A structural perspective of human RNA polymerase III

Wang, Qianmin; Lei, Ming; Wu, Jian

doi:10.1080/15476286.2021.2022293

Cited by 3 publications

(3 citation statements)

References 74 publications

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“…DNA and RNA were extracted simultaneously following the mirVana miRNA isolation kit for RNA protocol (Ambion, ThermoFisher Scientific, Waltham, MA). We chose this isolation kit as it is designed to efficiently isolate small RNAs (<200 nt) as well as total RNA which play a crucial role in regulating bacterial global gene expression and is routinely used for microbiome studies (Azpiroz et al 2021; Tong, Tang, and Wang 2023; Yost et al 2018). For RNA isolation, genomic DNA was removed using a Turbo DNA-free kit (Applied Biosystems, Ambion).…”

Section: Methodsmentioning

confidence: 99%

Heterogeneous lineage-specific arginine deiminase expression within dental microbiome species

Mann,

Chakraborty,

O’Connell

et al. 2023

Preprint

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Arginine catabolism by the bacterial arginine deiminase system (ADS) has anticariogenic properties through the production of ammonia, which modulates the pH of the oral environment. Given the potential protective capacity of the ADS pathway, the exploitation of ADS competent oral microbes through pre- or probiotic applications is a promising therapeutic target to prevent tooth decay. To date, most investigations of the ADS in the oral cavity and its relation to caries have focused on indirect measures of activity, or on specific bacterial groups, yet the pervasiveness and rate of expression of the ADS operon in diverse mixed microbial communities in oral health and disease remains an open question. Here we use a multivariate approach, combining ultra-deep metatranscriptomic sequencing with paired metataxonomic andin vitrocitrulline quantification to characterize the microbial community and ADS operon expression in healthy and late-stage cavitated teeth. While ADS activity is higher in healthy teeth, we identify multiple bacterial lineages with upregulated ADS activity on cavitated teeth that are distinct from those found on healthy teeth using both reference-based mapping anddenovoassembly methods. Our dual metataxonomic and metatranscriptomic approach demonstrates the importance of species abundance for gene expression data interpretation and that patterns of differential expression can be skewed by low abundance groups. Finally, we identify several potential candidate probiotic bacterial lineages within species that may be useful therapeutic targets for the prevention of tooth decay and propose that the development of a strain-specific, mixed-microbial probiotic may be a beneficial approach given the heterogeneity of taxa identified here across health groups.IMPORTANCETooth decay is the most common preventable chronic disease, globally affecting more than two billion people. The development of caries on teeth is primarily a consequence of acid production by cariogenic bacteria that inhabit the plaque microbiome. Other bacterial strains in the oral cavity may suppress or prevent tooth decay by producing ammonia as a byproduct of the arginine deiminase metabolic pathway, increasing the pH of the plaque biofilm. While the benefits of arginine metabolism on oral health have been extensively documented in specific bacterial groups, the prevalence and consistency of ADS activity among oral bacteria in a community context remains an open question. In the current study, we use a multi-omics approach to document the pervasiveness of expression of the ADS operon in both health and disease to better understand the conditions in which ADS activity may prevent tooth decay.

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Section: Methodsmentioning

confidence: 99%

Heterogeneous lineage-specific arginine deiminase expression within dental microbiome species

Mann,

Chakraborty,

O’Connell

et al. 2023

Preprint

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“…C-terminal deletion of the RPC7 ortholog in yeast, as well as alanine substitution at residues occupying the active center cause severe growth defects or death, suggesting an essential role in Pol III function ( Thuillier et al, 1995 ; Wang et al, 2021 ). Current models propose interactions between RPC7 and TFIIIB subunit BRF1 may restructure the RPC7 C-terminal tail to facilitate Pol III transcription initiation ( Wang et al, 2022 ). Further deconstructing the role of the N- and C-termini of RPC7 subunits is critical for understanding the functions and putative differences between RPC7α or RPC7β in Pol III transcription and regulation.…”

Section: Divergent Protein Sequence and Implications For Rpc7α And Rp...mentioning

confidence: 99%

RNA polymerase III transcription and cancer: A tale of two RPC7 subunits

Cheng

Bortle²

2023

Front. Mol. Biosci.

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RNA polymerase III composition is shaped by the mutually exclusive incorporation of two paralogous subunits, RPC7α and RPC7β, encoded by genes POLR3G and POLR3GL in vertebrates. The expression of POLR3G and POLR3GL is spatiotemporally regulated during development, and multiple reports point to RPC7α-enhanced Pol III activity patterns, indicating that Pol III identity may underly dynamic Pol III transcription patterns observed in higher eukaryotes. In cancer, upregulation of POLR3G, but not POLR3GL, is associated with poor survival outcomes among patients, suggesting differences between RPC7α and RPC7β further influence disease progression and may translate into future biomarkers and therapeutic strategies. Here, we outline our current understanding of Pol III identity and transcription and reexamine the distinct protein characteristics of Pol III subunits RPC7α and RPC7β. Drawing on both structural and genomic studies, we discuss differences between RPC7α and RPC7β and the potential mechanisms by which Pol III identity may establish differential activities during development and disease.

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“…The transcription process mainly involves initiation, elongation and termination, in which initiation is the most complicated ( 1 ). Promoters located proximal to the transcription start sites (TSS) are non-coding DNA regions, which are essential for initiating the transcription of a particular gene by cooperating with RNA polymerase (RNAP) ( 2 , 3 ) and are critical for gene expression in different species.…”

Section: Introductionmentioning

confidence: 99%

iPro-WAEL: a comprehensive and robust framework for identifying promoters in multiple species

Zhang

2022

Nucleic Acids Research

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Promoters are consensus DNA sequences located near the transcription start sites and they play an important role in transcription initiation. Due to their importance in biological processes, the identification of promoters is significantly important for characterizing the expression of the genes. Numerous computational methods have been proposed to predict promoters. However, it is difficult for these methods to achieve satisfactory performance in multiple species. In this study, we propose a novel weighted average ensemble learning model, termed iPro-WAEL, for identifying promoters in multiple species, including Human, Mouse, E.coli, Arabidopsis, B.amyloliquefaciens, B.subtilis and R.capsulatus. Extensive benchmarking experiments illustrate that iPro-WAEL has optimal performance and is superior to the current methods in promoter prediction. The experimental results also demonstrate a satisfactory prediction ability of iPro-WAEL on cross-cell lines, promoters annotated by other methods and distinguishing between promoters and enhancers. Moreover, we identify the most important transcription factor binding site (TFBS) motif in promoter regions to facilitate the study of identifying important motifs in the promoter regions. The source code of iPro-WAEL is freely available at https://github.com/HaoWuLab-Bioinformatics/iPro-WAEL.

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A structural perspective of human RNA polymerase III

Cited by 3 publications

References 74 publications

Heterogeneous lineage-specific arginine deiminase expression within dental microbiome species

Heterogeneous lineage-specific arginine deiminase expression within dental microbiome species

RNA polymerase III transcription and cancer: A tale of two RPC7 subunits

iPro-WAEL: a comprehensive and robust framework for identifying promoters in multiple species

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