ITQB: CGE - PhD Theses
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- Unraveling the role of the RNA chaperone Hfq in the human pathogen Listeria monocytogenes: Regulation of oxidative stress responsePublication . Seixas, André Filipe Coimbra e; Andrade, José; Arraiano, Cecília"The RNA chaperone Hfq is a well-established post-transcriptional regulator in Gram-negative bacteria, where it facilitates small RNA–mRNA interactions. However, its role in Gram-positive bacteria remains poorly understood. In this thesis, we uncover novel functions for Hfq in the human pathogen Listeria monocytogenes, the causative agent of listeriosis, a severe foodborne disease. L. monocytogenes is a facultative intracellular bacterium that must withstand oxidative stress during infection, particularly the reactive oxygen species (ROS) generated by host immune cells.(...)"
- Bacterial Survival Strategies: Unveiling the boIA gene, persistence and diversificationPublication . Silva, Ana Maria Da; Arraiano, Cecília Maria; Silva, Inês de Jesus"Bacteria are some of the most adaptable organisms on the planet and have developed a myriad of survival strategies that enable them to thrive in diverse and often challenging environments. These strategies allow them to withstand harsh conditions, compete with other organisms, and persist over time. Understanding these survival phenomena may be the key to control the spread of bacterial infections. This dissertation intends to explore some of these survival strategies and is organized in six main chapters.(...)"
- Deciphering the roles of ribonuclease PNPase in the human pathogen Listeria monocytogenes:Publication . Quendera, Ana Patrícia; Andrade, José; Arraiano, Cecília"PNPase is a 3’-5’ exoribonuclease that catalyses the degradation and processing of RNA. Although PNPase has been associated to virulence-related processes in bacteria, the regulatory networks under control of PNPase that contribute to virulence remain mostly elusive. Here, we studied the function of PNPase in the Gram-positive pathogenic bacterium Listeria monocytogenes, the infectious agent responsible for listeriosis, a foodborne infection associated with high morbidity and mortality in humans. L. monocytogenes is a facultative intracellular microorganism that thrives in a wide range of environmental conditions and endures different external stresses. Moreover, L. monocytogenes can adhere and form biofilms in several types of surfaces, namely in food-processing environments, making this bacterium a major burden for the food industry.(...)"
- Post-transcriptional Control Strategies in Synthetic BiologyPublication . Apura, Patrícia; Viegas, Sandra; Arraiano, Cecília"The revolution of genomics and growth of systems biology urged the creation of synthetic biology, an engineering discipline aiming at recreating and reprogramming cellular functions for industrial needs. There has been a large effort in synthetic biology to develop versatile and programmable genetic regulators that would enable the precise control of gene expression. Synthetic RNA components have emerged as a solution, offering a diverse range of programmable functions, including signal sensing, gene regulation and the modulation of molecular interactions. Owing to their compactness, structure and way of action, several types of RNA devices that act on DNA, RNA and protein have been characterized and applied in synthetic biology. RNA-based approaches are more ‘economical’ for the cell, since they are generally not translated. These RNA-based strategies act on a much shorter time scale than transcription-based ones and can be more efficient than protein-based mechanisms. In this PhD, we explored these RNA components as building blocks in the RNA synthetic biology field. The components were tested in two different model microorganisms, the widely studied and industrially used bacterium, Escherichia coli, and one of the most stress resistant and industrially promising bacteria, Pseudomonas putida.(...)"
- Dynamics and Function of Ribonuclease R in Streptococcus pneumoniaePublication . Bárria, Cátia; Arraiano, Cecília; Domingues, Susana"Ribonucleases (RNases) are key factors in the control of all biological processes. These enzymes ensure maturation, degradation and quality control of all types of RNAs. Some RNases are up-regulated under stress conditions and are also involved in virulence processes of pathogenic bacteria. The RNB family of enzymes is present in all domains of life and includes RNase R, RNase II and the eukaryotic Rrp44/Dis3, Dis3L1 and Dis3L2 proteins.(...)"
