DOCSLIB.ORG

1 Metabolic Engineering of Clostridium Cellulovorans For

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
1 Metabolic Engineering of Clostridium Cellulovorans For Metabolic engineering of Clostridium cellulovorans for selective n-butanol production from cellulose Dissertation Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Teng Bao, M.S. Graduate Program in Chemical Engineering The Ohio State University 2019 Dissertation Committee Shang-Tian Yang, Advisor Charles E. Bell Jeffrey Chalmers Eduardo Reátegui 1 Copyrighted by Teng Bao 2019 2 Abstract n-Butanol as a promising alternative biofuel has gained high interest. Especially, compared with methanol and ethanol, n-butanol presents superior fuel properties and can be used as an ideal substitute of gasoline because of its high energy density, low water solubility, and low vapor pressure. Unfortunately, bio-butanol production through the conventional acetone-butanol-ethanol (ABE) fermentation process is not economically feasible because of the co-production of other metabolites and the use of expensive food- based feedstock. Lignocellulosic biomass, an abundant, cheap, and renewable source, is a desired feedstock for biofuels production. Conventional biorefinery of lignocellulosic biomass requires different operations, which is not cost-effective due to the complex process and high equipment capital requirement. Currently, several process strategies have been developed for cellulosic butanol production. Among them, consolidated bioprocessing (CBP) combines enzyme production, biomass hydrolysis, and sugar fermentation into one step, which greatly simplifies the process and dramatically reduces the equipment investment. Clostridium cellulovorans is a strictly anaerobic, cellulolytic bacterium among the most interesting candidates for CBP of lignocellulosic biomass. Recently, a bifunctional aldehyde/alcohol dehydrogenase gene adhE2 from Clostridium acetobutylicum has been overexpressed in C. cellulovorans for n-butanol production from cellulose. However, this ii recombinant strain produced n-butanol from microcrystalline cellulose at a low titer and yield insufficient for industrial application. In addition, there are two type II restriction modification (RM) systems in C. cellulovorans and currently available plasmids would be digested by C. cellulovorans cell extract even after in vivo methylation, making it difficult to transfer and express genes in C. cellulovorans for further metabolic engineering. Therefore, efficient transformation for developing better recombinant C. cellulovorans for butanol production is urgently required. In this study, the RM system of C. cellulovorans was analyzed and a new Clostridium shuttle plasmid pYL001 without Cce743I and Cce743II restriction sites was constructed to overcome the transformation barrier in C. cellulovorans. The new plasmid with improved post-electroporation procedure significantly improved the transformation efficiency and allowed the use of unmethylated DNA for metabolic engineering of C. cellulovorans. Then a synthetic butanol formation pathway was introduced in C. cellulovorans by overexpressing three different aldehyde/alcohol dehydrogenases gene combinations (acidogenesis: adhE2-bdhB, solventogenesis: adhE1-bdhB, and alcohologenesis: adhE2) from C. acetobutylicum. Due to different substrate and cofactor specificities, overexpressing different ADH and BDH in C. cellulovorans resulted in different amounts of alcohols production. Among them, C. cellulovorans adhE2 with the highest aldehyde/alcohol dehydrogenase activities produced the highest n-butanol titer of ~4 g/L with a high yield of ~0.22 g/g. Finally, modular metabolic engineering strategies, including strengthening the butyryl-CoA biosynthesis and improving intracellular NADH availability, were applied to