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Fan W, Eklund E, Sherman RM, Liu H, Pitts S, Ford B, Rajeshkumar NV, Laiho M. Widespread genetic heterogeneity of human ribosomal RNA genes. RNA 2022; 28:478-492. [PMID: 35110373 PMCID: PMC8925967 DOI: 10.1261/rna.078925.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/28/2021] [Indexed: 05/28/2023]
Abstract
Polymorphism drives survival under stress and provides adaptability. Genetic polymorphism of ribosomal RNA (rRNA) genes derives from internal repeat variation of this multicopy gene, and from interindividual variation. A considerable amount of rRNA sequence heterogeneity has been proposed but has been challenging to estimate given the scarcity of accurate reference sequences. We identified four rDNA copies on chromosome 21 (GRCh38) with 99% similarity to recently introduced reference sequence KY962518.1. We customized a GATK bioinformatics pipeline using the four rDNA loci, spanning a total 145 kb, for variant calling and used high-coverage whole-genome sequencing (WGS) data from the 1000 Genomes Project to analyze variants in 2504 individuals from 26 populations. We identified a total of 3791 variant positions. The variants positioned nonrandomly on the rRNA gene. Invariant regions included the promoter, early 5' ETS, most of 18S, 5.8S, ITS1, and large areas of the intragenic spacer. A total of 470 variant positions were observed on 28S rRNA. The majority of the 28S rRNA variants were located on highly flexible human-expanded rRNA helical folds ES7L and ES27L, suggesting that these represent positions of diversity and are potentially under continuous evolution. Several variants were validated based on RNA-seq analyses. Population analyses showed remarkable ancestry-linked genetic variance and the presence of both high penetrance and frequent variants in the 5' ETS, ITS2, and 28S regions segregating according to the continental populations. These findings provide a genetic view of rRNA gene array heterogeneity and raise the need to functionally assess how the 28S rRNA variants affect ribosome functions.
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Affiliation(s)
- Wenjun Fan
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Eetu Eklund
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Rachel M Sherman
- Department of Computer Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Hester Liu
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Stephanie Pitts
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Brittany Ford
- Drug Research Program, Faculty of Pharmacy, University of Helsinki, 00014 Helsinki, Finland
| | - N V Rajeshkumar
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Marikki Laiho
- Department of Radiation Oncology and Molecular Radiation Sciences, and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
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Pérez-Ortín JE, Mena A, Barba-Aliaga M, Singh A, Chávez S, García-Martínez J. Cell volume homeostatically controls the rDNA repeat copy number and rRNA synthesis rate in yeast. PLoS Genet 2021; 17:e1009520. [PMID: 33826644 PMCID: PMC8055003 DOI: 10.1371/journal.pgen.1009520] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 04/19/2021] [Accepted: 03/25/2021] [Indexed: 01/20/2023] Open
Abstract
The adjustment of transcription and translation rates to the changing needs of cells is of utmost importance for their fitness and survival. We have previously shown that the global transcription rate for RNA polymerase II in budding yeast Saccharomyces cerevisiae is regulated in relation to cell volume. Total mRNA concentration is constant with cell volume since global RNApol II-dependent nascent transcription rate (nTR) also keeps constant but mRNA stability increases with cell size. In this paper, we focus on the case of rRNA and RNA polymerase I. Contrarily to that found for RNA pol II, we detected that RNA polymerase I nTR increases proportionally to genome copies and cell size in polyploid cells. In haploid mutant cells with larger cell sizes, the rDNA repeat copy number rises. By combining mathematical modeling and experimental work with the large-size cln3 strain, we observed that the increasing repeat copy number is based on a feedback mechanism in which Sir2 histone deacetylase homeostatically controls the amplification of rDNA repeats in a volume-dependent manner. This amplification is paralleled with an increase in rRNA nTR, which indicates a control of the RNA pol I synthesis rate by cell volume. Synthesis rates of biological macromolecules should be strictly regulated and adjusted to the changing conditions of cells. The change in volume is one of the commonest variables along individual cell life and also when comparing different cell types. We previously found that cells with asymmetric division, such as budding yeasts, use a compensatory change in the global RNA polymerase II synthesis rate and mRNA decay rate to maintain mRNA homeostasis. In the present study, we address the same issue for the RNA polymerase that makes rRNAs, which are essential components of ribosomes and the most abundant RNAs in the cell. We found that the copy number of the gene encoding 35S rRNA, transcribed by RNA polymerase I, changes proportionally to the cell volume in budding yeast via a feedback mechanism based on the Sir2 histone deacetylase, which guarantees that yeast cells have the appropriate RNA polymerase I synthesis rate required for rRNA homeostasis.
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Affiliation(s)
- José E. Pérez-Ortín
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, Burjassot, Spain
- * E-mail: (JEP-O); (JG-M)
| | - Adriana Mena
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, Burjassot, Spain
| | - Marina Barba-Aliaga
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, Burjassot, Spain
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of Delaware, Newark, DE, United States of America
| | - Sebastián Chávez
- Instituto de Biomedicina de Sevilla. Campus Hospital Universitario Virgen del Rocío, Seville, Spain
| | - José García-Martínez
- Instituto de Biotecnología y Biomedicina (Biotecmed), Universitat de València, Burjassot, Spain
- * E-mail: (JEP-O); (JG-M)
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Abstract
The maximum agreement subtree method determines the consensus of a collection of phylogenetic trees by identifying maximum cardinality subsets of leaves for which all input trees agree. The trees induced by these maximum cardinality subsets are maximum agreement subtrees (MASTs). A single MAST may be misleading, since there can exist two MASTs which share almost no leaves; nevertheless, it may be impossible to inspect all MASTs, since the number of MASTs can be exponential in the number of leaves. To overcome this drawback, Swenson et al. suggested to further summarize the information common to all MASTs by their intersection, which is called the kernel agreement subtree (KAST). The construction of the KAST is the focus of this paper. Swenson et al. had an O(kn3 + n4 + nd + 1) time algorithm for computing the KAST of k trees on n leaves, in which at least one tree has maximum degree d. In this paper, an O(kn3 + nd)-time algorithm is presented. We demonstrate the efficiency of our algorithm on simulated trees as well as on ribosomal RNA alignments, where trees with 13,000 taxa took only hours to process, whereas the previous algorithm did not terminate after a week of computation.
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Bittar F, Gouriet F, Khelaifia S, Raoult D, Ranque S. FastFung: A novel medium for the culture and isolation of fastidious fungal species from clinical samples. J Microbiol Methods 2020; 180:106108. [PMID: 33232796 DOI: 10.1016/j.mimet.2020.106108] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/26/2022]
Abstract
We developed a novel culture medium, referred to FastFung medium as suitable for the culture of clinical fungi, including fastidious ones, for both research and diagnostic studies. It is based on Schædler agar supplemented with many essential components for the growth of fastidious fungi. It also contains selective antibacterial agents for the inhibition of contaminant bacteria growth. In this preliminary study, the FastFung medium was compared to the gold standard Sabouraud medium for 98 fungal and 20 bacterial strains. The fungal strain positive culture rate was 100% vs. 95% and the bacterial strain inhibition was 100% vs. 20%, for the FastFung and Sabouraud media, respectively. When compared to the Sabouraud medium on 120 clinical samples, the FastFung medium displayed both a higher fungal colonies count, and a lower culture contamination rate. Storage at 4 °C for 4 weeks did not alter the FastFung culture medium performances for the six isolates of Candida, Cryptococcus, and Penicillium tested. These encouraging results suggest future development of using the FastFung medium in clinical mycology and in mycobiome characterization. Further prospective evaluation aiming at assessing whether implementing the FastFung medium in the routine workflow simplifies and strengthen fungal isolation capacities in the clinical laboratory is warranted.
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Affiliation(s)
- Fadi Bittar
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | - Frédérique Gouriet
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | - Saber Khelaifia
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France; IHU Méditerranée Infection, Marseille, France
| | - Stéphane Ranque
- Aix Marseille Univ, IRD, APHM, SSA, VITROME, Marseille, France; IHU Méditerranée Infection, Marseille, France.
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Borowska‐Zuchowska N, Kovarik A, Robaszkiewicz E, Tuna M, Tuna GS, Gordon S, Vogel JP, Hasterok R. The fate of 35S rRNA genes in the allotetraploid grass Brachypodium hybridum. Plant J 2020; 103:1810-1825. [PMID: 32506573 PMCID: PMC7497271 DOI: 10.1111/tpj.14869] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/20/2020] [Accepted: 05/28/2020] [Indexed: 05/22/2023]
Abstract
Nucleolar dominance (ND) consists of the reversible silencing of 35S/45S rDNA loci inherited from one of the ancestors of an allopolyploid. The molecular mechanisms by which one ancestral rDNA set is selected for silencing remain unclear. We applied a combination of molecular (Southern blot hybridization and reverse-transcription cleaved amplified polymorphic sequence analysis), genomic (analysis of variants) and cytogenetic (fluorescence in situ hybridization) approaches to study the structure, expression and epigenetic landscape of 35S rDNA in an allotetraploid grass that exhibits ND, Brachypodium hybridum (genome composition DDSS), and its putative progenitors, Brachypodium distachyon (DD) and Brachypodium stacei (SS). In progenitor genomes, B. stacei showed a higher intragenomic heterogeneity of rDNA compared with B. distachyon. In all studied accessions of B. hybridum, there was a reduction in the copy number of S homoeologues, which was accompanied by their inactive transcriptional status. The involvement of DNA methylation in CG and CHG contexts in the silencing of the S-genome rDNA loci was revealed. In the B. hybridum allotetraploid, ND is stabilized towards the D-genome units, irrespective of the polyphyletic origin of the species, and does not seem to be influenced by homoeologous 35S rDNA ratios and developmental stage.
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Affiliation(s)
- Natalia Borowska‐Zuchowska
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental ProtectionFaculty of Natural SciencesUniversity of Silesia in KatowiceJagiellonska 28Katowice40‐032Poland
| | - Ales Kovarik
- Department of Molecular EpigeneticsInstitute of BiophysicsAcademy of Sciences of the Czech Republic, v.v.i.Královopolská 135Brno612 65Czech Republic
| | - Ewa Robaszkiewicz
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental ProtectionFaculty of Natural SciencesUniversity of Silesia in KatowiceJagiellonska 28Katowice40‐032Poland
| | - Metin Tuna
- Department of Field CropsFaculty of AgricultureTekirdag Namik Kemal UniversitySuleymanpasaTekirdag59030Turkey
| | | | - Sean Gordon
- US Department of Energy (DOE) Joint Genome Institute (JGI)BerkeleyCA94720USA
| | - John P. Vogel
- US Department of Energy (DOE) Joint Genome Institute (JGI)BerkeleyCA94720USA
- University CaliforniaBerkeley, BerkeleyCA94720USA
| | - Robert Hasterok
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental ProtectionFaculty of Natural SciencesUniversity of Silesia in KatowiceJagiellonska 28Katowice40‐032Poland
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Horn IR, Verleg PA, Ibrahim NZ, Soeleman K, van Kampen F, Ruesen MO, Reulen NM, Breij H, Bakker RJ, Gravendeel B. Mushroom DNA barcoding project: Sequencing a segment of the 28S rRNA gene. Biochem Mol Biol Educ 2020; 48:404-410. [PMID: 32585770 PMCID: PMC7497104 DOI: 10.1002/bmb.21388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 04/22/2020] [Accepted: 05/18/2020] [Indexed: 06/11/2023]
Abstract
DNA barcoding is an important molecular methodology for species identification that was developed over the last two decades and it should be covered in the biology bachelor curriculum. Here, we present an example of DNA barcoding by sequencing a segment of the 28S nuclear ribosomal large subunit rRNA gene of wild mushrooms and framing the education in a project form for undergraduate students in biology. Students perform this project in 6-8 weeks, which also includes preparing a poster, writing a report and presenting a paper related to the work in a journal club format. First, fieldwork in the Netherlands was carried out, during which students collected mushrooms under supervision of a professional mycologist with the goal to (a) verify morphologically based identifications with a molecular method and (b) assess phylogenetic relationships of the different species collected. Next, DNA extractions and quantitation were performed, PCR amplification was done, and samples were sent out for Sanger sequencing. Students aligned and analyzed the sequences using BLAST and Geneious and subsequently created a phylogenetic tree. In case of collecting DNA barcodes of an earlier sequenced species, students could upload the data to a repository established for facilitation of future research projects. The method described is very robust, reagents and equipment are readily available, and costs are relatively low. In addition, the results can be compared to published fungal phylogenetic trees.
