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Okamura Y, Suemitsu M, Ishikawa T, Takahashi H. Nonribosomal Peptide Synthetase Specific Genome Amplification Using Rolling Circle Amplification for Targeted Gene Sequencing. Int J Mol Sci 2024; 25:5089. [PMID: 38791129 PMCID: PMC11121399 DOI: 10.3390/ijms25105089] [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: 03/31/2024] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
Next-generation sequencing has transformed the acquisition of vast amounts of genomic information, including the rapid identification of target gene sequences in metagenomic databases. However, dominant species can sometimes hinder the detection of rare bacterial species. Therefore, a highly sensitive amplification technique that can selectively amplify bacterial genomes containing target genes of interest was developed in this study. The rolling circle amplification (RCA) method can initiate amplification from a single locus using a specific single primer to amplify a specific whole genome. A mixed cell suspension was prepared using Pseudomonas fluorescens ATCC17400 (targeting nonribosomal peptide synthetase [NRPS]) and Escherichia coli (non-target), and a specific primer designed for the NRPS was used for the RCA reaction. The resulting RCA product (RCP) amplified only the Pseudomonas genome. The NRPS was successfully amplified using RCP as a template from even five cells, indicating that the single-priming RCA technique can specifically enrich the target genome using gene-specific primers. Ultimately, this specific genome RCA technique was applied to metagenomes extracted from sponge-associated bacteria, and NRPS sequences were successfully obtained from an unknown sponge-associated bacterium. Therefore, this method could be effective for accessing species-specific sequences of NRPS in unknown bacteria, including viable but non-culturable bacteria.
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Affiliation(s)
- Yoshiko Okamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima 739-8530, Japan; (T.I.); (H.T.)
- Graduate School of Advanced Science of Matter, Hiroshima University, Hiroshima 739-8530, Japan;
| | - Masahiro Suemitsu
- Graduate School of Advanced Science of Matter, Hiroshima University, Hiroshima 739-8530, Japan;
| | - Takato Ishikawa
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima 739-8530, Japan; (T.I.); (H.T.)
| | - Hirokazu Takahashi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima 739-8530, Japan; (T.I.); (H.T.)
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Horio K, Takahashi H, Kobori T, Watanabe K, Aki T, Nakashimada Y, Okamura Y. Visualization of Gene Reciprocity among Lactic Acid Bacteria in Yogurt by RNase H-Assisted Rolling Circle Amplification-Fluorescence In Situ Hybridization. Microorganisms 2021; 9:1208. [PMID: 34204984 PMCID: PMC8228470 DOI: 10.3390/microorganisms9061208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022] Open
Abstract
Recently, we developed an in situ mRNA detection method termed RNase H-assisted rolling circle amplification-fluorescence in situ hybridization (RHa-RCA-FISH), which can detect even short mRNA in a bacterial cell. However, because this FISH method is sensitive to the sample condition, it is necessary to find a suitable cell permeabilization and collection protocol. Here, we demonstrate its further applicability for detecting intrinsic mRNA expression using lactic acid bacteria (LAB) as a model consortium. Our results show that this method can visualize functional gene expression in LAB cells and can be used for monitoring the temporal transition of gene expression. In addition, we also confirmed that data obtained from bulk analyses such as RNA-seq or microarray do not always correspond to gene expression in individual cells. RHa-RCA-FISH will be a powerful tool to compensate for insufficient data from metatranscriptome analyses while clarifying the carriers of function in microbial consortia. By extending this technique to capture spatiotemporal microbial gene expression at the single-cell level, it will be able to characterize microbial interactions in phytoplankton-bacteria interactions.
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Affiliation(s)
- Kyohei Horio
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima 739-8530, Japan; (K.H.); (H.T.); (K.W.); (T.A.); (Y.N.)
| | - Hirokazu Takahashi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima 739-8530, Japan; (K.H.); (H.T.); (K.W.); (T.A.); (Y.N.)
| | - Toshiro Kobori
- Division of Food Biotechnology, Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8642, Japan;
| | - Kenshi Watanabe
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima 739-8530, Japan; (K.H.); (H.T.); (K.W.); (T.A.); (Y.N.)
| | - Tsunehiro Aki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima 739-8530, Japan; (K.H.); (H.T.); (K.W.); (T.A.); (Y.N.)
| | - Yutaka Nakashimada
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima 739-8530, Japan; (K.H.); (H.T.); (K.W.); (T.A.); (Y.N.)
| | - Yoshiko Okamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima 739-8530, Japan; (K.H.); (H.T.); (K.W.); (T.A.); (Y.N.)
