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Yoon H, Lee HH, Noh HS, Lee SJ. Identification of genus Deinococcus strains by PCR detection using the gyrB gene and its extension to Bacteria domain. J Microbiol Methods 2024; 223:106980. [PMID: 38936431 DOI: 10.1016/j.mimet.2024.106980] [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: 05/17/2024] [Revised: 06/24/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024]
Abstract
In radiation-resistant bacteria belonging to the genus Deinococcus, transposition events of insertion sequences (IS elements) leading to phenotypic changes from a reddish color to white were detected following exposure to gamma irradiation and hydrogen peroxide treatment. This change resulted from the integration of IS elements into the phytoene desaturase gene, a key enzyme in the carotenoid biosynthesis pathway. To facilitate species identification and distinguish among Deinococcus strains, the gyrB gene encoding the B subunit of DNA gyrase was utilized. The s gnificance of the gyrB gene is well recognized not only in genome replication through the regulation of supercoiling but also in phylogenetic analysis providing support for 16S rRNA-based identification. Its mutation rate surpasses that of the 16S rRNA gene, offering greater resolution between closely related species, particularly those exhibiting >99% similarity. In this study, phylogenetic analysis was conducted comparing the 16S rRNA and gyrB gene sequences of Deinococcus species. Species-specific and genus-specific primers targeting Deinococcus species were designed and experimentally validated for selective amplification and rapid identification of the targeted species. This approach allows for the omission of 16S rRNA sequencing in the targeted Deinococcus species. Therefore, the gyrB gene is useful for identifying bacterial species and genus-level detection from individual microbes or microbial consortia using specialized primer sets for PCR amplification.
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Affiliation(s)
- Hyeonsik Yoon
- Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Hyun Hee Lee
- Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Hee Seong Noh
- Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Sung-Jae Lee
- Department of Biology, Kyung Hee University, Seoul 02447, Republic of Korea.
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2
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Chen Z, Hu J, Dai J, Zhou C, Hua Y, Hua X, Zhao Y. Precise CRISPR/Cpf1 genome editing system in the Deinococcus radiodurans with superior DNA repair mechanisms. Microbiol Res 2024; 284:127713. [PMID: 38608339 DOI: 10.1016/j.micres.2024.127713] [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: 12/04/2023] [Revised: 02/20/2024] [Accepted: 04/06/2024] [Indexed: 04/14/2024]
Abstract
Deinococcus radiodurans, with its high homologous recombination (HR) efficiency of double-stranded DNA breaks (DSBs), is a model organism for studying genome stability maintenance and an attractive microbe for industrial applications. Here, we developed an efficient CRISPR/Cpf1 genome editing system in D. radiodurans by evaluating and optimizing double-plasmid strategies and four Cas effector proteins from various organisms, which can precisely introduce different types of template-dependent mutagenesis without off-target toxicity. Furthermore, the role of DNA repair genes in determining editing efficiency in D. radiodurans was evaluated by introducing the CRISPR/Cpf1 system into 13 mutant strains lacking various DNA damage response and repair factors. In addition to the crucial role of RecA-dependent HR required for CRISPR/Cpf1 editing, D. radiodurans showed higher editing efficiency when lacking DdrB, the single-stranded DNA annealing (SSA) protein involved in the RecA-independent DSB repair pathway. This suggests a possible competition between HR and SSA pathways in the CRISPR editing of D. radiodurans. Moreover, off-target effects were observed during the genome editing of the pprI knockout strain, a master DNA damage response gene in Deinococcus species, which suggested that precise regulation of DNA damage response is critical for a high-fidelity genome editing system.
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Affiliation(s)
- Zijing Chen
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jing Hu
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jingli Dai
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Congli Zhou
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuejin Hua
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Ye Zhao
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China.
