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Bodunova N, Tsapkova L, Polyakova V, Baratova I, Rumyantsev K, Dekhnich N, Nikolskaya K, Chebotareva M, Voynovan I, Parfenchikova E, Pronina G, Chernikova E, Bordin D. Genetic Markers of Helicobacter pylori Resistance to Clarithromycin and Levofloxacin in Moscow, Russia. Curr Issues Mol Biol 2024; 46:6665-6674. [PMID: 39057039 PMCID: PMC11276122 DOI: 10.3390/cimb46070397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 06/03/2024] [Accepted: 06/03/2024] [Indexed: 07/28/2024] Open
Abstract
The Maastricht VI/Florence consensus recommends, as one of the measures to enhance the efficacy of Helicobacter pylori infection eradication, a personalized treatment approach involving the selection of an antimicrobial agent based on the pre-determined resistance of H. pylori. To address the need to develop test systems for personalized drug selection, this study was designed to analyze the molecular resistance of H. pylori using a newly developed Sanger sequencing test platform. The characteristics of the test system were determined on 25 pure culture samples of H. pylori with known resistance. Sensitivity and specificity for detecting resistance to clarithromycin was 100% and those to levofloxacin were 93% and 92%, respectively. The test system has been tested in real clinical practice on 112 H. pylori-positive patients who had not previously received proton pump inhibitors (PPIs) or antibacterial drugs. Mutations indicating resistance to clarithromycin were found in 27 (24%) samples and those indicating resistance to levofloxacin were found in 26 (23%) samples. Double resistance was observed in 16 (14%) samples. The most common mutations leading to clarithromycin resistance were 2143G and 2142G and to levofloxacin resistance-261A and 271A in the gyrA gene, which account for 69% of all identified genetic determinants in levofloxacin-resistant bacteria. Thus, a personalized approach to the selection of H. pylori eradication therapy based on the detection of bacterial resistance before prescribing first-line therapy could help to avoid the prescription of ineffective H. pylori eradication therapies and, overall, contribute to the control of antibiotic resistance of H. pylori.
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Affiliation(s)
- Natalia Bodunova
- A.S. Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia; (V.P.); (I.B.); (K.R.); (K.N.); (M.C.); (E.P.); (G.P.); (E.C.); (D.B.)
| | - Larisa Tsapkova
- A.S. Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia; (V.P.); (I.B.); (K.R.); (K.N.); (M.C.); (E.P.); (G.P.); (E.C.); (D.B.)
| | - Vera Polyakova
- A.S. Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia; (V.P.); (I.B.); (K.R.); (K.N.); (M.C.); (E.P.); (G.P.); (E.C.); (D.B.)
| | - Irina Baratova
- A.S. Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia; (V.P.); (I.B.); (K.R.); (K.N.); (M.C.); (E.P.); (G.P.); (E.C.); (D.B.)
| | - Konstantin Rumyantsev
- A.S. Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia; (V.P.); (I.B.); (K.R.); (K.N.); (M.C.); (E.P.); (G.P.); (E.C.); (D.B.)
| | - Natalia Dekhnich
- Department of Faculty Therapy, Smolensk State Medical University of the Ministry of Health of Russia, 214019 Smolensk, Russia;
| | - Karina Nikolskaya
- A.S. Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia; (V.P.); (I.B.); (K.R.); (K.N.); (M.C.); (E.P.); (G.P.); (E.C.); (D.B.)
| | - Margarita Chebotareva
- A.S. Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia; (V.P.); (I.B.); (K.R.); (K.N.); (M.C.); (E.P.); (G.P.); (E.C.); (D.B.)
| | - Irina Voynovan
- A.S. Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia; (V.P.); (I.B.); (K.R.); (K.N.); (M.C.); (E.P.); (G.P.); (E.C.); (D.B.)
| | - Elena Parfenchikova
- A.S. Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia; (V.P.); (I.B.); (K.R.); (K.N.); (M.C.); (E.P.); (G.P.); (E.C.); (D.B.)
| | - Galina Pronina
- A.S. Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia; (V.P.); (I.B.); (K.R.); (K.N.); (M.C.); (E.P.); (G.P.); (E.C.); (D.B.)
| | - Ekaterina Chernikova
- A.S. Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia; (V.P.); (I.B.); (K.R.); (K.N.); (M.C.); (E.P.); (G.P.); (E.C.); (D.B.)
| | - Dmitry Bordin
- A.S. Loginov Moscow Clinical Scientific Center, 111123 Moscow, Russia; (V.P.); (I.B.); (K.R.); (K.N.); (M.C.); (E.P.); (G.P.); (E.C.); (D.B.)
- Department of Propaedeutics of Internal Diseases and Gastroenterology of the Faculty of Medicine, Russian University of Medicine, 127473 Moscow, Russia
- Department of Family Medicine and General Medical Practice, Tver State Medical University, 170100 Tver, Russia
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Jeong S, Singh H, Jung JH, Jung KW, Ryu S, Lim S. Comparative genomics of Deinococcus radiodurans: unveiling genetic discrepancies between ATCC 13939K and BAA-816 strains. Front Microbiol 2024; 15:1410024. [PMID: 38962131 PMCID: PMC11219805 DOI: 10.3389/fmicb.2024.1410024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 06/04/2024] [Indexed: 07/05/2024] Open
Abstract
The Deinococcus genus is renowned for its remarkable resilience against environmental stresses, including ionizing radiation, desiccation, and oxidative damage. This resilience is attributed to its sophisticated DNA repair mechanisms and robust defense systems, enabling it to recover from extensive damage and thrive under extreme conditions. Central to Deinococcus research, the D. radiodurans strains ATCC BAA-816 and ATCC 13939 facilitate extensive studies into this remarkably resilient genus. This study focused on delineating genetic discrepancies between these strains by sequencing our laboratory's ATCC 13939 specimen (ATCC 13939K) and juxtaposing it with ATCC BAA-816. We uncovered 436 DNA sequence differences within ATCC 13939K, including 100 single nucleotide variations, 278 insertions, and 58 deletions, which could induce frameshifts altering protein-coding genes. Gene annotation revisions accounting for gene fusions and the reconciliation of gene lengths uncovered novel protein-coding genes and refined the functional categorizations of established ones. Additionally, the analysis pointed out genome structural variations due to insertion sequence (IS) elements, underscoring the D. radiodurans genome's plasticity. Notably, ATCC 13939K exhibited a loss of six ISDra2 elements relative to BAA-816, restoring genes fragmented by ISDra2, such as those encoding for α/β hydrolase and serine protease, and revealing new open reading frames, including genes imperative for acetoin decomposition. This comparative genomic study offers vital insights into the metabolic capabilities and resilience strategies of D. radiodurans.
