scholarly journals Cyclases of the 3'-terminal phosphate in RNA: a new family of RNA processing enzymes conserved in eucarya, bacteria and archaea.

1998 ◽  
Vol 45 (4) ◽  
pp. 895-906 ◽  
Author(s):  
W Filipowicz ◽  
E Billy ◽  
K Drabikowski ◽  
P Genschik
Keyword(s):  
Escherichia Coli ◽  
Rna Processing ◽  
Rna Cleavage ◽  
Biological Functions ◽  
Rna Molecules ◽  
Cyclic Groups ◽  
Processing Enzymes ◽  
New Family ◽  
Genes Encoding ◽  
Cyclic Phosphate

The 2',3'-cyclic phosphate termini are produced, as either intermediates or final products, during RNA cleavage by many different endoribonucleases. Likewise, ribozymes such as hammerheads, hairpins, or the hepatitis delta ribozyme, generate 2',3'-cyclic phosphate ends. Discovery of the RNA 3'-terminal phosphate cyclase has indicated that cyclic phosphate termini in RNA can also be produced by an entirely different mechanism. The RNA 3'-phosphate cyclase converts the 3'-terminal phosphate in RNA into the 2',3'-cyclic phosphodiester in the ATP-dependent reaction which involves formation of the covalent cyclase-AMP and the RNA-N3' pp5' A intermediates. The findings that several eukaryotic and prokaryotic RNA ligases require the 2',3'-cyclic phosphate for the ligation of RNA molecules raised a possibility that the RNA 3'-phosphate cyclase may have an anabolic function in RNA metabolism by generating terminal cyclic groups required for ligation. Recent cloning of a cDNA encoding the human cyclase indicated that genes encoding cyclase-like proteins are conserved among Eucarya, Bacteria, and Archaea. The protein encoded by the Escherichia coli gene was overexpressed and shown to have the RNA 3'-phosphate cyclase activity. This article reviews properties of the human and bacterial cyclases, their mechanism of action and substrate specificity. Possible biological functions of the enzymes are also discussed.

scholarly journals RNA 3’-terminal phosphate cyclases and cyclase-like proteins

2016 ◽  
Vol 62 (3) ◽  
pp. 327-334
Author(s):  
Witold Filipowicz
Keyword(s):  
Rna Cleavage ◽  
Rna Molecules ◽  
Metabolic Reactions ◽  
Cyclic Phosphate ◽  
Cleavage Reactions

RNA molecules bearing terminal 2’,3’-cyclic phosphate are quite common in nature. For example, 2’,3’-cyclic phosphate termini are produced during RNA cleavage by many en-doribonucleases either as intermediates or final products. Many RNA-based nucleases (ribo-zymes) also generate cyclic phosphate termini. However, cleavage reactions are not the only way in which RNAs bearing cyclic phosphate ends are produced. They can also be generated by RNA 3’-terminal phosphate cyclases (RtcA), a family of enzymes conserved in eukaryotes, bacteria, and archaea. These enzymes catalyze the ATP-dependent conversion of the 3’-phos-phate to a 2’,3’-cyclic phosphodiester at the end of RNA. In this article, I review knowledge about the biochemistry and structure of RNA 3’-phosphate cyclases and also proteins of the RNA cyclase-like (Rcl1) family, and discuss their documented or possible roles in different RNA metabolic reactions.

scholarly journals Molecular Epidemiology of NDM-1-Producing Enterobacteriaceae and Acinetobacter baumannii Isolates from Pakistan

2014 ◽  
Vol 58 (9) ◽  
pp. 5589-5593 ◽  
Author(s):  
Anna L. Sartor ◽  
Muhammad W. Raza ◽  
Shahid A. Abbasi ◽  
Kathryn M. Day ◽  
John D. Perry ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Molecular Epidemiology ◽  
Genetic Relatedness ◽  
Antibiotic Resistance Genes ◽  
Enterobacter Cloacae ◽  
Content Type ◽  
Plasmid Replicon ◽  
Genes Encoding ◽  
Clonal Spread ◽  
Encoding Genes

ABSTRACTThe molecular epidemiology of 66 NDM-producing isolates from 2 Pakistani hospitals was investigated, with their genetic relatedness determined using repetitive sequence-based PCR (Rep-PCR). PCR-based replicon typing and screening for antibiotic resistance genes encoding carbapenemases, other β-lactamases, and 16S methylases were also performed. Rep-PCR suggested a clonal spread ofEnterobacter cloacaeandEscherichia coli. A number of plasmid replicon types were identified, with the incompatibility A/C group (IncA/C) being the most common (78%). 16S methylase-encoding genes were coharbored in 81% of NDM-producingEnterobacteriaceae.

scholarly journals Shiga Toxins, and the Genes Encoding Them, in Fecal Samples from Native Idaho Ungulates