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Affiliation(s)
- Ivo R. Horn
- University of Applied Sciences Leiden, Faculty of Science and TechnologyLeidenThe Netherlands
- Naturalis Biodiversity Center, Endless Forms GroupLeidenThe Netherlands
- Leiden Centre for Applied BioscienceLeidenThe Netherlands
| | - Peter A. Verleg
- University of Applied Sciences Leiden, Faculty of Science and TechnologyLeidenThe Netherlands
| | - Nafiesa Z. Ibrahim
- University of Applied Sciences Leiden, Faculty of Science and TechnologyLeidenThe Netherlands
| | - Khadiedjah Soeleman
- University of Applied Sciences Leiden, Faculty of Science and TechnologyLeidenThe Netherlands
| | - Floris van Kampen
- University of Applied Sciences Leiden, Faculty of Science and TechnologyLeidenThe Netherlands
| | - Mia O. Ruesen
- University of Applied Sciences Leiden, Faculty of Science and TechnologyLeidenThe Netherlands
| | - Naïsha M. Reulen
- University of Applied Sciences Leiden, Faculty of Science and TechnologyLeidenThe Netherlands
| | - Henk Breij
- University of Applied Sciences Leiden, Faculty of Science and TechnologyLeidenThe Netherlands
| | - Roderick J. Bakker
- University of Applied Sciences Leiden, Faculty of Science and TechnologyLeidenThe Netherlands
| | - Barbara Gravendeel
- University of Applied Sciences Leiden, Faculty of Science and TechnologyLeidenThe Netherlands
- Naturalis Biodiversity Center, Endless Forms GroupLeidenThe Netherlands
- Institute of Biology Leiden, Leiden UniversityLeidenThe Netherlands
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Kretzschmar AL, Verma A, Kohli G, Murray S. Development of a quantitative PCR assay for the detection and enumeration of a potentially ciguatoxin-producing dinoflagellate, Gambierdiscus lapillus (Gonyaulacales, Dinophyceae). PLoS One 2019; 14:e0224664. [PMID: 31730656 PMCID: PMC6857910 DOI: 10.1371/journal.pone.0224664] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 10/19/2019] [Indexed: 11/19/2022] Open
Abstract
Ciguatera fish poisoning (CFP) is an illness contracted through the ingestion of seafood containing ciguatoxins. It is prevalent in tropical regions worldwide, including in Australia. Ciguatoxins are produced by some species of Gambierdiscus. Therefore, screening of Gambierdiscus species identification through quantitative PCR (qPCR), along with the determination of species toxicity, can be useful in monitoring potential ciguatera risk in these regions. In Australia, CFP is prevalent in tropical Queensland and increasingly in sub-tropical regions of Australia, but has a report rate of approximately 10%. Yet the identity, distribution and abundance of ciguatoxin producing Gambierdiscus spp. is largely unknown. In this study, we developed a rapid qPCR assay to quantify the presence and abundance of Gambierdiscus lapillus, a likely ciguatoxic species first described from Australia. We assessed the specificity and efficiency of the qPCR assay. The assay was tested on 25 environmental samples from the Heron Island reef in the southern Great Barrier Reef, a ciguatera endemic region, to determine the presence and patchiness of this species across samples from Chnoospora sp., Padina sp. and Sargassum sp. macroalgal hosts.
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Affiliation(s)
- Anna Liza Kretzschmar
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, New South Wales, Australia
- ithree institute (i3), University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Arjun Verma
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Gurjeet Kohli
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, New South Wales, Australia
- Alfred Wegener-Institut Helmholtz-Zentrum fr Polar- und Meeresforschung, Bremerhaven, Germany
| | - Shauna Murray
- Climate Change Cluster (C3), University of Technology Sydney, Ultimo, New South Wales, Australia
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Kumar De A, Ponraj P, Malakar D, Muthiyan R, Kundu A, Bhattacharya D. Complete mitogenome sequencing of Andaman buffalo: an endangered germplasm of Andaman and Nicobar Islands, India. J Genet 2019; 98:97. [PMID: 31767814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Andaman buffalo is an indigenous buffalo of Andaman and Nicobar Islands, India. Over the last decade, it has witnessed a rapid decline in population, necessitating its immediate characterization and conservation. The present study reports the complete mitogenome profile of Andaman buffalo which is 16,359 bp in length and comprised of 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNAs and two ribosomal RNAs. In addition, one A + T rich region (D-loop) was also present. A biasness towards A and T base was observed in all the genes. All the PCGs except ND6 were present on heavy strand. Start codons for all the 13 PCGs were ATN codon and abbreviated/truncated stop codons were observed in ND1, ND2, COX3, ND3 and ND4. The phylogenetic analysis revealed that the Andaman buffalo is closely related to buffalo from India and China. The results from this study will help in sketching the conservation plan of the threatened breed.
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Affiliation(s)
- Arun Kumar De
- Animal Science Division, ICAR-Central Island Agricultural Research Institute, Port Blair 744 101, India.
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Yang SL, Wen YH, Wu YS, Wang MC, Chang PY, Yang S, Lu JJ. Diagnosis of Pneumocystis pneumonia by real-time PCR in patients with various underlying diseases. J Microbiol Immunol Infect 2019; 53:785-790. [PMID: 31635929 DOI: 10.1016/j.jmii.2019.08.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 08/16/2019] [Accepted: 08/22/2019] [Indexed: 11/19/2022]
Abstract
BACKGROUND Pneumocystis pneumonia (PCP) is a disease caused by the opportunistic infection of the fungus Pneumocystis jirovecii. Several PCR methods have been developed to aid in the diagnosis of PCP. In this study, we evaluated the performance of a real-time PCR in the diagnosis of PCP, in patients with various underlying diseases. METHODS Ninety-seven BAL samples and 94 sputum samples from 191 patients were used in the study. Patients were classified as PCP (121 patients) or non-PCP (70 patients) based on their clinical and radiological presentations. RESULTS Real time PCR amplified the P. jirovecii mitochondrial large-subunit rRNA gene with a detection limit of 68 copies of DNA per reaction. Non-PCP pathogens including 32 different fungi and bacteria were also evaluated. Overall, 71.9% of the samples from PCP patients and 14.5% of those from non-PCP patients were positive for the PCR test with a CT value of the real-time PCR below 45. The main underlying diseases of the patients were hematological or solid malignancies (47.1%) and HIV infection (8.9%). The CT values of the test were significantly lower in BAL samples from PCP patients than those from non-PCP patients (p = 0.024). No non-PCP patient had a CT value below 30, whereas samples from 24.8% of PCP patients with underlying diseases had a CT value below 30. CONCLUSION Since false positive PCR results were obtained, perhaps due to colonization, we suggest that the diagnosis of PCP should be based on a combination of clinical symptoms, underlying diseases, and PCR results.
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Affiliation(s)
- Shu-Li Yang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | - Ying-Hao Wen
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Yu-Shan Wu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Mei-Chia Wang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | - Pi-Yueh Chang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan; Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Shuan Yang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Jang-Jih Lu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan; Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan; Department of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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Korsholm LM, Gál Z, Lin L, Quevedo O, Ahmad DA, Dulina E, Luo Y, Bartek J, Larsen DH. Double-strand breaks in ribosomal RNA genes activate a distinct signaling and chromatin response to facilitate nucleolar restructuring and repair. Nucleic Acids Res 2019; 47:8019-8035. [PMID: 31184714 PMCID: PMC6735822 DOI: 10.1093/nar/gkz518] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 12/21/2022] Open
Abstract
The nucleolus is a nuclear sub-domain containing the most highly transcribed genes in the genome. Hundreds of human ribosomal RNA (rRNA) genes, located in the nucleolus, rely on constant maintenance. DNA double-strand breaks (DSBs) in rRNA genes activate the ATM kinase, repress rRNA transcription and induce nucleolar cap formation. Yet how ribosomal-DNA (rDNA) lesions are detected and processed remains elusive. Here, we use CRISPR/Cas9-mediated induction of DSBs and report a chromatin response unique to rDNA depending on ATM-phosphorylation of the nucleolar protein TCOF1 and recruitment of the MRE11-RAD50-NBS1 (MRN) complex via the NBS1-subunit. NBS1- and MRE11-depleted cells fail to suppress rRNA transcription and to translocate rDNA into nucleolar caps. Furthermore, the DNA damage response (DDR) kinase ATR operates downstream of the ATM-TCOF1-MRN interplay and is required to fully suppress rRNA transcription and complete DSB-induced nucleolar restructuring. Unexpectedly, we find that DSBs in rDNA neither activate checkpoint kinases CHK1/CHK2 nor halt cell-cycle progression, yet the nucleolar-DDR protects against genomic aberrations and cell death. Our data highlight the concept of a specialized nucleolar DNA damage response (n-DDR) with a distinct protein composition, spatial organization and checkpoint communication. The n-DDR maintains integrity of ribosomal RNA genes, with implications for cell physiology and disease.
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Affiliation(s)
- Lea M Korsholm
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Zita Gál
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Lin Lin
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
- China National GeneBank, BGI-Shenzhen, 518083 Shenzhen, China
| | - Oliver Quevedo
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Diana A Ahmad
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Ekaterina Dulina
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark
- China National GeneBank, BGI-Shenzhen, 518083 Shenzhen, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, 266555 Qingdao, China
| | - Jiri Bartek
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Department of Medical Biochemistry and Biophysics, Science for Life Laboratory, Division of Genome Biology, Karolinska Institutet, SE-171 65 Solna, Sweden
| | - Dorthe H Larsen
- Nucleolar Stress and Disease Group, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
- Genome Integrity Unit, Danish Cancer Society Research Center, Danish Cancer Society, Strandboulevarden 49, DK-2100 Copenhagen, Denmark
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Hou H, Zhao L, Zheng X, Gautam M, Yue M, Hou J, Chen Z, Wang P, Li L. Dynamic changes in histone modification are associated with upregulation of Hsf and rRNA genes during heat stress in maize seedlings. Protoplasma 2019; 256:1245-1256. [PMID: 31030267 DOI: 10.1007/s00709-019-01364-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 03/10/2019] [Indexed: 06/09/2023]
Abstract
Histone modification plays a significant role in plant responses to abiotic stress. However, there are little scientific studies available on the involvement of dynamic changes in histone modification in the heat stress response in maize. The present investigation was aimed to analyze the epigenetic mechanisms involved in regulating the physiological and biochemical alterations in maize seedlings under heat stress. Our results and observations indicated an increase in electrolyte leakage and hydrolytic activity of the plasma membrane H+-ATPase as well as the high pigment content and reactive oxygen species (ROS) content under high temperature. Furthermore, decondensation of ribosomal DNA (rDNA) chromatin and a simultaneous increase in rRNA gene expression were observed during heat stress, accompanied by a genome-wide increase in the levels of histone H3K4me2 and H3K9ac. Additionally, chromatin immunoprecipitation (ChIP) analysis revealed that alterations in H3K4me2 and H3K9ac levels occurred in promoter regions, which were found to be associated with the upregulation of heat stress factor (Hsf) and rRNA genes. In conclusion, short-term heat stress induces dynamic histone alterations which are associated with Hsf and rRNA gene transcription, accompanied by perturbations of cell membranes and an increase in ROS during acclimation in maize seedlings.
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Affiliation(s)
- Haoli Hou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- School of electrical engineering and Automation, Wuhan University, Wuhan, 430072, China
| | - Lin Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Institute of Food and Agriculture Standardization, China National Institute of Standardization, Beijing, 100191, China
| | - Xueke Zheng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Mayank Gautam
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Mengxia Yue
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jiaqi Hou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhenfei Chen
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Pu Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Lijia Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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12
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Manee MM, Alshehri MA, Binghadir SA, Aldhafer SH, Alswailem RM, Algarni AT, Al-Shomrani BM, Al-Fageeh MB. Comparative analysis of camelid mitochondrial genomes. J Genet 2019; 98:88. [PMID: 31544791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Camelus dromedarius has played a pivotal role in both culture and way of life in the Arabian peninsula, particularly in arid regions where other domestic animals cannot be easily domesticated. Although, the mitochondrial genomes have recently been sequenced for several camelid species, wider phylogenetic studies are yet to be performed. The features of conserved gene elements, rapid evolutionary rate, and rare recombination make the mitochondrial genome a useful molecular marker for phylogenetic studies of closely related species. Here we carried out a comparative analysis of previously sequenced mitochondrial genomes of camelids with an emphasis on C. dromedarius, revealing a number of noticeable findings. First, the arrangement of mitochondrial genes in C. dromedarius is similar to those of the other camelids. Second, multiple sequence alignment of intergenic regions shows up to 90% similarity across different kinds of camels, with dromedary camels to reach 99%. Third, we successfully identified the three domains (termination-associated sequence, conserved domain and conserved sequence block) of the control region structure. The phylogenetic tree analysis showed that C. dromedarius mitogenomes were significantly clustered in the same clade with Lama pacos mitogenome. These findings will enhance our understanding of the nucleotide composition and molecular evolution of the mitogenomes of the genus Camelus, and provide more data for comparative mitogenomics in the family Camelidae.
