Rational design of cyclic peptide inhibitors of U2AF homology motif (UHM) domains to modulate pre-mRNA splicing.

U2AF homology motifs (UHMs) are atypical RNA recognition motif domains that mediate critical protein-protein interactions during the regulation of alternative pre-mRNA splicing and other processes. The recognition of UHM domains by UHM ligand motif (Ulm) peptide sequences plays important roles during early steps of spliceosome assembly. Splicing factor 45 kDa (SPF45) is an alternative splicing factor implicated in breast and lung cancers, and splicing regulation of apoptosis-linked pre-mRNAs by SPF45 was shown to depend on interactions between its UHM domain and Ulm motifs in constitutive splicing factors. We have developed cyclic peptide inhibitors that target UHM domains. By screening a focused library of linear and cyclic peptides and performing structure-activity relationship analysis, we designed cyclic peptides with 4-fold improved binding affinity for the SPF45 UHM domain compared to native Ulm ligands and 270-fold selectivity to discriminate UHM domains from alternative and constitutive splicing factors. These inhibitors are useful tools to modulate and dissect mechanisms of alternative splicing regulation

Identification of phenothiazine derivatives as UHM-binding inhibitors of early spliceosome assembly.

Interactions between U2AF homology motifs (UHMs) and U2AF ligand motifs (ULMs) play a crucial role in early spliceosome assembly in eukaryotic gene regulation. UHM-ULM interactions mediate heterodimerization of the constitutive splicing factors U2AF65 and U2AF35 and between other splicing factors that regulate spliceosome assembly at the 3′ splice site, where UHM domains of alternative splicing factors, such as SPF45 and PUF60, contribute to alternative splicing regulation. Here, we performed high-throughput screening using fluorescence polarization assays with hit validation by NMR and identified phenothiazines as general inhibitors of UHM-ULM interactions. NMR studies show that these compounds occupy the tryptophan binding pocket of UHM domains. Co-crystal structures of the inhibitors with the PUF60 UHM domain and medicinal chemistry provide structure-activity-relationships and reveal functional groups important for binding. These inhibitors inhibit early spliceosome assembly on pre-mRNA substrates in vitro. Our data show that spliceosome assembly can be inhibited by targeting UHM-ULM interactions by small molecules, thus extending the toolkit of splicing modulators for structural and biochemical studies of the spliceosome and splicing regulation

Extinction risk assessment of the world's seagrass species

Seagrasses, a functional group of marine flowering plants rooted in the world's coastal oceans, support marine food webs and provide essential habitat for many coastal species, playing a critical role in the equilibrium of coastal ecosystems and human livelihoods. For the first time, the probability of extinction is determined for the world's seagrass species under the Categories and Criteria of the International Union for the Conservation of Nature (IUCN) Red List of Threatened Species. Several studies have indicated that seagrass habitat is declining worldwide. Our focus is to determine the risk of extinction for individual seagrass species, a 4-year process involving seagrass experts internationally, compilation of data on species' status, populations, and distribution, and review of the biology and ecology of each of the world's seagrass species. Ten seagrass species are at elevated risk of extinction (14% of all seagrass species), with three species qualifying as Endangered. Seagrass species loss and degradation of seagrass biodiversity will have serious repercussions for marine biodiversity and the human populations that depend upon the resources and ecosystem services that seagrasses provide