2008 ◽  
Vol 75 (3) ◽  
pp. 862-865 ◽  
Author(s):  
Jeremy J. Gilbreath ◽  
Malcolm S. Shields ◽  
Rebekah L. Smith ◽  
Larry D. Farrell ◽  
Peter P. Sheridan ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Shiga Toxin ◽  
Wild Ungulates ◽  
Fecal Samples ◽  
Shiga Toxins ◽  
Toxin Genes ◽  
Genes Encoding ◽  
Shiga Toxin Genes

ABSTRACT Cattle are a known reservoir of Shiga toxin-producing Escherichia coli. The prevalence and stability of Shiga toxin and/or Shiga toxin genes among native wild ungulates in Idaho were investigated. The frequency of both Shiga genes and toxin was similar to that reported for Idaho cattle (∼19%).

scholarly journals Insights into functional and evolutionary analysis of carbaryl metabolic pathway from Pseudomonas sp. strain C5pp

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Vikas D. Trivedi ◽  
Pramod Kumar Jangir ◽  
Rakesh Sharma ◽  
Prashant S. Phale
Keyword(s):  
Draft Genome ◽  
Degradation Pathway ◽  
Evolutionary Analysis ◽  
Extradiol Dioxygenase ◽  
Transfer Event ◽  
New Family ◽  
New Genes ◽  
Catabolic Genes ◽  
Soil Isolate ◽  
Genes Encoding

Abstract Carbaryl (1-naphthyl N-methylcarbamate) is a most widely used carbamate pesticide in the agriculture field. Soil isolate, Pseudomonas sp. strain C5pp mineralizes carbaryl via 1-naphthol, salicylate and gentisate, however the genetic organization and evolutionary events of acquisition and assembly of pathway have not yet been studied. The draft genome analysis of strain C5pp reveals that the carbaryl catabolic genes are organized into three putative operons, ‘upper’, ‘middle’ and ‘lower’. The sequence and functional analysis led to identification of new genes encoding: i) hitherto unidentified 1-naphthol 2-hydroxylase, sharing a common ancestry with 2,4-dichlorophenol monooxygenase; ii) carbaryl hydrolase, a member of a new family of esterase; and iii) 1,2-dihydroxy naphthalene dioxygenase, uncharacterized type-II extradiol dioxygenase. The ‘upper’ pathway genes were present as a part of a integron while the ‘middle’ and ‘lower’ pathway genes were present as two distinct class-I composite transposons. These findings suggest the role of horizontal gene transfer event(s) in the acquisition and evolution of the carbaryl degradation pathway in strain C5pp. The study presents an example of assembly of degradation pathway for carbaryl.

Characteristics of Shiga Toxin–Producing Escherichia coli Isolated from Swiss Raw Milk Cheese within a 3-Year Monitoring Program

2010 ◽  
Vol 73 (1) ◽  
pp. 88-91 ◽  
Author(s):  
C. ZWEIFEL ◽  
N. GIEZENDANNER ◽  
S. CORTI ◽  
G. KRAUSE ◽  
L. BEUTIN ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Shiga Toxin ◽  
Monitoring Program ◽  
Raw Milk ◽  
Health Impact ◽  
Toxin Gene ◽  
Genes Encoding ◽  
Raw Milk Cheese ◽  
Human Infections ◽  
Hard Cheese

Food is an important vehicle for transmission of Shiga toxin–producing Escherichia coli (STEC). To assess the potential public health impact of STEC in Swiss raw milk cheese produced from cow's, goat's, and ewe's milk, 1,422 samples from semihard or hard cheese and 80 samples from soft cheese were examined for STEC, and isolated strains were further characterized. By PCR, STEC was detected after enrichment in 5.7% of the 1,502 raw milk cheese samples collected at the producer level. STEC-positive samples comprised 76 semihard, 8 soft, and 1 hard cheese. By colony hybridization, 29 STEC strains were isolated from 24 semihard and 5 soft cheeses. Thirteen of the 24 strains typeable with O antisera belonged to the serogroups O2, O22, and O91. More than half (58.6%) of the 29 strains belonged to O:H serotypes previously isolated from humans, and STEC O22:H8, O91:H10, O91:H21, and O174:H21 have also been identified as agents of hemolytic uremic syndrome. Typing of Shiga toxin genes showed that stx1 was only found in 2 strains, whereas 27 strains carried genes encoding for the Stx2 group, mainly stx2 and stx2vh-a/b. Production of Stx2 and Stx2vh-a/b subtypes might be an indicator for a severe outcome in patients. Nine strains harbored hlyA (enterohemorrhagic E. coli hemolysin), whereas none tested positive for eae (intimin). Consequently, semihard and hard raw milk cheese may be a potential source of STEC, and a notable proportion of the isolated non-O157 STEC strains belonged to serotypes or harbored Shiga toxin gene variants associated with human infections.

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