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Bouam A, Vincent JJ, Drancourt M, Raoult D, Levy PY. Preventing contamination of PCR-based multiplex assays including the use of a dedicated biosafety cabinet. Lett Appl Microbiol 2021; 72:98-103. [PMID: 33245575 DOI: 10.1111/lam.13375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 08/11/2020] [Accepted: 08/11/2020] [Indexed: 01/15/2023]
Abstract
We retrospectively investigated cases of false-positive diagnoses using the BIOFIRE® FilmArray® meningitis/encephalitis (ME) panel to measure the impact of using a dedicated biosafety cabinet combined with preventive measures to reduce the prevalence of false-positive diagnoses due to pre-analytical in-laboratory contamination. False-positive results were identified by reviewing clinical data, biological parameters and cytology results of cerebrospinal fluid (CSF) samples showing discrepant results between the FilmArray ME panel and routine PCR assays. A total of 327 CSF were analysed over 16 weeks in point-of-care (POC) A and B, over two 8-week periods, periods 1 and 2. The analysis yielded 30 (9·17%) detection of at least one pathogen including 21/30 (70%) viruses and 9/30 (30%) bacteria. During period 1, POC-A and POC-B manipulated CSF under a non-dedicated hood featuring laminar flow, whereas during period 2, CSFs were manipulated under a dedicated biosafety cabinet without any airflow in POC-A. During period 1, false positives were detected in 3/114 CSF (2·63%) in POC-A and 1/36 (2·77%) in POC-B (P = 0·97); during period 2, false positives were detected in 0/139 CSF (0%) in POC-A and 1/38 (2·63%) in POC-B (P = 0·23). All false positives were bacterial. The use of a dedicated cabinet without ventilation along with preventive measures during period 2 in POC-A significantly reduced the number of false-positive results (P = 0·05). Preventive measures described in this study can mitigate false positives when using PCR-based multiplex assays such as the BIOFIRE FilmArray ME Panel for the diagnosis of meningitis and other infectious diseases.
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Affiliation(s)
- A Bouam
- POCRAMé, Marseille, France
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille University, Marseille, France
| | - J J Vincent
- IHU Méditerranée Infection, Marseille, France
| | - M Drancourt
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - D Raoult
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - P Y Levy
- POCRAMé, Marseille, France
- IHU Méditerranée Infection, Marseille, France
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Takahashi H, Horio K, Kato S, Kobori T, Watanabe K, Aki T, Nakashimada Y, Okamura Y. Direct detection of mRNA expression in microbial cells by fluorescence in situ hybridization using RNase H-assisted rolling circle amplification. Sci Rep 2020; 10:9588. [PMID: 32541674 PMCID: PMC7295810 DOI: 10.1038/s41598-020-65864-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 05/04/2020] [Indexed: 11/11/2022] Open
Abstract
Meta-analyses using next generation sequencing is a powerful strategy for studying microbiota; however, it cannot clarify the role of individual microbes within microbiota. To know which cell expresses what gene is important for elucidation of the individual cell’s function in microbiota. In this report, we developed novel fluorescence in situ hybridization (FISH) procedure using RNase-H-assisted rolling circle amplification to visualize mRNA of interest in microbial cells without reverse transcription. Our results show that this method is applicable to both Gram-negative and Gram-positive microbes without any noise from DNA, and it is possible to visualize the target mRNA expression directly at the single-cell level. Therefore, our procedure, when combined with data of meta-analyses, can help to understand the role of individual microbes in the microbiota.
