Ribonuclease E is a 5′-end-dependent endonuclease

Nature ◽  
10.1038/27246 ◽  
1998 ◽  
Vol 395 (6703) ◽  
pp. 720-724 ◽  
Author(s):  
George A. Mackie
Keyword(s):  
Ribonuclease E ◽  
Dependent Endonuclease

Assay Method for Femtogram Order of Ca2+,Mg2+-Dependent Endonuclease

1997 ◽  
Vol 247 (2) ◽  
pp. 428-433 ◽  
Author(s):  
Koichiro Yoshihara ◽  
Ichiro Ohta ◽  
Yasuharu Tanaka ◽  
Hiroto Fujita ◽  
Takeshi Ide ◽  
...  
Keyword(s):  
Assay Method ◽  
Dependent Endonuclease

scholarly journals Pseudomonas putida MPE, a manganese-dependent endonuclease of the binuclear metallophosphoesterase superfamily, incises single-strand DNA in two orientations to yield a mixture of 3′-PO4 and 3′-OH termini

2020 ◽  
Author(s):  
Shreya Ghosh ◽  
Anam Ejaz ◽  
Lucas Repeta ◽  
Stewart Shuman
Keyword(s):  
Pseudomonas Putida ◽  
Bound Water ◽  
Acid Catalyst ◽  
Nuclease Activity ◽  
Single Strand ◽  
Dna Endonuclease ◽  
Dependent Endonuclease ◽  
Leaving Group ◽  
Phosphodiester Hydrolysis ◽  
Hydrolysis Of

Abstract Pseudomonas putida MPE exemplifies a novel clade of manganese-dependent single-strand DNA endonuclease within the binuclear metallophosphoesterase superfamily. MPE is encoded within a widely conserved DNA repair operon. Via structure-guided mutagenesis, we identify His113 and His81 as essential for DNA nuclease activity, albeit inessential for hydrolysis of bis-p-nitrophenylphosphate. We propose that His113 contacts the scissile phosphodiester and serves as a general acid catalyst to expel the OH leaving group of the product strand. We find that MPE cleaves the 3′ and 5′ single-strands of tailed duplex DNAs and that MPE can sense and incise duplexes at sites of short mismatch bulges and opposite a nick. We show that MPE is an ambidextrous phosphodiesterase capable of hydrolyzing the ssDNA backbone in either orientation to generate a mixture of 3′-OH and 3′-PO4 cleavage products. The directionality of phosphodiester hydrolysis is dictated by the orientation of the water nucleophile vis-à-vis the OH leaving group, which must be near apical for the reaction to proceed. We propose that the MPE active site and metal-bound water nucleophile are invariant and the enzyme can bind the ssDNA productively in opposite orientations.

scholarly journals Maturation of UTR-Derived sRNAs Is Modulated during Adaptation to Different Growth Conditions

2021 ◽  
Vol 22 (22) ◽  
pp. 12260
Author(s):  
Daniel-Timon Spanka ◽  
Gabriele Klug
Keyword(s):  
Growth Conditions ◽  
Global Scale ◽  
Rnase E ◽  
Bacterial Gene ◽  
Ribonuclease E ◽  
Mrna Targets ◽  
Small Regulatory Rnas ◽  
The Stability ◽  
Ngs Data

Small regulatory RNAs play a major role in bacterial gene regulation by binding their target mRNAs, which mostly influences the stability or translation of the target. Expression levels of sRNAs are often regulated by their own promoters, but recent reports have highlighted the presence and importance of sRNAs that are derived from mRNA 3′ untranslated regions (UTRs). In this study, we investigated the maturation of 5′ and 3′ UTR-derived sRNAs on a global scale in the facultative phototrophic alphaproteobacterium Rhodobacter sphaeroides. Including some already known UTR-derived sRNAs like UpsM or CcsR1-4, 14 sRNAs are predicted to be located in 5′ UTRs and 16 in 3′ UTRs. The involvement of different ribonucleases during maturation was predicted by a differential RNA 5′/3′ end analysis based on RNA next generation sequencing (NGS) data from the respective deletion strains. The results were validated in vivo and underline the importance of polynucleotide phosphorylase (PNPase) and ribonuclease E (RNase E) during processing and maturation. The abundances of some UTR-derived sRNAs changed when cultures were exposed to external stress conditions, such as oxidative stress and also during different growth phases. Promoter fusions revealed that this effect cannot be solely attributed to an altered transcription rate. Moreover, the RNase E dependent cleavage of several UTR-derived sRNAs varied significantly during the early stationary phase and under iron depletion conditions. We conclude that an alteration of ribonucleolytic processing influences the levels of UTR-derived sRNAs, and may thus indirectly affect their mRNA targets.

