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Kumar Awasthi M, Ravindran B, Sarsaiya S, Chen H, Wainaina S, Singh E, Liu T, Kumar S, Pandey A, Singh L, Zhang Z. Metagenomics for taxonomy profiling: tools and approaches. Bioengineered 2020; 11:356-374. [PMID: 32149573 PMCID: PMC7161568 DOI: 10.1080/21655979.2020.1736238] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/20/2020] [Accepted: 02/21/2020] [Indexed: 12/25/2022] Open
Abstract
The study of metagenomics is an emerging field that identifies the total genetic materials in an organism along with the set of all genetic materials like deoxyribonucleic acid and ribose nucleic acid, which play a key role with the maintenance of cellular functions. The best part of this technology is that it gives more flexibility to environmental microbiologists to instantly pioneer the immense genetic variability of microbial communities. However, it is intensively complex to identify the suitable sequencing measures of any specific gene that can exclusively indicate the involvement of microbial metagenomes and be able to advance valuable results about these communities. This review provides an overview of the metagenomic advancement that has been advantageous for aggregation of more knowledge about specific genes, microbial communities and its metabolic pathways. More specific drawbacks of metagenomes technology mainly depend on sequence-based analysis. Therefore, this 'targeted based metagenomics' approach will give comprehensive knowledge about the ecological, evolutionary and functional sequence of significantly important genes that naturally exist in living beings either human, animal and microorganisms from distinctive ecosystems.
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Affiliation(s)
- Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, China
- Swedish Centre for Resource Recovery, University of Borås, Borås, Sweden
| | - B. Ravindran
- Department of Environmental Energy and Engineering, Kyonggi University Youngtong-Gu, Suwon, South Korea
| | - Surendra Sarsaiya
- Key Laboratory of Basic Pharmacology of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Hongyu Chen
- Institute of Biology, Freie Universität Berlin Altensteinstr, Berlin, Germany
| | - Steven Wainaina
- Swedish Centre for Resource Recovery, University of Borås, Borås, Sweden
| | - Ekta Singh
- CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Tao Liu
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Sunil Kumar
- CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Ashok Pandey
- Centre for Innovation and Translational Research CSIR-Indian Institute of Toxicology Research, Lucknow, India
| | - Lal Singh
- CSIR-National Environmental Engineering Research Institute, Nagpur, India
| | - Zengqiang Zhang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, China
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3
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Kugel S, Baunach M, Baer P, Ishida-Ito M, Sundaram S, Xu Z, Groll M, Hertweck C. Cryptic indole hydroxylation by a non-canonical terpenoid cyclase parallels bacterial xenobiotic detoxification. Nat Commun 2017. [PMID: 28643772 PMCID: PMC5481743 DOI: 10.1038/ncomms15804] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Terpenoid natural products comprise a wide range of molecular architectures that typically result from C–C bond formations catalysed by classical type I/II terpene cyclases. However, the molecular diversity of biologically active terpenoids is substantially increased by fully unrelated, non-canonical terpenoid cyclases. Their evolutionary origin has remained enigmatic. Here we report the in vitro reconstitution of an unusual flavin-dependent bacterial indoloterpenoid cyclase, XiaF, together with a designated flavoenzyme-reductase (XiaP) that mediates a key step in xiamycin biosynthesis. The crystal structure of XiaF with bound FADH2 (at 2.4 Å resolution) and phylogenetic analyses reveal that XiaF is, surprisingly, most closely related to xenobiotic-degrading enzymes. Biotransformation assays show that XiaF is a designated indole hydroxylase that can be used for the production of indigo and indirubin. We unveil a cryptic hydroxylation step that sets the basis for terpenoid cyclization and suggest that the cyclase has evolved from xenobiotics detoxification enzymes. The biosynthesis of xiamycin, an antimicrobial bacterial indolosesquiterpenoid, involves an unusual cyclization cascade. Here, the authors characterise the XiaF enzyme, which resembles xenobiont-degrading enzymes and is responsible for a hidden indole hydroxylation step that triggers the cyclization reaction.