redistribute the carbon flux towards butanol production in C. iii cellulovorans. Heterologous thiolase (thlA) and 3-hydroxybutyryl-CoA dehydrogenase (hbd) genes from C. acetobutylicum and Clostridium tyrobutyricum, respectively, were overexpressed in C. cellulovorans adhE2 to increase the flux from C2 to C4 metabolites. In addition, ferredoxin-NAD(P)+ oxidoreductase (fnr) from C. acetobutylicum, which can regenerate the intracellular NAD(P)H and thus increase alcohols formation, was also overexpressed. In batch fermentation with adding methyl viologen (MV) as an electron carrier, the recombinant C. cellulovorans adhE2-fnrCA-thlACA-hbdCT was able to direct the carbon flux towards n-butanol biosynthesis, leading to a high n-butanol titer of 5.56 g/L with a high yield of 0.34 g/g cellulose, which were the highest ever obtained for butanol production from cellulose in a mono-culture fermentation. These results indicated that C. cellulovorans is a promising CBP platform host for bio-butanol production from lignocellulosic biomass. iv Dedication This document is dedicated to my family and friends. v Acknowledgments I would like to express my deep and sincere gratitude to my advisor, Dr. Shang- Tian Yang for his continuous support of my Ph.D. study and research, for his insight, enthusiasm, and immense knowledge. He not only guided me how to solve the problems in studies, but also taught me how to face the difficulties in my life. His aggressive upward style also affected me a lot, from which I will benefit a lot in the future. I am also very thankful to the rest of my committee members, Prof. Jeffrey Chalmers and Prof. Eduardo Reátegui for their encouragement, insightful comments, and challenging questions. My sincere thanks also go to Dr. Mei Shao, Dr. Siguang Sui, Dr. Hungwei Chien, Mrs. Bianca Olson and Mr. David Ramey, for offering me summer internship opportunities to work on diverse exciting projects in their groups. I also want to thank all current and previous lab mates, including Dr. Jingbo Zhao, Dr. Meng Lin, Dr. Jin Huang, Dr. Xian Zhang, Dr. Xin Xin, Dr. Chi Cheng, Mrs. Li Lu, Ms. Fengli Zhang, Ms. You Li, and Ms. Zhen Qin for useful discussions. Especially, I would like to thank Dr. Zhao, who helped me with many experimental details, and taught me genetic engineering design when I first joined the project. In addition, I also would like to thank all my friends met at the Ohio State University. vi Financial supports from US Department of Energy EERE (DE-EE0007005) and SBIR (DE-FOA-0001771) program and ENGIE-Axium scholarship during the course of this research are acknowledged. Last but not the least, I would like to thank my girlfriend, Xuyao Liu, for her support and encouragement during my graduate study. I also want to deeply thank my parents, Jinhua Bao and Ji Guan, for giving me their selfless love and forever support. vii Vita November 1990……….……………………………………….Born-Jiashan, P.R. China 2012.…B.S. Bioengineering, Zhejiang University of Science & Technology, P.R. China 2015……………………………..M.S. Bioengineering, Jiangnan University, P.R. China 2015-2019…………..Graduate Teaching/Research Associate, Department of Chemical and Biomolecular Engineering, The Ohio State University Publications 1. Teng Bao, Jingbo Zhao, Jing Li, Xin Liu, and Shang-Tian Yang. 2019. n-Butanol and ethanol production from cellulose by Clostridium cellulovorans overexpressing heterologous aldehyde/alcohol dehydrogenases. Bioresource Technology, 3:121316. 2. Teng Bao, Jingbo Zhao, Qianxia Zhang, and Shang-Tian Yang. 2019. Development of a shuttle plasmid without host restriction sites for efficient transformation and heterologous gene expression in Clostridium cellulovorans. Applied Microbiology and Biotechnology, 103:5391-5400. 