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Abstract
Conservation agriculture practices that promote soil health have distinct and lasting effects on microbial populations involved with soil nitrogen (N) cycling. In particular, using a leguminous winter cover crop (hairy vetch) promoted the expression of key functional genes involved in soil N cycling, equaling or exceeding the effects of inorganic N fertilizer. Soil microbial transformations of nitrogen (N) can be affected by soil health management practices. Here, we report in situ seasonal dynamics of the population size (gene copy abundances) and functional activity (transcript copy abundances) of five bacterial genes involved in soil N cycling (ammonia-oxidizing bacteria [AOB] amoA, nifH, nirK, nirS, and nosZ) in a long-term continuous cotton production system under different management practices (cover crops, tillage, and inorganic N fertilization). Hairy vetch (Vicia villosa Roth), a leguminous cover crop, most effectively promoted the expression of N cycle genes, which persisted after cover crop termination throughout the growing season. Moreover, we observed similarly high or even higher N cycle gene transcript abundances under vetch with no fertilizer as no cover crop with N fertilization throughout the cover crop peak and cotton growing seasons (April, May, and October). Further, both the gene and transcript abundances of amoA and nosZ were positively correlated to soil nitrous oxide (N2O) emissions. We also found that the abundances of amoA genes and transcripts both positively correlated to field and incubated net nitrification rates. Together, our results revealed relationships between microbial functional capacity and activity and in situ soil N transformations under different agricultural seasons and soil management practices. IMPORTANCE Conservation agriculture practices that promote soil health have distinct and lasting effects on microbial populations involved with soil nitrogen (N) cycling. In particular, using a leguminous winter cover crop (hairy vetch) promoted the expression of key functional genes involved in soil N cycling, equaling or exceeding the effects of inorganic N fertilizer. Hairy vetch also left a legacy on soil nutrient capacity by promoting the continued activity of N cycling microbes after cover crop termination and into the main growing season. By examining both genes and transcripts involved in soil N cycling, we showed different responses of functional capacity (i.e., gene abundances) and functional activity (i.e., transcript abundances) to agricultural seasons and management practices, adding to our understanding of the effects of soil health management practices on microbial ecology.
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Miyazaki J, Ikuta T, Watsuji TO, Abe M, Yamamoto M, Nakagawa S, Takaki Y, Nakamura K, Takai K. Dual energy metabolism of the Campylobacterota endosymbiont in the chemosynthetic snail Alviniconcha marisindica. ISME JOURNAL 2020; 14:1273-1289. [PMID: 32051527 PMCID: PMC7174374 DOI: 10.1038/s41396-020-0605-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 01/16/2020] [Accepted: 01/30/2020] [Indexed: 11/09/2022]
Abstract
Some deep-sea chemosynthetic invertebrates and their symbiotic bacteria can use molecular hydrogen (H2) as their energy source. However, how much the chemosynthetic holobiont (endosymbiont-host association) physiologically depends on H2 oxidation has not yet been determined. Here, we demonstrate that the Campylobacterota endosymbionts of the gastropod Alviniconcha marisindica in the Kairei and Edmond fields (kAlv and eAlv populations, respectively) of the Indian Ocean, utilize H2 in response to their physical and environmental H2 conditions, although the 16S rRNA gene sequence of both the endosymbionts shared 99.6% identity. A thermodynamic calculation using in situ H2 and hydrogen sulfide (H2S) concentrations indicated that chemosynthetic symbiosis could be supported by metabolic energy via H2 oxidation, particularly for the kAlv holobiont. Metabolic activity measurements showed that both the living individuals and the gill tissues consumed H2 and H2S at similar levels. Moreover, a combination of fluorescence in situ hybridization, quantitative transcript analyses, and enzymatic activity measurements showed that the kAlv endosymbiont expressed the genes and enzymes for both H2- and sulfur-oxidations. These results suggest that both H2 and H2S could serve as the primary energy sources for the kAlv holobiont. The eAlv holobiont had the ability to utilize H2, but the gene expression and enzyme activity for hydrogenases were much lower than for sulfur-oxidation enzymes. These results suggest that the energy acquisitions of A. marisindica holobionts are dependent on H2- and sulfur-oxidation in the H2-enriched Kairei field and that the mechanism of dual metabolism is controlled by the in situ H2 concentration.
