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More than 150 different RNA modifications have been detected in all kingdoms of life and 60 are known to decorate bacterial RNA. Among them, pseudouridine is universally conserved and one of the most abundant modifications present in bacterial stable RNAs such as tRNAs and rRNAs. In bacteria, the nucleotide is posttranscriptionally generated by dedicated enzymes called pseudouridine synthases (PUSs). With the advent of sophisticated deep-sequencing technologies, this modification has been identified in different types of RNA classes (tRNAs, rRNAs, mRNAs, snRNAs, and lncRNAs) in diverse eukaryotic organisms. However, these techniques have never been applied to bacteria, generating a knowledge gap about the location of the modified nucleotide in prokaryotic RNAs. Mutations or deletions of specific eukaryotic PUS enzymes are linked to human diseases and therefore their absence is deleterious for the correct function of the cell. However, deletion of tRNA or rRNA PUS enzymes in the bacterial model organism E. coli have not revealed any such drastic phenotypes, suggesting a different role and function of the modification itself and of the enzymes in different kingdoms of life.
Since the roles of tRNA PUS enzymes in bacteria is still poorly understood, a functional characterization of these proteins is pursued in the Epsilonproteobacteria Campylobacter jejuni and Helicobacter pylori. While C. jejuni is the leading cause of bacterial foodborne gastroenteritis in humans, infection with H. pylori is associated with the development of gastric cancer. In particular, phenotypes were explored for the tRNA PUS enzymes TruA, TruB, and TruD in C. jejuni as well as TruA and TruD in H. pylori. Upon deletion of truD, a severe growth defect is observed for C. jejuni but not for H. pylori, highlighting a potential difference in function of the enzyme in the two related bacterial pathogens.
Moreover, a genome-wide approach called Pseudo-seq is established and applied for RNA of these two pathogens, which allows, for the first time, the global identification of pseudouridine modifications at single-nucleotide resolution in the bacterial transcriptome. Applying Pseudo-seq in RNAs of wildtype and diverse PUS enzyme deletion mutants enabled the identification of the distinct RNA substrates of tRNA PUS enyzmes in C. jejuni and H. pylori. Hereby, the tRNA-Glu was determined to be the major tRNA substrate of TruD in C. jejuni. Interestingly, the tRNA-Glu is expressed as a single copy in the C. jejuni genome. To link the growth defect observed for a C. jejuni ∆truD mutant strain to the pseudouridine modification of the tRNA-Glu, a catalytically inactive TruD complementation was generated. This strain is unable to restore the tRNA-Glu modification but surprisingly, was able to complement the growth defect. The same observation was made for a cross-complementation with a copy of H. pylori TruD. This indicates that there is a potential additional function of the TruD PUS enzyme in C. jejuni that is independent of the pseudouridine modification. Using a combination of deep-sequencing technologies (RIP-seq, RNA-seq, Ribo-seq, and CLIP-seq), the dual function of TruD is investigated.
Overall, this study provides the first in-depth investigation into pseudouridylation of bacteria in general and the bacterial pathogens C. jejuni and H. pylori in particular. The work presented in this thesis reveals not only a global map of pseudouridine in tRNAs and rRNAs of the two bacteria but it also explores the function of the responsible tRNA PUS enzymes. In addition, this study provides evidence for a dual function of the C. jejuni PUS enzyme TruD that goes beyond its RNA modifying function. Future research could focus on unravelling the function of TruD and its potential interaction partners and thus reveal new mechanisms of regulation of a protein previously only described as an RNA modification enzyme.
Low pH is the main environmental stress encountered by Helicobacter pylori in the human stomach. To ensure its survival under acidic conditions, this bacterium utilizes urease (encoded by the ureAB operon), a nickel-activated metalloenzyme, which cleaves urea into ammonia to buffer the periplasmic space. Expression of the ureAB operon is tightly regulated at the transcriptional level. Moreover, the urease activity is modulated post translationally via the activity of nickel-binding proteins such as HP1432 that act as nickel sponges to either sequester or release nickel depending on the pH. However, little is known how the levels of these nickel-binding proteins are regulated at the post-transcriptional level. Interestingly, more than 60 candidate small regulatory RNAs (sRNAs) have been identified in a differential RNA-seq approach in H. pylori strain 26695, suggesting an uncharacterized layer of post-transcriptional riboregulation in this pathogen. sRNAs control their trans- or cis- encoded targets by direct binding. Many of the characterized sRNAs are expressed in response to specific environmental cues and are ideal candidates to confer post-transcriptional regulation under different growth conditions.