3. Teng Bao, Chi Cheng, Xin Xin, Jufang Wang, Minqi Wang, and Shang-Tian Yang. 2019. Deciphering mixotrophic Clostridium formicoaceticum metabolism and energy conservation: Genomic analysis and experimental studies. Genomics, 111:1687-94. 4. Chi Cheng, Teng Bao, and Shang-Tian Yang. 2019. Engineering Clostridium for improved solvent production: Recent progress and perspective. Applied Microbiology and Biotechnology. 103:5549-5566. 5. Jianfa Ou, Teng Bao, Patrick Ernst, Yingnan Si, Sumanth Prabhu, Hui Wu, Jianyi viii Zhang, Lufang Zhou, Shang-Tian Yang, Xiaoguang Liu. 2019. Intracellular metabolism analysis of Clostridium cellulovorans via modeling integrating proteomics, metabolomics and fermentation. Process Biochemistry. In press. 6. Jing Li, Yinming Du, Teng Bao, Jie Dong, Meng Lin, Hojae Shim, Shang-Tian Yang. 2019. n-Butanol production from lignocellulosic biomass hydrolysates without detoxification by Clostridium tyrobutyricum Δack-adhE2 in a fibrous-bed bioreactor. Bioresource Technology. 289:121749. (Co-first author) 7. Jin Huang, Yinming Du, Teng Bao, Meng Lin, Jufang Wang, Shang-Tian Yang. 2019. Production of n-butanol from cassava bagasse hydrolysate by engineered Clostridium tyrobutyricum overexpressing adhE2: Kinetics and cost analysis. Bioresource Technology. 292:121969. (Co-first author) 8. Xian Zhang, Rumeng Han, Teng Bao, Xiaojing Zhao, Xiangfei Li, Manchi Zhu, Taowei Yang, Meijuan Xu, Minglong Shao, Youxi Zhao, Zhiming Rao. 2019. Synthetic engineering of Corynebacterium crenatum to selectively produce acetoin or 2,3-butanediol by one step bioconversion method. Microbial Cell Factories. 18:128. 9. Zhiping Xiao, Chu Cheng, Teng Bao, Lujie Liu, Bin Wang, Wenjing Tao, Xun Pei, Shang-Tian Yang, and Minqi Wang. 2018. Production of butyric acid from acid hydrolysate of corn husk in fermentation by Clostridium tyrobutyricum: kinetics and process economic analysis. Biotechnology for Biofuels, 11(1), 164. 10. Niyomukiza Samuel, Teng Bao, Xian Zhang, Taowei Yang, Meijuan Xu, Xin Li, Irene Komera, Tuyishime Philibert, and Zhiming
Load more

Recommended publications
  • From Sporulation to Intracellular Offspring Production: Evolution
    FROM SPORULATION TO INTRACELLULAR OFFSPRING PRODUCTION: EVOLUTION OF THE DEVELOPMENTAL PROGRAM OF EPULOPISCIUM A Dissertation Presented to the Faculty of the Graduate School of Cornell University In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by David Alan Miller January 2012 © 2012 David Alan Miller FROM SPORULATION TO INTRACELLULAR OFFSPRING PRODUCTION: EVOLUTION OF THE DEVELOPMENTAL PROGRAM OF EPULOPISCIUM David Alan Miller, Ph. D. Cornell University 2012 Epulopiscium sp. type B is an unusually large intestinal symbiont of the surgeonfish Naso tonganus. Unlike most other bacteria, Epulopiscium sp. type B has never been observed to undergo binary fission. Instead, to reproduce, it forms multiple intracellular offspring. We believe this process is related to endospore formation, an ancient and complex developmental process performed by certain members of the Firmicutes. Endospore formation has been studied for over 50 years and is best characterized in Bacillus subtilis. To study the evolution of endospore formation in the Firmicutes and the relatedness of this process to intracellular offspring formation in Epulopiscium, we have searched for sporulation genes from the B. subtilis model in all of the completed genomes of members of the Firmicutes, in addition to Epulopiscium sp. type B and its closest relative, the spore-forming Cellulosilyticum lentocellum. By determining the presence or absence of spore genes, we see the evolution of endospore formation in closely related bacteria within the Firmicutes and begin to predict if 19 previously characterized non-spore-formers have the genetic capacity to form a spore. We can also map out sporulation-specific mechanisms likely being used by Epulopiscium for offspring formation.