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Affiliation(s)
- Manee M Manee
- National Centre for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia.
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13
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Huggett MJ, Apprill A. Coral microbiome database: Integration of sequences reveals high diversity and relatedness of coral-associated microbes. Environ Microbiol Rep 2019; 11:372-385. [PMID: 30094953 PMCID: PMC7379671 DOI: 10.1111/1758-2229.12686] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 08/04/2018] [Indexed: 05/10/2023]
Abstract
Coral-associated microorganisms are thought to play a fundamental role in the health and ecology of corals, but understanding of specific coral-microbial interactions are lacking. In order to create a framework to examine coral-microbial specificity, we integrated and phylogenetically compared 21,100 SSU rRNA gene Sanger-produced sequences from bacteria and archaea associated with corals from previous studies, and accompanying host, location and publication metadata, to produce the Coral Microbiome Database. From this database, we identified 39 described and candidate phyla of Bacteria and two Archaea phyla associated with corals, demonstrating that corals are one of the most phylogenetically diverse animal microbiomes. Secondly, this new phylogenetic resource shows that certain microorganisms are indeed specific to corals, including evolutionary distinct hosts. Specifically, we identified 2-37 putative monophyletic, coral-specific sequence clusters within bacterial genera associated with the greatest number of coral species (Vibrio, Endozoicomonas and Ruegeria) as well as functionally relevant microbial taxa ("Candidatus Amoebophilus", "Candidatus Nitrosopumilus" and under recognized cyanobacteria). This phylogenetic resource provides a framework for more targeted studies of corals and their specific microbial associates, which is timely given the escalated need to understand the role of the coral microbiome and its adaptability to changing ocean and reef conditions.
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Affiliation(s)
- Megan J. Huggett
- School of Environmental and Life SciencesUniversity of NewcastleOurimbahNSW, 2258Australia
- School of ScienceEdith Cowan UniversityJoondalupWAAustralia
| | - Amy Apprill
- Marine Chemistry and Geochemistry DepartmentWoods Hole Oceanographic InstitutionWoods HoleMAUSA
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14
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Unubol N, Kizilkaya IT, Okullu SO, Koksalan K, Kocagoz T. Simple Identification of Mycobacterial Species by Sequence-Specific Multiple Polymerase Chain Reactions. Curr Microbiol 2019; 76:791-798. [PMID: 31073733 DOI: 10.1007/s00284-019-01661-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 02/28/2019] [Indexed: 12/29/2022]
Abstract
Several species of mycobacteria cause infections in humans. Species identification of clinical isolates of mycobacteria is very important for the decision of treatment and in choosing the appropriate treatment regimen. We have developed a multiplex PCR method that can identify practically all known species of mycobacteria, by determination of single-nucleotide differences at a total of 13 different polymorphic regions in the genes of rRNA and hsp65, in four PCR mixes. To achieve this goal, single-nucleotide differences in these polymorphic regions were used to divide mycobacterial species into two groups, than four, eight, etc., in an algorithmic manner. It was sufficient to reach single species level by evaluating 13 polymorphic regions. Evaluation of the multiplex PCR patterns by observable real-time electrophoresis (ORTE) simplified species identification. This new method may enable easy, rapid, and cost-effective identification of all species of mycobacteria.
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Affiliation(s)
- Nihan Unubol
- Department of Medical Microbiology, Faculty of Medicine, Acibadem Mehmet Ali Aydınlar University, Istanbul, Turkey
- Department of Medical Biotechnology, Institute of Health Sciences, Acibadem Mehmet Ali Aydınlar University, Istanbul, Turkey
| | | | - Sinem Oktem Okullu
- Department of Medical Microbiology, Faculty of Medicine, Acibadem Mehmet Ali Aydınlar University, Istanbul, Turkey
- Department of Medical Biotechnology, Institute of Health Sciences, Acibadem Mehmet Ali Aydınlar University, Istanbul, Turkey
| | - Kaya Koksalan
- Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Tanil Kocagoz
- Department of Medical Microbiology, Faculty of Medicine, Acibadem Mehmet Ali Aydınlar University, Istanbul, Turkey.
- Department of Medical Biotechnology, Institute of Health Sciences, Acibadem Mehmet Ali Aydınlar University, Istanbul, Turkey.
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15
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Lesuthu P, Mostert L, Spies CFJ, Moyo P, Regnier T, Halleen F. Diaporthe nebulae sp. nov. and First Report of D. cynaroidis, D. novem, and D. serafiniae on Grapevines in South Africa. Plant Dis 2019; 103:808-817. [PMID: 30920350 DOI: 10.1094/pdis-03-18-0433-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Diaporthe species cause Phomopsis cane and leaf spot as well as Phomopsis dieback on grapevines. Symptoms of Phomopsis dieback have increasingly been observed over the past few years. In order to assess the current status of Diaporthe on grapevines in the Western Cape Province of South Africa, isolations were made from dormant grafted nursery vines, dormant rootstock canes, and dying or dead spurs of field vines. Cultures identified as Diaporthe based on morphological features were further identified to species level by sequencing the internal transcribed spacers (ITS) 1 and 2 and 5.8S rRNA and, for a representative subsample of isolates, the partial beta-tubulin (tub2) and translation elongation factor 1-alpha (EF1-α) genes. Phylogenetic analysis of the combined ITS, tub2, and EF1-α data revealed nine Diaporthe species associated with grapevines during this survey. One of these represents a new species, D. nebulae sp. nov., and three other species, namely D. novem, D. cynaroidis, and D. serafiniae, are reported on grapevines in South Africa for the first time. Species-specific primers were designed for PCR identification of D. ampelina, D. ambigua, and D. foeniculina. Pathogenicity studies conducted on detached grapevine shoots indicated D. ampelina, D. novem, and D. nebulae sp. nov. as the most virulent species.
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Affiliation(s)
- Palesa Lesuthu
- 1 Plant Protection Division, ARC Infruitec-Nietvoorbij, Private Bag X5026, Stellenbosch, 7599, South Africa
- 3 Department of Biotechnology and Food Technology, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa
| | - Lizel Mostert
- 2 Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa; and
| | - Christoffel F J Spies
- 1 Plant Protection Division, ARC Infruitec-Nietvoorbij, Private Bag X5026, Stellenbosch, 7599, South Africa
- 2 Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa; and
| | - Providence Moyo
- 2 Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa; and
| | - Thierry Regnier
- 3 Department of Biotechnology and Food Technology, Tshwane University of Technology, Private Bag X680, Pretoria, 0001, South Africa
| | - Francois Halleen
- 1 Plant Protection Division, ARC Infruitec-Nietvoorbij, Private Bag X5026, Stellenbosch, 7599, South Africa
- 2 Department of Plant Pathology, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa; and
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16
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Imachi H, Tasumi E, Takaki Y, Hoshino T, Schubotz F, Gan S, Tu TH, Saito Y, Yamanaka Y, Ijiri A, Matsui Y, Miyazaki M, Morono Y, Takai K, Hinrichs KU, Inagaki F. Cultivable microbial community in 2-km-deep, 20-million-year-old subseafloor coalbeds through ~1000 days anaerobic bioreactor cultivation. Sci Rep 2019; 9:2305. [PMID: 30783143 PMCID: PMC6381156 DOI: 10.1038/s41598-019-38754-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/09/2019] [Indexed: 11/08/2022] Open
Abstract
Recent explorations of scientific ocean drilling have revealed the presence of microbial communities persisting in sediments down to ~2.5 km below the ocean floor. However, our knowledge of these microbial populations in the deep subseafloor sedimentary biosphere remains limited. Here, we present a cultivation experiment of 2-km-deep subseafloor microbial communities in 20-million-year-old lignite coalbeds using a continuous-flow bioreactor operating at 40 °C for 1029 days with lignite particles as the major energy source. Chemical monitoring of effluent samples via fluorescence emission-excitation matrices spectroscopy and stable isotope analyses traced the transformation of coalbed-derived organic matter in the dissolved phase. Hereby, the production of acetate and 13C-depleted methane together with the increase and transformation of high molecular weight humics point to an active lignite-degrading methanogenic community present within the bioreactor. Electron microscopy revealed abundant microbial cells growing on the surface of lignite particles. Small subunit rRNA gene sequence analysis revealed that diverse microorganisms grew in the bioreactor (e.g., phyla Proteobacteria, Firmicutes, Chloroflexi, Actinobacteria, Bacteroidetes, Spirochaetes, Tenericutes, Ignavibacteriae, and SBR1093). These results indicate that activation and adaptive growth of 2-km-deep microbes was successfully accomplished using a continuous-flow bioreactor, which lays the groundwork to explore networks of microbial communities of the deep biosphere and their physiologies.
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Affiliation(s)
- Hiroyuki Imachi
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan.
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan.
| | - Eiji Tasumi
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
- Project Team for Development of New-generation Research Protocol for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
| | - Tatsuhiko Hoshino
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
- Kochi Institute for Core Sample Research, JAMSTEC, Nankoku, Kochi, 783-8502, Japan
| | - Florence Schubotz
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, D-28359, Bremen, Germany
| | - Shuchai Gan
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, D-28359, Bremen, Germany
| | - Tzu-Hsuan Tu
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
- Institute of Oceanography, National Taiwan University, Taipei, 106, Taiwan
| | - Yumi Saito
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
| | - Yuko Yamanaka
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
| | - Akira Ijiri
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
- Project Team for Development of New-generation Research Protocol for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
| | - Yohei Matsui
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
- Project Team for Development of New-generation Research Protocol for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
| | - Masayuki Miyazaki
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
| | - Yuki Morono
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
- Kochi Institute for Core Sample Research, JAMSTEC, Nankoku, Kochi, 783-8502, Japan
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, 237-0061, Japan
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences and Department of Geosciences, University of Bremen, D-28359, Bremen, Germany
| | - Fumio Inagaki
- Research and Development Center for Submarine Resources, JAMSTEC, Yokosuka, Kanagawa, 237-0061, Japan
- Kochi Institute for Core Sample Research, JAMSTEC, Nankoku, Kochi, 783-8502, Japan
- Research and Development Center for Ocean Drilling Science, JAMSTEC, Yokohama, Kanagawa, 236-0001, Japan
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17
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Abstract
Ribosomal RNA gene repeats (rDNA) encode ribosomal RNA, a major component of ribosomes. Ribosome biogenesis is central to cellular metabolic regulation, and several diseases are associated with rDNA dysfunction, notably cancer, However, its highly repetitive nature has severely limited characterization of the elements responsible for rDNA function. Here we make use of phylogenetic footprinting to provide a comprehensive list of novel, potentially functional elements in the human rDNA. Complete rDNA sequences for six non-human primate species were constructed using de novo whole genome assemblies. These new sequences were used to determine the conservation profile of the human rDNA, revealing 49 conserved regions in the rDNA intergenic spacer (IGS). To provide insights into the potential roles of these conserved regions, the conservation profile was integrated with functional genomics datasets. We find two major zones that contain conserved elements characterised by enrichment of transcription-associated chromatin factors, and transcription. Conservation of some IGS transcripts in the apes underpins the potential functional significance of these transcripts and the elements controlling their expression. Our results characterize the conservation landscape of the human IGS and suggest that noncoding transcription and chromatin elements are conserved and important features of this unique genomic region.
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Affiliation(s)
- Saumya Agrawal
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Austen R. D. Ganley
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- * E-mail:
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18
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Menezes L, Alvarez TM, Persinoti GF, Franco JP, Squina F, Moreira EA, Alvaredo Paixão DA, Costa-Leonardo AM, da Silva VX, Clerici MTPS, Arab A. Food Storage by the Savanna Termite Cornitermes cumulans (Syntermitinae): a Strategy to Improve Hemicellulose Digestibility? Microb Ecol 2018; 76:492-505. [PMID: 29270662 DOI: 10.1007/s00248-017-1128-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 12/11/2017] [Indexed: 06/07/2023]
Abstract
It has been suggested that food storage inside the nest may offer termites with a nutritional provision during low resource availability. Additionally, feces employed as construction material provide an excellent environment for colonization by microorganisms and, together with the storage of plant material inside the nest, could thus provide some advantage to the termites in terms of lignocellulose decomposition. Here, we conducted for the first time a comprehensive study of the microbial communities associated to a termite exhibiting food storage behavior using Illumina sequencing of the 16S and (ITS2) regions of rRNA genes, together with enzymatic assays and data collected in the field. Cornitermes cumulans (Syntermitinae) stored grass litter in nodules made from feces and saliva located in the nest core. The amount of nodules increased with nest size and isolation, and interestingly, the soluble fraction of extracts from nodules showed a higher activity against hemicellulosic substrates compared to termite guts. Actinobacteria and Sordariales dominated microbial communities of food nodules and nest walls, whereas Spirochetes and Pleosporales dominated gut samples of C. cumulans. Within Syntermitinae, however, gut bacterial assemblages were dissimilar. On the other hand, there is a remarkable convergence of the bacterial community structure of Termitidae nests. Our results suggest that the role of nodules could be related to food storage; however, the higher xylanolytic activity in the nodules and their associated microbiota could also provide C. cumulans with an external source of predigested polysaccharides, which might be advantageous in comparison with litter-feeding termites that do not display food storage behavior.