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Affiliation(s)
- Junichi Miyazaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan.
| | - Tetsuro Ikuta
- Marine Biodiversity and Environmental Assessment Research Center (BioEnv), Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Tomo-O Watsuji
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan.,Department of Food and Nutrition, Higashi-Chikushi Junior College, 5-1-1 Shimoitozu, Kitakyusyu, 803-0846, Japan
| | - Mariko Abe
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Masahiro Yamamoto
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Satoshi Nakagawa
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan.,Laboratory of Marine Environmental Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Yoshihiro Takaki
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Kentaro Nakamura
- Department of Systems Innovation, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Ken Takai
- Super-cutting-edge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
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Hernández-Arriaga AM, Del Cerro C, Urbina L, Eceiza A, Corcuera MA, Retegi A, Auxiliadora Prieto M. Genome sequence and characterization of the bcs clusters for the production of nanocellulose from the low pH resistant strain Komagataeibacter medellinensis ID13488. Microb Biotechnol 2019; 12:620-632. [PMID: 30793484 PMCID: PMC6559206 DOI: 10.1111/1751-7915.13376] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/25/2019] [Accepted: 01/27/2019] [Indexed: 11/28/2022] Open
Abstract
Komagataeibacter medellinensis ID13488 (formerly Gluconacetobacter medellinensis ID13488) is able to produce crystalline bacterial cellulose (BC) under high acidic growth conditions. These abilities make this strain desirable for industrial BC production from acidic residues (e.g. wastes generated from cider production). To explore the molecular bases of the BC biosynthesis in this bacterium, the genome has been sequenced revealing a sequence of 3.4 Mb containing three putative plasmids of 38.1 kb (pKM01), 4.3 kb (pKM02) and 3.3 Kb (pKM03). Genome comparison analyses of K. medellinensis ID13488 with other cellulose‐producing related strains resulted in the identification of the bcs genes involved in the cellulose biosynthesis. Genes arrangement and composition of four bcs clusters (bcs1, bcs2, bcs3 and bcs4) was studied by RT‐PCR, and their organization in four operons transcribed as four independent polycistronic mRNAs was determined. qRT‐PCR experiments demonstrated that mostly bcs1 and bcs4 are expressed under BC production conditions, suggesting that these operons direct the synthesis of BC. Genomic differences with the close related strain K. medellinensis NBRC 3288 unable to produce BC were also described and discussed.
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Affiliation(s)
- Ana M Hernández-Arriaga
- Polymer Biotechnology Group, Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Carlos Del Cerro
- Polymer Biotechnology Group, Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Leire Urbina
- Materials + Technology' Group, Engineering School of Gipuzkoa, Department of Chemical and Environmental Engineering, University of the Basque Country (UPV/EHU), Pza. Europa 1, 20018, Donostia - San Sebastián, Spain
| | - Arantxa Eceiza
- Materials + Technology' Group, Engineering School of Gipuzkoa, Department of Chemical and Environmental Engineering, University of the Basque Country (UPV/EHU), Pza. Europa 1, 20018, Donostia - San Sebastián, Spain
| | - Mª Angeles Corcuera
- Materials + Technology' Group, Engineering School of Gipuzkoa, Department of Chemical and Environmental Engineering, University of the Basque Country (UPV/EHU), Pza. Europa 1, 20018, Donostia - San Sebastián, Spain
| | - Aloña Retegi
- Materials + Technology' Group, Engineering School of Gipuzkoa, Department of Chemical and Environmental Engineering, University of the Basque Country (UPV/EHU), Pza. Europa 1, 20018, Donostia - San Sebastián, Spain
| | - M Auxiliadora Prieto
- Polymer Biotechnology Group, Microbial and Plant Biotechnology Department, Centro de Investigaciones Biológicas, CIB-CSIC, Ramiro de Maeztu 9, 28040, Madrid, Spain
