Diversity of 5S rRNA genes within individual prokaryotic genomes

Pei, Anna; Li, Hongru; Oberdorf, William E.; Alekseyenko, Alexander V.; Parsons, Tamasha; Yang, Liying; Gerz, Erika A.; Lee, Peng; Xiang, Charlie; Nossa, Carlos W.; Pei, Zhiheng

doi:10.1111/j.1574-6968.2012.02632.x

Cited by 13 publications

(8 citation statements)

References 25 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…variecolor NRRL 1858 displays branched unpaired region where as isolate CLB38 appeared linear in structure and also variations in stem/loop transition were observed ( Fig 5 ). ITS2 RNA structures are sensible to single base changes which in turn can affect hydrogen base pairing in stem and loop secondary structures [ 50 ].A non-conserved mismatches might altered base-pairing and stem to loop transitions by counterparts [ 42 , 51 ]. Studies have reported many fungi might express different life-styles in response to environmental factors or host genotype [ 52 ].…”

Section: Resultsmentioning

confidence: 99%

“…Specifically, a series of emerimidine (A-B) derived from endophytic fungus Emericella sp. HK-ZJ which isolated from the inner bark of the mangrove plant Aegiceras corniculatum (Myrsinaceae) has been reported to show anti-influenza A viral (H 1 N 1 ) activity [ 51 ]. Thus, from the present study, it suggests that the antimicrobial potential of these isolated metabolites might play a significant role in symbiotic benefits of endosymbiont to the host.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Chemogenomics driven discovery of endogenous polyketide anti-infective compounds from endosymbiotic Emericella variecolor CLB38 and their RNA secondary structure analysis

et al. 2017

View full text Add to dashboard Cite

In the postgenomic era, a new strategy for chemical dereplication of polyketide anti-infective drugs requires novel genomics and chromatographic strategies. An endosymbiotic fungal strain CLB38 was isolated from the root tissue of Combretum latifolium Blume (Combretaceae) which was collected from the Western Ghats of India. The isolate CLB38 was then identified as Emericella variecolor by its characteristic stellate ascospores culture morphology and molecular analysis of ITS nuclear rDNA and intervening 5.8S rRNA gene sequence. ITS2 RNA secondary structure modeling clearly distinguished fungal endosymbiont E. variecolor CLB38 with other lifestyles in the same monophyletic clade. Ethyl acetate fraction of CLB38 explored a broad spectrum of antimicrobial activity against multidrug resistant pathogens. Biosynthetic PKS type-I gene and chromatographic approach afford two polyketide antimicrobial compounds which identified as evariquinone and isoindolones derivative emerimidine A. MIC of purified compounds against test microorganisms ranged between 3.12 μg/ml and 12.5 μg/ml. This research highlights the utility of E. variecolor CLB38 as an anticipate source for anti-infective polyketide metabolites evariquinone and emerimidine A to combat multidrug resistant microorganisms. Here we demonstrates a chemogenomics strategy via the feasibility of PKS type-I gene and chromatographic approach as a proficient method for the rapid prediction and discovery of new polyketides compounds from fungal endosymbionts.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Chemogenomics driven discovery of endogenous polyketide anti-infective compounds from endosymbiotic Emericella variecolor CLB38 and their RNA secondary structure analysis

et al. 2017

View full text Add to dashboard Cite

show abstract

“…Species of bacteria often contain multiple copies of the ribosomal operon, and each has its own distinct phylogenetic diversity; intragenomic variability in the 16S gene has been studied most commonly (Větrovský and Baldrian 2013;Coenye and Vandamme 2003) , but there are also studies on the 23S and 5S genes (Pei et al 2012(Pei et al , 2009) . When we consider the evolutionary history of all copies of the ribosomal RNA operons from a given species, one underlying assumption is that all those copies should be monophyletic, i.e.…”

mentioning

confidence: 99%

Taxonomic resolution of the ribosomal RNA operon in bacteria: Implications for its use with long read sequencing

Martins

Page

Charles

2019

Preprint

View full text Add to dashboard Cite

show abstract

“…Species of bacteria often contain multiple copies of the ribosomal operon, and each has its own distinct phylogenetic diversity; intragenomic variability in the 16S gene has been studied most commonly ( 20 , 21 ), but there are also studies on the 23S and 5S genes ( 22 , 23 ). When we consider the evolutionary history of all copies of the ribosomal RNA operons from a given species, one underlying assumption is that all those copies should be monophyletic, i.e.…”

Section: Resultsmentioning

confidence: 99%

Taxonomic resolution of the ribosomal RNA operon in bacteria: implications for its use with long-read sequencing

Martins

Page

Mather

et al. 2019

NAR Genomics and Bioinformatics

View full text Add to dashboard Cite

DNA barcoding through the use of amplified regions of the ribosomal operon, such as the 16S gene, is a routine method to gain an overview of the microbial taxonomic diversity within a sample without the need to isolate and culture the microbes present. However, bacterial cells usually have multiple copies of this ribosomal operon, and choosing the ‘wrong’ copy could provide a misleading species classification. While this presents less of a problem for well-characterized organisms with large sequence databases to interrogate, it is a significant challenge for lesser known organisms with unknown copy number and diversity. Using the entire length of the ribosomal operon, which encompasses the 16S, 23S, 5S and internal transcribed spacer regions, should provide greater taxonomic resolution but has not been well explored. Here, we use publicly available reference genomes and explore the theoretical boundaries when using concatenated genes and the full-length ribosomal operons, which has been made possible by the development and uptake of long-read sequencing technologies. We quantify the issues of both copy choice and operon length in a phylogenetic context to demonstrate that longer regions improve the phylogenetic signal while maintaining taxonomic accuracy.

show abstract

Diversity of 5S rRNA genes within individual prokaryotic genomes

Cited by 13 publications

References 25 publications

Chemogenomics driven discovery of endogenous polyketide anti-infective compounds from endosymbiotic Emericella variecolor CLB38 and their RNA secondary structure analysis

Chemogenomics driven discovery of endogenous polyketide anti-infective compounds from endosymbiotic Emericella variecolor CLB38 and their RNA secondary structure analysis

Taxonomic resolution of the ribosomal RNA operon in bacteria: Implications for its use with long read sequencing

Taxonomic resolution of the ribosomal RNA operon in bacteria: implications for its use with long-read sequencing

Contact Info

Product

Resources

About