    [Show full text]
  • EXPERIMENTAL STUDIES on FERMENTATIVE FIRMICUTES from ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, and THEIR GEOCHEMICAL IMPACTS By
    EXPERIMENTAL STUDIES ON FERMENTATIVE FIRMICUTES FROM ANOXIC ENVIRONMENTS: ISOLATION, EVOLUTION, AND THEIR GEOCHEMICAL IMPACTS By JESSICA KEE EUN CHOI A dissertation submitted to the School of Graduate Studies Rutgers, The State University of New Jersey In partial fulfillment of the requirements For the degree of Doctor of Philosophy Graduate Program in Microbial Biology Written under the direction of Nathan Yee And approved by _______________________________________________________ _______________________________________________________ _______________________________________________________ _______________________________________________________ New Brunswick, New Jersey October 2017 ABSTRACT OF THE DISSERTATION Experimental studies on fermentative Firmicutes from anoxic environments: isolation, evolution and their geochemical impacts by JESSICA KEE EUN CHOI Dissertation director: Nathan Yee Fermentative microorganisms from the bacterial phylum Firmicutes are quite ubiquitous in subsurface environments and play an important biogeochemical role. For instance, fermenters have the ability to take complex molecules and break them into simpler compounds that serve as growth substrates for other organisms. The research presented here focuses on two groups of fermentative Firmicutes, one from the genus Clostridium and the other from the class Negativicutes. Clostridium species are well-known fermenters. Laboratory studies done so far have also displayed the capability to reduce Fe(III), yet the mechanism of this activity has not been investigated
    [Show full text]
  • Development of a Metabolic Pathway Transfer and Genomic Integration
    Philipps et al. Biotechnol Biofuels (2019) 12:112 https://doi.org/10.1186/s13068-019-1448-1 Biotechnology for Biofuels RESEARCH Open Access Development of a metabolic pathway transfer and genomic integration system for the syngas-fermenting bacterium Clostridium ljungdahlii Gabriele Philipps1, Sebastian de Vries1,2 and Stefan Jennewein1* Abstract Background: Clostridium spp. can synthesize valuable chemicals and fuels by utilizing diverse waste-stream sub- strates, including starchy biomass, lignocellulose, and industrial waste gases. However, metabolic engineering in Clostridium spp. is challenging due to the low efciency of gene transfer and genomic integration of entire biosyn- thetic pathways. Results: We have developed a reliable gene transfer and genomic integration system for the syngas-fermenting bacterium Clostridium ljungdahlii based on the conjugal transfer of donor plasmids containing large transgene cas- settes (> 5 kb) followed by the inducible activation of Himar1 transposase to promote integration. We established a conjugation protocol for the efcient generation of transconjugants using the Gram-positive origins of replica- tion repL and repH. We also investigated the impact of DNA methylation on conjugation efciency by testing donor constructs with all possible combinations of Dam and Dcm methylation patterns, and used bisulfte conversion and PacBio sequencing to determine the DNA methylation profle of the C. ljungdahlii genome, resulting in the detection of four sequence motifs with N6-methyladenosine. As proof of concept, we demonstrated the transfer and genomic integration of a heterologous acetone biosynthesis pathway using a Himar1 transposase system regulated by a xylose-inducible promoter. The functionality of the integrated pathway was confrmed by detecting enzyme proteo- typic peptides and the formation of acetone and isopropanol by C.