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Affiliation(s)
- Susann Kugel
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Martin Baunach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Philipp Baer
- Center for Integrated Protein Science Munich (CIPSM), Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Mie Ishida-Ito
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Srividhya Sundaram
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Zhongli Xu
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Michael Groll
- Center for Integrated Protein Science Munich (CIPSM), Department Chemie, Technische Universität München, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745 Jena, Germany.,Natural Product Chemistry, Friedrich Schiller University, 07743 Jena, Germany
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6
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Bouhajja E, McGuire M, Liles MR, Bataille G, Agathos SN, George IF. Identification of novel toluene monooxygenase genes in a hydrocarbon-polluted sediment using sequence- and function-based screening of metagenomic libraries. Appl Microbiol Biotechnol 2016; 101:797-808. [PMID: 27785541 DOI: 10.1007/s00253-016-7934-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 10/06/2016] [Accepted: 10/12/2016] [Indexed: 11/25/2022]
Abstract
The microbial potential for toluene degradation within sediments from a tar oil-contaminated site in Flingern, Germany, was assessed using a metagenomic approach. High molecular weight environmental DNA from contaminated sediments was extracted, purified, and cloned into fosmid and BAC vectors and transformed into Escherichia coli. The fosmid library was screened by hybridization with a PCR amplicon of the α-subunit of the toluene 4-monooxygenase gene to identify genes and pathways encoding toluene degradation. Fourteen clones were recovered from the fosmid library, among which 13 were highly divergent from known tmoA genes and several had the closest relatives among Acinetobacter species. The BAC library was transferred to the heterologous hosts Cupriavidus metallidurans (phylum Proteobacteria) and Edaphobacter aggregans (phylum Acidobacteria). The resulting libraries were screened for expression of toluene degradation in the non-degradative hosts. From expression in C. metallidurans, three novel toluene monooxygenase-encoding operons were identified that were located on IncP1 plasmids. The E. aggregans-hosted BAC library led to the isolation of a cloned genetic locus putatively derived from an Acidobacteria taxon that contained genes involved in aerobic and anaerobic toluene degradation. These data suggest the important role of plasmids in the spread of toluene degradative capacity and indicate putative novel tmoA genes present in this hydrocarbon-polluted environment.
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Affiliation(s)
- E Bouhajja
- Earth and Life Institute, Laboratoire de Génie Biologique, Université catholique de Louvain, Place Croix du Sud 2, boite L7.05.19, 1348, Louvain-la-Neuve, Belgium
| | - M McGuire
- Department of Biological Sciences, Auburn University, 101 Rouse Life Science Building, Auburn, Alabama, 36849, USA
| | - M R Liles
- Department of Biological Sciences, Auburn University, 101 Rouse Life Science Building, Auburn, Alabama, 36849, USA
| | - G Bataille
- Earth and Life Institute, Biodiversity Research Centre, Université catholique de Louvain, Place Croix du Sud 4-5, Bte L.7.07.04, 1348, Louvain-la-Neuve, Belgium
| | - S N Agathos
- Earth and Life Institute, Laboratoire de Génie Biologique, Université catholique de Louvain, Place Croix du Sud 2, boite L7.05.19, 1348, Louvain-la-Neuve, Belgium.,School of Life Sciences and Biotechnology, Yachay Tech University, San Miguel de Urcuquí, Ecuador
| | - I F George
- Laboratoire d'Ecologie des Systèmes Aquatiques, Université libre de Bruxelles, Campus de la Plaine CP 221, Boulevard du Triomphe, 1050, Brussels, Belgium.
