A database search for hammerhead ribozyme motifs

2005 ◽  
Vol 33 (3) ◽  
pp. 477-478 ◽  
Author(s):  
S. Gräf ◽  
R. Przybilski ◽  
G. Steger ◽  
C. Hammann
Keyword(s):  
Plant Pathogens ◽  
Hammerhead Ribozyme ◽  
Database Search ◽  
Catalytic Rna ◽  
Magnesium Ion ◽  
In Planta ◽  
Hammerhead Ribozymes ◽  
Structural Requirements ◽  
Ion Concentrations ◽  
Naturally Occurring

The hammerhead ribozyme is the smallest naturally occurring RNA endonuclease. It is found in subviral plant pathogens and transcripts of satellite DNA from a limited number of organisms. We have performed a database search for novel examples of this catalytic RNA, taking into consideration the recently defined structural requirements for an efficient cleavage under physiological magnesium ion concentrations. In this search, we find, apart from the known examples, several hundreds of motifs in organisms of all kingdoms of life. In a first set of experiments, we analysed hammerhead ribozymes from Arabidopsis thaliana. We found that these sequences are tissue-specifically expressed and that they undergo self-cleavage in planta. Furthermore, their activity under physiological magnesium ion concentrations depends on functional loop–loop interactions, as shown by the lack of activity of appropriate mutants.

scholarly journals Intronic hammerhead ribozymes in mRNA biogenesis

2012 ◽  
Vol 393 (11) ◽  
pp. 1317-1326 ◽  
Author(s):  
Inmaculada García-Robles ◽  
Jesús Sánchez-Navarro ◽  
Marcos de la Peña
Keyword(s):  
Plant Pathogens ◽  
Hammerhead Ribozyme ◽  
Bioinformatic Analysis ◽  
Catalytic Rna ◽  
Splicing Regulation ◽  
Biological Characterization ◽  
Hammerhead Ribozymes ◽  
Endonucleolytic Cleavage ◽  
New Form

Abstract Small self-cleaving ribozymes are a group of natural RNAs that are capable of catalyzing their own and sequence-specific endonucleolytic cleavage. One of the most studied members is the hammerhead ribozyme (HHR), a catalytic RNA originally discovered in subviral plant pathogens but recently shown to reside in a myriad of genomes along the tree of life. In eukaryotes, most of the genomic HHRs seem to be related to short interspersed retroelements, with the main exception of a group of strikingly conserved ribozymes found in the genomes of all amniotes (reptiles, birds and mammals). These amniota HHRs occur in the introns of a few specific genes, and clearly point to a preserved biological role during pre-mRNA biosynthesis. More specifically, bioinformatic analysis suggests that these intronic ribozymes could offer a new form of splicing regulation of the mRNA of higher vertebrates. We review here the latest advances in the discovery and biological characterization of intronic HHRs of vertebrates, including new conserved examples in the genomes of the primitive turtle and coelacanth fish.

scholarly journals Idiosyncratic cleavage and ligation activity of individual hammerhead ribozymes and core sequence variants thereof

2007 ◽  
Vol 388 (7) ◽  
pp. 737-741 ◽  
Author(s):  
Rita Przybilski ◽  
Christian Hammann
Keyword(s):  
Small Rna ◽  
Plant Pathogens ◽  
Hammerhead Ribozyme ◽  
Structure And Function ◽  
Sequence Variants ◽  
Hammerhead Ribozymes ◽  
Satellite Dnas ◽  
Cleavage Reactions ◽  
The Individual ◽  
And Function

AbstractThe hammerhead ribozyme is a small RNA endonuclease found in sub-viral plant pathogens, in transcripts from certain animal satellite DNAs and encoded at distinct loci ofArabidopsis thaliana. Kinetic analyses of tertiary stabilised ribozymes from peach latent mosaic viroid (PLMVd),Schistosoma mansoniandA. thalianarevealed a ten-fold difference in cleavage rates. Core nucleotide variations affected cleavage reactions least in theA. thalianaribozyme, and most in theS. mansoniribozyme. The reverse ligation reaction was catalysed efficiently by the PLMVd andA. thalianaribozymes. The different behaviour of the individual hammerhead ribozymes is discussed in terms of structure and function.

scholarly journals Single Mutation in Hammerhead Ribozyme Favors Cleavage Activity with Manganese over Magnesium

2020 ◽  
Vol 6 (1) ◽  
pp. 14
Author(s):  
Mohammad Reza Naghdi ◽  
Emilie Boutet ◽  
Clarisse Mucha ◽  
Jonathan Ouellet ◽  
Jonathan Perreault
Keyword(s):  
Divalent Cations ◽  
Hammerhead Ribozyme ◽  
Single Mutation ◽  
Hammerhead Ribozymes ◽  
Catalytic Core ◽  
Cleavage Activity ◽  
Naturally Occurring