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Affiliation(s)
- Soyoung Jeong
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Harinder Singh
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS Deemed to be University, Mumbai, India
| | - Jong-Hyun Jung
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Kwang-Woo Jung
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Sangyong Lim
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
- Department of Radiation Science, University of Science and Technology, Daejeon, Republic of Korea
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Leunda-Esnaola A, Bunin E, Arrufat P, Pearman PB, Kaberdin VR. Harnessing the intragenomic variability of rRNA operons to improve differentiation of Vibrio species. Sci Rep 2024; 14:9908. [PMID: 38688963 PMCID: PMC11061105 DOI: 10.1038/s41598-024-60505-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 04/24/2024] [Indexed: 05/02/2024] Open
Abstract
Although the 16S rRNA gene is frequently used as a phylogenetic marker in analysis of environmental DNA, this marker often fails to distinguish closely related species, including those in the genus Vibrio. Here, we investigate whether inclusion and analysis of 23S rRNA sequence can help overcome the intrinsic weaknesses of 16S rRNA analyses for the differentiation of Vibrio species. We construct a maximum likelihood 16S rRNA gene tree to assess the use of this gene to identify clades of Vibrio species. Within the 16S rRNA tree, we identify the putative informative bases responsible for polyphyly, and demonstrate the association of these positions with tree topology. We demonstrate that concatenation of 16S and 23S rRNA genes increases the number of informative nucleotide positions, thereby overcoming ambiguities in 16S rRNA-based phylogenetic reconstructions. Finally, we experimentally demonstrate that this approach considerably improves the differentiation and identification of Vibrio species in environmental samples.
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Affiliation(s)
- Amaia Leunda-Esnaola
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHU, 48940, Leioa, Spain
- Research Centre for Experimental Marine Biology and Biotechnology (Plentzia Marine Station, PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain
| | - Evgeni Bunin
- Research Centre for Experimental Marine Biology and Biotechnology (Plentzia Marine Station, PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain
- CBET Research Group, Department of Zoology and Animal Cell Biology, University of the Basque Country (UPV/EHU), Leioa, Basque Country, Spain
| | - Pablo Arrufat
- Department of Plant Biology and Ecology, Faculty of Sciences and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Peter B Pearman
- Department of Plant Biology and Ecology, Faculty of Sciences and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain.
- IKERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, 48013, Bilbao, Spain.
- BC3 Basque Center for Climate Change, Scientific Campus of the University of the Basque Country, 48940, Leioa, Spain.
| | - Vladimir R Kaberdin
- Department of Immunology, Microbiology and Parasitology, University of the Basque Country UPV/EHU, 48940, Leioa, Spain.
- Research Centre for Experimental Marine Biology and Biotechnology (Plentzia Marine Station, PiE-UPV/EHU), University of the Basque Country (UPV/EHU), Plentzia, Basque Country, Spain.
- IKERBASQUE, Basque Foundation for Science, Maria Diaz de Haro 3, 48013, Bilbao, Spain.
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Petrone JR, Rios Glusberger P, George CD, Milletich PL, Ahrens AP, Roesch LFW, Triplett EW. RESCUE: a validated Nanopore pipeline to classify bacteria through long-read, 16S-ITS-23S rRNA sequencing. Front Microbiol 2023; 14:1201064. [PMID: 37547696 PMCID: PMC10402275 DOI: 10.3389/fmicb.2023.1201064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/03/2023] [Indexed: 08/08/2023] Open
Abstract
Despite the advent of third-generation sequencing technologies, modern bacterial ecology studies still use Illumina to sequence small (~400 bp) hypervariable regions of the 16S rRNA SSU for phylogenetic classification. By sequencing a larger region of the rRNA gene operons, the limitations and biases of sequencing small portions can be removed, allowing for more accurate classification with deeper taxonomic resolution. With Nanopore sequencing now providing raw simplex reads with quality scores above Q20 using the kit 12 chemistry, the ease, cost, and portability of Nanopore play a leading role in performing differential bacterial abundance analysis. Sequencing the near-entire rrn operon of bacteria and archaea enables the use of the universally conserved operon holding evolutionary polymorphisms for taxonomic resolution. Here, a reproducible and validated pipeline was developed, RRN-operon Enabled Species-level Classification Using EMU (RESCUE), to facilitate the sequencing of bacterial rrn operons and to support import into phyloseq. Benchmarking RESCUE showed that fully processed reads are now parallel or exceed the quality of Sanger, with median quality scores of approximately Q20+, using the R10.4 and Guppy SUP basecalling. The pipeline was validated through two complex mock samples, the use of multiple sample types, with actual Illumina data, and across four databases. RESCUE sequencing is shown to drastically improve classification to the species level for most taxa and resolves erroneous taxa caused by using short reads such as Illumina.
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Trabelsi I, Soltane R, Nejma MB, Albogami BM, Nour M. Genetic variability of the helix 54 of the 23S rDNA and its use as a molecular target for identification of species within the viridans group streptococci (VGS). INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 103:105321. [PMID: 35753621 DOI: 10.1016/j.meegid.2022.105321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 06/15/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
The aim of the present study is to establish a method, based on sequence analysis of the helix 54 of 23S rRNA gene, to identify clinical relevant strains belonging to viridans group streptococci (VGS). A set of 25 randomly selected clinical isolates of alpha-hemolytic streptococci from upper respiratory tract were characterized by the routine phenotypic methods (API 20 Strep test). Molecular characterization was assessed by genotypic analysis of the nucleotide sequence of the helix 54 of 23S rRNA and Intergenic spacer region 16S23S. Partial sequencing of the gdh gene was used on 10 strains of mitis group. Sequence variations of the helix 54 allowed the identification of strains to group level and even to species level for certain strains within sanguinis and anginosus groups. Infact, species identification was ambiguous for some strains belonged to the salivarius group (of VGS16 to VGS20) and the mitis group (of VGS1 to VGS14). These results are almost similar to those obtained by sequencing the 16S23S intergenic region. Thus, we use the gdh gene sequencing for the identification of strains, not recognized, within the mitis group. The results generated herein indicate that no single methodology can be used to provide an accurate identification to the species level of all VGS, although nucleotide sequence analysis of the helix 54 of 23S rRNA gene proved to be a reliable method for the identification of VGS to the group level and even to the species level within sanguinis and anginosus groups.
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Affiliation(s)
- Ines Trabelsi
- University of Monastir, Higher Institute of Biotechnology of Monastir, Bioresources: Integrative Biology & Valuation "BIOLIVAL", Avenue Taher Hadded, (BP 74), 5000 Monastir, Tunisia.
| | - Raya Soltane
- Departement of Basic Sciences, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia; Departement of Biology, Faculty of sciences, Tunis El Manar University, Tunis 1068, Tunisia.
