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Sharts DM, Almanza MT, Banks AV, Castellanos AM, Hernandez CGO, Lopez ML, Rodriguez D, Tong AY, Segeberg MR, Passalacqua LFM, Abdelsayed MM. Robo-Therm, a pipeline to RNA thermometer discovery and validation. RNA (NEW YORK, N.Y.) 2024; 30:760-769. [PMID: 38565243 PMCID: PMC11182007 DOI: 10.1261/rna.079980.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 03/20/2024] [Indexed: 04/04/2024]
Abstract
RNA thermometers are highly structured noncoding RNAs located in the 5'-untranslated regions (UTRs) of genes that regulate expression by undergoing conformational changes in response to temperature. The discovery of RNA thermometers through bioinformatics is difficult because there is little sequence conservation among their structural elements. Thus, the abundance of these thermosensitive regulatory structures remains unclear. Herein, to advance the discovery and validation of RNA thermometers, we developed Robo-Therm, a pipeline that combines an adaptive and user-friendly in silico motif search with a well-established reporter system. Through our application of Robo-Therm, we discovered two novel RNA thermometers in bacterial and bacteriophage genomes found in the human gut. One of these thermometers is present in the 5'-UTR of a gene that codes for σ 70 RNA polymerase subunit in the bacteria Mediterraneibacter gnavus and Bacteroides pectinophilus, and in the bacteriophage Caudoviricetes, which infects B. pectinophilus The other thermometer is in the 5'-UTR of a tetracycline resistance gene (tetR) in the intestinal bacteria Escherichia coli and Shigella flexneri Our Robo-Therm pipeline can be applied to discover multiple RNA thermometers across various genomes.
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Affiliation(s)
- Davis M Sharts
- Department of Biology, California Lutheran University, Thousand Oaks, California 91360, USA
| | - Maria T Almanza
- Department of Biology, California Lutheran University, Thousand Oaks, California 91360, USA
| | - Andrea V Banks
- Department of Biology, California Lutheran University, Thousand Oaks, California 91360, USA
| | - Alyssa M Castellanos
- Department of Biology, California Lutheran University, Thousand Oaks, California 91360, USA
| | | | - Monica L Lopez
- Department of Biology, California Lutheran University, Thousand Oaks, California 91360, USA
| | - Daniela Rodriguez
- Department of Biology, California Lutheran University, Thousand Oaks, California 91360, USA
| | - Alina Y Tong
- Department of Biology, California Lutheran University, Thousand Oaks, California 91360, USA
| | - Maximilian R Segeberg
- Department of Biology, California Lutheran University, Thousand Oaks, California 91360, USA
| | - Luiz F M Passalacqua
- Laboratory of Nucleic Acids, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Michael M Abdelsayed
- Department of Biology, California Lutheran University, Thousand Oaks, California 91360, USA
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Wang Q, Wang BY, Pratap S, Xie H. Oral microbiome associated with differential ratios of Porphyromonas gingivalis and Streptococcus cristatus. Microbiol Spectr 2024; 12:e0348223. [PMID: 38230927 PMCID: PMC10846039 DOI: 10.1128/spectrum.03482-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/18/2023] [Indexed: 01/18/2024] Open
Abstract
Periodontitis has recently been defined as a dysbiotic disease caused by an imbalanced oral microbiota. The transition from commensal microbial communities to periodontitis-associated ones requires colonization by specific pathogens, including Porphyromonas gingivalis. We previously reported an antagonistic relationship between Streptococcus cristatus and P. gingivalis. To determine the role of S. cristatus in altering the interactions of P. gingivalis with other oral bacteria in a complex context, we collected dental plaque samples from patients with periodontitis and assigned them to two groups based on the ratios of S. cristatus and P. gingivalis. We then characterized the microbial profiles of the dental plaque samples using shotgun metagenomic sequencing and compared the oral microbial composition and functional capabilities of the group with high S. cristatus-P. gingivalis ratios with the low ratio group. Taxonomic annotation revealed significant differences in the microbial composition at both the genus and species levels between the low and high S. cristatus-P. gingivalis ratio groups. Notably, a higher microbial diversity was observed in the samples with low S. cristatus-P. gingivalis ratios. Furthermore, the antibiotic resistance gene profiles of the two groups were also distinct, with a significantly increased abundance of the genes in the dental plaque samples with low S. cristatus-P. gingivalis ratios. It, therefore, indicates that the S. cristatus-P. gingivalis ratios influenced the virulence potential of the oral microbiome. Our work shows that enhancing the S. cristatus-P. gingivalis ratio in oral microbial communities can be an attractive approach for revising the dysbiotic oral microbiome.IMPORTANCEPeriodontitis, one of the most common chronic diseases, is linked to several systemic diseases, such as cardiovascular disease and diabetes. Although Porphyromonas gingivalis is a keystone pathogen that causes periodontitis, its levels, interactions with accessory bacteria and pathobionts in the oral microbiome, and its association with the pathogenic potential of the microbial communities are still not well understood. In this study, we revealed the role of Streptococcus cristatus and the ratios of S. cristatus and P. gingivalis in modulating the oral microbiome to facilitate a deeper understanding of periodontitis and its progression. The study has important clinical implications as it laid a foundation for developing novel non-antibiotic therapies against P. gingivalis and improving the efficiency of periodontal treatments.
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Affiliation(s)
- Qingguo Wang
- School of Applied Computational Sciences, Meharry Medical College, Nashville, Tennessee, USA
| | - Bing-Yan Wang
- School of Dentistry, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Siddharth Pratap
- School of Medicine, Meharry Medical College, Nashville, Tennessee, USA
| | - Hua Xie
- School of Dentistry, Meharry Medical College, Nashville, Tennessee, USA
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