1
|
Ma Y, Wang J, He X, Liu Y, Zhen S, An L, Yang Q, Niu F, Wang H, An B, Tai X, Yan Z, Wu C, Yang X, Liu X. Molecular mechanism of human ISG20L2 for the ITS1 cleavage in the processing of 18S precursor ribosomal RNA. Nucleic Acids Res 2024; 52:1878-1895. [PMID: 38153123 PMCID: PMC10899777 DOI: 10.1093/nar/gkad1210] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/03/2023] [Accepted: 12/10/2023] [Indexed: 12/29/2023] Open
Abstract
The exonuclease ISG20L2 has been initially characterized for its role in the mammalian 5.8S rRNA 3' end maturation, specifically in the cleavage of ITS2 of 12S precursor ribosomal RNA (pre-rRNA). Here, we show that human ISG20L2 is also involved in 18S pre-rRNA maturation through removing the ITS1 region, and contributes to ribosomal biogenesis and cell proliferation. Furthermore, we determined the crystal structure of the ISG20L2 nuclease domain at 2.9 Å resolution. It exhibits the typical αβα fold of the DEDD 3'-5' exonuclease with a catalytic pocket located in the hollow near the center. The catalytic residues Asp183, Glu185, Asp267, His322 and Asp327 constitute the DEDDh motif in ISG20L2. The active pocket represents conformational flexibility in the absence of an RNA substrate. Using structural superposition and mutagenesis assay, we mapped RNA substrate binding residues in ISG20L2. Finally, cellular assays revealed that ISG20L2 is aberrantly up-regulated in colon adenocarcinoma and promotes colon cancer cell proliferation through regulating ribosome biogenesis. Together, these results reveal that ISG20L2 is a new enzymatic member for 18S pre-rRNA maturation, provide insights into the mechanism of ISG20L2 underlying pre-rRNA processing, and suggest that ISG20L2 is a potential therapeutic target for colon adenocarcinoma.
Collapse
Affiliation(s)
- Yinliang Ma
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Jiaxu Wang
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
- College of Life Sciences, State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453002 Henan, China
| | - Xingyi He
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Yuhang Liu
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Shuo Zhen
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Lina An
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Qian Yang
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Fumin Niu
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Hong Wang
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Boran An
- Affiliated Hospital of Hebei University, Hebei University, Baoding 071002 Hebei, China
| | - Xinyue Tai
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Zhenzhen Yan
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Chen Wu
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Xiaoyun Yang
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
| | - Xiuhua Liu
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| |
Collapse
|
2
|
Lambert M, Benmoussa A, Diallo I, Ouellet-Boutin K, Dorval V, Majeau N, Joly-Beauparlant C, Droit A, Bergeron A, Têtu B, Fradet Y, Pouliot F, Provost P. Identification of Abundant and Functional dodecaRNAs (doRNAs) Derived from Ribosomal RNA. Int J Mol Sci 2021; 22:9757. [PMID: 34575920 PMCID: PMC8467515 DOI: 10.3390/ijms22189757] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 08/04/2021] [Revised: 09/02/2021] [Accepted: 09/05/2021] [Indexed: 12/17/2022] Open
Abstract
Using a modified RNA-sequencing (RNA-seq) approach, we discovered a new family of unusually short RNAs mapping to ribosomal RNA 5.8S, which we named dodecaRNAs (doRNAs), according to the number of core nucleotides (12 nt) their members contain. Using a new quantitative detection method that we developed, we confirmed our RNA-seq data and determined that the minimal core doRNA sequence and its 13-nt variant C-doRNA (doRNA with a 5' Cytosine) are the two most abundant doRNAs, which, together, may outnumber microRNAs. The C-doRNA/doRNA ratio is stable within species but differed between species. doRNA and C-doRNA are mainly cytoplasmic and interact with heterogeneous nuclear ribonucleoproteins (hnRNP) A0, A1 and A2B1, but not Argonaute 2. Reporter gene activity assays suggest that C-doRNA may function as a regulator of Annexin II receptor (AXIIR) expression. doRNAs are differentially expressed in prostate cancer cells/tissues and may control cell migration. These findings suggest that unusually short RNAs may be more abundant and important than previously thought.
Collapse
Affiliation(s)
- Marine Lambert
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Department of Microbiology, Infectious Diseases and Immunology, Université Laval, Quebec City, QC G1V 4G2, Canada
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Abderrahim Benmoussa
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Department of Microbiology, Infectious Diseases and Immunology, Université Laval, Quebec City, QC G1V 4G2, Canada
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Idrissa Diallo
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Department of Microbiology, Infectious Diseases and Immunology, Université Laval, Quebec City, QC G1V 4G2, Canada
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Katheryn Ouellet-Boutin
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Department of Microbiology, Infectious Diseases and Immunology, Université Laval, Quebec City, QC G1V 4G2, Canada
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Véronique Dorval
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
| | - Nathalie Majeau
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
| | - Charles Joly-Beauparlant
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Department of Molecular Medicine, Université Laval, Quebec City, QC G1V 4G2, Canada
| | - Arnaud Droit
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Department of Molecular Medicine, Université Laval, Quebec City, QC G1V 4G2, Canada
| | - Alain Bergeron
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Department of Surgery, Université Laval, Quebec City, QC G1R 2J6, Canada
| | - Bernard Têtu
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
| | - Yves Fradet
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Department of Surgery, Université Laval, Quebec City, QC G1R 2J6, Canada
| | - Frédéric Pouliot
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Department of Surgery, Université Laval, Quebec City, QC G1R 2J6, Canada
| | - Patrick Provost
- CHU de Québec Research Center/CHUL Pavilion—Université Laval, 2705 boulevard Laurier, Quebec City, QC G1V 4G2, Canada; (M.L.); (A.B.); (I.D.); (K.O.-B.); (N.M.); (C.J.-B.); (A.D.); (A.B.); (B.T.); (Y.F.); (F.P.)
- Department of Microbiology, Infectious Diseases and Immunology, Université Laval, Quebec City, QC G1V 4G2, Canada
- Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
| |
Collapse
|
3
|
Abstract
The use of potent fungal mixed cultures is a promising technique for the biodegradation of crude oil. Four isolates of fungi, namely, Alternaria alternata (AA-1), Aspergillus flavus (AF-3), Aspergillus terreus (AT-7), and Trichoderma harzianum (TH-5), were isolated from date palm soil in Saudi Arabia. The mixed fungal of the four isolates have a powerful tool for biodegradation up to 73.6% of crude oil (1%, w/v) in 14 days. The fungal consortium no. 15 containing the four isolates (1:1:1:1) performed significantly better as a biodegradation agent than other consortium in a variety of environmental factors containing crude oil concentration, incubation temperature, initial pH, biodegradation time and the salinity of the medium. The fungal consortium showed better performance in the biodegradation of normal alkanes (n-alkanes) than that of the polycyclic aromatic hydrocarbons (PAHs); the biodegradation efficiency of normal alkanes of the fungal consortium (67.1%) was clearly high than that of the PAHs (56.8%).
Collapse
Affiliation(s)
- Abeer R. M. Abd El-Aziz
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- * E-mail:
| | - Monira R. Al-Othman
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Sameh M. Hisham
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Shereen M. Shehata
- Pharmaceutical Chemistry Department, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| |
Collapse
|
4
|
Aykur M, Dagci H. Evaluation of molecular characterization and phylogeny for quantification of Acanthamoeba and Naegleria fowleri in various water sources, Turkey. PLoS One 2021; 16:e0256659. [PMID: 34437614 PMCID: PMC8389491 DOI: 10.1371/journal.pone.0256659] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 04/22/2021] [Accepted: 08/11/2021] [Indexed: 01/02/2023] Open
Abstract
Free-living amoeba (FLA) is widely distributed in the natural environment. Since these amoebae are widely found in various waters, they pose an important public health problem. The aim of this study was to detect the presence of Acanthamoeba, B. mandrillaris, and N. fowleri in various water resources by qPCR in Izmir, Turkey. A total of (n = 27) 18.24% Acanthamoeba and (n = 4) 2.7% N. fowleri positives were detected in six different water sources using qPCR with ITS regions (ITS1) specific primers. The resulting concentrations varied in various water samples for Acanthamoeba in the range of 3.2x105-1.4x102 plasmid copies/l and for N. fowleri in the range of 8x103-11x102 plasmid copies/l. The highest concentration of Acanthamoeba and N. fowleri was found in seawater and damp samples respectively. All 27 Acanthamoeba isolates were identified in genotype level based on the 18S rRNA gene as T4 (51.85%), T5 (22.22%), T2 (14.81%) and T15 (11.11%). The four positive N. fowleri isolate was confirmed by sequencing the ITS1, ITS2 and 5.8S rRNA regions using specific primers. Four N. fowleri isolates were genotyped (three isolate as type 2 and one isolate as type 5) and detected for the first time from water sources in Turkey. Acanthamoeba and N. fowleri genotypes found in many natural environments are straightly related to human populations to have pathogenic potentials that may pose a risk to human health. Public health professionals should raise awareness on this issue, and public awareness education should be provided by the assistance of civil authorities. To the best of our knowledge, this is the first study on the quantitative detection and distribution of Acanthamoeba and N. fowleri genotypes in various water sources in Turkey.
Collapse
Affiliation(s)
- Mehmet Aykur
- Department of Parasitology, Faculty of Medicine, Tokat Gaziosmanpasa University Tokat, Tokat, Turkey
- Department of Parasitology, Faculty of Medicine, Ege University, Bornova, İzmir, Turkey
- * E-mail:
| | - Hande Dagci
- Department of Parasitology, Faculty of Medicine, Ege University, Bornova, İzmir, Turkey
| |
Collapse
|
5
|
Li X, Zengel JM, Lindahl L. A Novel Model for the RNase MRP-Induced Switch between the Formation of Different Forms of 5.8S rRNA. Int J Mol Sci 2021; 22:6690. [PMID: 34206573 PMCID: PMC8268776 DOI: 10.3390/ijms22136690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 04/27/2021] [Revised: 06/14/2021] [Accepted: 06/17/2021] [Indexed: 01/12/2023] Open
Abstract
Processing of the RNA polymerase I pre-rRNA transcript into the mature 18S, 5.8S, and 25S rRNAs requires removing the "spacer" sequences. The canonical pathway for the removal of the ITS1 spacer involves cleavages at the 3' end of 18S rRNA and at two sites inside ITS1. The process can generate either a long or a short 5.8S rRNA that differs in the number of ITS1 nucleotides retained at the 5.8S 5' end. Here we document a novel pathway to the long 5.8S, which bypasses cleavage within ITS1. Instead, the entire ITS1 is degraded from its 5' end by exonuclease Xrn1. Mutations in RNase MRP increase the accumulation of long relative to short 5.8S rRNA. Traditionally this is attributed to a decreased rate of RNase MRP cleavage at its target in ITS1, called A3. However, results from this work show that the MRP-induced switch between long and short 5.8S rRNA formation occurs even when the A3 site is deleted. Based on this and our published data, we propose that the link between RNase MRP and 5.8S 5' end formation involves RNase MRP cleavage at unknown sites elsewhere in pre-rRNA or in RNA molecules other than pre-rRNA.
Collapse
MESH Headings
- DNA, Ribosomal Spacer
- Endoribonucleases
- Gene Expression Regulation, Fungal
- Nucleic Acid Conformation
- RNA Processing, Post-Transcriptional
- RNA, Fungal
- RNA, Ribosomal, 5.8S/chemistry
- RNA, Ribosomal, 5.8S/genetics
- RNA, Ribosomal, 5.8S/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Sequence Deletion
Collapse
Affiliation(s)
- Xiao Li
- Department of Biological Sciences, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA; (X.L.); (J.M.Z.)
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Janice M. Zengel
- Department of Biological Sciences, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA; (X.L.); (J.M.Z.)
| | - Lasse Lindahl
- Department of Biological Sciences, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA; (X.L.); (J.M.Z.)
| |
Collapse
|
6
|
Micol-Ponce R, Sarmiento-Mañús R, Fontcuberta-Cervera S, Cabezas-Fuster A, de Bures A, Sáez-Vásquez J, Ponce MR. SMALL ORGAN4 Is a Ribosome Biogenesis Factor Involved in 5.8S Ribosomal RNA Maturation. Plant Physiol 2020; 184:2022-2039. [PMID: 32913045 PMCID: PMC7723108 DOI: 10.1104/pp.19.01540] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 08/27/2020] [Indexed: 05/09/2023]
Abstract
Ribosome biogenesis is crucial for cellular metabolism and has important implications for disease and aging. Human (Homo sapiens) glioma tumor-suppressor candidate region gene2 (GLTSCR2) and yeast (Saccharomyces cerevisiae) Nucleolar protein53 (Nop53) are orthologous proteins with demonstrated roles as ribosome biogenesis factors; knockdown of GLTSCR2 impairs maturation of 18S and 5.8S ribosomal RNAs (rRNAs), and Nop53 is required for maturation of 5.8S and 25S rRNAs. Here, we characterized SMALL ORGAN4 (SMO4), the most likely ortholog of human GLTSCR2 and yeast Nop53 in Arabidopsis (Arabidopsis thaliana). Loss of function of SMO4 results in a mild morphological phenotype; however, we found that smo4 mutants exhibit strong cytological and molecular phenotypes: nucleolar hypertrophy and disorganization, overaccumulation of 5.8S and 18S rRNA precursors, and an imbalanced 40S:60S ribosome subunit ratio. Like yeast Nop53 and human GLTSCR2, Arabidopsis SMO4 participates in 5.8S rRNA maturation. In yeast, Nop53 cooperates with mRNA transport4 (Mtr4) for 5.8S rRNA maturation. In Arabidopsis, we found that SMO4 plays similar roles in the 5.8S rRNA maturation pathway than those described for MTR4. However, SMO4 seems not to participate in the degradation of by-products derived from the 5'-external transcribed spacer (ETS) of 45S pre-rRNA, as MTR4 does.
