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Evaluation of candidate reference genes stability for gene expression analysis by reverse transcription qPCR in Clostridium perfringens. Sci Rep 2022; 12:19434. [PMID: 36372839 PMCID: PMC9659559 DOI: 10.1038/s41598-022-23804-7] [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: 11/23/2021] [Accepted: 11/06/2022] [Indexed: 11/14/2022] Open
Abstract
Identification of stable reference genes for normalization purposes is necessary for obtaining reliable and accurate results of reverse transcription quantitative polymerase chain reaction (RT-qPCR) analyses. To our knowledge, no reference gene(s) have been validated for this purpose in Clostridium perfringens. In this study, the expression profile of ten candidate reference genes from three strains of C. perfringens were assessed for stability under various experimental conditions using geNorm in qbase + . These stability rankings were then compared to stability assessments evaluated by BestKeeper, NormFinder, delta Ct, and RefFinder algorithms. When comparing all the analyses; gyrA, ftsZ, and recA were identified within the most stable genes under the different experimental conditions and were further tested as a set of reference genes for normalization of alpha toxin gene expression over a 22-h period. Depending on the condition, rpoA and rho might also be suitable to include as part of the reference set. Although commonly used for the purpose of normalizing RT-qPCR data, the 16S rRNA gene (rrs) was found to be an unsuitable gene to be used as a reference. This work provides a framework for the selection of a suitable stable reference gene set for data normalization of C. perfringens gene expression.
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2
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Klask CM, Jäger B, Casini I, Angenent LT, Molitor B. Genetic Evidence Reveals the Indispensable Role of the rseC Gene for Autotrophy and the Importance of a Functional Electron Balance for Nitrate Reduction in Clostridium ljungdahlii. Front Microbiol 2022; 13:887578. [PMID: 35615511 PMCID: PMC9124969 DOI: 10.3389/fmicb.2022.887578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 03/31/2022] [Indexed: 11/20/2022] Open
Abstract
For Clostridium ljungdahlii, the RNF complex plays a key role for energy conversion from gaseous substrates such as hydrogen and carbon dioxide. In a previous study, a disruption of RNF-complex genes led to the loss of autotrophy, while heterotrophy was still possible via glycolysis. Furthermore, it was shown that the energy limitation during autotrophy could be lifted by nitrate supplementation, which resulted in an elevated cellular growth and ATP yield. Here, we used CRISPR-Cas12a to delete: (1) the RNF complex-encoding gene cluster rnfCDGEAB; (2) the putative RNF regulator gene rseC; and (3) a gene cluster that encodes for a putative nitrate reductase. The deletion of either rnfCDGEAB or rseC resulted in a complete loss of autotrophy, which could be restored by plasmid-based complementation of the deleted genes. We observed a transcriptional repression of the RNF-gene cluster in the rseC-deletion strain during autotrophy and investigated the distribution of the rseC gene among acetogenic bacteria. To examine nitrate reduction and its connection to the RNF complex, we compared autotrophic and heterotrophic growth of our three deletion strains with either ammonium or nitrate. The rnfCDGEAB- and rseC-deletion strains failed to reduce nitrate as a metabolic activity in non-growing cultures during autotrophy but not during heterotrophy. In contrast, the nitrate reductase deletion strain was able to grow in all tested conditions but lost the ability to reduce nitrate. Our findings highlight the important role of the rseC gene for autotrophy, and in addition, contribute to understand the connection of nitrate reduction to energy metabolism.
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Affiliation(s)
- Christian-Marco Klask
- Environmental Biotechnology Group, Geo- and Environmental Science Center, University of Tübingen, Tübingen, Germany
| | - Benedikt Jäger
- Environmental Biotechnology Group, Geo- and Environmental Science Center, University of Tübingen, Tübingen, Germany
| | - Isabella Casini
- Environmental Biotechnology Group, Geo- and Environmental Science Center, University of Tübingen, Tübingen, Germany
| | - Largus T. Angenent
- Environmental Biotechnology Group, Geo- and Environmental Science Center, University of Tübingen, Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Bastian Molitor
- Environmental Biotechnology Group, Geo- and Environmental Science Center, University of Tübingen, Tübingen, Germany
- Cluster of Excellence – Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- *Correspondence: Bastian Molitor,
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3
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Patakova P, Branska B, Vasylkivska M, Jureckova K, Musilova J, Provaznik I, Sedlar K. Transcriptomic studies of solventogenic clostridia, Clostridium acetobutylicum and Clostridium beijerinckii. Biotechnol Adv 2021; 58:107889. [PMID: 34929313 DOI: 10.1016/j.biotechadv.2021.107889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/10/2021] [Accepted: 12/14/2021] [Indexed: 12/13/2022]
Abstract
Solventogenic clostridia are not a strictly defined group within the genus Clostridium but its representatives share some common features, i.e. they are anaerobic, non-pathogenic, non-toxinogenic and endospore forming bacteria. Their main metabolite is typically 1-butanol but depending on species and culture conditions, they can form other metabolites such as acetone, isopropanol, ethanol, butyric, lactic and acetic acids, and hydrogen. Although these organisms were previously used for the industrial production of solvents, they later fell into disuse, being replaced by more efficient chemical production. A return to a more biological production of solvents therefore requires a thorough understanding of clostridial metabolism. Transcriptome analysis, which reflects the involvement of individual genes in all cellular processes within a population, at any given (sampling) moment, is a valuable tool for gaining a deeper insight into clostridial life. In this review, we describe techniques to study transcription, summarize the evolution of these techniques and compare methods for data processing and visualization of solventogenic clostridia, particularly the species Clostridium acetobutylicum and Clostridium beijerinckii. Individual approaches for evaluating transcriptomic data are compared and their contributions to advancements in the field are assessed. Moreover, utilization of transcriptomic data for reconstruction of computational clostridial metabolic models is considered and particular models are described. Transcriptional changes in glucose transport, central carbon metabolism, the sporulation cycle, butanol and butyrate stress responses, the influence of lignocellulose-derived inhibitors on growth and solvent production, and other respective topics, are addressed and common trends are highlighted.
