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Daakour S, Nelson DR, Fu W, Jaiswal A, Dohai B, Alzahmi AS, Koussa J, Huang X, Shen Y, Twizere JC, Salehi-Ashtiani K. Adaptive Evolution Signatures in Prochlorococcus: Open Reading Frame (ORF)eome Resources and Insights from Comparative Genomics. Microorganisms 2024; 12:1720. [PMID: 39203562 PMCID: PMC11357015 DOI: 10.3390/microorganisms12081720] [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: 05/07/2024] [Revised: 07/30/2024] [Accepted: 08/13/2024] [Indexed: 09/03/2024] Open
Abstract
Prochlorococcus, a cyanobacteria genus of the smallest and most abundant oceanic phototrophs, encompasses ecotype strains adapted to high-light (HL) and low-light (LL) niches. To elucidate the adaptive evolution of this genus, we analyzed 40 Prochlorococcus marinus ORFeomes, including two cornerstone strains, MED4 and NATL1A. Employing deep learning with robust statistical methods, we detected new protein family distributions in the strains and identified key genes differentiating the HL and LL strains. The HL strains harbor genes (ABC-2 transporters) related to stress resistance, such as DNA repair and RNA processing, while the LL strains exhibit unique chlorophyll adaptations (ion transport proteins, HEAT repeats). Additionally, we report the finding of variable, depth-dependent endogenous viral elements in the 40 strains. To generate biological resources to experimentally study the HL and LL adaptations, we constructed the ORFeomes of two representative strains, MED4 and NATL1A synthetically, covering 99% of the annotated protein-coding sequences of the two species, totaling 3976 cloned, sequence-verified open reading frames (ORFs). These comparative genomic analyses, paired with MED4 and NATL1A ORFeomes, will facilitate future genotype-to-phenotype mappings and the systems biology exploration of Prochlorococcus ecology.
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Affiliation(s)
- Sarah Daakour
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
| | - David R. Nelson
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
| | - Weiqi Fu
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
- Department of Marine Science, Ocean College, Zhejiang University, Zhoushan 316021, China
| | - Ashish Jaiswal
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
| | - Bushra Dohai
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
- Helmholtz Center Munich, Institute of Network Biology (INET), German Research Center for Environmental Health, 85764 Munich, Germany
| | - Amnah Salem Alzahmi
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
- Laboratory of Viral Interactomes Networks, Unit of Molecular & Computational Biology, Interdisciplinary Cluster for Applied Genoproteomics (GIGA Institute), University of Liège, 4000 Liège, Belgium
| | - Joseph Koussa
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
- Department of Biology, New York University, New York, NY 10012, USA
- Department of Chemical and Biological Sciences, Montgomery College, Germantown, MD 20850, USA
| | - Xiaoluo Huang
- Genome Synthesis and Editing Platform, China National GeneBank (CNGB), BGI-Research, Shenzhen 518120, China; (X.H.); (Y.S.)
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Beijing 100045, China
| | - Yue Shen
- Genome Synthesis and Editing Platform, China National GeneBank (CNGB), BGI-Research, Shenzhen 518120, China; (X.H.); (Y.S.)
| | - Jean-Claude Twizere
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
- Laboratory of Viral Interactomes Networks, Unit of Molecular & Computational Biology, Interdisciplinary Cluster for Applied Genoproteomics (GIGA Institute), University of Liège, 4000 Liège, Belgium
| | - Kourosh Salehi-Ashtiani
- Center for Genomics and Systems Biology (CGSB), New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates; (S.D.); (D.R.N.); (W.F.); (A.J.); (B.D.); (A.S.A.); (J.K.); (J.-C.T.)
- Division of Science and Math, New York University-Abu Dhabi, Abu Dhabi P.O. Box 129188, United Arab Emirates
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Li Z, Li S, Chen L, Sun T, Zhang W. Fast-growing cyanobacterial chassis for synthetic biology application. Crit Rev Biotechnol 2024; 44:414-428. [PMID: 36842999 DOI: 10.1080/07388551.2023.2166455] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/19/2022] [Accepted: 12/28/2022] [Indexed: 02/28/2023]
Abstract
Carbon neutrality by 2050 has become one of the most urgent challenges the world faces today. To address the issue, it is necessary to develop and promote new technologies related with CO2 recycling. Cyanobacteria are the only prokaryotes performing oxygenic photosynthesis, capable of fixing CO2 into biomass under sunlight and serving as one of the most important primary producers on earth. Notably, recent progress on synthetic biology has led to utilizing model cyanobacteria such as Synechocystis sp. PCC 6803 and Synechococcus elongatus PCC 7942 as chassis for "light-driven autotrophic cell factories" to produce several dozens of biofuels and various fine chemicals directly from CO2. However, due to the slow growth rate and low biomass accumulation in the current chassis, the productivity for most products is still lower than the threshold necessary for large-scale commercial application, raising the importance of developing high-efficiency cyanobacterial chassis with fast growth and/or higher biomass accumulation capabilities. In this article, we critically reviewed recent progresses on identification, systems biology analysis, and engineering of fast-growing cyanobacterial chassis. Specifically, fast-growing cyanobacteria identified in recent years, such as S. elongatus UTEX 2973, S. elongatus PCC 11801, S. elongatus PCC 11802 and Synechococcus sp. PCC 11901 was comparatively analyzed. In addition, the progresses on their recent application in converting CO2 into chemicals, and genetic toolboxes developed for these new cyanobacterial chassis were discussed. Finally, the article provides insights into future challenges and perspectives on the synthetic biology application of cyanobacterial chassis.
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Affiliation(s)
- Zhixiang Li
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, P.R. China
| | - Shubin Li
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, P.R. China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, P.R. China
| | - Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, P.R. China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, P.R. China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, P.R. China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, P.R. China
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Irit N, Hana B, Laura R, Arielle K, Mariela P, Esti KW, Guadalupe P, Katja S, Ariel K. Trichocoleus desertorum isolated from Negev desert petroglyphs: Characterization, adaptation and bioerosion potential. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166739. [PMID: 37673239 DOI: 10.1016/j.scitotenv.2023.166739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 08/23/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023]
Abstract
The Negev petroglyphs are considered valuable cultural heritage sites, but unfortunately, they are exposed to deterioration processes caused by anthropogenic and natural forces. Despite the many studies that have already pointed to the role of cyanobacteria in biogenic rock weathering, the knowledge involved in the process is still lacking. In this study, a cyanobacterial strain was isolated from the Negev Desert petroglyphs aiming to reveal its involvement in geochemical cycles and in the weathering processes of the rock substrate. The strain was characterized using morphological, molecular, and microscopic studies. The morphological research revealed a green-bluish, bundle-forming filamentous strain characterized by trichomes embedded in a common sheath. A combination of Nanopore and Illumina sequencing technologies facilitated the assembly of a near-complete genome containing 5,458,034 base pairs. A total of 5027 coding sequences were revealed by implementing PROKKA software. Annotation of five replicas of the 16S ribosomal RNA genes revealed that the Negev cyanobacteria isolate is closely (99.73 %) related to Trichocoleus desertorum LSB90_MW403957 isolated from the Sahara Desert, Algeria. The local strain was thus named Trichocoleus desertorum NBK24 CP116619. Several gene sequences that code for possible environmental adaptation mechanisms were found. Our study also identified genes for membrane transporters involved in the exchange of chemical elements, suggesting a possible interaction with rock minerals. Microscopic observations of T. desertorum NBK24 CP116619 infected onto calcareous stone slabs under laboratory conditions demonstrated the effect of the isolated cyanobacteria on stone surface degradation. In conclusion, the findings of this study further our understanding of terrestrial cyanobacterial genomes and functions and highlight the role of T. desertorum NBK24 CP116619 in stone weathering processes. This information may contribute to the creation of efficient restoration strategies for stone monuments affected by cyanobacteria.
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Affiliation(s)
- Nir Irit
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Barak Hana
- Department of Civil and Environmental Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Rabbachin Laura
- Institute of Natural Sciences and Technology in the Arts (INTK), Academy of Fine Arts Vienna, Vienna, Austria
| | - Kahn Arielle
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Pavan Mariela
- The Ilse Katz Center for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Kramarsky-Winter Esti
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Piñar Guadalupe
- Institute of Natural Sciences and Technology in the Arts (INTK), Academy of Fine Arts Vienna, Vienna, Austria
| | - Sterflinger Katja
- Institute of Natural Sciences and Technology in the Arts (INTK), Academy of Fine Arts Vienna, Vienna, Austria
| | - Kushmaro Ariel
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel; The Ilse Katz Center for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel; School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
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Singh PR, Pathak J, Rajneesh, Ahmed H, Häder DP, Sinha RP. Physiological responses of the cyanobacterium Synechocystis sp. PCC 6803 under rhythmic light variations. Photochem Photobiol Sci 2023; 22:2055-2069. [PMID: 37227683 DOI: 10.1007/s43630-023-00429-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/26/2023] [Indexed: 05/26/2023]
Abstract
Cyanobacteria are challenged by daily fluctuations of light intensities and photoperiod in their natural habitats, which affect the physiology and fitness of cyanobacteria. Circadian rhythms (CRs), an important endogenous process found in all organisms including cyanobacteria, control their physiological activities and helps in coping with 24-h light/dark (LD) cycle. In cyanobacteria, physiological responses under rhythmic ultraviolet radiation (UVR) are poorly studied. Therefore, we studied the changes in photosynthetic pigments, and physiological parameters of Synechocystis sp. PCC 6803 under UVR and photosynthetically active radiation (PAR) of light/dark (LD) oscillations having the combinations of 0, 4:20, 8:16, 12:12, 16:8, 20:4, and 24:24 h. The LD 16:8 enhanced the growth, pigments, proteins, photosynthetic efficiency, and physiology of Synechocystis sp. PCC6803. Continuous light (LL 24) of UVR and PAR exerted negative impact on the photosynthetic pigments, and chlorophyll fluorescence. Significant increase in reactive oxygen species (ROS) resulted in loss of plasma membrane integrity followed by decreased viability of cells. The dark phase played a significant role in Synechocystis to withstand the LL 24 under PAR and UVR. This study offers detailed understanding of the physiological responses of the cyanobacterium to changing light environment.
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Affiliation(s)
- Prashant R Singh
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Jainendra Pathak
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
- Department of Botany, Pt. Jawaharlal Nehru College (Affiliated to Bundelkhand University, Jhansi), Banda, 210001, India
| | - Rajneesh
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Haseen Ahmed
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Donat-P Häder
- Department of Biology, Emeritus From Friedrich-Alexander University, Neue Str. 9, 91096, Möhrendorf, Germany
| | - Rajeshwar P Sinha
- Laboratory of Photobiology and Molecular Microbiology, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi, 221005, India.
- University Center for Research and Development (UCRD), Chandigarh University, Chandigarh, India.