Collapse
Affiliation(s)
- Rosa Micol-Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Alicante, Spain
| | - Raquel Sarmiento-Mañús
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Alicante, Spain
| | - Sara Fontcuberta-Cervera
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Alicante, Spain
| | - Adrián Cabezas-Fuster
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Alicante, Spain
| | - Anne de Bures
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, 66860 Perpignan, France
- Universite Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, 66860 Perpignan, France
| | - Julio Sáez-Vásquez
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, 66860 Perpignan, France
- Universite Perpignan Via Domitia, Laboratoire Génome et Développement des Plantes, Unité Mixte de Recherche 5096, 66860 Perpignan, France
| | - María Rosa Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Alicante, Spain
| |
Collapse
|
7
|
Wang J, Zhao Y, Lu X, Lyu Z, Warren A, Shao C. Does the Gonostomum-patterned oral apparatus in hypotrichia carry a phylogenetic signal? Evidence from morphological and molecular data based on extended taxon sampling using three nuclear genes (Ciliophora, Spirotrichea). Sci China Life Sci 2020; 64:311-322. [PMID: 32572808 DOI: 10.1007/s11427-020-1667-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [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: 01/13/2020] [Accepted: 02/12/2020] [Indexed: 11/26/2022]
Abstract
The classification of hypotrichs based on the gonostomatid oral structure is widely accepted, but the phylogenetic signal of this character is unknown. Here, we infer the species phylogeny of those gonostomatids for which molecular data are available, plus 26 new sequences of SSU-rDNA, ITS1-5.8S-ITS2 and LSU-rDNA genes. The results indicate that: (i) the endoral is more phylogenetically informative than the paroral; (ii) the structure of the endoral and the Gonostomum-pattern adoral zone of membranelles are plesiomorphies for the hypotrichs sensu stricto; (iii) the group of species possessing these features is monophyletic in all our phylogenetic analyses, except that for the SSU-rDNA; (iv) Schmidingerotrichidae is monophyletic in all trees, suggesting that it is a well-defined family; (v) the Gonostomatidae is polyphyletic in the SSU-rDNA and ITS1-5.8S-ITS2 trees, with Gonostomum, Cladotricha, Cotterillia, Metagonostomum, Paragonostomum and Wallackia distributed among separate clades, but monophyletic in the LSU-rDNA and concatenated trees; (vi) higher hypotrich taxa such as core urostyloids and core sporadotrichids/stichotrichids might have evolved from species that possessed a gonostomatid oral apparatus.
Collapse
Affiliation(s)
- Jingyi Wang
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Yan Zhao
- College of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Xiaoteng Lu
- Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Zhao Lyu
- College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Alan Warren
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
| | - Chen Shao
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China.
| |
Collapse
|
8
|
Natsidis P, Schiffer PH, Salvador-Martínez I, Telford MJ. Computational discovery of hidden breaks in 28S ribosomal RNAs across eukaryotes and consequences for RNA Integrity Numbers. Sci Rep 2019; 9:19477. [PMID: 31863008 PMCID: PMC6925239 DOI: 10.1038/s41598-019-55573-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 10/14/2019] [Accepted: 11/27/2019] [Indexed: 11/09/2022] Open
Abstract
In some eukaryotes, a 'hidden break' has been described in which the 28S ribosomal RNA molecule is cleaved into two subparts. The break is common in protostome animals (arthropods, molluscs, annelids etc.), but a break has also been reported in some vertebrates and non-metazoan eukaryotes. We present a new computational approach to determine the presence of the hidden break in 28S rRNAs using mapping of RNA-Seq data. We find a homologous break is present across protostomes although it has been lost in a small number of taxa. We show that rare breaks in vertebrate 28S rRNAs are not homologous to the protostome break. A break is found in just 4 out of 331 species of non-animal eukaryotes studied and, in three of these, the break is located in the same position as the protostome break suggesting a striking instance of convergent evolution. RNA Integrity Numbers (RIN) rely on intact 28S rRNA and will be consistently underestimated in the great majority of animal species with a break.
Collapse
Affiliation(s)
- Paschalis Natsidis
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - Philipp H Schiffer
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - Irepan Salvador-Martínez
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - Maximilian J Telford
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK.
| |
Collapse
|
9
|
Jankowiak R, Bilański P, Strzałka B, Linnakoski R, Bosak A, Hausner G. Four new Ophiostoma species associated with conifer- and hardwood-infesting bark and ambrosia beetles from the Czech Republic and Poland. Antonie Van Leeuwenhoek 2019; 112:1501-1521. [PMID: 31140027 PMCID: PMC6748885 DOI: 10.1007/s10482-019-01277-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 11/30/2018] [Accepted: 05/14/2019] [Indexed: 12/24/2022]
Abstract
Fungi under the order Ophiostomatales (Ascomycota) are known to associate with various species of bark beetles (Coleoptera: Curculionidae: Scolytinae). In addition this group of fungi contains many taxa that can impart blue-stain on sapwood and some are important tree pathogens. A recent survey that focussed on the diversity of the Ophiostomatales in the forest ecosystems of the Czech Republic and Poland uncovered four putative new species. Phylogenetic analyses of four gene regions (ITS1-5.8S-ITS2 region, ß-tubulin, calmodulin, and translation elongation factor 1-α) indicated that these four species are members of the genus Ophiostoma. All four newly described species can be distinguished from each other and from closely related species based on DNA sequence comparisons, morphological characters, growth rates, and their insect associations. Based on this study four new taxa can be circumscribed and the following names are provided: Ophiostoma pityokteinis sp. nov., Ophiostoma rufum sp. nov., Ophiostoma solheimii sp. nov., and Ophiostoma taphrorychi sp. nov. O. rufum sp. nov. is a member of the Ophiostoma piceae species complex, while O. pityokteinis sp. nov. resides in a discrete lineage within Ophiostoma s. stricto. O. taphrorychi sp. nov. together with O. distortum formed a well-supported clade in Ophiostoma s. stricto close to O. pityokteinis sp. nov. O. solheimii sp. nov. groups within a currently undefined lineage A, which also includes Ophiostoma grandicarpum and Ophiostoma microsporum. This study highlights the need for more intensive surveys that should include additional countries of Central Europe, insect vectors and host tree species in order to elucidate Ophiostoma species diversity in this region.
Collapse
Affiliation(s)
- Robert Jankowiak
- Department of Forest Pathology, Mycology and Tree Physiology, Institute of Forest Ecosystem Protection, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425, Kraków, Poland.
| | - Piotr Bilański
- Department of Forest Protection, Entomology and Forest Climatology, Institute of Forest Ecosystem Protection, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425, Kraków, Poland
| | - Beata Strzałka
- Department of Forest Pathology, Mycology and Tree Physiology, Institute of Forest Ecosystem Protection, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425, Kraków, Poland
| | - Riikka Linnakoski
- Natural Resources Institute Finland (Luke), Latokartanonkaari 9, 00790, Helsinki, Finland
| | - Agnieszka Bosak
- Department of Forest Pathology, Mycology and Tree Physiology, Institute of Forest Ecosystem Protection, University of Agriculture in Krakow, Al. 29 Listopada 46, 31-425, Kraków, Poland
| | - Georg Hausner
- Department of Microbiology, Buller Building 213, University of Manitoba, Winnipeg, R3T 2N2, Canada
| |
Collapse
|
10
|
Grab DJ, Nikolskaia OV, Courtioux B, Thekisoe OMM, Magez S, Bogorad M, Dumler JS, Bisser S. Using detergent-enhanced LAMP for African trypanosome detection in human cerebrospinal fluid and implications for disease staging. PLoS Negl Trop Dis 2019; 13:e0007631. [PMID: 31425540 PMCID: PMC6715242 DOI: 10.1371/journal.pntd.0007631] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 03/09/2019] [Revised: 08/29/2019] [Accepted: 07/13/2019] [Indexed: 12/12/2022] Open
Abstract
Objective Where human African trypanosomiasis (HAT) patients are seen, failure to microscopically diagnose infections by Trypanosoma brucei gambiense in blood smears and/or cerebrospinal fluid (CSF) in the critical early stages of the disease is the single most important factor in treatment failure, a result of delayed treatment onset or its absence. We hypothesized that the enhanced sensitivity of detergent-enhanced loop-mediated isothermal amplification (LAMP) will allow for point of care (POC) detection of African trypanosomes in the CSF of HAT patients where the probability for detecting a single parasite or parasite DNA molecule in 1 μL of CSF sample is negligible by current methods. Methodology We used LAMP targeting the multicopy pan-T. brucei repetitive insertion mobile element (RIME LAMP) and the Trypanosoma brucei gambiense 5.8S rRNA-internal transcribed spacer 2 gene (TBG1 LAMP). We tested 1 μL out of 20 μL sham or Triton X-100 treated CSFs from 73 stage-1 and 77 stage-2 HAT patients from the Central African Republic and 100 CSF negative controls. Results Under sham conditions, parasite DNA was detected by RIME and TBG1 LAMP in 1.4% of the stage-1 and stage-2 gambiense HAT CSF samples tested. After sample incubation with detergent, the number of LAMP parasite positive stage-2 CSF’s increased to 26%, a value which included the 2 of the 4 CSF samples where trypanosomes were identified microscopically. Unexpected was the 41% increase in parasite positive stage-1 CSF’s detected by LAMP. Cohen’s kappa coefficients for RIME versus TBG1 LAMP of 0.92 (95%CI: 0.82–1.00) for stage-1 and 0.90 (95%CI: 0.80–1.00) for stage-2 reflected a high level of agreement between the data sets indicating that the results were not due to amplicon contamination, data confirmed in χ2 tests (p<0.001) and Fisher’s exact probability test (p = 4.7e-13). Conclusion This study detected genomic trypanosome DNA in the CSF independent of the HAT stage and may be consistent with early CNS entry and other scenarios that identify critical knowledge gaps for future studies. Detergent-enhanced LAMP could be applicable for non-invasive African trypanosome detection in human skin and saliva or as an epidemiologic tool for the determination of human (or animal) African trypanosome prevalence in areas where chronically low parasitemias are present. Human African trypanosomiasis is a fatal disease (if untreated) spread by bloodsucking tsetse flies. These protozoan parasites first enter the lymph and blood to invade many organ systems (early stage sleeping sickness). Weeks to months later, the parasites invade the brain causing a wide variety of neurological symptoms (late stage sleeping sickness). In rural clinical settings, diagnosis still relies on the detection of these microbes in blood and cerebrospinal fluid (CSF) by microscopy. LAMP, or loop-mediated isothermal amplification of DNA, is a technique that can specifically detect very small amounts of DNA from an organism. We previously showed that by simply adding detergent during sample preparation, the analytical sensitivity of LAMP targeting many gene copies is greatly improved, presumably because DNA is released from the pathogen cells and dispersed through the sample. We demonstrated proof of principle using pathogenic trypanosomes in different human body fluids (CSF or blood) and showed that this simple modification should be applicable for diagnosis of other microbial infections where cells are sensitive to detergent lysis. After completion of the above published study, we tested a collection of clinical CSF samples from African patients diagnosed with early or late stage sleeping sickness based on current World Health Organization (WHO) guidelines. For proof-of-concept we tested only a single microliter of detergent-treated CSF to test for late stage disease. We predicted that a significant number of the late stage samples would be LAMP positive, while the early stage CSFs would yield predominantly negative results. Instead, our study detected trypanosome DNA in patient CSF independent of African sleeping sickness stage, results that may be consistent with early brain entry and other scenarios that identify critical knowledge gaps for future studies.
Collapse
MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Central African Republic
- Cerebrospinal Fluid/parasitology
- Child
- Child, Preschool
- DNA, Protozoan/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/genetics
- Detergents/metabolism
- Female
- Humans
- Infant
- Infant, Newborn
- Male
- Middle Aged
- Molecular Diagnostic Techniques/methods
- Nucleic Acid Amplification Techniques/methods
- RNA, Ribosomal, 5.8S/genetics
- Sensitivity and Specificity
- Severity of Illness Index
- Trypanosoma/genetics
- Trypanosoma/isolation & purification
- Trypanosomiasis, African/diagnosis
- Trypanosomiasis, African/pathology
- Young Adult
Collapse
Affiliation(s)
- Dennis J. Grab
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
| | - Olga V. Nikolskaia
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Bertrand Courtioux
- Institute of Neuroepidemiology and Tropical Neurology, School of Medicine, CNRS FR 3503 GEIST, University of Limoges, INSERM UMR1094 Tropical Neuroepidemiology, Limoges, France
| | - Oriel M. M. Thekisoe
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Stefan Magez
- Laboratory for Biomedical Research, Ghent University Global Campus, Incheon, South Korea
- Laboratory for Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Maxim Bogorad
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - J. Stephen Dumler
- Department of Pathology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Sylvie Bisser
- Institute of Neuroepidemiology and Tropical Neurology, School of Medicine, CNRS FR 3503 GEIST, University of Limoges, INSERM UMR1094 Tropical Neuroepidemiology, Limoges, France
- Pasteur Institute, Cayenne, French Guiana, France
| |
Collapse
|
11
|
Milyutina IA, Belevich TA, Ilyash LV, Troitsky AV. Insight into picophytoplankton diversity of the subarctic White Sea-The first recording of Pedinophyceae in environmental DNA. Microbiologyopen 2019; 8:e892. [PMID: 31184446 PMCID: PMC6813492 DOI: 10.1002/mbo3.892] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 01/04/2019] [Revised: 05/02/2019] [Accepted: 05/20/2019] [Indexed: 12/17/2022] Open
Abstract
Operational taxonomic units 94%-95% similar to the known Pedinophyceae were found as a result of high-through sequencing of 18S rDNA V4 amplicons of environmental DNA from the summer picophytoplankton samples from the White Sea. Partial sequence of a ribosomal operon (the 5,298 bp includes partial 18S and 28S rDNA, complete 5.8S rDNA, ITS1, and ITS2 sequences) and a partial 2,112 bp chloroplast 23S rDNA sequence White Sea Pedinophyceae was amplified from metagenomic DNA by specific primers and sequenced. A new phylotype was designated as uncultured Pedinophyceae WS. On Chlorophyta phylogenetic trees the discovered phylotype occupies a basal position in the Marsupiomonadales clade. The synapomorphic base substitutions in rRNA hairpins confirm the relationship of Pedinophyceae WS to Marsupiomonadales and its difference from known genera of the order. The obtained results extend knowledge of picophytoplankton diversity in subarctic waters.
Collapse
MESH Headings
- Arctic Regions
- Biodiversity
- Cluster Analysis
- DNA, Chloroplast/chemistry
- DNA, Chloroplast/genetics
- DNA, Environmental/chemistry
- DNA, Environmental/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Phylogeny
- Phytoplankton/classification
- Phytoplankton/genetics
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 23S/genetics
- RNA, Ribosomal, 28S/genetics
- RNA, Ribosomal, 5.8S/genetics
- Seawater/microbiology
- Sequence Analysis, DNA
Collapse
Affiliation(s)
- Irina A. Milyutina
- Belozersky Institute of Physico‐Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
| | | | | | - Aleksey V. Troitsky
- Belozersky Institute of Physico‐Chemical BiologyLomonosov Moscow State UniversityMoscowRussia
| |
Collapse
|
12
|
Chaudhary A, Amin OM, Singh HS. Molecular Characterization and Phylogenetic Relationships of Pallisentis ( Brevitritospinus) Indica (Acanthocephala: Quadrigyridae), A Parasite of the Spotted Snakehead ( Channa punctatus). J Parasitol 2019; 105:180-185. [PMID: 30817218] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023] Open
Abstract
Pallisentis ( Brevitritospinus) indica Mittal and Lal, 1976 was found infecting the spotted snakehead Channa punctatus Bloch and Schneider (Channidae) from Meerut, Uttar Pradesh (U.P.), India. The species was identified on the basis of proboscis hooks, trunk spines, and other structures that separate it from all described species. Molecular analysis based on 18S rDNA placed the P. indica isolates within a clade of Pallisentis spp. but distinct from other representatives of the same genus. This study documents the first molecular characterization of P. indica from India.
