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At least 19 recordsLinked to original sources
PubMed1991

sRNA of phage phi 29 of Bacillus subtilis mediates DNA packaging of phi 29 proheads assembled in Escherichia coli.

The structural genes of the prohead of phage phi 29 of Bacillus subtilis and a small phi 29 RNA (sRNA) were cloned and expressed in Escherichia coli individually or in combination to study the role of the sRNA in prohead assembly and the mechanism of prohead morphogenesis. The genes coding for the proteins of the scaffold (gp7), the capsid (gp8), the portal vertex (gp10), and the dispensable head fiber (gp8.5) were expressed in E. coli and the gene products were assembled, with and without the presence of the sRNA, into uniform and prolate particles that resembled the typical native phi 29 prohead. No differences in particle size and shape were found between the particles of 7-8-8.5-10 (scaffold-capsid-fiber-portal vertex) and 7-8-8.5-10-RNA (scaffold-capsid-fiber-portal vertex-RNA), suggesting that the phi 29 sRNA was not required for phi 29 prohead assembly. The 7-8-8.5-10 particles produced in E. coli in the absence of phi 29 sRNA were fully competent to package phi 29 DNA in the defined in vitro DNA packaging system by the addition of purified sRNA. Moreover, these DNA-filled heads were assembled into infectious virions in extracts. Without the addition of the sRNA, the 7-8-8.5-10 particles were incompetent while the 7-8-8.5-10-RNA particles were competent in DNA packaging. Bacterial sRNA present in E. coli cannot substitute for the phi 29 sRNA. The assembly of prohead particles in E. coli indicated that host factors unique to B. subtilis were not required. The evidence that the phi 29 sRNA was not required for phi 29 prohead assembly and was not a fixed structural component of the phi 29 prohead favors the conclusion that the phi 29 sRNA is a specific enzyme or morphogenetic factor in DNA packaging.

Bacillus subtilis↗
PubMed2006

Assembly of the archaeal box C/D sRNP can occur via alternative pathways and requires temperature-facilitated sRNA remodeling.

Archaeal dual-guide box C/D small nucleolar RNA-like RNAs (sRNAs) bind three core proteins in sequential order at both terminal box C/D and internal C'/D' motifs to assemble two ribonuclear protein (RNP) complexes active in guiding nucleotide methylation. Experiments have investigated the process of box C/D sRNP assembly and the resultant changes in sRNA structure or "remodeling" as a consequence of sRNP core protein binding. Hierarchical assembly of the Methanocaldococcus jannaschii sR8 box C/D sRNP is a temperature-dependent process with binding of L7 and Nop56/58 core proteins to the sRNA requiring elevated temperature to facilitate necessary RNA structural dynamics. Circular dichroism (CD) spectroscopy and RNA thermal denaturation revealed an increased order and stability of sRNA folded structure as a result of L7 binding. Subsequent binding of the Nop56/58 and fibrillarin core proteins to the L7-sRNA complex further remodeled sRNA structure. Assessment of sR8 guide region accessibility using complementary RNA oligonucleotide probes revealed significant changes in guide region structure during sRNP assembly. A second dual-guide box C/D sRNA from M. jannaschii, sR6, also exhibited RNA remodeling during temperature-dependent sRNP assembly, although core protein binding was affected by sR6's distinct folded structure. Interestingly, the sR6 sRNP followed an alternative assembly pathway, with both guide regions being continuously exposed during sRNP assembly. Further experiments using sR8 mutants possessing alternative guide regions demonstrated that sRNA folded structure induced by specific guide sequences impacted the sRNP assembly pathway. Nevertheless, assembled sRNPs were active for sRNA-guided methylation independent of the pathway followed. Thus, RNA remodeling appears to be a common and requisite feature of archaeal dual-guide box C/D sRNP assembly and formation of the mature sRNP can follow different assembly pathways in generating catalytically active complexes.

Amino Acid Sequence↗
PubMed2006

Identification of 17 Pseudomonas aeruginosa sRNAs and prediction of sRNA-encoding genes in 10 diverse pathogens using the bioinformatic tool sRNAPredict2.

sRNAs are small, non-coding RNA species that control numerous cellular processes. Although it is widely accepted that sRNAs are encoded by most if not all bacteria, genome-wide annotations for sRNA-encoding genes have been conducted in only a few of the nearly 300 bacterial species sequenced to date. To facilitate the efficient annotation of bacterial genomes for sRNA-encoding genes, we developed a program, sRNAPredict2, that identifies putative sRNAs by searching for co-localization of genetic features commonly associated with sRNA-encoding genes. Using sRNAPredict2, we conducted genome-wide annotations for putative sRNA-encoding genes in the intergenic regions of 11 diverse pathogens. In total, 2759 previously unannotated candidate sRNA loci were predicted. There was considerable range in the number of sRNAs predicted in the different pathogens analyzed, raising the possibility that there are species-specific differences in the reliance on sRNA-mediated regulation. Of 34 previously unannotated sRNAs predicted in the opportunistic pathogen Pseudomonas aeruginosa, 31 were experimentally tested and 17 were found to encode sRNA transcripts. Our findings suggest that numerous genes have been missed in the current annotations of bacterial genomes and that, by using improved bioinformatic approaches and tools, much remains to be discovered in 'intergenic' sequences.

Computational Biology↗
PubMed2005

The Monte Carlo SRNA-VOX code for 3D proton dose distribution in voxelized geometry using CT data.

