SLAIN2’s interactions with multiple different microtubule plus end–tracking proteins stimulate processive microtubule polymerization and ensure proper microtubule organization.

Alternative splicing plays an important role in generating proteome diversity. The polypyrimidine tract-binding protein (PTB) is a key alternative splicing factor involved in exon repression. It has been proposed that PTB acts by looping out exons flanked by pyrimidine tracts. We present fluorescence, NMR, and in vivo splicing data in support of a role of PTB in inducing RNA loops. We show that the RNA recognition motifs (RRMs) 3 and 4 of PTB can bind two distant pyrimidine tracts and bring their 5′ and 3′ ends in close proximity, thus looping the RNA. Efficient looping requires an intervening sequence of 15 nucleotides or longer between the pyrimidine tracts. RRM3 and RRM4 bind the 5′ and the 3′ pyrimidine tracts, respectively, in a specific directionality and work synergistically for efficient splicing repression in vivo.alternative splicing | polypyrimidine tract-binding protein | protein-RNA interactions A lternative splicing is a highly regulated biological process that plays a crucial role in generating high proteomic diversity. It has been estimated that >90% of human genes are alternatively spliced (1). Alternative splicing occurs frequently in cells, and most RNA-binding proteins that influence alternative splicing were found to be nonspliceosomal (2). The polypyrimidine tract (PPT)-binding protein (PTB) is one of the major trans-acting factors involved in splicing regulation. PTB is most often associated with its role as a splicing repressor (3-5), but it is also involved in other aspects of mRNA processing including 3′ end processing (6, 7), mRNA localization and stability (8), and internal ribosome entry site (IRES)-mediated translation (9).PTB is a 58-kDa member of the hnRNP family consisting of four RNA recognition motifs (RRMs) joined by three linkers (10, 11). PTB recognizes PPTs in the RNA target containing CU-rich elements (12, 13). The mechanism by which PTB promotes exon exclusion is poorly understood. Our NMR structure of RNAbound PTB has suggested a potential mechanism of PTB action in splicing whereby RRM3 and RRM4 bind the PPTs flanking an alternative exon and loop out the intervening RNA, thus repressing the exon (Fig. 1A) (14). The two RRM-bound PPTs appear in opposite direction as if forming a loop to exclude the intervening exon or the branched adenosine from the spliceosomal machinery. Other mechanistic models for PTB repression have proposed a direct (5) and an indirect (5, 15) competition between PTB and other splicing factors like U2AF65, corepression with Raver-1 (16) and PTB preventing exon (15) or intron definition (17). However, all proposed mechanisms are consistent with RNA looping between RRM3 and RRM4.Here, we have sought to test and characterize this suggested looping mechanism using FRET, NMR spectroscopy, and in vivo splicing assays. Results PTB34 Binds PPTs and Brings Their 5′ and 3′ Ends into Close Proximity.First, we tested the binding of RRM3 and RRM4 of PTB (PTB34, Fig. 1A) to several model RNAs using a FRET-based gel shift assay (18). We prepared a series of singl...

Secondary active transporters of the SLC11/NRAMP family catalyse the uptake of iron and manganese into cells. These proteins are highly conserved across all kingdoms of life and thus likely share a common transport mechanism. Here we describe the structural and functional properties of the prokaryotic SLC11 transporter EcoDMT. Its crystal structure reveals a previously unknown outward-facing state of the protein family. In proteoliposomes EcoDMT mediates proton-coupled uptake of manganese at low micromolar concentrations. Mutants of residues in the transition-metal ion-binding site severely affect transport, whereas a mutation of a conserved histidine located near this site results in metal ion transport that appears uncoupled to proton transport. Combined with previous results, our study defines the conformational changes underlying transition-metal ion transport in the SLC11 family and it provides molecular insight to its coupling to protons.

Like many asymmetrically dividing cells, budding yeast segregates mitotic spindle poles nonrandomly between mother and daughter cells. During metaphase, the spindle positioning protein Kar9 accumulates asymmetrically, localizing specifically to astral microtubules emanating from the old spindle pole body (SPB) and driving its segregation to the bud. Here, we show that the SPB component Nud1/centriolin acts through the mitotic exit network (MEN) to specify asymmetric SPB inheritance. In the absence of MEN signaling, Kar9 asymmetry is unstable and its preference for the old SPB is disrupted. Consistent with this, phosphorylation of Kar9 by the MEN kinases Dbf2 and Dbf20 is not required to break Kar9 symmetry but is instead required to maintain stable association of Kar9 with the old SPB throughout metaphase. We propose that MEN signaling links Kar9 regulation to SPB identity through biasing and stabilizing the age-insensitive, cyclin-B-dependent mechanism of symmetry breaking.