| | - Mouna Ben Nejma
- University of Monastir, Higher Institute of Biotechnology of Monastir, Bioresources: Integrative Biology & Valuation "BIOLIVAL", Avenue Taher Hadded, (BP 74), 5000 Monastir, Tunisia
| | - Bander M Albogami
- Taif University, College of Science, Laboratory of Applied and Molecular Microbiology, Saudi Arabia
| | - Mohamed Nour
- University of Monastir, Higher Institute of Biotechnology of Monastir, Bioresources: Integrative Biology & Valuation "BIOLIVAL", Avenue Taher Hadded, (BP 74), 5000 Monastir, Tunisia
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Carvalho TLG, Rosman AC, Grativol C, de M. Nogueira E, Baldani JI, Hemerly AS. Sugarcane Genotypes with Contrasting Biological Nitrogen Fixation Efficiencies Differentially Modulate Nitrogen Metabolism, Auxin Signaling, and Microorganism Perception Pathways. PLANTS (BASEL, SWITZERLAND) 2022; 11:1971. [PMID: 35956449 PMCID: PMC9370643 DOI: 10.3390/plants11151971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 06/15/2023]
Abstract
Sugarcane is an economically important crop that is used for the production of fuel ethanol. Diazotrophic bacteria have been isolated from sugarcane tissues, without causing visible plant anatomical changes or disease symptoms. These bacteria can be beneficial to the plant by promoting root growth and an increase in plant yield. Different rates of Biological Nitrogen Fixation (BNF) were observed in different genotypes. The aim of this work was to conduct a comprehensive molecular and physiological analysis of two model genotypes for contrasting BNF efficiency in order to unravel plant genes that are differentially regulated during a natural association with diazotrophic bacteria. A next-generation sequencing of RNA samples from the genotypes SP70-1143 (high-BNF) and Chunee (low-BNF) was performed. A differential transcriptome analysis showed that several pathways were differentially regulated among the two BNF-contrasting genotypes, including nitrogen metabolism, hormone regulation and bacteria recognition. Physiological analyses, such as nitrogenase and GS activity quantification, bacterial colonization, auxin response and root architecture evaluation, supported the transcriptome expression analyses. The differences observed between the genotypes may explain, at least in part, the differences in BNF contributions. Some of the identified genes might be involved in key regulatory processes for a beneficial association and could be further used as tools for obtaining more efficient BNF genotypes.
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Affiliation(s)
- Thais Louise G. Carvalho
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, RJ, Brazil; (T.L.G.C.); (A.C.R.); (C.G.); (E.d.M.N.)
| | - Aline C. Rosman
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, RJ, Brazil; (T.L.G.C.); (A.C.R.); (C.G.); (E.d.M.N.)
| | - Clícia Grativol
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, RJ, Brazil; (T.L.G.C.); (A.C.R.); (C.G.); (E.d.M.N.)
- Laboratório de Química e Funções de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense, Campos dos Goytacazes 28015-622, RJ, Brazil
| | - Eduardo de M. Nogueira
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, RJ, Brazil; (T.L.G.C.); (A.C.R.); (C.G.); (E.d.M.N.)
| | - José Ivo Baldani
- Laboratório de Genética e Bioquímica, Centro Nacional de Pesquisa de Agrobiologia, Embrapa Agrobiologia, Rio de Janeiro 23897-970, RJ, Brazil;
| | - Adriana S. Hemerly
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, RJ, Brazil; (T.L.G.C.); (A.C.R.); (C.G.); (E.d.M.N.)
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New Insights into the Taxonomy of Bacteria in the Genomic Era and a Case Study with Rhizobia. Int J Microbiol 2022; 2022:4623713. [PMID: 35637770 PMCID: PMC9148247 DOI: 10.1155/2022/4623713] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/09/2022] [Indexed: 12/15/2022] Open
Abstract
Since early studies, the history of prokaryotes taxonomy has dealt with many changes driven by the development of new and more robust technologies. As a result, the number of new taxa descriptions is exponentially increasing, while an increasing number of others has been subject of reclassification, demanding from the taxonomists more effort to maintain an organized hierarchical system. However, expectations are that the taxonomy of prokaryotes will acquire a more stable status with the genomic era. Other analyses may continue to be necessary to determine microbial features, but the use of genomic data might be sufficient to provide reliable taxa delineation, helping taxonomy to reach the goal of correct classification and identification. Here we describe the evolution of prokaryotes' taxonomy until the genomic era, emphasizing bacteria and taking as an example the history of rhizobia taxonomy. This example was chosen because of the importance of the symbiotic nitrogen fixation of legumes with rhizobia to the nitrogen input to both natural ecosystems and agricultural crops. This case study reports the technological advances and the methodologies used to classify and identify bacterial species and indicates the actual rules required for an accurate description of new taxa.
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Silva DP, Epstein HE, Vega Thurber RL. Best practices for generating and analyzing 16S rRNA amplicon data to track coral microbiome dynamics. Front Microbiol 2022; 13:1007877. [PMID: 36891260 PMCID: PMC9987214 DOI: 10.3389/fmicb.2022.1007877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 12/30/2022] [Indexed: 02/22/2023] Open
Abstract
Over the past two decades, researchers have searched for methods to better understand the relationship between coral hosts and their microbiomes. Data on how coral-associated bacteria are involved in their host's responses to stressors that cause bleaching, disease, and other deleterious effects can elucidate how they may mediate, ameliorate, and exacerbate interactions between the coral and the surrounding environment. At the same time tracking coral bacteria dynamics can reveal previously undiscovered mechanisms of coral resilience, acclimatization, and evolutionary adaptation. Although modern techniques have reduced the cost of conducting high-throughput sequencing of coral microbes, to explore the composition, function, and dynamics of coral-associated bacteria, it is necessary that the entire procedure, from collection to sequencing, and subsequent analysis be carried out in an objective and effective way. Corals represent a difficult host with which to work, and unique steps in the process of microbiome assessment are necessary to avoid inaccuracies or unusable data in microbiome libraries, such as off-target amplification of host sequences. Here, we review, compare and contrast, and recommend methods for sample collection, preservation, and processing (e.g., DNA extraction) pipelines to best generate 16S amplicon libraries with the aim of tracking coral microbiome dynamics. We also discuss some basic quality assurance and general bioinformatic methods to analyze the diversity, composition, and taxonomic profiles of the microbiomes. This review aims to be a generalizable guide for researchers interested in starting and modifying the molecular biology aspects of coral microbiome research, highlighting best practices and tricks of the trade.
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Affiliation(s)
- Denise P Silva
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Hannah E Epstein
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
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Wen JD, Kuo ST, Chou HHD. The diversity of Shine-Dalgarno sequences sheds light on the evolution of translation initiation. RNA Biol 2020; 18:1489-1500. [PMID: 33349119 DOI: 10.1080/15476286.2020.1861406] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Shine-Dalgarno (SD) sequences, the core element of prokaryotic ribosome-binding sites, facilitate mRNA translation by base-pair interaction with the anti-SD (aSD) sequence of 16S rRNA. In contrast to this paradigm, an inspection of thousands of prokaryotic species unravels tremendous SD sequence diversity both within and between genomes, whereas aSD sequences remain largely static. The pattern has led many to suggest unidentified mechanisms for translation initiation. Here we review known translation-initiation pathways in prokaryotes. Moreover, we seek to understand the cause and consequence of SD diversity through surveying recent advances in biochemistry, genomics, and high-throughput genetics. These findings collectively show: (1) SD:aSD base pairing is beneficial but nonessential to translation initiation. (2) The 5' untranslated region of mRNA evolves dynamically and correlates with organismal phylogeny and ecological niches. (3) Ribosomes have evolved distinct usage of translation-initiation pathways in different species. We propose a model portraying the SD diversity shaped by optimization of gene expression, adaptation to environments and growth demands, and the species-specific prerequisite of ribosomes to initiate translation. The model highlights the coevolution of ribosomes and mRNA features, leading to functional customization of the translation apparatus in each organism.