This study demonstrates that a small RNA termed ArsZ (Acid Responsive sRNA Z) and its target HP1432 constitute yet another level of urease regulation. In-vitro and in-vivo experiments show that ArsZ interacts with the ribosome binding site (RBS) of HP1432 mRNA, effectively repressing translation of HP1432. During acid adaptation, the acid-responsive ArsRS two-component system represses expression of ArsZ. ArsRS and ArsZ work in tandem to regulate expression of HP1432 via a coherent feedforward loop (FFL). ArsZ acts as a delay mechanism in this feedforward loop to ensure that HP1432 protein levels do not abruptly change upon transient pH drops encountered by the bacteria. ArsZ “fine-tunes” the dynamics of urease activity after pH shift presumably by altering nickel availability through post transcriptional control of HP1432 expression. Interestingly, after adaptation to acid stress, ArsZ indirectly activates the transcription of HP1432 and forms an incoherent FFL with ArsRS to regulate HP1432. This study identified a non-standard FFL in which ArsZ can participate directly or indirectly in two different network configurations depending on the state of acid stress adaptation. The importance of ArsZ in the acid response of H. pylori is further supported by bioinformatics analysis showing that the evolution of ArsZ is closely related to the emergence of modern H. pylori strains that globally infect humans. No homologs of arsZ were found in the non-pylori species of Helicobacter. Moreover, this study also demonstrates that the physiological role of a sRNA can be elucidated without the artificial overexpression of the respective sRNA, a method commonly used to characterize sRNAs. Coupled with time-course experiments, this approach allows the kinetics of ArsZ regulation to be studied under more native conditions. ArsZ is the first example of a trans-acting sRNA that regulates a nickel storage protein to modulate apo-urease maturation. These findings may have important implications in understanding the details of urease activation and hence the colonization capability of H. pylori, the only bacterial class I carcinogen to date (WHO, 1994).
Bacterial small non-coding RNAs (sRNAs) play fundamental roles in controlling and finetuning gene expression in a wide variety of cellular processes, including stress responses, environmental signaling and virulence in pathogens. Despite the identification of hundreds of sRNA candidates in diverse bacteria by genomics approaches, the mechanisms and regulatory capabilities of these posttranscriptional regulators have most intensively been studied in Gram-negative Gammaproteobacteria such as Escherichia coli and Salmonella. So far, almost nothing is known about sRNA-mediated regulation (riboregulation) in Epsilonproteobacteria, including the major human pathogen Helicobacter pylori. H. pylori was even thought to be deficient for riboregulation as none of the sRNAs known from enterobacteria are conserved in Helicobacter and since it lacks the major RNA chaperone Hfq, which is crucial for sRNA function as well as stability in many bacteria. Nonetheless, more than 60 cis- and trans-acting sRNA candidates were recently identified in H. pylori by a global RNA sequencing approach, indicating that this pathogen, in principle, has the capability to use riboregulation for its gene expression control. However, the functions and underlying mechanisms of H. pylori sRNAs remained unclear.
This thesis focused on the first functional characterization and target gene identification of a trans-acting sRNA, RepG (Regulator of polymeric G-repeats), in H. pylori. Using in-vitro and in-vivo approaches, RepG was shown to directly base-pair with its C/Urich terminator loop to a variable homopolymeric G-repeat in the 5’ untranslated region (UTR) of the tlpB mRNA, thereby regulating expression of the chemotaxis receptor TlpB. While the RepG sRNA is highly conserved, the length of the G-repeat in the tlpB mRNA leader varies among different H. pylori isolates, resulting in a strain-specific tlpB regulation. The modification of the number of guanines within the G-stretch in H. pylori strain 26695 demonstrated that the length of the homopolymeric G-repeat determines the outcome of posttranscriptional control (repression or activation) of tlpB by RepG. This lengthdependent targeting of a simple sequence repeat by a trans-acting sRNA represents a new twist in sRNA-mediated regulation and a novel mechanism of gene expression control, since it uniquely links phase variation by simple sequence repeats to posttranscriptional regulation.
In almost all sequenced H. pylori strains, tlpB is encoded in a two gene operon upstream of HP0102, a gene of previously unknown function. This study provided evidence that HP0102 encodes a glycosyltransferase involved in LPS O-chain and Lewis x antigen production. Accordingly, this glycosyltransferase was shown to be essential for mice colonization by H. pylori. The coordinated posttranscriptional regulation of the tlpB-HP0102 operon by antisense base-pairing of RepG to the phase-variable G-repeat in the 5’ UTR of the tlpB mRNA allows for a gradual, rather than ON/OFF, control of HP0102 expression, thereby affecting LPS biosynthesis in H. pylori. This fine-tuning of O-chain and Lewis x antigen expression modulates H. pylori antibiotics sensitivity and thus, might be advantageous for Helicobacter colonization and persistence.
Whole transcriptome analysis based on microarray and RNA sequencing was used to identify additional RepG target mRNAs and uncover the physiological role of this riboregulator in H. pylori. Altogether, repG deletion affected expression of more than 40 target gene candidates involved various cellular processes, including membrane transport and adhesion, LPS modification, amino acid metabolism, oxidative and nitrosative stress, and nucleic acid modification. The presence of homopolymeric G-repeats/G-rich sequences in almost all target mRNA candidates indicated that RepG hijacks a conserved motif to
recognize and regulate multiple target mRNAs in H. pylori.
Overall, this study demonstrates that H. pylori employs riboregulation in stress response and virulence control. In addition, this thesis has successfully established Helicobacter as a new model organism for investigating general concepts of gene expression control by Hfq-independent sRNAs and sRNAs in bacterial pathogens.