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Affiliation(s)
- Petra Patakova
- University of Chemistry and Technology Prague, Technicka 5, 16628 Prague 6, Czech Republic.
| | - Barbora Branska
- University of Chemistry and Technology Prague, Technicka 5, 16628 Prague 6, Czech Republic
| | - Maryna Vasylkivska
- University of Chemistry and Technology Prague, Technicka 5, 16628 Prague 6, Czech Republic
| | | | - Jana Musilova
- Brno University of Technology, Technicka 10, 61600 Brno, Czech Republic
| | - Ivo Provaznik
- Brno University of Technology, Technicka 10, 61600 Brno, Czech Republic
| | - Karel Sedlar
- Brno University of Technology, Technicka 10, 61600 Brno, Czech Republic
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Fan YX, Zhang JZ, Zhang Q, Ma XQ, Liu ZY, Lu M, Qiao K, Li FL. Biofuel and chemical production from carbon one industry flux gas by acetogenic bacteria. ADVANCES IN APPLIED MICROBIOLOGY 2021; 117:1-34. [PMID: 34742365 DOI: 10.1016/bs.aambs.2021.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Carbon one industry flux gas generated from fossil fuels, various industrial and domestic waste, as well as lignocellulosic biomass provides an innovative raw material to lead the sustainable development. Through the chemical and biological processing, the gas mixture composed of CO, CO2, and H2, also termed as syngas, is converted to biofuels and high-value chemicals. Here, the syngas fermentation process is elaborated to provide an overview. Sources of syngas are summarized and the influences of impurities on biological fermentation are exhibited. Acetogens and carboxydotrophs are the two main clusters of syngas utilizing microorganisms, their essential characters are presented, especially the energy metabolic scheme with CO, CO2, and H2. Synthetic biology techniques and microcompartment regulation are further discussed and proposed to create a high-efficiency cell factory. Moreover, the influencing factors in fermentation and products in carboxylic acids, alcohols, and others such like polyhydroxyalkanoate and poly-3-hydroxybutyrate are addressed. Biological fermentation from carbon one industry flux gas is a promising alternative, the latest scientific advances are expatiated hoping to inspire more creative transformation.
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Affiliation(s)
- Yi-Xuan Fan
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jun-Zhe Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China
| | - Quan Zhang
- Sinopec Dalian (Fushun) Research Institute of Petroleum and Petrochemicals, Dalian, China
| | - Xiao-Qing Ma
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China
| | - Zi-Yong Liu
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China
| | - Ming Lu
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China
| | - Kai Qiao
- Sinopec Dalian (Fushun) Research Institute of Petroleum and Petrochemicals, Dalian, China.
| | - Fu-Li Li
- Shandong Provincial Key Laboratory of Synthetic Biology, Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Dalian National Laboratory for Clean Energy, Dalian, China.
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5
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Zhao N, Xu J, Jiao L, Qiu M, Zhang J, Wei X, Fan M. Transcriptome-Based Selection and Validation of Reference Genes for Gene Expression Analysis of Alicyclobacillus acidoterrestris Under Acid Stress. Front Microbiol 2021; 12:731205. [PMID: 34512609 PMCID: PMC8430261 DOI: 10.3389/fmicb.2021.731205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 08/10/2021] [Indexed: 11/13/2022] Open
Abstract
Alicyclobacillus acidoterrestris is a major concern in fruit juice industry due to its spoilage potential of acidic fruit juice. Quantifying the expression levels of functional genes by real-time quantitative polymerase chain reaction (RT-qPCR) is necessary to elucidate the response mechanisms of A. acidoterrestris to acid stress. However, appropriate reference genes (RGs) for data normalization are required to obtain reliable RT-qPCR results. In this study, eight novel candidate RGs were screened based on transcriptome datasets of A. acidoterrestris under acid stress. The expression stability of eight new RGs and commonly used RG 16s rRNA was assessed using geNorm, NormFinder, and BestKeeper algorithms. Moreover, the comprehensive analysis using the RefFinder program and the validation using target gene ctsR showed that dnaG and dnaN were the optimal multiple RGs for normalization at pH 4.0; ytvI, dnaG, and 16s rRNA at pH 3.5; icd and dnaG at pH 3.0; and ytvI, dnaG, and spoVE at pH 2.5. This study revealed for the first time that A. acidoterrestris had different suitable RGs under different acid conditions, with implications for further deciphering the acid response mechanisms of this spoilage-causing bacterium.
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Affiliation(s)
- Ning Zhao
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China
| | - Junnan Xu
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China
| | - Lingxia Jiao
- School of Food Science, Henan Institute of Science and Technology, Xinxiang, China
| | - Mengzhen Qiu
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China
| | - Jie Zhang
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China
| | - Xinyuan Wei
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China
| | - Mingtao Fan
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China
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Jureckova K, Raschmanova H, Kolek J, Vasylkivska M, Branska B, Patakova P, Provaznik I, Sedlar K. Identification and Validation of Reference Genes in Clostridium beijerinckii NRRL B-598 for RT-qPCR Using RNA-Seq Data. Front Microbiol 2021; 12:640054. [PMID: 33815328 PMCID: PMC8012504 DOI: 10.3389/fmicb.2021.640054] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/17/2021] [Indexed: 11/23/2022] Open
Abstract
Gene expression analysis through reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) depends on correct data normalization by reference genes with stable expression. Although Clostridium beijerinckii NRRL B-598 is a promising Gram-positive bacterium for the industrial production of biobutanol, validated reference genes have not yet been reported. In this study, we selected 160 genes with stable expression based on an RNA sequencing (RNA-Seq) data analysis, and among them, seven genes (zmp, rpoB1, rsmB, greA, rpoB2, topB2, and rimO) were selected for experimental validation by RT-qPCR and gene ontology (GO) enrichment analysis. According to statistical analyses, zmp and greA were the most stable and suitable reference genes for RT-qPCR normalization. Furthermore, our methodology can be useful for selection of the reference genes in other strains of C. beijerinckii and it also suggests that the RNA-Seq data can be used for the initial selection of novel reference genes, however, their validation is required.