    [Show full text]
  • ABSTRACT WHITHAM, JASON MICHAEL. Identifying Genetic
    ABSTRACT WHITHAM, JASON MICHAEL. Identifying Genetic Targets and Growth Conditions for Higher Ethanol Production by the Synthesis Gas Fermenting Bacterium Clostridium ljungdahlii (Under direction of Dr. Amy M. Grunden and Dr. Joel J. Pawlak). The United States has increasing volume mandates for cellulosic biofuels production to reduce our dependence on foreign oil for the sake of transportation fuel security. For the past few years, mandated volumes have not been met by industry though for a variety of reasons. Clostridium ljungdahlii, an established cellulosic ethanol- producing industrial biocatalyst can produce ethanol from synthesis gas; however, relatively low concentrations of ethanol compared to traditional yeast fermentations of sugar are costly to separate from the fermentation medium, and C. ljungdahlii’s growth and productivity can be inhibited by contaminants in syngas which are expensive to remove. Synthesis gas is predominantly composed of carbon monoxide, carbon dioxide, and hydrogen, but also can contain a variety of contaminants (e.g. hydrogen cyanide, mono-nitrogen oxides, ammonia, sulfur dioxide, carbonyl sulfide, hydrogen sulfide, oxygen) depending on the carbonaceous feedstock from which it is produced (e.g. biomass, agricultural waste, municipal waste, industrial waste). The purpose of this work was, therefore, to identify genetic targets and growth conditions for higher ethanol production. To accomplish this, the metabolic and physiological response of C. ljungdahlii PETC to oxygen was investigated and a lab-derived hyper ethanol-producing strain of C. ljungdahlii (designated OTA1) was characterized. Preliminary investigation showed that C. ljungdahlii PETC has some tolerance to oxygen when cultured in a rich mixotrophic medium. Batch cultures not only continued to grow and consume H2, CO, and fructose after 8% O2 exposure, but fermentation product analysis revealed an increase in ethanol yield and decreased acetate yield compared to non-oxygen exposed cultures.
    [Show full text]
  • Genome Diversity of Spore-Forming Firmicutes MICHAEL Y
    Genome Diversity of Spore-Forming Firmicutes MICHAEL Y. GALPERIN National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 ABSTRACT Formation of heat-resistant endospores is a specific Vibrio subtilis (and also Vibrio bacillus), Ferdinand Cohn property of the members of the phylum Firmicutes (low-G+C assigned it to the genus Bacillus and family Bacillaceae, Gram-positive bacteria). It is found in representatives of four specifically noting the existence of heat-sensitive vegeta- different classes of Firmicutes, Bacilli, Clostridia, Erysipelotrichia, tive cells and heat-resistant endospores (see reference 1). and Negativicutes, which all encode similar sets of core sporulation fi proteins. Each of these classes also includes non-spore-forming Soon after that, Robert Koch identi ed Bacillus anthracis organisms that sometimes belong to the same genus or even as the causative agent of anthrax in cattle and the species as their spore-forming relatives. This chapter reviews the endospores as a means of the propagation of this orga- diversity of the members of phylum Firmicutes, its current taxon- nism among its hosts. In subsequent studies, the ability to omy, and the status of genome-sequencing projects for various form endospores, the specific purple staining by crystal subgroups within the phylum. It also discusses the evolution of the violet-iodine (Gram-positive staining, reflecting the pres- Firmicutes from their apparently spore-forming common ancestor ence of a thick peptidoglycan layer and the absence of and the independent loss of sporulation genes in several different lineages (staphylococci, streptococci, listeria, lactobacilli, an outer membrane), and the relatively low (typically ruminococci) in the course of their adaptation to the saprophytic less than 50%) molar fraction of guanine and cytosine lifestyle in a nutrient-rich environment.
    [Show full text]
  • One-Step Production of C6–C8 Carboxylates by Mixed Culture Solely Grown on CO
    He et al. Biotechnol Biofuels (2018) 11:4 https://doi.org/10.1186/s13068-017-1005-8 Biotechnology for Biofuels RESEARCH Open Access One‑step production of C6–C8 carboxylates by mixed culture solely grown on CO Pinjing He1,2,3, Wenhao Han1, Liming Shao2,3 and Fan Lü1,2,4* Abstract Background: This study aimed at producing C6–C8 medium-chain carboxylates (MCCAs) directly from gaseous CO using mixed culture. The yield and C2–C8 product composition were investigated when CO was continuously fed with gradually increasing partial pressure. Results: The maximal concentrations of n-caproate, n-heptylate, and n-caprylate were 1.892, 1.635, and 1 1 1 1.033 mmol L− , which were achieved at the maximal production rates of 0.276, 0.442, and 0.112 mmol L− ­day− , respectively. Microbial analysis revealed that long-term acclimation and high CO partial pressure were important to establish a CO-tolerant and CO-utilizing chain-elongating microbiome, rich in Acinetobacter, Alcaligenes, and Rhodo- bacteraceae and capable of forming MCCAs solely from CO. Conclusions: These results demonstrated that carboxylate and syngas platform could be integrated in a shared growth vessel, and could be a promising one-step technique to convert gaseous syngas to preferable liquid biochem- icals, thereby avoiding the necessity to coordinate syngas fermentation to short-chain carboxylates and short-to- medium-chain elongation. Thus, this method could provide an alternative solution for the utilization of waste-derived syngas and expand the resource of promising biofuels. Keywords: Syngas fermentation, Chain elongation, Carboxylates, One-step production, Mixed culture Background the thermal treatment of biowaste or artifcial polymers In recent times, conversion of waste to biochemicals [3–5].