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Charubin K, Papoutsakis ET. Direct cell-to-cell exchange of matter in a synthetic Clostridium syntrophy enables CO 2 fixation, superior metabolite yields, and an expanded metabolic space. Metab Eng 2018; 52:9-19. [PMID: 30391511 DOI: 10.1016/j.ymben.2018.10.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 10/19/2018] [Accepted: 10/25/2018] [Indexed: 11/24/2022]
Abstract
In microbial fermentations at least 33% of the sugar-substrate carbon is lost as CO2 during pyruvate decarboxylation to acetyl-CoA, with the corresponding electrons lost in the form of H2. Previous attempts to reduce this carbon and electron loss focused on engineering of a single organism. In nature, most microorganisms live in complex communities where syntrophic interactions result in superior resource utilization. Here, we show that a synthetic syntrophy consisting of the solventogen Clostridium acetobutylicum, which converts simple and complex carbohydrates into a variety of chemicals, and the acetogen C. ljungdahlii which fixes CO2, achieved carbon recoveries into C2-C4 alcohols almost to the limit of substrate-electron availability, with minimal H2 and CO2 release. The syntrophic co-culture produced robust metabolic outcomes over a broad range of starting population ratios of the two organisms. We show that direct cell-to-cell interactions and material exchange among the two microbes enabled unforeseen rearrangements in the metabolism of the individual species that resulted in the production of non-native metabolites, namely isopropanol and 2,3-butanediol. This was accomplished by pathway-specific alterations of gene expression brought about by one organism on the other, and vice versa. While some of these gene-expression alterations can be explained by the exchange of metabolites that induce specific gene expression patterns, others, as demonstrated by co-culture setup in a transwell system, cannot. The latter, for now, would be attributed to complex direct physical interactions among the two organisms, thus providing a glimpse of the potential microbial complexity of simple or multicomponent microbiomes. Such direct material-transfer phenomena have not been documented in the literature. Furthermore, our study shows that syntrophic cultures offer a flexible platform for metabolite production with superior carbon recovery that can also be applied to electron-enhanced fermentations enabling even higher carbon recoveries.
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Affiliation(s)
- Kamil Charubin
- Department of Chemical and Biomolecular Engineering, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA; Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA.
| | - Eleftherios Terry Papoutsakis
- Department of Chemical and Biomolecular Engineering, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA; Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA.
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Najar IN, Sherpa MT, Das S, Verma K, Dubey VK, Thakur N. Geobacillus yumthangensis sp. nov., a thermophilic bacterium isolated from a north-east Indian hot spring. Int J Syst Evol Microbiol 2018; 68:3430-3434. [PMID: 30222099 DOI: 10.1099/ijsem.0.003002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A thermophilic, spore-forming, rod-shaped bacterium isolated from the Yumthang hot spring in North Sikkim, India was subjected to taxonomic studies. The thermophilic bacterial isolate was designated as strain AYN2T. Cells were Gram-stain-positive, aerobic, motile, rod-shaped, catalase-positive and methyl red-negative. Strain AYN2T was able to grow in the pH range from 6 to 10 (optimum, pH 7.5-8.0), at 40-70 °C (60 °C) and in NaCl concentrations of 0-4 % (1 %). The major cellular fatty acids were iso-C15 : 0 (12.8 %), iso-C16 : 0 (13.9 %) and iso-C17 : 0 (13.8 %). No matches were found in the rtsba6 Sherlock libraries. The G+C content of the genomic DNA was 42.11 mol%. Based on phylogenetic analysis of the 16S rRNA gene sequences, strain AYNT showed highest sequence similarity to the type strain of Geobacillus toebii (96 %). However, the phenotypic properties of strain AYN2T were clearly distinct from those of G. toebii and related species. On the basis of polyphasic analysis, strain AYN2T represents a novel species in the genus Geobacillus, for which the name Geobacillus yumthangensis sp. nov. is proposed. The type strain is AYN2T(MTCC=12749=KCTC=33950= JCM 32596).
