The Many Faces of RNA

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Rudd KE. Novel intergenic repeats of Escherichia coli K The tyrT locus of Escherichia coli B.

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How does Europe PMC derive its citations network? Protein Interactions. Protein Families. Nucleotide Sequences. Functional Genomics Experiments. Protein Structures. Gene Ontology GO Terms. Data Citations. Proteomics Data. Menu Formats.

Loose RNA molecules rejuvenate skin

It highlights a rapidly developing area of scientific investigation. The style and format are deliberately designed to promote in-depth presentations and discussions and to facilitate the forging of collaborations between academic and industrial partners. This symposium focuses on several of the many fundamental, advancing strategies for exploring RNA and its functions.

It emphasizes the interplay between biology, chemistry, genomics, and molecular biology which is leading to exciting new insights and avenues of investigation. Gait, D. Earnshaw, M. Farrow, and N. Cusack, A. Yaremchuk, and M. Prescott, L. Hegg, K. Nurse, R. Gontarek, H. Li, V. Emerick, T. Sterner, M. Gress, G. Thom, S. Guth, and D. In phylogenetic trees of the YhbY proteins, the archaeal and bacterial groups form distinct clusters which are clearly separated from each other by a distinct branch Figure 2b.

Furthermore, the archaeal and bacterial versions of YhbY are distinguished by specific sequence motifs. The tree topology, conservation pattern and function suggest that the YhbY domain was also likely to have been present in the LUCA. Hence, at least three ancient members of the IF3-C fold which possess RNA-binding properties potentially can be traced back to the point prior to the split between the bacteria and the archaeo-eukaryotic lineages, that is, the LUCA.

The shared loop seen in YhbY and Alba Figure 1 is in orange. Clustering, based on pairwise-structural-alignment Z-scores obtained using the DALI program and sequence similarity, suggests that the closest relatives of the Alba superfamily are IF3 and YhbY Figures 2c and 3.

Furthermore, Alba and YhbY domains share a distinct basic loop, bounded by two small residues between the first strand and helix Figures 1 and 3 , which may participate in RNA binding. These observations suggest that Alba and YhbY probably diverged from each other early in the evolution of the archaeo-eukaryotic lineage.

mRNA, tRNA, and rRNA function - Types of RNA

Only three sets of proteins of the Alba superfamily are experimentally characterized: Sulfolobus Alba, Rpp20 proteins from yeast and vertebrates and the Rpp25 protein from vertebrates. The former has been shown to be the major chromosomal DNA-binding protein in the crenarchaeon Sulfolobus. However, even in Sulfolobus , Alba coats DNA densely but does not elicit significant compaction, suggesting that it is not sufficient for chromatin organization and requires functional partners, such as Sul7d [ 6 ].

Experimental studies on euryarchaeal chromatin have, so far, not yielded much evidence for a major chromosomal role for Alba [ 5 , 8 , 27 ]. Hence, it is conceivable that Alba was specifically recruited for a major chromosomal function only in a particular lineage of crenarchaea. It is likely that other members of the Rpp20 family, which are conserved widely across the eukaryotic tree, perform a similar function in RNase P.

Human Rpp25, the only experimentally characterized member of the second eukaryotic family Mdp2 family , is also a RNase P subunit [ 18 ]. Several uncharacterized members of the Mdp2 family contain tripeptide RGG repeats carboxy-terminal to their globular Alba domain Figure 1. As in the case of these eukaryotic Alba proteins, they occur typically in conjunction with some other globular RNA-binding domain. The ciliate Mdp2, which is a member of the second eukaryotic family, is exclusively co-expressed along with Mdp1 and Mdp3 during macronuclear development [ 19 ]. The ciliate Piwi homologs, such as Mdp1, have been proposed to bind small RNAs that direct the process of DNA reorganization in macronucleus development, in a process related to gene silencing and repeat-induced mutagenesis in fungi [ 19 , 32 ].

The exclusive co-expression of Mdp2 with Mdp1 suggests that the two may interact functionally with each other. The above observations suggest that Mdp2 and some of its relatives could potentially form other ribonucleoprotein complexes, which may perform functions in relation to the small RNAs involved in ciliate DNA reorganization, gene-silencing or allied processes. Members of the Mdp2 family are present in multiple copies in plants Figure 2a and may correlate with a well-developed gene-silencing system in this lineage [ 23 , 33 ]. Thus, an ancestral role in RNA metabolism may be interpolated for both eukaryotic families of the Alba superfamily.