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Affiliation(s)
- Jin-Der Wen
- Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan.,Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
| | - Syue-Ting Kuo
- Department of Life Science, National Taiwan University, Taipei, Taiwan
| | - Hsin-Hung David Chou
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan.,Department of Life Science, National Taiwan University, Taipei, Taiwan
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Djemiel C, Plassard D, Terrat S, Crouzet O, Sauze J, Mondy S, Nowak V, Wingate L, Ogée J, Maron PA. µgreen-db: a reference database for the 23S rRNA gene of eukaryotic plastids and cyanobacteria. Sci Rep 2020; 10:5915. [PMID: 32246067 PMCID: PMC7125122 DOI: 10.1038/s41598-020-62555-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 03/09/2020] [Indexed: 11/29/2022] Open
Abstract
Studying the ecology of photosynthetic microeukaryotes and prokaryotic cyanobacterial communities requires molecular tools to complement morphological observations. These tools rely on specific genetic markers and require the development of specialised databases to achieve taxonomic assignment. We set up a reference database, called µgreen-db, for the 23S rRNA gene. The sequences were retrieved from generalist (NCBI, SILVA) or Comparative RNA Web (CRW) databases, in addition to a more original approach involving recursive BLAST searches to obtain the best possible sequence recovery. At present, µgreen-db includes 2,326 23S rRNA sequences belonging to both eukaryotes and prokaryotes encompassing 442 unique genera and 736 species of photosynthetic microeukaryotes, cyanobacteria and non-vascular land plants based on the NCBI and AlgaeBase taxonomy. When PR2/SILVA taxonomy is used instead, µgreen-db contains 2,217 sequences (399 unique genera and 696 unique species). Using µgreen-db, we were able to assign 96% of the sequences of the V domain of the 23S rRNA gene obtained by metabarcoding after amplification from soil DNA at the genus level, highlighting good coverage of the database. µgreen-db is accessible at http://microgreen-23sdatabase.ea.inra.fr.
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Affiliation(s)
- Christophe Djemiel
- Agroécologie, AgroSup Dijon, INRA, University Bourgogne Franche-Comté, Dijon, France
| | | | - Sébastien Terrat
- Agroécologie, AgroSup Dijon, INRA, University Bourgogne Franche-Comté, Dijon, France
| | - Olivier Crouzet
- Univ. Paris Saclay, AgroParisTech, UMR ECOSYS, INRA, F-78206, Versailles, France
| | - Joana Sauze
- INRA, Bordeaux Science Agro, UMR 1391 ISPA, 33140, Villenave d'Ornon, France
| | - Samuel Mondy
- Agroécologie, AgroSup Dijon, INRA, University Bourgogne Franche-Comté, Dijon, France
| | - Virginie Nowak
- Agroécologie, AgroSup Dijon, INRA, University Bourgogne Franche-Comté, Dijon, France
| | - Lisa Wingate
- INRA, Bordeaux Science Agro, UMR 1391 ISPA, 33140, Villenave d'Ornon, France
| | - Jérôme Ogée
- INRA, Bordeaux Science Agro, UMR 1391 ISPA, 33140, Villenave d'Ornon, France
| | - Pierre-Alain Maron
- Agroécologie, AgroSup Dijon, INRA, University Bourgogne Franche-Comté, Dijon, France.
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11
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de Oliveira Martins L, Page AJ, Mather AE, Charles IG. Taxonomic resolution of the ribosomal RNA operon in bacteria: implications for its use with long-read sequencing. NAR Genom Bioinform 2019; 2:lqz016. [PMID: 33575567 PMCID: PMC7671355 DOI: 10.1093/nargab/lqz016] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 10/03/2019] [Accepted: 10/24/2019] [Indexed: 01/02/2023] Open
Abstract
DNA barcoding through the use of amplified regions of the ribosomal operon, such as the 16S gene, is a routine method to gain an overview of the microbial taxonomic diversity within a sample without the need to isolate and culture the microbes present. However, bacterial cells usually have multiple copies of this ribosomal operon, and choosing the 'wrong' copy could provide a misleading species classification. While this presents less of a problem for well-characterized organisms with large sequence databases to interrogate, it is a significant challenge for lesser known organisms with unknown copy number and diversity. Using the entire length of the ribosomal operon, which encompasses the 16S, 23S, 5S and internal transcribed spacer regions, should provide greater taxonomic resolution but has not been well explored. Here, we use publicly available reference genomes and explore the theoretical boundaries when using concatenated genes and the full-length ribosomal operons, which has been made possible by the development and uptake of long-read sequencing technologies. We quantify the issues of both copy choice and operon length in a phylogenetic context to demonstrate that longer regions improve the phylogenetic signal while maintaining taxonomic accuracy.
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Affiliation(s)
| | - Andrew J Page
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Alison E Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK.,Faculty of Medicine and Health Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Ian G Charles
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK.,Faculty of Medicine and Health Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
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12
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Unlinked rRNA genes are widespread among bacteria and archaea. ISME JOURNAL 2019; 14:597-608. [PMID: 31712737 DOI: 10.1038/s41396-019-0552-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/23/2019] [Accepted: 10/29/2019] [Indexed: 02/06/2023]
Abstract
Ribosomes are essential to cellular life and the genes for their RNA components are the most conserved and transcribed genes in bacteria and archaea. Ribosomal RNA genes are typically organized into a single operon, an arrangement thought to facilitate gene regulation. In reality, some bacteria and archaea do not share this canonical rRNA arrangement-their 16S and 23S rRNA genes are separated across the genome and referred to as "unlinked". This rearrangement has previously been treated as an anomaly or a byproduct of genome degradation in intracellular bacteria. Here, we leverage complete genome and long-read metagenomic data to show that unlinked 16S and 23S rRNA genes are more common than previously thought. Unlinked rRNA genes occur in many phyla, most significantly within Deinococcus-Thermus, Chloroflexi, and Planctomycetes, and occur in differential frequencies across natural environments. We found that up to 41% of rRNA genes in soil were unlinked, in contrast to the human gut, where all sequenced rRNA genes were linked. The frequency of unlinked rRNA genes may reflect meaningful life history traits, as they tend to be associated with a mix of slow-growing free-living species and intracellular species. We speculate that unlinked rRNA genes may confer selective advantages in some environments, though the specific nature of these advantages remains undetermined and worthy of further investigation. More generally, the prevalence of unlinked rRNA genes in poorly-studied taxa serves as a reminder that paradigms derived from model organisms do not necessarily extend to the broader diversity of bacteria and archaea.
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13
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Chiu JKH, Dillon TS, Chen YPP. Large-scale frequent stem pattern mining in RNA families. J Theor Biol 2018; 455:131-139. [PMID: 30036526 DOI: 10.1016/j.jtbi.2018.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 07/09/2018] [Accepted: 07/11/2018] [Indexed: 11/19/2022]
Abstract
Functionally similar non-coding RNAs are expected to be similar in certain regions of their secondary structures. These similar regions are called common structure motifs, and are structurally conserved throughout evolution to maintain their functional roles. Common structure motif identification is one of the critical tasks in RNA secondary structure analysis. Nevertheless, current approaches suffer several limitations, and/or do not scale with both structure size and the number of input secondary structures. In this work, we present a method to transform the conserved base pair stems into transaction items and apply frequent itemset mining to identify common structure motifs existing in a majority of input structures. Our experimental results on telomerase and ribosomal RNA secondary structures report frequent stem patterns that are of biological significance. Moreover, the algorithms utilized in our method are scalable and frequent stem patterns can be identified efficiently among many large structures.