This paper describes the application of the SRNA Monte Carlo package for proton transport simulations in complex geometry and different material compositions. The SRNA package was developed for 3D dose distribution calculation in proton therapy and dosimetry and it was based on the theory of multiple scattering. The decay of proton induced compound nuclei was simulated by the Russian MSDM model and our own using ICRU 63 data. The developed package consists of two codes: the SRNA-2KG, which simulates proton transport in combinatorial geometry and the SRNA-VOX, which uses the voxelized geometry using the CT data and conversion of the Hounsfield's data to tissue elemental composition. Transition probabilities for both codes are prepared by the SRNADAT code. The simulation of the proton beam characterization by multi-layer Faraday cup, spatial distribution of positron emitters obtained by the SRNA-2KG code and intercomparison of computational codes in radiation dosimetry, indicate immediate application of the Monte Carlo techniques in clinical practice. In this paper, we briefly present the physical model implemented in the SRNA package, the ISTAR proton dose planning software, as well as the results of the numerical experiments with proton beams to obtain 3D dose distribution in the eye and breast tumour.

Algorithms↗
PubMed2006

Computer simulation of chaperone effects of Archaeal C/D box sRNA binding on rRNA folding.

Archaeal C/D box small RNAs (sRNAs) are homologues of eukaryotic C/D box small nucleolar RNAs (snoRNAs). Their main function is guiding 2'-O-ribose methylation of nucleotides in rRNAs. The methylation requires the pairing of an sRNA antisense element to an rRNA target site with formation of an RNA-RNA duplex. The temporary formation of such a duplex during rRNA maturation is expected to influence rRNA folding in a chaperone-like way, in particular in thermophilic Archaea, where multiple sRNAs with two binding sites are found. Here we investigate possible mechanisms of chaperone function of Archaeoglobus fulgidus and Pyrococcus abyssi C/D box sRNAs using computer simulations of rRNA secondary structure formation by genetic algorithm. The effects of sRNA binding on rRNA structure are introduced as temporary structural constraints during co-transcriptional folding. Comparisons of the final predictions with simulations without sRNA binding and with phylogenetic structures show that sRNAs with two antisense elements may significantly facilitate the correct formation of long-range interactions in rRNAs, in particular at elevated temperatures. The simulations suggest that the main mechanism of this effect is a transient restriction of folding in rRNA domains where the termini are brought together by binding to double-guide sRNAs.

Archaeoglobus fulgidus↗
PubMed2003

A novel sRNA component of the carbon storage regulatory system of Escherichia coli.

Small untranslated RNAs (sRNAs) perform a variety of important functions in bacteria. The 245 nucleotide sRNA of Escherichia coli, CsrC, was discovered using a genetic screen for factors that regulate glycogen biosynthesis. CsrC RNA binds multiple copies of CsrA, a protein that post-transcriptionally regulates central carbon flux, biofilm formation and motility in E. coli. CsrC antagonizes the regulatory effects of CsrA, presumably by sequestering this protein. The discovery of CsrC is intriguing, in that a similar sRNA, CsrB, performs essentially the same function. Both sRNAs possess similar imperfect repeat sequences (18 in CsrB, nine in CsrC), primarily localized in the loops of predicted hairpins, which may serve as CsrA binding elements. Transcription of csrC increases as the culture approaches the stationary phase of growth and is indirectly activated by CsrA via the response regulator UvrY. Because CsrB and CsrC antagonize CsrA activity and depend on CsrA for their synthesis, a csrB null mutation causes a modest compensatory increase in CsrC levels and vice versa. Homologues of csrC are apparent in several Enterobacteriaceae. The regulatory and evolutionary implications of these findings are discussed.

Base Sequence↗
PubMed1969

A Study of the Aminoacyl-sRNA Synthetases of Phaseolus vulgaris in Relation to Germination.

Optimum conditions for the extraction and assay by ATP-pyrophosphate exchange of the aminoacyl-sRNA synthetases of the various tissues of french bean (Phaseolus vulgaris) seeds and seedlings are described. Extracts of plumules, after passage through Sephadex G-25, were assayed for synthetase activity using an amino acid mixture as substrate, when a 30 to 100-fold stimulation of exchange above the endogenous level was obtained. This marked enhancement of exchange by added amino acids is largely attributed to the use of dilute extracts.The total synthetase activity of the cotyledons was studied in relation to germination. Synthetase activity was highest in the dry cotyledon; activity decreased in proportion to the loss of protein during germination, i.e. the specific activity of the synthetases remained constant for at least the first 6 days of germination. With a few minor exceptions, the specific activity of the individual synthetases remained constant during germination.The absolute activity of the synthetases of the plumule and radicle increased exponentially during germination. The specific activity of the synthetases in both tissues increased approximately 2-fold during the first 2 to 3 days of germination, then gradually decreased. However the asparaginyl-, valyl-, and histidinyl-sRNA synthetases in the plumule did not conform with this general pattern.

Journal Article↗
PubMed1964

AMINOACYL POSITION IN AMINOACYL SRNA.

Chromatographic systems capable of resolving the 2'- and 3'-isomers of valyladenosine and N-acetylvalyladenosine are used to show that valyladenosine isolated from valyl-sRNA is the equilibrium mixture of 2'- and 3'-acyl isomers by the time of chromatography. Acyl migration in N-acetylvalyladenosine is shown to be a rapid, base-catalyzed reaction with a rate 40,000 times the rate of hydrolysis under equivalent conditions. Calculations indicate that the pool of free aminoacyl sRNA exists in vivo as the equilibrium mixture of the 2'- and 3'-aminoacyl isomers

Carbon Isotopes↗