Hammerhead ribozymes are one of the most studied classes of ribozymes so far, from both the structural and biochemical point of views. The activity of most hammerhead ribozymes is cation-dependent. Mg2+ is one of the most abundant divalent cations in the cell and therefore plays a major role in cleavage activity for most hammerhead ribozymes. Besides Mg2+, cleavage can also occur in the presence of other cations such as Mn2+. The catalytic core of hammerhead ribozymes is highly conserved, which could contribute to a preference of hammerhead ribozymes toward certain cations. Here, we show a naturally occurring variation in the catalytic core of hammerhead ribozymes, A6C, that can favor one metallic ion, Mn2+, over several other cations.

STUDY OF SOME FACTORS THAT AFFECT THE DISTRIBUTION OF NUCLEAR VOLUMES IN PREPARATIONS OF RAT LIVER NUCLEI

1967 ◽  
Vol 45 (7) ◽  
pp. 1175-1183 ◽  
Author(s):  
Roberto Umaña
Keyword(s):  
Rat Liver ◽  
Dna Content ◽  
Direct Relationship ◽  
Magnesium Ion ◽  
Homogenization Procedure ◽  
Ion Concentrations ◽  
Ph Values ◽  
Sucrose Solutions ◽  
Liver Nuclei ◽  
Calcium And Magnesium

The effect of the homogenization procedure, the centrifugation scheme, and the composition of the suspension medium on the distribution of nuclear volumes has been studied.It has been shown that the Waring Blendor not only destroys a greater number of the nuclei during homogenization, but also that this destruction is a selective one. At neutral pH values, no direct relationship appears to exist between the DNA content of the nuclei and their density. For this reason, purification in concentrated sucrose solutions produces a selective loss of the lighter nuclei, which includes small diploid stromal nuclei and some of the larger polyploid type of parenchymal nuclei.The study of the effect of increasing the calcium and magnesium ion concentrations (from 0.001 to 0.005 M) on the nuclear distribution showed that these ions produce a selective shrinkage and condensation of the nuclei, probably through different mechanisms.

Thermal stability of ribosomes from a thermophilic and a mesophilic fungus

1973 ◽  
Vol 19 (6) ◽  
pp. 761-763 ◽  
Author(s):  
H. M. Miller ◽  
M. G. Shepherd
Keyword(s):  
Thermal Stability ◽  
Ion Concentration ◽  
Magnesium Ion ◽  
Penicillium Notatum ◽  
Ribosomal Subunits ◽  
Ion Concentrations ◽  
Thermal Stability Of

Ribosomes and ribosomal subunits from the thermophile Penicillium duponti were found to be more thermostable than the corresponding particles from the mesophile Penicillium notatum. The thermostability of the ribosomes from both organisms was dependent on magnesium ion concentration. The dissociation of the 80-S ribosomes into 60-S and 40-S subunits occurred at higher magnesium ion concentrations for the mesophile than the thermophile.

scholarly journals In planta bacterial multi-omics analysis illuminates regulatory principles underlying plant-pathogen interactions

2019 ◽  
Author(s):  
Tatsuya Nobori ◽  
Yiming Wang ◽  
Jingni Wu ◽  
Sara Christina Stolze ◽  
Yayoi Tsuda ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Pseudomonas Syringae ◽  
Protein Level ◽  
Plant Pathogens ◽  
Plant Immunity ◽  
Bacterial Pathogen ◽  
Bacterial Virulence ◽  
In Planta ◽  
Bacterial Gene ◽  
Global Food Security

AbstractUnderstanding how gene expression is regulated in plant pathogens is crucial for pest control and thus global food security. An integrated understanding of bacterial gene regulation in the host is dependent on multi-omic datasets, but these are largely lacking. Here, we simultaneously characterized the transcriptome and proteome of a foliar bacterial pathogen, Pseudomonas syringae, in Arabidopsis thaliana and identified a number of bacterial processes influenced by plant immunity at the mRNA and the protein level. We found instances of both concordant and discordant regulation of bacterial mRNAs and proteins. Notably, the tip component of bacterial type III secretion system was selectively suppressed by the plant salicylic acid pathway at the protein level, suggesting protein-level targeting of the bacterial virulence system by plant immunity. Furthermore, gene co-expression analysis illuminated previously unknown gene regulatory modules underlying bacterial virulence and their regulatory hierarchy. Collectively, the integrated in planta bacterial omics approach provides molecular insights into multiple layers of bacterial gene regulation that contribute to bacterial growth in planta and elucidate the role of plant immunity in controlling pathogens.

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