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Affiliation(s)
- Jimmy Ka Ho Chiu
- Department of Computer Science and Information, Technology, La Trobe University, Melbourne VIC 3086, Australia.
| | - Tharam S Dillon
- Department of Computer Science and Information, Technology, La Trobe University, Melbourne VIC 3086, Australia.
| | - Yi-Ping Phoebe Chen
- Department of Computer Science and Information, Technology, La Trobe University, Melbourne VIC 3086, Australia.
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14
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Borsetti F, Dal Piaz F, D'Alessio F, Stefan A, Brandimarti R, Sarkar A, Datta A, Montón Silva A, den Blaauwen T, Alberto M, Spisni E, Hochkoeppler A. Manganese is a Deinococcus radiodurans growth limiting factor in rich culture medium. MICROBIOLOGY-SGM 2018; 164:1266-1275. [PMID: 30052171 DOI: 10.1099/mic.0.000698] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
To understand the effects triggered by Mn2+ on Deinococcus radiodurans, the proteome patterns associated with different growth phases were investigated. In particular, under physiological conditions we tested the growth rate and the biomass yield of D. radiodurans cultured in rich medium supplemented or not with MnCl2. The addition of 2.5-5.0 µM MnCl2 to the medium neither altered the growth rate nor the lag phase, but significantly increased the biomass yield. When higher MnCl2 concentrations were used (10-250 µM), biomass was again found to be positively affected, although we did observe a concentration-dependent lag phase increase. The in vivo concentration of Mn2+ was determined in cells grown in rich medium supplemented or not with 5 µM MnCl2. By atomic absorption spectroscopy, we estimated 0.2 and 0.75 mM Mn2+ concentrations in cells grown in control and enriched medium, respectively. We qualitatively confirmed this observation using a fluorescent turn-on sensor designed to selectively detect Mn2+in vivo. Finally, we investigated the proteome composition of cells grown for 15 or 19 h in medium to which 5 µM MnCl2 was added, and we compared these proteomes with those of cells grown in the control medium. The presence of 5 µM MnCl2 in the culture medium was found to alter the pI of some proteins, suggesting that manganese affects post-translational modifications. Further, we observed that Mn2+ represses enzymes linked to nucleotide recycling, and triggers overexpression of proteases and enzymes linked to the metabolism of amino acids.
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Affiliation(s)
- Francesca Borsetti
- 1Department of Biology, Geology and Environmental Sciences, University of Bologna, Via Selmi 3, 40125 Bologna, Italy
| | - Fabrizio Dal Piaz
- 2Department of Medicine, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano SA, Italy
| | - Federico D'Alessio
- 3Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136 Bologna, Italy
| | - Alessandra Stefan
- 3Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136 Bologna, Italy.,4CSGI, University of Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino FI, Italy
| | - Renato Brandimarti
- 3Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136 Bologna, Italy
| | - Anindita Sarkar
- 5Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Ankona Datta
- 5Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Alejandro Montón Silva
- 6Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Tanneke den Blaauwen
- 6Bacterial Cell Biology and Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Mucchi Alberto
- 7Department of Industrial Chemistry "Toson Montanari", University of Bologna, Viale Risorgimento 4, 40136 Bologna, Italy
| | - Enzo Spisni
- 1Department of Biology, Geology and Environmental Sciences, University of Bologna, Via Selmi 3, 40125 Bologna, Italy
| | - Alejandro Hochkoeppler
- 4CSGI, University of Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino FI, Italy.,3Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136 Bologna, Italy
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15
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Franke JD, Blomberg WR, Todd RT, Thomas RW, Selmecki AM. Assembly of a complete genome sequence for Gemmata obscuriglobus reveals a novel prokaryotic rRNA operon gene architecture. Antonie van Leeuwenhoek 2018; 111:2095-2105. [DOI: 10.1007/s10482-018-1102-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 05/16/2018] [Indexed: 11/28/2022]
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16
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Community-like genome in single cells of the sulfur bacterium Achromatium oxaliferum. Nat Commun 2017; 8:455. [PMID: 28878209 PMCID: PMC5587575 DOI: 10.1038/s41467-017-00342-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 06/22/2017] [Indexed: 01/01/2023] Open
Abstract
Polyploid bacteria are common, but the genetic and functional diversity resulting from polyploidy is unknown. Here we use single-cell genomics, metagenomics, single-cell amplicon sequencing, and fluorescence in situ hybridization, to show that individual cells of Achromatium oxaliferum, the world’s biggest known freshwater bacterium, harbor genetic diversity typical of whole bacterial communities. The cells contain tens of transposable elements, which likely cause the unprecedented diversity that we observe in the sequence and synteny of genes. Given the high within-cell diversity of the usually conserved 16S ribosomal RNA gene, we suggest that gene conversion occurs in multiple, separated genomic hotspots. The ribosomal RNA distribution inside the cells hints to spatially differential gene expression. We also suggest that intracellular gene transfer may lead to extensive gene reshuffling and increased diversity. The cells of Achromatium bacteria are remarkably large and contain multiple chromosome copies. Here, Ionescu et al. show that chromosome copies within individual cells display high diversity, similar to that of bacterial communities, and contain tens of transposable elements.
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17
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Khalid SAL, Omar AH, Abdel FMEZ. Phylogenetic analysis of 23S rRNA gene sequences of some Rhizobium leguminosarum isolates and their tolerance to drought. ACTA ACUST UNITED AC 2016. [DOI: 10.5897/ajb2016.15450] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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18
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Comparative genome analysis of Lysinibacillus B1-CDA, a bacterium that accumulates arsenics. Genomics 2015; 106:384-92. [DOI: 10.1016/j.ygeno.2015.09.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 07/29/2015] [Accepted: 09/15/2015] [Indexed: 11/18/2022]
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19
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Sarshar M, Shahrokhi N, Ranjbar R, Mammina C. Simultaneous Detection of Escherichia coli, Salmonella enterica, Listeria monocytogenes and Bacillus cereus by Oligonucleotide Microarray. INTERNATIONAL JOURNAL OF ENTERIC PATHOGENS 2015. [DOI: 10.17795/ijep30187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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20
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Šmajs D, Paštěková L, Grillová L. Macrolide Resistance in the Syphilis Spirochete, Treponema pallidum ssp. pallidum: Can We Also Expect Macrolide-Resistant Yaws Strains? Am J Trop Med Hyg 2015; 93:678-83. [PMID: 26217043 PMCID: PMC4596581 DOI: 10.4269/ajtmh.15-0316] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 06/05/2015] [Indexed: 11/07/2022] Open
Abstract
Treponema pallidum ssp. pallidum (TPA) causes over 10 million new cases of syphilis worldwide whereas T. pallidum ssp. pertenue (TPE), the causative agent of yaws, affects about 2.5 million people. Although penicillin remains the drug of choice in the treatment of syphilis, in penicillin-allergic patients, macrolides have been used in this indication since the 1950s. Failures of macrolides in syphilis treatment have been well documented in the literature and since 2000, there has been a dramatic increase in a number of clinical samples with macrolide-resistant TPA. Scarce data regarding the genetics of macrolide-resistant mutations in TPA suggest that although macrolide-resistance mutations have emerged independently several times, the increase in the proportion of TPA strains resistant to macrolides is mainly due to the spread of resistant strains, especially in developed countries. The emergence of macrolide resistance in TPA appears to require a two-step process including either A2058G or A2059G mutation in one copy of the 23S rRNA gene and a subsequent gene conversion unification of both rRNA genes. Given the enormous genetic similarity that was recently revealed between TPA and TPE strains, there is a low but reasonable risk of emergence and spread of macrolide-resistant yaws strains following azithromycin treatment.
