Characterization of MazF-Mediated Sequence-Specific RNA Cleavage in Pseudomonas putida Using Massive Parallel Sequencing

PloS One
Tatsuki MiyamotoNaohiro Noda

Abstract

Under environmental stress, microbes are known to alter their translation patterns using sequence-specific endoribonucleases that we call RNA interferases. However, there has been limited insight regarding which RNAs are specifically cleaved by these RNA interferases, hence their physiological functions remain unknown. In the current study, we developed a novel method to effectively identify cleavage specificities with massive parallel sequencing. This approach uses artificially designed RNAs composed of diverse sequences, which do not form extensive secondary structures, and it correctly identified the cleavage sequence of a well-characterized Escherichia coli RNA interferase, MazF, as ACA. In addition, we also determined that an uncharacterized MazF homologue isolated from Pseudomonas putida specifically recognizes the unique triplet, UAC. Using a real-time fluorescence resonance energy transfer assay, the UAC triplet was further proved to be essential for cleavage in P. putida MazF. These results highlight an effective method to determine cleavage specificity of RNA interferases.

References

Jun 11, 1996·Proceedings of the National Academy of Sciences of the United States of America·E AizenmanG Glaser
Feb 27, 2001·Journal of Bacteriology·B SatH Engelberg-Kulka
Jun 6, 2003·Molecular Microbiology·Susanne K Christensen, Kenn Gerdes
Mar 17, 2004·The Journal of Biological Chemistry·Junjie ZhangMasayori Inouye
May 20, 2004·Journal of Bacteriology·Ronen HazanHanna Engelberg-Kulka
Jun 3, 2004·Genome Research·Gavin E CrooksSteven E Brenner
Nov 13, 2004·The Journal of Biological Chemistry·Yonglong ZhangMasayori Inouye
Feb 19, 2005·Nucleic Acids Research·Deo Prakash Pandey, Kenn Gerdes
May 20, 2005·The Journal of Biological Chemistry·Yonglong ZhangMasayori Inouye
Apr 14, 2006·The Journal of Biological Chemistry·Ling ZhuMasayori Inouye
Oct 6, 2006·Molecular Microbiology·Mikkel Christensen-Dalsgaard, Kenn Gerdes
Aug 21, 2007·Analytical Biochemistry·Nora R Wang, Paul J Hergenrother
Sep 27, 2007·Genes & Genetic Systems·Yuichi OtsukaTetsuro Yonesaki
Jan 7, 2009·The Journal of Biological Chemistry·Yonglong Zhang, Masayori Inouye
Jul 21, 2009·The Journal of Biological Chemistry·Yonglong ZhangMasayori Inouye
Aug 20, 2009·The Journal of Biological Chemistry·Yoshihiro YamaguchiMasayori Inouye
Dec 1, 2009·Molecular Microbiology·Mikkel Christensen-DalsgaardKenn Gerdes
Oct 12, 2010·Nucleic Acids Research·Yucheng ShaoZixin Deng
Oct 29, 2010·Genetics·Mitsunori KogaTetsuro Yonesaki
Jul 19, 2011·FEBS Letters·Jung-Ho ParkMasayori Inouye
Jul 27, 2011·Proceedings of the National Academy of Sciences of the United States of America·Etienne MaisonneuveKenn Gerdes
Sep 20, 2011·Nature Reviews. Microbiology·Yoshihiro Yamaguchi, Masayori Inouye
Jan 5, 2012·Nature Communications·Yoshihiro YamaguchiMasayori Inouye
Feb 22, 2012·Applied Microbiology and Biotechnology·Ignacio Poblete-CastroChristoph Wittmann
Feb 23, 2012·The Journal of Biological Chemistry·Jared D SharpNancy A Woychik
May 1, 2012·Journal of Bacteriology·Francesca P RothenbacherNancy A Woychik
Oct 30, 2012·Journal of Bacteriology·Christopher F SchusterRalph Bertram
Jan 8, 2013·FEMS Microbiology Letters·Christopher F Schuster, Ralph Bertram
May 8, 2013·Proceedings of the National Academy of Sciences of the United States of America·Jason M SchifanoNancy A Woychik
Oct 29, 2013·Journal of Bacteriology·Hedvig TammanRita Hõrak
Nov 23, 2013·Genome Biology and Evolution·Nikita ChopraSonika Bhatnagar
Jun 29, 2014·Biochemical and Biophysical Research Communications·Shashikala Verma, Rakesh Bhatnagar
Jul 6, 2014·Biochimica Et Biophysica Acta·H P J Buermans, J T den Dunnen
Jan 23, 2015·Nature Communications·Prabhakar TiwariRamandeep Singh
Apr 8, 2015·Proceedings of the National Academy of Sciences of the United States of America·Elsa GermainEtienne Maisonneuve
Jul 15, 2015·Nature Communications·Jonathan W CruzNancy A Woychik

❮ Previous
Next ❯

Citations

Nov 15, 2016·RNA Biology·Jason M Schifano, Nancy A Woychik
Jul 5, 2017·MicrobiologyOpen·Tatsuki MiyamotoNaohiro Noda
Nov 28, 2019·International Journal of Molecular Sciences·Rawana N AlkhaliliBjörn Canbäck
May 5, 2020·Frontiers in Genetics·Dukas Jurėnas, Laurence Van Melderen
Oct 24, 2018·Frontiers in Microbiology·Tatsuki MiyamotoNaohiro Noda
Aug 25, 2021·Microbial Biotechnology·Patrícia ApuraCecília M Arraiano
Mar 21, 2019·Journal of Molecular Microbiology and Biotechnology·Mao ShakuYoshihiro Yamaguchi

❮ Previous
Next ❯

Methods Mentioned

BETA
electrophoresis
RNA-seq
PCR
Protein Assay
in vitro transcription
RNA Assay
environmental stresses

Software Mentioned

SOLiD
MORE
WebLogo

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.