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Affiliation(s)
- Letícia Menezes
- Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro, SP, Brazil
| | - Thabata Maria Alvarez
- Universidade Positivo, Curitiba, PR, Brazil
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - Gabriela Félix Persinoti
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - João Paulo Franco
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - Fábio Squina
- Programa em Processos Tecnológicos e Ambientais, Universidade de Sorocaba (UNISO), Sorocaba, SP, Brazil
| | - Edimar Agnaldo Moreira
- CCNH-Center for Natural Sciences and Humanities, Federal University of ABC (UFABC), Santo André, SP, Brazil
| | - Douglas Antonio Alvaredo Paixão
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil
| | - Ana Maria Costa-Leonardo
- Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro, SP, Brazil
| | | | | | - Alberto Arab
- CCNH-Center for Natural Sciences and Humanities, Federal University of ABC (UFABC), Santo André, SP, Brazil.
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19
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Cornet L, Meunier L, Van Vlierberghe M, Léonard RR, Durieu B, Lara Y, Misztak A, Sirjacobs D, Javaux EJ, Philippe H, Wilmotte A, Baurain D. Consensus assessment of the contamination level of publicly available cyanobacterial genomes. PLoS One 2018; 13:e0200323. [PMID: 30044797 PMCID: PMC6059444 DOI: 10.1371/journal.pone.0200323] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 06/22/2018] [Indexed: 12/31/2022] Open
Abstract
Publicly available genomes are crucial for phylogenetic and metagenomic studies, in which contaminating sequences can be the cause of major problems. This issue is expected to be especially important for Cyanobacteria because axenic strains are notoriously difficult to obtain and keep in culture. Yet, despite their great scientific interest, no data are currently available concerning the quality of publicly available cyanobacterial genomes. As reliably detecting contaminants is a complex task, we designed a pipeline combining six methods in a consensus strategy to assess the contamination level of 440 genome assemblies of Cyanobacteria. Two methods are based on published reference databases of ribosomal genes (SSU rRNA 16S and ribosomal proteins), one is indirectly based on a reference database of marker genes (CheckM), and three are based on complete genome analysis. Among those genome-wide methods, Kraken and DIAMOND blastx share the same reference database that we derived from Ensembl Bacteria, whereas CONCOCT does not require any reference database, instead relying on differences in DNA tetramer frequencies. Given that all the six methods appear to have their own strengths and limitations, we used the consensus of their rankings to infer that >5% of cyanobacterial genome assemblies are highly contaminated by foreign DNA (i.e., contaminants were detected by 5 or 6 methods). Our results will help researchers to check the quality of publicly available genomic data before use in their own analyses. Moreover, we argue that journals should make mandatory the submission of raw read data along with genome assemblies in order to facilitate the detection of contaminants in sequence databases.
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Affiliation(s)
- Luc Cornet
- InBioS–PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
- UR Geology–Palaeobiogeology-Palaeobotany-Palaeopalynology, University of Liège, Liège, Belgium
| | - Loïc Meunier
- InBioS–PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
| | - Mick Van Vlierberghe
- InBioS–PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
| | - Raphaël R. Léonard
- InBioS–PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
- InBioS–CIP, Macromolecular Crystallography, University of Liège, Liège, Belgium
| | - Benoit Durieu
- InBioS–CIP, Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Yannick Lara
- InBioS–CIP, Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Agnieszka Misztak
- InBioS–PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
- Intercollegiate Faculty of Biotechnology UG-MUG, Gdansk, Poland
| | - Damien Sirjacobs
- InBioS–PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
| | - Emmanuelle J. Javaux
- UR Geology–Palaeobiogeology-Palaeobotany-Palaeopalynology, University of Liège, Liège, Belgium
| | - Hervé Philippe
- Centre for Biodiversity Theory and Modelling, Moulis, France
| | - Annick Wilmotte
- InBioS–CIP, Centre for Protein Engineering, University of Liège, Liège, Belgium
| | - Denis Baurain
- InBioS–PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
- * E-mail:
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20
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Röhl O, Graupner N, Peršoh D, Kemler M, Mittelbach M, Boenigk J, Begerow D. Flooding Duration Affects the Structure of Terrestrial and Aquatic Microbial Eukaryotic Communities. Microb Ecol 2018; 75:875-887. [PMID: 29026984 DOI: 10.1007/s00248-017-1085-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/29/2017] [Indexed: 05/22/2023]
Abstract
The increasing number and duration of inundations is reported to be a consequence of climate change and may severely compromise non-adapted macroorganisms. The effect of flooding events on terrestrial and aquatic microbial communities is, however, less well understood. They may respond to the changed abiotic properties of their native habitat, and the native community may change due to the introduction of alien species. We designed an experiment to investigate the effect of five different flooding durations on the terrestrial and aquatic communities of eukaryotic microorganism, using the AquaFlow mesocosms. With amplicon sequencing of the small subunit (SSU) and internal transcribed spacer (ITS) rRNA gene regions, we analyzed community compositions directly before and after flooding. Subsequently, they were monitored for another 28 days, to determine the sustainability of community changes. Our results revealed a temporary increase in similarity between terrestrial and aquatic communities according to OTU composition (operational taxonomic unit, serves as a proxy for species). Increased similarity was mainly caused by the transmission of OTUs from water to soil. A minority of these were able to persist in soil until the end of the experiment. By contrast, the vast majority of soil OTUs was not transmitted to water. Flooding duration affected the community structure (abundance) more than composition (occurrence). Terrestrial communities responded immediately to flooding and the flooding duration influenced the community changes. Independent from flooding duration, all terrestrial communities recovered largely after flooding, indicating a remarkable resilience to the applied disturbances. Aquatic communities responded immediately to the applied inundations too. At the end of the experiment, they grouped according to the applied flooding duration and the amount of ammonium and chloride that leached from the soil. This indicates a sustained long-term response of the aquatic communities to flooding events.
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Affiliation(s)
- Oliver Röhl
- AG Geobotany, Faculty of Biology and Biotechnology, Ruhr Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany.
| | - Nadine Graupner
- Department of Biodiversity, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Derek Peršoh
- AG Geobotany, Faculty of Biology and Biotechnology, Ruhr Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Martin Kemler
- AG Geobotany, Faculty of Biology and Biotechnology, Ruhr Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Moritz Mittelbach
- AG Ökologie der Pflanzen; Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
| | - Jens Boenigk
- Department of Biodiversity, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Dominik Begerow
- AG Geobotany, Faculty of Biology and Biotechnology, Ruhr Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
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Schwarz A, Adetutu EM, Juhasz AL, Aburto-Medina A, Ball AS, Shahsavari E. Microbial Degradation of Phenanthrene in Pristine and Contaminated Sandy Soils. Microb Ecol 2018; 75:888-902. [PMID: 29080101 DOI: 10.1007/s00248-017-1094-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/15/2017] [Indexed: 06/07/2023]
Abstract
Phenanthrene mineralisation studies in both pristine and contaminated sandy soils were undertaken through detailed assessment of the activity and diversity of the microbial community. Stable isotope probing (SIP) was used to assess and identify active 13C-labelled phenanthrene degraders. Baseline profiling indicated that there was little difference in fungal diversity but a significant difference in bacterial diversity dependent on contamination history. Identification of dominant fungal and bacterial species highlighted the presence of organisms capable of degrading various petroleum-based compounds together with other anthropogenic compounds, regardless of contamination history. Community response following a simulated contamination event (14C-phenanthrene) showed that the microbial community in deep pristine and shallow contaminated soils adapted most to the presence of phenanthrene. The similarity in microbial community structure of well-adapted soils demonstrated that a highly adaptable fungal community in these soils enabled a rapid response to the introduction of a contaminant. Ten fungal and 15 bacterial species were identified as active degraders of phenanthrene. The fungal degraders were dominated by the phylum Basidiomycota including the genus Crypotococcus, Cladosporium and Tremellales. Bacterial degraders included the genera Alcanivorax, Marinobacter and Enterococcus. There was little synergy between dominant baseline microbes, predicted degraders and those that were determined to be actually degrading the contaminant. Overall, assessment of baseline microbial community in contaminated soils provides useful information; however, additional laboratory assessment of the microbial community's ability to degrade pollutants allows for better prediction of the bioremediation potential of a soil.
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Affiliation(s)
- Alexandra Schwarz
- Discipline of Biological Sciences, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Eric M Adetutu
- Medical Biotechnology, School of Medicine, Flinders University, Adelaide, Australia
| | - Albert L Juhasz
- Future Industries Institute, University of South Australia, Adelaide, Australia
| | - Arturo Aburto-Medina
- Centre for Environmental Sustainability and Remediation, School of Sciences, RMIT University, Bundoora, Australia
| | - Andrew S Ball
- Centre for Environmental Sustainability and Remediation, School of Sciences, RMIT University, Bundoora, Australia
| | - Esmaeil Shahsavari
- Centre for Environmental Sustainability and Remediation, School of Sciences, RMIT University, Bundoora, Australia.
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Jones AC, Hambright KD, Caron DA. Ecological Patterns Among Bacteria and Microbial Eukaryotes Derived from Network Analyses in a Low-Salinity Lake. Microb Ecol 2018; 75:917-929. [PMID: 29110066 DOI: 10.1007/s00248-017-1087-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 10/09/2017] [Indexed: 06/07/2023]
Abstract
Microbial communities are comprised of complex assemblages of highly interactive taxa. We employed network analyses to identify and describe microbial interactions and co-occurrence patterns between microbial eukaryotes and bacteria at two locations within a low salinity (0.5-3.5 ppt) lake over an annual cycle. We previously documented that the microbial diversity and community composition within Lake Texoma, southwest USA, were significantly affected by both seasonal forces and a site-specific bloom of the harmful alga, Prymnesium parvum. We used network analyses to answer ecological questions involving both the bacterial and microbial eukaryotic datasets and to infer ecological relationships within the microbial communities. Patterns of connectivity at both locations reflected the seasonality of the lake including a large rain disturbance in May, while a comparison of the communities between locations revealed a localized response to the algal bloom. A network built from shared nodes (microbial operational taxonomic units and environmental variables) and correlations identified conserved associations at both locations within the lake. Using network analyses, we were able to detect disturbance events, characterize the ecological extent of a harmful algal bloom, and infer ecological relationships not apparent from diversity statistics alone.
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Affiliation(s)
- Adriane Clark Jones
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-0371, USA.
- Department of Biological Sciences, Mount Saint Mary's University, Los Angeles, CA, 90049, USA.
| | - K David Hambright
- Program in Ecology and Evolutionary Biology, Department of Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - David A Caron
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-0371, USA
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Raghunathan N, Kapshikar RM, Leela JK, Mallikarjun J, Bouloc P, Gowrishankar J. Genome-wide relationship between R-loop formation and antisense transcription in Escherichia coli. Nucleic Acids Res 2018; 46:3400-3411. [PMID: 29474582 PMCID: PMC5909445 DOI: 10.1093/nar/gky118] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 01/30/2018] [Accepted: 02/09/2018] [Indexed: 12/22/2022] Open
Abstract
Transcription termination by Rho is essential for viability in various bacteria, including some major pathogens. Since Rho acts by targeting nascent RNAs that are not simultaneously translated, it also regulates antisense transcription. Here we show that RNase H-deficient mutants of Escherichia coli exhibit heightened sensitivity to the Rho inhibitor bicyclomycin, and that Rho deficiency provokes increased formation of RNA-DNA hybrids (R-loops) which is ameliorated by expression of the phage T4-derived R-loop helicase UvsW. We also provide evidence that in Rho-deficient cells, R-loop formation blocks subsequent rounds of antisense transcription at more than 500 chromosomal loci. Hence these antisense transcripts, which can extend beyond 10 kb in their length, are only detected when Rho function is absent or compromised and the UvsW helicase is concurrently expressed. Thus the potential for antisense transcription in bacteria is much greater than hitherto recognized; and the cells are able to retain viability even when nearly one-quarter of their total non-rRNA abundance is accounted for by antisense transcripts, provided that R-loop formation from them is curtailed.