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Affiliation(s)
- Katerina Jureckova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Hana Raschmanova
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Jan Kolek
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Maryna Vasylkivska
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Barbora Branska
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Petra Patakova
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Ivo Provaznik
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Karel Sedlar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
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Silva Rabelo CAB, Okino CH, Sakamoto IK, Varesche MBA. Isolation of Paraclostridium CR4 from sugarcane bagasse and its evaluation in the bioconversion of lignocellulosic feedstock into hydrogen by monitoring cellulase gene expression. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 715:136868. [PMID: 32014768 DOI: 10.1016/j.scitotenv.2020.136868] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 05/15/2023]
Abstract
Bioconversion of sugarcane bagasse (SCB) into hydrogen (H2) and organic acids was evaluated using a biomolecular approach to monitor the quantity and expression of the cellulase (Cel) gene. Batch reactors at 37 °C were operated with Paraclostridium sp. (10% v/v) and different substrates (5 g/L): glucose, cellulose and SCB in natura and pre-heat treated and hydrothermally. H2 production from glucose was 162.4 mL via acetic acid (2.9 g/L) and 78.4 mL from cellulose via butyric acid (2.9 g/L). H2 production was higher in hydrothermally pretreated SCB reactors (92.0 mL), heat treated (62.5 mL), when compared to in natura SCB (51.4 mL). Butyric acid (5.8, 4.9 and 4.0 g/L) was the main acid observed in hydrothermally, thermally pretreated, and in natura SCB, respectively. In the reactors with cellulose and reactors with hydrothermally pretreated SCB, the Cel gene copy number 3 and 2 log were higher, respectively, during the stage of maximum H2 production rate, when compared to the initial stage. Differences in Cel gene expression were observed according to the concentration of soluble sugars in the reaction medium. That is, there was no gene expression at the initial phase of the experiment using SCB with 2.6 g/L of sugars and increase of 2.2 log in gene expression during the phases with soluble sugars of <1.4 g/L.
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Affiliation(s)
- Camila Abreu B Silva Rabelo
- Laboratory of Biological Processes, Department of Hydraulics and Sanitation, Engineering School of São Carlos, University of São Paulo (EESC - USP) Campus II, São Carlos, SP CEP 13563-120, Brazil.
| | - Cintia Hiromi Okino
- Embrapa Pecuária Sudeste, Rod Washington Luiz, Km 234, Fazenda Canchim, PO Box 339, São Carlos, SP, Brazil
| | - Isabel Kimiko Sakamoto
- Laboratory of Biological Processes, Department of Hydraulics and Sanitation, Engineering School of São Carlos, University of São Paulo (EESC - USP) Campus II, São Carlos, SP CEP 13563-120, Brazil
| | - Maria Bernadete Amâncio Varesche
- Laboratory of Biological Processes, Department of Hydraulics and Sanitation, Engineering School of São Carlos, University of São Paulo (EESC - USP) Campus II, São Carlos, SP CEP 13563-120, Brazil
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Zhao R, Liu Y, Zhang H, Chai C, Wang J, Jiang W, Gu Y. CRISPR-Cas12a-Mediated Gene Deletion and Regulation in Clostridium ljungdahlii and Its Application in Carbon Flux Redirection in Synthesis Gas Fermentation. ACS Synth Biol 2019; 8:2270-2279. [PMID: 31526005 DOI: 10.1021/acssynbio.9b00033] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Uncovering the full potential of gas-fermenting Clostridia, attractive autotrophic bacteria capable of using synthesis gases (CO-CO2-H2) to produce a range of chemicals and fuels, for industrial applications relies on having efficient molecular tools for genetic modifications. Although the CRISPR-Cas9-mediated genome editing system has been developed in Clostridia, its use is limited owing to low GC content (approx. 30%) in these anaerobes. Therefore, the effector protein Cas12a, which recognizes T-rich instead of G-rich protospacer-adjacent motifs (PAMs), has evident advantages over Cas9 in CRISPR genome editing in Clostridia. Here, we developed the CRISPR-Cas12a system for efficient gene deletion and regulation in the gas-fermenting Clostridium ljungdahlii species. On the basis of screening for the most suitable Cas12a and significantly improved electrotransformation efficiency that bypassed poor repair efficiency of the Cas12a-caused DNA double-strand break (DSB) in C. ljungdahlii, efficient deletion (80-100%) of four genes (pyrE, pta, adhE1, and ctf) was achieved by using the CRISPR-FnCas12a system. Furthermore, a DNase-deactivated FnCas12a (ddCas12a) was adopted to construct a CRISPRi system to downregulate targeted genes, reaching over 80% repression for most of the chosen binding sites. This CRISPRi system was also used in a butyric acid-producing C. ljungdahlii strain to redirect carbon flux, leading to 20-40% reductions in ethanol titer that were accompanied by increased butyric acid titer. These results demonstrate the high efficiency of the CRISPR-FnCas12a system for genome engineering in C. ljungdahlii, which effectively expands the existing CRISPR-Cas toolbox in gas-fermenting Clostridium species and may play important roles in genetic manipulations where CRISPR-Cas9 is incompetent.
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Affiliation(s)
- Ran Zhao
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- School of Life Sciences, Henan University, Kaifeng 475001, China
| | - Yanqiang Liu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Huan Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Changsheng Chai
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jin Wang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Weihong Jiang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yang Gu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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Yang L, Chen J, Liu Y, Zhang S, Li S, Ding W. Validation of reference genes for quantitative gene expression analysis in Ralstonia pseudosolanacearum CQPS-1 under environment stress. J Microbiol Methods 2018; 148:104-109. [PMID: 29653150 DOI: 10.1016/j.mimet.2018.04.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/31/2018] [Accepted: 04/08/2018] [Indexed: 11/19/2022]
Abstract
Quantitative real-time reverse transcriptase PCR (qRT-PCR) has become the method choice for quantification of gene expression changes, however, the accuracy of the method depends on the stability of reference genes. Ralstonia pseudosolanacearum (R. pseudosolanacearum) is an important plant pathogen, infecting >450 plant species and causing bacterial wilt. In order to identify stable reference genes in R. pseudosolanacearum CQPS-1 under different environment stresses. We used five tools (△Ct method, GeNorm, NormFinder, BestKeeper, and RefFinder) to evaluate the stability of seven candidate reference genes including phosphoglycerate kinase (PGK), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), 16S ribosomal RNA (16S), cell division protein ftsZ (ftsZ), DNA gyrase subunit A (gyrA), Ribosomal protein L13 (rplM), and phosphoserine aminotransferase (serC) under biotic (growth phases) and abiotic stress (temperature, hydroxycoumarins, nutrition). Overall, gyrA and serC were the most stable genes under different growth phases, while serC, gyrA and ftsZ during temperature stress, gyrA, ftsZ and 16S under hydroxycoumarins stress, and serC and 16S under nutrition stress conditions. This study provides useful resources for normalizing expression changes of target genes in R. pseudosolanacearum subjected to environment stress.