Collapse
Affiliation(s)
- Anshu Chaudhary
- 1 Molecular Taxonomy Laboratory, Department of Zoology, Chaudhary Charan Singh University, Meerut (U.P.), 250004, India
| | - Omar M Amin
- 2 Institute of Parasitic Diseases, 11445 E. Via Linda 2-419, Scottsdale, Arizona 85259
| | - Hridaya S Singh
- 1 Molecular Taxonomy Laboratory, Department of Zoology, Chaudhary Charan Singh University, Meerut (U.P.), 250004, India
| |
Collapse
|
13
|
Sereno-Uribe AL, Gómez LA, de Núñez MO, de León GPP, García-Varela M. Assessing the Taxonomic Validity of Austrodiplostomum SPP. (Digenea: Diplostomidae) Through Nuclear and Mitochondrial Data. J Parasitol 2019; 105:102-112. [PMID: 30807727] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023] Open
Abstract
Adults of the genus Austrodiplostomum are parasites in cormorants of the New World, whereas metacercariae are parasites from eye globe and brain of freshwater and brackish water fishes. In this study, specimens of Austrodiplostomum mordax from South America (type-species) were analyzed together with other specimens of Austrodiplostomum spp. collected from several locations across Middle America and North America. Partial DNA sequences of the mitochondrial gene cytochrome c oxidase subunit I ( COI), the internal transcribed spacers ( ITS1, ITS2, and 5.8S gene), and the D2-D3, domains of the large subunit ( LSU) of nuclear ribosomal DNA, were generated for both developmental stages and compared with available sequences of Austrodiplostomum spp. Phylogenetic analyses inferred with each molecular marker using maximum likelihood and Bayesian inference revealed the existence of 4 lineages representing 2 described species, A. mordax and Austrodiplostomum compactum (syn. Austrodiplostomum ostrowskiae) and 2 undescribed species of Austrodiplostomum recognized in previous studies. The COI haplotype network inferred with 172 sequences detected 28 haplotypes divided into 4 clusters, separating each other by 33 and 40 substitutions and with a genetic divergence ranging from 9 to 12%. The largest group included specimens identified as A. compactum plus those identified as A. ostrowskiae, supporting the synonymy of both species. As a result, we conclude that A. compactum is widely distributed across the Americas, in locations of the United States, Mexico, El Salvador, Honduras, Costa Rica, Venezuela, Peru, and Brazil. The other 2 undescribed species of the genus Austrodiplostomum were previously recorded in the United States and now are reported in Mexico. These 2 species cannot be described because adult forms have not been found in their definitive hosts. Finally, the species A. mordax has been found only in some lakes from Argentina, and it was validated in this study through molecular analyses.
Collapse
Affiliation(s)
- Ana Lucia Sereno-Uribe
- 1 Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), Avenida Universidad 3000, Ciudad Universitaria, CP 04510, Distrito Federal, México
| | - Leopoldo Andrade Gómez
- 1 Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), Avenida Universidad 3000, Ciudad Universitaria, CP 04510, Distrito Federal, México
- 2 Universidad Nacional Autónoma de México (UNAM), Posgrado en Ciencias Biológicas, Avenida Universidad 3000, Ciudad Universitaria, CP 04510, Distrito Federal, México
| | - Margarita Ostrowski de Núñez
- 3 Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón II, 1428 Buenos Aires, Argentina
| | - Gerardo Pérez-Ponce de León
- 1 Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), Avenida Universidad 3000, Ciudad Universitaria, CP 04510, Distrito Federal, México
| | - Martín García-Varela
- 1 Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México (UNAM), Avenida Universidad 3000, Ciudad Universitaria, CP 04510, Distrito Federal, México
| |
Collapse
|
14
|
Mitchell D, Renda AJ, Douds CA, Babitzke P, Assmann SM, Bevilacqua PC. In vivo RNA structural probing of uracil and guanine base-pairing by 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC). RNA 2019; 25:147-157. [PMID: 30341176 PMCID: PMC6298566 DOI: 10.1261/rna.067868.118] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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: 06/26/2018] [Accepted: 10/18/2018] [Indexed: 05/09/2023]
Abstract
Many biological functions performed by RNAs arise from their in vivo structures. The structure of the same RNA can differ in vitro and in vivo owing in part to the influence of molecules ranging from protons to secondary metabolites to proteins. Chemical reagents that modify the Watson-Crick (WC) face of unprotected RNA bases report on the absence of base-pairing and so are of value to determining structures adopted by RNAs. Reagents have thus been sought that can report on the native RNA structures that prevail in living cells. Dimethyl sulfate (DMS) and glyoxal penetrate cell membranes and inform on RNA secondary structure in vivo through modification of adenine (A), cytosine (C), and guanine (G) bases. Uracil (U) bases, however, have thus far eluded characterization in vivo. Herein, we show that the water-soluble carbodiimide 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) is capable of modifying the WC face of U and G in vivo, favoring the former nucleobase by a factor of ∼1.5, and doing so in the eukaryote rice, as well as in the Gram-negative bacterium Escherichia coli While both EDC and glyoxal target Gs, EDC reacts with Gs in their typical neutral state, while glyoxal requires Gs to populate the rare anionic state. EDC may thus be more generally useful; however, comparison of the reactivity of EDC and glyoxal may allow the identification of Gs with perturbed pKas in vivo and genome-wide. Overall, use of EDC with DMS allows in vivo probing of the base-pairing status of all four RNA bases.
Collapse
MESH Headings
- Base Pairing
- Base Sequence
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Ethyldimethylaminopropyl Carbodiimide
- Glyoxal
- Guanine/chemistry
- Indicators and Reagents
- Molecular Probe Techniques
- Molecular Probes
- Molecular Structure
- Nucleic Acid Conformation
- Oryza/chemistry
- Oryza/genetics
- RNA/chemistry
- RNA/genetics
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Plant/chemistry
- RNA, Plant/genetics
- RNA, Ribosomal, 16S/chemistry
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 5.8S/chemistry
- RNA, Ribosomal, 5.8S/genetics
- Uracil/chemistry
Collapse
Affiliation(s)
- David Mitchell
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Andrew J Renda
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Catherine A Douds
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Paul Babitzke
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Sarah M Assmann
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Philip C Bevilacqua
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| |
Collapse
|
15
|
Andersen KL, Nielsen H. Knock-Down of a Novel snoRNA in Tetrahymena Reveals a Dual Role in 5.8S rRNA Processing and Generation of a 26S rRNA Fragment. Biomolecules 2018; 8:E128. [PMID: 30380771 PMCID: PMC6315972 DOI: 10.3390/biom8040128] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/24/2018] [Accepted: 10/25/2018] [Indexed: 11/30/2022] Open
Abstract
In eukaryotes, 18S, 5.8S, and 28S rRNAs are transcribed as precursor molecules that undergo extensive modification and nucleolytic processing to form the mature rRNA species. Central in the process are the small nucleolar RNAs (snoRNAs). The majority of snoRNAs guide site specific chemical modifications but a few are involved in defining pre-rRNA cleavages. Here, we describe an unusual snoRNA (TtnuCD32) belonging to the box C/D subgroup from the ciliate Tetrahymena thermophila. We show that TtnuCD32 is unlikely to function as a modification guide snoRNA and that it is critical for cell viability. Cell lines with genetic knock-down of TtnuCD32 were impaired in growth and displayed two novel and apparently unrelated phenotypes. The most prominent phenotype is the accumulation of processing intermediates of 5.8S rRNA. The second phenotype is the decrease in abundance of a ~100 nt 26S rRNA fragment of unknown function. Sequence analysis demonstrated that TtnuCD32 share features with the essential snoRNA U14 but an alternative candidate (TtnuCD25) was more closely related to other U14 sequences. This, together with the fact that the observed rRNA processing phenotypes were not similar to what has been observed in U14 depleted cells, suggests that TtnuCD32 is a U14 homolog that has gained novel functions.
Collapse
MESH Headings
- Base Sequence
- Cell Survival
- Conserved Sequence
- Gene Expression Regulation
- Gene Knockdown Techniques
- Genome
- Methylation
- Nucleic Acid Conformation
- Protozoan Proteins/chemistry
- Protozoan Proteins/metabolism
- RNA Processing, Post-Transcriptional/genetics
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 5.8S/chemistry
- RNA, Ribosomal, 5.8S/genetics
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- Tetrahymena/genetics
- RNA, Guide, CRISPR-Cas Systems
Collapse
Affiliation(s)
- Kasper L Andersen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200N Copenhagen, Denmark.
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Blegdamsvej 5b, DK-2200N Copenhagen, Denmark.
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, Blegdamsvej 5b, DK-2200N Copenhagen, Denmark.
| |
Collapse
|
16
|
Mowna Sundari T, Alwin Prem Anand A, Jenifer P, Shenbagarathai R. Bioprospection of Basidiomycetes and molecular phylogenetic analysis using internal transcribed spacer (ITS) and 5.8S rRNA gene sequence. Sci Rep 2018; 8:10720. [PMID: 30013072 PMCID: PMC6048145 DOI: 10.1038/s41598-018-29046-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 11/10/2017] [Accepted: 07/04/2018] [Indexed: 11/23/2022] Open
Abstract
Macrofungi belonging to the phylum Basidiomycota are mostly used as medicinal mushrooms in many countries. In the present study, hundred basidiocarp of macrofungi were collected from Tamilnadu during rainy season. The basidiocarp was found in association with root/trunk of living trees, wood log and decayed matter. Among the hundred basidiocarp, 49 were grown into axenic cultures. Notable variations in the macroscopic characteristics of the basidiome and culture morphology were observed. To study the genetic diversity, the molecular taxonomy of the isolates was carried out using internal transcribed spacer (ITS) and 5.8S rRNA gene sequence marker. Thirty-two strains belonging to the order Polyporales, Hymenochataeles and Russuales under the division Basidiomycota were classified based on phylogeny analysis. This study provides first evidence for the occurrence of species Fulvifomes fastuosus (LDCMY39 and LDCMY43) and Ganoderma wiiroense (LDCMY02, LDCMY08, LDCMY11, LDCMY17 and LDCMY19) from southern India. Molecular evidence for the existence of Phellinus badius was given for the first time as well. These data enhance our understanding on the diversity of macrofungi in India, which could be further exploited for biomedical applications.
Collapse
Affiliation(s)
- Thangamalai Mowna Sundari
- DBT - BIF centre, Lady Doak College, Madurai, 625 002, Tamilnadu, India
- Department of Biotechnology, Lady Doak College, Madurai, 625 002, Tamilnadu, India
- PG and Research Department of Zoology, Lady Doak College, Madurai, 625 002, Tamilnadu, India
| | | | - Packiaraj Jenifer
- DBT - BIF centre, Lady Doak College, Madurai, 625 002, Tamilnadu, India
| | - Rajaiah Shenbagarathai
- DBT - BIF centre, Lady Doak College, Madurai, 625 002, Tamilnadu, India.
- Department of Biotechnology, Lady Doak College, Madurai, 625 002, Tamilnadu, India.
- PG and Research Department of Zoology, Lady Doak College, Madurai, 625 002, Tamilnadu, India.
| |
Collapse
|
17
|
Unger P, Neubert K, Palm HW. Metazoan parasite fauna of migrating common garfish, Belone belone (L.), in the Baltic Sea. Acta Parasitol 2018; 63:99-105. [PMID: 29351069 DOI: 10.1515/ap-2018-0011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 07/21/2017] [Indexed: 11/15/2022]
Abstract
A total of 35 common garfish, Belone belone (Linnaeus, 1761), were studied for metazoan parasites on their spawning grounds in the western Baltic Sea. Nine parasite species were found, and six new locality records could be established for German coastal waters (Axine belones, Monogenea; Proteocephalus sp., Cestoda; Anisakis simplex (s.s.), Contracaecum rudolphii A and Hysterothylacium aduncum, Nematoda; Echinorhynchus gadi, Acanthocephala). For the first time, the marine ectoparasite A. belones was recorded from the gills of garfish inside the Baltic Sea, indicating its ability to survive the spawning migration as well as the brackish water conditions at its reproduction grounds. This is alike the endohelminth A. simplex (s.s.), that was identified by molecular analyses of the internal transcribed spacer (ITS-1, 5.8S, ITS-2) region. Almost all isolated metazoans were parasites commonly recorded from the northeast Atlantic Ocean and the North Sea. The lower number of typical generalist Baltic Sea parasites indicates the rapid migration of common garfish onto the spawning grounds, reducing the access and uptake of these species.