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Affiliation(s)
- David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lenka Paštěková
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Linda Grillová
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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21
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Ecotype diversity and conversion in Photobacterium profundum strains. PLoS One 2014; 9:e96953. [PMID: 24824441 PMCID: PMC4019646 DOI: 10.1371/journal.pone.0096953] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 04/12/2014] [Indexed: 12/03/2022] Open
Abstract
Photobacterium profundum is a cosmopolitan marine bacterium capable of growth at low temperature and high hydrostatic pressure. Multiple strains of P. profundum have been isolated from different depths of the ocean and display remarkable differences in their physiological responses to pressure. The genome sequence of the deep-sea piezopsychrophilic strain Photobacterium profundum SS9 has provided some clues regarding the genetic features required for growth in the deep sea. The sequenced genome of Photobacterium profundum strain 3TCK, a non-piezophilic strain isolated from a shallow-water environment, is now available and its analysis expands the identification of unique genomic features that correlate to environmental differences and define the Hutchinsonian niche of each strain. These differences range from variations in gene content to specific gene sequences under positive selection. Genome plasticity between Photobacterium bathytypes was investigated when strain 3TCK-specific genes involved in photorepair were introduced to SS9, demonstrating that horizontal gene transfer can provide a mechanism for rapid colonisation of new environments.
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22
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Yadegar A, Alebouyeh M, Lawson AJ, Mirzaei T, Nazemalhosseini Mojarad E, Zali MR. Differentiation of non-pylori Helicobacter species based on PCR-restriction fragment length polymorphism of the 23S rRNA gene. World J Microbiol Biotechnol 2014; 30:1909-17. [PMID: 24493015 DOI: 10.1007/s11274-014-1615-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 01/27/2014] [Indexed: 01/21/2023]
Abstract
Phenotypic identification of non-pylori Helicobacter species has always been problematic and time-consuming in comparison with many other bacteria. We developed a rapid two-step identification assay based on PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of the 23S rRNA gene for differentiating between non-pylori Helicobacter species. A new genus-specific primer pair based on all available complete and partial 23S rRNA sequences of Helicobacter species was designed. In silico restriction analysis of variable regions of the 23S rRNA gene suggested SmaI and HindIII endonucleases would provide a good level of differentiation. Analysis of the obtained 23S rRNA RFLP patterns divided all Helicobacter study strains into three species groups (groups A-C) and 12 unique restriction patterns. Wolinella succinogenes also gave a unique pattern. Our proposed PCR-RFLP method was found to be as a valuable tool for routine identification of non-pylori Helicobacter species from human or animal samples.
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Affiliation(s)
- Abbas Yadegar
- Gastroenterology and Liver Diseases Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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23
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Tagawa M, Matsumoto K, Yokoyama N, Inokuma H. Prevalence and molecular analyses of hemotrophic Mycoplasma spp. (hemoplasmas) detected in sika deer (Cervus nippon yesoensis) in Japan. J Vet Med Sci 2013; 76:401-7. [PMID: 24270803 PMCID: PMC4013367 DOI: 10.1292/jvms.13-0486] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Hemotropic mycoplasmas (hemoplasmas) are cell-wall deficient, epierythrocytic
bacteria that cause infectious anemia in several mammalian species. The prevalence of
hemoplasma species was examined by screening and species-specific PCR using blood samples
collected from 51 sika deer in Hokkaido, Japan. Molecular analyses were performed for the
16S rRNA, 23S rRNA and RNase P RNA (rnpB) gene sequences. A total of
23/51 (45%) deer DNA samples were positive for hemoplasmas in the screening PCR. Using
species-specific PCR, 12 and 17 samples were positive for ‘Candidatus
Mycoplasma haemocervae’ and ‘Candidatus M. erythrocervae’, respectively.
Sequencing and phylogenetic trees of those three genes indicate that the
‘Candidatus M. haemocervae’ and ‘Candidatus M.
erythrocervae’ detected in Japanese deer are potentially different species from the
cervine hemoplasma found in deer from America and Brazil.
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Affiliation(s)
- Michihito Tagawa
- Department of Clinical Veterinary Medicine, Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, Hokkaido, 080-8555, Japan
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24
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Development of a broad-range 23S rDNA real-time PCR assay for the detection and quantification of pathogenic bacteria in human whole blood and plasma specimens. BIOMED RESEARCH INTERNATIONAL 2013; 2013:264651. [PMID: 23586027 PMCID: PMC3613074 DOI: 10.1155/2013/264651] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 01/15/2013] [Accepted: 01/29/2013] [Indexed: 01/02/2023]
Abstract
Molecular methods are important tools in the diagnosis of bloodstream bacterial infections, in particular in patients treated with antimicrobial therapy, due to their quick turn-around time. Here we describe a new broad-range real-time PCR targeting the 23S rDNA gene and capable to detect as low as 10 plasmid copies per reaction of targeted bacterial 23S rDNA gene. Two commercially available DNA extraction kits were evaluated to assess their efficiency for the extraction of plasma and whole blood samples spiked with different amount of either Staphylococcus aureus or Escherichia coli, in order to find the optimal extraction method to be used. Manual QIAmp extraction method with enzyme pre-treatment resulted the most sensitive for detection of bacterial load. Sensitivity of this novel assay ranged between 10 and 103 CFU per PCR reaction for E. coli and S. aureus in human whole blood samples depending on the extraction methods used. Analysis of plasma samples showed a 10- to 100-fold reduction of bacterial 23S rDNA in comparison to the corresponding whole blood specimens, thus indicating that whole blood is the preferential sample type to be used in this real-time PCR protocol. Our results thus show that the 23S rDNA gene represents an optimal target for bacteria quantification in human whole blood.
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25
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Čejková D, Zobaníková M, Pospíšilová P, Strouhal M, Mikalová L, Weinstock GM, Šmajs D. Structure of rrn operons in pathogenic non-cultivable treponemes: sequence but not genomic position of intergenic spacers correlates with classification of Treponema pallidum and Treponema paraluiscuniculi strains. J Med Microbiol 2012; 62:196-207. [PMID: 23082031 PMCID: PMC3755535 DOI: 10.1099/jmm.0.050658-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This study examined the sequences of the two rRNA (rrn) operons of pathogenic non-cultivable treponemes, comprising 11 strains of T. pallidum ssp. pallidum (TPA), five strains of T. pallidum ssp. pertenue (TPE), two strains of T. pallidum ssp. endemicum (TEN), a simian Fribourg-Blanc strain and a rabbit T. paraluiscuniculi (TPc) strain. PCR was used to determine the type of 16S–23S ribosomal intergenic spacers in the rrn operons from 30 clinical samples belonging to five different genotypes. When compared with the TPA strains, TPc Cuniculi A strain had a 17 bp deletion, and the TPE, TEN and Fribourg-Blanc isolates had a deletion of 33 bp. Other than these deletions, only 17 heterogeneous sites were found within the entire region (excluding the 16S–23S intergenic spacer region encoding tRNA-Ile or tRNA-Ala). The pattern of nucleotide changes in the rrn operons corresponded to the classification of treponemal strains, whilst two different rrn spacer patterns (Ile/Ala and Ala/Ile) appeared to be distributed randomly across species/subspecies classification, time and geographical source of the treponemal strains. It is suggested that the random distribution of tRNA genes is caused by reciprocal translocation between repetitive sequences mediated by a recBCD-like system.