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Affiliation(s)
- Liang Yang
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Juanni Chen
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Ying Liu
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Shuting Zhang
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Shili Li
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Wei Ding
- Laboratory of Natural Products Pesticides, College of Plant Protection, Southwest University, Chongqing 400715, China.
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Effects of zinc on the production of alcohol by Clostridium carboxidivorans P7 using model syngas. ACTA ACUST UNITED AC 2018; 45:61-69. [DOI: 10.1007/s10295-017-1992-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 11/26/2017] [Indexed: 01/03/2023]
Abstract
Abstract
Renewable energy, including biofuels such as ethanol and butanol from syngas bioconversed by Clostridium carboxidivorans P7, has been drawing extensive attention due to the fossil energy depletion and global eco-environmental issues. Effects of zinc on the growth and metabolites of C. carboxidivorans P7 were investigated with model syngas as the carbon source. The cell concentration was doubled, the ethanol content increased 3.02-fold and the butanol content increased 7.60-fold, the hexanol content increased 44.00-fold in the medium with 280 μM Zn2+, when comparing with those in the control medium [Zn2+, (7 μM)]. Studies of the genes expression involved in the carbon fixation as well as acid and alcohol production in the medium with 280 μM Zn2+ indicated that fdhII was up-regulated on the second day, acs A, fdhII, bdh35 and bdh50 were up-regulated on the third day and bdh35, acsB, fdhI, fdhIII, fdhIV, buk, bdh10, bdh35, bdh40 and bdh50 were up-regulated on the fourth day. The results indicated that the increased Zn2+ content increased the alcohol production through increase in the gene expression of the carbon fixation and alcohol dehydrogenase.
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11
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Polese V, de Paula Soares C, da Silva PRA, Simões-Araújo JL, Baldani JI, Vidal MS. Selection and validation of reference genes for RT-qPCR indicates that juice of sugarcane varieties modulate the expression of C metabolism genes in the endophytic diazotrophic Herbaspirillum rubrisubalbicans strain HCC103. Antonie Van Leeuwenhoek 2017; 110:1555-1568. [DOI: 10.1007/s10482-017-0906-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 06/28/2017] [Indexed: 12/24/2022]
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12
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Metabolic pathway analysis of the xylose-metabolizing yeast protoplast fusant ZLYRHZ7. J Biosci Bioeng 2017; 124:386-391. [DOI: 10.1016/j.jbiosc.2017.04.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 04/06/2017] [Accepted: 04/20/2017] [Indexed: 11/19/2022]
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Udaondo Z, Duque E, Ramos JL. The pangenome of the genus Clostridium. Environ Microbiol 2017; 19:2588-2603. [PMID: 28321969 DOI: 10.1111/1462-2920.13732] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 03/15/2017] [Accepted: 03/15/2017] [Indexed: 11/26/2022]
Abstract
The pangenome for the genus Clostridium sensu stricto, which was obtained using highly curated and annotated genomes from 16 species is presented; some of these cause disease, while others are used for the production of added-value chemicals. Multilocus sequencing analysis revealed that species of this genus group into at least two clades that include non-pathogenic and pathogenic strains, suggesting that pathogenicity is dispersed across the phylogenetic tree. The core genome of the genus includes 546 protein families, which mainly comprise those involved in protein translation and DNA repair. The GS-GOGAT may represent the central pathway for generating organic nitrogen from inorganic nitrogen sources. Glycerol and glucose metabolism genes are well represented in the core genome together with a set of energy conservation systems. A metabolic network comprising proteins/enzymes, RNAs and metabolites, whose topological structure is a non-random and scale-free network with hierarchically structured modules was built. These modules shed light on the interactions between RNAs, proteins and metabolites, revealing biological features of transcription and translation, cell wall biosynthesis, C1 metabolism and N metabolism. Network analysis identified four nodes that function as hubs and bottlenecks, namely, coenzyme A, HPr kinases, S-adenosylmethionine and the ribonuclease P-protein, suggesting pivotal roles for them in Clostridium.
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Affiliation(s)
- Zulema Udaondo
- Calle Energía Solar 1, Building D, Campus Palmas Altas, Abengoa Research, Biotechnology Technological Area, Sevilla, 41014, Spain.,Consejo Superior de Investigaciones Científicas, EEZ, Environmental Protection Department, C/Profesor Albareda 1, Granada, 18008, Spain
| | - Estrella Duque
- Calle Energía Solar 1, Building D, Campus Palmas Altas, Abengoa Research, Biotechnology Technological Area, Sevilla, 41014, Spain.,Consejo Superior de Investigaciones Científicas, EEZ, Environmental Protection Department, C/Profesor Albareda 1, Granada, 18008, Spain
| | - Juan-Luis Ramos
- Calle Energía Solar 1, Building D, Campus Palmas Altas, Abengoa Research, Biotechnology Technological Area, Sevilla, 41014, Spain.,Consejo Superior de Investigaciones Científicas, EEZ, Environmental Protection Department, C/Profesor Albareda 1, Granada, 18008, Spain
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14
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Biofilm Formation by Clostridium ljungdahlii Is Induced by Sodium Chloride Stress: Experimental Evaluation and Transcriptome Analysis. PLoS One 2017; 12:e0170406. [PMID: 28118386 PMCID: PMC5261816 DOI: 10.1371/journal.pone.0170406] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/04/2017] [Indexed: 01/08/2023] Open
Abstract
The acetogen Clostridium ljungdahlii is capable of syngas fermentation and microbial electrosynthesis. Biofilm formation could benefit both these applications, but was not yet reported for C. ljungdahlii. Biofilm formation does not occur under standard growth conditions, but attachment or aggregation could be induced by different stresses. The strongest biofilm formation was observed with the addition of sodium chloride. After 3 days of incubation, the biomass volume attached to a plastic surface was 20 times higher with than without the addition of 200 mM NaCl to the medium. The addition of NaCl also resulted in biofilm formation on glass, graphite and glassy carbon, the latter two being often used electrode materials for microbial electrosynthesis. Biofilms were composed of extracellular proteins, polysaccharides, as well as DNA, while pilus-like appendages were observed with, but not without, the addition of NaCl. A transcriptome analysis comparing planktonic (no NaCl) and biofilm (NaCl addition) cells showed that C. ljungdahlii coped with the salt stress by the upregulation of the general stress response, Na+ export and osmoprotectant accumulation. A potential role for poly-N-acetylglucosamines and D-alanine in biofilm formation was found. Flagellar motility was downregulated, while putative type IV pili biosynthesis genes were not expressed. Moreover, the gene expression analysis suggested the involvement of the transcriptional regulators LexA, Spo0A and CcpA in stress response and biofilm formation. This study showed that NaCl addition might be a valuable strategy to induce biofilm formation by C. ljungdahlii, which can improve the efficacy of syngas fermentation and microbial electrosynthesis applications.