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Affiliation(s)
- Nalini Raghunathan
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500039, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Rajvardhan M Kapshikar
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500039, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Jakku K Leela
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500039, India
| | - Jillella Mallikarjun
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500039, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Philippe Bouloc
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, F-91198, Gif-sur-Yvette cedex, France
| | - Jayaraman Gowrishankar
- Laboratory of Bacterial Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana 500039, India
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Matta AJ, Zambrano DC, Pazos AJ. Punctual mutations in 23S rRNA gene of clarithromycin-resistant Helicobacter pylori in Colombian populations. World J Gastroenterol 2018; 24:1531-1539. [PMID: 29662291 PMCID: PMC5897857 DOI: 10.3748/wjg.v24.i14.1531] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 02/25/2018] [Accepted: 03/18/2018] [Indexed: 02/06/2023] Open
Abstract
AIM To characterize punctual mutations in 23S rRNA gene of clarithromycin-resistant Helicobacter pylori (H. pylori) and determine their association with therapeutic failure.
METHODS PCR products of 23S rRNA gene V domain of 74 H. pylori isolates; 34 resistant to clarithromycin (29 from a low-risk gastric cancer (GC) population: Tumaco-Colombia, and 5 from a high-risk population: Tuquerres-Colombia) and 40 from a susceptible population (28 from Tumaco and 12 from Túquerres) were sequenced using capillary electrophoresis. The concordance between mutations of V domain 23S rRNA gene of H. pylori and therapeutic failure was determined using the Kappa coefficient and McNemar’s test was performed to determine the relationship between H. pylori mutations and clarithromycin resistance.
RESULTS 23S rRNA gene from H. pylori was amplified in 56/74 isolates, of which 25 were resistant to clarithromycin (20 from Tumaco and 5 from Túquerres, respectively). In 17 resistant isolates (13 from Tumaco and 4 from Túquerres) the following mutations were found: A1593T1, A1653G2, C1770T, C1954T1, and G1827C in isolates from Tumaco, and A2144G from Túquerres. The mutations T2183C, A2144G and C2196T in H. pylori isolates resistant to clarithromycin from Colombia are reported for the first time. No association between the H. pylori mutations and in vitro clarithromycin resistance was found. However, therapeutic failure of eradication treatment was associated with mutations of 23S rRNA gene in clarithromycin-resistant H. pylori (κ = 0.71).
CONCLUSION The therapeutic failure of eradication treatment in the two populations from Colombia was associated with mutations of the 23S rRNA gene in clarithromycin-resistant H. pylori.
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Affiliation(s)
- Andrés Jenuer Matta
- Registro Poblacional de Cáncer de Cali, Department of Pathology, School of Medicine, Universidad del Valle, Cali 760043, Colombia
- Faculty of Education and Sports Sciences, Institución Universitaria Escuela Nacional del Deporte, Cali 760043, Colombia
| | - Diana Carolina Zambrano
- Faculty of Education and Sports Sciences, Institución Universitaria Escuela Nacional del Deporte, Cali 760043, Colombia
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Herklotz V, Kovařík A, Lunerová J, Lippitsch S, Groth M, Ritz CM. The fate of ribosomal RNA genes in spontaneous polyploid dogrose hybrids [Rosa L. sect. Caninae (DC.) Ser.] exhibiting non-symmetrical meiosis. Plant J 2018; 94:77-90. [PMID: 29385286 DOI: 10.1111/tpj.13843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 01/03/2018] [Accepted: 01/15/2018] [Indexed: 05/02/2023]
Abstract
Dogroses represent an exceptional system for studying the effects of genome doubling and hybridization: their asymmetrical meiosis enables recombination in bi-parentally inherited chromosomes but prevents it in maternally inherited ones. We employed fluorescent in situ hybridization, genome skimming, amplicon sequencing of genomic and cDNA as well as conventional cloning of nuclear ribosomal DNA in two phylogenetically distinct pentaploid (2n = 5x = 35) species, Rosa canina and Rosa inodora, and their naturally occurring reciprocal hybrids, Rosa dumalis (5x) and Rosa agrestis (5x, 6x). Both progenitor species differed in composition, meiotic behaviour and expression of rDNA loci: R. canina (five 18S and 5-8 5S loci) was dominated by the Canina ribotypes, but R. inodora (four 18S loci and 7-8 5S loci) by the Rubiginosa ribotype. The co-localized 5S/18S loci occurred on either bivalent-forming (R. canina) or univalent-forming (R. inodora) chromosomes. Ribosomal DNA loci were additively inherited; however, the Canina ribotypes were dominantly expressed, even in genotypes with relatively low copy number of these genes. Moreover, we observed rDNA homogenization towards the paternally transmitted Canina ribotype in 6x R. agrestis. The here-observed variation in arrangement and composition of rDNA types between R. canina and R. inodora suggests the involvement of different genomes in bivalent formation. This results supports the hypothesis that the asymmetrical meiosis arose at least twice by independent ancient hybridization events.
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Affiliation(s)
- Veit Herklotz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Am Museum 1, D-02826, Görlitz, Germany
| | - Aleš Kovařík
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Jana Lunerová
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65, Brno, Czech Republic
| | - Susan Lippitsch
- Department of Ecology and Environment Protection, University of Applied Sciences Zittau/Görlitz, Theodor-Körner-Allee 16, D-02763, Zittau, Germany
| | - Marco Groth
- Leibniz Institute on Aging - Fritz Lipmann Institute, Beutenbergstr. 11, D-07745, Jena, Germany
| | - Christiane M Ritz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Am Museum 1, D-02826, Görlitz, Germany
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Zhao LL, Zhai XD, Zhang Z, Lü Z, Xia ZY, Mo YN. [Molecular Identification of Sarcosaphagous Flies in Luoyang Based on 28S rRNA Gene Sequence]. Fa Yi Xue Za Zhi 2018; 34:114-119. [PMID: 29923373 DOI: 10.3969/j.issn.1004-5619.2018.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Indexed: 06/08/2023]
Abstract
OBJECTIVES To detect 715 bp sequence of 28S rRNA in sarcosaphagous flies, and to identify their common species for solving the problem of morphological identification, as well as providing technical support for postmortem interval (PMI) estimation. METHODS Twenty-nine common sarcosaphagous flies were collected in Luoyang and classified by morphological characteristics. The DNA was extracted from the fly's legs by Chelex-100 method and then the fragments of 28S rRNA were amplified and sequenced. The results were compared with twenty-eight corresponding fly species of GenBank and EMBL databases. All the sequences were analyzed by MEGA7.0 software, and sequence alignment was performed by the searching in BLAST. The nucleotide composition was analysed, and the intraspecific and interspecific genetic distance and phylogenetic tree were established. RESULTS Twenty-nine sarcosaphagous flies were classified into 6 species of 5 genera, 3 families by morphological characteristics. In the obtained 715 bp sequence of 28S rRNA, the comparison result of online BLAST showed that the similarity was 100%. Five species were well clustered by a phylogenetic tree. Between different groups, the interspecific and intraspecific differences ranged from 0.007 to 0.045 and 0 to 0.001, respectively. CONCLUSIONS The 28S rRNA target gene sequences shows a good identification capability, which can be a new genetic marker for the identification of sarcosaphagous flies.
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Affiliation(s)
- L L Zhao
- School of Forensic Medicine, Henan University of Science and Technology, Luoyang 471003, China
| | - X D Zhai
- School of Forensic Medicine, Henan University of Science and Technology, Luoyang 471003, China
| | - Z Zhang
- School of Forensic Medicine, Henan University of Science and Technology, Luoyang 471003, China
| | - Z Lü
- School of Criminal Investigation, Southwest University of Political Science & Law, Chongqing 400031, China
| | - Z Y Xia
- School of Forensic Medicine, Henan University of Science and Technology, Luoyang 471003, China
| | - Y N Mo
- School of Forensic Medicine, Henan University of Science and Technology, Luoyang 471003, China
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Marić Pfannkuchen D, Godrijan J, Smodlaka Tanković M, Baričević A, Kužat N, Djakovac T, Pustijanac E, Jahn R, Pfannkuchen M. The Ecology of One Cosmopolitan, One Newly Introduced and One Occasionally Advected Species from the Genus Skeletonema in a Highly Structured Ecosystem, the Northern Adriatic. Microb Ecol 2018; 75:674-687. [PMID: 28951994 DOI: 10.1007/s00248-017-1069-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/05/2017] [Indexed: 06/07/2023]
Abstract
The diatom genus Skeletonema is globally distributed and often an important constituent of the phytoplankton community. In the marine phytoplankton of the northern Adriatic Sea, we found three species of the genus Skeletonema: Skeletonema menzelii, Skeletonema marinoi and Skeletonema grevillei. Making use of the steep ecological gradients that characterise the northern Adriatic, along which we could observe those species, we report here on the ecological circumstances under which those species thrive and how their respective populations are globally connected. This is the first detailed ecological study for the species S. grevillei. This study is also the first report for S. grevillei for the Adriatic Sea and Mediterranean together with additional electron microscopic details on fresh in situ samples for this species. S. marinoi appears to clearly prefer strong freshwater influence and high nutrient concentrations delivered by low salinity waters. It can outcompete other diatom species and dominate microphytoplankton blooms. S. grevillei on the other hand appears to thrive in high nutrient concentrations triggered by water column mixing. It also appears to prefer higher salinity waters and coastal embayments. Genetic analysis of S. grevillei demonstrated a peculiar dissimilarity with isolates from coastal waters off Yemen, India, Oman and China. However, a closely related sequence was isolated from coastal waters off Japan. These results indicate that S. grevillei is an introduced species, possibly transported by ballast waters. S. menzelii is a sporadic visitor in the northern Adriatic, advected from rather oligotrophic middle Adriatic waters and never dominates the phytoplankton community in the northern Adriatic.
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Affiliation(s)
| | - Jelena Godrijan
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, Zagreb, Croatia
| | - Mirta Smodlaka Tanković
- Ruđer Bošković Institute, Center for Marine Research, G. Paliaga 5, HR-52210, Rovinj, Croatia
| | - Ana Baričević
- Ruđer Bošković Institute, Center for Marine Research, G. Paliaga 5, HR-52210, Rovinj, Croatia
| | - Nataša Kužat
- Ruđer Bošković Institute, Center for Marine Research, G. Paliaga 5, HR-52210, Rovinj, Croatia
| | - Tamara Djakovac
- Ruđer Bošković Institute, Center for Marine Research, G. Paliaga 5, HR-52210, Rovinj, Croatia
| | - Emina Pustijanac
- Department for Natural and Health Sciences, Juraj Dobrila University of Pula, Zagrebačka 30, HR-52100, Pula, Croatia
| | - Regina Jahn
- Botanischer Garten und Botanisches Museum Berlin-Dahlem, Freie Universität Berlin, Königin-Luise-Str.6-8, Berlin, Germany
| | - Martin Pfannkuchen
- Ruđer Bošković Institute, Center for Marine Research, G. Paliaga 5, HR-52210, Rovinj, Croatia.
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Ghilamicael AM, Boga HI, Anami SE, Mehari T, Budambula NLM. Potential human pathogenic bacteria in five hot springs in Eritrea revealed by next generation sequencing. PLoS One 2018; 13:e0194554. [PMID: 29566040 PMCID: PMC5864021 DOI: 10.1371/journal.pone.0194554] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 03/06/2018] [Indexed: 01/15/2023] Open
Abstract
Human pathogens can survive and grow in hot springs. For water quality assessment, Escherichia coli or Enterococci are the main thermotolerant enteric bacteria commonly used to estimate the load of pathogenic bacteria in water. However, most of the environmental bacteria are unculturable thus culture methods may cause bias in detection of most pathogens. Illumina sequencing can provide a more comprehensive and accurate insight into environmental bacterial pathogens, which can be used to develop better risk assessment methods and promote public health awareness. In this study, high-throughput Illumina sequencing was used to identify bacterial pathogens from five hot springs; Maiwooi, Akwar, Garbanabra, Elegedi and Gelti, in Eritrea. Water samples were collected from the five hot springs. Total community DNA was extracted from samples using the phenol-chloroform method. The 16S rRNA gene variable region (V4—V7) of the extracted DNA was amplified and library construction done according to Illumina sequencing protocol. The sequence reads (length >200 bp) from Illumina sequencing libraries ranged from 22,091 sequences in the wet sediment sample from Garbanabra to 155,789 sequences in the mat sample from Elegedi. Taxonomy was assigned to each OTU using BLASTn against a curated database derived from GreenGenes, RDPII, SILVA SSU Reference 119 and NCBI. The proportion of potential pathogens from the water samples was highest in Maiwooi (17.8%), followed by Gelti (16.7%), Akwar (13.6%) and Garbanabra (10.9%). Although the numbers of DNA sequence reads from Illumina sequencing were very high for the Elegedi (104,328), corresponding proportion of potential pathogens very low (3.6%). Most of the potential pathogenic bacterial sequences identified were from Proteobacteria and Firmicutes. Legionella and Clostridium were the most common detected genera with different species. Most of the potential pathogens were detected from the water samples. However, sequences belonging to Clostridium were observed more abundantly from the mat samples. This study employed high-throughput sequencing technologies to determine the presence of pathogenic bacteria in the five hot springs in Eritrea.
