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14 results on '"Schwenk, Stefan"'

1. Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing

Author

Deshpande, Aditya S., Ulahannan, Netha, Pendleton, Matthew, Dai, Xiaoguang, Ly, Lynn, Behr, Julie M., Schwenk, Stefan, Liao, Will, Augello, Michael A., Tyer, Carly, Rughani, Priyesh, Kudman, Sarah, Tian, Huasong, Otis, Hannah G., Adney, Emily, Wilkes, David, Mosquera, Juan Miguel, Barbieri, Christopher E., Melnick, Ari, Stoddart, David, Turner, Daniel J., Juul, Sissel, Harrington, Eoghan, and Imieliński, Marcin

Published
2022
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2. Riboswitch-mediated regulation of the Mycobacterium tuberculosis resuscitation promoting factor, rpfB

Author

Schwenk, Stefan, Arnvig, K., and McHugh, T.

Subjects
570
Abstract

Mycobacterium tuberculosis, the causative agent of tuberculosis, results in over 1.5 million deaths every year. An estimated third of the world’s population may harbour a latent infection with risk of reactivation under permissive conditions. M. tuberculosis expresses a number of homologous resuscitation promoting factors (Rpfs) believed to facilitate resuscitation from dormancy. However, little is known about the regulation of Rpf expression. This study identifies a putative novel riboswitch in the 5’UTR of rpfB, which appears to be conserved in pathogenic mycobacteria, but not in non-pathogenic species. Northern blot analysis of M. tuberculosis RNA reveals short terminated transcripts and longer read-through transcripts suggesting transcription attenuation mediated by a transcriptional riboswitch. This has been further supported by 3’RACE, reporter gene assays and in vitro transcription. Findings indicate that rpfB is co-transcribed with the universally conserved rRNA methyltransferase ksgA, implicating the riboswitch in ksgA expression regulation, thereby linking resuscitation with ribosome maturation. Moreover, through translation start site mapping the RpfB start codon has been re-annotated and a ribosome binding site has been validated. This ribosome binding site is likely targeted by an rpfB antisense RNA produced from an antisense promoter that may also serve to regulate rpfB expression either by RNA polymerase clashing, sense antisense interaction, mRNA processing or all of the above. Expression of the rpfB locus has been investigated under multiple physiological stresses and throughout biofilm formation. Collectively, findings support the presence of a novel rpfB riboswitch transcriptional ‘on-switch’ capable of regulating expression through transcription attenuation. Understanding the stimuli and regulation of Rpf gene expression will improve understanding of their role in disease and resuscitation.

Published
2018

4. Nanopore sequencing of DNA concatemers reveals higher-order features of chromatin structure

Author

Ulahannan, Netha, primary, Pendleton, Matthew, additional, Deshpande, Aditya, additional, Schwenk, Stefan, additional, Behr, Julie M., additional, Dai, Xiaoguang, additional, Tyer, Carly, additional, Rughani, Priyesh, additional, Kudman, Sarah, additional, Adney, Emily, additional, Tian, Huasong, additional, Wilkes, David, additional, Mosquera, Juan Miguel, additional, Stoddart, David, additional, Turner, Daniel J., additional, Juul, Sissel, additional, Harrington, Eoghan, additional, and Imielinski, Marcin, additional

Published
2019
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5. Cell-wall synthesis and ribosome maturation are co-regulated by an RNA switch in Mycobacterium tuberculosis

Author

Schwenk, Stefan, Moores, Alexandra, Nobeli, Irene, McHugh, Timothy D., Arnvig, Kristine B., Schwenk, Stefan, Moores, Alexandra, Nobeli, Irene, McHugh, Timothy D., and Arnvig, Kristine B.

Abstract

The success of Mycobacterium tuberculosis relies on the ability to switch between active growth and non-replicating persistence, associated with latent TB infection. Resuscitation promoting factors (Rpfs) are essential for the transition between these states. Rpf expression is tightly regulated as these enzymes are able to degrade the cell wall, and hence potentially lethal to the bacterium itself. We have identified a regulatory element in the 5' untranslated region (UTR) of rpfB. We demonstrate that this element is a transcriptionally regulated RNA switch/riboswitch candidate, which appears to be restricted to pathogenic mycobacteria, suggesting a role in virulence. We have used translation start site mapping to re-annotate the RpfB start codon and identified and validated a ribosome binding site that is likely to be targeted by an rpfB antisense RNA. Finally, we show that rpfB is co-transcribed with ksgA and ispE downstream. ksgA encodes a universally conserved methyltransferase involved in ribosome maturation and ispE encodes an essential kinase involved in cell wall synthesis. This arrangement implies co-regulation of resuscitation, cell wall synthesis and ribosome maturation via the RNA switch.