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15
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Liew F, Henstra AM, Kӧpke M, Winzer K, Simpson SD, Minton NP. Metabolic engineering of Clostridium autoethanogenum for selective alcohol production. Metab Eng 2017; 40:104-114. [PMID: 28111249 PMCID: PMC5367853 DOI: 10.1016/j.ymben.2017.01.007] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 11/01/2016] [Accepted: 01/19/2017] [Indexed: 01/27/2023]
Abstract
Gas fermentation using acetogenic bacteria such as Clostridium autoethanogenum offers an attractive route for production of fuel ethanol from industrial waste gases. Acetate reduction to acetaldehyde and further to ethanol via an aldehyde: ferredoxin oxidoreductase (AOR) and alcohol dehydrogenase has been postulated alongside the classic pathway of ethanol formation via a bi-functional aldehyde/alcohol dehydrogenase (AdhE). Here we demonstrate that AOR is critical to ethanol formation in acetogens and inactivation of AdhE led to consistently enhanced autotrophic ethanol production (up to 180%). Using ClosTron and allelic exchange mutagenesis, which was demonstrated for the first time in an acetogen, we generated single mutants as well as double mutants for both aor and adhE isoforms to confirm the role of each gene. The aor1+2 double knockout strain lost the ability to convert exogenous acetate, propionate and butyrate into the corresponding alcohols, further highlighting the role of these enzymes in catalyzing the thermodynamically unfavourable reduction of carboxylic acids into alcohols. 180% improvement in C. autoethanogenum ethanol production via metabolic engineering. Confirmed role of AOR in autotrophic ethanol production of acetogens. Generated both aor and adhE mutants of C. autoethanogenum.. Demonstrated allelic exchange mutagenesis for stable deletions in acetogens. Inactivation of adhE and aor2, but not aor1, improves autotrophic ethanol production.
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Affiliation(s)
- Fungmin Liew
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham NG7 2RD, UK; LanzaTech Inc., 8045 Lamon Avenue, Suite 400, Skokie, IL, USA
| | - Anne M Henstra
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham NG7 2RD, UK
| | - Michael Kӧpke
- LanzaTech Inc., 8045 Lamon Avenue, Suite 400, Skokie, IL, USA
| | - Klaus Winzer
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham NG7 2RD, UK
| | - Sean D Simpson
- LanzaTech Inc., 8045 Lamon Avenue, Suite 400, Skokie, IL, USA
| | - Nigel P Minton
- BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham NG7 2RD, UK.
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16
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Whitham JM, Schulte MJ, Bobay BG, Bruno-Barcena JM, Chinn MS, Flickinger MC, Pawlak JJ, Grunden AM. Characterization of Clostridium ljungdahlii OTA1: a non-autotrophic hyper ethanol-producing strain. Appl Microbiol Biotechnol 2016; 101:1615-1630. [PMID: 27866253 DOI: 10.1007/s00253-016-7978-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 10/27/2016] [Accepted: 10/31/2016] [Indexed: 02/07/2023]
Abstract
A Clostridium ljungdahlii lab-isolated spontaneous-mutant strain, OTA1, has been shown to produce twice as much ethanol as the C. ljungdahlii ATCC 55383 strain when cultured in a mixotrophic medium containing fructose and syngas. Whole-genome sequencing identified four unique single nucleotide polymorphisms (SNPs) in the C. ljungdahlii OTA1 genome. Among these, two SNPs were found in the gene coding for AcsA and HemL, enzymes involved in acetyl-CoA formation from CO/CO2. Homology models of the respective mutated enzymes revealed alterations in the size and hydrogen bonding of the amino acids in their active sites. Failed attempts to grow OTA1 autotrophically suggested that one or both of these mutated genes prevented acetyl-CoA synthesis from CO/CO2, demonstrating that its activity was required for autotrophic growth by C. ljungdahlii. An inoperable Wood-Ljungdahl pathway resulted in higher CO2 and ethanol yields and lower biomass and acetate yields compared to WT for multiple growth conditions including heterotrophic and mixotrophic conditions. The two other SNPs identified in the C. ljungdahlii OTA1 genome were in genes coding for transcriptional regulators (CLJU_c09320 and CLJU_c18110) and were found to be responsible for deregulated expression of co-localized arginine catabolism and 2-deoxy-D-ribose catabolism genes. Growth medium supplementation experiments suggested that increased arginine metabolism and 2-deoxy-D-ribose were likely to have minor effects on biomass and fermentation product yields. In addition, in silico flux balance analysis simulating mixotrophic and heterotrophic conditions showed no change in flux to ethanol when flux through HemL was changed whereas limited flux through AcsA increased the ethanol flux for both simulations. In characterizing the effects of the SNPs identified in the C. ljungdahlii OTA1 genome, a non-autotrophic hyper ethanol-producing strain of C. ljungdahlii was identified that has utility for further physiology and strain performance studies and as a biocatalyst for industrial applications.
