Comparative systems biological analysis of the potential of a high-performance expression platform – Bacillus pumilus

by Stefani Díaz Valerio
Doctoral thesis
Date of Examination:2023-03-28
Date of issue:2023-06-29
Advisor:Dr. Heiko Liesegang
Referee:Dr. Heiko Liesegang
Referee:Prof. Dr. Jan de Vries
Referee:Prof. Dr. Rolf Daniel
Referee:Prof. Dr. Jörg Stülke
Referee:PD Dr. Michael Hoppert
Referee:Prof. Dr. Kai Heimel
Persistent Address: http://dx.doi.org/10.53846/goediss-9957

 

 

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Abstract

English

This project was supported by the German Federal Ministry of Education and Research (BMBF) with the grant ID: Fkz.031B057 under the Industrial Biotechnology Innovation Initiative. The particular program corresponds to the Bioeconomy Initiative (UfiB, for "Umsetzungsfördernde Maßnahme in der Initiative Bioökonomie") and aims to investigate and establish more sustainable (waste-avoiding, energy, and resource saving) production strategies to replace conventional methods in the manufacturing industry. The framework includes strategic alliances between universities and industrial companies. The present work is part of the base-ground studies required to assess the biotechnological potential of a promising expression platform, B. pumilus. This comparative systems biology approach allows to better understand what makes this organism unique regarding other well characterized and established productions hosts, like B. subtilis and B. licheniformis. Given the close relatedness of these Bacillus, it has been suggested that differences in productive performance lay in regulatory elements, such as small non-coding RNAs. Therefore, comparative transcriptomics was proposed as the approach to identify and characterize potential regulators. The final section of this project explores state of the art bioinformatic methods for RNA-seq studies. Special attention is given to detection of small regulatory RNAs and expression profiles of B. pumilus and B. licheniformis during fermentation conditions within small-scale bioreactors. By this approach, the bacterial behavior in conditions closer to industrial production is revealed. Moreover, it allows the direct comparative transcriptomic analysis between these two species. Species-specific differences in regulation and transcription of genomic features are discussed. The insights generated are relevant for selection, development, and optimization of Bacillus species as microbial cell factories. These findings not only promise to increase the understanding of Bacillus biology, but also to aid in the rational optimization of Bacillus as industrial production hosts.
Keywords: Bacillus; RNA-seq; trancriptomics; fermentation; comparative genomics; B. pumilus; sRNA
 
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