a key organelle of membrane biogenesis and crucial for the folding of both membrane and secretory proteins. Sensors of the unfolded protein response (UPR) monitor the unfolded protein load in the ER and convey effector functions for maintaining ER homeostasis. Aberrant compositions of the ER membrane, referred to as lipid bilayer stress, are equally potent activators of the UPR. How the distinct signals from lipid bilayer stress and unfolded proteins are processed by the conserved UPR transducer Ire1 remains unknown. Here, we have generated a functional, cysteine-less variant of Ire1 and performed systematic cysteine crosslinking experiments in native membranes to establish its transmembrane architecture in signaling-active clusters. We show that the transmembrane helices of two neighboring Ire1 molecules adopt an X-shaped configuration independent of the primary cause for ER stress. This suggests that different forms of stress converge in a common, signaling-active transmembrane architecture of Ire1. SummaryThe endoplasmic reticulum (ER) is a hotspot of lipid biosynthesis and crucial for the folding of membrane and secretory proteins. The unfolded protein response (UPR) controls the size and folding capacity of the ER. The conserved UPR transducer Ire1 senses both unfolded proteins and aberrant lipid compositions to mount adaptive responses. Using a biochemical assay to study Ire1 in signaling-active clusters, Vath et al. provide evidence that the neighboring transmembrane helices of clustered Ire1 form an X irrespectively of the primary cause of ER stress. Hence, different forms of ER stress converge in a common, signaling-active transmembrane architecture of Ire1.

biochemistry↗