Mycobacterial RNA Polymerase Requires a U-Tract at Intrinsic Terminators and Is Aided by NusG at Suboptimal Terminators

ABSTRACT Intrinsic terminators, which encode GC-rich RNA hairpins followed immediately by a 7-to-9-nucleotide (nt) U-rich “U-tract,” play principal roles of punctuating and regulating transcription in most bacteria. However, canonical intrinsic terminators with strong U-tracts are underrepresented i...

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Autores principales:	Agata Czyz, Rachel A. Mooney, Ala Iaconi, Robert Landick
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2014
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/97483c40eae04b599fd751b684cea533
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spelling	oai:doaj.org-article:97483c40eae04b599fd751b684cea5332021-11-15T15:45:13ZMycobacterial RNA Polymerase Requires a U-Tract at Intrinsic Terminators and Is Aided by NusG at Suboptimal Terminators10.1128/mBio.00931-142150-7511https://doaj.org/article/97483c40eae04b599fd751b684cea5332014-05-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00931-14https://doaj.org/toc/2150-7511ABSTRACT Intrinsic terminators, which encode GC-rich RNA hairpins followed immediately by a 7-to-9-nucleotide (nt) U-rich “U-tract,” play principal roles of punctuating and regulating transcription in most bacteria. However, canonical intrinsic terminators with strong U-tracts are underrepresented in some bacterial lineages, notably mycobacteria, leading to proposals that their RNA polymerases stop at noncanonical intrinsic terminators encoding various RNA structures lacking U-tracts. We generated recombinant forms of mycobacterial RNA polymerase and its major elongation factors NusA and NusG to characterize mycobacterial intrinsic termination. Using in vitro transcription assays devoid of possible mycobacterial contaminants, we established that mycobacterial RNA polymerase terminates more efficiently than Escherichia coli RNA polymerase at canonical terminators with imperfect U-tracts but does not terminate at putative terminators lacking U-tracts even in the presence of mycobacterial NusA and NusG. However, mycobacterial NusG exhibits a novel termination-stimulating activity that may allow intrinsic terminators with suboptimal U-tracts to function efficiently. IMPORTANCE Bacteria rely on transcription termination to define and regulate units of gene expression. In most bacteria, precise termination and much regulation by attenuation are accomplished by intrinsic terminators that encode GC-rich hairpins and U-tracts necessary to disrupt stable transcription elongation complexes. Thus, the apparent dearth of canonical intrinsic terminators with recognizable U-tracts in mycobacteria is of significant interest both because noncanonical intrinsic terminators could reveal novel routes to destabilize transcription complexes and because accurate understanding of termination is crucial for strategies to combat mycobacterial diseases and for computational bioinformatics generally. Our finding that mycobacterial RNA polymerase requires U-tracts for intrinsic termination, which can be aided by NusG, will guide future study of mycobacterial transcription and aid improvement of predictive algorithms to annotate bacterial genome sequences.Agata CzyzRachel A. MooneyAla IaconiRobert LandickAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 5, Iss 2 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Agata Czyz Rachel A. Mooney Ala Iaconi Robert Landick Mycobacterial RNA Polymerase Requires a U-Tract at Intrinsic Terminators and Is Aided by NusG at Suboptimal Terminators
description	ABSTRACT Intrinsic terminators, which encode GC-rich RNA hairpins followed immediately by a 7-to-9-nucleotide (nt) U-rich “U-tract,” play principal roles of punctuating and regulating transcription in most bacteria. However, canonical intrinsic terminators with strong U-tracts are underrepresented in some bacterial lineages, notably mycobacteria, leading to proposals that their RNA polymerases stop at noncanonical intrinsic terminators encoding various RNA structures lacking U-tracts. We generated recombinant forms of mycobacterial RNA polymerase and its major elongation factors NusA and NusG to characterize mycobacterial intrinsic termination. Using in vitro transcription assays devoid of possible mycobacterial contaminants, we established that mycobacterial RNA polymerase terminates more efficiently than Escherichia coli RNA polymerase at canonical terminators with imperfect U-tracts but does not terminate at putative terminators lacking U-tracts even in the presence of mycobacterial NusA and NusG. However, mycobacterial NusG exhibits a novel termination-stimulating activity that may allow intrinsic terminators with suboptimal U-tracts to function efficiently. IMPORTANCE Bacteria rely on transcription termination to define and regulate units of gene expression. In most bacteria, precise termination and much regulation by attenuation are accomplished by intrinsic terminators that encode GC-rich hairpins and U-tracts necessary to disrupt stable transcription elongation complexes. Thus, the apparent dearth of canonical intrinsic terminators with recognizable U-tracts in mycobacteria is of significant interest both because noncanonical intrinsic terminators could reveal novel routes to destabilize transcription complexes and because accurate understanding of termination is crucial for strategies to combat mycobacterial diseases and for computational bioinformatics generally. Our finding that mycobacterial RNA polymerase requires U-tracts for intrinsic termination, which can be aided by NusG, will guide future study of mycobacterial transcription and aid improvement of predictive algorithms to annotate bacterial genome sequences.
format	article
author	Agata Czyz Rachel A. Mooney Ala Iaconi Robert Landick
author_facet	Agata Czyz Rachel A. Mooney Ala Iaconi Robert Landick
author_sort	Agata Czyz
title	Mycobacterial RNA Polymerase Requires a U-Tract at Intrinsic Terminators and Is Aided by NusG at Suboptimal Terminators
title_short	Mycobacterial RNA Polymerase Requires a U-Tract at Intrinsic Terminators and Is Aided by NusG at Suboptimal Terminators
title_full	Mycobacterial RNA Polymerase Requires a U-Tract at Intrinsic Terminators and Is Aided by NusG at Suboptimal Terminators
title_fullStr	Mycobacterial RNA Polymerase Requires a U-Tract at Intrinsic Terminators and Is Aided by NusG at Suboptimal Terminators
title_full_unstemmed	Mycobacterial RNA Polymerase Requires a U-Tract at Intrinsic Terminators and Is Aided by NusG at Suboptimal Terminators
title_sort	mycobacterial rna polymerase requires a u-tract at intrinsic terminators and is aided by nusg at suboptimal terminators
publisher	American Society for Microbiology
publishDate	2014
url	https://doaj.org/article/97483c40eae04b599fd751b684cea533
work_keys_str_mv	AT agataczyz mycobacterialrnapolymeraserequiresautractatintrinsicterminatorsandisaidedbynusgatsuboptimalterminators AT rachelamooney mycobacterialrnapolymeraserequiresautractatintrinsicterminatorsandisaidedbynusgatsuboptimalterminators AT alaiaconi mycobacterialrnapolymeraserequiresautractatintrinsicterminatorsandisaidedbynusgatsuboptimalterminators AT robertlandick mycobacterialrnapolymeraserequiresautractatintrinsicterminatorsandisaidedbynusgatsuboptimalterminators
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Mycobacterial RNA Polymerase Requires a U-Tract at Intrinsic Terminators and Is Aided by NusG at Suboptimal Terminators

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