Collapse
MESH Headings
- Animals
- Beloniformes/parasitology
- Biodiversity
- DNA, Helminth/chemistry
- DNA, Helminth/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Ectoparasitic Infestations/parasitology
- Ectoparasitic Infestations/veterinary
- Fish Diseases/parasitology
- Intestinal Diseases, Parasitic/parasitology
- Intestinal Diseases, Parasitic/veterinary
- Parasites/classification
- Parasites/isolation & purification
- RNA, Ribosomal, 5.8S/genetics
- Sequence Analysis, DNA
Collapse
Affiliation(s)
- Patrick Unger
- Aquaculture and Sea-Ranching, Faculty of Agricultural and Environmental Sciences, University of Rostock, Justus-von-Liebig-Weg 6, 18059 Rostock, Germany
| | - Kilian Neubert
- Aquaculture and Sea-Ranching, Faculty of Agricultural and Environmental Sciences, University of Rostock, Justus-von-Liebig-Weg 6, 18059 Rostock, Germany
| | - Harry W Palm
- Aquaculture and Sea-Ranching, Faculty of Agricultural and Environmental Sciences, University of Rostock, Justus-von-Liebig-Weg 6, 18059 Rostock, Germany
| |
Collapse
|
18
|
Saeed EE, Sham A, AbuZarqa A, A Al Shurafa K, S Al Naqbi T, Iratni R, El-Tarabily K, F AbuQamar S. Detection and Management of Mango Dieback Disease in the United Arab Emirates. Int J Mol Sci 2017; 18:E2086. [PMID: 29053600 PMCID: PMC5666768 DOI: 10.3390/ijms18102086] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 09/14/2017] [Revised: 09/28/2017] [Accepted: 09/28/2017] [Indexed: 11/20/2022] Open
Abstract
Mango is affected by different decline disorders causing significant losses to mango growers. In the United Arab Emirates (UAE), the pathogen was isolated from all tissues sampled from diseased trees affected by Lasiodiplodia theobromae. Symptoms at early stages of the disease included general wilting appearance of mango trees, and dieback of twigs. In advanced stages, the disease symptoms were also characterized by the curling and drying of leaves, leading to complete defoliation of the tree and discolouration of vascular regions of the stems and branches. To substantially reduce the devastating impact of dieback disease on mango, the fungus was first identified based on its morphological and cultural characteristics. Target regions of 5.8S rRNA (ITS) and elongation factor 1-α (EF1-α) genes of the pathogen were amplified and sequenced. We also found that the systemic chemical fungicides, Score®, Cidely® Top, and Penthiopyrad®, significantly inhibited the mycelial growth of L. theobromae both in vitro and in the greenhouse. Cidely® Top proved to be a highly effective fungicide against L. theobromae dieback disease also under field conditions. Altogether, the morphology of the fruiting structures, molecular identification and pathogenicity tests confirm that the causal agent of the mango dieback disease in the UAE is L. theobromae.
Collapse
Affiliation(s)
- Esam Eldin Saeed
- Department of Biology, United Arab Emirates University, Al-Ain 15551, UAE.
| | - Arjun Sham
- Department of Biology, United Arab Emirates University, Al-Ain 15551, UAE.
| | - Ayah AbuZarqa
- Department of Biology, United Arab Emirates University, Al-Ain 15551, UAE.
| | | | | | - Rabah Iratni
- Department of Biology, United Arab Emirates University, Al-Ain 15551, UAE.
| | - Khaled El-Tarabily
- Department of Biology, United Arab Emirates University, Al-Ain 15551, UAE.
| | - Synan F AbuQamar
- Department of Biology, United Arab Emirates University, Al-Ain 15551, UAE.
| |
Collapse
|
19
|
Locati MD, Pagano JFB, Girard G, Ensink WA, van Olst M, van Leeuwen S, Nehrdich U, Spaink HP, Rauwerda H, Jonker MJ, Dekker RJ, Breit TM. Expression of distinct maternal and somatic 5.8S, 18S, and 28S rRNA types during zebrafish development. RNA 2017; 23:1188-1199. [PMID: 28500251 PMCID: PMC5513064 DOI: 10.1261/rna.061515.117] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [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: 03/29/2017] [Accepted: 05/09/2017] [Indexed: 05/27/2023]
Abstract
There is mounting evidence that the ribosome is not a static translation machinery, but a cell-specific, adaptive system. Ribosomal variations have mostly been studied at the protein level, even though the essential transcriptional functions are primarily performed by rRNAs. At the RNA level, oocyte-specific 5S rRNAs are long known for Xenopus. Recently, we described for zebrafish a similar system in which the sole maternal-type 5S rRNA present in eggs is replaced completely during embryonic development by a somatic-type. Here, we report the discovery of an analogous system for the 45S rDNA elements: 5.8S, 18S, and 28S. The maternal-type 5.8S, 18S, and 28S rRNA sequences differ substantially from those of the somatic-type, plus the maternal-type rRNAs are also replaced by the somatic-type rRNAs during embryogenesis. We discuss the structural and functional implications of the observed sequence differences with respect to the translational functions of the 5.8S, 18S, and 28S rRNA elements. Finally, in silico evidence suggests that expansion segments (ES) in 18S rRNA, previously implicated in ribosome-mRNA interaction, may have a preference for interacting with specific mRNA genes. Taken together, our findings indicate that two distinct types of ribosomes exist in zebrafish during development, each likely conducting the translation machinery in a unique way.
Collapse
MESH Headings
- Animals
- Base Pairing
- Base Sequence
- DNA, Ribosomal/genetics
- Embryo, Nonmammalian/cytology
- Embryo, Nonmammalian/metabolism
- Nucleic Acid Conformation
- RNA Processing, Post-Transcriptional
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/metabolism
- RNA, Ribosomal, 28S/genetics
- RNA, Ribosomal, 28S/metabolism
- RNA, Ribosomal, 5.8S/genetics
- RNA, Ribosomal, 5.8S/metabolism
- Ribosomes/metabolism
- Sequence Alignment
- Zebrafish/genetics
- Zebrafish/growth & development
- Zebrafish/metabolism
Collapse
Affiliation(s)
- Mauro D Locati
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Johanna F B Pagano
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Geneviève Girard
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Wim A Ensink
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Marina van Olst
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Selina van Leeuwen
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Ulrike Nehrdich
- Department of Molecular Cell Biology, Institute of Biology, Leiden University, Gorlaeus Laboratories-Cell Observatorium, Leiden 2333 CE, the Netherlands
| | - Herman P Spaink
- Department of Molecular Cell Biology, Institute of Biology, Leiden University, Gorlaeus Laboratories-Cell Observatorium, Leiden 2333 CE, the Netherlands
| | - Han Rauwerda
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Martijs J Jonker
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Rob J Dekker
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| | - Timo M Breit
- RNA Biology and Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, the Netherlands
| |
Collapse
|
20
|
Murúa P, Goecke F, Westermeier R, van West P, Küpper FC, Neuhauser S. Maullinia braseltonii sp. nov. (Rhizaria, Phytomyxea, Phagomyxida): A Cyst-forming Parasite of the Bull Kelp Durvillaea spp. (Stramenopila, Phaeophyceae, Fucales). Protist 2017; 168:468-480. [PMID: 28822911 PMCID: PMC5673062 DOI: 10.1016/j.protis.2017.07.001] [Citation(s) in RCA: 16] [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: 02/22/2017] [Revised: 06/22/2017] [Accepted: 07/01/2017] [Indexed: 11/08/2022]
Abstract
Phytomyxea are obligate endoparasites of angiosperm plants and Stramenopiles characterised by a complex life cycle. Here Maullinia braseltonii sp. nov., an obligate parasite infecting the bull kelp Durvillaea (Phaeophyceae, Fucales) from the South-Eastern Pacific (Central Chile and Chiloe Island) and South-Western Atlantic (Falkland Islands, UK) is described. M. braseltonii causes distinct hypertrophies (galls) on the host thalli making it easily identifiable in the field. Sequence comparisons based on the partial 18S and the partial 18S-5.8S-28S regions confirmed its placement within the order Phagomyxida (Phytomyxea, Rhizaria), as a sister species of the marine parasite Maullinia ectocarpii, which is also a parasite of brown algae. The development of resting spores in M. braseltonii is described by light and electron microscopy and confirmed by FISH experiments, which visually showed the differential expression of the 28S non-coding gene, strongly in early plasmodia and weakly in late cysts. M. braseltonii is, so far, the only phytomyxean parasite of brown algae for which the formation of resting spores has been reported, and which is widely distributed in Durvillaea stocks from the Southeastern Pacific and Southwestern Atlantic.
Collapse
Affiliation(s)
- Pedro Murúa
- Oceanlab, School of Biological Sciences, University of Aberdeen, Main street, Newburgh, AB41 6AA, United Kingdom; Aberdeen Oomycete Laboratory, International Centre for Aquaculture Research and Development, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom; The Scottish Association for Marine Science, Scottish Marine Institute, Culture Collection for Algae and Protozoa, Oban, Argyll, PA37 1QA, United Kingdom
| | - Franz Goecke
- Department of Plant and Environmental Science (IPV), Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Renato Westermeier
- Laboratorio de Macroalgas, Instituto de Acuicultura, Universidad Austral de Chile, Sede Puerto Montt. PO box 1327, Puerto Montt, Chile
| | - Pieter van West
- Aberdeen Oomycete Laboratory, International Centre for Aquaculture Research and Development, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom
| | - Frithjof C Küpper
- Oceanlab, School of Biological Sciences, University of Aberdeen, Main street, Newburgh, AB41 6AA, United Kingdom
| | - Sigrid Neuhauser
- Institute of Microbiology, University of Innsbruck, Innsbruck, Tyrol, Austria.
| |
Collapse
|
21
|
Deutscher AT, Reynolds OL, Chapman TA. Yeast: An Overlooked Component of Bactrocera tryoni (Diptera: Tephritidae) Larval Gut Microbiota. J Econ Entomol 2017; 110:298-300. [PMID: 28039426 DOI: 10.1093/jee/tow262] [Citation(s) in RCA: 14] [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] [Indexed: 06/06/2023]
Abstract
Yeasts, often in hydrolyzed form, are key ingredients in the larval and adult diets of tephritid fruit fly colonies. However, very little is known about the presence or role of yeasts in the diets of tephritid fruit flies in nature. Previous studies have identified bacteria but not detected yeasts in the gut of Queensland fruit fly, Bactrocera tryoni (Froggatt), one of Australia's most economically damaging insect pests of horticultural crops and of significant biosecurity concern domestically and internationally. Here we demonstrate that cultivable yeasts are commonly found in the gut of B. tryoni larvae from fruit hosts. Analysis of the ITS1, 5.8S rRNA gene, and ITS2 sequences of randomly selected isolates identified yeasts and yeast-like fungi of the genera Aureobasidium, Candida, Cryptococcus, Hanseniaspora, Pichia, and Starmerella. The prevalence of these yeasts in fruits suggests that larvae consume the yeasts as part of their diet. This work highlights that yeasts should be considered in future tephritid larval gut microbiota studies. Understanding tephritid-microbial symbiont interactions will lead to improvements in artificial diets and the quality of mass-reared tephritids for the sterile insect technique.
Collapse
Affiliation(s)
- Ania T Deutscher
- Biosecurity and Food Safety, NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Narellan, New South Wales, Australia
- Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Elizabeth Macarthur Agricultural Institute, Private Mail Bag 4008, Narellan, New South Wales, Australia
| | - Olivia L Reynolds
- Biosecurity and Food Safety, NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Narellan, New South Wales, Australia
- Graham Centre for Agricultural Innovation (an alliance between NSW Department of Primary Industries and Charles Sturt University), Elizabeth Macarthur Agricultural Institute, Private Mail Bag 4008, Narellan, New South Wales, Australia
| | - Toni A Chapman
- Biosecurity and Food Safety, NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Narellan, New South Wales, Australia
| |
Collapse
|
22
|
Yang X, Hameed U, Zhang AF, Zang HY, Gu CY, Chen Y, Xu YL. Development of a nested-PCR assay for the rapid detection of Pilidiella granati in pomegranate fruit. Sci Rep 2017; 7:40954. [PMID: 28106107 PMCID: PMC5247718 DOI: 10.1038/srep40954] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [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: 06/17/2016] [Accepted: 12/14/2016] [Indexed: 12/03/2022] Open
Abstract
Pilidiella granati, a causal agent of twig blight and crown rot of pomegranate, is an emerging threat that may cause severe risk to the pomegranate industry in the future. Development of a rapid assay for the timely and accurate detection of P. granati will be helpful in the active surveillance and management of the disease caused by this pathogen. In this study, a nested PCR method was established for the detection of P. granati. Comparative analysis of genetic diversity within 5.8S rDNA internal transcribed spacer (ITS) sequences of P. granati and 21 other selected fungal species was performed to design species-specific primers (S1 and S2). This primer pair successfully amplified a 450 bp product exclusively from the genomic DNA of P. granati. The developed method can detect 10 pg genomic DNA of the pathogen in about 6 h. This technique was successfully applied to detect the natural infection of P. granati in the pomegranate fruit. The designed protocol is rapid and precise with a high degree of sensitivity.
Collapse
Affiliation(s)
- Xue Yang
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China
- Laboratory of Quality and Safety Risk Assessment for Agro-Products (Hefei), Ministry of Agriculture, China
| | - Uzma Hameed
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Ai-Fang Zhang
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China
- Laboratory of Quality and Safety Risk Assessment for Agro-Products (Hefei), Ministry of Agriculture, China
| | - Hao-Yu Zang
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China
- Laboratory of Quality and Safety Risk Assessment for Agro-Products (Hefei), Ministry of Agriculture, China
| | - Chun-Yan Gu
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China
- Laboratory of Quality and Safety Risk Assessment for Agro-Products (Hefei), Ministry of Agriculture, China
| | - Yu Chen
- Institute of Plant Protection and Agro-products Safety, Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Scientific Observing and Experimental Station of Crop Pests in Hefei, Ministry of Agriculture, China
- Laboratory of Quality and Safety Risk Assessment for Agro-Products (Hefei), Ministry of Agriculture, China
| | - Yi-Liu Xu
- Anhui Academy of Agricultural Sciences, Hefei 230031, China
- Key Laboratory of Genetic Improvement and Ecophysiology of Horticultural Crop, Anhui Province, China
| |
Collapse
|
23
|
Drumonde-Neves J, Franco-Duarte R, Lima T, Schuller D, Pais C. Association between Grape Yeast Communities and the Vineyard Ecosystems. PLoS One 2017; 12:e0169883. [PMID: 28085916 PMCID: PMC5234834 DOI: 10.1371/journal.pone.0169883] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [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: 09/08/2016] [Accepted: 12/24/2016] [Indexed: 11/19/2022] Open
Abstract
The grape yeast biota from several wine-producing areas, with distinct soil types and grapevine training systems, was assessed on five islands of Azores Archipelago, and differences in yeast communities composition associated with the geographic origin of the grapes were explored. Fifty-seven grape samples belonging to the Vitis vinifera grapevine cultivars Verdelho dos Açores (Verdelho), Arinto da Terceira (Arinto) and Terrantez do Pico (Terrantez) were collected in two consecutive years and 40 spontaneous fermentations were achieved. A total of 1710 yeast isolates were obtained from freshly crushed grapes and 1200 from final stage of fermentations. Twenty-eight species were identified, Hanseniaspura uvarum, Pichia terricola and Metschnikowia pulcherrima being the three most representative species isolated. Candida carpophila was encountered for the first time as an inhabitant of grape or wine-associated environments. In both sampling years, a higher proportion of H. uvarum in fresh grapes from Verdelho cultivar was observed, in comparison with Arinto cultivar. Qualitatively significant differences were found among yeast communities from several locations on five islands of the Archipelago, particularly in locations with distinctive agro-ecological compositions. Our results are in agreement with the statement that grape-associated microbial biogeography is non-randomly associated with interactions of climate, soil, cultivar, and vine training systems in vineyard ecosystems. Our observations strongly support a possible linkage between grape yeast and wine typicality, reinforcing the statement that different viticultural terroirs harbor distinctive yeast biota, in particular in vineyards with very distinctive environmental conditions.
