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Gtari M. Taxogenomic status of phylogenetically distant Frankia clusters warrants their elevation to the rank of genus: A description of Protofrankia gen. nov., Parafrankia gen. nov., and Pseudofrankia gen. nov. as three novel genera within the family Frankiaceae. Front Microbiol 2022; 13:1041425. [PMID: 36425027 PMCID: PMC9680954 DOI: 10.3389/fmicb.2022.1041425] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/12/2022] [Indexed: 11/10/2022] Open
Abstract
The genus Frankia is at present the sole genus in the family Frankiaceae and encompasses filamentous, sporangia-forming actinomycetes principally isolated from root nodules of taxonomically disparate dicotyledonous hosts named actinorhizal plants. Multiple independent phylogenetic analyses agree with the division of the genus Frankia into four well-supported clusters. Within these clusters, Frankia strains are well defined based on host infectivity range, mode of infection, morphology, and their behaviour in culture. In this study, phylogenomics, overall genome related indices (OGRI), together with available data sets for phenotypic and host-plant ranges available for the type strains of Frankia species, were considered. The robustness and the deep radiation observed in Frankia at the subgeneric level, fulfilling the primary principle of phylogenetic systematics, were strengthened by establishing genome criteria for new genus demarcation boundaries. Therefore, the taxonomic elevation of the Frankia clusters to the rank of the genus is proposed. The genus Frankia should be revised to encompass cluster 1 species only and three novel genera, Protofrankia gen. nov., Parafrankia gen. nov., and Pseudofrankia gen. nov., are proposed to accommodate clusters 2, 3, and 4 species, respectively. New combinations for validly named species are also provided.
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Affiliation(s)
- Maher Gtari
- USCR Bactériologie Moléculaire & Génomique, Institut National des Sciences Appliquées et de Technologie, Université de Carthage, Tunis, Tunisia
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Alnus glutinosa seedlings grown following co-inoculation with Frankia torreyi strain CpI1 and Frankia asymbiotica strain NRRL B-16386. Symbiosis 2022. [DOI: 10.1007/s13199-022-00845-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Spink BC, Bloom MS, Wu S, Sell S, Schneider E, Ding X, Spink DC. Analysis of the AHR gene proximal promoter GGGGC-repeat polymorphism in lung, breast, and colon cancer. Toxicol Appl Pharmacol 2014; 282:30-41. [PMID: 25447411 DOI: 10.1016/j.taap.2014.10.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 09/26/2014] [Accepted: 10/27/2014] [Indexed: 02/05/2023]
Abstract
The aryl hydrocarbon receptor (AhR) regulates expression of numerous genes, including those of the CYP1 gene family. With the goal of determining factors that control AHR gene expression, our studies are focused on the role of the short tandem repeat polymorphism, (GGGGC)n, located in the proximal promoter of the human AHR gene. When luciferase constructs containing varying GGGGC repeats were transfected into cancer cell lines derived from the lung, colon, and breast, the number of GGGGC repeats affected AHR promoter activity. The number of GGGGC repeats was determined in DNA from 327 humans and from 38 samples representing 5 species of non-human primates. In chimpanzees and 3 species of macaques, only (GGGGC)2 alleles were observed; however, in western gorilla, (GGGGC)n alleles with n=2, 4, 5, 6, 7, and 8 were identified. In all human populations examined, the frequency of (GGGGC)n was n=4>5≫2, 6. When frequencies of the (GGGGC)n alleles in DNA from patients with lung, colon, or breast cancer were evaluated, the occurrence of (GGGGC)2 was found to be 8-fold more frequent among lung cancer patients in comparison with its incidence in the general population, as represented by New York State neonates. Analysis of matched tumor and non-tumor DNA samples from the same individuals provided no evidence of microsatellite instability. These studies indicate that the (GGGGC)n short tandem repeats are inherited, and that the (GGGGC)2 allele in the AHR proximal promoter region should be further investigated with regard to its potential association with lung cancer susceptibility.
