Structural and functional annotation of small RNA sequences in non-model bacteria

Structural and functional annotation of small RNA sequences in non-model bacteria

Abstract

Although the bacterial transcription and consequent translation represent a tightly coupled process, small RNAs (sRNAs) are non-coding genomic elements that regulate the number of specific transcripts in the cell, primarily in response to changes in the environment. Non-model bacteria represent a renewable source of value-added chemicals, thus embodying the concept of white biotechnology. While the annotation of bacterial genomes, even in non-model bacteria, has moved forward, the annotation of non-coding elements is still lagging. This limits the process of fine-tuning the bacterial production of valuable bio-based chemicals and, hence, sustainable production. Main focus is on bacteria producing polyhydroxyalkanoates (PHA), microbial polyesters used for the production of bioplastics. The lack of annotated non-coding elements in bacterial genomes keeps us from understanding how bacteria adapt their metabolism in reaction to changing environments. Therefore, the main goal of this PhD project is to provide a computational solution of the insufficient knowledge about non-coding regulatory mechanisms in non-model bacteria. The information about non-coding regulatory elements will provide another piece to the puzzle of bacterial cell complexity and help us reveal the potential of bacteria for white biotechnology.

Although the bacterial transcription and consequent translation represent a tightly coupled process, small RNAs (sRNAs) are non-coding genomic elements that regulate the number of specific transcripts in the cell, primarily in response to changes in the environment. Non-model bacteria represent a renewable source of value-added chemicals, thus embodying the concept of white biotechnology. While the annotation of bacterial genomes, even in non-model bacteria, has moved forward, the annotation of non-coding elements is still lagging. This limits the process of fine-tuning the bacterial production of valuable bio-based chemicals and, hence, sustainable production. Main focus is on bacteria producing polyhydroxyalkanoates (PHA), microbial polyesters used for the production of bioplastics. The lack of annotated non-coding elements in bacterial genomes keeps us from understanding how bacteria adapt their metabolism in reaction to changing environments. Therefore, the main goal of this PhD project is to provide a computational solution of the insufficient knowledge about non-coding regulatory mechanisms in non-model bacteria. The information about non-coding regulatory elements will provide another piece to the puzzle of bacterial cell complexity and help us reveal the potential of bacteria for white biotechnology.

small RNA;non-model bacteria;polyhydroxyalkanoates;genomes

small RNA;non-model bacteria;polyhydroxyalkanoates;genomes

HEŘMÁNKOVÁ, K.; SEDLÁŘ, K.

28.03.2025

1st Czech PhD Bioinformatics Conference

Telč

https://bioinformatics.cuni.cz/phdconf2025/#schedule