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Affiliation(s)
- Jason M Whitham
- Department of Plant and Microbial Biology, North Carolina State University, 4548 Thomas Hall, Campus Box 7615, Raleigh, NC, 27695-7615, USA
| | - Mark J Schulte
- Department of Chemical and Biomolecular Engineering, 196 Golden LEAF Biomanufacturing Training and Education Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Benjamin G Bobay
- Duke University NMR Center, Duke University Medical Center, Duke University, Durham, NC, 27710, USA
| | - Jose M Bruno-Barcena
- Department of Plant and Microbial Biology, North Carolina State University, 4548 Thomas Hall, Campus Box 7615, Raleigh, NC, 27695-7615, USA
| | - Mari S Chinn
- Department of Biological and Agricultural Engineering, North Carolina State University, 277 Weaver Labs, Campus Box 7625, Raleigh, NC, 27695-7625, USA
| | - Michael C Flickinger
- Department of Chemical and Biomolecular Engineering, 196 Golden LEAF Biomanufacturing Training and Education Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Joel J Pawlak
- Department of Forest Biomaterials, North Carolina State University, 2028C Biltmore Hall, Campus Box 8001, Raleigh, NC, 27695-8001, USA
| | - Amy M Grunden
- Department of Plant and Microbial Biology, North Carolina State University, 4548 Thomas Hall, Campus Box 7615, Raleigh, NC, 27695-7615, USA.
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17
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Wu BY, Ye JR, Huang L, He LM, Li DW. Validation of reference genes for RT-qPCR analysis in Burkholderia pyrrocinia JK-SH007. J Microbiol Methods 2016; 132:95-98. [PMID: 27725176 DOI: 10.1016/j.mimet.2016.10.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 10/06/2016] [Accepted: 10/06/2016] [Indexed: 11/18/2022]
Abstract
Burkholderia pyrrocinia strain JK-SH007 isolated from poplar stems plays a highly significant role in the growth promotion and the biocontrol of poplar canker during colonization in poplar. In this research, the ideal reference gene was filtered and determined for the transcript normalization. Additionally, the expression of pyrG under all four conditions was relatively stable in B. pyrrocinia JK-SH007.
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Affiliation(s)
- Bin-Yan Wu
- College of Forestry and Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Jian-Ren Ye
- College of Forestry and Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu, China.
| | - Lin Huang
- College of Forestry and Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Ling-Min He
- College of Forestry and Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - De-Wei Li
- College of Forestry and Co-Innovation Center for Sustainable Forestry in Southern China, Jiangsu Key Laboratory for Prevention and Management of Invasive Species, Nanjing Forestry University, Nanjing, Jiangsu, China; The Connecticut Agricultural Experiment Station, Valley Laboratory, 153 Cook Hill Road, Windsor, CT, United States
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18
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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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19
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Hu Y, Xie S, Yao J. Identification of Novel Reference Genes Suitable for qRT-PCR Normalization with Respect to the Zebrafish Developmental Stage. PLoS One 2016; 11:e0149277. [PMID: 26891128 PMCID: PMC4758726 DOI: 10.1371/journal.pone.0149277] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 01/29/2016] [Indexed: 12/20/2022] Open
Abstract
Reference genes used in normalizing qRT-PCR data are critical for the accuracy of gene expression analysis. However, many traditional reference genes used in zebrafish early development are not appropriate because of their variable expression levels during embryogenesis. In the present study, we used our previous RNA-Seq dataset to identify novel reference genes suitable for gene expression analysis during zebrafish early developmental stages. We first selected 197 most stably expressed genes from an RNA-Seq dataset (29,291 genes in total), according to the ratio of their maximum to minimum RPKM values. Among the 197 genes, 4 genes with moderate expression levels and the least variation throughout 9 developmental stages were identified as candidate reference genes. Using four independent statistical algorithms (delta-CT, geNorm, BestKeeper and NormFinder), the stability of qRT-PCR expression of these candidates was then evaluated and compared to that of actb1 and actb2, two commonly used zebrafish reference genes. Stability rankings showed that two genes, namely mobk13 (mob4) and lsm12b, were more stable than actb1 and actb2 in most cases. To further test the suitability of mobk13 and lsm12b as novel reference genes, they were used to normalize three well-studied target genes. The results showed that mobk13 and lsm12b were more suitable than actb1 and actb2 with respect to zebrafish early development. We recommend mobk13 and lsm12b as new optimal reference genes for zebrafish qRT-PCR analysis during embryogenesis and early larval stages.
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Affiliation(s)
- Yu Hu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Shuying Xie
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Jihua Yao
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
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20
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Goret J, Le Roy C, Touati A, Mesureur J, Renaudin H, Claverol S, Bébéar C, Béven L, Pereyre S. Surface lipoproteome of Mycoplasma hominis PG21 and differential expression after contact with human dendritic cells. Future Microbiol 2016; 11:179-94. [DOI: 10.2217/fmb.15.130] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To assess the lipoproteins that are involved in the interaction between Mycoplasma hominis and human dendritic cells. Materials & methods: The surface lipoproteome of M. hominis PG21 was characterized by using Triton X-114 extraction and LC–MS/MS identification. The transcriptional changes in lipoprotein genes upon contact with human dendritic cells were determined by using reverse transcription quantitative PCR after identification of reference genes suitable for normalization. Results: A large-scale overexpression of lipoprotein genes was observed with 21 upregulated transcripts. Seven genes of unknown function were M. hominis species specific and six genes were putatively associated with increased nutrient capture from the host cell and adhesion. Conclusion: M. hominis regulates lipoprotein gene expression and may use species-specific mechanisms during the host colonization process.