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Okubo T, Tsukui T, Maita H, Okamoto S, Oshima K, Fujisawa T, Saito A, Futamata H, Hattori R, Shimomura Y, Haruta S, Morimoto S, Wang Y, Sakai Y, Hattori M, Aizawa SI, Nagashima KVP, Masuda S, Hattori T, Yamashita A, Bao Z, Hayatsu M, Kajiya-Kanegae H, Yoshinaga I, Sakamoto K, Toyota K, Nakao M, Kohara M, Anda M, Niwa R, Jung-Hwan P, Sameshima-Saito R, Tokuda SI, Yamamoto S, Yamamoto S, Yokoyama T, Akutsu T, Nakamura Y, Nakahira-Yanaka Y, Hoshino YT, Hirakawa H, Mitsui H, Terasawa K, Itakura M, Sato S, Ikeda-Ohtsubo W, Sakakura N, Kaminuma E, Minamisawa K. Complete genome sequence of Bradyrhizobium sp. S23321: insights into symbiosis evolution in soil oligotrophs. Microbes Environ 2012; 27:306-15. [PMID: 22452844 PMCID: PMC4036050 DOI: 10.1264/jsme2.me11321] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 02/28/2012] [Indexed: 11/12/2022] Open
Abstract
Bradyrhizobium sp. S23321 is an oligotrophic bacterium isolated from paddy field soil. Although S23321 is phylogenetically close to Bradyrhizobium japonicum USDA110, a legume symbiont, it is unable to induce root nodules in siratro, a legume often used for testing Nod factor-dependent nodulation. The genome of S23321 is a single circular chromosome, 7,231,841 bp in length, with an average GC content of 64.3%. The genome contains 6,898 potential protein-encoding genes, one set of rRNA genes, and 45 tRNA genes. Comparison of the genome structure between S23321 and USDA110 showed strong colinearity; however, the symbiosis islands present in USDA110 were absent in S23321, whose genome lacked a chaperonin gene cluster (groELS3) for symbiosis regulation found in USDA110. A comparison of sequences around the tRNA-Val gene strongly suggested that S23321 contains an ancestral-type genome that precedes the acquisition of a symbiosis island by horizontal gene transfer. Although S23321 contains a nif (nitrogen fixation) gene cluster, the organization, homology, and phylogeny of the genes in this cluster were more similar to those of photosynthetic bradyrhizobia ORS278 and BTAi1 than to those on the symbiosis island of USDA110. In addition, we found genes encoding a complete photosynthetic system, many ABC transporters for amino acids and oligopeptides, two types (polar and lateral) of flagella, multiple respiratory chains, and a system for lignin monomer catabolism in the S23321 genome. These features suggest that S23321 is able to adapt to a wide range of environments, probably including low-nutrient conditions, with multiple survival strategies in soil and rhizosphere.
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Affiliation(s)
- Takashi Okubo
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Takahiro Tsukui
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Hiroko Maita
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
- Laboratory for Plant Genome Informatics, Kazusa DNA Research Institute, 2–6–7 Kazusakamatari, Kisarazu, Chiba 292–0818, Japan
| | - Shinobu Okamoto
- Database Center for Life Science (DBCLS), Research Organization of Information and Systems (ROIS), 2–11–16 Yayoi, Bunkyo-ku, Tokyo 113–0032, Japan
| | - Kenshiro Oshima
- Graduate School of Frontier Sciences, University of Tokyo, 5–1–5, Kashiwa-no-ha, Kashiwa, Chiba 277–8561, Japan
| | - Takatomo Fujisawa
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Shizuoka 411–85, Japan
| | - Akihiro Saito
- Department of Material and Life Science, Faculty of Science and Technology, Shizuoka Institute of Science and Technology 2200–2 Toyosawa, Fukuroi, Shizuoka 437–8555, Japan
| | - Hiroyuki Futamata
- Department of Material Science and Chemical Engineering, Shizuoka University, 3–5–1 Jyohoku, Naka-ku, Hamamatsu, Shizuoka, 432–8561, Japan
| | - Reiko Hattori
- Attic Lab, 1–6–2–401 Komegafukuro, Aobaku, Sendai, Miyagi 980–0813, Japan
| | - Yumi Shimomura
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Shin Haruta
- Graduate School of Science and Engineering, Tokyo Metropolitan University, 1–1 Minami-Osawa, Hachioji-shi, Tokyo 192–0397, Japan