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Olina A, Agapov A, Yudin D, Sutormin D, Galivondzhyan A, Kuzmenko A, Severinov K, Aravin AA, Kulbachinskiy A. Bacterial Argonaute Proteins Aid Cell Division in the Presence of Topoisomerase Inhibitors in Escherichia coli. Microbiol Spectr 2023; 11:e0414622. [PMID: 37102866 PMCID: PMC10269773 DOI: 10.1128/spectrum.04146-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/29/2023] [Indexed: 04/28/2023] Open
Abstract
Prokaryotic Argonaute (pAgo) proteins are guide-dependent nucleases that function in host defense against invaders. Recently, it was shown that TtAgo from Thermus thermophilus also participates in the completion of DNA replication by decatenating chromosomal DNA. Here, we show that two pAgos from cyanobacteria Synechococcus elongatus (SeAgo) and Limnothrix rosea (LrAgo) are active in heterologous Escherichia coli and aid cell division in the presence of the gyrase inhibitor ciprofloxacin, depending on the host double-strand break repair machinery. Both pAgos are preferentially loaded with small guide DNAs (smDNAs) derived from the sites of replication termination. Ciprofloxacin increases the amounts of smDNAs from the termination region and from the sites of genomic DNA cleavage by gyrase, suggesting that smDNA biogenesis depends on DNA replication and is stimulated by gyrase inhibition. Ciprofloxacin enhances asymmetry in the distribution of smDNAs around Chi sites, indicating that it induces double-strand breaks that serve as a source of smDNA during their processing by RecBCD. While active in E. coli, SeAgo does not protect its native host S. elongatus from ciprofloxacin. These results suggest that pAgo nucleases may help to complete replication of chromosomal DNA by promoting chromosome decatenation or participating in the processing of gyrase cleavage sites, and may switch their functional activities depending on the host species. IMPORTANCE Prokaryotic Argonautes (pAgos) are programmable nucleases with incompletely understood functions in vivo. In contrast to eukaryotic Argonautes, most studied pAgos recognize DNA targets. Recent studies suggested that pAgos can protect bacteria from invader DNA and counteract phage infection and may also have other functions including possible roles in DNA replication, repair, and gene regulation. Here, we have demonstrated that two cyanobacterial pAgos, SeAgo and LrAgo, can assist DNA replication and facilitate cell division in the presence of topoisomerase inhibitors in Escherichia coli. They are specifically loaded with small guide DNAs from the region of replication termination and protect the cells from the action of the gyrase inhibitor ciprofloxacin, suggesting that they help to complete DNA replication and/or repair gyrase-induced breaks. The results show that pAgo proteins may serve as a backup to topoisomerases under conditions unfavorable for DNA replication and may modulate the resistance of host bacterial strains to antibiotics.
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Affiliation(s)
- Anna Olina
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Aleksei Agapov
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Denis Yudin
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Dmitry Sutormin
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | | | - Anton Kuzmenko
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, Russia
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | | | - Alexei A. Aravin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Andrey Kulbachinskiy
- Institute of Molecular Genetics, National Research Center “Kurchatov Institute”, Moscow, Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
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Fagliarone C, Mosca C, Di Stefano G, Leuko S, Moeller R, Rabbow E, Rettberg P, Billi D. Enabling deep-space experimentations on cyanobacteria by monitoring cell division resumption in dried Chroococcidiopsis sp. 029 with accumulated DNA damage. Front Microbiol 2023; 14:1150224. [PMID: 37266021 PMCID: PMC10229888 DOI: 10.3389/fmicb.2023.1150224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/21/2023] [Indexed: 06/03/2023] Open
Abstract
Cyanobacteria are gaining considerable interest as a method of supporting the long-term presence of humans on the Moon and settlements on Mars due to their ability to produce oxygen and their potential as bio-factories for space biotechnology/synthetic biology and other applications. Since many unknowns remain in our knowledge to bridge the gap and move cyanobacterial bioprocesses from Earth to space, we investigated cell division resumption on the rehydration of dried Chroococcidiopsis sp. CCMEE 029 accumulated DNA damage while exposed to space vacuum, Mars-like conditions, and Fe-ion radiation. Upon rehydration, the monitoring of the ftsZ gene showed that cell division was arrested until DNA damage was repaired, which took 48 h under laboratory conditions. During the recovery, a progressive DNA repair lasting 48 h of rehydration was revealed by PCR-stop assay. This was followed by overexpression of the ftsZ gene, ranging from 7.5- to 9-fold compared to the non-hydrated samples. Knowing the time required for DNA repair and cell division resumption is mandatory for deep-space experiments that are designed to unravel the effects of reduced/microgravity on this process. It is also necessary to meet mission requirements for dried-sample implementation and real-time monitoring upon recovery. Future experiments as part of the lunar exploration mission Artemis and the lunar gateway station will undoubtedly help to move cyanobacterial bioprocesses beyond low Earth orbit. From an astrobiological perspective, these experiments will further our understanding of microbial responses to deep-space conditions.
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Affiliation(s)
| | - Claudia Mosca
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Giorgia Di Stefano
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
- PhD Program in Cellular and Molecular Biology, Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Stefan Leuko
- Aerospace Microbiology Research Group, Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
| | - Ralf Moeller
- Aerospace Microbiology Research Group, Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Department of Natural Sciences, University of Applied Sciences Bonn-Rhein-Sieg (BRSU), Rheinbach, Germany
| | - Elke Rabbow
- Astrobiology Research Group, Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
| | - Petra Rettberg
- Astrobiology Research Group, Radiation Biology Department, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
| | - Daniela Billi
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
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Sun H, Luan G, Ma Y, Lou W, Chen R, Feng D, Zhang S, Sun J, Lu X. Engineered hypermutation adapts cyanobacterial photosynthesis to combined high light and high temperature stress. Nat Commun 2023; 14:1238. [PMID: 36871084 PMCID: PMC9985602 DOI: 10.1038/s41467-023-36964-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 02/23/2023] [Indexed: 03/06/2023] Open
Abstract
Photosynthesis can be impaired by combined high light and high temperature (HLHT) stress. Obtaining HLHT tolerant photoautotrophs is laborious and time-consuming, and in most cases the underlying molecular mechanisms remain unclear. Here, we increase the mutation rates of cyanobacterium Synechococcus elongatus PCC 7942 by three orders of magnitude through combinatory perturbations of the genetic fidelity machinery and cultivation environment. Utilizing the hypermutation system, we isolate Synechococcus mutants with improved HLHT tolerance and identify genome mutations contributing to the adaptation process. A specific mutation located in the upstream non-coding region of the gene encoding a shikimate kinase results in enhanced expression of this gene. Overexpression of the shikimate kinase encoding gene in both Synechococcus and Synechocystis leads to improved HLHT tolerance. Transcriptome analysis indicates that the mutation remodels the photosynthetic chain and metabolism network in Synechococcus. Thus, mutations identified by the hypermutation system are useful for engineering cyanobacteria with improved HLHT tolerance.
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Affiliation(s)
- Huili Sun
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Shandong Energy Institute, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, 266101, Qingdao, Shandong, China
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Guodong Luan
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, 266101, Qingdao, Shandong, China.
- Shandong Energy Institute, No. 189 Songling Road, 266101, Qingdao, Shandong, China.
- Qingdao New Energy Shandong Laboratory, 266101, Qingdao, Shandong, China.
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, China.
- Dalian National Laboratory for Clean Energy, 116023, Dalian, Liaoning, China.
| | - Yifan Ma
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Shandong Energy Institute, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, 266101, Qingdao, Shandong, China
- College of Life Science and Technology, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China
| | - Wenjing Lou
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Shandong Energy Institute, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, 266101, Qingdao, Shandong, China
| | - Rongze Chen
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Shandong Energy Institute, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, 266101, Qingdao, Shandong, China
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Dandan Feng
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Shandong Energy Institute, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, 266101, Qingdao, Shandong, China
| | - Shanshan Zhang
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Shandong Energy Institute, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, 266101, Qingdao, Shandong, China
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Jiahui Sun
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Shandong Energy Institute, No. 189 Songling Road, 266101, Qingdao, Shandong, China
- Qingdao New Energy Shandong Laboratory, 266101, Qingdao, Shandong, China
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Xuefeng Lu
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, 266101, Qingdao, Shandong, China.
- Shandong Energy Institute, No. 189 Songling Road, 266101, Qingdao, Shandong, China.
- Qingdao New Energy Shandong Laboratory, 266101, Qingdao, Shandong, China.
- College of Life Science, University of Chinese Academy of Sciences, 100049, Beijing, China.
- Dalian National Laboratory for Clean Energy, 116023, Dalian, Liaoning, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, 266237, Qingdao, Shandong, China.
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8
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Singh PR, Gupta A, Rajneesh, Pathak J, Sinha RP. Phylogenetic distribution, structural analysis and interaction of nucleotide excision repair proteins in cyanobacteria. DNA Repair (Amst) 2023; 126:103487. [PMID: 37054651 DOI: 10.1016/j.dnarep.2023.103487] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 03/25/2023] [Accepted: 03/26/2023] [Indexed: 03/30/2023]
Abstract
Cyanobacteria are photosynthetic Gram-negative, oxygen evolving prokaryotes with cosmopolitan distribution. Ultraviolet radiation (UVR) and other abiotic stresses result in DNA lesions in cyanobacteria. Nucleotide excision repair (NER) pathway removes the DNA lesions produced by UVR to normal DNA sequence. In cyanobacteria, detailed knowledge about NER proteins is poorly studied. Therefore, we have studied the NER proteins in cyanobacteria. Analyses of 289 amino acids sequence from 77 cyanobacterial species have revealed the presence of a minimum of one copy of NER protein in their genome. Phylogenetic analysis of NER protein shows that UvrD has maximal rate of amino acid substitutions which resulted in increased branch length. The motif analysis shows that UvrABC proteins is more conserved than UvrD, Further, UvrA with UvrB protein interacts with each other and form stable complex which have DNA binding domain on the surface of the complex. UvrB also have DNA binding domain. Positive electrostatic potential was found in the DNA binding region, which is followed by negative and neutral electrostatic potential. Additionally, the surface accessibility values at the DNA strands of T5-T6 dimer binding site were maximal. Protein nucleotide interaction shows the strong binding of T5-T6 dimer with NER proteins of Synechocystis sp. PCC 6803. This process repairs the UV-induced DNA lesions in dark when photoreactivation is inactive. Regulation of NER proteins protect cyanobacterial genome and maintain the fitness of organism under different abiotic stresses.
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Watanabe S, Stazic D, Georg J, Ohtake S, Sakamaki Y, Numakura M, Asayama M, Chibazakura T, Wilde A, Steglich C, Hess WR. Regulation of RNase E during the UV stress response in the cyanobacterium Synechocystis sp. PCC 6803. MLIFE 2023; 2:43-57. [PMID: 38818332 PMCID: PMC10989929 DOI: 10.1002/mlf2.12056] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 12/07/2022] [Accepted: 12/15/2022] [Indexed: 06/01/2024]
Abstract
Endoribonucleases govern the maturation and degradation of RNA and are indispensable in the posttranscriptional regulation of gene expression. A key endoribonuclease in Gram-negative bacteria is RNase E. To ensure an appropriate supply of RNase E, some bacteria, such as Escherichia coli, feedback-regulate RNase E expression via the rne 5'-untranslated region (5' UTR) in cis. However, the mechanisms involved in the control of RNase E in other bacteria largely remain unknown. Cyanobacteria rely on solar light as an energy source for photosynthesis, despite the inherent ultraviolet (UV) irradiation. In this study, we first investigated globally the changes in gene expression in the cyanobacterium Synechocystis sp. PCC 6803 after a brief exposure to UV. Among the 407 responding genes 2 h after UV exposure was a prominent upregulation of rne mRNA level. Moreover, the enzymatic activity of RNase E rapidly increased as well, although the protein stability decreased. This unique response was underpinned by the increased accumulation of full-length rne mRNA caused by the stabilization of its 5' UTR and suppression of premature transcriptional termination, but not by an increased transcription rate. Mapping of RNA 3' ends and in vitro cleavage assays revealed that RNase E cleaves within a stretch of six consecutive uridine residues within the rne 5' UTR, indicating autoregulation. These observations suggest that RNase E in cyanobacteria contributes to reshaping the transcriptome during the UV stress response and that its required activity level is secured at the RNA level despite the enhanced turnover of the protein.