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Affiliation(s)
- Darina Čejková
- The Genome Institute, Washington University in St Louis, 4444 Forest Park Avenue, St Louis, MO 63108, USA.,Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 62500 Brno, Czech Republic
| | - Marie Zobaníková
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 62500 Brno, Czech Republic
| | - Petra Pospíšilová
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 62500 Brno, Czech Republic
| | - Michal Strouhal
- The Genome Institute, Washington University in St Louis, 4444 Forest Park Avenue, St Louis, MO 63108, USA.,Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 62500 Brno, Czech Republic
| | - Lenka Mikalová
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 62500 Brno, Czech Republic
| | - George M Weinstock
- The Genome Institute, Washington University in St Louis, 4444 Forest Park Avenue, St Louis, MO 63108, USA
| | - David Šmajs
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5, Building A6, 62500 Brno, Czech Republic
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26
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Pei A, Li H, Oberdorf WE, Alekseyenko AV, Parsons T, Yang L, Gerz EA, Lee P, Xiang C, Nossa CW, Pei Z. Diversity of 5S rRNA genes within individual prokaryotic genomes. FEMS Microbiol Lett 2012; 335:11-8. [PMID: 22765222 DOI: 10.1111/j.1574-6968.2012.02632.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2012] [Revised: 06/14/2012] [Accepted: 06/30/2012] [Indexed: 11/28/2022] Open
Abstract
We examined intragenomic variation of paralogous 5S rRNA genes to evaluate the concept of ribosomal constraints. In a dataset containing 1161 genomes from 779 unique species, 96 species exhibited > 3% diversity. Twenty-seven species with > 10% diversity contained a total of 421 mismatches between all pairs of the most dissimilar copies of 5S rRNA genes. The large majority (401 of 421) of the diversified positions were conserved at the secondary structure level. The high diversity was associated with partial rRNA operon, split operon, or spacer length-related divergence. In total, these findings indicated that there are tight ribosomal constraints on paralogous 5S rRNA genes in a genome despite of the high degree of diversity at the primary structure level.
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Affiliation(s)
- Anna Pei
- New York University College of Arts and Science, New York, NY, USA
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27
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Steven B, McCann S, Ward NL. Pyrosequencing of plastid 23S rRNA genes reveals diverse and dynamic cyanobacterial and algal populations in two eutrophic lakes. FEMS Microbiol Ecol 2012; 82:607-15. [DOI: 10.1111/j.1574-6941.2012.01429.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2012] [Revised: 05/24/2012] [Accepted: 06/06/2012] [Indexed: 11/26/2022] Open
Affiliation(s)
- Blaire Steven
- Department of Molecular Biology; University of Wyoming; Laramie; WY; USA
| | - Sage McCann
- Department of Molecular Biology; University of Wyoming; Laramie; WY; USA
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28
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Yilmaz P, Kottmann R, Pruesse E, Quast C, Glöckner FO. Analysis of 23S rRNA genes in metagenomes – A case study from the Global Ocean Sampling Expedition. Syst Appl Microbiol 2011; 34:462-9. [DOI: 10.1016/j.syapm.2011.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 04/04/2011] [Accepted: 04/04/2011] [Indexed: 12/19/2022]
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29
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López-Ramírez V, Alcaraz LD, Moreno-Hagelsieb G, Olmedo-Álvarez G. Phylogenetic distribution and evolutionary history of bacterial DEAD-Box proteins. J Mol Evol 2011; 72:413-31. [PMID: 21437710 PMCID: PMC3093544 DOI: 10.1007/s00239-011-9441-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Accepted: 03/04/2011] [Indexed: 01/24/2023]
Abstract
DEAD-box proteins are found in all domains of life and participate in almost all cellular processes that involve RNA. The presence of DEAD and Helicase_C conserved domains distinguish these proteins. DEAD-box proteins exhibit RNA-dependent ATPase activity in vitro, and several also show RNA helicase activity. In this study, we analyzed the distribution and architecture of DEAD-box proteins among bacterial genomes to gain insight into the evolutionary pathways that have shaped their history. We identified 1,848 unique DEAD-box proteins from 563 bacterial genomes. Bacterial genomes can possess a single copy DEAD-box gene, or up to 12 copies of the gene, such as in Shewanella. The alignment of 1,208 sequences allowed us to perform a robust analysis of the hallmark motifs of DEAD-box proteins and determine the residues that occur at high frequency, some of which were previously overlooked. Bacterial DEAD-box proteins do not generally contain a conserved C-terminal domain, with the exception of some members that possess a DbpA RNA-binding domain (RBD). Phylogenetic analysis showed a separation of DbpA-RBD-containing and DbpA-RBD-lacking sequences and revealed a group of DEAD-box protein genes that expanded mainly in the Proteobacteria. Analysis of DEAD-box proteins from Firmicutes and γ-Proteobacteria, was used to deduce orthologous relationships of the well-studied DEAD-box proteins from Escherichia coli and Bacillus subtilis. These analyses suggest that DbpA-RBD is an ancestral domain that most likely emerged as a specialized domain of the RNA-dependent ATPases. Moreover, these data revealed numerous events of gene family expansion and reduction following speciation.
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Affiliation(s)
- Varinia López-Ramírez
- Departamento de Ingeniería Genética de Plantas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Irapuato, Km. 9.6 Libramiento Norte Carr. Irapuato-León CP, 36821 Irapuato, Guanajuato Mexico
| | - Luis D. Alcaraz
- Departamento de Ingeniería Genética de Plantas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Irapuato, Km. 9.6 Libramiento Norte Carr. Irapuato-León CP, 36821 Irapuato, Guanajuato Mexico
- Present Address: Department of Genomics and Health, Centro Superior de Investigación en Salud Pública, Avda. Cataluña 21, Valencia, Spain
| | - Gabriel Moreno-Hagelsieb
- Department of Biology, Wilfrid Laurier University, 75 University Ave. W., Waterloo, ON N2L 3C5 Canada
| | - Gabriela Olmedo-Álvarez
- Departamento de Ingeniería Genética de Plantas, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional Unidad Irapuato, Km. 9.6 Libramiento Norte Carr. Irapuato-León CP, 36821 Irapuato, Guanajuato Mexico
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Lange C, Zerulla K, Breuert S, Soppa J. Gene conversion results in the equalization of genome copies in the polyploid haloarchaeon Haloferax volcanii. Mol Microbiol 2011; 80:666-77. [PMID: 21338422 DOI: 10.1111/j.1365-2958.2011.07600.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Haloferax volcanii is highly polyploid and contains about 20 copies of the major chromosome. A heterozygous strain was constructed that contained two different types of genomes: the leuB locus contained either the wild-type leuB gene or a leuB:trpA gene introduced by gene replacement. As the trpA locus is devoid of the wild-type trpA gene, growth in the absence of both amino acids is only possible when both types of genomes are simultaneously present, exemplifying gene redundancy and the potential to form heterozygous cells as one possible evolutionary advantage of polyploidy. The heterozygous strain was grown (i) in the presence of tryptophan, selecting for the presence of leuB, (ii) in the presence of leucine selecting for leuB:trpA and (iii) in the absence of selection. Both types of genomes were quantified with real-time PCR. The first condition led to a complete loss of leuB:trpA-containing genomes, while under the second condition leuB-containing genomes were lost. Also in the absence of selection gene conversion led to a fast equalization of genomes and resulted in homozygous leuB-containing cells. Gene conversion leading to genome equalization can explain the escape from 'Muller's ratchet' as well as the ease of mutant construction using polyploid haloarchaea.
