Comprehensive transcription terminator atlas for Bacillus subtilis

Mandell, Zachary F.; Vishwakarma, Rishi K.; Yakhnin, Helen; Murakami, Katsuhiko; Kashlev, Mikhail; Babitzke, Paul

doi:10.1038/s41564-022-01240-7

Cited by 18 publications

(38 citation statements)

References 64 publications

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“…In bacteria, the factor-dependent termination is mediated by the transcription termination factor Rho, which terminates transcription at the Rho-dependent terminators present in many genes (2)(3)(4)(5). These two mechanisms can be combined: Rho stimulates termination at some intrinsic terminators (6,7) and at Rho-dependent terminators after readthrough of the Rho-stimulated intrinsic terminators (6). Thus, Rho plays a crucial role in defining the ends of genes and gene boundaries.…”

Section: Introductionmentioning

confidence: 99%

Structural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase from Thermus thermophilus

et al. 2023

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Transcription termination is an essential step in transcription by RNA polymerase (RNAP) and crucial for gene regulation. For many bacterial genes, transcription termination is mediated by the adenosine triphosphate–dependent RNA translocase/helicase Rho, which causes RNA/DNA dissociation from the RNAP elongation complex (EC). However, the structural basis of the interplay between Rho and RNAP remains obscure. Here, we report the cryo–electron microscopy structure of the Thermus thermophilus RNAP EC engaged with Rho. The Rho hexamer binds RNAP through the carboxyl-terminal domains, which surround the RNA exit site of RNAP, directing the nascent RNA seamlessly from the RNA exit to its central channel. The β-flap tip at the RNA exit is critical for the Rho-dependent RNA release, and its deletion causes an alternative Rho-RNAP binding mode, which is irrelevant to termination. The Rho binding site overlaps with the binding sites of other macromolecules, such as ribosomes, providing a general basis of gene regulation.

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Section: Introductionmentioning

confidence: 99%

Structural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase from Thermus thermophilus

et al. 2023

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“…Tandem terminations where both RITs and RDTs are involved in the termination process are attracting attention ( 43 , 44 ). The RDTs in these tandem terminators can be further classified as pure RDTs and hybrid RDTs.…”

Section: Discussionmentioning

confidence: 99%

“…This phenomenon leads to an indirect stimulatory effect of Rho on RIT. For hybrid RDTs, Rho stimulates termination at Rho-independent terminators by remodeling the RNA upstream of the Rho-independent terminators to prevent the formation of RNA structures that could otherwise compete with the terminator hairpin ( 43 ). In these cases, Rho showed a direct activating effect on RIT.…”

Section: Discussionmentioning

confidence: 99%

Identification of a Rho-Dependent Termination Site In Vivo Using Synthetic Small RNA

Wang

Jeon

et al. 2023

Microbiol Spectr

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“…We also observed that 45.2% of predicted mRNA intrinsic terminators have downstream Rho regions. An overlap between intrinsic and Rho-mediated termination was also observed in E. coli (Adams et al, 2021) and B. subtilis (Mandell et al, 2022). We carried out northern analysis on two B. burgdorferi examples, manA and ospD, with both significant intrinsic terminator scores and a downstream Rho region.…”

Section: Mechanisms Of B Burgdorferi Transcription Terminationmentioning

confidence: 96%

“…Recent studies have challenged the general view of two distinct termination processes. For example, intrinsic and Rho-mediated termination has been observed simultaneously at the same site, which may indicate they can function cooperatively (Adams et al, 2021; Mandell et al, 2022; Nagaraja et al, 2022). Protein factors, like the transcription-elongation factors NusA and NusG, may also play a role in stimulating intrinsic termination, as recently implicated in B. subtilis (Mandell et al, 2021; Mandell et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogenB. burgdorferi

Petroni

Esnault

Tetreault

et al. 2023

Preprint

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Transcription termination is an essential and dynamic process that can tune gene expression in response to diverse molecular signals. Yet, the genomic positions, molecular mechanisms, and regulatory consequences of termination have only been studied thoroughly in model bacteria. We employed complementary RNA-seq approaches to map RNA ends for the transcriptome of the spirochete Borrelia burgdorferi, the etiological agent of Lyme disease. By systematically mapping B. burgdorferi RNA ends at single nucleotide resolution, we delineated complex gene arrangements and operons and mapped untranslated regions (UTRs) and small RNAs (sRNAs). We experimentally tested modes of B. burgdorferi transcription termination and compared our findings to observations in E. coli, P. aeruginosa, and B. subtilis. We discovered 63% of B. burgdorferi RNA 3′ ends map upstream or internal to open reading frames (ORFs), suggesting novel mechanisms of regulation. Northern analysis confirmed the presence of stable 5′ derived RNAs from mRNAs encoding gene products involved in the unique infectious cycle of B. burgdorferi. We suggest these RNAs resulted from premature termination and regulatory events, including forms of cis-acting regulation. For example, we documented that the polyamine spermidine globally influences the generation of truncated mRNAs. In one case, we showed that high spermidine concentrations increased levels of RNA fragments derived from an mRNA encoding a spermidine import system, with a concomitant decrease in levels of the full-length mRNA. Collectively, our findings revealed new insight into transcription termination and uncovered an abundance of potential RNA regulators.

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Comprehensive transcription terminator atlas for Bacillus subtilis

Cited by 18 publications

References 64 publications

Structural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase from Thermus thermophilus

Structural basis of the transcription termination factor Rho engagement with transcribing RNA polymerase from Thermus thermophilus

Identification of a Rho-Dependent Termination Site In Vivo Using Synthetic Small RNA

Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogenB. burgdorferi

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