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The role of the sequence and structure of mRNAs and anti-sRNAs in their interactions with bacterial noncoding RNAs

Daria Sobańska

Abstract

In the presented PhD dissertation, the role of sequence and structure of mRNAs, and anti-sRNA for their interactions sRNAs was elucidated. So far, the significance of the evolutionally conserved mRNA sequences located in the neighborhood to the sRNA binding sites was not resolved. Little is known about the mode of Hfq action in sRNA interactions with anti-sRNAs. To determine the first issue, S. enterica RybB sRNA interactions with complementary mRNAs containing different nucleotides located 3ʹ to the RybB binding sites were analyzed. To aim the second part of the study, E. coli class I and II sRNA interactions with complementary anti-sRNA and mRNA molecules were compared. The results showed that thermodynamic stability, and the rate of RybB-mRNA complex association were increased, and RybB-dependent ompC mRNA translation repression was more efficient, when purine residues were located 3ʹ to the RybB binding sites in mRNA. It was proposed that the evolutionary preference for purine residues in the mRNA sequences close to the sRNA binding sites enables efficient interactions of those RNAs, which leads to effective mRNA translation repression. Studies concerning second part indicated that RNA binding sites in anti-sRNAs and sRNAs are located in the regions with structure available for binding. sRNA and anti-sRNA molecules specifically interact with Hfq protein. Moreover, it was determined that Hfq-dependent sRNA binding with anti-sRNAs and mRNAs shows similar mechanism, which can be explained by the resemblance of sequences recognized by sRNAs and Hfq in mRNAs and anti-sRNAs.
Record ID
UAM1cbf995a924a40e29fd208999f630f08
Diploma type
Doctor of Philosophy
Author
Daria Sobańska (SNP/WB/FoB) Daria Sobańska,,
Title in Polish
Znaczenie sekwencji i struktury mRNA i anty-sRNA w ich odziaływaniach z niekodującymi RNA bakterii
Title in English
The role of the sequence and structure of mRNAs and anti-sRNAs in their interactions with bacterial noncoding RNAs
Language
pl Polish
Certifying Unit
Faculty of Biology (SNP/WB/FoB)
Discipline
biochemistry / (biological sciences domain) / (biological sciences)
Scientific discipline (2.0)
6.4 biological sciences
Defense Date
16-04-2018
End date
16-04-2018
Supervisor
URL
http://hdl.handle.net/10593/22728 opening in a new tab
Keywords in English
bacterial sRNAs anti-sRNAs
Abstract in English
In the presented PhD dissertation, the role of sequence and structure of mRNAs, and anti-sRNA for their interactions sRNAs was elucidated. So far, the significance of the evolutionally conserved mRNA sequences located in the neighborhood to the sRNA binding sites was not resolved. Little is known about the mode of Hfq action in sRNA interactions with anti-sRNAs. To determine the first issue, S. enterica RybB sRNA interactions with complementary mRNAs containing different nucleotides located 3ʹ to the RybB binding sites were analyzed. To aim the second part of the study, E. coli class I and II sRNA interactions with complementary anti-sRNA and mRNA molecules were compared. The results showed that thermodynamic stability, and the rate of RybB-mRNA complex association were increased, and RybB-dependent ompC mRNA translation repression was more efficient, when purine residues were located 3ʹ to the RybB binding sites in mRNA. It was proposed that the evolutionary preference for purine residues in the mRNA sequences close to the sRNA binding sites enables efficient interactions of those RNAs, which leads to effective mRNA translation repression. Studies concerning second part indicated that RNA binding sites in anti-sRNAs and sRNAs are located in the regions with structure available for binding. sRNA and anti-sRNA molecules specifically interact with Hfq protein. Moreover, it was determined that Hfq-dependent sRNA binding with anti-sRNAs and mRNAs shows similar mechanism, which can be explained by the resemblance of sequences recognized by sRNAs and Hfq in mRNAs and anti-sRNAs.
Thesis file

Uniform Resource Identifier
https://researchportal.amu.edu.pl/info/phd/UAM1cbf995a924a40e29fd208999f630f08/

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