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Affiliation(s)
- Satoru Watanabe
- Faculty of Biology, Genetics and Experimental BioinformaticsUniversity of FreiburgFreiburgGermany
| | - Damir Stazic
- Department of BioscienceTokyo University of AgricultureSetagaya‐kuTokyoJapan
- Present address:
NexxiotPrime Tower (Hardstrasse 201)ZurichSwitzerland
| | - Jens Georg
- Department of BioscienceTokyo University of AgricultureSetagaya‐kuTokyoJapan
| | - Shota Ohtake
- Faculty of Biology, Genetics and Experimental BioinformaticsUniversity of FreiburgFreiburgGermany
| | - Yutaka Sakamaki
- Faculty of Biology, Genetics and Experimental BioinformaticsUniversity of FreiburgFreiburgGermany
| | - Megumi Numakura
- Faculty of Biology, Genetics and Experimental BioinformaticsUniversity of FreiburgFreiburgGermany
| | - Munehiko Asayama
- School of Agriculture, Molecular GeneticsIbaraki UniversityIbarakiJapan
| | - Taku Chibazakura
- Faculty of Biology, Genetics and Experimental BioinformaticsUniversity of FreiburgFreiburgGermany
| | - Annegret Wilde
- Faculty of Biology, Molecular GeneticsUniversity of FreiburgFreiburgGermany
| | - Claudia Steglich
- Department of BioscienceTokyo University of AgricultureSetagaya‐kuTokyoJapan
| | - Wolfgang R. Hess
- Department of BioscienceTokyo University of AgricultureSetagaya‐kuTokyoJapan
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10
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Blanc-Garin V, Chenebault C, Diaz-Santos E, Vincent M, Sassi JF, Cassier-Chauvat C, Chauvat F. Exploring the potential of the model cyanobacterium Synechocystis PCC 6803 for the photosynthetic production of various high-value terpenes. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:110. [PMID: 36242067 PMCID: PMC9564069 DOI: 10.1186/s13068-022-02211-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022]
Abstract
Background The robust model cyanobacterium Synechocystis PCC 6803 is increasingly explored for its potential to use solar energy, water and atmospheric CO2 for the carbon-neutral production of terpenes, the high-value chemicals that can be used for the production of drugs, flavors, fragrances and biofuels. However, as terpenes are chemically diverse, it is extremely difficult to predict whether Synechocystis is a suitable chassis for the photosynthetic production of various terpenes or only a few of them. Results We have performed the first-time engineering and comparative analysis of the best-studied cyanobacterium Synechocystis PCC 6803 for the photosynthetic production of five chemically diverse high-value terpenes: two monoterpenes (C10H16) limonene (cyclic molecule) and pinene (bicyclic), and three sesquiterpenes (C15H24) bisabolene (cyclic), farnesene (linear) and santalene (cyclic). All terpene producers appeared to grow well and to be genetically stable, as shown by the absence of changes in their production levels during the 5–9-month periods of their sub-cultivation under photoautotrophic conditions). We also found that Synechocystis PCC 6803 can efficiently and stably produce farnesene and santalene, which had never been produced before by this model organism or any other cyanobacteria, respectively. Similar production levels were observed for cells growing on nitrate (the standard nitrogen source for cyanobacteria) or urea (cheaper than nitrate). Furthermore, higher levels of farnesene were produced by cloning the heterologous farnesene synthase gene in a RSF1010-derived replicating plasmid as compared to the well-used slr0168 neutral cloning site of the chromosome. Conclusions Altogether, the present results indicate that Synechocystis PCC 6803 is better suited to produce sesquiterpenes (particularly farnesene, the most highly produced terpene of this study) than monoterpenes (especially pinene). Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02211-0.
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Affiliation(s)
- Victoire Blanc-Garin
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif‐sur‐Yvette, France
| | - Célia Chenebault
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif‐sur‐Yvette, France
| | - Encarnación Diaz-Santos
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif‐sur‐Yvette, France
| | - Marine Vincent
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif‐sur‐Yvette, France
| | - Jean-François Sassi
- Commissariat À L’énergie Atomique Et Aux Énergies Alternatives (CEA), Centre de Cadarache, 13108 St Paul Lez Durance, France
| | - Corinne Cassier-Chauvat
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif‐sur‐Yvette, France
| | - Franck Chauvat
- grid.457334.20000 0001 0667 2738Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif‐sur‐Yvette, France
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11
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Mackelprang R, Vaishampayan P, Fisher K. Adaptation to Environmental Extremes Structures Functional Traits in Biological Soil Crust and Hypolithic Microbial Communities. mSystems 2022; 7:e0141921. [PMID: 35852333 PMCID: PMC9426607 DOI: 10.1128/msystems.01419-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 06/30/2022] [Indexed: 12/24/2022] Open
Abstract
Biological soil crusts (biocrusts) are widespread in drylands and deserts. At the microhabitat scale, they also host hypolithic communities that live under semitranslucent stones. Both environmental niches experience exposure to extreme conditions such as high UV radiation, desiccation, temperature fluctuations, and resource limitation. However, hypolithic communities are somewhat protected from extremes relative to biocrust communities. Conditions are otherwise similar, so comparing them can answer outstanding questions regarding adaptations to environmental extremes. Using metagenomic sequencing, we assessed the functional potential of dryland soil communities and identified the functional underpinnings of ecological niche differentiation in biocrusts versus hypoliths. We also determined the effect of the anchoring photoautotroph (moss or cyanobacteria). Genes and pathways differing in abundance between biocrusts and hypoliths indicate that biocrust communities adapt to the higher levels of UV radiation, desiccation, and temperature extremes through an increased ability to repair damaged DNA, sense and respond to environmental stimuli, and interact with other community members and the environment. Intracellular competition appears to be crucial to both communities, with biocrust communities using the Type VI Secretion System (T6SS) and hypoliths favoring a diversity of antibiotics. The dominant primary producer had a reduced effect on community functional potential compared with niche, but an abundance of genes related to monosaccharide, amino acid, and osmoprotectant uptake in moss-dominated communities indicates reliance on resources provided to heterotrophs by mosses. Our findings indicate that functional traits in dryland communities are driven by adaptations to extremes and we identify strategies that likely enable survival in dryland ecosystems. IMPORTANCE Biocrusts serve as a keystone element of desert and dryland ecosystems, stabilizing soils, retaining moisture, and serving as a carbon and nitrogen source in oligotrophic environments. Biocrusts cover approximately 12% of the Earth's terrestrial surface but are threatened by climate change and anthropogenic disturbance. Given their keystone role in ecosystem functioning, loss will have wide-spread consequences. Biocrust microbial constituents must withstand polyextreme environmental conditions including high UV exposure, desiccation, oligotrophic conditions, and temperature fluctuations over short time scales. By comparing biocrust communities with co-occurring hypolithic communities (which inhabit the ventral sides of semitranslucent stones and are buffered from environmental extremes), we identified traits that are likely key adaptations to extreme conditions. These include DNA damage repair, environmental sensing and response, and intracellular competition. Comparison of the two niches, which differ primarily in exposure levels to extreme conditions, makes this system ideal for understanding how functional traits are structured by the environment.
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Affiliation(s)
- Rachel Mackelprang
- Department of Biology, California State University Northridge, Northridge, California, USA
| | - Parag Vaishampayan
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, California, USA
| | - Kirsten Fisher
- Department of Biological Sciences, California State University, Los Angeles, Los Angeles, California, USA
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12
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McCarthy B, O’Neill G, Abu-Ghannam N. Potential Psychoactive Effects of Microalgal Bioactive Compounds for the Case of Sleep and Mood Regulation: Opportunities and Challenges. Mar Drugs 2022; 20:493. [PMID: 36005495 PMCID: PMC9410000 DOI: 10.3390/md20080493] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 01/25/2023] Open
Abstract
Sleep deficiency is now considered an emerging global epidemic associated with many serious health problems, and a major cause of financial and social burdens. Sleep and mental health are closely connected, further exacerbating the negative impact of sleep deficiency on overall health and well-being. A major drawback of conventional treatments is the wide range of undesirable side-effects typically associated with benzodiazepines and antidepressants, which can be more debilitating than the initial disorder. It is therefore valuable to explore the efficiency of other remedies for complementarity and synergism with existing conventional treatments, leading to possible reduction in undesirable side-effects. This review explores the relevance of microalgae bioactives as a sustainable source of valuable phytochemicals that can contribute positively to mood and sleep disorders. Microalgae species producing these compounds are also catalogued, thus creating a useful reference of the state of the art for further exploration of this proposed approach. While we highlight possibilities awaiting investigation, we also identify the associated issues, including minimum dose for therapeutic effect, bioavailability, possible interactions with conventional treatments and the ability to cross the blood brain barrier. We conclude that physical and biological functionalization of microalgae bioactives can have potential in overcoming some of these challenges.
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Affiliation(s)
- Bozena McCarthy
- Environmental Sustainability & Health Institute (ESHI), Technological University Dublin, Grangegorman, D07 H6K8 Dublin 7, Ireland; (B.M.); (G.O.)
| | - Graham O’Neill
- Environmental Sustainability & Health Institute (ESHI), Technological University Dublin, Grangegorman, D07 H6K8 Dublin 7, Ireland; (B.M.); (G.O.)
- School of Food Science and Environmental Health, College of Sciences and Health, Technological University Dublin, Grangegorman, D07 H6K8 Dublin 7, Ireland
| | - Nissreen Abu-Ghannam
- Environmental Sustainability & Health Institute (ESHI), Technological University Dublin, Grangegorman, D07 H6K8 Dublin 7, Ireland; (B.M.); (G.O.)
- School of Food Science and Environmental Health, College of Sciences and Health, Technological University Dublin, Grangegorman, D07 H6K8 Dublin 7, Ireland
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13
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Suzuki S, Kawachi M, Tsukakoshi C, Nakamura A, Hagino K, Inouye I, Ishida KI. Unstable Relationship Between Braarudosphaera bigelowii (= Chrysochromulina parkeae) and Its Nitrogen-Fixing Endosymbiont. FRONTIERS IN PLANT SCIENCE 2021; 12:749895. [PMID: 34925404 PMCID: PMC8679911 DOI: 10.3389/fpls.2021.749895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/10/2021] [Indexed: 06/14/2023]
Abstract
Marine phytoplankton are major primary producers, and their growth is primarily limited by nitrogen in the oligotrophic ocean environment. The haptophyte Braarudosphaera bigelowii possesses a cyanobacterial endosymbiont (UCYN-A), which plays a major role in nitrogen fixation in the ocean. However, host-symbiont interactions are poorly understood because B. bigelowii was unculturable. In this study, we sequenced the complete genome of the B. bigelowii endosymbiont and showed that it was highly reductive and closely related to UCYN-A2 (an ecotype of UCYN-A). We succeeded in establishing B. bigelowii strains and performed microscopic observations. The detailed observations showed that the cyanobacterial endosymbiont was surrounded by a single host derived membrane and divided synchronously with the host cell division. The transcriptome of B. bigelowii revealed that B. bigelowii lacked the expression of many essential genes associated with the uptake of most nitrogen compounds, except ammonia. During cultivation, some of the strains completely lost the endosymbiont. Moreover, we did not find any evidence of endosymbiotic gene transfer from the endosymbiont to the host. These findings illustrate an unstable morphological, metabolic, and genetic relationship between B. bigelowii and its endosymbiont.