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Affiliation(s)
- Hirokazu Takahashi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, 739-8530, Japan.
| | - Kyohei Horio
- Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima, 739-8530, Japan
| | - Setsu Kato
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, 739-8530, Japan.,Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima, 739-8530, Japan
| | - Toshiro Kobori
- Division of Food Biotechnology, Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8642, Japan
| | - Kenshi Watanabe
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, 739-8530, Japan.,Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima, 739-8530, Japan
| | - Tsunehiro Aki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, 739-8530, Japan.,Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima, 739-8530, Japan
| | - Yutaka Nakashimada
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, 739-8530, Japan.,Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima, 739-8530, Japan
| | - Yoshiko Okamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashihiroshima, 739-8530, Japan. .,Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima, 739-8530, Japan.
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Sasagawa Y, Hayashi T, Nikaido I. Strategies for Converting RNA to Amplifiable cDNA for Single-Cell RNA Sequencing Methods. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1129:1-17. [PMID: 30968357 DOI: 10.1007/978-981-13-6037-4_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
This review describes the features of molecular biology techniques for single-cell RNA sequencing (scRNA-seq), including methods developed in our laboratory. Existing scRNA-seq methods require the conversion of first-strand cDNA to amplifiable cDNA followed by whole-transcript amplification. There are three primary strategies for this conversion: poly-A tagging, template switching, and RNase H-DNA polymerase I-mediated second-strand cDNA synthesis for in vitro transcription. We discuss the merits and limitations of these strategies and describe our Reverse Transcription with Random Displacement Amplification technology that allows for direct first-strand cDNA amplification from RNA without the need for conversion to an amplifiable cDNA. We believe that this review provides all users of single-cell transcriptome technologies with an understanding of the relationship between the quantitative performance of various methods and their molecular features.
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Affiliation(s)
- Yohei Sasagawa
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, Wako, Saitama, Japan
| | - Tetsutaro Hayashi
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, Wako, Saitama, Japan
| | - Itoshi Nikaido
- Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research, Wako, Saitama, Japan.
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Takahashi H, Ohkawachi M, Horio K, Kobori T, Aki T, Matsumura Y, Nakashimada Y, Okamura Y. RNase H-assisted RNA-primed rolling circle amplification for targeted RNA sequence detection. Sci Rep 2018; 8:7770. [PMID: 29773824 PMCID: PMC5958062 DOI: 10.1038/s41598-018-26132-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 03/21/2018] [Indexed: 12/20/2022] Open
Abstract
RNA-primed rolling circle amplification (RPRCA) is a useful laboratory method for RNA detection; however, the detection of RNA is limited by the lack of information on 3′-terminal sequences. We uncovered that conventional RPRCA using pre-circularized probes could potentially detect the internal sequence of target RNA molecules in combination with RNase H. However, the specificity for mRNA detection was low, presumably due to non-specific hybridization of non-target RNA with the circular probe. To overcome this technical problem, we developed a method for detecting a sequence of interest in target RNA molecules via RNase H-assisted RPRCA using padlocked probes. When padlock probes are hybridized to the target RNA molecule, they are converted to the circular form by SplintR ligase. Subsequently, RNase H creates nick sites only in the hybridized RNA sequence, and single-stranded DNA is finally synthesized from the nick site by phi29 DNA polymerase. This method could specifically detect at least 10 fmol of the target RNA molecule without reverse transcription. Moreover, this method detected GFP mRNA present in 10 ng of total RNA isolated from Escherichia coli without background DNA amplification. Therefore, this method can potentially detect almost all types of RNA molecules without reverse transcription and reveal full-length sequence information.
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Affiliation(s)
- Hirokazu Takahashi
- Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima, 739-8530, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo, 102-0075, Japan
| | - Masahiko Ohkawachi
- Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima, 739-8530, Japan
| | - Kyohei Horio
- Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima, 739-8530, Japan
| | - Toshiro Kobori
- Division of Food Biotechnology, Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8642, Japan
| | - Tsunehiro Aki
- Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima, 739-8530, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo, 102-0075, Japan
| | - Yukihiko Matsumura
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo, 102-0075, Japan.,Division of Energy and Environmental Engineering, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8527, Japan
| | - Yutaka Nakashimada
- Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima, 739-8530, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo, 102-0075, Japan
| | - Yoshiko Okamura
- Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashihiroshima, Hiroshima, 739-8530, Japan. .,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Sanbancho 5, Chiyoda-ku, Tokyo, 102-0075, Japan.
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