scholarly journals Ribonuclease P

2011 ◽  
Vol 366 (1580) ◽  
pp. 2936-2941 ◽  
Author(s):  
Sidney Altman
Keyword(s):  
Rnase P ◽  
Evolutionary Tree ◽  
Ancient World ◽  
Ribonuclease P ◽  
Free Living ◽  
Rna Molecules ◽  
Gene Coding ◽  
Living Organisms

The gene coding for the RNA subunit of ribonuclease P (RNase P) is essential in all free-living organisms. The RNA subunit, itself, is an enzyme and, from its evolutionary tree, we can infer that it is a very ancient molecule. The specificity of this enzyme is that it cleaves other RNA molecules at the junction of single-stranded and the 5′ end of double-stranded regions of RNA. One can speculate that this molecule was very useful in an ancient world in cleaving long pieces of RNA, which must have contained hairpin regions in it, into shorter molecules with the capability of different functions from the longer parent. Today, the specificity of the enzyme can be used in designing drug therapies.

scholarly journals An open‐source sensor‐logger for recording vertical movement in free‐living organisms

2017 ◽  
Vol 9 (3) ◽  
pp. 465-471 ◽  
Author(s):  
J. Ryan Shipley ◽  
Julian Kapoor ◽  
Richard A. Dreelin ◽  
David W. Winkler
Keyword(s):  
Open Source ◽  
Vertical Movement ◽  
Free Living ◽  
Living Organisms

scholarly journals Interplay between substrate recognition, 5’ end tRNA processing and methylation activity of human mitochondrial RNase P

2018 ◽  
Author(s):  
Agnes Karasik ◽  
Carol A. Fierke ◽  
Markos Koutmos
Keyword(s):  
Mitochondrial Diseases ◽  
Protein S ◽  
Rnase P ◽  
Ribonuclease P ◽  
Mitochondrial Rna ◽  
P Protein ◽  
Adenosyl Methionine ◽  
Methylation Activity

ABSTRACTHuman mitochondrial ribonuclease P (mtRNase P) is an essential three protein complex that catalyzes the 5’ end maturation of mitochondrial precursor tRNAs (pre-tRNAs). MRPP3 (Mitochondrial RNase P Protein 3), a protein-only RNase P (PRORP), is the nuclease component of the mtRNase P complex and requires a two-protein S-adenosyl methionine (SAM)-dependent methyltransferase MRPP1/2 sub-complex to function. Dysfunction of mtRNase P is linked to several human mitochondrial diseases, such as mitochondrial myopathies. Despite its central role in mitochondrial RNA processing, little is known about how the protein subunits of mtRNase P function synergistically. Here we use purified mtRNase P to demonstrate that mtRNase P recognizes, cleaves, and methylates some, but not all, mitochondrial pre-tRNAs in vitro. Additionally, mtRNase P does not process all mitochondrial pre-tRNAs uniformly, suggesting the possibility that some pre-tRNAs require additional factors to be cleaved in vivo. Consistent with this, we found that addition of the MRPP1 co-factor SAM enhances the ability of mtRNase P to bind and cleave some mitochondrial pre-tRNAs. Furthermore, the presence of MRPP3 can enhance the methylation activity of MRPP1/2. Taken together, our data demonstrate that the subunits of mtRNase P work together to efficiently recognize, process and methylate human mitochondrial pre-tRNAs.

Regulatory aspects of RNAi in plant production.

2021 ◽  
pp. 154-158
Author(s):  
Werner Schenkel ◽  
Achim Gathmann
Keyword(s):  
Small Rna ◽  
Plant Protection ◽  
Plant Protection Products ◽  
Plant Production ◽  
The European Union ◽  
Relevant Aspect ◽  
Rna Molecules ◽  
Rnai Technology ◽  
Living Organisms ◽  
Intended Use

Abstract Technologies based on RNA interference (RNAi) may be used in plant production in different contexts. With respect to applicable regulations, a major distinction is to be made between plants producing small RNA molecules due to modifications of the genome and topically applied plant protection products (PPPs) based on double-stranded RNA (dsRNA). The first group may be further divided into those using RNAi technology to achieve changes in the plant's metabolism and those where plant-produced RNA molecules are intended to impact other organisms that interact with the plant. For PPPs, relevant aspects are whether the product contains living organisms or only purified molecules. The intended use of the product is another relevant aspect with respect to regulation. It is expected that PPPs will be among the first products utilizing the RNAi mechanism in the European Union. This chapter discusses the regulation of modified RNAi plants and the regulation of PPPs utilizing RNAi mechanisms.

scholarly journals A screening platform to monitor RNA processing and protein-RNA interactions in ribonuclease P uncovers a small molecule inhibitor