Potential activity of Ca2+/Mg2+-dependent endonuclease in endometrial hyperplasia and cancer

1999 ◽  
Vol 127 (6) ◽  
pp. 624-627
Author(s):  
E. A. Kolobova ◽  
A. V. Zhdanov ◽  
D. A. Varlamov ◽  
M. M. Dement'eva ◽  
G. E. Chernukha ◽  
...  
Keyword(s):  
Endometrial Hyperplasia ◽  
Dependent Endonuclease ◽  
Potential Activity

scholarly journals Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome

1998 ◽  
Vol 12 (17) ◽  
pp. 2770-2781 ◽  
Author(s):  
N. F. Vanzo ◽  
Y. S. Li ◽  
B. Py ◽  
E. Blum ◽  
C. F. Higgins ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Protein Interactions ◽  
Ribonuclease E ◽  
Rna Degradosome

Structural and functional studies of SAV1707 from Staphylococcus aureus elucidate its distinct metal-dependent activity and a crucial residue for catalysis

2021 ◽  
Vol 77 (5) ◽  
pp. 587-598
Author(s):  
Dong-Gyun Kim ◽  
Kyu-Yeon Lee ◽  
Sang Jae Lee ◽  
Seung-Ho Cheon ◽  
Yuri Choi ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Metal Binding ◽  
Binding Mode ◽  
Structure And Function ◽  
Functional Study ◽  
Functional Studies ◽  
Dependent Endonuclease ◽  
Metal Selectivity ◽  
Metal Binding Domain ◽  
And Function

The metallo-β-lactamase fold is the most abundant metal-binding domain found in two major kingdoms: bacteria and archaea. Despite the rapid growth in genomic information, most of these enzymes, which may play critical roles in cellular metabolism, remain uncharacterized in terms of structure and function. In this study, X-ray crystal structures of SAV1707, a hypothetical metalloenzyme from Staphylococcus aureus, and its complex with cAMP are reported at high resolutions of 2.05 and 1.55 Å, respectively, with a detailed atomic description. Through a functional study, it was verified that SAV1707 has Ni2+-dependent phosphodiesterase activity and Mn2+-dependent endonuclease activity, revealing a different metal selectivity depending on the reaction. In addition, the crystal structure of cAMP-bound SAV1707 shows a unique snapshot of cAMP that reveals the binding mode of the intermediate, and a key residue Phe511 that forms π–π interactions with cAMP was verified as contributing to substrate recognition by functional studies of its mutant. Overall, these findings characterized the relationship between the structure and function of SAV1707 and may provide further understanding of metalloenzymes possessing the metallo-β-lactamase fold.

Heterogeneous nuclear RNA promotes synthesis of (2',5')oligoadenylate and is cleaved by the (2',5')oligoadenylate-activated endoribonuclease

1982 ◽  
Vol 2 (2) ◽  
pp. 154-160
Author(s):  
T W Nilsen ◽  
P A Maroney ◽  
H D Robertson ◽  
C Baglioni
Keyword(s):  
Ethidium Bromide ◽  
Hela Cells ◽  
Competitive Inhibition ◽  
Double Stranded Rna ◽  
Processing Enzymes ◽  
Dependent Endonuclease ◽  
Nuclear Rna ◽  
Recognition Elements

Heterogeneous nuclear RNA contains double-stranded regions that are not found in mRNA and that may serve as recognition elements for processing enzymes. The double-stranded regions of heterogeneous nuclear RNA prepared from HeLa cells promoted the synthesis of (2',5')oligoadenylate [(2',5')oligo(A) or (2'5')An] when incubated with (2',5')An polymerase. This enzyme is present in elevated levels in interferon-treated cells, and labeled heterogeneous nuclear RNA incubated with extracts of these cells is preferentially cleaved, since mRNA included in the same incubations is not appreciably degraded. The cleavage of heterogenous nuclear RNA is caused by the synthesis of (2'5')An and by a "localized" activation of the (2',5')An-dependent endonuclease, since it was enhanced by ATP, the substrate of the (2',5')An polymerase, and inhibited by 2'-dATP and ethidium bromide. Both of these compounds suppress the synthesis of (2',5')An, the first by competitive inhibition and the latter by intercalating into double-stranded RNA. The possible role of double-stranded regions and of the (2',5')An polymerase-endonuclease system in the processing of heterogeneous nuclear RNA is discussed.

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