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Affiliation(s)
- Shigekatsu Suzuki
- Biodiversity Division, National Institute for Environmental Studies, Ibaraki, Japan
| | - Masanobu Kawachi
- Biodiversity Division, National Institute for Environmental Studies, Ibaraki, Japan
| | - Chinatsu Tsukakoshi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Atsushi Nakamura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Kyoko Hagino
- Center for Advanced Marine Core Research, Kochi University, Kochi, Japan
| | - Isao Inouye
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Ken-ichiro Ishida
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
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14
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Racharaks R, Arnold W, Peccia J. Development of CRISPR-Cas9 knock-in tools for free fatty acid production using the fast-growing cyanobacterial strain Synechococcus elongatus UTEX 2973. J Microbiol Methods 2021; 189:106315. [PMID: 34454980 DOI: 10.1016/j.mimet.2021.106315] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/23/2021] [Accepted: 08/23/2021] [Indexed: 12/26/2022]
Abstract
Synechococcus elongatus UTEX 2973 has one of the fastest measured doubling time of cyanobacteria making it an important candidate for metabolic engineering. Traditional genetic engineering methods, which rely on homologous recombination, however, are inefficient, labor-intensive, and time-consuming due to the oligoploidy or polyploidy nature of cyanobacteria and the reliance on unique antibiotic resistance markers. CRISPR-Cas9 has emerged as an effective and versatile editing platform in a wide variety of organisms, but its application for cyanobacterial engineering is limited by the inherent toxicity of Cas9 resulting in poor transformation efficiencies. Here, we demonstrated that a single-plasmid CRISPR-Cas9 system, pCRISPOmyces-2, can effectively knock-in a truncated thioesterase gene from Escherichia coli to generate free fatty acid (FFA) producing mutants of Syn2973. To do so, three parameters were evaluated on the effect of generating recipient colonies after conjugation with pCRISPOmyces-2-based plasmids: 1) a modified conjugation protocol termed streaked conjugation, 2) the deletion of the gene encoding RecJ exonuclease, and 3) single guide RNA (sgRNA) sequence. With the use of the streaked conjugation protocol and a ΔrecJ mutant strain of Syn2973, the conjugation efficiency for the pCRISPomyces-2 plasmid could be improved by 750-fold over the wildtype (WT) for a conjugation efficiency of 2.0 × 10-6 transconjugants/recipient cell. While deletion of the RecJ exonuclease alone increased the conjugation efficiency by 150-fold over the WT, FFA generation was impaired in FFA-producing mutants with the ΔrecJ background, and the large number of poor FFA-producing isolates indicated the potential increase in spontaneous mutation rates. The sgRNA sequence was found to be critical in achieving the desired CRISPR-Cas9-mediated knock-in mutation as the sgRNA impacts conjugation efficiency, likelihood of homogenous recombinants, and free fatty acid production in engineered strains.
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Affiliation(s)
- Ratanachat Racharaks
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA
| | - Wyatt Arnold
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA
| | - Jordan Peccia
- Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA.
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15
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Mosca C, Fagliarone C, Napoli A, Rabbow E, Rettberg P, Billi D. Revival of Anhydrobiotic Cyanobacterium Biofilms Exposed to Space Vacuum and Prolonged Dryness: Implications for Future Missions beyond Low Earth Orbit. ASTROBIOLOGY 2021; 21:541-550. [PMID: 33956489 DOI: 10.1089/ast.2020.2359] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Dried biofilms of Chroococcidiopsis sp. CCMEE 029 were revived after a 672-day exposure to space vacuum outside the International Space Station during the EXPOSE-R2 space mission. After retrieval, they were air-dried stored for 3.5 years. Space vacuum reduced cell viability and increased DNA damage compared to air-dried storage for 6 years under laboratory conditions. Long exposure times to space vacuum and extreme dryness decrease the changes of survival that ultimately depend on DNA damage repair upon rehydration, and hence, an in silico analysis of Chroococcidiopsis sp. CCMEE 029's genome was performed with a focus on DNA repair pathways. The analysis identified a high number of genes that encode proteins of the homologous recombination RecF pathway and base excision repair that were over-expressed during 1 and 6 h rehydration of space-vacuum exposed biofilms. This suggests that Chroococcidiopsis developed a survival strategy against desiccation, with DNA repair playing a key role, which allowed the revival of biofilms exposed to space vacuum. Unravelling how long anhydrobiotic cyanobacteria can persist under space vacuum followed by prolonged air-dried storage is relevant to future astrobiological experiments that use space platforms and might require prolonged air-dried storage of the exposed samples before retrieval to Earth.
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Affiliation(s)
- Claudia Mosca
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | | | | | - Elke Rabbow
- German Aerospace Center, Institute of Aerospace Medicine, Cologne, Germany
| | - Petra Rettberg
- German Aerospace Center, Institute of Aerospace Medicine, Cologne, Germany
| | - Daniela Billi
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
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16
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Pandey S, Kumar A, Kirti A, Gupta GD, Rajaram H. Rec(F/O/R) proteins of the nitrogen-fixing cyanobacterium Nostoc PCC7120: In silico and expression analysis. Gene 2021; 788:145663. [PMID: 33887372 DOI: 10.1016/j.gene.2021.145663] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/01/2021] [Accepted: 04/15/2021] [Indexed: 01/19/2023]
Abstract
The high radioresistance of Nostoc sp. strain PCC7120 is indicative of a robust DNA repair pathway. In the absence of NHEJ pathway and the canonical RecBCD proteins, the RecF pathway proteins are expected to play an important role in double strand break repair in this organism. The RecF, RecO and RecR proteins which are central to the RecF pathway have not been characterised in the ancient cyanobacteria, several of which are known to be radioresistant. The characterisation of these proteins was initiated through a mix of in silico, expression and complementation analysis. Differential expression of the recF, recO and recR genes was observed both at the transcript and the protein level under normal growth condition, which did not change significantly upon exposure to DNA damage stresses. Expression of RecR as a 23 kDa protein in vivo in Nostoc PCC7120 confirmed the re-annotation of the initiation codon of the gene (alr4977) to a rare initiation codon 'GTT' 267 bases upstream of the annotated initiation codon. Of the three proteins, Nostoc RecO and RecR proteins could complement the corresponding mutations in Escherichia coli, but not RecF. The Nostoc RecO protein exhibited low sequence and structural homology with other bacterial RecO protein, and was predicted to have a longer loop region. Phylogenetic as well as sequence analysis revealed high conservation among bacterial RecR proteins and least for RecO. In silico analysis revealed a comparatively smaller interactome for the Nostoc RecF, RecO and RecR proteins compared to other bacteria, with RecO predicted to interact with both RecF and RecR. The information gathered can form a stepping stone to further characterise these proteins in terms of deciphering their interactome, biochemical and physiological activities. This would help in establishing their importance in RecF pathway of DSB repair in Nostoc PCC7120.
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Affiliation(s)
- Sarita Pandey
- Cyanobacterial Stress Biology and Biotechnology Section, Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Arvind Kumar
- Cyanobacterial Stress Biology and Biotechnology Section, Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Anurag Kirti
- Cyanobacterial Stress Biology and Biotechnology Section, Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Gagan D Gupta
- Radiaiton Biology and Health Sciences Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Hema Rajaram
- Cyanobacterial Stress Biology and Biotechnology Section, Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India.
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17
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Genetic, Genomics, and Responses to Stresses in Cyanobacteria: Biotechnological Implications. Genes (Basel) 2021; 12:genes12040500. [PMID: 33805386 PMCID: PMC8066212 DOI: 10.3390/genes12040500] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/25/2021] [Accepted: 03/25/2021] [Indexed: 02/07/2023] Open
Abstract
Cyanobacteria are widely-diverse, environmentally crucial photosynthetic prokaryotes of great interests for basic and applied science. Work to date has focused mostly on the three non-nitrogen fixing unicellular species Synechocystis PCC 6803, Synechococcus PCC 7942, and Synechococcus PCC 7002, which have been selected for their genetic and physiological interests summarized in this review. Extensive "omics" data sets have been generated, and genome-scale models (GSM) have been developed for the rational engineering of these cyanobacteria for biotechnological purposes. We presently discuss what should be done to improve our understanding of the genotype-phenotype relationships of these models and generate robust and predictive models of their metabolism. Furthermore, we also emphasize that because Synechocystis PCC 6803, Synechococcus PCC 7942, and Synechococcus PCC 7002 represent only a limited part of the wide biodiversity of cyanobacteria, other species distantly related to these three models, should be studied. Finally, we highlight the need to strengthen the communication between academic researchers, who know well cyanobacteria and can engineer them for biotechnological purposes, but have a limited access to large photobioreactors, and industrial partners who attempt to use natural or engineered cyanobacteria to produce interesting chemicals at reasonable costs, but may lack knowledge on cyanobacterial physiology and metabolism.
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18
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Double strand break (DSB) repair in Cyanobacteria: Understanding the process in an ancient organism. DNA Repair (Amst) 2020; 95:102942. [DOI: 10.1016/j.dnarep.2020.102942] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/19/2020] [Accepted: 07/26/2020] [Indexed: 02/07/2023]
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Schirmacher AM, Hanamghar SS, Zedler JAZ. Function and Benefits of Natural Competence in Cyanobacteria: From Ecology to Targeted Manipulation. Life (Basel) 2020; 10:E249. [PMID: 33105681 PMCID: PMC7690421 DOI: 10.3390/life10110249] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/18/2020] [Accepted: 10/20/2020] [Indexed: 02/03/2023] Open
Abstract
Natural competence is the ability of a cell to actively take up and incorporate foreign DNA in its own genome. This trait is widespread and ecologically significant within the prokaryotic kingdom. Here we look at natural competence in cyanobacteria, a group of globally distributed oxygenic photosynthetic bacteria. Many cyanobacterial species appear to have the genetic potential to be naturally competent, however, this ability has only been demonstrated in a few species. Reasons for this might be due to a high variety of largely uncharacterised competence inducers and a lack of understanding the ecological context of natural competence in cyanobacteria. To shed light on these questions, we describe what is known about the molecular mechanisms of natural competence in cyanobacteria and analyse how widespread this trait might be based on available genomic datasets. Potential regulators of natural competence and what benefits or drawbacks may derive from taking up foreign DNA are discussed. Overall, many unknowns about natural competence in cyanobacteria remain to be unravelled. A better understanding of underlying mechanisms and how to manipulate these, can aid the implementation of cyanobacteria as sustainable production chassis.
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Affiliation(s)
| | | | - Julie A. Z. Zedler
- Matthias Schleiden Institute for Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany; (A.M.S.); (S.S.H.)
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20
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Chenebault C, Diaz-Santos E, Kammerscheit X, Görgen S, Ilioaia C, Streckaite S, Gall A, Robert B, Marcon E, Buisson DA, Benzerara K, Sassi JF, Cassier-Chauvat C, Chauvat F. A Genetic Toolbox for the New Model Cyanobacterium Cyanothece PCC 7425: A Case Study for the Photosynthetic Production of Limonene. Front Microbiol 2020; 11:586601. [PMID: 33042102 PMCID: PMC7530172 DOI: 10.3389/fmicb.2020.586601] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 08/31/2020] [Indexed: 12/17/2022] Open
Abstract
Cyanobacteria, the largest phylum of prokaryotes, perform oxygenic photosynthesis and are regarded as the ancestors of the plant chloroplast and the purveyors of the oxygen and biomass that shaped the biosphere. Nowadays, cyanobacteria are attracting a growing interest in being able to use solar energy, H2O, CO2 and minerals to produce biotechnologically interesting chemicals. This often requires the introduction and expression of heterologous genes encoding the enzymes that are not present in natural cyanobacteria. However, only a handful of model strains with a well-established genetic system are being studied so far, leaving the vast biodiversity of cyanobacteria poorly understood and exploited. In this study, we focused on the robust unicellular cyanobacterium Cyanothece PCC 7425 that has many interesting attributes, such as large cell size; capacity to fix atmospheric nitrogen (under anaerobiosis) and to grow not only on nitrate but also on urea (a frequent pollutant) as the sole nitrogen source; capacity to form CO2-sequestrating intracellular calcium carbonate granules and to produce various biotechnologically interesting products. We demonstrate for the first time that RSF1010-derived plasmid vectors can be used for promoter analysis, as well as constitutive or temperature-controlled overproduction of proteins and analysis of their sub-cellular localization in Cyanothece PCC 7425. These findings are important because no gene manipulation system had been developed for Cyanothece PCC 7425, yet, handicapping its potential to serve as a model host. Furthermore, using this toolbox, we engineered Cyanothece PCC 7425 to produce the high-value terpene, limonene which has applications in biofuels, bioplastics, cosmetics, food and pharmaceutical industries. This is the first report of the engineering of a Cyanothece strain for the production of a chemical and the first demonstration that terpene can be produced by an engineered cyanobacterium growing on urea as the sole nitrogen source.