2019 ◽  
Vol 47 (12) ◽  
pp. 6425-6438 ◽  
Author(s):  
Ezequiel-Alejandro Madrigal-Carrillo ◽  
Carlos-Alejandro Díaz-Tufinio ◽  
Hugo-Aníbal Santamaría-Suárez ◽  
Marcelino Arciniega ◽  
Alfredo Torres-Larios
Keyword(s):  
Rna Processing ◽  
Rnase P ◽  
Ribonuclease P ◽  
Binding Assays ◽  
Antibiotic Development ◽  
Processing Enzymes ◽  
P Protein ◽  
Molecule Inhibitor ◽  
Screening Platform ◽  
Dynamics Simulations

AbstractRibonucleoprotein (RNP) complexes and RNA-processing enzymes are attractive targets for antibiotic development owing to their central roles in microbial physiology. For many of these complexes, comprehensive strategies to identify inhibitors are either lacking or suffer from substantial technical limitations. Here, we describe an activity-binding-structure platform for bacterial ribonuclease P (RNase P), an essential RNP ribozyme involved in 5′ tRNA processing. A novel, real-time fluorescence-based assay was used to monitor RNase P activity and rapidly identify inhibitors using a mini-helix and a pre-tRNA-like bipartite substrate. Using the mini-helix substrate, we screened a library comprising 2560 compounds. Initial hits were then validated using pre-tRNA and the pre-tRNA-like substrate, which ultimately verified four compounds as inhibitors. Biolayer interferometry-based binding assays and molecular dynamics simulations were then used to characterize the interactions between each validated inhibitor and the P protein, P RNA and pre-tRNA. X-ray crystallographic studies subsequently elucidated the structure of the P protein bound to the most promising hit, purpurin, and revealed how this inhibitor adversely affects tRNA 5′ leader binding. This integrated platform affords improved structure-function studies of RNA processing enzymes and facilitates the discovery of novel regulators or inhibitors.

A survey on bioconcentration capacities of some marine parasitic and free-living organisms in the Gulf of Oman

2014 ◽  
Vol 37 ◽  
pp. 99-104 ◽  
Author(s):  
M. Golestaninasab ◽  
M. Malek ◽  
A. Roohi ◽  
A.R. Karbassi ◽  
E. Amoozadeh ◽  
...  
Keyword(s):  
Free Living ◽  
Gulf Of Oman ◽  
Living Organisms

scholarly journals HPrK Regulates Succinate-Mediated Catabolite Repression in the Gram-Negative Symbiont Sinorhizobium meliloti

2008 ◽  
Vol 191 (1) ◽  
pp. 298-309 ◽  
Author(s):  
Catalina Arango Pinedo ◽  
Daniel J. Gage
Keyword(s):  
Catabolite Repression ◽  
Sinorhizobium Meliloti ◽  
Root Nodules ◽  
Phosphotransferase System ◽  
Free Living ◽  
Gene Encoding ◽  
Common Component ◽  
Gram Negative ◽  
Gram Positive Bacteria ◽  
Living Organisms

ABSTRACT The HPrK kinase/phosphatase is a common component of the phosphotransferase system (PTS) of gram-positive bacteria and regulates catabolite repression through phosphorylation/dephosphorylation of its substrate, the PTS protein HPr, at a conserved serine residue. Phosphorylation of HPr by HPrK also affects additional phosphorylation of HPr by the PTS enzyme EI at a conserved histidine residue. Sinorhizobium meliloti can live as symbionts inside legume root nodules or as free-living organisms and is one of the relatively rare gram-negative bacteria known to have a gene encoding HPrK. We have constructed S. meliloti mutants that lack HPrK or that lack key amino acids in HPr that are likely phosphorylated by HPrK and EI. Deletion of hprK in S. meliloti enhanced catabolite repression caused by succinate, as did an S53A substitution in HPr. Introduction of an H22A substitution into HPr alleviated the strong catabolite repression phenotypes of strains carrying ΔhprK or hpr(S53A) mutations, demonstrating that HPr-His22-P is needed for strong catabolite repression. Furthermore, strains with a hpr(H22A) allele exhibited relaxed catabolite repression. These results suggest that HPrK phosphorylates HPr at the serine-53 residue, that HPr-Ser53-P inhibits phosphorylation at the histidine-22 residue, and that HPr-His22-P enhances catabolite repression in the presence of succinate. Additional experiments show that ΔhprK mutants overproduce exopolysaccharides and form nodules that do not fix nitrogen.

scholarly journals Stressful colours: corticosterone concentrations in a free-living songbird vary with the spectral composition of experimental illumination