Collapse
Affiliation(s)
- João Drumonde-Neves
- CITAA—Research Center for Agricultural Technology of Azores, University of Azores, Angra do Heroísmo, Portugal
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
| | - Ricardo Franco-Duarte
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
| | - Teresa Lima
- CITAA—Research Center for Agricultural Technology of Azores, University of Azores, Angra do Heroísmo, Portugal
| | - Dorit Schuller
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
| | - Célia Pais
- Centre of Molecular and Environmental Biology (CBMA), Department of Biology, University of Minho, Braga, Portugal
| |
Collapse
|
24
|
Xu B, Zeng XM, Gao XF, Jin DP, Zhang LB. ITS non-concerted evolution and rampant hybridization in the legume genus Lespedeza (Fabaceae). Sci Rep 2017; 7:40057. [PMID: 28051161 PMCID: PMC5209741 DOI: 10.1038/srep40057] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [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: 08/15/2016] [Accepted: 11/30/2016] [Indexed: 12/27/2022] Open
Abstract
The internal transcribed spacer (ITS) as one part of nuclear ribosomal DNA is one of the most extensively sequenced molecular markers in plant systematics. The ITS repeats generally exhibit high-level within-individual homogeneity, while relatively small-scale polymorphism of ITS copies within individuals has often been reported in literature. Here, we identified large-scale polymorphism of ITS copies within individuals in the legume genus Lespedeza (Fabaceae). Divergent paralogs of ITS sequences, including putative pseudogenes, recombinants, and multiple functional ITS copies were sometimes detected in the same individual. Thirty-seven ITS pseudogenes could be easily detected according to nucleotide changes in conserved 5.8S motives, the significantly lower GC contents in at least one of three regions, and the lost ability of 5.8S rDNA sequence to fold into a conserved secondary structure. The distribution patterns of the putative functional clones were highly different between the traditionally recognized two subgenera, suggesting different rates of concerted evolution in two subgenera which could be attributable to their different extents/frequencies of hybridization, confirmed by our analysis of the single-copy nuclear gene PGK. These findings have significant implications in using ITS marker for reconstructing phylogeny and studying hybridization.
Collapse
MESH Headings
- Base Composition
- Cluster Analysis
- DNA, Plant/chemistry
- DNA, Plant/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Evolution, Molecular
- Lespedeza/classification
- Lespedeza/genetics
- Nucleic Acid Hybridization
- Phylogeny
- Polymorphism, Genetic
- RNA, Ribosomal, 5.8S/genetics
- Sequence Analysis, DNA
Collapse
Affiliation(s)
- Bo Xu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan 610041, China
| | - Xiao-Mao Zeng
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan 610041, China
| | - Xin-Fen Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, P.O. Box 416, Chengdu, Sichuan 610041, China
| | - Dong-Pil Jin
- Department of Biological Sciences, Inha University, Incheon 402-751, Republic of Korea
| | - Li-Bing Zhang
- Missouri Botanical Garden, P.O. Box 299, St. Louis, Missouri 63166, USA
| |
Collapse
|
25
|
Souza ARCD, Baldoni DB, Lima J, Porto V, Marcuz C, Machado C, Ferraz RC, Kuhn RC, Jacques RJS, Guedes JVC, Mazutti MA. Selection, isolation, and identification of fungi for bioherbicide production. Braz J Microbiol 2017; 48:101-108. [PMID: 27769882 PMCID: PMC5220639 DOI: 10.1016/j.bjm.2016.09.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [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: 08/19/2015] [Accepted: 05/02/2016] [Indexed: 11/24/2022] Open
Abstract
Production of a bioherbicide for biological control of weeds requires a series of steps, from selection of a suitable microbial strain to final formulation. Thus, this study aimed to select fungi for production of secondary metabolites with herbicidal activity using biological resources of the Brazilian Pampa biome. Phytopathogenic fungi were isolated from infected tissues of weeds in the Pampa biome. A liquid synthetic culture medium was used for production of metabolites. The phytotoxicity of fungal metabolites was assessed via biological tests using the plant Cucumis sativus L., and the most promising strain was identified by molecular analysis. Thirty-nine fungi were isolated, and 28 presented some phytotoxic symptoms against the target plant. Fungus VP51 belonging to the genus Diaporthe showed the most pronounced herbicidal activity. The Brazilian Pampa biome is a potential resource for the development of new and sustainable chemical compounds for modern agriculture.
Collapse
Affiliation(s)
| | - Daiana Bortoluzzi Baldoni
- Universidade Federal de Santa Maria (UFSM), Departamento em ciência do solo, Santa Maria, RS, Brazil
| | - Jessica Lima
- Universidade Federal de Santa Maria (UFSM), Departamento de engenharia química, Santa Maria, RS, Brazil
| | - Vitória Porto
- Universidade Federal de Santa Maria (UFSM), Departamento de engenharia química, Santa Maria, RS, Brazil
| | - Camila Marcuz
- Universidade Federal de Santa Maria (UFSM), Departamento de engenharia química, Santa Maria, RS, Brazil
| | - Carolina Machado
- Universidade Federal de Santa Maria (UFSM), Departamento de engenharia química, Santa Maria, RS, Brazil
| | | | - Raquel C Kuhn
- Universidade Federal de Santa Maria (UFSM), Departamento de engenharia química, Santa Maria, RS, Brazil
| | - Rodrigo J S Jacques
- Universidade Federal de Santa Maria (UFSM), Departamento em ciência do solo, Santa Maria, RS, Brazil
| | - Jerson V C Guedes
- Universidade Federal de Santa Maria (UFSM), Departamento de proteção de plantas, Santa Maria, RS, Brazil
| | - Marcio A Mazutti
- Universidade Federal de Santa Maria (UFSM), Departamento de engenharia química, Santa Maria, RS, Brazil.
| |
Collapse
|
26
|
Gomes FCO, Safar SVB, Santos ARO, Lachance MA, Rosa CA. Kockovaella libkindii sp. nov., a yeast species isolated from water tanks of bromeliad. Int J Syst Evol Microbiol 2016; 66:5066-5069. [PMID: 27601234 DOI: 10.1099/ijsem.0.001471] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During a study of yeast community associated with water tanks (phytotelmata) of the bromeliad Vriesea minarum, two strains of a novel stalk-forming yeast species were found. The sequences of the region spanning the ITS and D1/D2 domains of the large subunit rRNA gene showed that this species belongs to the genus Kockovaella. The novel species differs by 14 or more nucleotide substitutions in the D1/D2 domains and by 26 or more substitutions in the ITS-5.8S region from all other Kockovaella species. We describe this species as Kockovaella libkindii sp. nov. The type strain of Kockovaella libkindii sp. nov. is UFMG-CM-Y6053T (=UFMG-BRO-488T=CBS 12685T). The MycoBank number is MB 817710.
Collapse
Affiliation(s)
- Fatima C O Gomes
- Departamento de Química, Centro Federal de Educação Tecnológica de Minas Gerais, Belo Horizonte, MG 30421-169, Brazil
| | - Silvana V B Safar
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Ana Raquel O Santos
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Marc-André Lachance
- Department of Biology, University of Western Ontario, London, Ontario, Canada N6A 5B7
| | - Carlos A Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| |
Collapse
|
27
|
Kondova I, Simon MA, Klumpp SA, MacKey J, Widmer G, Domingues HG, Persengiev SP, O'Neil SP. Trichomonad Gastritis in Rhesus Macaques (Macaca mulatta) Infected with Simian Immunodeficiency Virus. Vet Pathol 2016; 42:19-29. [PMID: 15657268 DOI: 10.1354/vp.42-1-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In a retrospective study, 51 cases of gastritis (14%) were identified from among 341 necropsies performed on simian immunodeficiency virus (SlV)-infected rhesus macaques ( Macaca mulatta) at the New England Primate Research Center from 1993 to 2001. Protozoa were seen in the stomach of 13 monkeys (25%) with gastritis. Two histopathologic manifestations of gastritis were observed: seven cases of lymphoplasmacytic gastritis with trichomonad trophozoites within lumens of gastric glands and four cases of necrosuppurative gastritis containing intralesional periodic acid-Schiff-positive protozoa; two cases of gastritis had morphologic features of both types of gastritis. In instances of necrosuppurative and combined lymphoplasmacytic and necrosuppurative gastritis, protozoa were 4-35 μm in diameter and round to tear-shaped. Because of the unusual morphology of the protozoa in these latter cases, transmission electron microscopy and polymerase chain reaction (PCR) were used to further identify these organisms. The protozoa were definitively identified as Tritrichomonas in all cases on the basis of ultrastructural characteristics (flagella and undulating membranes) and amplification of a 347-bp product of the 5.8S ribosomal RNA gene of Tritrichomonas foetus, Tritrichomonas suis and Tritrichomonas mobilensis by PCR using DNA extracted from stomach tissue. On the basis of these observations, we conclude that Tritrichomonas can be a significant cofactor in the development of necrosup-purative gastritis in SIV-infected rhesus macaques.
Collapse
MESH Headings
- Animals
- DNA, Protozoan/chemistry
- DNA, Protozoan/genetics
- Female
- Gastritis/pathology
- Gastritis/veterinary
- Gastritis/virology
- Immunohistochemistry/veterinary
- In Situ Hybridization/veterinary
- Macaca mulatta
- Male
- Microscopy, Electron, Transmission/veterinary
- Monkey Diseases/parasitology
- Monkey Diseases/pathology
- Monkey Diseases/virology
- Polymerase Chain Reaction/veterinary
- Protozoan Infections/parasitology
- Protozoan Infections/pathology
- Protozoan Infections/virology
- Protozoan Infections, Animal
- RNA, Protozoan/chemistry
- RNA, Protozoan/genetics
- RNA, Ribosomal, 5.8S/chemistry
- RNA, Ribosomal, 5.8S/genetics
- Retrospective Studies
- Simian Acquired Immunodeficiency Syndrome/parasitology
- Simian Acquired Immunodeficiency Syndrome/pathology
- Simian Acquired Immunodeficiency Syndrome/virology
- Simian Immunodeficiency Virus/growth & development
- Tritrichomonas/genetics
- Tritrichomonas/growth & development
- Tritrichomonas/ultrastructure
Collapse
Affiliation(s)
- I Kondova
- Division of Comparative Pathology, New England Primate Research Center, Harvard Medical School, Southborough, MA 01772-9102, USA
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Dyomin AG, Koshel EI, Kiselev AM, Saifitdinova AF, Galkina SA, Fukagawa T, Kostareva AA, Gaginskaya ER. Chicken rRNA Gene Cluster Structure. PLoS One 2016; 11:e0157464. [PMID: 27299357 PMCID: PMC4907446 DOI: 10.1371/journal.pone.0157464] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 03/10/2016] [Accepted: 05/31/2016] [Indexed: 11/18/2022] Open
Abstract
Ribosomal RNA (rRNA) genes, whose activity results in nucleolus formation, constitute an extremely important part of genome. Despite the extensive exploration into avian genomes, no complete description of avian rRNA gene primary structure has been offered so far. We publish a complete chicken rRNA gene cluster sequence here, including 5'ETS (1836 bp), 18S rRNA gene (1823 bp), ITS1 (2530 bp), 5.8S rRNA gene (157 bp), ITS2 (733 bp), 28S rRNA gene (4441 bp) and 3'ETS (343 bp). The rRNA gene cluster sequence of 11863 bp was assembled from raw reads and deposited to GenBank under KT445934 accession number. The assembly was validated through in situ fluorescent hybridization analysis on chicken metaphase chromosomes using computed and synthesized specific probes, as well as through the reference assembly against de novo assembled rRNA gene cluster sequence using sequenced fragments of BAC-clone containing chicken NOR (nucleolus organizer region). The results have confirmed the chicken rRNA gene cluster validity.
Collapse
Affiliation(s)
| | - Elena I. Koshel
- Saint Petersburg State University, Saint Petersburg, 199034, Russia
| | - Artem M. Kiselev
- Almazov Federal Medical Research Centre, Saint Petersburg, 197341, Russia
- ITMO University, Saint Petersburg, 197101, Russia
| | | | | | | | - Anna A. Kostareva
- Almazov Federal Medical Research Centre, Saint Petersburg, 197341, Russia
- ITMO University, Saint Petersburg, 197101, Russia
| | - Elena R. Gaginskaya
- Saint Petersburg State University, Saint Petersburg, 199034, Russia
- * E-mail:
| |
Collapse
|
29
|
Kinoshita A, Ogura-Tsujita Y, Umata H, Sato H, Hashimoto T, Yukawa T. How do fungal partners affect the evolution and habitat preferences of mycoheterotrophic plants? A case study in Gastrodia. Am J Bot 2016; 103:207-20. [PMID: 26838365 DOI: 10.3732/ajb.1500082] [Citation(s) in RCA: 14] [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: 03/02/2015] [Accepted: 11/25/2015] [Indexed: 05/20/2023]
Abstract
PREMISE OF THE STUDY Since mycoheterotrophic plants (MHPs) completely depend on their mycorrhizal fungi for carbon, selection of fungal partners has an important role in the speciation of MHPs. However, the causes and mechanisms of mycobiont changes during speciation are not clear. We tested fungal partner shifts and changes in mycorrhizal specificity during speciation of three closely related MHPs-Gastrodia confusa (Gc), G. pubilabiata (Gp), and G. nipponica (Gn) (Orchidaceae)-and correlations between these changes and the vegetation types where each species grows. METHODS We investigated the diversity of mycobionts of the three species by sequencing nrDNA ITS, and the sequence data were subjected to test changes in fungal specificity and fungal partner shifts among the three species. Furthermore, we conducted multivariate analysis to test for differences in mycobiont communities of vegetation types where each species grows. KEY RESULTS Two saprobic Basidiomycota, Marasmiaceae and Mycenaceae, were dominant fungal partners of the three species, and Gn was simultaneously associated with the ectomycorrhizal Russulaceae and Sebacinaceae. Although mycobiont composition differed among the three species, they also sometimes shared identical fungal species. Multivariate analysis revealed that mycobiont communities of the three species in bamboo thickets differed significantly from those in other vegetation types. CONCLUSIONS Fungal partner shifts are not necessarily associated with the evolution of MHPs, and fungal specificity of Gc and Gp was significantly higher than that of Gn, implying that the specificity fluctuates during speciation. Further, Gc exclusively inhabits bamboo thickets, which suggests that adaptation to particular fungi specific to bamboo thickets triggered speciation of this species.
