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Transcriptional and translational control through the 5 '-leader region of the dmpR master regulatory gene of phenol metabolism
Umeå University, Faculty of Science and Technology, Department of Molecular Biology (Faculty of Science and Technology). (Victoria Shingler)
Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine). (Felipe Cava)
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2015 (English)In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 17, no 1, 119-133 p.Article in journal (Refereed) Published
Abstract [en]

Expression of pathways for dissimilation of toxic aromatic compounds such as (methyl)phenols interfaces both stress-response and carbon catabolite repression control cascades. In Pseudomonas putida, carbon catabolite repression is mediated by the protein Crc - a translational repressor that counteracts utilization of less-preferred carbon sources as growth substrates until they are needed. In this work we dissect the regulatory role of the 5-leader region (5-LR) of the dmpR gene that encodes the master regulator of (methyl)phenol catabolism. Using deletion and substitution mutants combined with artificial manipulations of Crc availability in P.putida, we present evidence that a DNA motif within the 5-leader region is critical for inhibition of the output from the Pr promoter that drives transcription of dmpR, while the RNA chaperone Hfq facilitates Crc-mediated translation repression through the 5-leader region of the dmpR mRNA. The results are discussed in the light of a model in which Hfq assists Crc to target a sequence within a loop formed by secondary structure of the 5-LR mRNA. Our results support the idea that Crc functions as a global translational inhibitor to co-ordinate hierarchical carbon utilization in Pseudomonads.

Place, publisher, year, edition, pages
2015. Vol. 17, no 1, 119-133 p.
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
URN: urn:nbn:se:umu:diva-100785DOI: 10.1111/1462-2920.12511ISI: 000349152800011PubMedID: 24889314OAI: diva2:794518
Available from: 2015-03-11 Created: 2015-03-09 Last updated: 2015-08-12Bibliographically approved
In thesis
1. Multiple regulatory inputs for hierarchical control of phenol catabolism by Pseudomonas putida
Open this publication in new window or tab >>Multiple regulatory inputs for hierarchical control of phenol catabolism by Pseudomonas putida
2015 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Metabolically versatile bacteria have evolved diverse strategies to adapt to different environmental niches and respond to fluctuating physico-chemical parameters. In order to survive in soil and water habitats, they employ specific and global regulatory circuits to integrate external and internal signals to counteract stress and optimise their energy status. One strategic endurance mechanism is the ability to choose the most energetically favourable carbon source amongst a number on offer.

Pseudomonas putida strains possess large genomes that underlie much of their ability to use diverse carbon sources as growth substrates. Their metabolic potential is frequently expanded by possession of catabolic plasmids to include the ability to grow at the expense of seemingly obnoxious carbon sources such as phenols. However, this ability comes with a metabolic price tag. Carbon source repression is one of the main regulatory networks employed to subvert use of these expensive pathways in favour of alternative sources that provide a higher metabolic gain. This thesis identifies some of the key regulatory elements and factors used by P. putida to supress expression of plasmid-encoded enzymes for degradation of phenols until they are beneficial.

I first present evidence for a newly identified DNA and RNA motif within the regulatory region of the gene encoding the master regulator of phenol catabolism – DmpR. The former of these motifs functions to decrease the number of transcripts originating from the dmpR promoter, while the latter mediates a regulatory checkpoint for translational repression by Crc – the carbon repression control protein of P. putida. The ability of Crc to form repressive riboprotein complexes with RNA is shown to be dependent on the RNA chaperone protein Hfq – a co-partnership demonstrated to be required for many previously identified Crc-targets implicated in hierarchical assimilation of different carbon sources in P. putida. Finally, I present evidence for a model in which Crc and Hfq co-target multiple RNA motifs to bring about a two-tiered regulation to subvert catabolism of phenols in the face of preferred substrates – one at the level of the regulator DmpR and another at the level of translation of the catabolic enzymes.

Place, publisher, year, edition, pages
Umeå: Umeå University, 2015. 46 p.
P. putida, Phenol catabolism, dmpR, dmp-System, 5’-LR, Carbon Catabolite Repression, Transcriptional & Translational regulation, Crc, CrcZ, CrcY, Hfq
National Category
Cell and Molecular Biology
urn:nbn:se:umu:diva-106878 (URN)978-91-7601-313-7 (ISBN)
Public defence
2015-09-07, E04, Unod R1, Norrlands universitetssjukhus, Umeå, 10:00 (English)
Available from: 2015-08-17 Created: 2015-08-11 Last updated: 2015-08-12Bibliographically approved

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Madhushani, Anjanadel Peso-Santos, TeresaShingler, Victoria
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