| | - Sho Morimoto
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Yong Wang
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Yoriko Sakai
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Masahira Hattori
- Graduate School of Frontier Sciences, University of Tokyo, 5–1–5, Kashiwa-no-ha, Kashiwa, Chiba 277–8561, Japan
| | - Shin-ichi Aizawa
- Department of Life Sciences, Prefectural University of Hiroshima, 562 Nanatsuka, Shobara, Hiroshima 727–0023, Japan
| | - Kenji V. P. Nagashima
- Graduate School of Science and Engineering, Tokyo Metropolitan University, 1–1 Minami-Osawa, Hachioji-shi, Tokyo 192–0397, Japan
| | - Sachiko Masuda
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Tsutomu Hattori
- Attic Lab, 1–6–2–401 Komegafukuro, Aobaku, Sendai, Miyagi 980–0813, Japan
| | - Akifumi Yamashita
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Zhihua Bao
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Masahito Hayatsu
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Hiromi Kajiya-Kanegae
- Database Center for Life Science (DBCLS), Research Organization of Information and Systems (ROIS), 2–11–16 Yayoi, Bunkyo-ku, Tokyo 113–0032, Japan
| | - Ikuo Yoshinaga
- Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606–8502, Japan
| | - Kazunori Sakamoto
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba 271–8510, Japan
| | - Koki Toyota
- Tokyo University of Agriculture and Technology, 2–24–16, Naka, Koganei, Tokyo 184–8588, Japan
| | - Mitsuteru Nakao
- Database Center for Life Science (DBCLS), Research Organization of Information and Systems (ROIS), 2–11–16 Yayoi, Bunkyo-ku, Tokyo 113–0032, Japan
| | - Mitsuyo Kohara
- Laboratory for Plant Genome Informatics, Kazusa DNA Research Institute, 2–6–7 Kazusakamatari, Kisarazu, Chiba 292–0818, Japan
| | - Mizue Anda
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Rieko Niwa
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Park Jung-Hwan
- Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606–8502, Japan
| | - Reiko Sameshima-Saito
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422–8529, Japan
| | - Shin-ichi Tokuda
- National Institute of Vegetable and Tea Sciences, National Agriculture and Food Research Organization, 3–1–1 Kannondai, Tsukuba, Ibaraki 305–8666, Japan
| | - Sumiko Yamamoto
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Shizuoka 411–85, Japan
| | - Syuji Yamamoto
- Department of Material Science and Chemical Engineering, Shizuoka University, 3–5–1 Jyohoku, Naka-ku, Hamamatsu, Shizuoka, 432–8561, Japan
| | - Tadashi Yokoyama
- Institute of Agriculture, Tokyo university of Agriculture and Technology, 3–5–8 Saiwaicho, Fuchu, Tokyo 183–8509, Japan
| | - Tomoko Akutsu
- Laboratory for Plant Genome Informatics, Kazusa DNA Research Institute, 2–6–7 Kazusakamatari, Kisarazu, Chiba 292–0818, Japan
| | - Yasukazu Nakamura
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Shizuoka 411–85, Japan
| | - Yuka Nakahira-Yanaka
- Graduate School of Life and Environment Sciences, University of Tsukuba, 1–1–1 Ten-noudai, Tsukuba, Ibaraki 305–8572, Japan
| | - Yuko Takada Hoshino
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Hideki Hirakawa
- Laboratory for Plant Genome Informatics, Kazusa DNA Research Institute, 2–6–7 Kazusakamatari, Kisarazu, Chiba 292–0818, Japan
| | - Hisayuki Mitsui
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Kimihiro Terasawa
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Manabu Itakura
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
- Laboratory for Plant Genome Informatics, Kazusa DNA Research Institute, 2–6–7 Kazusakamatari, Kisarazu, Chiba 292–0818, Japan
| | - Wakako Ikeda-Ohtsubo
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Natsuko Sakakura
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Shizuoka 411–85, Japan
| | - Eli Kaminuma
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Shizuoka 411–85, Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
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