Collapse
MESH Headings
- Biological Evolution
- Ecosystem
- Gastrodia/genetics
- Gastrodia/microbiology
- Gastrodia/physiology
- Molecular Sequence Data
- Mycorrhizae/genetics
- Mycorrhizae/physiology
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/metabolism
- RNA, Ribosomal, 28S/genetics
- RNA, Ribosomal, 28S/metabolism
- RNA, Ribosomal, 5.8S/genetics
- RNA, Ribosomal, 5.8S/metabolism
- Sequence Analysis, DNA
- Symbiosis
Collapse
Affiliation(s)
- Akihiko Kinoshita
- Tsukuba Botanical Garden, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki 305-0005, Japan
| | - Yuki Ogura-Tsujita
- Faculty of Agriculture, Saga University, Honjo-machi, Saga 840-8502, Japan
| | - Hidetaka Umata
- 5211 Kita-Takanabe, Takanabe-cho, Koyu-gun, Miyazaki 888-0002, Japan
| | - Hiroki Sato
- Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki 305-8687, Japan
| | - Toshimasa Hashimoto
- Japan Wildlife Research Center, 3-3-7 Kotobashi Sumida-ku, Tokyo 130-8606, Japan
| | - Tomohisa Yukawa
- Tsukuba Botanical Garden, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba, Ibaraki 305-0005, Japan
| |
Collapse
|
30
|
Taştan BE, Çakir DN, Dönmez G. A new and effective approach to boron removal by using novel boron-specific fungi isolated from boron mining wastewater. Water Sci Technol 2016; 73:543-549. [PMID: 26877036 DOI: 10.2166/wst.2015.519] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Boron-resistant fungi were isolated from the wastewater of a boron mine in Turkey. Boron removal efficiencies of Penicillium crustosum and Rhodotorula mucilaginosa were detected in different media compositions. Minimal Salt Medium (MSM) and two different waste media containing molasses (WM-1) or whey + molasses (WM-2) were tested to make this process cost effective when scaled up. Both isolates achieved high boron removal yields at the highest boron concentrations tested in MSM and WM-1. The maximum boron removal yield by P. crustosum was 45.68% at 33.95 mg l(-1) initial boron concentration in MSM, and was 38.97% at 42.76 mg l(-1) boron for R. mucilaginosa, which seemed to offer an economically feasible method of removing boron from the effluents.
Collapse
Affiliation(s)
- Burcu Ertit Taştan
- Life Sciences Application and Research Center, Gazi University, 06830 Gölbaşı, Ankara, Turkey and Health Services Vocational School, Gazi University, 06830 Gölbaşı, Ankara, Turkey E-mail:
| | - Dilara Nur Çakir
- Department of Biology, Faculty of Science, Ankara University, 06100 Beşevler, Ankara, Turkey
| | - Gönül Dönmez
- Department of Biology, Faculty of Science, Ankara University, 06100 Beşevler, Ankara, Turkey
| |
Collapse
|
31
|
Kuuskeri J, Mäkelä MR, Isotalo J, Oksanen I, Lundell T. Lignocellulose-converting enzyme activity profiles correlate with molecular systematics and phylogeny grouping in the incoherent genus Phlebia (Polyporales, Basidiomycota). BMC Microbiol 2015; 15:217. [PMID: 26482661 PMCID: PMC4610053 DOI: 10.1186/s12866-015-0538-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [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: 01/20/2015] [Accepted: 09/25/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The fungal genus Phlebia consists of a number of species that are significant in wood decay. Biotechnological potential of a few species for enzyme production and degradation of lignin and pollutants has been previously studied, when most of the species of this genus are unknown. Therefore, we carried out a wider study on biochemistry and systematics of Phlebia species. METHODS Isolates belonging to the genus Phlebia were subjected to four-gene sequence analysis in order to clarify their phylogenetic placement at species level and evolutionary relationships of the genus among phlebioid Polyporales. rRNA-encoding (5.8S, partial LSU) and two protein-encoding gene (gapdh, rpb2) sequences were adopted for the evolutionary analysis, and ITS sequences (ITS1+5.8S+ITS2) were aligned for in-depth species-level phylogeny. The 49 fungal isolates were cultivated on semi-solid milled spruce wood medium for 21 days in order to follow their production of extracellular lignocellulose-converting oxidoreductases and carbohydrate active enzymes. RESULTS Four-gene phylogenetic analysis confirmed the polyphyletic nature of the genus Phlebia. Ten species-level subgroups were formed, and their lignocellulose-converting enzyme activity profiles coincided with the phylogenetic grouping. The highest enzyme activities for lignin modification (manganese peroxidase activity) were obtained for Phlebia radiata group, which supports our previous studies on the enzymology and gene expression of this species on lignocellulosic substrates. CONCLUSIONS Our study implies that there is a species-level connection of molecular systematics (genotype) to the efficiency in production of both lignocellulose-converting carbohydrate active enzymes and oxidoreductases (enzyme phenotype) on spruce wood. Thus, we may propose a similar phylogrouping approach for prediction of lignocellulose-converting enzyme phenotypes in new fungal species or genetically and biochemically less-studied isolates of the wood-decay Polyporales.
Collapse
MESH Headings
- Basidiomycota/classification
- Basidiomycota/enzymology
- Basidiomycota/genetics
- Basidiomycota/metabolism
- Biotransformation
- Cluster Analysis
- Culture Media/chemistry
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating)/genetics
- Lignin/metabolism
- Microbiological Techniques
- Molecular Sequence Data
- Phylogeny
- RNA Polymerase II/genetics
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 5.8S/genetics
- Sequence Analysis, DNA
Collapse
Affiliation(s)
- Jaana Kuuskeri
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Viikki Biocenter 1, P.O.B. 56, FIN-00014, Helsinki, Finland.
| | - Miia R Mäkelä
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Viikki Biocenter 1, P.O.B. 56, FIN-00014, Helsinki, Finland.
| | - Jarkko Isotalo
- Department of Forest Sciences, University of Helsinki, Helsinki, Finland.
| | - Ilona Oksanen
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Viikki Biocenter 1, P.O.B. 56, FIN-00014, Helsinki, Finland.
| | - Taina Lundell
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, Viikki Biocenter 1, P.O.B. 56, FIN-00014, Helsinki, Finland.
| |
Collapse
|
32
|
Mehrdana F, Marana MH, Skov J, Bahlool QZM, Sindberg D, Mundeling M, Overgaard BC, Kania PW, Buchmann K. Eye fluke infection status in Baltic cod, Gadus morhua, after three decades and their use as ecological indicators. Acta Parasitol 2015. [PMID: 26204178 DOI: 10.1515/ap-2015-0058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Eye flukes of the genus Diplostomum were recorded with a prevalence of 7.4% and a mean intensity of 11.9 (range 1-75) parasites per fish in eye lenses of a total of 188 Atlantic cod, Gadus morhua, sampled in the Southeastern Baltic Sea from March 2013 to February 2014. A slight decrease of infection level, among the fish with body length ranging from 30 to 89.5 cm, was found when data were compared to a corresponding survey in the 1980s. Due to imprecise species identification of eye flukes based on morphometric analyses we present, as a baseline for further studies, rDNA sequences from a subsample of 19 eye flukes based on sequencing of a part of 18S, ITS-1, 5.8S, ITS-2 and part of 28S. We discuss the use of eye fluke recordings in Baltic cod as an environmental indicator due to the dependence of the parasite's life cycle on biotic (occurrence of snail and bird hosts) and abiotic (temperature and salinity) parameters.
Collapse
MESH Headings
- Animals
- DNA, Helminth/chemistry
- DNA, Helminth/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Eye Diseases/epidemiology
- Eye Diseases/veterinary
- Fish Diseases/epidemiology
- Fish Diseases/parasitology
- Gadus morhua/parasitology
- Molecular Sequence Data
- Parasite Load
- Prevalence
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 28S/genetics
- RNA, Ribosomal, 5.8S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Trematoda/classification
- Trematoda/genetics
- Trematoda/isolation & purification
- Trematode Infections/epidemiology
- Trematode Infections/veterinary
Collapse
|
33
|
Freitas LA, Russo CAM, Voloch CM, Mutaquiha OCF, Marques LP, Schrago CG. Diversification of the Genus Anopheles and a Neotropical Clade from the Late Cretaceous. PLoS One 2015; 10:e0134462. [PMID: 26244561 PMCID: PMC4526650 DOI: 10.1371/journal.pone.0134462] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [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: 01/26/2015] [Accepted: 07/10/2015] [Indexed: 11/18/2022] Open
Abstract
The Anopheles genus is a member of the Culicidae family and consists of approximately 460 recognized species. The genus is composed of 7 subgenera with diverse geographical distributions. Despite its huge medical importance, a consensus has not been reached on the phylogenetic relationships among Anopheles subgenera. We assembled a comprehensive dataset comprising the COI, COII and 5.8S rRNA genes and used maximum likelihood and Bayesian inference to estimate the phylogeny and divergence times of six out of the seven Anopheles subgenera. Our analysis reveals a monophyletic group composed of the three exclusively Neotropical subgenera, Stethomyia, Kerteszia and Nyssorhynchus, which began to diversify in the Late Cretaceous, at approximately 90 Ma. The inferred age of the last common ancestor of the Anopheles genus was ca. 110 Ma. The monophyly of all Anopheles subgenera was supported, although we failed to recover a significant level of statistical support for the monophyly of the Anopheles genus. The ages of the last common ancestors of the Neotropical clade and the Anopheles and Cellia subgenera were inferred to be at the Late Cretaceous (ca. 90 Ma). Our analysis failed to statistically support the monophyly of the Anopheles genus because of an unresolved polytomy between Bironella and A. squamifemur.
Collapse
Affiliation(s)
- Lucas A. Freitas
- Departamento de Genética, Universidade Federal do Rio de Janeiro, RJ, Brazil
| | - Claudia A. M. Russo
- Departamento de Genética, Universidade Federal do Rio de Janeiro, RJ, Brazil
| | - Carolina M. Voloch
- Departamento de Genética, Universidade Federal do Rio de Janeiro, RJ, Brazil
| | | | - Lucas P. Marques
- Departamento de Genética, Universidade Federal do Rio de Janeiro, RJ, Brazil
| | - Carlos G. Schrago
- Departamento de Genética, Universidade Federal do Rio de Janeiro, RJ, Brazil
- * E-mail:
| |
Collapse
|
34
|
Slugina MA, Torres Minho K, Filiushin MA. [Analysis of the sequences of internal transcribed spacers ITS1, ITS2 and the 5.8S ribosomal gene of species of the Amaranthus genus]. Izv Akad Nauk Ser Biol 2014:631-635. [PMID: 25739312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Analysis of the sequence ITS1-5.8S-ITS2 in 11 samples of the amaranth species (Amaranthus caudatus, A. cruentus, A. hybridus, A. tricolor, A. paniculatus, A. hypohondriacus) was performed. It has been shown that the variability of the sequences of the intergenic spacers ITS1, ITS2 and 5.8S rRNA gene of the amaranth species analyzed is extremely low. A possible secondary structure of the 5.8S rRNA molecule was determined for the first time; three conservative motifs were identified. A single nucleotide substitution found in A. hybridus did not change the loop topology. In the sample of Celosia cristata taken as an external group, a four-nucleotide insertion in the 5'-end of the gene and a one-nucleotide deletion in the fourth hairpin not affecting the general topology of the 5.8S rRNA molecule were found.
Collapse
|
35
|
Filyushin MA, Kochieva EZ. [5.8S rDNA variability in Allium species belonging to the third evolutionary group]. Genetika 2014; 50:1263-1268. [PMID: 25720260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Sequence analysis of 5.8S rDNA in 67 accessions of the subgenus Allium and six other subgenera belonging to the third evolutionary group of Allium genus (Friesen et al., 2006) was performed. Nucleotide substitutions in 5.8S rDNA sequences ofAllium accessions were identified and, studied for the first time. The probable secondary structure of 5.8S rRNA was constructed. It was shown that mutations in 5.8S rDNA do not involve conserved motifs, and they did not significantly affect the Secondary structure of the RNA molecule in Allium accessions.
Collapse
|
36
|
Beroiz B, Couso-Ferrer F, Ortego F, Chamorro MJ, Arteaga C, Lombardero M, Castañera P, Hernández-Crespo P. Mite species identification in the production of allergenic extracts for clinical use and in environmental samples by ribosomal DNA amplification. Med Vet Entomol 2014; 28:287-96. [PMID: 24617319 DOI: 10.1111/mve.12052] [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] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 08/01/2013] [Accepted: 11/06/2013] [Indexed: 05/09/2023]
Abstract
The identification of allergy-causing mites is conventionally based on morphological characters. However, molecular taxonomy using ribosomal DNA (rDNA) may be particularly useful in the analysis of mite cultures and purified mite fractions in the production of allergenic extracts. Full-length internal transcribed spacers (ITS1 and ITS2) were obtained from Dermatophagoides farinae, Dermatophagoides pteronyssinus, Dermatophagoides microceras and Euroglyphus maynei (Astigmata: Pyroglyphidae), Glycyphagus domesticus and Lepidoglyphus destructor (Astigmata: Glycyphagidae), Tyrophagus fanetzhangorum, Tyrophagus putrescentiae, Tyrophagus longior, Tyrophagus neiswanderi, Acarus farris and Acarus siro (Astigmata: Acaridae), and Blomia tropicalis (Astigmata: Echymopodidae), using mite-specific primers. Polymerase chain reaction (PCR) products were digested with HpaII and RsaI restriction enzymes in order to produce species-specific PCR restricted fragment length polymorphism (RFLP) profiles. A semi-nested re-amplification step was introduced before the RFLP in order to apply the method to environmental samples. Results demonstrate that rDNA sequences can be used for the unambiguous identification of mite species. The PCR-RFLP system allows the identification of species in purified mite fractions when the availability of intact adult mite bodies for morphological identification is limited. This reliable and straightforward PCR-RFLP system and the rDNA sequences obtained can be of use in the identification of allergy-causing mite species.