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Affiliation(s)
- Barbara C Spink
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States
| | - Michael S Bloom
- Department of Environmental Health Sciences, School of Public Health, University at Albany, State University of New York, Albany, NY 12201, United States
| | - Susan Wu
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States
| | - Stewart Sell
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States; Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Albany, NY 12201, United States
| | - Erasmus Schneider
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States; Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Albany, NY 12201, United States
| | - Xinxin Ding
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States; Department of Environmental Health Sciences, School of Public Health, University at Albany, State University of New York, Albany, NY 12201, United States; Department of Biomedical Sciences, School of Public Health, University at Albany, State University of New York, Albany, NY 12201, United States
| | - David C Spink
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, United States; Department of Environmental Health Sciences, School of Public Health, University at Albany, State University of New York, Albany, NY 12201, United States.
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Ghodhbane-Gtari F, Nouioui I, Chair M, Boudabous A, Gtari M. 16S-23S rRNA intergenic spacer region variability in the genus Frankia. MICROBIAL ECOLOGY 2010; 60:487-495. [PMID: 20179918 DOI: 10.1007/s00248-010-9641-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2009] [Accepted: 02/02/2010] [Indexed: 05/28/2023]
Abstract
16S-23S rRNA internally transcribed spacer (ITS) sequences from 53 Frankia strains were sequenced and sized from polymerase chain reaction amplification products and compiled with 14 selected 16S-23S ITS sequences from public database. Frankia genomes included two to three ITS copies lacking length polymorphism except for nine strains. No tRNA gene was encountered in this region. Frankia strains exhibited various lengths (369 to 452 nt) and a wide range of sequence similarity (35-100%) in the ITS region. The average pairwise distance varied from 0.368 (clusters 1 and 2) to 0.964 (clusters 3 and 4) and was 0.397, 0.138, 0.129, and 0.016, respectively, for cluster 4 (saprophytic non-infective/non-effective), clusters 1 and 3 (facultative symbiotic), and cluster 2 (obligate symbiotic). This suggests a gradual erosion of Frankia diversity concomitantly with a shift from saprophytic non-infective/non-effective to facultative and symbiotic lifestyle. Comparative sequence analyses of the 16S-23S rRNA intergenic spacer region of Frankia strains are not useful to assign them to their respective cluster or host infection group. Accurate assignment required the inclusion of the adjacent 16S and 23S rRNA gene fragments.
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Affiliation(s)
- Faten Ghodhbane-Gtari
- Laboratoire Microorganismes and Biomolécules Actives, Département de Biologie, Faculté des Sciences de Tunis, Campus Universitaire, 2092 Tunis, Tunisia
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Reverse transcription of 16S rRNA to monitor ribosome-synthesizing bacterial populations in the environment. Appl Environ Microbiol 2009; 75:4589-98. [PMID: 19395563 DOI: 10.1128/aem.02970-08] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Identification and quantification of phylogenetically defined bacterial populations in the environment are often performed using molecular tools targeting 16S rRNA. Fluorescence in situ hybridization has been used to monitor the expression and processing of rRNA by targeting the 3' tail of precursor 16S rRNA. To expand this approach, we employed reverse transcription of total RNA using primer S-D-Bact-0338-a-A-18. Length heterogeneity detected by slab gel analysis, denaturing high-performance liquid chromatography (DHPLC) was used to differentiate the 5' tail of the precursor from mature 16S rRNA, and the relative abundance of the precursor compared to the abundance of mature 16S rRNA was shown to be a sensitive indicator of the physiologic state of Acinetobacter calcoaceticus ATCC 23055(T). Our results demonstrate that this is a sensitive and reliable method with a detection limit of 10 ng of single-stranded DNA. The assay was also used to differentiate among precursor 16S rRNA levels with mixed pure cultures, as well as to examine the response of a mixed activated sludge culture exposed to fresh growth medium and the antibiotic chloramphenicol. The results of this study demonstrate that this assay is a novel reverse transcription assay that simultaneously measures the mature and precursor 16S rRNA pools for mixed bacterial populations in an engineered environment. Furthermore, collection of the reverse transcription products derived from activated sludge samples by the DHPLC approach enabled identification of the active bacterial genera. Comparison of 16S and precursor 16S rRNA clone library results indicated that the precursor 16S rRNA library is a more sensitive indicator for active bacteria in engineered environmental samples.
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