Is the Trypanosoma brucei REL1 RNA ligase specific for U-deletion RNA editing,and is the REL2 RNA ligase specific for U-insertion editing?

It was shown previously that the REL1 mitochondrial RNA ligase in Trypanosoma brucei was a vital gene and disruption affected RNA editing in vivo, whereas the REL2 RNA ligase gene could be down-regulated with no effect on cell growth or on RNA editing. We performed down-regulation of REL1 in procyclic T. brucei (midgut insect forms) by RNA interference and found a 40-50% inhibition of Cyb editing, which has only U-insertions, as well as a similar inhibition of ND7 editing, which has both U-insertions and U-deletions. In addition, both U-insertion and U-deletion in vitro pre-cleaved editing were inhibited to similar extents. We also found little if any effect of REL1 down-regulation on the sedimentation coefficient or abundance of the RNA ligase-containing L-complex (Aphasizhev, R., Aphasizheva, I., Nelson, R. E., Gao, G., Simpson, A. M., Kang, X., Falick, A. M., Sbicego, S., and Simpson, L. (2003) EMBO J. 22, 913-924), suggesting that the inhibition of both insertion and deletion editing was not due to a disruption of the L-complex. Together with the evidence that down-regulation of REL2 has no effect on cell growth or on RNA editing in vivo or in vitro, these data suggest that the REL1 RNA ligase may be active in vivo in both U-insertion and U-deletion editing. The in vivo biological role of REL2 remains obscure.     

4SALE – A tool for synchronous RNA sequence and secondary structure alignment and editing

Background  

In sequence analysis the multiple alignment builds the fundament of all proceeding analyses. Errors in an alignment could strongly influence all succeeding analyses and therefore could lead to wrong predictions. Hand-crafted and hand-improved alignments are necessary and meanwhile good common practice. For RNA sequences often the primary sequence as well as a secondary structure consensus is well known, e.g., the cloverleaf structure of the t-RNA. Recently, some alignment editors are proposed that are able to include and model both kinds of information. However, with the advent of a large amount of reliable RNA sequences together with their solved secondary structures (available from e.g. the ITS2 Database), we are faced with the problem to handle sequences and their associated secondary structures synchronously.     

Regulation of RNA function by aminoacylation and editing?

The chemical modification of nucleic acids is a ubiquitous phenomenon. Aminoacylation of tRNAs by aminoacyl-tRNA synthetases (ARSs) is a reaction essentially devoted to protein synthesis but it is used also as an emergency mechanism to recycle stalled ribosomes, and it is required for genome replication in some RNA viruses. In several aminoacyl-tRNA synthetases a correction mechanism known as editing is present to prevent aminoacylation errors. Genome data reveal a growing number of open reading frames encoding ARS-like proteins. This strongly suggests the existence of a widespread and nonconventional machinery for aminoacylation and editing. Here we review the different biological functions of aminoacylation and editing; also we propose an evolutionary scenario for the origin of these two reactions, and hypothesize an extant role for RNA charging and editing outside the genetic code.     

Chirality-induced budding: a raft-mediated mechanism for endocytosis and morphology of caveolae?

The formation of transport carriers (spherical vesicles and tubules) involves membrane budding, growth, and ultimately fission. We propose a mechanism of membrane budding, wherein the tilt and chirality of constituent molecules, confined to a patch of area A, induces buds of approximately 50-100 nm that are comparable to vesicles involved in endocytosis. Because such chiral and tilted lipid molecules are likely to exist in "rafts", we suggest the involvement of this mechanism in generating membrane buds in the clathrin and dynamin-independent, raft-component mediated endocytosis of glycosylphosphatidylinositol-anchored proteins. We argue that caveolae, permanent cell surface structures with characteristic morphology and enriched in raft constituents, are also likely to be formed by this mechanism. Thus, molecular chirality and tilt, and its expression over large spatial scales may be a common organizing principle in membrane budding of transport carriers.     

Cysteine residues as catalysts for covalent peptide and protein modification: a role for thiyl radicals?

Cysteine thiyl radicals engage in reversible intramolecular hydrogen-transfer reactions with amino acid residues in peptides and proteins. These reactions can be experimentally demonstrated through covalent hydrogen-deuterium exchange when experiments are carried out in (2)H2O. To this end, hydrogen-transfer reactions have been observed between cysteine thiyl radicals and glycine, alanine, serine, valine and leucine in both model peptides and a protein, insulin. The relevance of such reactions for protein oxidation under conditions of oxidative stress is discussed.     

Synchrony: a neuronal mechanism for attentional selection?

Attentional selection involves brain processes that select and control the flow of information into the mechanisms that underlie perception and consciousness. One theory proposes that the neural activity that represents the stimuli or events to be attended to is selected through modification of its synchrony. Recent experimental evidence supports this theory, by showing that changes in attentional focus increase the synchrony of neural firing in some neuron pairs and decrease it in others.     

The β subunit gate loop is required for RNA polymerase modification by RfaH and NusG

In all organisms, RNA polymerase (RNAP) relies on accessory factors to complete synthesis of long RNAs. These factors increase RNAP processivity by reducing pausing and termination, but their molecular mechanisms remain incompletely understood. We identify the β gate loop as an RNAP element required for antipausing activity of a bacterial virulence factor RfaH, a member of the universally conserved NusG family. Interactions with the gate loop are necessary for suppression of pausing and termination by RfaH, but are dispensable for RfaH binding to RNAP mediated by the β' clamp helices. We hypothesize that upon binding to the clamp helices and the gate loop RfaH bridges the gap across the DNA channel, stabilizing RNAP contacts with nucleic acid and disfavoring isomerization into a paused state. We show that contacts with the gate loop are also required for antipausing by NusG and propose that most NusG homologs use similar mechanisms to increase RNAP processivity.     

Natural folding of airborne fungal spores: a mechanism for dispersal and long-term survival?

Analysis of numerous air samples has indicated that dormant, viable fungal spores are highly present, which suggests that aerial dispersion is important for fungi. Whereas the majority of the spores may travel only very short distances, there is indication that a notable number of them cover much longer distances. Harmomegathy is a terminology coined by Wodehouse (1935) describing the natural folding of pollen to accommodate controlled and reversible water loss. Here, we discuss evidence that this concept may also apply to airborne fungal spores that face similar challenges and have to survive periods of drought and low temperatures while retaining viability to germinate after deposition upon a suitable moist substrate. In fact, (air)dried conidia, appear collapsed, survive for much longer times compared to spores in liquid, that deteriorate in time. This indicates that for some types of fungal spores, true dormancy is reached in the desiccated state. For these airborne spores this might be regarded as a pre-adaptation that supports long-distance transport of viable cells through air. We state that spores are naturally folded during transport in air if the humidity is low enough. We hypothesize that this is a pre-adaptation supporting release, dispersal and survival of airborne spores. Moreover, the smaller size of dry naturally-folded spores may also be relevant, e.g. for the opportunistic pathogenic fungus Aspergillus fumigatus reduced spore size supports deposition within the alveoli in the lung.