Collapse
Affiliation(s)
- B Beroiz
- Department of Environmental Biology, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | | | | | | | | | | | | | | |
Collapse
|
37
|
Hou XQ, Guo SX. [Screening and identification of endophytic fungi with growth promoting effect on Dendrobium officinale]. Zhongguo Zhong Yao Za Zhi 2014; 39:3232-3237. [PMID: 25522603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The endophytic fungi with plant growth promoting effects were screened by co-culture of each endophytic fungus and seedlings of Dendrobium officinale. Anatomical features of the inoculated roots were studied by paraffin sectioning. Morphological characteristics and rDNA ITS1-5. 8S-ITS2 sequences were applied for the taxonomy of endophytic fungi. The results showed that 8 strains inoculated to D. officinale seedlings greatly enhanced plant height, stem diameter, new roots number and biomass. According to the anatomical features of the inoculated roots, each fungus could infect the velamina of seedlings. The hyphae or pelotons were existed in the exodermis passage cells and cortex cells. The effective fungi could not infect the endodermis and vascular bundle sheath, but which was exception for other fungi with harmful to seedlings. Combined with classic morphologic classification, 2 effective strains were identified which were subjected to Pestalotiopsis and Eurotium. Six species of fungi without conidiophore belonged to Pyrenochaeta, Coprinellus, Pholiota, Alternaria, Helotiales, which were identified by sequencing the PCR-amplified rDNA ITS1-5. 8S-ITS2 regions. The co-culture technology of effective endophytic fungi and plant can apply to cultivate the seedlings of D. officinale. It is feasible to shorten growth cycle of D. officinale and increase the resource of Chinese herbs.
Collapse
|
38
|
Wei YC, Chen Y, Luo LQ, Yang QX, Chen YJ, Liang YC, Chen SR. [Study on identification of Sarcandra glabra and Chloranthus spicatus's leaves by PCR amplification of specific alleles]. Zhongguo Zhong Yao Za Zhi 2014; 39:3259-3262. [PMID: 25522607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The paper is aimed to identify SNP in Sarcandra glabra and Chloranthus spicatus, and authenticate S. glabra from Ch. spicatus and the mixture by using PCR amplification of specific alleles. SNPs in the ITS sequences of S. glabra and Ch. spicatus were found by ClustulX 2. 1 program and Bioedit software. Primers for authentic S. glabra and Ch. spicatus was designed according to the SNP site, and ITS sequence universal primers plus to the authentic primer to construct a multi-PCR reaction system, and then optimized the PCR reaction system. Five hundred and eighty band special for S. glabra and 470 bp band special for Ch. spicatus were found by using multi-PCR reaction. The multi-PCR reaction system could be applied to identify S. glabra and Ch. spicatus's leaves.
Collapse
MESH Headings
- DNA, Plant/analysis
- DNA, Plant/genetics
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/analysis
- DNA, Ribosomal Spacer/genetics
- Magnoliopsida/classification
- Magnoliopsida/genetics
- Plant Leaves/genetics
- Polymerase Chain Reaction
- Polymorphism, Single Nucleotide
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 5.8S/genetics
- Species Specificity
Collapse
|
39
|
Senés-Guerrero C, Torres-Cortés G, Pfeiffer S, Rojas M, Schüßler A. Potato-associated arbuscular mycorrhizal fungal communities in the Peruvian Andes. Mycorrhiza 2014; 24:405-417. [PMID: 24356891 DOI: 10.1007/s00572-013-0549-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 12/03/2013] [Indexed: 06/03/2023]
Abstract
The world's fourth largest food crop, potato, originates in the Andes. Here, the community composition of arbuscular mycorrhizal fungi (AMF) associated with potato in Andean ecosystems is described for the first time. AMF were studied in potato roots and rhizosphere soil at four different altitudes from 2,658 to 4,075 m above mean sea level (mamsl) and in three plant growth stages (emergence, flowering, and senescence). AMF species were distinguished by sequencing an approx. 1,500 bp nuclear rDNA region. Twenty species of AMF were identified, of which 12 came from potato roots and 15 from rhizosphere soil. Seven species were found in both roots and soil. Interestingly, altitude affected species composition with the highest altitude exhibiting the greatest species diversity. The three most common colonizers of potato roots detected were Funneliformis mosseae, an unknown Claroideoglomus sp., and Rhizophagus irregularis. Notably, the potato-associated AMF diversity observed in this Andean region is much higher than that reported for potato in other ecosystems. Potato plants were colonized by diverse species from 8 of the 11 Glomeromycota families. Identification of the AMF species is important for their potential use in sustainable management practices to improve potato production in the Andean region.
Collapse
MESH Headings
- Altitude
- Biodiversity
- Cluster Analysis
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Genes, rRNA
- Molecular Sequence Data
- Mycorrhizae/classification
- Mycorrhizae/genetics
- Mycorrhizae/isolation & purification
- Peru
- Phylogeny
- RNA, Fungal/genetics
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 5.8S/genetics
- Rhizosphere
- Sequence Analysis, DNA
- Soil Microbiology
- Solanum tuberosum/microbiology
Collapse
Affiliation(s)
- Carolina Senés-Guerrero
- Department of Biology, Genetics, Ludwig-Maximilians University, Grosshadernerstr. 4, 82152, Planegg-Martinsried, Germany
| | | | | | | | | |
Collapse
|
40
|
Neto JBA, da Silva CR, Neta MAS, Campos RS, Siebra JT, Silva RAC, Gaspar DM, Magalhães HIF, de Moraes MO, Lobo MDP, Grangeiro TB, Carvalho TSC, Diogo EBT, da Silva Júnior EN, Rodrigues FAR, Cavalcanti BC, Júnior HVN. Antifungal activity of naphthoquinoidal compounds in vitro against fluconazole-resistant strains of different Candida species: a special emphasis on mechanisms of action on Candida tropicalis. PLoS One 2014; 9:e93698. [PMID: 24817320 PMCID: PMC4015898 DOI: 10.1371/journal.pone.0093698] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [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: 03/26/2013] [Accepted: 03/09/2014] [Indexed: 11/19/2022] Open
Abstract
In recent decades, the incidence of candidemia in tertiary hospitals worldwide has substantially increased. These infections are a major cause of morbidity and mortality; in addition, they prolong hospital stays and raise the costs associated with treatment. Studies have reported a significant increase in infections by non-albicans Candida species, especially C. tropicalis. The number of antifungal drugs on the market is small in comparison to the number of antibacterial agents available. The limited number of treatment options, coupled with the increasing frequency of cross-resistance, makes it necessary to develop new therapeutic strategies. The objective of this study was to evaluate and compare the antifungal activities of three semisynthetic naphthofuranquinone molecules against fluconazole-resistant Candida spp. strains. These results allowed to us to evaluate the antifungal effects of three naphthofuranquinones on fluconazole-resistant C. tropicalis. The toxicity of these compounds was manifested as increased intracellular ROS, which resulted in membrane damage and changes in cell size/granularity, mitochondrial membrane depolarization, and DNA damage (including oxidation and strand breakage). In conclusion, the tested naphthofuranquinones (compounds 1-3) exhibited in vitro cytotoxicity against fluconazole-resistant Candida spp. strains.
Collapse
MESH Headings
- Animals
- Antifungal Agents/chemical synthesis
- Antifungal Agents/chemistry
- Antifungal Agents/pharmacology
- Candida/classification
- Candida/drug effects
- Candida/genetics
- Candida tropicalis/drug effects
- Candida tropicalis/genetics
- Candida tropicalis/metabolism
- Cell Line
- Cell Survival/drug effects
- DNA Damage
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- DNA, Fungal/metabolism
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Drug Resistance, Fungal/drug effects
- Fibroblasts/cytology
- Fibroblasts/drug effects
- Fluconazole/pharmacology
- Membrane Potential, Mitochondrial/drug effects
- Microbial Sensitivity Tests
- Models, Chemical
- Molecular Sequence Data
- Molecular Structure
- Naphthoquinones/chemical synthesis
- Naphthoquinones/chemistry
- Naphthoquinones/pharmacology
- Phosphatidylserines
- RNA, Ribosomal, 5.8S/genetics
- Reactive Oxygen Species/metabolism
- Sequence Analysis, DNA
Collapse
Affiliation(s)
- João B. A. Neto
- Department of Clinical and Toxicological Analysis, School of Pharmacy, Laboratory of Bioprospection and Experiments in Yeast (LABEL), Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Cecília R. da Silva
- Department of Clinical and Toxicological Analysis, School of Pharmacy, Laboratory of Bioprospection and Experiments in Yeast (LABEL), Federal University of Ceará, Fortaleza, Ceará, Brazil
- Department of Pathology and Legal Medicine, School of Medicine, Laboratory of Bioprospection and Experiments in Yeast (LABEL), Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Maria A. S. Neta
- Department of Clinical and Toxicological Analysis, School of Pharmacy, Laboratory of Bioprospection and Experiments in Yeast (LABEL), Federal University of Ceará, Fortaleza, Ceará, Brazil
- Department of Pathology and Legal Medicine, School of Medicine, Laboratory of Bioprospection and Experiments in Yeast (LABEL), Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Rosana S. Campos
- Department of Clinical and Toxicological Analysis, School of Pharmacy, Laboratory of Bioprospection and Experiments in Yeast (LABEL), Federal University of Ceará, Fortaleza, Ceará, Brazil
- Department of Pathology and Legal Medicine, School of Medicine, Laboratory of Bioprospection and Experiments in Yeast (LABEL), Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Janaína T. Siebra
- Department of Clinical and Toxicological Analysis, School of Pharmacy, Laboratory of Bioprospection and Experiments in Yeast (LABEL), Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Rose A. C. Silva
- Department of Clinical and Toxicological Analysis, School of Pharmacy, Laboratory of Bioprospection and Experiments in Yeast (LABEL), Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Danielle M. Gaspar
- Department of Physiology and Pharmacology, Laboratory of Experimental Oncology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Hemerson I. F. Magalhães
- Department of Clinical and Toxicological Analysis, School of Pharmacy, Laboratory of Bioprospection and Experiments in Yeast (LABEL), Federal University of Ceará, Fortaleza, Ceará, Brazil
- Department of Pharmaceutical Sciences, Center for Toxicological Assistance, University Federal of Paraíba, Paraíba, Brazil
| | - Manoel O. de Moraes
- Department of Physiology and Pharmacology, Laboratory of Experimental Oncology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Marina D. P. Lobo
- Department of Biology, ScienceCenter, Molecular Genetics Laboratory, Federal University of Ceará, Ceará, Brazil
| | - Thalles B. Grangeiro
- Department of Biology, ScienceCenter, Molecular Genetics Laboratory, Federal University of Ceará, Ceará, Brazil
| | - Tatiane S. C. Carvalho
- Natural Products Research Nucleus, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Emilay B. T. Diogo
- Department of Chemistry, Institute of Exact Sciences, Laboratory of Synthetic and Heterocyclic Chemistry, Federal University of Minas Gerais, Minas Gerais, Brazil
| | - Eufrânio N. da Silva Júnior
- Department of Chemistry, Institute of Exact Sciences, Laboratory of Synthetic and Heterocyclic Chemistry, Federal University of Minas Gerais, Minas Gerais, Brazil
| | - Felipe A. R. Rodrigues
- Department of Physiology and Pharmacology, Laboratory of Experimental Oncology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Bruno C. Cavalcanti
- Department of Pathology and Legal Medicine, School of Medicine, Laboratory of Bioprospection and Experiments in Yeast (LABEL), Federal University of Ceará, Fortaleza, Ceará, Brazil
- Department of Physiology and Pharmacology, Laboratory of Experimental Oncology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Hélio V. N. Júnior
- Department of Clinical and Toxicological Analysis, School of Pharmacy, Laboratory of Bioprospection and Experiments in Yeast (LABEL), Federal University of Ceará, Fortaleza, Ceará, Brazil
- Department of Pathology and Legal Medicine, School of Medicine, Laboratory of Bioprospection and Experiments in Yeast (LABEL), Federal University of Ceará, Fortaleza, Ceará, Brazil
- Department of Physiology and Pharmacology, Laboratory of Experimental Oncology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| |
Collapse
|
41
|
Shentu X, Zhan X, Ma Z, Yu X, Zhang C. Antifungal activity of metabolites of the endophytic fungus Trichoderma brevicompactum from garlic. Braz J Microbiol 2014; 45:248-54. [PMID: 24948941 PMCID: PMC4059306 DOI: 10.1590/s1517-83822014005000036] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [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: 06/25/2012] [Accepted: 04/01/2013] [Indexed: 11/30/2022] Open
Abstract
The endophytic fungus strain 0248, isolated from garlic, was identified as Trichoderma brevicompactum based on morphological characteristics and the nucleotide sequences of ITS1-5.8S- ITS2 and tef1. The bioactive compound T2 was isolated from the culture extracts of this fungus by bioactivity-guided fractionation and identified as 4β-acetoxy-12,13- epoxy-Δ(9)-trichothecene (trichodermin) by spectral analysis and mass spectrometry. Trichodermin has a marked inhibitory activity on Rhizoctonia solani, with an EC50 of 0.25 μg mL(-1). Strong inhibition by trichodermin was also found for Botrytis cinerea, with an EC50 of 2.02 μg mL(-1). However, a relatively poor inhibitory effect was observed for trichodermin against Colletotrichum lindemuthianum (EC50 = 25.60 μg mL(-1)). Compared with the positive control Carbendazim, trichodermin showed a strong antifungal activity on the above phytopathogens. There is little known about endophytes from garlic. This paper studied in detail the identification of endophytic T. brevicompactum from garlic and the characterization of its active metabolite trichodermin.
Collapse
Affiliation(s)
- Xuping Shentu
- Institute of Insect ScienceZhejiang UniversityHangzhouChina
- College of Life ScienceChina Jiliang UniversityZhejiang Provincial Key Laboratory of Biometrology and Inspection & QuarantineHangzhouChina
| | - Xiaohuan Zhan
- College of Life ScienceChina Jiliang UniversityZhejiang Provincial Key Laboratory of Biometrology and Inspection & QuarantineHangzhouChina
| | - Zheng Ma
- College of Life ScienceChina Jiliang UniversityZhejiang Provincial Key Laboratory of Biometrology and Inspection & QuarantineHangzhouChina
| | - Xiaoping Yu
- College of Life ScienceChina Jiliang UniversityZhejiang Provincial Key Laboratory of Biometrology and Inspection & QuarantineHangzhouChina
| | - Chuanxi Zhang
- Institute of Insect ScienceZhejiang UniversityHangzhouChina
| |
Collapse
|
42
|
Cavassin FB, Kuehn CC, Kopp RL, Thomaz-Soccol V, Da Rosa JA, Luz E, Mas-Coma S, Bargues MD. Genetic variability and geographical diversity of the main Chagas' disease vector Panstrongylus megistus (Hemiptera: Triatominae) in Brazil based on ribosomal DNA intergenic sequences. J Med Entomol 2014; 51:616-628. [PMID: 24897854 DOI: 10.1603/me13073] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Studies were made on the ribosomal DNA intergenic region, comprising complete internal transcribed spacer (ITS)-1, 5.8S, and ITS-2 sequences, of populations of the triatomine Panstrongylus megistus, the most important vector of Chagas' disease in Brazil since Triatoma infestans eradication. Specimens were from 26 localities of Rio Grande do Sul, Santa Catarina, Paraná, São Paulo, Minas Gerais, Bahia, and Sergipe states. In total, 21 ITS-1 and 12 ITS-2 haplotypes were found. Nucleotide differences were higher in ITS-1 (3.00%) than in ITS-2 (1.33%). The intergenic region was 1,513-1,522-bp-long (mean 1,516.9 bp), providing 26 combined haplotypes. The combination of microsatellites found in both ITSs may be of applied usefulness, to assess interpopulation specimen exchange and potential recolonizations after vector elimination by control implementation. Network results suggest that São Paulo may be considered one of the spreading centers of this species. Molecular clock datation suggests that P. megistus populations are diversifying at least since 4.54 million years ago, with diversification still ongoing today by geographical isolation of populations. Evidence is provided about the relationship of genetic diversity with geographical spread that characterizes a major vector and explains its ability to colonize distant areas and different ecotopes, including human habitats, and consequently its importance in Chagas' disease epidemiology.
