A three-dimensional model of the U1 small nuclear ribonucleoprotein particle

Most of the pre-mRNAs in the eukaryotic cell are comprised of protein-coding exons and non-protein-coding introns. The introns are removed and the exons are ligated together, or spliced, by a large, macromolecular complex known as the spliceosome. This RNA-protein assembly is made up of five uridine-rich small nuclear RNAs (U1-, U2-, U4-, U5- and U6-snRNA) as well over 300 proteins, which form small nuclear ribonucleoprotein particles (snRNPs). Initial recognition of the 5′ exon/intron splice site is mediated by the U1 snRNP, which is composed of the U1 snRNA as well as at least ten proteins. By combining structural informatics tools with the available biochemical and crystallographic data, we attempted to simulate a complete, three dimensional U1 snRNP from the silk moth, Bombyx mori. Comparison of our model with empirically derived crystal structures and electron micrographs pinpoints both the strengths and weaknesses in the in silico determination of macromolecular complexes. One of the most striking differences between our model and experimentally generated structures is in the positioning of the U1 snRNA stem-loops. This highlights the continuing difficulties in generating reliable, complex RNA structures; however, three-dimensional modeling of individual protein subunits by threading provided models of biological significance and the use of both automated and manual docking strategies generated a complex that closely reflects the assembly found in nature. Yet, without utilizing experimentally-derived contacts to select the most likely docking scenario, ab initio docking would fall short of providing a reliable model. Our work shows that the combination of experimental data with structural informatics tools can result in generation of near-native macromolecular complexes.     

Heat maps for intramolecular communication in an RNP enzyme encoding glutamine

Allosteric signaling within large ribonucleoproteins modulates both catalytic function and biological specificity, but the spatial extent and quantitative magnitudes of long-distance free-energy couplings have yet to be well characterized. Here, we employ pre-steady-state kinetics to generate a comprehensive mapping of intramolecular communication in the glutaminyl-tRNA synthetase:tRNA(Gln) complex. Alanine substitution at 29 positions across the protein-RNA interface reveals distinct coupling amplitudes for glutamine binding and aminoacyl-tRNA formation on the enzyme, respectively, implying the existence of multiple signaling pathways. Structural models suggest that long-range signal propagation from the tRNA anticodon is dynamically driven, whereas shorter pathways are mediated by induced-fit rearrangements. Seven protein contacts with the distal tRNA vertical arm each weaken glutamine binding affinity across distances up to 40 ?, demonstrating that negative allosteric coupling plays a key role in enforcing the selective RNA-amino acid pairing at the heart of the genetic code.     

Facilitated invasion of an overseas invader: human mediated settlement and expansion of the giant African snail, <Emphasis Type="Italic">Lissachatina fulica</Emphasis>, in Cuba

The giant African snail, Lissachatina fulica, is considered one of the most invasive species worldwide, acting as a crop pest and diseases vector. It was first detected in Cuba in 2014 and is dispersing throughout Havana. We mapped 34 sites in the vicinity of Havana to assess its spread and analysed ecological (forestation and humidity) and anthropogenic (pollution and religious sites) factors in relation to the presence/absence of the snails using multivariate correspondence analysis. There were 14 sites at which the snail was present and where religious rituals of the Yoruba creed, an African rooted religion, were observed. No other variables showed significant relationships. This indicates that the rituals may be a major factor in the dispersal of the snail in Havana and more widely in Cuba. In light of this an outreach program with key Yoruba leaders may help in slowing the dispersal of the snail within Cuba, once the threats posed by this species are known.     

Spliceosomal immunophilins

The spliceosome is a dynamic, macromolecular complex, which removes non-protein-coding introns from pre-mRNA to form mature mRNA in a process known as splicing. This ribonucleoprotein assembly is comprised of five uridine-rich small nuclear RNAs (snRNAs) as well as over 300 proteins. In humans, several of the known proteinaceous splicing factors are members of the immunophilin superfamily. Immunophilins are peptidyl-prolyl cis-trans isomerases that catalyze the conversion of proteins from cis to trans at Xaa-Pro bonds. Our review of the data indicates that some members of this protein family are activators of spliceosomal proteins by way of folding and transport.     

Echolocation calls of free-flying common vampire bats Desmodus rotundus (Chiroptera: Phyllostomidae) in Chile

We recorded and characterized the echolocation calls emitted by the common vampire bat Desmodus rotundus during foraging in natural habitats in Chile. Signal design typically shows multiple harmonics consisting of a brief quasi-constant frequency (QCF) component at the beginning of the pulse followed by a downward frequency modulated component. Calls are characterized by long durations (5.5 ms) and emitted as single pulses or in groups of 2–3 pulses at a repetition rate of 29 Hz. The higher frequency ranges (85–35 kHz) and the unusual QCF component that characterized multiharmonic signals of free-flying D. rotundus in Chile is a remarkable feature for acoustic identification with other Chilean bats.     

New Brazilian species of Endecous Saussure, 1878: Phallic sclerites, calling song and tegmen morphometry (Orthoptera: Grylloidea: Phalangopsinae)

In this paper we describe the phalangopsid cricket Endecous alejomesai n. sp. collected from the cave "Lapa do Fuzil", Vila Propício, State of Goiás, Brazil. Diagnosis has been acquired by the combination of the following characteristics: phallic sclerite features; calling song with dominant frequency of 4.8 kHz and 52.9 ± 5.8 (42–60, n  = 22) cycles of sound per pulse; pars stridens with 90 ± 6.84 (78–99, n  = 12) teeth; mirror with one or two cross-veins; harp with two, three or four cross-veins.     

U1 small nuclear RNA variants differentially form ribonucleoprotein particles in vitro

The U1 small nuclear (sn)RNA participates in splicing of pre-mRNAs by recognizing and binding to 5′ splice sites at exon/intron boundaries. U1 snRNAs associate with 5′ splice sites in the form of ribonucleoprotein particles (snRNPs) that are comprised of the U1 snRNA and 10 core components, including U1A, U1-70K, U1C and the ‘Smith antigen’, or Sm, heptamer. The U1 snRNA is highly conserved across a wide range of taxa; however, a number of reports have identified the presence of expressed U1-like snRNAs in multiple species, including humans. While numerous U1-like molecules have been shown to be expressed, it is unclear whether these variant snRNAs have the capacity to form snRNPs and participate in splicing. The purpose of the present study was to further characterize biochemically the ability of previously identified human U1-like variants to form snRNPs and bind to U1 snRNP proteins. A bioinformatics analysis provided support for the existence of multiple expressed variants. In vitro gel shift assays, competition assays, and immunoprecipitations (IPs) revealed that the variants formed high molecular weight assemblies to varying degrees and associated with core U1 snRNP proteins to a lesser extent than the canonical U1 snRNA. Together, these data suggest that the human U1 snRNA variants analyzed here are unable to efficiently bind U1 snRNP proteins. The current work provides additional biochemical insights into the ability of the variants to assemble into snRNPs.