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Affiliation(s)
- Julien Goret
- Université de Bordeaux, USC EA 3671 Mycoplasmal & Chlamydial Infections in Humans, Bordeaux, France
- INRA, USC EA 3671 Mycoplasmal & Chlamydial Infections in Humans, Bordeaux, France
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
| | - Chloé Le Roy
- Université de Bordeaux, USC EA 3671 Mycoplasmal & Chlamydial Infections in Humans, Bordeaux, France
- INRA, USC EA 3671 Mycoplasmal & Chlamydial Infections in Humans, Bordeaux, France
| | - Arabella Touati
- Université de Bordeaux, USC EA 3671 Mycoplasmal & Chlamydial Infections in Humans, Bordeaux, France
- INRA, USC EA 3671 Mycoplasmal & Chlamydial Infections in Humans, Bordeaux, France
| | | | - Hélène Renaudin
- Université de Bordeaux, USC EA 3671 Mycoplasmal & Chlamydial Infections in Humans, Bordeaux, France
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
| | - Stéphane Claverol
- Pôle Protéomique, Plateforme Génomique Fonctionnelle de Bordeaux, Université de Bordeaux, Bordeaux, France
| | - Cécile Bébéar
- Université de Bordeaux, USC EA 3671 Mycoplasmal & Chlamydial Infections in Humans, Bordeaux, France
- INRA, USC EA 3671 Mycoplasmal & Chlamydial Infections in Humans, Bordeaux, France
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
| | - Laure Béven
- INRA, UMR 1332, Biologie du Fruit et Pathologie, Villenave d'Ornon, France
- Université de Bordeaux, UMR 1332, Biologie du Fruit et Pathologie, Bordeaux, France
| | - Sabine Pereyre
- Université de Bordeaux, USC EA 3671 Mycoplasmal & Chlamydial Infections in Humans, Bordeaux, France
- INRA, USC EA 3671 Mycoplasmal & Chlamydial Infections in Humans, Bordeaux, France
- Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
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21
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Metabolic response of Clostridium ljungdahlii to oxygen exposure. Appl Environ Microbiol 2015; 81:8379-91. [PMID: 26431975 DOI: 10.1128/aem.02491-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 09/23/2015] [Indexed: 12/31/2022] Open
Abstract
Clostridium ljungdahlii is an important synthesis gas-fermenting bacterium used in the biofuels industry, and a preliminary investigation showed that it has some tolerance to oxygen when cultured in rich mixotrophic medium. Batch cultures not only continue to grow and consume H2, CO, and fructose after 8% O2 exposure, but fermentation product analysis revealed an increase in ethanol concentration and decreased acetate concentration compared to non-oxygen-exposed cultures. In this study, the mechanisms for higher ethanol production and oxygen/reactive oxygen species (ROS) detoxification were identified using a combination of fermentation, transcriptome sequencing (RNA-seq) differential expression, and enzyme activity analyses. The results indicate that the higher ethanol and lower acetate concentrations were due to the carboxylic acid reductase activity of a more highly expressed predicted aldehyde oxidoreductase (CLJU_c24130) and that C. ljungdahlii's primary defense upon oxygen exposure is a predicted rubrerythrin (CLJU_c39340). The metabolic responses of higher ethanol production and oxygen/ROS detoxification were found to be linked by cofactor management and substrate and energy metabolism. This study contributes new insights into the physiology and metabolism of C. ljungdahlii and provides new genetic targets to generate C. ljungdahlii strains that produce more ethanol and are more tolerant to syngas contaminants.
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22
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Bacterial reference genes for gene expression studies by RT-qPCR: survey and analysis. Antonie van Leeuwenhoek 2015; 108:685-93. [PMID: 26149127 DOI: 10.1007/s10482-015-0524-1] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Accepted: 06/29/2015] [Indexed: 10/23/2022]
Abstract
The appropriate choice of reference genes is essential for accurate normalization of gene expression data obtained by the method of reverse transcription quantitative real-time PCR (RT-qPCR). In 2009, a guideline called the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) highlighted the importance of the selection and validation of more than one suitable reference gene for obtaining reliable RT-qPCR results. Herein, we searched the recent literature in order to identify the bacterial reference genes that have been most commonly validated in gene expression studies by RT-qPCR (in the first 5 years following publication of the MIQE guidelines). Through a combination of different search parameters with the text mining tool MedlineRanker, we identified 145 unique bacterial genes that were recently tested as candidate reference genes. Of these, 45 genes were experimentally validated and, in most of the cases, their expression stabilities were verified using the software tools geNorm and NormFinder. It is noteworthy that only 10 of these reference genes had been validated in two or more of the studies evaluated. An enrichment analysis using Gene Ontology classifications demonstrated that genes belonging to the functional categories of DNA Replication (GO: 0006260) and Transcription (GO: 0006351) rendered a proportionally higher number of validated reference genes. Three genes in the former functional class were also among the top five most stable genes identified through an analysis of gene expression data obtained from the Pathosystems Resource Integration Center. These results may provide a guideline for the initial selection of candidate reference genes for RT-qPCR studies in several different bacterial species.
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Cusick KD, Fitzgerald LA, Cockrell AL, Biffinger JC. Selection and Evaluation of Reference Genes for Reverse Transcription-Quantitative PCR Expression Studies in a Thermophilic Bacterium Grown under Different Culture Conditions. PLoS One 2015; 10:e0131015. [PMID: 26115538 PMCID: PMC4482720 DOI: 10.1371/journal.pone.0131015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 05/26/2015] [Indexed: 11/18/2022] Open
Abstract
The phylum Deinococcus-Thermus is a deeply-branching lineage of bacteria widely recognized as one of the most extremophilic. Members of the Thermus genus are of major interest due to both their bioremediation and biotechnology potentials. However, the molecular mechanisms associated with these key metabolic pathways remain unknown. Reverse-transcription quantitative PCR (RT-qPCR) is a high-throughput means of studying the expression of a large suite of genes over time and under different conditions. The selection of a stably-expressed reference gene is critical when using relative quantification methods, as target gene expression is normalized to expression of the reference gene. However, little information exists as to reference gene selection in extremophiles. This study evaluated 11 candidate reference genes for use with the thermophile Thermus scotoductus when grown under different culture conditions. Based on the combined stability values from BestKeeper and NormFinder software packages, the following are the most appropriate reference genes when comparing: (1) aerobic and anaerobic growth: TSC_c19900, polA2, gyrA, gyrB; (2) anaerobic growth with varied electron acceptors: TSC_c19900, infA, pfk, gyrA, gyrB; (3) aerobic growth with different heating methods: gyrA, gap, gyrB; (4) all conditions mentioned above: gap, gyrA, gyrB. The commonly-employed rpoC does not serve as a reliable reference gene in thermophiles, due to its expression instability across all culture conditions tested here. As extremophiles exhibit a tendency for polyploidy, absolute quantification was employed to determine the ratio of transcript to gene copy number in a subset of the genes. A strong negative correlation was found to exist between ratio and threshold cycle (CT) values, demonstrating that CT changes reflect transcript copy number, and not gene copy number, fluctuations. Even with the potential for polyploidy in extremophiles, the results obtained via absolute quantification indicate that relative quantification is appropriate for RT-qPCR studies with this thermophile.