Collapse
|
43
|
Ieshko E, Lebedeva D, Lumme J. A new Gyrodactylus strain on brown trout (Salmo trutta) in Jänisjärvi, Russian Karelia, and a literature revision of salmonid parasites of the genus Gyrodactylus in North-Western Russia and adjacent areas. Acta Parasitol 2014. [PMID: 26204023 DOI: 10.1515/ap-2015-0010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A Gyrodactylus parasite infected juveniles of brown trout (Salmo trutta L.) in a hatchery in Lake Janisjarvi, Russian Karelia. Molecular identification by ITS1-5.8S-ITS2 of ribosomal DNA indicated that the infection was caused by a non-segregating hybrid clone between unknown Gyrodactylus species and Gyrodactylus teuchis Lautraite, Blanc, Thiery, Daniel & Vigneulle, 1999, described from brown trout collected in France. The mitochondrial CO1 was sequenced from the hybrid, but it is not available from pure G. teuchis from type locality. The mitochondrial DNA was an independent clade among the wageneri group parasites, differing from the nearest relative G. derjavinoides by 19%. Morphometric measurements of the Janisjarvi parasite were compared with separate (host specific) G. salaris strains from farmed rainbow trout and salmon in Lake Onega, and with available data on G. teuchis from Western Europe, Austria and Poland. All isolates were distinguishable by morphometry, and the measurements are a useful primary diagnostic tool for the salmonid parasites in Karelian great lakes and fish farms. Pure G. teuchis is not found on Russian territory, and the other parent of the hybrid has not been discovered yet in any other country. A mini review of Gyrodactylus on salmonids in the Russian Karelia is presented.
Collapse
MESH Headings
- Animals
- Cluster Analysis
- DNA, Helminth/chemistry
- DNA, Helminth/genetics
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/chemistry
- DNA, Ribosomal Spacer/genetics
- Electron Transport Complex IV/genetics
- Lakes
- Microscopy
- Molecular Sequence Data
- Phylogeny
- Platyhelminths/anatomy & histology
- Platyhelminths/classification
- Platyhelminths/genetics
- Platyhelminths/isolation & purification
- RNA, Ribosomal, 5.8S/genetics
- Russia
- Sequence Analysis, DNA
- Trout/parasitology
Collapse
|
44
|
Savel'eva EN, Boris KV, Kochieva EZ, Kudryavtsev AM. [Analysis of sequences of ITS1 internal transcribed spacer and 5.8S ribosome gene of Malus species]. Genetika 2013; 49:1345-1352. [PMID: 25470936 DOI: 10.7868/s0016675813110143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The nucleotide sequence of the ITS1-5.8S ribosomal DNA spacer fragment was determined for 41 samples of the Malus species. The total length of compared sequences ranged from 389 to 392 bp. The nucleotide sequence of the 5.8S gene within the genus was highly conserved. The level of polymorphism of ITS 1 region comprised 14%. Both species- and group-specific substitutions were identified. The analysis of M. orientalis and M. turkmenorum sequences revealed their full identity, which indicates the need to perform more research with a larger number of samples of both species from other collections to clarify the taxonomic status of the M. turkmenorum species. The previous findings on the synonymy of species M. baccata, M. mandshurica, M. pallasiana, and M. sachalinensis were also confirmed.
Collapse
|
45
|
Joel EL, Bhimba BV. Biological activity of secondary metabolites isolated from mangrove fungi Neurospora crassa. J Environ Biol 2013; 34:729-732. [PMID: 24640249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The screening of antimicrobial compounds from mangrove-associated fungi is a promising way to meet the increasing threat of drug-resistant strains of human pathogens. In the present study, a novel foliar fungus was isolated from the leaves of Rhizophora mucronata. Crude fungal extracts were obtained through solvent extraction. The fungal extracts exhibited an effective antimicrobial activity against bacterial strains. This study reports the cytotoxic activity of the secondary metabolite produced by the fungus against Hep 2 (HeLa derivative) cell line by 3-(4,5-dimethylthiazol-2-yl) -2,5-diphenyltetrazolium bromide (MTT) assay. GC-MS investigation of the secondary metabolites revealed the active components of the fungal metabolite. The DNA of the fungus was sequenced by amplifying the ITS region of the 5.8s rRNA to be submitted in the Genbank and an accession number was assigned confirming it to be a new strain.
Collapse
|
46
|
Čadež N, Dlauchy D, Raspor P, Péter G. Ogataea kolombanensis sp. nov., Ogataea histrianica sp. nov. and Ogataea deakii sp. nov., three novel yeast species from plant sources. Int J Syst Evol Microbiol 2013; 63:3115-3123. [PMID: 23749284 DOI: 10.1099/ijs.0.052589-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nine methanol-assimilating yeast strains isolated from olive oil sediments in Slovenia, extra virgin olive oil from Italy and rotten wood collected in Hungary were found to form three genetically separated groups, distinct from the currently recognized yeast species. Sequence analysis from genes of the small subunit (SSU) rRNA, internal transcribed spacer region/5.8S rRNA, large subunit (LSU) rRNA D1/D2 domains and translational elongation factor-1α (EF-1α) revealed that the three closely related groups represent three different undescribed yeast species. Sequence analysis of the LSU rRNA gene D1/D2 domains placed the novel species in the Ogataea clade. The three novel species are designated as Ogataea kolombanensis sp. nov. (type strain: ZIM 2322(T) = CBS 12778(T) = NRRL Y-63657(T)), Ogataea histrianica sp. nov. (type strain: ZIM 2463(T) = CBS 12779(T) = NRRL Y-63658(T)) and Ogataea deakii sp. nov. (type strain: NCAIM Y.01896(T) = CBS 12735(T) = NRRL Y-63656(T)).
Collapse
Affiliation(s)
- Neža Čadež
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Dénes Dlauchy
- National Collection of Agricultural and Industrial Microorganisms, Faculty of Food Science, Corvinus University of Budapest, Somlói út 14-16. H-1118 Budapest, Hungary
| | - Peter Raspor
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Gábor Péter
- National Collection of Agricultural and Industrial Microorganisms, Faculty of Food Science, Corvinus University of Budapest, Somlói út 14-16. H-1118 Budapest, Hungary
| |
Collapse
|
47
|
Ruffini Castiglione M, Gelati MT, Cremonini R, Frediani M. The intergenic spacer region of the rDNA in Haplopappus gracilis (Nutt.) Gray. Protoplasma 2013; 250:683-689. [PMID: 22948831 DOI: 10.1007/s00709-012-0441-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 07/24/2012] [Indexed: 06/01/2023]
Abstract
In this paper, we provide further information on the genome organisation of Haplopappus gracilis, one of the six angiosperms showing the lowest chromosome number, i.e. 2n = 4, by determining the nucleotide sequence of the intergenic spacer region of the ribosomal RNA genes and its cytological localization on metaphase chromosomes. DNA sequence analysis reveals the occurring of a product of 4,382 bp in length, characterised by the presence of four blocks of different repeated sequences. Our analysis also evidenced putative promoter regions with three transcription initiation sites for polymerase I, as previously reported in Artemisia absinthium, belonging to the same Asteraceae family. A fluorescent in situ hybridization with the intergenic spacer probe indicates the presence of rDNA genes only in the satellited chromosomes of H. gracilis; besides, differences in the signal intensity between homologous chromosomes were frequently observed, thus suggesting for these chromosome sites the presence of a variable number of rDNA gene copies, even if a divergent chromatin organisation in corresponding regions cannot be ruled out.
Collapse
MESH Headings
- Base Sequence
- Chromosome Mapping
- Chromosomes, Plant
- DNA, Ribosomal Spacer/genetics
- Genes, Plant
- Haplopappus/genetics
- Molecular Sequence Annotation
- Molecular Sequence Data
- Promoter Regions, Genetic
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 5.8S/genetics
- Sequence Analysis, DNA
- Transcription Initiation Site
Collapse
|
48
|
Daboit TC, Magagnin CM, Heidrich D, Castrillón MR, Mendes SDC, Vettorato G, Valente P, Scroferneker ML. A case of relapsed chromoblastomycosis due to Fonsecaea monophora: antifungal susceptibility and phylogenetic analysis. Mycopathologia 2013; 176:139-44. [PMID: 23645135 DOI: 10.1007/s11046-013-9660-1] [Citation(s) in RCA: 13] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 04/19/2013] [Indexed: 11/25/2022]
Abstract
Chromoblastomycosis is a chronic cutaneous and subcutaneous mycosis. The management of this infection continues to be challenging because there is no consensus on the therapeutic regimen. We report here a case of a 69-year-old male patient with cauliflower-like lesions on his left leg and foot. He had already been treated with itraconazole at a dose of 200 mg/day for 5 months, with mycological cure for all the affected areas. However, the lesions relapsed at both sites, and treatment with itraconazole was resumed at the dose previously used. Initially, direct mycological examination, cultural, and microculture slide observation were performed. Afterward, sequencing of the ITS1-5.8S rDNA-ITS2 region of the fungal DNA and evaluation of its susceptibility to antifungal agents alone and in combination were performed. In direct mycological examination, the presence of sclerotic cells was verified, and the fungus was identified as Fonsecaea based on cultural and microscopic examinations. Identification as Fonsecaea monophora was confirmed after sequencing of the ITS region and phylogenetic analysis. The isolate was susceptible to itraconazole and terbinafine. The combinations of amphotericin B and terbinafine and terbinafine and voriconazole were synergistic. The use of drugs for which the causative agent is susceptible to singly or in combination may be an alternative for the treatment of mycosis. Furthermore, the identification of the agent by molecular techniques is important for epidemiological purposes. To the best of our knowledge, this is the first case of relapsed chromoblastomycosis caused by F. monophora in Brazil.
Collapse
Affiliation(s)
- Tatiane Caroline Daboit
- Graduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Rua Ramiro Barcelos, 2400-2º andar, Porto Alegre, Rio Grande do Sul, CEP 90035-003, Brazil,
| | | | | | | | | | | | | | | |
Collapse
|
49
|
Jung J, Choi HK. Recognition of two major clades and early diverged groups within the subfamily Cyperoideae (Cyperaceae) including Korean sedges. J Plant Res 2013; 126:335-349. [PMID: 23114970 DOI: 10.1007/s10265-012-0534-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Accepted: 10/02/2012] [Indexed: 06/01/2023]
Abstract
We aim to present phylogenetic major groups within the subfamily Cyperoideae (Cyperaceae) on the basis of three molecular data sets; nuclear ribosomal internal transcribed spacer and 5.8S ribosomal RNA region, the ribulose-1, 5-bisphosphate carboxylase/oxygenase large subunit gene, and trnL intron and trnL-F intergenic spacer. Three molecular data and two combined data sets were used to obtain robust and detailed phylogenetic trees by using maximum parsimony and Bayesian inference, respectively. We analyzed 81 genera and 426 species of Cyperaceae, including Korean species. We suggest one early diverged group (EDGs), and two major clades (FAEC and SDC) within the subfamily Cyperoideae. And the clade EDGs comprises six tribes (Schoeneae, Bisboeckelereae, Sclerieae, Cryptangieae, Trilepideae, and Rhynchosporeae) at the basal nodes of Cyperoideae. The FAEC clade (posterior probability [PP]/bootstrap value [BS] = 1.00/85) comprises four tribes (Fuireneae, Abildgaardieae, Eleocharideae, Cypereae), and the SDC clade (PP/BS = 1.00/86) comprises three tribes (Scirpeae, Dulichieae, Cariceae). These three clades used for phylogenetic groups in our study will be useful for establishing the major lineage of the sedge family. The phylogeny of Korean sedges was also investigated within the whole phylogeny of Cyperaceae. The 20 genera of Korean sedges were placed in 10 tribes forming 14 clades.
Collapse
Affiliation(s)
- Jongduk Jung
- Department of Biological Science, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon, South Korea
| | | |
Collapse
|
50
|
Shalaby I, Gherbawy Y, Banaja A. Molecular characterization of Fasciola species isolated from imported sheep in Taif region (Saudi Arabia). Trop Biomed 2013; 30:15-26. [PMID: 23665704] [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: 06/02/2023]
Abstract
Accurate identification of Fasciola species, followed by biological and ecological characterization, is important with concern to the planning for field control. Because there are many variations in morphological characteristics, exact distinguishing of Fasciola species is usually difficult by simple traditional microscopic measurements and, therefore, the morphometric characterization may be insufficient for the species identification. Hence, the present work was proposed to collect 100 liver samples from 100 imported sheep from Sudan from slaughterhouses in Taif region. The samples were firstly examined macroscopically and microscopically to ensure the presence or absence of infection. The collected worms were subjected for RAPD-PCR analysis using different primers and ITS1 sequences for accurate identification. Using RAPD-PCR analysis, two primers were selected to amplify the DNA of each Fasciola. The results show that the amplification fragments were between 500 and 1500 bp and, the use of random genetic markers allowed to discriminate among the different collected species. Using Internal transcribed spacer region (ITS) sequencing, the imported sheep in Taif region consisted of 630 bps including complete ITS1, partial 18S and 5.8S and had 5 variable nucleotide positions. This is the first demonstration of the existence of both F. hepatica, F. gigantica and hybrid and/or introgressed populations of liver flukes bearing genetic material from both F. hepatica and F. gigantica in the imported sheep in Saudi Arabia by a genetic approach.
Collapse
Affiliation(s)
- I Shalaby
- Department of Biological Sciences, Faculty of Science, Taif University, Taif, KSA
| | | | | |
Collapse
|