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Affiliation(s)
- Célia Chenebault
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Encarnación Diaz-Santos
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Xavier Kammerscheit
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Sigrid Görgen
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.,Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Cristian Ilioaia
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Simona Streckaite
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Andrew Gall
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Bruno Robert
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Elodie Marcon
- Université Paris-Saclay, Service de Chimie Bio-organique et Marquage (SCBM), CEA/DRF/JOLIOT, Gif-sur-Yvette, France
| | - David-Alexandre Buisson
- Université Paris-Saclay, Service de Chimie Bio-organique et Marquage (SCBM), CEA/DRF/JOLIOT, Gif-sur-Yvette, France
| | - Karim Benzerara
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Jean-François Sassi
- Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), Centre de Cadarache, Saint-Paul-lez-Durance, France
| | - Corinne Cassier-Chauvat
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Franck Chauvat
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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21
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Methylglyoxal Detoxification Revisited: Role of Glutathione Transferase in Model Cyanobacterium Synechocystis sp. Strain PCC 6803. mBio 2020; 11:mBio.00882-20. [PMID: 32753490 PMCID: PMC7407080 DOI: 10.1128/mbio.00882-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In most organisms, methylglyoxal (MG), a toxic metabolite by-product that causes diabetes in humans, is predominantly detoxified by the glyoxalase enzymes. This process begins with the so-called “spontaneous” conjugation of MG with the cytoprotectant metabolite glutathione (GSH). In this study, we unravel a logical, but as yet unsuspected, link between MG detoxification and a (prokaryotic) representative of the ubiquitous glutathione transferase (GST) enzymes. We show that a GST of a model cyanobacterium plays a prominent role in the detoxification of MG in catalyzing its conjugation with GSH. This finding is important because this reaction, always regarded as nonenzymatic, could exist in plants and/or human and thus have an impact on agriculture and/or human health. Methylglyoxal (MG) is a detrimental metabolic by-product that threatens most organisms (in humans MG causes diabetes). MG is predominantly detoxified by the glyoxalase pathway. This process begins with the conjugation of MG with glutathione (GSH), yielding a hemithioacetal product that is subsequently transformed by the glyoxalase enzymes into d-lactate and GSH. MG has been overlooked in photosynthetic organisms, although they inevitably produce it not only by the catabolism of sugars, lipids, and amino acids, as do heterotrophic organisms, but also by their active photoautotrophic metabolism. This is especially true for cyanobacteria that are regarded as having developed photosynthesis and GSH-dependent enzymes to detoxify the reactive oxygen species produced by their photosynthesis (CO2 assimilation) and respiration (glucose catabolism), which they perform in the same cell compartment. In this study, we used a combination of in vivo and in vitro approaches to characterize a logical, but as yet never described, link between MG detoxification and a (prokaryotic) representative of the evolutionarily conserved glutathione transferase (GST) detoxification enzymes. We show that the Sll0067 GST of the model cyanobacterium Synechocystis sp. strain PCC 6803 plays a prominent role in MG tolerance and detoxification, unlike the other five GSTs of this organism. Sll0067 catalyzes the conjugation of MG with GSH to initiate its elimination driven by glyoxalases. These results are novel because the conjugation of MG with GSH is always described as nonenzymatic. They will certainly stimulate the analysis of Sll0067 orthologs from other organisms with possible impacts on human health (development of biomarkers or drugs) and/or agriculture.
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22
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Guyet U, Nguyen NA, Doré H, Haguait J, Pittera J, Conan M, Ratin M, Corre E, Le Corguillé G, Brillet-Guéguen L, Hoebeke M, Six C, Steglich C, Siegel A, Eveillard D, Partensky F, Garczarek L. Synergic Effects of Temperature and Irradiance on the Physiology of the Marine Synechococcus Strain WH7803. Front Microbiol 2020; 11:1707. [PMID: 32793165 PMCID: PMC7393227 DOI: 10.3389/fmicb.2020.01707] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/29/2020] [Indexed: 11/18/2022] Open
Abstract
Understanding how microorganisms adjust their metabolism to maintain their ability to cope with short-term environmental variations constitutes one of the major current challenges in microbial ecology. Here, the best physiologically characterized marine Synechococcus strain, WH7803, was exposed to modulated light/dark cycles or acclimated to continuous high-light (HL) or low-light (LL), then shifted to various stress conditions, including low (LT) or high temperature (HT), HL and ultraviolet (UV) radiations. Physiological responses were analyzed by measuring time courses of photosystem (PS) II quantum yield, PSII repair rate, pigment ratios and global changes in gene expression. Previously published membrane lipid composition were also used for correlation analyses. These data revealed that cells previously acclimated to HL are better prepared than LL-acclimated cells to sustain an additional light or UV stress, but not a LT stress. Indeed, LT seems to induce a synergic effect with the HL treatment, as previously observed with oxidative stress. While all tested shift conditions induced the downregulation of many photosynthetic genes, notably those encoding PSI, cytochrome b6/f and phycobilisomes, UV stress proved to be more deleterious for PSII than the other treatments, and full recovery of damaged PSII from UV stress seemed to involve the neo-synthesis of a fairly large number of PSII subunits and not just the reassembly of pre-existing subunits after D1 replacement. In contrast, genes involved in glycogen degradation and carotenoid biosynthesis pathways were more particularly upregulated in response to LT. Altogether, these experiments allowed us to identify responses common to all stresses and those more specific to a given stress, thus highlighting genes potentially involved in niche acclimation of a key member of marine ecosystems. Our data also revealed important specific features of the stress responses compared to model freshwater cyanobacteria.
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Affiliation(s)
- Ulysse Guyet
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Ngoc A Nguyen
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Hugo Doré
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Julie Haguait
- LS2N, UMR CNRS 6004, IMT Atlantique, ECN, Université de Nantes, Nantes, France
| | - Justine Pittera
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Maël Conan
- DYLISS (INRIA-IRISA)-INRIA, CNRS UMR 6074, Université de Rennes 1, Rennes, France
| | - Morgane Ratin
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Erwan Corre
- CNRS, FR2424, ABiMS, Station Biologique, Sorbonne Université, Roscoff, France
| | - Gildas Le Corguillé
- CNRS, FR2424, ABiMS, Station Biologique, Sorbonne Université, Roscoff, France
| | - Loraine Brillet-Guéguen
- CNRS, FR2424, ABiMS, Station Biologique, Sorbonne Université, Roscoff, France.,CNRS, UMR 8227 Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Mark Hoebeke
- CNRS, FR2424, ABiMS, Station Biologique, Sorbonne Université, Roscoff, France
| | - Christophe Six
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | | | - Anne Siegel
- DYLISS (INRIA-IRISA)-INRIA, CNRS UMR 6074, Université de Rennes 1, Rennes, France
| | - Damien Eveillard
- LS2N, UMR CNRS 6004, IMT Atlantique, ECN, Université de Nantes, Nantes, France
| | - Frédéric Partensky
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Laurence Garczarek
- CNRS, UMR 7144 Adaptation and Diversity in the Marine Environment, Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
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23
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Crits-Christoph A, Olm MR, Diamond S, Bouma-Gregson K, Banfield JF. Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow. THE ISME JOURNAL 2020; 14:1834-1846. [PMID: 32327732 PMCID: PMC7305173 DOI: 10.1038/s41396-020-0655-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 03/22/2020] [Accepted: 04/02/2020] [Indexed: 01/25/2023]
Abstract
Soil microbial diversity is often studied from the perspective of community composition, but less is known about genetic heterogeneity within species. The relative impacts of clonal interference, gene-specific selection, and recombination in many abundant but rarely cultivated soil microbes remain unknown. Here we track genome-wide population genetic variation for 19 highly abundant bacterial species sampled from across a grassland meadow. Genomic inferences about population structure are made using the millions of sequencing reads that are assembled de novo into consensus genomes from metagenomes, as each read pair describes a short genomic sequence from a cell in each population. Genomic nucleotide identity of assembled genomes was significantly associated with local geography for over half of the populations studied, and for a majority of populations within-sample nucleotide diversity could often be as high as meadow-wide nucleotide diversity. Genes involved in metabolite biosynthesis and extracellular transport were characterized by elevated nucleotide diversity in multiple species. Microbial populations displayed varying degrees of homologous recombination and recombinant variants were often detected at 7-36% of loci genome-wide. Within multiple populations we identified genes with unusually high spatial differentiation of alleles, fewer recombinant events, elevated ratios of nonsynonymous to synonymous variants, and lower nucleotide diversity, suggesting recent selective sweeps for gene variants. Taken together, these results indicate that recombination and gene-specific selection commonly shape genetic variation in several understudied soil bacterial lineages.
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Affiliation(s)
| | - Matthew R Olm
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Spencer Diamond
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Keith Bouma-Gregson
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA
| | - Jillian F Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, CA, USA.
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA.
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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24
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Nies F, Mielke M, Pochert J, Lamparter T. Natural transformation of the filamentous cyanobacterium Phormidium lacuna. PLoS One 2020; 15:e0234440. [PMID: 32530971 PMCID: PMC7292380 DOI: 10.1371/journal.pone.0234440] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/25/2020] [Indexed: 02/06/2023] Open
Abstract
Research for biotechnological applications of cyanobacteria focuses on synthetic pathways and bioreactor design, while little effort is devoted to introduce new, promising organisms in the field. Applications are most often based on recombinant work, and the establishment of transformation can be a risky, time-consuming procedure. In this work we demonstrate the natural transformation of the filamentous cyanobacterium Phormidium lacuna and insertion of a selection marker into the genome by homologous recombination. This is the first example for natural transformation filamentous non-heterocystous cyanobacterium. We found that Phormidium lacuna is polyploid, each cell has about 20-90 chromosomes. Transformed filaments were resistant against up to 14 mg/ml of kanamycin. Formerly, natural transformation in cyanobacteria has been considered a rare and exclusive feature of a few unicellular species. Our finding suggests that natural competence is more distributed among cyanobacteria than previously thought. This is supported by bioinformatic analyses which show that all protein factors for natural transformation are present in the majority of the analyzed cyanobacteria.
