scholarly journals Sequence-dependent Cleavage Site Selection by RNase Z from the CyanobacteriumSynechocystissp. PCC 6803

2005 ◽  
Vol 280 (39) ◽  
pp. 33461-33469 ◽  
Author(s):  
María Ceballos-Chávez ◽  
Agustín Vioque
Keyword(s):  
Site Selection ◽  
Cleavage Site ◽  
Sequence Dependent ◽  
Rnase Z ◽  
Pcc 6803

Recombinant RNase Z Does Not Recognize CCA as Part of the tRNA and Its Cleavage Efficieny Is Influenced by Acceptor Stem Length

2003 ◽  
Vol 384 (3) ◽  
pp. 333-342 ◽  
Author(s):  
S. Schiffer ◽  
S. Rösch ◽  
A. Marchfelder
Keyword(s):  
Site Selection ◽  
Cleavage Site ◽  
Stem Length ◽  
Wild Type ◽  
Base Pairs ◽  
Acceptor Stem ◽  
Recombinant Plant ◽  
Nucleotidyl Transferase ◽  
Rnase Z

Abstract One of the essential maturation steps to yield functional tRNA molecules is the removal of 3'-trailer sequences by RNase Z. After RNase Z cleavage the tRNA nucleotidyl transferase adds the CCA sequence to the tRNA 3terminus, thereby generating the mature tRNA. Here we investigated whether a terminal CCA triplet as 3'-trailer or embedded in a longer 3'- trailer influences cleavage site selection by RNase Z using three activities: a recombinant plant RNase Z, a recombinant archaeal RNase Z and an RNase Z active wheat extract. A trailer of only the CCA trinucleotide is left intact by the wheat extract RNase Z but is removed by the recombinant plant and archaeal enzymes. Thus the CCA triplet is not recognized by the RNase Z enzyme itself, but rather requires cofactors still present in the extract. In addition, we investigated the influence of acceptor stem length on cleavage by RNase Z using variants of wildtype tRNATyr. While the wild type and the variant with 8 base pairs in the acceptor stem were processed efficiently by all three activities, variants with shorter and longer acceptor stems were poor substrates or were not cleaved at all.

scholarly journals DNA translocation blockage, a general mechanism of cleavage site selection by type I restriction enzymes

1999 ◽  
Vol 18 (9) ◽  
pp. 2638-2647 ◽  
Author(s):  
Pavel Janscak ◽  
Maria P. MacWilliams ◽  
Ursula Sandmeier ◽  
Valakunja Nagaraja ◽  
Thomas A. Bickle
Keyword(s):  
Site Selection ◽  
Cleavage Site ◽  
Restriction Enzymes ◽  
General Mechanism ◽  
Type I ◽  
Dna Translocation

scholarly journals DNA cleavage site selection by Type III restriction enzymes provides evidence for head-on protein collisions following 1D bidirectional motion

2011 ◽  
Vol 39 (18) ◽  
pp. 8042-8051 ◽  
Author(s):  
Friedrich W. Schwarz ◽  
Kara van Aelst ◽  
Júlia Tóth ◽  
Ralf Seidel ◽  
Mark D. Szczelkun
Keyword(s):  
Site Selection ◽  
Dna Cleavage ◽  
Cleavage Site ◽  
Restriction Enzymes ◽  
Type Iii

scholarly journals Cleavage of model substrates by archaeal RNase P: role of protein cofactors in cleavage-site selection

2010 ◽  
Vol 39 (3) ◽  
pp. 1105-1116 ◽  
Author(s):  
Sylvie Sinapah ◽  
Shiying Wu ◽  
Yu Chen ◽  
B. M. Fredrik Pettersson ◽  
Venkat Gopalan ◽  
...  
Keyword(s):  
Site Selection ◽  
Cleavage Site ◽  
Rnase P

scholarly journals Substrate-Dependent Cleavage Site Selection by Unconventional Radical S-Adenosylmethionine Enzymes in Diphthamide Biosynthesis

2017 ◽  
Vol 139 (16) ◽  
pp. 5680-5683 ◽  
Author(s):  
Min Dong ◽  
Masaki Horitani ◽  
Boris Dzikovski ◽  
Jack H. Freed ◽  
Steven E. Ealick ◽  
...  
Keyword(s):  
Site Selection ◽  
Cleavage Site

scholarly journals A Sequence Element Downstream of the Yeast HTB1 Gene Contributes to mRNA 3′ Processing and Cell Cycle Regulation

2002 ◽  
Vol 22 (24) ◽  
pp. 8415-8425 ◽  
Author(s):  
Susan G. Campbell ◽  
Marcel li del Olmo ◽  
Paul Beglan ◽  
Ursula Bond
Keyword(s):  
Cell Cycle ◽  
Site Selection ◽  
Cleavage Site ◽  
Cell Cycle Regulation ◽  
Binding Activity ◽  
S Phase ◽  
Sequence Element ◽  
Reading Frame ◽  
Protein Factor ◽  
Cycle Regulation

ABSTRACT Histone mRNAs accumulate in the S phase and are rapidly degraded as cells progress into the G2 phase of the cell cycle. In Saccharomyces cerevisiae, fusion of the 3′ untranslated region and downstream sequences of the yeast histone gene HTB1 to a neomycin phosphotransferase open reading frame is sufficient to confer cell cycle regulation on the resulting chimera gene (neo-HTB1). We have identified a sequence element, designated the distal downstream element (DDE), that influences both the 3′-end cleavage site selection and the cell cycle regulation of the neo-HTB1 mRNA. Mutations in the DDE, which is located approximately 110 nucleotides downstream of the HTB1 gene, lead to a delay in the accumulation of the neo-HTB1 mRNA in the S phase and a lack of mRNA turnover in the G2 phase. The DDE is transcribed as part of the primary transcript and binds a protein factor(s). Maximum binding is observed in the S phase of the cell cycle, and mutations that affect the turnover of the HTB1 mRNA alter the binding activity. While located in the same general region, mutations that affect 3′-end cleavage site selection act independently from those that alter the cell cycle regulation.

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