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Loh, Edmund
Publications (9 of 9) Show all publications
Loh, E., Memarpour, F., Vaitkevicius, K., Kallipolitis, B. H., Johansson, J. & Sondén, B. (2012). An unstructured 5'-coding region of the prfA mRNA is required for efficient translation. Nucleic Acids Research, 40(4), 1818-1827
Open this publication in new window or tab >>An unstructured 5'-coding region of the prfA mRNA is required for efficient translation
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2012 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 40, no 4, p. 1818-1827Article in journal (Refereed) Published
Abstract [en]

Expression of virulence factors in the human bacterial pathogen Listeria monocytogenes is almost exclusively regulated by the transcriptional activator PrfA. The translation of prfA is controlled by a thermosensor located in the 5'-untranslated RNA (UTR), and is high at 37 degrees C and low at temperatures < 30 degrees C. In order to develop a thermoregulated translational expression system, the 5'-UTR and different lengths of the prfA-coding sequences were placed in front of lacZ. When expressed in Escherichia coli, the beta-galactosidase expression was directly correlated to the length of the prfA-coding mRNA lying in front of lacZ. A similar effect was detected with gfp as a reporter gene in both L. monocytogenes and E. coli, emphasizing the requirement of the prfA-coding RNA for maximal expression. In vitro transcription/translation and mutational analysis suggests a role for the first 20 codons of the native prfA-mRNA for maximal expression. By toe-print and RNA-probing analysis, a flexible hairpin-loop located immediately downstream of the start-codon was shown to be important for ribosomal binding. The present work determines the importance of an unstructured part of the 5'-coding region of the prfA-mRNA for efficient translation.

Place, publisher, year, edition, pages
Oxford, England: Oxford University Press, 2012
Keywords
Listeris-monocytogenes virulence, Escherichia-coli, Bacterial translation, Controls expression, Secondary structure, Ribosome binding, Initiation condon, Gene-expression, Shuttle vectors, Determinants
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:umu:diva-54341 (URN)10.1093/nar/gkr850 (DOI)000301069400041 ()
Available from: 2012-04-24 Created: 2012-04-24 Last updated: 2020-02-21Bibliographically approved
Loh, E. (2010). RNA-mediated virulence gene regulation in the human pathogen Listeria monocytogenes. (Doctoral dissertation). Umeå, Sweden: Print & Media
Open this publication in new window or tab >>RNA-mediated virulence gene regulation in the human pathogen Listeria monocytogenes
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The Gram-positive human pathogen Listeria monocytogenes uses a wide range of virulence factors for its pathogenesis. The majority of its virulence genes are encoded on a 9-kb pathogenicity island and are controlled by the transcriptional activator PrfA. Expression of these genes is maximal at 37°C and minimal at 30°C in a mechanism involving an RNA thermosensor. This thesis brings up different aspects of RNA-mediated regulation, including regulatory RNA structures within coding mRNA controlling expression to 5-untranslated RNA (5´-UTR) that controls downstream genes (cis-acting) as well as small non-coding RNAs (ncRNAs) that bind other target RNA (trans-acting).

We investigated the importance of the coding region of the prfA-mRNA for its expression. Various lengths of prfA-mRNA were fused with reporter genes. Our finding suggested that the first 20 codons of prfA-mRNA were essential for efficient translation in Listeria monocytogenes. Translation of the shorter constructs was shown to be reduced. The expression level showed an inverse correlation with the RNA secondary structure stability in the beginning of the coding region. Riboswitches have previously been known to control expression of their downstream mRNA in a cis-acting manner. A trans-acting S-adenosylmethionine-binding riboswitch termed SreA was identified in Listeria monocytogenes. It was found to control the expression of the virulence regulator PrfA, by binding to the prfA-UTR and thereby affecting its translation. We examined the RNA locus encoding different virulence factors in Listeria monocytogenes. Several of them were preceded by 5´-UTRs of various lengths. We speculate that these 5´-UTRs could control expression of the downstream mRNA, provided they are of sufficient length. These findings prompted us to examine where and when Listeria monocytogenes switches on gene expression. Tiling array was used to compare RNAs isolated from wild-type and mutant bacteria grown at different growth conditions. Antisense RNAs covering parts of or whole open-reading frames as well as 29 new ncRNAs were identified. Several novel riboswitches possibly functioning as upstream terminators were also found.

My thesis work compiles together a variety of novel RNA-mediated gene regulatory entities. A first coordinated transcriptional map of Listeria monocytogenes has been set up. My work has also revealed that the expression of the virulence regulator PrfA is controlled at several levels, indicating the importance of both the 5´-UTR and the coding RNA for regulated expression.