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Affiliation(s)
- Amanuel Menghs Ghilamicael
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
- * E-mail:
| | | | - Sylvester Elikana Anami
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Tadesse Mehari
- National Commission for Higher Education in Eritrea, Asmara, Eritrea
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Mirzaghaderi G, Abdolmalaki Z, Zohouri M, Moradi Z, Mason AS. Dynamic nucleolar activity in wheat × Aegilops hybrids: evidence of C-genome dominance. Plant Cell Rep 2017; 36:1277-1285. [PMID: 28456843 DOI: 10.1007/s00299-017-2152-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 04/27/2017] [Indexed: 06/07/2023]
Abstract
NOR loci of C-subgenome are dominant in wheat × Aegilops interspecific hybrids, which may have evolutionary implications for wheat group genome dynamics and evolution. After interspecific hybridisation, some genes are often expressed from only one of the progenitor species, shaping subsequent allopolyploid genome evolution processes. A well-known example is nucleolar dominance, i.e. the formation of cell nucleoli from chromosomes of only one parental species. We studied nucleolar organizing regions (NORs) in diploid Aegilops markgrafii (syn: Ae. caudata; CC), Ae. umbellulata (UU), allotetraploids Aegilops cylindrica (CcCcDcDc) and Ae. triuncialis (CtCtUtUt), synthetic interspecific F1 hybrids between these two allotetraploids and bread wheat (Triticum aestivum, AABBDD) and in F3 generation hybrids with genome composition AABBDDCtCtUtUt using silver staining and fluorescence in situ hybridization (FISH). In Ae. markgrafii (CC), NORs of both 1C and 5C or only 5C chromosome pairs were active in different individual cells, while only NORs on 1U chromosomes were active in Ae. umbellulata (UU). Although all 35S rDNA loci of the Ct subgenome (located on 1Ct and 5Ct) were active in Ae. triuncialis, only one pair (occupying either 1Cc or 5Cc) was active in Ae. cylindrica, depending on the genotype studied. These C-genome expression patterns were transmitted to the F1 and F3 generations. Wheat chromosome NOR activity was variable in Ae. triuncialis × T. aestivum F1 seeds, but silenced by the F3 generation. No effect of maternal or paternal cross direction was observed. These results indicate that C-subgenome NOR loci are dominant in wheat × Aegilops interspecific hybrids, which may have evolutionary implications for wheat group genome dynamics and allopolyploid evolution.
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Affiliation(s)
- Ghader Mirzaghaderi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, P. O. Box 416, Sanandaj, Iran.
| | - Zinat Abdolmalaki
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, P. O. Box 416, Sanandaj, Iran
| | - Mohsen Zohouri
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, P. O. Box 416, Sanandaj, Iran
| | - Zeinab Moradi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, P. O. Box 416, Sanandaj, Iran
| | - Annaliese S Mason
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
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Garcia S, Kovařík A, Leitch AR, Garnatje T. Cytogenetic features of rRNA genes across land plants: analysis of the Plant rDNA database. Plant J 2017; 89:1020-1030. [PMID: 27943584 DOI: 10.1111/tpj.13442] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 11/22/2016] [Accepted: 11/24/2016] [Indexed: 05/09/2023]
Abstract
The online resource http://www.plantrdnadatabase.com/ stores information on the number, chromosomal locations and structure of the 5S and 18S-5.8S-26S (35S) ribosomal DNAs (rDNA) in plants. This resource was exploited to study relationships between rDNA locus number, distribution, the occurrence of linked (L-type) and separated (S-type) 5S and 35S rDNA units, chromosome number, genome size and ploidy level. The analyses presented summarise current knowledge on rDNA locus numbers and distribution in plants. We analysed 2949 karyotypes, from 1791 species and 86 plant families, and performed ancestral character state reconstructions. The ancestral karyotype (2n = 16) has two terminal 35S sites and two interstitial 5S sites, while the median (2n = 24) presents four terminal 35S sites and three interstitial 5S sites. Whilst 86.57% of karyotypes show S-type organisation (ancestral condition), the L-type arrangement has arisen independently several times during plant evolution. A non-terminal position of 35S rDNA was found in about 25% of single-locus karyotypes, suggesting that terminal locations are not essential for functionality and expression. Single-locus karyotypes are very common, even in polyploids. In this regard, polyploidy is followed by subsequent locus loss. This results in a decrease in locus number per monoploid genome, forming part of the diploidisation process returning polyploids to a diploid-like state over time.
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Affiliation(s)
- Sònia Garcia
- Institut Botànic de Barcelona (IBB-CSIC-ICUB), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
| | - Ales Kovařík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno, 612 65, Czech Republic
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Teresa Garnatje
- Institut Botànic de Barcelona (IBB-CSIC-ICUB), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
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Robinson CK, Brotman RM, Ravel J. Intricacies of assessing the human microbiome in epidemiologic studies. Ann Epidemiol 2016; 26:311-21. [PMID: 27180112 PMCID: PMC4892937 DOI: 10.1016/j.annepidem.2016.04.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/29/2016] [Accepted: 04/05/2016] [Indexed: 12/11/2022]
Abstract
PURPOSE In the past decade, remarkable relationships have been documented between dysbiosis of the human microbiota and adverse health outcomes. This review seeks to highlight some of the challenges and pitfalls that may be encountered during all stages of microbiota research, from study design and sample collection, to nucleic acid extraction and sequencing, and bioinformatic and statistical analysis. METHODS Literature focused on human microbiota research was reviewed and summarized. RESULTS Although most studies have focused on surveying the composition of the microbiota, fewer have explored the causal roles of these bacteria, archaea, viruses, and fungi in affecting disease states. Microbiome research is in its relatively early years and many aspects remain challenging, including the complexity and personalized aspects of microbial communities, the influence of exogenous and often confounding factors, the need to apply fundamental principles of ecology and epidemiology, the necessity for new software tools, and the rapidly evolving genomic, technological, and analytical landscapes. CONCLUSIONS Incorporating human microbiome research in large epidemiologic studies will soon help us unravel the intricate relationships that we have with our microbial partners and provide interventional opportunities to improve human health.
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Affiliation(s)
- Courtney K Robinson
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore
| | - Rebecca M Brotman
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore; Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore.
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore; Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore.
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Chandrasekhara C, Mohannath G, Blevins T, Pontvianne F, Pikaard CS. Chromosome-specific NOR inactivation explains selective rRNA gene silencing and dosage control in Arabidopsis. Genes Dev 2016; 30:177-90. [PMID: 26744421 PMCID: PMC4719308 DOI: 10.1101/gad.273755.115] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 12/04/2015] [Indexed: 02/03/2023]
Abstract
In eukaryotes, scores of excess ribosomal RNA (rRNA) genes are silenced by repressive chromatin modifications. Given the near sequence identity of rRNA genes within a species, it is unclear how specific rRNA genes are reproducibly chosen for silencing. Using Arabidopsis thaliana ecotype (strain) Col-0, a systematic search identified sequence polymorphisms that differ between active and developmentally silenced rRNA gene subtypes. Recombinant inbred mapping populations derived from three different ecotype crosses were then used to map the chromosomal locations of silenced and active RNA gene subtypes. Importantly, silenced and active rRNA gene subtypes are not intermingled. All silenced rRNA gene subtypes mapped to the nucleolus organizer region (NOR) on chromosome 2 (NOR2). All active rRNA gene subtypes mapped to NOR4. Using an engineered A. thaliana line in which a portion of Col-0 chromosome 4 was replaced by sequences of another ecotype, we show that a major rRNA gene subtype silenced at NOR2 is active when introgressed into the genome at NOR4. Collectively, these results reveal that selective rRNA gene silencing is not regulated gene by gene based on mechanisms dependent on subtle gene sequence variation. Instead, we propose that a subchromosomal silencing mechanism operates on a multimegabase scale to inactivate NOR2.
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Affiliation(s)
- Chinmayi Chandrasekhara
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA; Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Gireesha Mohannath
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA; Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Todd Blevins
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA; Department of Biology, Indiana University, Bloomington, Indiana 47405, USA; Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana 47405, USA
| | - Frederic Pontvianne
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA; Department of Biology, Indiana University, Bloomington, Indiana 47405, USA
| | - Craig S Pikaard
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, USA; Department of Biology, Indiana University, Bloomington, Indiana 47405, USA; Howard Hughes Medical Institute, Indiana University, Bloomington, Indiana 47405, USA
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Poidevin L, Andreeva K, Khachatoorian C, Judelson HS. Comparisons of Ribosomal Protein Gene Promoters Indicate Superiority of Heterologous Regulatory Sequences for Expressing Transgenes in Phytophthora infestans. PLoS One 2015; 10:e0145612. [PMID: 26716454 PMCID: PMC4696810 DOI: 10.1371/journal.pone.0145612] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 12/07/2015] [Indexed: 12/14/2022] Open
Abstract
Molecular genetics approaches in Phytophthora research can be hampered by the limited number of known constitutive promoters for expressing transgenes and the instability of transgene activity. We have therefore characterized genes encoding the cytoplasmic ribosomal proteins of Phytophthora and studied their suitability for expressing transgenes in P. infestans. Phytophthora spp. encode a standard complement of 79 cytoplasmic ribosomal proteins. Several genes are duplicated, and two appear to be pseudogenes. Half of the genes are expressed at similar levels during all stages of asexual development, and we discovered that the majority share a novel promoter motif named the PhRiboBox. This sequence is enriched in genes associated with transcription, translation, and DNA replication, including tRNA and rRNA biogenesis. Promoters from the three P. infestans genes encoding ribosomal proteins S9, L10, and L23 and their orthologs from P. capsici were tested for their ability to drive transgenes in stable transformants of P. infestans. Five of the six promoters yielded strong expression of a GUS reporter, but the stability of expression was higher using the P. capsici promoters. With the RPS9 and RPL10 promoters of P. infestans, about half of transformants stopped making GUS over two years of culture, while their P. capsici orthologs conferred stable expression. Since cross-talk between native and transgene loci may trigger gene silencing, we encourage the use of heterologous promoters in transformation studies.
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Affiliation(s)
- Laetitia Poidevin
- Department of Plant Pathology and Microbiology, University of California, Riverside, California, United States of America
| | - Kalina Andreeva
- Department of Plant Pathology and Microbiology, University of California, Riverside, California, United States of America
| | - Careen Khachatoorian
- Department of Plant Pathology and Microbiology, University of California, Riverside, California, United States of America
| | - Howard S. Judelson
- Department of Plant Pathology and Microbiology, University of California, Riverside, California, United States of America
- * E-mail:
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Ramos V, Salvi D, Machado JP, Vale M, Azevedo J, Vasconcelos V. Culture-Independent Study of the Late-Stage of a Bloom of the Toxic Dinoflagellate Ostreopsis cf. ovata: Preliminary Findings Suggest Genetic Differences at the Sub-Species Level and Allow ITS2 Structure Characterization. Toxins (Basel) 2015; 7:2514-33. [PMID: 26134259 PMCID: PMC4516926 DOI: 10.3390/toxins7072514] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 06/06/2015] [Accepted: 06/24/2015] [Indexed: 02/03/2023] Open
Abstract
Available genomic data for the toxic, bloom-forming, benthic Ostreopsis spp. are traditionally obtained from isolates rather than from individuals originally present in environmental samples. Samples from the final phase of the first reported Ostreopsis bloom in European North Atlantic waters (Algarve, south coast of Portugal) were studied and characterized, using a culture-independent approach. In the first instance, a microscopy-based analysis revealed the intricate complexity of the samples. Then, we evaluated the adequacy of commonly used molecular tools (i.e., primers and nuclear ribosomal markers) for the study of Ostreopsis diversity in natural samples. A PCR-based methodology previously developed to identify/detect common Ostreopsis species was tested, including one new combination of existing PCR primers. Two sets of environmental rRNA sequences were obtained, one of them (1052 bp) with the newly tested primer set. These latter sequences encompass both the ITS1-5.8S-ITS2 region and the D1/D2 domain of the LSU rRNA gene, leading us to an accurate identification of ITS2. In turn, this allowed us to predict and show for the first time the ITS2 secondary structure of Ostreopsis. With 92 bp in length and a two-helix structure, the ITS2 of this genus revealed to be unique among the dinoflagellates. Both the PCR approach as the phylogenetic analyses allowed to place the Ostreopsis cells observed in the samples within the O. cf. ovata phylospecies’ complex, discarding the presence of O. cf. siamensis. The (phylo)genetic results point out a certain level of nucleotide sequence divergence, but were inconclusive in relation to a possible geographic origin of the O. cf. ovata population from the Algarve’s bloom.