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Affiliation(s)
- Ishfaq Nabi Najar
- 1Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Tadong, Gangtok - 737102, Sikkim, India
| | - Mingma Thundu Sherpa
- 1Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Tadong, Gangtok - 737102, Sikkim, India
| | - Sayak Das
- 1Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Tadong, Gangtok - 737102, Sikkim, India
| | - Kamalesh Verma
- 2Centre for the Environment, Indian Institute of Technology Guwahati, Guwahati-781039, Assam, India
| | - Vikash Kumar Dubey
- 2Centre for the Environment, Indian Institute of Technology Guwahati, Guwahati-781039, Assam, India.,3Department of Biosciences and Bioengineering, Indian Institute ofTechnology Guwahati, Guwahati-781039, Assam, India
| | - Nagendra Thakur
- 1Department of Microbiology, School of Life Sciences, Sikkim University, 6th Mile, Samdur, Tadong, Gangtok - 737102, Sikkim, India
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Liu S, Meng C, Xu G, Jian H, Wang F. Validation of reference genes for reverse transcription real-time quantitative PCR analysis in the deep-sea bacterium Shewanella psychrophila WP2. FEMS Microbiol Lett 2018. [DOI: 10.1093/femsle/fny048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Shunzhang Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 Shanghai, PR China
| | - Canxin Meng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 Shanghai, PR China
| | - Guanpeng Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 Shanghai, PR China
| | - Huahua Jian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 Shanghai, PR China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 Shanghai, PR China
- State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, 200240 Shanghai, PR China
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Low-Molecular-Weight Thiols and Thioredoxins Are Important Players in Hg(II) Resistance in Thermus thermophilus HB27. Appl Environ Microbiol 2018; 84:AEM.01931-17. [PMID: 29150497 DOI: 10.1128/aem.01931-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/24/2017] [Indexed: 12/31/2022] Open
Abstract
Mercury (Hg), one of the most toxic and widely distributed heavy metals, has a high affinity for thiol groups. Thiol groups reduce and sequester Hg. Therefore, low-molecular-weight (LMW) and protein thiols may be important cell components used in Hg resistance. To date, the role of low-molecular-weight thiols in Hg detoxification remains understudied. The mercury resistance (mer) operon of Thermus thermophilus suggests an evolutionary link between Hg(II) resistance and low-molecular-weight thiol metabolism. The mer operon encodes an enzyme involved in methionine biosynthesis, Oah. Challenge with Hg(II) resulted in increased expression of genes involved in the biosynthesis of multiple low-molecular-weight thiols (cysteine, homocysteine, and bacillithiol), as well as the thioredoxin system. Phenotypic analysis of gene replacement mutants indicated that Oah contributes to Hg resistance under sulfur-limiting conditions, and strains lacking bacillithiol and/or thioredoxins are more sensitive to Hg(II) than the wild type. Growth in the presence of either a thiol-oxidizing agent or a thiol-alkylating agent increased sensitivity to Hg(II). Furthermore, exposure to 3 μM Hg(II) consumed all intracellular reduced bacillithiol and cysteine. Database searches indicate that oah2 is present in all Thermus sp. mer operons. The presence of a thiol-related gene was also detected in some alphaproteobacterial mer operons, in which a glutathione reductase gene was present, supporting the role of thiols in Hg(II) detoxification. These results have led to a working model in which LMW thiols act as Hg(II)-buffering agents while Hg is reduced by MerA.IMPORTANCE The survival of microorganisms in the presence of toxic metals is central to life's sustainability. The affinity of thiol groups for toxic heavy metals drives microbe-metal interactions and modulates metal toxicity. Mercury detoxification (mer) genes likely originated early in microbial evolution in geothermal environments. Little is known about how mer systems interact with cellular thiol systems. Thermus spp. possess a simple mer operon in which a low-molecular-weight thiol biosynthesis gene is present, along with merR and merA In this study, we present experimental evidence for the role of thiol systems in mercury resistance. Our data suggest that, in T. thermophilus, thiolated compounds may function side by side with mer genes to detoxify mercury. Thus, thiol systems function in consort with mer-mediated resistance to mercury, suggesting exciting new questions for future research.