2015 ◽  
Vol 11 (8) ◽  
pp. 20150517 ◽  
Author(s):  
Jenny Q. Ouyang ◽  
Maaike de Jong ◽  
Michaela Hau ◽  
Marcel E. Visser ◽  
Roy H. A. van Grunsven ◽  
...  
Keyword(s):  
Large Scale ◽  
Red Light ◽  
Spectral Composition ◽  
Parus Major ◽  
Light Spectrum ◽  
Night Time ◽  
Free Living ◽  
Treatment Type ◽  
Artificial Illumination ◽  
Living Organisms

Organisms have evolved under natural daily light/dark cycles for millions of years. These cycles have been disturbed as night-time darkness is increasingly replaced by artificial illumination. Investigating the physiological consequences of free-living organisms in artificially lit environments is crucial to determine whether nocturnal lighting disrupts circadian rhythms, changes behaviour, reduces fitness and ultimately affects population numbers. We make use of a unique, large-scale network of replicated field sites which were experimentally illuminated at night using lampposts emanating either red, green, white or no light to test effect on stress hormone concentrations (corticosterone) in a songbird, the great tit ( Parus major ). Adults nesting in white-light transects had higher corticosterone concentrations than in the other treatments. We also found a significant interaction between distance to the closest lamppost and treatment type: individuals in red light had higher corticosterone levels when they nested closer to the lamppost than individuals nesting farther away, a decline not observed in the green or dark treatment. Individuals with high corticosterone levels had fewer fledglings, irrespective of treatment. These results show that artificial light can induce changes in individual hormonal phenotype. As these effects vary considerably with light spectrum, it opens the possibility to mitigate these effects by selecting street lighting of specific spectra.

scholarly journals The Comprehensive Antibiotic Resistance Database

2013 ◽  
Vol 57 (7) ◽  
pp. 3348-3357 ◽  
Author(s):  
Andrew G. McArthur ◽  
Nicholas Waglechner ◽  
Fazmin Nizam ◽  
Austin Yan ◽  
Marisa A. Azad ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Sequence Data ◽  
Antibiotic Resistance Genes ◽  
Research Database ◽  
Free Living ◽  
Bacterial Populations ◽  
Bioinformatic Tools ◽  
Antibiotic Drug ◽  
Genetics And Genomics ◽  
Living Organisms

ABSTRACTThe field of antibiotic drug discovery and the monitoring of new antibiotic resistance elements have yet to fully exploit the power of the genome revolution. Despite the fact that the first genomes sequenced of free living organisms were those of bacteria, there have been few specialized bioinformatic tools developed to mine the growing amount of genomic data associated with pathogens. In particular, there are few tools to study the genetics and genomics of antibiotic resistance and how it impacts bacterial populations, ecology, and the clinic. We have initiated development of such tools in the form of the Comprehensive Antibiotic Research Database (CARD;http://arpcard.mcmaster.ca). The CARD integrates disparate molecular and sequence data, provides a unique organizing principle in the form of the Antibiotic Resistance Ontology (ARO), and can quickly identify putative antibiotic resistance genes in new unannotated genome sequences. This unique platform provides an informatic tool that bridges antibiotic resistance concerns in health care, agriculture, and the environment.

Nitrogen fixation and acetylene reduction in decaying conifer boles: effects of incubation time, aeration, and moisture content

1982 ◽  
Vol 12 (3) ◽  
pp. 646-652 ◽  
Author(s):  
Warwick B. Silvester ◽  
Phillip Sollins ◽  
Thomas Verhoeven ◽  
Steven P. Cline
Keyword(s):  
Nitrogen Fixation ◽  
Moisture Content ◽  
Forest Ecosystem ◽  
Acetylene Reduction ◽  
Preliminary Survey ◽  
Anaerobic Conditions ◽  
Free Living ◽  
Living Organisms ◽  
Low Activity

Free-living microaerophiles fixed 15N2 and reduced acetylene in fallen tree boles at two old-growth Pseudotsugamenziesii stands in western Oregon. Acetylene reduction was most rapid under an atmosphere of 2–10% O2, whereas under prolonged anaerobic conditions it was at or below detection limits. Acetylene reduction rates increased up to fourfold during long-term incubations in acetylene (> 12 h). Ratios of acetylene reduction to N2 fixation frequently exceeded 6.0 during such long-term incubations but averaged 3.5 when samples were incubated < 7 h; consequently, long-term incubation of low-activity material in acetylene should be avoided. A preliminary survey indicated that N2 fixation by free-living organisms in fallen boles was less than other potential N inputs to fallen boles and to the forest ecosystem.

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