Faculty Opinions recommendation of Conserved functions of the trigger loop and Gre factors in RNA cleavage by bacterial RNA polymerases.

Author(s):  
Katsuhiko Murakami
2017 ◽  
Vol 292 (16) ◽  
pp. 6744-6752 ◽  
Author(s):  
Nataliya Miropolskaya ◽  
Daria Esyunina ◽  
Andrey Kulbachinskiy

2016 ◽  
Vol 44 (3) ◽  
pp. 1298-1308 ◽  
Author(s):  
Daria Esyunina ◽  
Matti Turtola ◽  
Danil Pupov ◽  
Irina Bass ◽  
Saulius Klimašauskas ◽  
...  

2019 ◽  
Vol 47 (19) ◽  
pp. 10296-10312 ◽  
Author(s):  
Ranjit K Prajapati ◽  
Petja Rosenqvist ◽  
Kaisa Palmu ◽  
Janne J Mäkinen ◽  
Anssi M Malinen ◽  
...  

Abstract Oxazinomycin is a C-nucleoside antibiotic that is produced by Streptomyces hygroscopicus and closely resembles uridine. Here, we show that the oxazinomycin triphosphate is a good substrate for bacterial and eukaryotic RNA polymerases (RNAPs) and that a single incorporated oxazinomycin is rapidly extended by the next nucleotide. However, the incorporation of several successive oxazinomycins or a single oxazinomycin in a certain sequence context arrested a fraction of the transcribing RNAP. The addition of Gre RNA cleavage factors eliminated the transcriptional arrest at a single oxazinomycin and shortened the nascent RNAs arrested at the polythymidine sequences suggesting that the transcriptional arrest was caused by backtracking of RNAP along the DNA template. We further demonstrate that the ubiquitous C-nucleoside pseudouridine is also a good substrate for RNA polymerases in a triphosphorylated form but does not inhibit transcription of the polythymidine sequences. Our results collectively suggest that oxazinomycin functions as a Trojan horse substrate and its inhibitory effect is attributable to the oxygen atom in the position corresponding to carbon five of the uracil ring.


2008 ◽  
Vol 7 (10) ◽  
pp. 40 ◽  
Author(s):  
Lin Tan ◽  
Simone Wiesler ◽  
Dominika Trzaska ◽  
Hannah C Carney ◽  
Robert OJ Weinzierl
Keyword(s):  

Author(s):  
John Harbottle ◽  
Hamed Mosaei ◽  
Nicholas Allenby ◽  
Nikolay Zenkin

Rifamycins, such as rifampicin, are potent inhibitors of bacterial RNA polymerases and widely used antibiotics. Usually rifamycin-resistance is associated with mutations in RNAP that preclude rifamycins binding. However, some bacteria have ADP-ribosyl transferases Arr that ADP-ribosylate rifamycin molecules, thus inactivating their antimicrobial activity. Here we directly show that ADP-ribosylation abolishes inhibition of transcription by rifampicin, the most widely used rifamycin antibiotic. We also show that natural rifamycin, Kanglemycin A, which has a unique sugar moiety at the ansa-chain close to the Arr-modification site, does not bind to Arr from M. smegmatis , and thus is not susceptible to inactivation. We, however, found that Kanglemycin A can still be ADP-ribosylated by Arr of an emerging pathogen M. abscessus . Interestingly, the only part of Arr which exhibits no homology between the species is the part that sterically clashes with sugar moiety of Kanglemycin A in M. smegmatis Arr. This suggests that M. abscessus has encountered KglA or rifamycin with similar sugar modification in the course of evolution. The results show that KglA could be effective antimicrobial against some of the Arr encoding bacteria.


2016 ◽  
Vol 44 (7) ◽  
pp. 3000-3012 ◽  
Author(s):  
Veronika Raindlová ◽  
Martina Janoušková ◽  
Michaela Slavíčková ◽  
Pavla Perlíková ◽  
Soňa Boháčová ◽  
...  

1979 ◽  
Vol 13 (1) ◽  
pp. 59-97 ◽  
Author(s):  
T Yura ◽  
A Ishihama

2016 ◽  
Vol 113 (11) ◽  
pp. 2946-2951 ◽  
Author(s):  
Ana Lisica ◽  
Christoph Engel ◽  
Marcus Jahnel ◽  
Édgar Roldán ◽  
Eric A. Galburt ◽  
...  

During DNA transcription, RNA polymerases often adopt inactive backtracked states. Recovery from backtracks can occur by 1D diffusion or cleavage of backtracked RNA, but how polymerases make this choice is unknown. Here, we use single-molecule optical tweezers experiments and stochastic theory to show that the choice of a backtrack recovery mechanism is determined by a kinetic competition between 1D diffusion and RNA cleavage. Notably, RNA polymerase I (Pol I) and Pol II recover from shallow backtracks by 1D diffusion, use RNA cleavage to recover from intermediary depths, and are unable to recover from extensive backtracks. Furthermore, Pol I and Pol II use distinct mechanisms to avoid nonrecoverable backtracking. Pol I is protected by its subunit A12.2, which decreases the rate of 1D diffusion and enables transcript cleavage up to 20 nt. In contrast, Pol II is fully protected through association with the cleavage stimulatory factor TFIIS, which enables rapid recovery from any depth by RNA cleavage. Taken together, we identify distinct backtrack recovery strategies of Pol I and Pol II, shedding light on the evolution of cellular functions of these key enzymes.


2019 ◽  
Vol 47 (2) ◽  
pp. 679-689 ◽  
Author(s):  
Amber Riaz-Bradley

Abstract Transcription in cyanobacteria involves several fascinating features. Cyanobacteria comprise one of the very few groups in which no proofreading factors (Gre homologues) have been identified. Gre factors increase the efficiency of RNA cleavage, therefore helping to maintain the fidelity of the RNA transcript and assist in the resolution of stalled RNAPs to prevent genome damage. The vast majority of bacterial species encode at least one of these highly conserved factors and so their absence in cyanobacteria is intriguing. Additionally, the largest subunit of bacterial RNAP has undergone a split in cyanobacteria to form two subunits and the SI3 insertion within the integral trigger loop element is roughly 3.5 times larger than in Escherichia coli. The Rho termination factor also appears to be absent, leaving cyanobacteria to rely solely on an intrinsic termination mechanism. Furthermore, cyanobacteria must be able to respond to environment signals such as light intensity and tightly synchronise gene expression and other cell activities to a circadian rhythm.


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