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Molecular Mechanisms Contributing to the Growth and Physiology of an Extremophile Cultured with Dielectric Heating. Appl Environ Microbiol 2016; 82:6233-6246. [PMID: 27520819 DOI: 10.1128/aem.02020-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 08/08/2016] [Indexed: 11/20/2022] Open
Abstract
The effect of microwave frequency electromagnetic fields on living microorganisms is an active and highly contested area of research. One of the major drawbacks to using mesophilic organisms to study microwave radiation effects is the unavoidable heating of the organism, which has limited the scale (<5 ml) and duration (<1 h) of experiments. However, the negative effects of heating a mesophile can be mitigated by employing thermophiles (organisms able to grow at temperatures of >60°C). This study identified changes in global gene expression profiles during the growth of Thermus scotoductus SA-01 at 65°C using dielectric (2.45 GHz, i.e., microwave) heating. RNA sequencing was performed on cultures at 8, 14, and 24 h after inoculation to determine the molecular mechanisms contributing to long-term cellular growth and survival under microwave heating conditions. Over the course of growth, genes associated with amino acid metabolism, carbohydrate metabolism, and defense mechanisms were upregulated; the number of repressed genes with unknown function increased; and at all time points, transposases were upregulated. Genes involved in cell wall biogenesis and elongation were also upregulated, consistent with the distinct elongated cell morphology observed after 24 h using microwave heating. Analysis of the global differential gene expression data enabled the identification of molecular processes specific to the response of T. scotoductus SA-01 to dielectric heating during growth. IMPORTANCE The residual heating of living organisms in the microwave region of the electromagnetic spectrum has complicated the identification of radiation-only effects using microorganisms for 50 years. A majority of the previous experiments used either mature cells or short exposure times with low-energy high-frequency radiation. Using global differential gene expression data, we identified molecular processes unique to dielectric heating using Thermus scotoductus SA-01 cultured over 30 h in a commercial microwave digestor. Genes associated with amino acid metabolism, carbohydrate metabolism, and defense mechanisms were upregulated; the number of repressed genes with unknown function increased; and at all time points, transposases were upregulated. These findings serve as a platform for future studies with mesophiles in order to better understand the response of microorganisms to microwave radiation.
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11
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Pessoa DDV, Vidal MS, Baldani JI, Simoes-Araujo JL. Validation of reference genes for RT-qPCR analysis in Herbaspirillum seropedicae. J Microbiol Methods 2016; 127:193-196. [PMID: 27302038 DOI: 10.1016/j.mimet.2016.06.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/09/2016] [Accepted: 06/10/2016] [Indexed: 11/17/2022]
Abstract
The RT-qPCR technique needs a validated set of reference genes for ensuring the consistency of the results from the gene expression. Expression stabilities for 9 genes from Herbaspirillum seropedicae, strain HRC54, grown with different carbon sources were calculated using geNorm and NormFinder, and the gene rpoA showed the best stability values.