- More than an RNA matchmaker: Expanding the roles of Hfq into ribosome biogenesisPublication . dos Santos, Ricardo F.; Arraiano, Cecília; Andrade, JoséRibosome biogenesis is a complex process involving multiple factors. The work described here is primarily centered in the study of ribosomal RNA, highlighting its central role in translation regulation. We have uncovered new regulators involved in rRNA processing, folding and degradation pathways. For the first time, we demonstrate that the widely conserved RNA chaperone Hfq, mostly known as the sRNA-mRNA matchmaker, acts as a ribosomal assembly factor in Escherichia coli, affecting rRNA processing, ribosome levels, translation efficiency and accuracy. This function is suggested to be independent of its activity as sRNA-regulator.(...)
- The Relevance of Ribonuclease III in Pathogenic BacteriaPublication . Saramago, Ana Margarida Teixeira; Arraiano, Cecília; Domingues, SusanaRibonucleases (RNases) are key factors in the control of all biological processes, since they modulate the stability of RNA transcripts, allowing rapid changes in gene expression. Some RNases are up-regulated under stress situations and are involved in virulence processes in pathogenic microorganisms. RNases also control the levels of regulatory RNAs, which play very important roles in cell physiology.(...)
- Interplay of Exoribonucleases, Hfq and Small RNAs Structural Determinants in the Control of Gene ExpressionPublication . Pobre, Vânia Sofia Fidalgo; Arraiano, Cecília MariaSmall non-coding RNAs (sRNAs) are regulatory molecules that typically are not translated into proteins. These molecules are often highly structured and very stable and can affect many genetic pathways in all domains of life. Bacterial small regulatory RNAs (sRNAs) parallel microRNAs in their ability to control multiple targets. Small RNAs can bind to proteins or to mRNA targets. The sRNAs that act by an antisense mechanism can have full (cis-encoded) or partial complementarity (trans-encoded) with their targets. Most of the trans-encoded sRNAs studied so far in Escherichia coli bind the RNA chaperone Hfq. The 5’ end of antisense RNAs is usually found to be critical for the interaction with targets, generally inhibiting translation and promoting mRNA decay. RNases are key elements in the control of RNA levels in the cell and not surprisingly are also critical in the regulation of sRNAs. In E. coli there are three 3’-5’exoribonucleases that accomplish most of the mRNA exodegradative activity: ribonuclease II (RNase II), ribonuclease R (RNase R) and polynucleotide phosphorylase (PNPase).(...)
- The Role of Small RNAs and Ribonucleases in the Control of Gene Expression in Salmonella TyphimuriumPublication . Silva, Inês de Jesus de Almeida; Arraiano, Cecília MariaRNAs are important effectors in the process of gene expression. In bacteria, the levels of the transcripts have to be rapidly adjusted in response to constantly changing environmental demands. The cellular concentration of a given RNA is the result of the balance between its synthesis and degradation. RNA degradation is a complex process encompassing multiple pathways. Ribonucleases are the enzymes that directly process and degrade RNA transcripts, regulating their cellular amounts. The rate at which RNA decay occurs depends on the availability of ribonucleases and their specificities according to the sequence and/or the structural elements of the RNA molecule. Several other factors modulate RNA degradation, namely polyadenylation, which plays a multifunctional role in RNA metabolism. Additionally, small non-coding RNAs are crucial regulators of gene expression, and can directly modulate the stability of their mRNA targets. In many cases this regulation is dependent on Hfq, an RNA binding protein which can act in concert with polyadenylation enzymes and is often necessary for the activity of the sRNAs.(...)
- Biological and Biochemical Characterization of Mutants of the RNase II family of enzymesPublication . Reis, Ana Filipa de Melo Tadeu Pereira dos; Arraiano, CecíliaThe cellular concentration of a given RNA is the result of the balance between its synthesis and degradation. RNA degradation plays a fundamental role in RNA metabolism, since the fast turnover of mRNA is important for the control of gene expression. One of the key components of RNA metabolism are enzymes from the RNase II family.(...)