    [Show full text]
  • Insights Into Key Parameters for Bio-Alcohol Production in Syngas Fermentation Using Model Carboxydotrophic Bacteria
    INSIGHTS INTO KEY PARAMETERS FOR BIO-ALCOHOL PRODUCTION IN SYNGAS FERMENTATION USING MODEL CARBOXYDOTROPHIC BACTERIA Sara Ramió Pujol Per citar o enllaçar aquest document: Para citar o enlazar este documento: Use this url to cite or link to this publication: http://hdl.handle.net/10803/388041 ADVERTIMENT. L'accés als continguts d'aquesta tesi doctoral i la seva utilització ha de respectar els drets de la persona autora. Pot ser utilitzada per a consulta o estudi personal, així com en activitats o materials d'investigació i docència en els termes establerts a l'art. 32 del Text Refós de la Llei de Propietat Intel·lectual (RDL 1/1996). Per altres utilitzacions es requereix l'autorització prèvia i expressa de la persona autora. En qualsevol cas, en la utilització dels seus continguts caldrà indicar de forma clara el nom i cognoms de la persona autora i el títol de la tesi doctoral. No s'autoritza la seva reproducció o altres formes d'explotació efectuades amb finalitats de lucre ni la seva comunicació pública des d'un lloc aliè al servei TDX. Tampoc s'autoritza la presentació del seu contingut en una finestra o marc aliè a TDX (framing). Aquesta reserva de drets afecta tant als continguts de la tesi com als seus resums i índexs. ADVERTENCIA. El acceso a los contenidos de esta tesis doctoral y su utilización debe respetar los derechos de la persona autora. Puede ser utilizada para consulta o estudio personal, así como en actividades o materiales de investigación y docencia en los términos establecidos en el art.
    [Show full text]
  • Identification of a Non-Coding RNA and Its Putative Involvement in The
    www.nature.com/scientificreports OPEN Identifcation of a non‑coding RNA and its putative involvement in the regulation of tetanus toxin synthesis in Clostridium tetani Holger Brüggemann1,4, Diana Chapeton‑Montes2,4, Lucile Plourde3 & Michel R. Popof 2* Clostridium tetani produces the tetanus toxin (TeNT), one of the most powerful bacterial toxins known to humankind and responsible for tetanus. The regulation of toxin expression is complex and involves the alternative sigma factor TetR as well as other regulators. Here, a transcriptional analysis of the TeNT‑encoding large plasmid of C. tetani identifed a putative non‑coding small RNA (sRNA), located in close vicinity of the 3′ untranslated region of the tent gene. A northern blot experiment could identify a respective sRNA with a size of approx. 140 nucleotides. Sequence analysis showed that the sRNA contains a 14‑nucleotide region that is complementary to a 5′ located region of tent. In order to investigate the function of the sRNA, we applied a RNA interference approach targeting the sRNA in two C. tetani wild‑type strains; the constructed antisense C. tetani strains showed an approx. threefold increase in both extracellular and total TeNT production compared to the respective wild‑type strains. In addition, recombinant C. tetani strains were constructed that contained tent- locus harboring plasmids with and without the sRNA. However, the introduction of the tent-locus without the sRNA in a C. tetani strain lacking the wild‑type TeNT‑encoding large plasmid resulted in a lower TeNT production compared to the same strain with recombinant tent‑locus with the sRNA. This suggests that the expression or the efect of the sRNA is modulated by the C.