Published
2018

6. Expression, maturation and turnover of DrrS, an unusually stable, DosR regulated small RNA in Mycobacterium tuberculosis

Author

Moores, Alexandra, Riesco, Ana B., Schwenk, Stefan, and Arnvig, Kristine B.

Subjects
Science, Medicine, QR
Abstract

Mycobacterium tuberculosis depends on the ability to adjust to stresses encountered in a range of host environments, adjustments that require significant changes in gene expression. Small RNAs (sRNAs) play an important role as post-transcriptional regulators of prokaryotic gene expression, where they are associated with stress responses and, in the case of pathogens, adaptation to the host environment. In spite of this, the understanding of M. tuberculosis RNA biology remains limited. Here we have used a DosR-associated sRNA as an example to investigate multiple aspects of mycobacterial RNA biology that are likely to apply to other M. tuberculosis sRNAs and mRNAs. We have found that accumulation of this particular sRNA is slow but robust as cells enter stationary phase. Using reporter gene assays, we find that the sRNA core promoter is activated by DosR, and we have renamed the sRNA DrrS for DosR Regulated sRNA. Moreover, we show that DrrS is transcribed as a longer precursor, DrrS+, which is rapidly processed to the mature and highly stable DrrS. We characterise, for the first time in mycobacteria, an RNA structural determinant involved\ud in this extraordinary stability and we show how the addition of a few nucleotides can lead to acute destabilisation. Finally, we show how this RNA element can enhance expression of a heterologous gene. Thus, the element, as well as its destabilising derivatives may be employed to post-transcriptionally regulate gene expression in mycobacteria in combination with different promoter variants. Moreover, our findings will facilitate further investigations into the severely understudied topic of mycobacterial RNA biology and into the role that regulatory RNA plays in M. tuberculosis pathogenesis.

Published
2017

12. Comparison of Established Diagnostic Methodologies and a Novel Bacterial smpB Real-Time PCR Assay for Specific Detection of Haemophilus influenzae Isolates Associated with Respiratory Tract Infections

Author

Reddington, Kate, primary, Schwenk, Stefan, additional, Tuite, Nina, additional, Platt, Gareth, additional, Davar, Danesh, additional, Coughlan, Helena, additional, Personne, Yoann, additional, Gant, Vanya, additional, Enne, Virve I., additional, Zumla, Alimuddin, additional, and Barry, Thomas, additional

Published
2015
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13. Comparison of Established Diagnostic Methodologies and a Novel Bacterial smpBReal-Time PCR Assay for Specific Detection of Haemophilus influenzaeIsolates Associated with Respiratory Tract Infections

Author

Reddington, Kate, Schwenk, Stefan, Tuite, Nina, Platt, Gareth, Davar, Danesh, Coughlan, Helena, Personne, Yoann, Gant, Vanya, Enne, Virve I., Zumla, Alimuddin, and Barry, Thomas

Abstract

ABSTRACTHaemophilus influenzaeis a significant causative agent of respiratory tract infections (RTI) worldwide. The development of a rapid H. influenzaediagnostic assay that would allow for the implementation of infection control measures and also improve antimicrobial stewardship for patients is required. A number of nucleic acid diagnostics approaches that detect H. influenzaein RTIs have been described in the literature; however, there are reported specificity and sensitivity limitations for these assays. In this study, a novel real-time PCR diagnostic assay targeting the smpBgene was designed to detect all serogroups of H. influenzae. The assay was validated using a panel of well-characterized Haemophilusspp. Subsequently, 44 Haemophilusclinical isolates were collected, and 36 isolates were identified as H. influenzaeusing a gold standard methodology that combined the results of matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) and a fucKdiagnostic assay. Using the novel smpBdiagnostic assay, 100% concordance was observed with the gold standard, demonstrating a sensitivity of 100% (95% confidence interval [CI], 90.26% to 100.00%) and a specificity of 100% (95% CI, 63.06% to 100.00%) when used on clinical isolates. To demonstrate the clinical utility of the diagnostic assay presented, a panel of lower RTI samples (n= 98) were blindly tested with the gold standard and smpBdiagnostic assays. The results generated were concordant for 94/98 samples tested, demonstrating a sensitivity of 90.91% (95% CI, 78.33% to 97.47%) and a specificity of 100% (95% CI, 93.40% to 100.00%) for the novel smpBassay when used directly on respiratory specimens.

Published
2015
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14. Untersuchungen zur Bedeutung toxischer Stoffwechselprodukte des Pilzes Trichothecium roseum Link ex Fr. für den Weinbau.

Author

Schwenk, Stefan, Altmayer, Bernd, and Eichhorn, Klaus

Abstract

Copyright of Zeitschrift für Lebensmittel-Untersuchung und -Forschung is the property of Springer Nature and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Published
1989
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