Place, publisher, year, edition, pages
Umeå, Sweden: Print & Media, 2010. p. 90
Series
Umeå University medical dissertations, ISSN 0346-6612 ; 1337
Keywords
Listeria monocytogenes, virulence, ncRNAs, PrfA, 5´-UTRs
National Category
Biochemistry and Molecular Biology
Research subject
Molecular Biology
Identifiers
urn:nbn:se:umu:diva-33096 (URN)0346-6612 (ISBN)
Public defence
2010-05-12, Major Groove, Department of Molecular Biology, Umeå University, 10:00 (English)
Opponent
Supervisors
Available from: 2010-04-20 Created: 2010-04-12 Last updated: 2018-06-08Bibliographically approved
Gripenland, J., Netterling, S., Loh, E., Tiensuu, T., Toledo-Arana, A. & Johansson, J. (2010). RNAs: regulators of bacterial virulence. Nature Reviews Microbiology, 8(12), 857-866
Open this publication in new window or tab >>RNAs: regulators of bacterial virulence
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2010 (English)In: Nature Reviews Microbiology, ISSN 1740-1526, E-ISSN 1740-1534, Vol. 8, no 12, p. 857-866Article in journal (Refereed) Published
Abstract [en]

RNA-based pathways that regulate protein expression are much more widespread than previously thought. Regulatory RNAs, including 5' and 3' untranslated regions next to the coding sequence, cis-acting antisense RNAs and trans-acting small non-coding RNAs, are effective regulatory molecules that can influence protein expression and function in response to external cues such as temperature, pH and levels of metabolites. This Review discusses the mechanisms by which these regulatory RNAs, together with accessory proteins such as RNases, control the fate of mRNAs and proteins and how this regulation influences virulence in pathogenic bacteria.

National Category
Microbiology in the medical area
Research subject
Microbiology
Identifiers
urn:nbn:se:umu:diva-38680 (URN)10.1038/nrmicro2457 (DOI)000284308200011 ()21079634 (PubMedID)
Available from: 2010-12-20 Created: 2010-12-20 Last updated: 2018-06-08Bibliographically approved
Loh, E., Dussurget, O., Gripenland, J., Vaitkevicius, K., Tiensuu, T., Mandin, P., . . . Johansson, J. (2009). A trans-acting riboswitch controls expression of the virulence regulator PrfA in Listeria monocytogenes. Cell, 139(4), 770-779
Open this publication in new window or tab >>A trans-acting riboswitch controls expression of the virulence regulator PrfA in Listeria monocytogenes
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2009 (English)In: Cell, ISSN 0092-8674, E-ISSN 1097-4172, Vol. 139, no 4, p. 770-779Article in journal (Refereed) Published
Abstract [en]

Riboswitches are RNA elements acting in cis, controlling expression of their downstream genes through a metabolite-induced alteration of their secondary structure. Here, we demonstrate that two S-adenosylmethionine (SAM) riboswitches, SreA and SreB, can also function in trans and act as noncoding RNAs in Listeria monocytogenes. SreA and SreB control expression of the virulence regulator PrfA by binding to the 5´-untranslated region of its mRNA. Absence of the SAM riboswitches SreA and SreB increases the level of PrfA and virulence gene expression in L. monocytogenes. Thus, the impact of the SAM riboswitches on PrfA expression highlights a link between bacterial virulence and nutrient availability. Together, our results uncover an unexpected role for riboswitches and a distinct class of regulatory noncoding RNAs in bacteria.

Keywords
Listeria, riboswitch, SreA, PrfA
National Category
Biochemistry and Molecular Biology
Research subject
Molecular Biology
Identifiers
urn:nbn:se:umu:diva-33105 (URN)10.1016/j.cell.2009.08.046 (DOI)19914169 (PubMedID)
Available from: 2010-04-12 Created: 2010-04-12 Last updated: 2018-06-08Bibliographically approved
Jöchl, C., Loh, E., Ploner, A., Haas, H. & Hüttenhofer, A. (2009). Development-dependent scavenging of nucleic acids in the filamentous fungus Aspergillus fumigatus.. RNA biology, 6(2), 179-186
Open this publication in new window or tab >>Development-dependent scavenging of nucleic acids in the filamentous fungus Aspergillus fumigatus.
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2009 (English)In: RNA biology, ISSN 1555-8584, Vol. 6, no 2, p. 179-186Article in journal (Refereed) Published
Abstract [en]