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Affiliation(s)
- Daniella Duarte Villarinho Pessoa
- Universidade Federal do Rio de Janeiro - UFRJ, Programa de Pós-Graduação em Biotecnologia Vegetal, Centro de Ciências da Saúde - CCS, Campus Ilha do Fundão, Av. Carlos Chagas Filho, 373 - Cidade Universitária, CEP: 21941-590 Rio de Janeiro, RJ, Brazil; Centro Nacional de Pesquisa de Agrobiologia, CNPAB, Embrapa, Laboratório de Genética e Bioquímica, Embrapa Agrobiologia, BR 465, Km 7, s/n, Pavilhão Johanna Döbereiner, Bairro Ecologia, CEP: 23890-000 Seropédica, RJ, Brazil.
| | - Marcia Soares Vidal
- Centro Nacional de Pesquisa de Agrobiologia, CNPAB, Embrapa, Laboratório de Genética e Bioquímica, Embrapa Agrobiologia, BR 465, Km 7, s/n, Pavilhão Johanna Döbereiner, Bairro Ecologia, CEP: 23890-000 Seropédica, RJ, Brazil
| | - José Ivo Baldani
- Centro Nacional de Pesquisa de Agrobiologia, CNPAB, Embrapa, Laboratório de Genética e Bioquímica, Embrapa Agrobiologia, BR 465, Km 7, s/n, Pavilhão Johanna Döbereiner, Bairro Ecologia, CEP: 23890-000 Seropédica, RJ, Brazil
| | - Jean Luiz Simoes-Araujo
- Centro Nacional de Pesquisa de Agrobiologia, CNPAB, Embrapa, Laboratório de Genética e Bioquímica, Embrapa Agrobiologia, BR 465, Km 7, s/n, Pavilhão Johanna Döbereiner, Bairro Ecologia, CEP: 23890-000 Seropédica, RJ, Brazil.
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Zhao Y, Luo J, Xu S, Wang W, Liu T, Han C, Chen Y, Kong L. Selection of Reference Genes for Gene Expression Normalization in Peucedanum praeruptorum Dunn under Abiotic Stresses, Hormone Treatments and Different Tissues. PLoS One 2016; 11:e0152356. [PMID: 27022972 PMCID: PMC4811526 DOI: 10.1371/journal.pone.0152356] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 03/14/2016] [Indexed: 12/29/2022] Open
Abstract
Peucedanum praeruptorum Dunn is one of the main traditional Chinese medicines producing coumarins and plenty of literatures are focused on the biosynthesis of coumarins. Quantitative real-time reverse transcription PCR (qRT-PCR) is a widely used method in studying the biosynthesis pathway and the selection of reference genes plays a crucial role in accurate normalization. To facilitate biosynthesis study of coumarins, twelve candidate reference genes were selected from the transcriptome database of P. praeruptorum according to previous studies. Then, BestKeeper, geNoFrm and NormFinder were used for selecting stably expressed reference genes in different tissues and under various stress treatments. The results indicated that, among the twelve candidate reference genes, the SAND family protein (SAND), actin 2 (ACT2), ubiquitin-conjugating enzyme 9 (UBC9), protein phosphatase 2A gene (PP2A) and polypyrimidine tract-binding protein (PTBP1) were the most stable reference genes under different experimental treatments, while glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and tubulin beta-6 (TUB6) were the least stable genes. In addition, the suitability of SAND, TIP41-like protein (TIP41), UBC9, ACT2, TUB6 and their combination as reference genes were confirmed by normalizing the expression of 1-aminocyclopropane-1-carboxylate oxidase (ACO) in different treatments. This work is the first survey of the stability of reference genes in P. praeruptorum and provides guidelines to obtain more accurate qRT-PCR results in P. praeruptorum and other plant species.
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Affiliation(s)
- Yucheng Zhao
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing, Jiangsu, P. R. China
| | - Jun Luo
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing, Jiangsu, P. R. China
| | - Sheng Xu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, Jiangsu, P. R. China
| | - Wei Wang
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing, Jiangsu, P. R. China
| | - Tingting Liu
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing, Jiangsu, P. R. China
| | - Chao Han
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing, Jiangsu, P. R. China
| | - Yijun Chen
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing, Jiangsu, P. R. China
| | - Lingyi Kong
- State Key Laboratory of Natural Medicines, Department of Natural Medicinal Chemistry, China Pharmaceutical University, Nanjing, Jiangsu, P. R. China
- * E-mail:
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