TY - JOUR

T1 - Proteomic and transcriptomic experiments reveal an essential role of RNA degradosome complexes in shaping the transcriptome of Mycobacterium tuberculosis

AU - Płociński, Przemysław

AU - MacIos, Maria

AU - Houghton, Joanna

AU - Niemiec, Emilia

AU - Płocińska, Renata

AU - Brzostek, Anna

AU - Słomka, Marcin

AU - Dziadek, Jarosław

AU - Young, Douglas

AU - Dziembowski, Andrzej

N1 - Funding Information: European Community’s Seventh Framework Programme (Health) [241587, SysteMTb to A.D., D.Y.]; National Science Centre, Poland [2015/19/D/NZ1/02842, SONATA 10 to P.P.]; at IBB PAS, experiments were carried out with the use of CePT infrastructure financed by the European Union: the European Regional Development Fund [Innovative economy 2007–13, Agreement POIG.02.02.00-14-024/08-00]. Funding for open access charge: National Science Centre, Poland [2015/19/D/NZ1/02842, SONATA 10 to P.P.]. Conflict of interest statement. None declared. Publisher Copyright: © The Author(s) 2019.

PY - 2019/6/20

Y1 - 2019/6/20

N2 - 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-thiouridinelabelled RNA, we mapped the mycobacterial RNAbound 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.

AB - 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-thiouridinelabelled RNA, we mapped the mycobacterial RNAbound 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.

UR - http://www.scopus.com/inward/record.url?scp=85068489657&partnerID=8YFLogxK

U2 - 10.1093/nar/gkz251

DO - 10.1093/nar/gkz251

M3 - Journal article

C2 - 30957850

AN - SCOPUS:85068489657

VL - 47

SP - 5892

EP - 5905

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - 11

ER -