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Affiliation(s)
- Vitor Ramos
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal.
| | - Daniele Salvi
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal.
| | - João Paulo Machado
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal.
| | - Micaela Vale
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal.
| | - Joana Azevedo
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal.
| | - Vitor Vasconcelos
- CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal.
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal.
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Abdel-Baki AAS, Mansour L, Al-Qahtani HA, Al Omar SY, Al-Quraishy S. Morphology, seasonality and phylogenetic relationships of Ceratomyxa husseini n. sp. from the gall-bladder of Cephalopholis hemistiktos (Rüppell) (Perciformes: Serranidae) in the Arabian Gulf off Saudi Arabia. Syst Parasitol 2015; 91:91-9. [PMID: 25862036 DOI: 10.1007/s11230-015-9554-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 02/18/2015] [Indexed: 11/26/2022]
Abstract
During a survey of myxosporean parasites of marine fishes from the Arabian Gulf in Saudi Arabia, spores of Ceratomyxa husseini n. sp. were found in the gall-bladders of 50 out of 148 specimens (33.8%) of the yellowfin hind Cephalopholis hemistiktos (Rüppell) (Perciformes: Serranidae). The rates of infection showed a seasonal fluctuation, with the highest prevalence in winter and the lowest in autumn. The mature spores appeared arched in frontal view with rounded valve ends and a slightly discriminated curved suture line and measured 8-9 × 14-18 (9 × 16) μm. The two polar capsules were spherical and equal in size, 4-5 (4.5) μm in diameter. The polar filament showed four turns obliquely to the longitudinal axis of the capsules and the sporoplasm filled half of the entire spore cavity. Partial sequences of the small subunit rRNA gene of C. husseini n. sp. showed percentage of identity with other species of Ceratomyxa ranging between 79.8 and 92.7%. The morphometric and molecular data, in association, confirmed that the present new species differs from all other Ceratomyxa spp. reported to date.
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Affiliation(s)
- Abdel-Azeem S Abdel-Baki
- Zoology Department, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia,
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Shao C, Li L, Zhang Q, Song W, Berger H. Molecular phylogeny and ontogeny of a new ciliate genus, Paracladotricha salina n. g., n. sp. (Ciliophora, Hypotrichia). J Eukaryot Microbiol 2014; 61:371-80. [PMID: 24773314 PMCID: PMC4140608 DOI: 10.1111/jeu.12117] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 01/28/2014] [Accepted: 02/27/2014] [Indexed: 11/29/2022]
Abstract
A hypotrichous ciliate, Paracladotricha salina n. g., n. sp., was discovered in hypersaline waters (salinity about 80‰) from Qingdao, China. Its morphology and some major ontogenetic stages were studied and the phylogenetic position was estimated using standard methods. Paracladotricha salina is characterized by a flexible, more or less slender body (size 50-120 × 20-35 μm), a gonostomatid oral apparatus, one short and two long frontoventral rows, four macronuclear nodules, almost completely reduced dorsal kineties 1-3, and a loss of several parts of the ciliature, namely, the slightly shortened ciliary row of the adoral membranelles, the paroral, and the buccal, the postoral and pretransverse ventral, the transverse, and the caudal cirri. The ontogenesis is rather simple: anlage II of both filial products and anlage III of the opisthe originate de novo, while anlagen IV and V are formed within the parental rows. This combination of features requires the establishment of a new genus, Paracladotricha, which is, according to the morphological data, closely related to Schmidingerothrix and Cladotricha. The small-subunit rRNA gene was sequenced, indicating that P. salina is, as also demonstrated by the oral apparatus, a member of the gonostomatids. We provide a first, vague hypothesis about the phylogenetic relationships of the Gonostomatidae, Cladotrichidae, and Schmidingerotrichidae. However, since molecular data of the type species of these higher taxa are lacking, their validity and relationships remain obscure.
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Affiliation(s)
- Chen Shao
- The Key Laboratory of Biomedical Information Engineering, Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
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Burow LC, Woebken D, Marshall IPG, Singer SW, Pett-Ridge J, Prufert-Bebout L, Spormann AM, Bebout BM, Weber PK, Hoehler TM. Identification of Desulfobacterales as primary hydrogenotrophs in a complex microbial mat community. Geobiology 2014; 12:221-230. [PMID: 24730641 DOI: 10.1111/gbi.12080] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 01/22/2014] [Indexed: 06/03/2023]
Abstract
Hypersaline microbial mats have been shown to produce significant quantities of H2 under dark, anoxic conditions via cyanobacterial fermentation. This flux of a widely accessible microbial substrate has potential to significantly influence the ecology of the mat, and any consumption will affect the net efflux of H2 that might otherwise be captured as a resource. Here, we focus on H2 consumption in a microbial mat from Elkhorn Slough, California, USA, for which H2 production has been previously characterized. Active biologic H2 consumption in this mat is indicated by a significant time-dependent decrease in added H2 compared with a killed control. Inhibition of sulfate reduction, as indicated by a decrease in hydrogen sulfide production relative to controls, resulted in a significant increase in H2 efflux, suggesting that sulfate-reducing bacteria (SRB) are important hydrogenotrophs. Low methane efflux under these same conditions indicated that methanogens are likely not important hydrogenotrophs. Analyses of genes and transcripts that encode for rRNA or dissimilatory sulfite reductase, using both PCR-dependent and PCR-independent metatranscriptomic sequencing methods, demonstrated that Desulfobacterales are the dominant, active SRB in the upper, H2-producing layer of the mat (0-2 mm). This hypothesis was further supported by the identification of transcripts encoding hydrogenases derived from Desulfobacterales capable of H2 oxidation. Analysis of molecular data provided no evidence for the activity of hydrogenotrophic methanogens. The combined biogeochemical and molecular data strongly indicate that SRB belonging to the Desulfobacterales are the quantitatively important hydrogenotrophs in the Elkhorn Slough mat.
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Affiliation(s)
- L C Burow
- Departments of Chemical, Civil and Environmental Engineering, Stanford University, Stanford, CA, USA; Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA
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Gittel A, Bárta J, Kohoutová I, Mikutta R, Owens S, Gilbert J, Schnecker J, Wild B, Hannisdal B, Maerz J, Lashchinskiy N, Čapek P, Šantrůčková H, Gentsch N, Shibistova O, Guggenberger G, Richter A, Torsvik VL, Schleper C, Urich T. Distinct microbial communities associated with buried soils in the Siberian tundra. ISME J 2014; 8:841-53. [PMID: 24335828 PMCID: PMC3960545 DOI: 10.1038/ismej.2013.219] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 10/21/2013] [Accepted: 11/06/2013] [Indexed: 01/22/2023]
Abstract
Cryoturbation, the burial of topsoil material into deeper soil horizons by repeated freeze-thaw events, is an important storage mechanism for soil organic matter (SOM) in permafrost-affected soils. Besides abiotic conditions, microbial community structure and the accessibility of SOM to the decomposer community are hypothesized to control SOM decomposition and thus have a crucial role in SOM accumulation in buried soils. We surveyed the microbial community structure in cryoturbated soils from nine soil profiles in the northeastern Siberian tundra using high-throughput sequencing and quantification of bacterial, archaeal and fungal marker genes. We found that bacterial abundances in buried topsoils were as high as in unburied topsoils. In contrast, fungal abundances decreased with depth and were significantly lower in buried than in unburied topsoils resulting in remarkably low fungal to bacterial ratios in buried topsoils. Fungal community profiling revealed an associated decrease in presumably ectomycorrhizal (ECM) fungi. The abiotic conditions (low to subzero temperatures, anoxia) and the reduced abundance of fungi likely provide a niche for bacterial, facultative anaerobic decomposers of SOM such as members of the Actinobacteria, which were found in significantly higher relative abundances in buried than in unburied topsoils. Our study expands the knowledge on the microbial community structure in soils of Northern latitude permafrost regions, and attributes the delayed decomposition of SOM in buried soils to specific microbial taxa, and particularly to a decrease in abundance and activity of ECM fungi, and to the extent to which bacterial decomposers are able to act as their functional substitutes.
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Affiliation(s)
- Antje Gittel
- Department of Biology, Centre for Geobiology, University of Bergen, Bergen, Norway
- Austrian Polar Research Institute, Vienna, Austria
| | - Jiří Bárta
- Department of Ecosystems Biology, University of South Bohemia, České Budějovice, Czech Republic
| | - Iva Kohoutová
- Department of Ecosystems Biology, University of South Bohemia, České Budějovice, Czech Republic
| | - Robert Mikutta
- Institut für Bodenkunde, Leibniz Universität Hannover, Hannover, Germany
| | - Sarah Owens
- Institute of Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL, USA
- Computation Institute, University of Chicago, Chicago, IL, USA
| | - Jack Gilbert
- Institute of Genomics and Systems Biology, Argonne National Laboratory, Argonne, IL, USA
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Jörg Schnecker
- Austrian Polar Research Institute, Vienna, Austria
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Birgit Wild
- Austrian Polar Research Institute, Vienna, Austria
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Bjarte Hannisdal
- Department of Earth Science, Centre for Geobiology, University of Bergen, Bergen, Norway
| | - Joeran Maerz
- Division of Ecosystem Modelling, Institute of Coastal Research, Helmholtz Zentrum Geesthacht, Geesthacht, Germany
| | - Nikolay Lashchinskiy
- Central Siberian Botanical Garden, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Petr Čapek
- Department of Ecosystems Biology, University of South Bohemia, České Budějovice, Czech Republic
| | - Hana Šantrůčková
- Department of Ecosystems Biology, University of South Bohemia, České Budějovice, Czech Republic
| | - Norman Gentsch
- Institut für Bodenkunde, Leibniz Universität Hannover, Hannover, Germany
| | - Olga Shibistova
- Institut für Bodenkunde, Leibniz Universität Hannover, Hannover, Germany
- VN Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, Akademgorodok, Russia
| | - Georg Guggenberger
- Institut für Bodenkunde, Leibniz Universität Hannover, Hannover, Germany
| | - Andreas Richter
- Austrian Polar Research Institute, Vienna, Austria
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Vigdis L Torsvik
- Department of Biology, Centre for Geobiology, University of Bergen, Bergen, Norway
| | - Christa Schleper
- Department of Biology, Centre for Geobiology, University of Bergen, Bergen, Norway
- Austrian Polar Research Institute, Vienna, Austria
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Tim Urich
- Austrian Polar Research Institute, Vienna, Austria
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
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KOBAYASHI T. Ribosomal RNA gene repeats, their stability and cellular senescence. Proc Jpn Acad Ser B Phys Biol Sci 2014; 90:119-29. [PMID: 24727936 PMCID: PMC4055705 DOI: 10.2183/pjab.90.119] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 01/08/2014] [Indexed: 05/19/2023]
Abstract
The ribosomal RNA gene (rDNA) repeats form a historically well-researched region in the chromosome. Their highly repetitive structure can be identified easily which has enabled studies on DNA replication, recombination, and transcription. The region is one of the most unstable regions in the genome because of deleterious recombination among the repeats. The ribosomal RNA gene repeats use a unique gene amplification system to restore the copy number after this has been reduced due to recombination. It has been shown that unstable features in the genome can accelerate cellular senescence that restricts the lifespan of a cell. Here, I will introduce a study by our group that shows how the stability of rDNA is maintained and affects lifespan. I propose that the ribosomal RNA gene repeats constitute a center from which the stability of the whole genome is regulated and the lifespan of the cell is controlled.