Aspergillus fumigatus is an ubiquitous, filamentous and opportunistic pathogenic fungus which causes fatal invasive aspergillosis among immuno-compromised patients. Since therapeutic strategies are currently limited, the mortality rate of invasive aspergillosis is high and thus, alternative antifungal strategies are required. In this study, we demonstrate that during vegetative growth Aspergillus fumigatus is able to scavenge nucleic acids within its cell wall with accumulation rates of several thousand-fold, compared to the surrounding medium. To investigate, whether nucleic acids, attached to the fungal cell wall, are able to move further into the cytoplasm of fungal cells, we directly applied siRNAs, in the absence of lipo-transfection reagents, to growing A. fumigatus cells. In fact, addition of two 21-nt siRNA duplexes resulted in knock-down of their corresponding target mRNAs, odcA and pyrG, respectively. These findings indicate that RNA interference, mediated by siRNAs, can be used as a fast and efficient tool to investigate the functions of genes within filamentous fungi. In addition, siRNA-based therapies may provide novel approaches for antifungal treatment.

National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:umu:diva-33158 (URN)10.4161/rna.6.2.7717 (DOI)19246986 (PubMedID)
Available from: 2010-04-13 Created: 2010-04-13 Last updated: 2018-06-08Bibliographically approved
Toledo-Arana, A., Dussurget, O., Nikitas, G., Sesto, N., Guet-Revillet, H., Balestrino, D., . . . Cossart, P. (2009). The Listeria transcriptional landscape from saprophytism to virulence. Nature, 459(7249), 950-956
Open this publication in new window or tab >>The Listeria transcriptional landscape from saprophytism to virulence
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2009 (English)In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 459, no 7249, p. 950-956Article in journal (Refereed) Published
Abstract [en]

The bacterium Listeria monocytogenes is ubiquitous in the environment and can lead to severe food-borne infections. It has recently emerged as a multifaceted model in pathogenesis. However, how this bacterium switches from a saprophyte to a pathogen is largely unknown. Here, using tiling arrays and RNAs from wild-type and mutant bacteria grown in vitro, ex vivo and in vivo, we have analysed the transcription of its entire genome. We provide the complete Listeria operon map and have uncovered far more diverse types of RNAs than expected: in addition to 50 small RNAs (<500 nucleotides), at least two of which are involved in virulence in mice, we have identified antisense RNAs covering several open-reading frames and long overlapping 5' and 3' untranslated regions. We discovered that riboswitches can act as terminators for upstream genes. When Listeria reaches the host intestinal lumen, an extensive transcriptional reshaping occurs with a SigB-mediated activation of virulence genes. In contrast, in the blood, PrfA controls transcription of virulence genes. Remarkably, several non-coding RNAs absent in the non-pathogenic species Listeria innocua exhibit the same expression patterns as the virulence genes. Together, our data unravel successive and coordinated global transcriptional changes during infection and point to previously unknown regulatory mechanisms in bacteria.

Keywords
11-beta-Hydroxysteroid Dehydrogenase Type 1/*genetics/metabolism, Animals, Cerebral Cortex/enzymology/metabolism, Circadian Rhythm, Corticosterone/blood, Gene Expression Regulation; Enzymologic, Hippocampus/enzymology/*metabolism, Male, Obesity/blood/enzymology/*genetics, RNA; Messenger/metabolism, Rats, Rats; Sprague-Dawley, Rats; Zucker
National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:umu:diva-33159 (URN)10.1038/nature08080 (DOI)19448609 (PubMedID)
Available from: 2010-04-13 Created: 2010-04-13 Last updated: 2018-06-08Bibliographically approved
Buren, J., Bergström, S.-A., Loh, E., Söderström, I., Olsson, T. & Mattsson, C. (2007). Hippocampal 11beta-hydroxysteroid dehydrogenase type 1 messenger ribonucleic acid expression has a diurnal variability that is lost in the obese Zucker rat.. Endocrinology, 148(6), 2716-22
Open this publication in new window or tab >>Hippocampal 11beta-hydroxysteroid dehydrogenase type 1 messenger ribonucleic acid expression has a diurnal variability that is lost in the obese Zucker rat.
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2007 (English)In: Endocrinology, ISSN 0013-7227, Vol. 148, no 6, p. 2716-22Article in journal (Refereed) Published
Keywords
11-beta-Hydroxysteroid Dehydrogenase Type 1/*genetics/metabolism, Animals, Cerebral Cortex/enzymology/metabolism, Circadian Rhythm, Corticosterone/blood, Gene Expression Regulation; Enzymologic, Hippocampus/enzymology/*metabolism, Male, Obesity/blood/enzymology/*genetics, RNA; Messenger/metabolism, Rats, Rats; Sprague-Dawley, Rats; Zucker
Identifiers
urn:nbn:se:umu:diva-16974 (URN)doi:10.1210/en.2006-0897 (DOI)17332068 (PubMedID)
Available from: 2008-01-13 Created: 2008-01-13 Last updated: 2018-06-09Bibliographically approved
Loh, E., Gripenland, J. & Johansson, J. (2006). Control of Listeria monocytogenes virulence by 5´-untranslated RNA. Trends in Microbiology, 14(7), 294-298
Open this publication in new window or tab >>Control of Listeria monocytogenes virulence by 5´-untranslated RNA
2006 (English)In: Trends in Microbiology, ISSN 0966-842X, E-ISSN 1878-4380, Vol. 14, no 7, p. 294-298Article in journal (Refereed) Published
Abstract [en]