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Affiliation(s)
- Kathleen D Cusick
- National Research Council Associateship, US Naval Research Laboratory, 4555 Overlook Ave., SW, Washington DC, 20375, United States of America
| | - Lisa A Fitzgerald
- Chemistry Division, US Naval Research Laboratory, 4555 Overlook Ave., SW, Washington DC, 20375, United States of America
| | - Allison L Cockrell
- National Research Council Associateship, US Naval Research Laboratory, 4555 Overlook Ave., SW, Washington DC, 20375, United States of America
| | - Justin C Biffinger
- Chemistry Division, US Naval Research Laboratory, 4555 Overlook Ave., SW, Washington DC, 20375, United States of America
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24
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Xie BT, Liu ZY, Tian L, Li FL, Chen XH. Physiological response of Clostridium ljungdahlii DSM 13528 of ethanol production under different fermentation conditions. BIORESOURCE TECHNOLOGY 2015; 177:302-7. [PMID: 25496952 DOI: 10.1016/j.biortech.2014.11.101] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 11/24/2014] [Accepted: 11/25/2014] [Indexed: 05/24/2023]
Abstract
In this study, cell growth, gene expression and ethanol production were monitored under different fermentation conditions. Like its heterotrophical ABE-producing relatives, a switch from acidogenesis to solventogenesis of Clostridium ljungdahlii during the autotrophic fermentation with CO/CO2 could be observed, which occurred surprisingly in the late-log phase rather than in the transition phase. The gene expression profiles indicated that aor1, one of the putative aldehyde oxidoreductases in its genome played a critical role in the formation of ethanol, and its transcription could be induced by external acids. Moreover, a low amount of CaCO3 was proved to have positive influences on the cell density and substrate utilization, followed by an increase of over 40% ethanol and 30% acetate formation.
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Affiliation(s)
- Bin-Tao Xie
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Road 189, Qingdao 266101, China; University of Chinese Academy of Sciences, Yuquan Road 19A, Beijing 100049, China
| | - Zi-Yong Liu
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Road 189, Qingdao 266101, China
| | - Lei Tian
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Road 189, Qingdao 266101, China
| | - Fu-Li Li
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Road 189, Qingdao 266101, China
| | - Xiao-Hua Chen
- Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Songling Road 189, Qingdao 266101, China.
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Tan Y, Liu ZY, Liu Z, Zheng HJ, Li FL. Comparative transcriptome analysis between csrA-disruption Clostridium acetobutylicum and its parent strain. MOLECULAR BIOSYSTEMS 2015; 11:1434-42. [DOI: 10.1039/c4mb00600c] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This study represented the first attempt to investigate the global regulation of CsrA through transcriptome analysis in Gram-positive bacteria.
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Affiliation(s)
- Yang Tan
- Key Laboratory of Biofuels
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- China
| | - Zi-Yong Liu
- Key Laboratory of Biofuels
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- China
| | - Zhen Liu
- Key Laboratory of Biofuels
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- China
| | - Hua-Jun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics
- Chinese National Human Genome Center at Shanghai
- Shanghai 201203
- China
| | - Fu-Li Li
- Key Laboratory of Biofuels
- Qingdao Institute of Bioenergy and Bioprocess Technology
- Chinese Academy of Sciences
- Qingdao 266101
- China
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Converting carbon dioxide to butyrate with an engineered strain of Clostridium ljungdahlii. mBio 2014; 5:e01636-14. [PMID: 25336453 PMCID: PMC4212834 DOI: 10.1128/mbio.01636-14] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Microbial conversion of carbon dioxide to organic commodities via syngas metabolism or microbial electrosynthesis is an attractive option for production of renewable biocommodities. The recent development of an initial genetic toolbox for the acetogen Clostridium ljungdahlii has suggested that C. ljungdahlii may be an effective chassis for such conversions. This possibility was evaluated by engineering a strain to produce butyrate, a valuable commodity that is not a natural product of C. ljungdahlii metabolism. Heterologous genes required for butyrate production from acetyl-coenzyme A (CoA) were identified and introduced initially on plasmids and in subsequent strain designs integrated into the C. ljungdahlii chromosome. Iterative strain designs involved increasing translation of a key enzyme by modifying a ribosome binding site, inactivating the gene encoding the first step in the conversion of acetyl-CoA to acetate, disrupting the gene which encodes the primary bifunctional aldehyde/alcohol dehydrogenase for ethanol production, and interrupting the gene for a CoA transferase that potentially represented an alternative route for the production of acetate. These modifications yielded a strain in which ca. 50 or 70% of the carbon and electron flow was diverted to the production of butyrate with H2 or CO as the electron donor, respectively. These results demonstrate the possibility of producing high-value commodities from carbon dioxide with C. ljungdahlii as the catalyst. Importance: The development of a microbial chassis for efficient conversion of carbon dioxide directly to desired organic products would greatly advance the environmentally sustainable production of biofuels and other commodities. Clostridium ljungdahlii is an effective catalyst for microbial electrosynthesis, a technology in which electricity generated with renewable technologies, such as solar or wind, powers the conversion of carbon dioxide and water to organic products. Other electron donors for C. ljungdahlii include carbon monoxide, which can be derived from industrial waste gases or the conversion of recalcitrant biomass to syngas, as well as hydrogen, another syngas component. The finding that carbon and electron flow in C. ljungdahlii can be diverted from the production of acetate to butyrate synthesis is an important step toward the goal of renewable commodity production from carbon dioxide with this organism.
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Engineering microbial electrocatalysis for chemical and fuel production. Curr Opin Biotechnol 2014; 29:93-8. [DOI: 10.1016/j.copbio.2014.03.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Revised: 03/07/2014] [Accepted: 03/11/2014] [Indexed: 11/19/2022]
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Carvalho DM, de Sá PH, Castro TLP, Carvalho RD, Pinto A, Gil DJP, Bagano P, Bastos B, Costa LFM, Meyer R, Silva A, Azevedo V, Ramos RTJ, Pacheco LGC. Reference genes for RT-qPCR studies in Corynebacterium pseudotuberculosis identified through analysis of RNA-seq data. Antonie van Leeuwenhoek 2014; 106:605-14. [DOI: 10.1007/s10482-014-0231-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 07/02/2014] [Indexed: 11/27/2022]
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