Skip to main content

Lund University Publications

LUND UNIVERSITY LIBRARIES

Proteomic and transcriptomic experiments reveal an essential role of RNA degradosome complexes in shaping the transcriptome of Mycobacterium tuberculosis

Płociński, Przemysław ; Macios, Maria ; Houghton, Joanna ; Niemiec, Emilia LU orcid ; Płocińska, Renata ; Brzostek, Anna ; Słomka, Marcin ; Dziadek, Jarosław ; Young, Douglas and Dziembowski, Andrzej (2019) In Nucleic Acids Research 47(11). p.5892-5905
Abstract

The phenotypic adjustments of Mycobacterium tuberculosis are commonly inferred from the analysis of transcript abundance. While mechanisms of transcriptional regulation have been extensively analysed in mycobacteria, little is known about mechanisms that shape the transcriptome by regulating RNA decay rates. The aim of the present study is to identify the core components of the RNA degradosome of M. tuberculosis and to analyse their function in RNA metabolism. Using an approach involving cross-linking to 4-thiouridine-labelled RNA, we mapped the mycobacterial RNA-bound proteome and identified degradosome-related enzymes polynucleotide phosphorylase (PNPase), ATP-dependent RNA helicase (RhlE), ribonuclease E (RNase E) and ribonuclease J... (More)

The phenotypic adjustments of Mycobacterium tuberculosis are commonly inferred from the analysis of transcript abundance. While mechanisms of transcriptional regulation have been extensively analysed in mycobacteria, little is known about mechanisms that shape the transcriptome by regulating RNA decay rates. The aim of the present study is to identify the core components of the RNA degradosome of M. tuberculosis and to analyse their function in RNA metabolism. Using an approach involving cross-linking to 4-thiouridine-labelled RNA, we mapped the mycobacterial RNA-bound proteome and identified degradosome-related enzymes polynucleotide phosphorylase (PNPase), ATP-dependent RNA helicase (RhlE), ribonuclease E (RNase E) and ribonuclease J (RNase J) as major components. We then carried out affinity purification of eGFP-tagged recombinant constructs to identify protein-protein interactions. This identified further interactions with cold-shock proteins and novel KH-domain proteins. Engineering and transcriptional profiling of strains with a reduced level of expression of core degradosome ribonucleases provided evidence of important pleiotropic roles of the enzymes in mycobacterial RNA metabolism highlighting their potential vulnerability as drug targets.

(Less)
Please use this url to cite or link to this publication:
author
; ; ; ; ; ; ; ; and
publishing date
type
Contribution to journal
publication status
published
subject
keywords
DEAD-box RNA Helicases/metabolism, Endoribonucleases/metabolism, Escherichia coli/genetics, Escherichia coli Proteins/metabolism, Multienzyme Complexes, Mycobacterium smegmatis/metabolism, Mycobacterium tuberculosis/metabolism, Polyribonucleotide Nucleotidyltransferase/genetics, Proteome, Proteomics, RNA/analysis, RNA Helicases/metabolism, RNA Stability, RNA, Bacterial/metabolism, Ribonuclease III/metabolism, Ribonucleases/metabolism, Thiouridine/chemistry, Transcriptome
in
Nucleic Acids Research
volume
47
issue
11
pages
14 pages
publisher
Oxford University Press
external identifiers
  • scopus:85068489657
  • pmid:30957850
ISSN
1362-4962
DOI
10.1093/nar/gkz251
language
English
LU publication?
no
additional info
© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.
id
34bb855a-b175-4dab-ac47-c800425f30a8
date added to LUP
2020-11-17 17:40:43
date last changed
2025-07-13 03:03:06
@article{34bb855a-b175-4dab-ac47-c800425f30a8,
  abstract     = {{<p>The phenotypic adjustments of Mycobacterium tuberculosis are commonly inferred from the analysis of transcript abundance. While mechanisms of transcriptional regulation have been extensively analysed in mycobacteria, little is known about mechanisms that shape the transcriptome by regulating RNA decay rates. The aim of the present study is to identify the core components of the RNA degradosome of M. tuberculosis and to analyse their function in RNA metabolism. Using an approach involving cross-linking to 4-thiouridine-labelled RNA, we mapped the mycobacterial RNA-bound proteome and identified degradosome-related enzymes polynucleotide phosphorylase (PNPase), ATP-dependent RNA helicase (RhlE), ribonuclease E (RNase E) and ribonuclease J (RNase J) as major components. We then carried out affinity purification of eGFP-tagged recombinant constructs to identify protein-protein interactions. This identified further interactions with cold-shock proteins and novel KH-domain proteins. Engineering and transcriptional profiling of strains with a reduced level of expression of core degradosome ribonucleases provided evidence of important pleiotropic roles of the enzymes in mycobacterial RNA metabolism highlighting their potential vulnerability as drug targets.</p>}},
  author       = {{Płociński, Przemysław and Macios, Maria and Houghton, Joanna and Niemiec, Emilia and Płocińska, Renata and Brzostek, Anna and Słomka, Marcin and Dziadek, Jarosław and Young, Douglas and Dziembowski, Andrzej}},
  issn         = {{1362-4962}},
  keywords     = {{DEAD-box RNA Helicases/metabolism; Endoribonucleases/metabolism; Escherichia coli/genetics; Escherichia coli Proteins/metabolism; Multienzyme Complexes; Mycobacterium smegmatis/metabolism; Mycobacterium tuberculosis/metabolism; Polyribonucleotide Nucleotidyltransferase/genetics; Proteome; Proteomics; RNA/analysis; RNA Helicases/metabolism; RNA Stability; RNA, Bacterial/metabolism; Ribonuclease III/metabolism; Ribonucleases/metabolism; Thiouridine/chemistry; Transcriptome}},
  language     = {{eng}},
  month        = {{06}},
  number       = {{11}},
  pages        = {{5892--5905}},
  publisher    = {{Oxford University Press}},
  series       = {{Nucleic Acids Research}},
  title        = {{Proteomic and transcriptomic experiments reveal an essential role of RNA degradosome complexes in shaping the transcriptome of Mycobacterium tuberculosis}},
  url          = {{http://dx.doi.org/10.1093/nar/gkz251}},
  doi          = {{10.1093/nar/gkz251}},
  volume       = {{47}},
  year         = {{2019}},
}