The Gram-positive bacterium Listeria monocytogenes uses a wide range of virulence factors for its pathogenesis. Expression of five of these factors has previously been shown to be subjected to posttranscriptional regulation as a result of their long 5´-untranslated region (5´-UTR). We have investigated the presence of 5´-UTRs among the other known virulence genes and genes that encode putatively virulence-associated surface proteins. Our results strongly suggest that L. monocytogenes controls many of its virulence genes by a mechanism that involves the 5´-UTR. These findings further emphasize the importance of post-transcriptional control for L. monocytogenes virulence.

Keywords
5´-UTRs, Listeria monocytogenes, virulence genes
National Category
Biochemistry and Molecular Biology
Research subject
Molecular Biology
Identifiers
urn:nbn:se:umu:diva-33106 (URN)10.1016/j.tim.2006.05.001 (DOI)
Available from: 2010-04-12 Created: 2010-04-12 Last updated: 2018-06-08Bibliographically approved
Loh, E., Memarpour, F., Johansson, J. & Sondén, B. The first 20 codons of the prfA-mRNA are required for efficient translation in Listeria monocytogenes.
Open this publication in new window or tab >>The first 20 codons of the prfA-mRNA are required for efficient translation in Listeria monocytogenes
(English)Manuscript (preprint) (Other academic)
Abstract [en]

Expression of virulence factors in the human pathogen Listeria monocytogenes is almost exclusively regulated by the transcriptional activator PrfA. The translation of prfA is controlled by a thermosensor located in the 5´-untranslated RNA (UTR), which is high at 37°C and low at temperatures below 30°C. Also, translation of the prfA transcript is inhibited by a trans-acting riboswitch RNA, SreA, which binds to the 5´-end of the thermosensor. In order to develop a thermoregulated translational expression system in Mycobacterial species, the 5´-UTR and different lengths of the prfA-coding sequences were placed in front of lacZ. When expressed in Escherichia coli, the constructs retained their thermoregulation. However, the β-galactosidase expression was directly correlated to the length of the prfA-coding mRNA fused in front of lacZ. A similar regulation was also detected when gfp was used as a reporter gene. Transcriptional stability experiments indicated that the observed difference in expression was not due to a decreased stability of transcripts lacking more of the prfA-coding RNA. The gfp constructs behaved similarly in L. monocytogenes as in E. coli, emphasizing the requirement of the prfA-coding RNA for maximal expression, also in its natural genetic background. Moreover, the different PrfA-LacZ fusion proteins showed the same proteolytic stability, ruling out post-translational mechanisms. Instead, in vitro transcription/translation experiments suggest a role of the first 20 codons of the native prfA-mRNA for maximal expression. Our data indicated that the difference in expression was not due to rare codons, stretches of certain bases or a putative downstream box. We observed an inverse correlation between the stability of the RNA secondary structure and protein expression. The first 12 codons of prfA displayed a very weak RNA secondary structure. Similar weak stabilities were detected also for thermosensors in other species, indicating a common strategy of regulation. In summary, the present work determines the importance of an unstructured 5´-coding region of the prfA-RNA for efficient translation.

Keywords
Listeria, prfA-mRNA
National Category
Biochemistry and Molecular Biology
Research subject
Molecular Biology
Identifiers
urn:nbn:se:umu:diva-33103 (URN)
Available from: 2010-04-12 Created: 2010-04-12 Last updated: 2018-06-08Bibliographically approved
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