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Affiliation(s)
- Takehiko KOBAYASHI
- National Institute of Genetics, Division of Cytogenetics/Dept. of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Shizuoka, Japan
- Correspondence should be addressed: T. Kobayashi, National Institute of Genetics, Division of Cytogenetics/Dept. of Genetics, The Graduate University for Advanced Studies, SOKENDAI, 1111 Yata, Mishima, Shizuoka 411-8540, Japan (e-mail: )
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Kokhanenko A, Anan'ina T, Stegniy V. Localization of rRNA genes in the nuclear space of Calliphora erythrocephala Mg. nurse cells during polytenization. Protoplasma 2014; 251:93-101. [PMID: 23873188 DOI: 10.1007/s00709-013-0529-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 07/03/2013] [Indexed: 06/02/2023]
Abstract
Multicolor 3D fluorescence in situ hybridization was used to study arrangement of rRNA genes in Calliphora erythrocephala nurse cell nuclei with different levels of polyteny. It has been shown that the rRNA genes are exclusively localized to chromosome 6, suggesting that chromosome 6 is the only C. erythrocephala chromosome responsible for nucleolar formation. We have also described changes in localization of ribosomal genes within the chromosome territory during polytenization, namely, that rDNA signals are detected in the peripheral region of chromosome territory starting from the stage of polytene chromosomes. In addition, it has emerged that large nucleolus associated with chromosome 6 starts to develop in the central nuclear region in the C. erythrocephala nurse cell nuclei at the stage of a primary reticular structure. The central position and nucleolar structure are retained at the stages when chromosome 6 occupies the central position, that is, at the stages of polytene and bloblike chromosomes. When the nucleus restores a reticular structure but at a higher polyteny level, the displacement of chromosome 6 to the nuclear periphery is accompanied by disruption of the large nucleolus into micronucleoli. The micronucleoli are distributed in the nuclear space retaining their association with the nucleolar-organizing regions of chromosome 6. Thus, our data suggest that the large-scale alterations in the organization of chromosome 6 and the nucleolus during polytenization are the correlated processes directly dependent on the rRNA gene activity. The earlier described dynamics of nucleolar-organizing chromosome territory and nucleolus in the nuclear space is likely to be associated with the change in the total expression activity of the nucleus, which complies with the hypothesis on the correlation between spatial nuclear organization and expression regulation of genetic material.
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Affiliation(s)
- Alina Kokhanenko
- Tomsk State University, 36 Lenin Prospekt, Tomsk, 634050, Russian Federation,
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Pombert JF, Otis C, Turmel M, Lemieux C. The mitochondrial genome of the prasinophyte Prasinoderma coloniale reveals two trans-spliced group I introns in the large subunit rRNA gene. PLoS One 2013; 8:e84325. [PMID: 24386369 PMCID: PMC3873408 DOI: 10.1371/journal.pone.0084325] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Accepted: 11/20/2013] [Indexed: 12/05/2022] Open
Abstract
Organelle genes are often interrupted by group I and or group II introns. Splicing of these mobile genetic occurs at the RNA level via serial transesterification steps catalyzed by the introns'own tertiary structures and, sometimes, with the help of external factors. These catalytic ribozymes can be found in cis or trans configuration, and although trans-arrayed group II introns have been known for decades, trans-spliced group I introns have been reported only recently. In the course of sequencing the complete mitochondrial genome of the prasinophyte picoplanktonic green alga Prasinoderma coloniale CCMP 1220 (Prasinococcales, clade VI), we uncovered two additional cases of trans-spliced group I introns. Here, we describe these introns and compare the 54,546 bp-long mitochondrial genome of Prasinoderma with those of four other prasinophytes (clades II, III and V). This comparison underscores the highly variable mitochondrial genome architecture in these ancient chlorophyte lineages. Both Prasinoderma trans-spliced introns reside within the large subunit rRNA gene (rnl) at positions where cis-spliced relatives, often containing homing endonuclease genes, have been found in other organelles. In contrast, all previously reported trans-spliced group I introns occur in different mitochondrial genes (rns or coxI). Each Prasinoderma intron is fragmented into two pieces, forming at the RNA level a secondary structure that resembles those of its cis-spliced counterparts. As observed for other trans-spliced group I introns, the breakpoint of the first intron maps to the variable loop L8, whereas that of the second is uniquely located downstream of P9.1. The breakpoint In each Prasinoderma intron corresponds to the same region where the open reading frame (ORF) occurs when present in cis-spliced orthologs. This correlation between the intron breakpoint and the ORF location in cis-spliced orthologs also holds for other trans-spliced introns; we discuss the possible implications of this interesting observation for trans-splicing of group I introns.
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Affiliation(s)
- Jean-François Pombert
- Department of Biological and Chemical Sciences, Illinois Institute of Technology, Chicago, Illinois, United States of America
| | - Christian Otis
- Institut de Biologie Intégrative et des Systèmes, Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Québec, Canada
| | - Monique Turmel
- Institut de Biologie Intégrative et des Systèmes, Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Québec, Canada
| | - Claude Lemieux
- Institut de Biologie Intégrative et des Systèmes, Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Québec, Canada
- * E-mail:
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Matsumoto T, Sugano M. [16S rRNA gene sequence analysis for bacterial identification in the clinical laboratory]. Rinsho Byori 2013; 61:1107-1115. [PMID: 24605544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The traditional identification of bacteria on the basis of phenotypic characteristics is generally not as accurate as identification based on genotypic methods. For many years, sequencing of the 16S ribosomal RNA (rRNA) gene has served as an important tool for determining phylogenetic relationships between bacteria. The features of this molecular target that make it a useful phylogenetic tool also make it useful for bacterial detection and identification in the clinical laboratory. 16S rRNA gene sequence analysis can better identify poorly described, rarely isolated, or phenotypically aberrant strains, and can lead to the recognition of novel pathogens and noncultured bacteria. In clinical microbiology, molecular identification based on 16S rDNA sequencing is applied fundamentally to bacteria whose identification by means of other types of techniques is impossible or difficult. However, there are some cases in which 16S rRNA gene sequence analysis can not differentiate closely related bacteria such as Shigella spp. and Escherichia coli at the species level. Thus, it is important to understand the advantages and disadvantages of 16S rRNA gene sequence analysis.
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Affiliation(s)
- Takehisa Matsumoto
- Department of Laboratory Medicine, Shinshu University Hospital, Matsumoto 390-8621, Japan.
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Zhu D, Tanabe SH, Yang C, Zhang W, Sun J. Bacterial community composition of South China Sea sediments through pyrosequencing-based analysis of 16S rRNA genes. PLoS One 2013; 8:e78501. [PMID: 24205246 PMCID: PMC3804488 DOI: 10.1371/journal.pone.0078501] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 09/14/2013] [Indexed: 01/12/2023] Open
Abstract
Background Subseafloor sediments accumulate large amounts of organic and inorganic materials that contain a highly diverse microbial ecosystem. The aim of this study was to survey the bacterial community of subseafloor sediments from the South China Sea. Methodology/Principal Findings Pyrosequencing of over 265,000 amplicons of the V3 hypervariable region of the 16S ribosomal RNA gene was performed on 16 sediment samples collected from multiple locations in the northern region of the South China Sea from depths ranging from 35 to 4000 m. A total of 9,726 operational taxonomic units (OTUs; between 695 and 2819 unique OTUs per sample) at 97% sequence similarity level were generated. In total, 40 bacterial phyla including 22 formally described phyla and 18 candidate phyla, with Proteobacteria, Firmicutes, Planctomycetes, Actinobacteria and Chloroflexi being most diverse, were identified. The most abundant phylotype, accounting for 42.6% of all sequences, belonged to Gammaproteobacteria, which possessed absolute predominance in the samples analyzed. Among the 18 candidate phyla, 12 were found for the first time in the South China Sea. Conclusions This study provided a novel insight into the composition of bacterial communities of the South China Sea subseafloor. Furthermore, abundances and community similarity analysis showed that the compositions of the bacterial communities are very similar at phylum level at different depths from 35-4000 m.
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Affiliation(s)
- Daochen Zhu
- School of Environmental Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
- State Key Laboratory of Applied Microbiology in South China (Ministry-Guangdong Province Jointly Breeding Base), Guangdong Institute of Microbiology, Guangzhou, China
- * E-mail: (DZ); (WZ)
| | - Shoko-Hosoi Tanabe
- School of Environmental Science, University of Shiga Prefecture, Hikone, Shiga, Japan
| | - Chong Yang
- Department of R&D, Zhenjiang Bio-innova Biotech Co, Ltd., Zhenjiang, Jiangsu, China
| | - Weimin Zhang
- State Key Laboratory of Applied Microbiology in South China (Ministry-Guangdong Province Jointly Breeding Base), Guangdong Institute of Microbiology, Guangzhou, China
- * E-mail: (DZ); (WZ)
| | - Jianzhong Sun
- School of Environmental Engineering, Jiangsu University, Zhenjiang, Jiangsu, China
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Tanaka Y, Tsuneoka M. [Control mechanisms of ribosomal RNA transcription]. Seikagaku 2013; 85:852-860. [PMID: 24392584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Affiliation(s)
- Yuji Tanaka
- Faculty of Pharmacy, Takasaki University of Health and Welfare, 60 Nakaoruimachi, Takasaki-shi, Gunma 370-0033, Japan
| | - Makoto Tsuneoka
- Faculty of Pharmacy, Takasaki University of Health and Welfare, 60 Nakaoruimachi, Takasaki-shi, Gunma 370-0033, Japan
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Kitabatake M. [Quality control of ribosomes]. Seikagaku 2013; 85:889-895. [PMID: 24392588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Affiliation(s)
- Makoto Kitabatake
- Institute for Virus Research, Kyoto University, Shougoin-Kawaharacho 53, Sakyo-ku, Kyoto 606-8507, Japan
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Kobayashi T, Akamatsu Y. [Instability of the ribosomal RNA gene cluster and its physiological functions]. Seikagaku 2013; 85:839-844. [PMID: 24392582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Affiliation(s)
- Takehiko Kobayashi
- Division of Cytogenetics, National Institute of Genetics, The Graduate University for Advanced Studies, SOKENDAI, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Yufuko Akamatsu
- Division of Cytogenetics, National Institute of Genetics, The Graduate University for Advanced Studies, SOKENDAI, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
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Uchiumi T, Baba K, Onozuka M. [The dynamic functional structure of the ribosome discovered by the analysis of the autoimmune target]. Seikagaku 2013; 85:924-931. [PMID: 24392592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Affiliation(s)
- Toshio Uchiumi
- Department of Biology, Faculty of Science, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan
| | - Kentaro Baba
- Department of Biology, Faculty of Science, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan
| | - Miho Onozuka
- Department of Biology, Faculty of Science, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan
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Okuwaki M. [The ribosome RNA gene and nucleolar structure]. Seikagaku 2013; 85:845-851. [PMID: 24392583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Affiliation(s)
- Mitsuru Okuwaki
- Faculty of Medicine, University of Tsukuba, 1-1-1Tennodai, Tsukuba, Ibaraki 305-8575, Japan
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Nagahama M. [Regulation of ribosome assembly by molecular chaperones --functional analysis of nucleolar AAA-ATPase NVL2]. Seikagaku 2013; 85:880-888. [PMID: 24392587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Affiliation(s)
- Masami Nagahama
- Department of Biochemistry, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose-shi, Tokyo 204-8588, Japan
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50
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Duan YQ, He ST, Li QQ, Wang MF, Wang WY, Zhe W, Cao YH, Mo MH, Zhai YL, Li WJ. Lysinibacillus tabacifolii sp. nov., a novel endophytic bacterium isolated from Nicotiana tabacum leaves. J Microbiol 2013; 51:289-94. [PMID: 23812807 DOI: 10.1007/s12275-013-2338-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 02/07/2013] [Indexed: 11/25/2022]
Abstract
A Gram-positive, catalase- and oxidase-positive, strictly aerobic, endospore-forming rod bacterium, designated K3514(T), was isolated from the leaves of Nicotiana tabacum. The strain was able to grow at temperatures of 8-40°C, pH 5.0-10.0 and NaCl concentrations of 0-7%. The predominant quinones (>30%) of this strain were MK-7(H2) and MK-7. Phylogenetic analysis of 16S rRNA gene sequence showed that strain K3514(T) was affiliated to the genus Lysinibacillus, with its closest relatives being Lysinibacillus mangiferihumi (98.3% sequence similarity), Lysinibacillus sphaericus (97.9% sequence similarity), Lysinibacillus fusiformis (97.4% sequence similarity), and Lysinibacillus xylanilyticus (97.3% sequence similarity). However, low levels of DNA-DNA relatedness values suggested that the isolate was distinct from the other closest Lysinibacillus species. Additionally, based on analysis of morphological, physiological, and biochemical characteristics, the isolate could be differentiated from the closest known relatives. Therefore, based on polyphasic taxonomic data, the novel isolate likely represents a novel species, for which the name Lysinibacillus tabacifolii sp. nov. and the type strain K3514(T) (=KCTC 33042(T) =CCTCC AB 2012050(T)) are proposed.
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Affiliation(s)
- Yan-Qing Duan
- Technology Center of Hongyun Honghe Tobacco Group Co, Ltd, Kunming 650202, PR China
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