The microtubule plus-end tracking protein Kar9 forms different types of complexes with Bim1 (orthologue of the end-binding protein EB1) to control nuclear fusion during mating and spindle alignment during metaphase in budding yeast.

Microtubule plus-end tracking proteins (+TIPs) are involved in virtually all microtubule-based processes. End-binding (EB) proteins are considered master regulators of +TIP interaction networks, since they autonomously track growing microtubule ends and recruit a plethora of proteins to this location. Two major EB-interacting elements have been described: CAP-Gly domains and linear SxIP sequence motifs. Here, we identified LxxPTPh as a third EB-binding motif that enables major +TIPs to interact with EBs at microtubule ends. In contrast to EB-SxIP and EB-CAP-Gly, the EB-LxxPTPh binding mode does not depend on the C-terminal tail region of EB. Our study reveals that +TIPs developed additional strategies besides CAP-Gly and SxIP to target EBs at growing microtubule ends. They further provide a unique basis to discover novel +TIPs, and to dissect the role of key interaction nodes and their differential regulation for hierarchical +TIP network organization and function in eukaryotic organisms.

Members of the ubiquitous SLC11/NRAMP family catalyze the uptake of divalent transition metal ions into cells. They have evolved to efficiently select these trace elements from a large pool of Ca2+ and Mg2+, which are both orders of magnitude more abundant, and to concentrate them in the cytoplasm aided by the cotransport of H+ serving as energy source. In the present study, we have characterized a member of a distant clade of the family found in prokaryotes, termed NRMTs, that were proposed to function as transporters of Mg2+. The protein transports Mg2+ and Mn2+ but not Ca2+ by a mechanism that is not coupled to H+. Structures determined by cryo-EM and X-ray crystallography revealed a generally similar protein architecture compared to classical NRAMPs, with a restructured ion binding site whose increased volume provides suitable interactions with ions that likely have retained much of their hydration shell.

Functional reconstitution of membrane proteins within lipid bilayers is crucial for understanding their biological function in living cells. While this strategy has been extensively used with liposomes, reconstitution of membrane proteins in lipidic cubic mesophases presents significant challenges related to the structural complexity of the lipid bilayer, organized on saddle-like minimal surfaces. Although reconstitution of membrane proteins in lipidic cubic mesophases plays a prominent role in membrane protein crystallization, nanotechnology, controlled drug delivery, and pathology of diseased cells, little is known about the molecular mechanism of protein reconstitution and about how transport properties of the doped mesophase mirror the original molecular gating features of the reconstituted membrane proteins. In this work we design a general strategy to demonstrate correct functional reconstitution of active and selective membrane protein transporters in lipidic mesophases, exemplified by the bacterial ClC exchanger from Escherichia coli (EcClC) as a model ion transporter. We show that its correct reconstitution in the lipidic matrix can be used to generate macroscopic proton and chloride pumps capable of selectively transporting charges over the length scale of centimeters. By further exploiting the coupled chloride/proton exchange of this membrane protein and by combining parallel or antiparallel chloride and proton gradients, we show that the doped mesophase can operate as a charge separation device relying only on the reconstituted EcClC protein and an external bias potential. These results may thus also pave the way to possible applications in supercapacitors, ion batteries, and molecular pumps.ipidic lyotropic liquid crystals (LLCs) are systems based on the spontaneous self-assembly of lipids in an aqueous environment. Hydrated neutral monoacylglycerols such as monolinolein (1) and monoolein (2), along with phospholipids in presence of hydrophobic species (3), can form liquid crystalline phases of various 3D architectures, which vary depending on temperature and composition, reflecting a complex lipid polymorphism.A particularly fascinating class of lipidic mesophases consists of bicontinuous cubic phases of double gyroid (Ia3d), double diamond (Pn3m), and primitive (Im3m) symmetry, in which the lipid molecules form a highly curved continuous bilayer organized through triply periodic minimal surfaces that separate two interpenetrating but nonintersecting aqueous channels (4). The latter two symmetries are of particular significance in fundamental and applied sciences because they coexist at thermodynamic equilibrium with excess water (1, 4), involving an immediate plethora of direct implications. For example, bicontinuous lipidic cubic phases are now recognized as a powerful tool for drug delivery (5, 6) and as efficient vectors for siRNA and DNA transfection (7,8) and have been observed in numerous biological systems, where they seem to have an apparent relation to pathological states of the cell (9)....