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Affiliation(s)
- Fabian Nies
- Botanical Institute, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Marion Mielke
- Botanical Institute, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Janko Pochert
- Botanical Institute, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Tilman Lamparter
- Botanical Institute, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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25
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Koksharova OA, Butenko IO, Pobeguts OV, Safronova NA, Govorun VM. Proteomic Insights into Starvation of Nitrogen-Replete Cells of Nostoc sp. PCC 7120 under β-N-Methylamino-L-Alanine (BMAA) Treatment. Toxins (Basel) 2020; 12:toxins12060372. [PMID: 32512731 PMCID: PMC7354497 DOI: 10.3390/toxins12060372] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/16/2020] [Accepted: 06/01/2020] [Indexed: 01/05/2023] Open
Abstract
All cyanobacteria produce a neurotoxic non-protein amino acid β-N-methylamino-L-alanine (BMAA). However, the biological function of BMAA in the regulation of cyanobacteria metabolism still remains undetermined. It is known that BMAA suppresses the formation of heterocysts in diazotrophic cyanobacteria under nitrogen starvation conditions, and BMAA induces the formation of heterocyst-like cells under nitrogen excess conditions, by causing the expression of heterocyst-specific genes that are usually “silent” under nitrogen-replete conditions, as if these bacteria receive a nitrogen deficiency intracellular molecular signal. In order to find out the molecular mechanisms underlying this unexpected BMAA effect, we studied the proteome of cyanobacterium Nostoc sp. PCC 7120 grown under BMAA treatment in nitrogen-replete medium. Experiments were performed in two experimental settings: (1) in control samples consisted of cells grown without the BMAA treatment and (2) the treated samples consisted of cells grown with addition of an aqueous solution of BMAA (20 µM). In total, 1567 different proteins of Nostoc sp. PCC 7120 were identified by LC-MS/MS spectrometry. Among them, 80 proteins belonging to different functional categories were chosen for further functional analysis and interpretation of obtained proteomic data. Here, we provide the evidence that a pleiotropic regulatory effect of BMAA on the proteome of cyanobacterium was largely different under conditions of nitrogen-excess compared to its effect under nitrogen starvation conditions (that was studied in our previous work). The most significant difference in proteome expression between the BMAA-treated and untreated samples under different growth conditions was detected in key regulatory protein PII (GlnB). BMAA downregulates protein PII in nitrogen-starved cells and upregulates this protein in nitrogen-replete conditions. PII protein is a key signal transduction protein and the change in its regulation leads to the change of many other regulatory proteins, including different transcriptional factors, enzymes and transporters. Complex changes in key metabolic and regulatory proteins (RbcL, RbcS, Rca, CmpA, GltS, NodM, thioredoxin 1, RpbD, ClpP, MinD, RecA, etc.), detected in this experimental study, could be a reason for the appearance of the “starvation” state in nitrogen-replete conditions in the presence of BMAA. In addition, 15 proteins identified in this study are encoded by genes, which are under the control of NtcA—a global transcriptional regulator—one of the main protein partners and transcriptional regulators of PII protein. Thereby, this proteomic study gives a possible explanation of cyanobacterium starvation under nitrogen-replete conditions and BMAA treatment. It allows to take a closer look at the regulation of cyanobacteria metabolism affected by this cyanotoxin.
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Affiliation(s)
- Olga A. Koksharova
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 1-40, 119992 Moscow, Russia;
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Square, 2, 123182 Moscow, Russia
- Correspondence: ; Tel.: +7-917-534-7543
| | - Ivan O. Butenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (I.O.B.); (O.V.P.); (V.M.G.)
| | - Olga V. Pobeguts
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (I.O.B.); (O.V.P.); (V.M.G.)
| | - Nina A. Safronova
- Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, Leninskie Gory, 1-40, 119992 Moscow, Russia;
| | - Vadim M. Govorun
- Federal Research and Clinical Centre of Physical-Chemical Medicine, 119435 Moscow, Russia; (I.O.B.); (O.V.P.); (V.M.G.)
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26
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Resilience and self-regulation processes of microalgae under UV radiation stress. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C: PHOTOCHEMISTRY REVIEWS 2020. [DOI: 10.1016/j.jphotochemrev.2019.100322] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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27
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Veaudor T, Blanc-Garin V, Chenebault C, Diaz-Santos E, Sassi JF, Cassier-Chauvat C, Chauvat F. Recent Advances in the Photoautotrophic Metabolism of Cyanobacteria: Biotechnological Implications. Life (Basel) 2020; 10:E71. [PMID: 32438704 PMCID: PMC7281370 DOI: 10.3390/life10050071] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/16/2020] [Accepted: 05/18/2020] [Indexed: 12/13/2022] Open
Abstract
Cyanobacteria constitute the only phylum of oxygen-evolving photosynthetic prokaryotes that shaped the oxygenic atmosphere of our planet. Over time, cyanobacteria have evolved as a widely diverse group of organisms that have colonized most aquatic and soil ecosystems of our planet and constitute a large proportion of the biomass that sustains the biosphere. Cyanobacteria synthesize a vast array of biologically active metabolites that are of great interest for human health and industry, and several model cyanobacteria can be genetically manipulated. Hence, cyanobacteria are regarded as promising microbial factories for the production of chemicals from highly abundant natural resources, e.g., solar energy, CO2, minerals, and waters, eventually coupled to wastewater treatment to save costs. In this review, we summarize new important discoveries on the plasticity of the photoautotrophic metabolism of cyanobacteria, emphasizing the coordinated partitioning of carbon and nitrogen towards growth or compound storage, and the importance of these processes for biotechnological perspectives. We also emphasize the importance of redox regulation (including glutathionylation) on these processes, a subject which has often been overlooked.
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Affiliation(s)
- Théo Veaudor
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (T.V.); (V.B.-G.); (C.C.); (E.D.-S.); (C.C.-C.)
| | - Victoire Blanc-Garin
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (T.V.); (V.B.-G.); (C.C.); (E.D.-S.); (C.C.-C.)
| | - Célia Chenebault
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (T.V.); (V.B.-G.); (C.C.); (E.D.-S.); (C.C.-C.)
| | - Encarnación Diaz-Santos
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (T.V.); (V.B.-G.); (C.C.); (E.D.-S.); (C.C.-C.)
| | - Jean-François Sassi
- Commissariat à l’énergie atomique et aux énergies alternatives (CEA), Centre de Cadarache St Paul Lez, 13108 Durance, France;
| | - Corinne Cassier-Chauvat
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (T.V.); (V.B.-G.); (C.C.); (E.D.-S.); (C.C.-C.)
| | - Franck Chauvat
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, 91198 Gif-sur-Yvette, France; (T.V.); (V.B.-G.); (C.C.); (E.D.-S.); (C.C.-C.)
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28
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Olina A, Kuzmenko A, Ninova M, Aravin AA, Kulbachinskiy A, Esyunina D. Genome-wide DNA sampling by Ago nuclease from the cyanobacterium Synechococcus elongatus. RNA Biol 2020; 17:677-688. [PMID: 32013676 PMCID: PMC7237159 DOI: 10.1080/15476286.2020.1724716] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 01/03/2020] [Accepted: 01/12/2020] [Indexed: 12/17/2022] Open
Abstract
Members of the conserved Argonaute (Ago) protein family provide defence against invading nucleic acids in eukaryotes in the process of RNA interference. Many prokaryotes also contain Ago proteins that are predicted to be active nucleases; however, their functional activities in host cells remain poorly understood. Here, we characterize the in vitro and in vivo properties of the SeAgo protein from the mesophilic cyanobacterium Synechococcus elongatus. We show that SeAgo is a DNA-guided nuclease preferentially acting on single-stranded DNA targets, with non-specific guide-independent activity observed for double-stranded substrates. The SeAgo gene is steadily expressed in S. elongatus; however, its deletion or overexpression does not change the kinetics of cell growth. When purified from its host cells or from heterologous E. coli, SeAgo is loaded with small guide DNAs whose formation depends on the endonuclease activity of the argonaute protein. SeAgo co-purifies with SSB proteins suggesting that they may also be involved in DNA processing. The SeAgo-associated small DNAs are derived from diverse genomic locations, with certain enrichment for the proposed sites of chromosomal replication initiation and termination, but show no preference for an endogenous plasmid. Therefore, promiscuous genome sampling by SeAgo does not have great effects on cell physiology and plasmid maintenance.
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Affiliation(s)
- Anna Olina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Anton Kuzmenko
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Maria Ninova
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Alexei A. Aravin
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | - Daria Esyunina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
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Chen Z, Li X, Tan X, Zhang Y, Wang B. Recent Advances in Biological Functions of Thick Pili in the Cyanobacterium Synechocystis sp. PCC 6803. FRONTIERS IN PLANT SCIENCE 2020; 11:241. [PMID: 32210999 PMCID: PMC7076178 DOI: 10.3389/fpls.2020.00241] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 02/17/2020] [Indexed: 05/05/2023]
Abstract
Cyanobacteria have evolved various strategies to sense and adapt to biotic and abiotic stresses including active movement. Motility in cyanobacteria utilizing the type IV pili (TFP) is useful to cope with changing environmental conditions. The model cyanobacterium Synechocystis sp. PCC 6803 (hereafter named Synechocystis) exhibits motility via TFP called thick pili, and uses it to seek out favorable light/nutrition or escape from unfavorable conditions. Recently, a number of studies on Synechocystis thick pili have been undertaken. Molecular approaches support the role of the pilin in motility, cell adhesion, metal utilization, and natural competence in Synechocystis. This review summarizes the most recent studies on the function of thick pili as well as their formation and regulation in this cyanobacterium.
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Affiliation(s)
- Zhuo Chen
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Xitong Li
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Xiaoming Tan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Yan Zhang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Baoshan Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
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Cas4 Facilitates PAM-Compatible Spacer Selection during CRISPR Adaptation. Cell Rep 2019; 22:3377-3384. [PMID: 29590607 PMCID: PMC5896167 DOI: 10.1016/j.celrep.2018.02.103] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/25/2018] [Accepted: 02/27/2018] [Indexed: 12/20/2022] Open
Abstract
CRISPR-Cas systems adapt their immunological memory against their invaders by integrating short DNA fragments into clustered regularly interspaced short palindromic repeat (CRISPR) loci. While Cas1 and Cas2 make up the core machinery of the CRISPR integration process, various class I and II CRISPR-Cas systems encode Cas4 proteins for which the role is unknown. Here, we introduced the CRISPR adaptation genes cas1, cas2, and cas4 from the type I-D CRISPR-Cas system of Synechocystis sp. 6803 into Escherichia coli and observed that cas4 is strictly required for the selection of targets with protospacer adjacent motifs (PAMs) conferring I-D CRISPR interference in the native host Synechocystis. We propose a model in which Cas4 assists the CRISPR adaptation complex Cas1-2 by providing DNA substrates tailored for the correct PAM. Introducing functional spacers that target DNA sequences with the correct PAM is key to successful CRISPR interference, providing a better chance of surviving infection by mobile genetic elements. Cas4 facilitates the integration of PAM-compatible spacers Spacer length variation is dictated by Cas1-2 Cas4 shortens spacer length Cas4-selected PAMs license type I-D CRISPR interference
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A Comparison of Constitutive and Inducible Non-Endogenous Keto-Carotenoids Biosynthesis in Synechocystis sp. PCC 6803. Microorganisms 2019; 7:microorganisms7110501. [PMID: 31661899 PMCID: PMC6920976 DOI: 10.3390/microorganisms7110501] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 10/14/2019] [Accepted: 10/26/2019] [Indexed: 12/05/2022] Open
Abstract
The model cyanobacterium Synechocystis sp. PCC 6803 has gained significant attention as an alternative and sustainable source for biomass, biofuels and added-value compounds. The latter category includes keto-carotenoids, which are molecules largely employed in a wide spectrum of industrial applications in the food, feed, nutraceutical, cosmetic and pharmaceutical sectors. Keto-carotenoids are not naturally synthesized by Synechocystis, at least in any significant amounts, but their accumulation can be induced by metabolic engineering of the endogenous carotenoid biosynthetic pathway. In this study, the accumulation of the keto-carotenoids astaxanthin and canthaxanthin, resulting from the constitutive or temperature-inducible expression of the CrtW and CrtZ genes from Brevundimonas, is compared. The benefits and drawbacks of the two engineering approaches are discussed.