    [Show full text]
  • Biofilm Formation by Clostridium Ljungdahlii Is Induced by Sodium Chloride Stress: Experimental Evaluation and Transcriptome Analysis
    RESEARCH ARTICLE Biofilm Formation by Clostridium ljungdahlii Is Induced by Sodium Chloride Stress: Experimental Evaluation and Transcriptome Analysis Jo Philips1,2*, Korneel Rabaey1, Derek R. Lovley2, Madeline Vargas3 1 Center of Microbial Ecology and Technology (CMET), Ghent University, Ghent, Belgium, 2 Department of a1111111111 Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America, 3 Department of Biology, College of the Holy Cross, Worcester, Massachusetts, United States of America a1111111111 a1111111111 * [email protected] a1111111111 a1111111111 Abstract The acetogen Clostridium ljungdahlii is capable of syngas fermentation and microbial elec- OPEN ACCESS trosynthesis. Biofilm formation could benefit both these applications, but was not yet reported for C. ljungdahlii. Biofilm formation does not occur under standard growth condi- Citation: Philips J, Rabaey K, Lovley DR, Vargas M (2017) Biofilm Formation by Clostridium ljungdahlii tions, but attachment or aggregation could be induced by different stresses. The strongest Is Induced by Sodium Chloride Stress: biofilm formation was observed with the addition of sodium chloride. After 3 days of incuba- Experimental Evaluation and Transcriptome tion, the biomass volume attached to a plastic surface was 20 times higher with than without Analysis. PLoS ONE 12(1): e0170406. doi:10.1371/ the addition of 200 mM NaCl to the medium. The addition of NaCl also resulted in biofilm journal.pone.0170406 formation on glass, graphite and glassy carbon, the latter two being often used electrode Editor: Shihui Yang, National Renewable Energy materials for microbial electrosynthesis. Biofilms were composed of extracellular proteins, Laboratory, UNITED STATES polysaccharides, as well as DNA, while pilus-like appendages were observed with, but not Received: November 16, 2016 without, the addition of NaCl.
    [Show full text]
  • Synthetic Biology on Acetogenic Bacteria for Highly Efficient Conversion of C1 Gases to Biochemicals
    International Journal of Molecular Sciences Review Synthetic Biology on Acetogenic Bacteria for Highly Efficient Conversion of C1 Gases to Biochemicals 1,2, 1,2, 1,2 3 1,2 Sangrak Jin y , Jiyun Bae y, Yoseb Song , Nicole Pearcy , Jongoh Shin , Seulgi Kang 1,2, Nigel P. Minton 3 , Philippe Soucaille 3,4,5,6 and Byung-Kwan Cho 1,2,7,8,* 1 Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea; [email protected] (S.J.); [email protected] (J.B.); [email protected] (Y.S.); [email protected] (J.S.); [email protected] (S.K.) 2 KAIST Institute for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea 3 BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, University Park, The University of Nottingham, Nottingham NG7 2RD, UK; [email protected] (N.P.); [email protected] (N.P.M.); [email protected] (P.S.) 4 Université de Toulouse, INSA, UPS, INP, LISBP, 31400 Toulouse, France 5 Institut National de la Recherche Agronomique (INRA), UMR 792, 31077 Toulouse, France 6 Centre National de la Recherche Scientifique (CNRS), UMR 5504, 31400 Toulouse, France 7 Innovative Biomaterials Center, Daejeon 34141, Korea 8 Intelligent Synthetic Biology Center, Daejeon 34141, Korea * Correspondence: [email protected]; Tel.: +82-042-350-2660 These authors contributed equally to this work. y Received: 25 September 2020; Accepted: 13 October 2020; Published: 15 October 2020 Abstract: Synthesis gas, which is mainly produced from fossil fuels or biomass gasification, consists of C1 gases such as carbon monoxide, carbon dioxide, and methane as well as hydrogen.