The high degree of conservation of Alba in both euryarchaea and crenarchaea is in contrast with the heterogeneity seen in the phyletic patterns of other major DNA-packaging proteins within archaea see below. Hence, based on its conserved archaeo-eukaryotic phyletic pattern, which is typical of several RNA-metabolism proteins [ 23 ], and by the principle of phylogenetic bracketing Figure 2c , we would predict that most archaeal members of the Alba superfamily could have an additional or exclusive role in RNA metabolism.

This prediction is consistent with both the phyletic pattern of Alba in archaea and the requirement of Rpp20 for viability in yeast. This is also consistent with Alba retaining the basic ancestral RNA-binding property, after divergence from its functionally-related RNA-binding domains at the base of the archaeo-eukaryotic lineage. In light of these predictions, it would be of interest to investigate if the deacetylation of Alba by the Sir2 homologs might have any relevance to RNA metabolism.

The recruitment of RNA-binding domains for DNA-binding roles in chromatin appears to have occurred on different occasions in the course of eukaryotic evolution.

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This fold is also present in proteins associated with RNA metabolism, such as a domain of the lysyl-tRNA synthetase and the bacterial transcription terminator protein Rho [ 35 ]. There is considerable diversity of chromosomal proteins across the archaea, with no major type being universally conserved [ 6 ]. All known crenarchaea lack histones but possess other proteins such as Alba or Sul7d, which is restricted to Sulfolobus [ 6 ].

Several euryarchaea possess histones, but others, for example, Thermoplasma , lack them and contain the bacterial-type HU protein instead [ 6 ]. Some euryarchaea also possess a distinct chromosomal protein of the MC1 family incorporated into a multi-domain protein with helicase and nuclease modules in some archaea , which is also found in the PBCV virus [ 36 , 37 ]. Hence, it is conceivable that the archaea have explored a number of strategies for DNA organization, with different strategies being selected by different local, extreme niches.

This diversity of chromosomal proteins in archaea is consistent with a model where a conserved protein such as Alba, with an original function in RNA metabolism, was recruited in some crenarchaea for chromatin-related functions. Interestingly, particular versions of Sso10b from Sulfolobales [ 10 ] are considerably divergent compared to all other archaeal Alba homologs Figure 2a , suggesting that they may have undergone divergence to perform exclusive roles in chromatin.

The Alba domain superfamily comprises three well-defined families, namely the archaeal family and two eukaryotic families, typified by the Rpp20 and Mdp2 proteins, respectively. We present data which suggest that the ancestral function of the IF3-C fold was related to RNA interaction, and we present evidence that both the eukaryotic lineages of the Alba superfamily are principally involved in RNA metabolism.

In addition to the RNase P complex, some of the Alba proteins may form complexes with other RNAs and participate in other regulatory processes, such as ciliate macronuclear development. The high degree of conservation of Alba in the archaea contrasts the poor conservation or mosaic phyletic distribution of other chromosomal proteins such as Sul7d, 7KMK, HU, MC1 and histones.


These observations, along with the principle of phylogenetic bracketing, suggest that Alba in archaea may additionally or, in some lineages, exclusively, possess a role in RNA metabolism. Thus, starting as an ancestral RNA binding module, the Alba superfamily has colonized two functionally-distinct but biochemically similar niches in RNA metabolism and chromatin structure. Experimental exploration of the observations and the functional predictions reported here may help in improving our understanding of key processes in RNA metabolism.

Profile searches were conducted using the PSI-BLAST program with either a single sequence or an alignment used as the query, with a default profile inclusion expectation e value threshold of 0. All large-scale sequence analysis procedures, such as determination of phyletic patterns, were carried out using the SEALS package [ 39 , 40 ]. The MEGA program version 2. The pairwise distances were estimated using the p-distance method. This was followed by local rearrangements using the ProtML program of the Molphy package to arrive at the maximum likelihood ML tree [ 45 — 47 ].

The statistical significance of various nodes of this ML tree was assessed using the relative estimate of logarithmic likelihood bootstrap Protml RELL-BP , with 10, replicates. Structural manipulations were carried out using the Swiss-PDB viewer version 3. Curr Opin Genet Dev. Methods Enzymol. Nucleic Acids Res. Trends Genet. EMBO J.