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Mosca C, Rothschild LJ, Napoli A, Ferré F, Pietrosanto M, Fagliarone C, Baqué M, Rabbow E, Rettberg P, Billi D. Over-Expression of UV-Damage DNA Repair Genes and Ribonucleic Acid Persistence Contribute to the Resilience of Dried Biofilms of the Desert Cyanobacetrium Chroococcidiopsis Exposed to Mars-Like UV Flux and Long-Term Desiccation. Front Microbiol 2019; 10:2312. [PMID: 31681194 PMCID: PMC6798154 DOI: 10.3389/fmicb.2019.02312] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 09/23/2019] [Indexed: 12/20/2022] Open
Abstract
The survival limits of the desert cyanobacterium Chroococcidiopsis were challenged by rewetting dried biofilms and dried biofilms exposed to 1.5 × 103 kJ/m2 of a Mars-like UV, after 7 years of air-dried storage. PCR-stop assays revealed the presence of DNA lesions in dried biofilms and an increased accumulation in dried-UV-irradiated biofilms. Different types and/or amounts of DNA lesions were highlighted by a different expression of uvrA, uvrB, uvrC, phrA, and uvsE genes in dried-rewetted biofilms and dried-UV-irradiated-rewetted biofilms, after rehydration for 30 and 60 min. The up-regulation in dried-rewetted biofilms of uvsE gene encoding an UV damage endonuclease, suggested that UV-damage DNA repair contributed to the repair of desiccation-induced damage. While the phrA gene encoding a photolyase was up-regulated only in dried-UV-irradiated-rewetted biofilms. Nucleotide excision repair genes were over-expressed in dried-rewetted biofilms and dried-UV-irradiated-rewetted biofilms, with uvrC gene showing the highest increase in dried-UV-irradiated-rewetted biofilms. Dried biofilms preserved intact mRNAs (at least of the investigated genes) and 16S ribosomal RNA that the persistence of the ribosome machinery and mRNAs might have played a key role in the early phase recovery. Results have implications for the search of extra-terrestrial life by contributing to the definition of habitability of astrobiologically relevant targets such as Mars or planets orbiting around other stars.
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Affiliation(s)
- Claudia Mosca
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Lynn J Rothschild
- Earth Sciences Division, NASA Ames Research Center, Mountain View, CA, United States
| | | | - Fabrizio Ferré
- Department of Pharmacy and Biotechnology, University of Bologna Alma Mater, Bologna, Italy
| | | | | | - Mickael Baqué
- Astrobiological Laboratories Research Group, German Aerospace Center, Institute of Planetary Research, Management and Infrastructure, Berlin, Germany
| | - Elke Rabbow
- German Aerospace Center, Institute of Aerospace Medicine, Cologne, Germany
| | - Petra Rettberg
- German Aerospace Center, Institute of Aerospace Medicine, Cologne, Germany
| | - Daniela Billi
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
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Kammerscheit X, Chauvat F, Cassier-Chauvat C. From Cyanobacteria to Human, MAPEG-Type Glutathione-S-Transferases Operate in Cell Tolerance to Heat, Cold, and Lipid Peroxidation. Front Microbiol 2019; 10:2248. [PMID: 31681188 PMCID: PMC6798054 DOI: 10.3389/fmicb.2019.02248] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 09/13/2019] [Indexed: 11/18/2022] Open
Abstract
The MAPEG2 sub-family of glutathione-S-transferase proteins (GST) has been poorly investigated in vivo, even in prokaryotes such as cyanobacteria the organisms that are regarded as having developed glutathione-dependent enzymes to protect themselves against the reactive oxygen species (ROS) often produced by their powerful photosynthesis. We report the first in vivo analysis of a cyanobacterial MAPEG2-like protein (Sll1147) in the model cyanobacterium Synechocystis PCC 6803. While Sll1147 is dispensable to cell growth in standard photo-autotrophic conditions, it plays an important role in the resistance to heat and cold, and to n-tertbutyl hydroperoxide (n-tBOOH) that induces lipid peroxidation. These findings suggest that Sll1147 could be involved in membrane fluidity, which is critical for photosynthesis. Attesting its sensitivity to these stresses, the Δsll1147 mutant lacking Sll1147 challenged by heat, cold, or n-tBOOH undergoes transient accumulation of peroxidized lipids and then of reduced and oxidized glutathione. These results are welcome because little is known concerning the signaling and/or protection mechanisms used by cyanobacteria to cope with heat and cold, two inevitable environmental stresses that limit their growth, and thus their production of biomass for our food chain and of biotechnologically interesting chemicals. Also interestingly, the decreased resistance to heat, cold and n-tBOOH of the Δsll1147 mutant could be rescued back to normal (wild-type) levels upon the expression of synthetic MAPEG2-encoding human genes adapted to the cyanobacterial codon usage. These synthetic hmGST2 and hmGST3 genes were also able to increase the Escherichia coli tolerance to heat and n-tBOOH. Collectively, these finding indicate that the activity of the MAPEG2 proteins have been conserved, at least in part, during evolution from (cyano)bacteria to human.
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Affiliation(s)
| | - Franck Chauvat
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University of Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Corinne Cassier-Chauvat
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University of Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
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Veaudor T, Cassier-Chauvat C, Chauvat F. Genomics of Urea Transport and Catabolism in Cyanobacteria: Biotechnological Implications. Front Microbiol 2019; 10:2052. [PMID: 31551986 PMCID: PMC6737895 DOI: 10.3389/fmicb.2019.02052] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/20/2019] [Indexed: 11/13/2022] Open
Abstract
Cyanobacteria are widely-diverse prokaryotes that colonize our planet. They use solar energy to assimilate huge amounts of atmospheric CO2 and produce a large part of the biomass and oxygen that sustain most life forms. Cyanobacteria are therefore increasingly studied for basic research objectives, as well as for the photosynthetic production of chemicals with industrial interests. One potential approach to reduce the cost of future bioproduction processes is to couple them with wastewater treatment, often polluted with urea, which in any case is cheaper than nitrate. As of yet, however, research has mostly focused on a very small number of model cyanobacteria growing on nitrate. Thus, the genetic inventory of the cyanobacterial phylum is still insufficiently employed to meaningfully select the right host for the right purpose. This review reports what is known about urea transport and catabolism in cyanobacteria, and what can be inferred from the comparative analysis of the publicly available genome sequence of the 308 cyanobacteria. We found that most cyanobacteria mostly harbor the genes encoding the urea catabolytic enzymes urease (ureABCDEFG), but not systematically, together with the urea transport (urtABCDE). These findings are consistent with the capacity of the few tested cyanobacteria that grow on urea as the sole nitrogen source. They also indicate that urease is important for the detoxification of internally generated urea (re-cycling its carbon and nitrogen). In contrast, several cyanobacteria have urtABCDE but not ureABCDEFG, suggesting that urtABCDE could operate in the transport of not only urea but also of other nutrients. Only four cyanobacteria appeared to have the genes encoding the urea carboxylase (uc) and allophanate hydrolase (ah) enzymes that sequentially catabolize urea. Three of these cyanobacteria belongs to the genera Gloeobacter and Gloeomargarita that have likely diverged early from other cyanobacteria, suggesting that the urea carboxylase and allophanate hydrolase enzymes appeared in cyanobacteria before urease.
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Affiliation(s)
- Théo Veaudor
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Corinne Cassier-Chauvat
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Franck Chauvat
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
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Kammerscheit X, Chauvat F, Cassier-Chauvat C. First in vivo Evidence That Glutathione-S-Transferase Operates in Photo-Oxidative Stress in Cyanobacteria. Front Microbiol 2019; 10:1899. [PMID: 31456794 PMCID: PMC6700277 DOI: 10.3389/fmicb.2019.01899] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/31/2019] [Indexed: 11/13/2022] Open
Abstract
Although glutathione (GSH) and GSH-dependent enzymes, such as glutathione transferases (GSTs), are thought to have been developed by cyanobacteria to cope with the reactive oxygen species (ROS) that they massively produced by their active photosynthesis, there had been no in vivo analysis of the role of GSTs in cyanobacteria so far. Consequently, we have analyzed two of the six GSTs of the model cyanobacterium Synechocystis PCC 6803, namely Sll1545 (to extend its in vitro study) and Slr0236 (because it is the best homolog to Sll1545). We report that Sll1545 is essential to cell growth in standard photo-autotrophic conditions, whereas Slr0236 is dispensable. Furthermore, both Sll1545 and Slr0236 operate in the protection against stresses triggered by high light, H2O2, menadione and methylene blue. The absence of Slr0236 and the depletion of Sll1545 decrease the tolerance to methylene blue in a cumulative way. Similarly, the combined absence of Slr0236 and depletion of Sll1545 decrease the resistance to high light. Attesting their sensitivity to high-light or methylene blue, these Δslr0236-sll1545 cells transiently accumulate ROS, and then reduced and oxidized glutathione in that order. In contrast, the absence of Slr0236 and the depletion of Sll1545 increase the tolerance to menadione in a cumulative way. This increased menadione resistance is due, at least in part, to the higher level of catalase and/or peroxidase activity of these mutants. Similarly, the increased H2O2 resistance of the Δslr0236-sll1545 cells is due, at least in part, to its higher level of peroxidase activity.
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Affiliation(s)
- Xavier Kammerscheit
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Franck Chauvat
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Corinne Cassier-Chauvat
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
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Wendt KE, Pakrasi HB. Genomics Approaches to Deciphering Natural Transformation in Cyanobacteria. Front Microbiol 2019; 10:1259. [PMID: 31231343 PMCID: PMC6567925 DOI: 10.3389/fmicb.2019.01259] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 05/21/2019] [Indexed: 12/24/2022] Open
Abstract
Natural transformation is the process by which bacteria actively take up and maintain extracellular DNA. This naturally occurring process is widely used as a genetic modification method in bacterial species, and is crucial for the efficient genetic modification of organisms in an industrial setting. Cyanobacteria are oxygenic photosynthetic microbes that are promising platforms for bioproduction of fuels, chemicals, and feedstocks. Using CO2 and sunlight alone, cyanobacteria can make these valuable bioproducts in a carbon-neutral manner. While genetic modifications have been performed in a number of cyanobacterial strains, natural transformation has been successfully demonstrated in only a handful of species. Even though thousands of cyanobacterial strains have been deposited in culture collections and hundreds of these species have had their genomes sequenced, only a few of these organisms have been experimentally transformed. Although there are many aspects of cyanobacterial biology that provide exciting opportunities for biological investigation, the absence of a rapid and straightforward genetic modification method such as natural transformation hinders research efforts to understand some of the fascinating nuances of cyanobacterial physiology. The ability to use natural transformation in more strains of cyanobacteria would facilitate the rapid employment of these organisms in bioproduction settings. This article discusses recent advances in the understanding of natural transformation in cyanobacteria. Additionally, it identifies gaps in the current knowledge about cyanobacterial natural transformation and provides an overview of how new genomic technologies may be implemented to understand this important process.
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Affiliation(s)
- Kristen E Wendt
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Himadri B Pakrasi
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
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Economic feasibility and long-term sustainability criteria on the path to enable a transition from fossil fuels to biofuels. Curr Opin Biotechnol 2019; 57:175-182. [DOI: 10.1016/j.copbio.2019.04.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 03/31/2019] [Accepted: 04/16/2019] [Indexed: 12/19/2022]
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Kumar P, Hegde K, Brar SK, Cledon M, Kermanshahi-Pour A. Potential of biological approaches for cyanotoxin removal from drinking water: A review. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 172:488-503. [PMID: 30738231 DOI: 10.1016/j.ecoenv.2019.01.066] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 01/20/2019] [Accepted: 01/22/2019] [Indexed: 05/20/2023]
Abstract
Biological treatment of cyanotoxins has gained much importance in recent decades and holds a promise to work in coordination with various physicochemical treatments. In drinking water treatment plants (DWTPs), effective removal of cyanotoxins with reduced toxicity is a primary concern. Commonly used treatments, such as ozonation, chlorination or activated carbon, undergo significant changes in their operating conditions (mainly dosage) to counter the variation in different environmental parameters, such as pH, temperature, and high cyanotoxin concentration. Presence of metal ions, natural organic matter (NOM), and other chemicals demand higher dosage and hence affect the activation energy to efficiently break down the cyanotoxin molecule. Due to these higher dose requirements, the treatment leads to the formation of toxic metabolites at a concentration high enough to break the guideline values. Biological methods of cyanotoxin removal proceed via enzymatic pathway where the protein-encoding genes are often responsible for the compound breakdown into non-toxic metabolites. However, in contrast to the chemical treatment, the biological processes advance at a much slower kinetic rate, predominantly due to a longer onset period (high lag phase). In fact, more than 90% of the studies reported on the biological degradation of the cyanotoxins attribute the biodegradation to the bacterial suspension. This suspended growth limits the mass transfer kinetics due to the presence of metal ions, NOMs and, other oxidizable matter, which further prolongs the lag phase and makes biological process toxic-free, albeit less efficient. In this context, this review attempts to bring out the importance of the attached growth mechanism, in particular, the biofilm-based treatment approaches which can enhance the biodegradation rate.