    [Show full text]
  • Non-Contiguous Finished Genome Sequence and Description of Clostridium Saudii Sp
    Angelakis et al. Standards in Genomic Sciences 2014, 9:8 http://www.standardsingenomics.com/content/9/1/8 SHORT GENOME REPORT Open Access Non-contiguous finished genome sequence and description of Clostridium saudii sp. nov Emmanouil Angelakis1, Fehmida Bibi2, Dhamodharan Ramasamy1, Esam I Azhar2,3, Asif A Jiman-Fatani4, Sally M Aboushoushah2, Jean-Christophe Lagier1, Catherine Robert1, Aurelia Caputo1, Muhammad Yasir2, Pierre-Edouard Fournier1 and Didier Raoult1,2* Abstract Clostridium saudii strain JCCT sp. nov. is the type strain of C. saudii sp. nov., a new species within the genus Clostridia. This strain, whose genome is described here, was isolated from a fecal sample collected from an obese 24-year-old (body mass index 52 kg/m2) man living in Jeddah, Saudi Arabia. C. saudii is a Gram-positive, anaerobic bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,653,762 bp long genome contains 3,452 protein-coding and 53 RNA genes, including 4 rRNA genes. Keywords: Clostridium saudii, Genome, Culturomics, Taxono-genomics Introduction which integrates genomic information in the taxonomic Clostridium saudii strain JCCT (=CSUR P697 = DSM framework, combining phenotypic characteristics, including 27835) is the type strain of C. saudii sp. nov. This bac- MALDI-TOF MS spectra, and genomic analysis [8-38]. terium is a Gram-positive, anaerobic, spore-forming in- The genus Clostridium was first created in 1880 [39] dole negative bacillus that was isolated from the stool and consists of obligate anaerobic rod-shaped bacilli able sample of an obese 24 year-old Saudi individual, as a to produce endospores [39].
    [Show full text]
  • Advancing Towards Biomass-Derived Syngas Fermentation
    ADVANCING TOWARDS BIOMASS-DERIVED SYNGAS FERMENTATION EVALUATION OF PROCESS PARAMETERS AND GAS COMPOSITION EFFECTS Zur Erlangung des akademischen Grades einer DOKTORIN DER INGENIEURWISSENSCHAFTEN (DR.-ING.) von der KIT-Fakultät für Chemieingenieurwesen und Verfahrenstechnik des Karlsruher Instituts für Technologie (KIT) genehmigte DISSERTATION von M. Sc Alba Infantes-López aus Mataró (Barcelona), Spain Tag der mündlichen Prüfung: 14.08.2020 Erstgutachter: Prof. Dr. Christoph Syldatk Zweitgutachter: Prof. Dr. Nicolaus Dahmen Zweitgutachterin: Dr. Anke Neumann This document is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License (CC BY-SA 4.0): https://creativecommons.org/licenses/by-sa/4.0/deed.en “Le rêve c’est tout – la technique, ça s’apprend.” Dreams are everything, technique can be learned. Jean Tinguely PREAMBLE Parts of this thesis have been published as peer reviewed research articles. They describe the main findings of my work. At the end of any applicable paragraph a reference note states the publication in which the content has been previously published. The text of these paragraphs is partially identical to the content of the publications. Layout, citation style, figures and formatting have been modified and adjusted to the style of this dissertation. Chapters that contain contents of previously published work are as follows: Chapters with the heading “General procedures for STR experiments”, “Impact of medium components and process parameters”, the discussion and the conclusion include content of the publication Infantes, A., Kugel, M., and Neumann, A. (2020). Evaluation of media components and process parameters in a sensitive and robust fed-batch syngas fermentation system with Clostridium ljungdahlii. Fermentation. 6(2), 61.
    [Show full text]