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Affiliation(s)
- Christian Lange
- Johann Wolfgang Goethe University, Institute for Molecular Biosciences, Max-von-Laue-Strasse 9, 60438 Frankfurt a.M., Germany
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Sahota G, Stormo GD. Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes. ACTA ACUST UNITED AC 2010; 26:2672-7. [PMID: 20807838 DOI: 10.1093/bioinformatics/btq501] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION Computational techniques for microbial genomic sequence analysis are becoming increasingly important. With next-generation sequencing technology and the human microbiome project underway, current sequencing capacity is significantly greater than the speed at which organisms of interest can be studied experimentally. Most related computational work has been focused on sequence assembly, gene annotation and metabolic network reconstruction. We have developed a method that will primarily use available sequence data in order to determine prokaryotic transcription factor (TF) binding specificities. RESULTS Specificity determining residues (critical residues) were identified from crystal structures of DNA-protein complexes and TFs with the same critical residues were grouped into specificity classes. The putative binding regions for each class were defined as the set of promoters for each TF itself (autoregulatory) and the immediately upstream and downstream operons. MEME was used to find putative motifs within each separate class. Tests on the LacI and TetR TF families, using RegulonDB annotated sites, showed the sensitivity of prediction 86% and 80%, respectively. AVAILABILITY http://ural.wustl.edu/∼gsahota/HTHmotif/
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Affiliation(s)
- Gurmukh Sahota
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63108, USA
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The insertion sequences of Anabaena sp. strain PCC 7120 and their effects on its open reading frames. J Bacteriol 2010; 192:5289-303. [PMID: 20656907 DOI: 10.1128/jb.00460-10] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Anabaena sp. strain PCC 7120, widely studied, has 145 annotated transposase genes that are part of transposable elements called insertion sequences (ISs). To determine the entirety of the ISs, we aligned transposase genes and their flanking regions; identified the ISs' possible terminal inverted repeats, usually flanked by direct repeats; and compared IS-interrupted sequences with homologous sequences. We thereby determined both ends of 87 ISs bearing 110 transposase genes in eight IS families (http://www-is.biotoul.fr/) and in a cluster of unclassified ISs, and of hitherto unknown miniature inverted-repeat transposable elements. Open reading frames were then identified to which ISs contributed and others--some encoding proteins of predictable function, including protein kinases, and restriction endonucleases--that were interrupted by ISs. Anabaena sp. ISs were often more closely related to exogenous than to other endogenous ISs, suggesting that numerous variant ISs were not degraded within PCC 7120 but transferred from without. This observation leads to the expectation that further sequencing projects will extend this and similar analyses. We also propose an adaptive role for poly(A) sequences in ISs.
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Winderl C, Penning H, Netzer FV, Meckenstock RU, Lueders T. DNA-SIP identifies sulfate-reducing Clostridia as important toluene degraders in tar-oil-contaminated aquifer sediment. ISME JOURNAL 2010; 4:1314-25. [PMID: 20428224 DOI: 10.1038/ismej.2010.54] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Global groundwater resources are constantly challenged by a multitude of contaminants such as aromatic hydrocarbons. Especially in anaerobic habitats, a large diversity of unrecognized microbial populations may be responsible for their degradation. Still, our present understanding of the respective microbiota and their ecophysiology is almost exclusively based on a small number of cultured organisms, mostly within the Proteobacteria. Here, by DNA-based stable isotope probing (SIP), we directly identified the most active sulfate-reducing toluene degraders in a diverse sedimentary microbial community originating from a tar-oil-contaminated aquifer at a former coal gasification plant. On incubation of fresh sediments with (13)C(7)-toluene, the production of both sulfide and (13)CO(2) was clearly coupled to the (13)C-labeling of DNA of microbes related to Desulfosporosinus spp. within the Peptococcaceae (Clostridia). The screening of labeled DNA fractions also suggested a novel benzylsuccinate synthase alpha-subunit (bssA) sequence type previously only detected in the environment to be tentatively affiliated with these degraders. However, carbon flow from the contaminant into degrader DNA was only ∼50%, pointing toward high ratios of heterotrophic CO(2)-fixation during assimilation of acetyl-CoA originating from the contaminant by these degraders. These findings demonstrate that the importance of non-proteobacterial populations in anaerobic aromatics degradation, as well as their specific ecophysiology in the subsurface may still be largely ungrasped.
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Affiliation(s)
- Christian Winderl
- Institute of Groundwater Ecology, Helmholtz Zentrum München-German Research Centre for Environmental Health, Neuherberg, Germany
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Abstract
Analysis of intragenomic variation of 16S rRNA genes is a unique approach to examining the concept of ribosomal constraints on rRNA genes; the degree of variation is an important parameter to consider for estimation of the diversity of a complex microbiome in the recently initiated Human Microbiome Project (http://nihroadmap.nih.gov/hmp). The current GenBank database has a collection of 883 prokaryotic genomes representing 568 unique species, of which 425 species contained 2 to 15 copies of 16S rRNA genes per genome (2.22 +/- 0.81). Sequence diversity among the 16S rRNA genes in a genome was found in 235 species (from 0.06% to 20.38%; 0.55% +/- 1.46%). Compared with the 16S rRNA-based threshold for operational definition of species (1 to 1.3% diversity), the diversity was borderline (between 1% and 1.3%) in 10 species and >1.3% in 14 species. The diversified 16S rRNA genes in Haloarcula marismortui (diversity, 5.63%) and Thermoanaerobacter tengcongensis (6.70%) were highly conserved at the 2 degrees structure level, while the diversified gene in B. afzelii (20.38%) appears to be a pseudogene. The diversified genes in the remaining 21 species were also conserved, except for a truncated 16S rRNA gene in "Candidatus Protochlamydia amoebophila." Thus, this survey of intragenomic diversity of 16S rRNA genes provides strong evidence supporting the theory of ribosomal constraint. Taxonomic classification using the 16S rRNA-based operational threshold could misclassify a number of species into more than one species, leading to an overestimation of the diversity of a complex microbiome. This phenomenon is especially seen in 7 bacterial species associated with the human microbiome or diseases.
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