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Affiliation(s)
- Pratik Kumar
- INRS-ETE, Université du Québec, 490, Rue de la Couronne, Québec, Canada G1K 9A9
| | | | - Satinder Kaur Brar
- INRS-ETE, Université du Québec, 490, Rue de la Couronne, Québec, Canada G1K 9A9; Department of Civil Engineering, Lassonde School of Engineering, York University, North York, Toronto, Ontario, Canada M3J 1P3.
| | - Maximiliano Cledon
- CIMAS (CONICET, UnComa, Rio Negro), Güemes 1030, San Antonio Oeste, Rio Negro, Argentina
| | - Azadeh Kermanshahi-Pour
- Biorefining and Remediation Laboratory, Department of Process Engineering and Applied Science, Dalhousie University, 1360 Barrington Street, Halifax, Nova Scotia, Canada B3J 1Z1
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Pérez AA, Chen Q, Hernández HP, Branco dos Santos F, Hellingwerf KJ. On the use of oxygenic photosynthesis for the sustainable production of commodity chemicals. PHYSIOLOGIA PLANTARUM 2019; 166:413-427. [PMID: 30829400 PMCID: PMC6850307 DOI: 10.1111/ppl.12946] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/15/2019] [Accepted: 02/18/2019] [Indexed: 05/13/2023]
Abstract
A sustainable society will have to largely refrain from the use of fossil carbon deposits. In such a regime, renewable electricity can be harvested as a primary source of energy. However, as for the synthesis of carbon-based materials from bulk chemicals, an alternative is required. A sustainable approach towards this is the synthesis of commodity chemicals from CO2 , water and sunlight. Multiple paths to achieve this have been designed and tested in the domains of chemistry and biology. In the latter, the use of both chemotrophic and phototrophic organisms has been advocated. 'Direct conversion' of CO2 and H2 O, catalyzed by an oxyphototroph, has excellent prospects to become the most economically competitive of these transformations, because of the relative ease of scale-up of this process. Significantly, for a wide range of energy and commodity products, a proof of principle via engineering of the corresponding production organism has been provided. In the optimization of a cyanobacterial production organism, a wide range of aspects has to be addressed. Of these, here we will put our focus on: (1) optimizing the (carbon) flux to the desired product; (2) increasing the genetic stability of the producing organism and (3) maximizing its energy conversion efficiency. Significant advances have been made on all these three aspects during the past 2 years and these will be discussed: (1) increasing the carbon partitioning to >50%; (2) aligning product formation with the growth of the cells and (3) expanding the photosynthetically active radiation region for oxygenic photosynthesis.
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Affiliation(s)
- Adam A. Pérez
- Molecular Microbial Physiology GroupSwammerdam Institute for Life Sciences, University of Amsterdam1098 XH AmsterdamThe Netherlands
- Photanol BVMatrix VAmsterdam, 1098 XHThe Netherlands
| | - Que Chen
- Molecular Microbial Physiology GroupSwammerdam Institute for Life Sciences, University of Amsterdam1098 XH AmsterdamThe Netherlands
| | - Hugo Pineda Hernández
- Molecular Microbial Physiology GroupSwammerdam Institute for Life Sciences, University of Amsterdam1098 XH AmsterdamThe Netherlands
| | - Filipe Branco dos Santos
- Molecular Microbial Physiology GroupSwammerdam Institute for Life Sciences, University of Amsterdam1098 XH AmsterdamThe Netherlands
| | - Klaas J. Hellingwerf
- Molecular Microbial Physiology GroupSwammerdam Institute for Life Sciences, University of Amsterdam1098 XH AmsterdamThe Netherlands
- Photanol BVMatrix VAmsterdam, 1098 XHThe Netherlands
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Lu J, Cui L, Lin S, Hao L, Cao N, Yi J, Liu X, Lu L, Kang Q. Short communication: Global transcriptome analysis of Lactococcus lactis ssp. lactis in response to gradient freezing. J Dairy Sci 2019; 102:3933-3938. [PMID: 30852017 DOI: 10.3168/jds.2018-15972] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Accepted: 01/07/2019] [Indexed: 11/19/2022]
Abstract
Lactic acid bacteria are often preserved as starter cultures by freezing to extend shelf stability as well as maintain cell viability and acidification activity. Previous studies showed that the endocyte extracted from gradient-freezing pretreated cells could act as lyoprotectant in the lyophilization process of Lactococcus lactis ssp. lactis. In this study, the molecular mechanisms of L. lactis in response to gradient freezing exposure are described using high-throughput sequencing. Nineteen of 56 genes were upregulated after gradient freezing, whereas 37 genes were downregulated. Further validation results of quantitative real-time PCR experiments were consistent with the RNA sequencing. Gene Ontology (http://www.geneontology.org/) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG; https://www.genome.jp/kegg/) pathway were used to analyze the differentially expressed genes. Several pathways, such as glutathione metabolism, ATP-binding cassette transport, metabolism of cell wall and cell membrane components, and stress response-related pathways, were affected by gradient freezing. Six genes relevant to freezing stress response were selected for quantitative real-time PCR, including 3 upregulated genes (hisK, eutD, dukA) and 3 downregulated genes (als, yedF, pepN). The Gene Ontology enrichment and KEGG pathway analyses showed these genes may influence stress response-related pathways, improving the survival of the L. lactis under freezing stress. The identification of these genes deepened an understanding about their response under freezing stress, helping us find potential genes or pathways related to gradient freezing for further research on lyoprotectants.
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Affiliation(s)
- Jike Lu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China.
| | - Lianming Cui
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Songyang Lin
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Limin Hao
- The Quartermaster Equipment Institute, Academy of Military Sciences PLA China, Beijing 100010, China
| | - Nana Cao
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Juanjuan Yi
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Xin Liu
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Laizheng Lu
- Zhengzhou Mindtek Biotechnology Co. Ltd., Zhengzhou, Henan 450001, China
| | - Qiaozhen Kang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China.
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An improved estimation of tRNA expression to better elucidate the coevolution between tRNA abundance and codon usage in bacteria. Sci Rep 2019; 9:3184. [PMID: 30816249 PMCID: PMC6395768 DOI: 10.1038/s41598-019-39369-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 01/23/2019] [Indexed: 12/16/2022] Open
Abstract
The degree to which codon usage can be explained by tRNA abundance in bacterial species is often inadequate, partly because differential tRNA abundance is often approximated by tRNA copy numbers. To better understand the coevolution between tRNA abundance and codon usage, we provide a better estimate of tRNA abundance by profiling tRNA mapped reads (tRNA tpm) using publicly available RNA Sequencing data. To emphasize the feasibility of our approach, we demonstrate that tRNA tpm is consistent with tRNA abundances derived from RNA fingerprinting experiments in Escherichia coli, Bacillus subtilis, and Salmonella enterica. Furthermore, we do not observe an appreciable reduction in tRNA sequencing efficiency due to post-transcriptional methylations in the seven bacteria studied. To determine optimal codons, we calculate codon usage in highly and lowly expressed genes determined by protein per transcript. We found that tRNA tpm is sensitive to identify more translationally optimal codons than gene copy number and early tRNA fingerprinting abundances. Additionally, tRNA tpm improves the predictive power of tRNA adaptation index over codon preference. Our results suggest that dependence of codon usage on tRNA availability is not always associated with species growth-rate. Conversely, tRNA availability is better optimized to codon usage in fast-growing than slow-growing species.
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Santos-Merino M, Singh AK, Ducat DC. New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering. Front Bioeng Biotechnol 2019; 7:33. [PMID: 30873404 PMCID: PMC6400836 DOI: 10.3389/fbioe.2019.00033] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/05/2019] [Indexed: 01/25/2023] Open
Abstract
Cyanobacteria are promising microorganisms for sustainable biotechnologies, yet unlocking their potential requires radical re-engineering and application of cutting-edge synthetic biology techniques. In recent years, the available devices and strategies for modifying cyanobacteria have been increasing, including advances in the design of genetic promoters, ribosome binding sites, riboswitches, reporter proteins, modular vector systems, and markerless selection systems. Because of these new toolkits, cyanobacteria have been successfully engineered to express heterologous pathways for the production of a wide variety of valuable compounds. Cyanobacterial strains with the potential to be used in real-world applications will require the refinement of genetic circuits used to express the heterologous pathways and development of accurate models that predict how these pathways can be best integrated into the larger cellular metabolic network. Herein, we review advances that have been made to translate synthetic biology tools into cyanobacterial model organisms and summarize experimental and in silico strategies that have been employed to increase their bioproduction potential. Despite the advances in synthetic biology and metabolic engineering during the last years, it is clear that still further improvements are required if cyanobacteria are to be competitive with heterotrophic microorganisms for the bioproduction of added-value compounds.
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Affiliation(s)
- María Santos-Merino
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
| | - Amit K. Singh
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
| | - Daniel C. Ducat
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, United States
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Xue Y, He Q. Synthetic Biology Approaches to the Sustainable Production of p-Coumaric Acid and Its Derivatives in Cyanobacteria. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1080:261-277. [PMID: 30091099 DOI: 10.1007/978-981-13-0854-3_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The photosynthetic cyanobacteria are promising candidates for the sustainable production of a plethora of plant secondary metabolites, which are beneficial to human health but are difficult to produce and purify in other systems. This chapter focuses on genetic engineering of Synechocystis PCC 6803 for production of p-coumaric acid and its derivatives. Cyanobacterial engineering approaches are briefly reviewed. Strategies to increase production yield are discussed, including codon optimization of genes expressing enzymatic proteins and a laccase-coding gene knockout from Synechocystis genome which degrades polyphenols.
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Affiliation(s)
- Yong Xue
- Division of Microbiology, Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, USA
| | - Qingfang He
- Department of Biology, University of Arkansas at Little Rock, Little Rock, AR, USA.
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Recombination. Mol Biol 2019. [DOI: 10.1016/b978-0-12-813288-3.00027-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Sun T, Li S, Song X, Diao J, Chen L, Zhang W. Toolboxes for cyanobacteria: Recent advances and future direction. Biotechnol Adv 2018; 36:1293-1307. [DOI: 10.1016/j.biotechadv.2018.04.007] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/09/2018] [Accepted: 04/26/2018] [Indexed: 12/20/2022]
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Du W, Jongbloets JA, van Boxtel C, Pineda Hernández H, Lips D, Oliver BG, Hellingwerf KJ, Branco dos Santos F. Alignment of microbial fitness with engineered product formation: obligatory coupling between acetate production and photoautotrophic growth. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:38. [PMID: 29456625 PMCID: PMC5809919 DOI: 10.1186/s13068-018-1037-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 01/31/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Microbial bioengineering has the potential to become a key contributor to the future development of human society by providing sustainable, novel, and cost-effective production pipelines. However, the sustained productivity of genetically engineered strains is often a challenge, as spontaneous non-producing mutants tend to grow faster and take over the population. Novel strategies to prevent this issue of strain instability are urgently needed. RESULTS In this study, we propose a novel strategy applicable to all microbial production systems for which a genome-scale metabolic model is available that aligns the production of native metabolites to the formation of biomass. Based on well-established constraint-based analysis techniques such as OptKnock and FVA, we developed an in silico pipeline-FRUITS-that specifically 'Finds Reactions Usable in Tapping Side-products'. It analyses a metabolic network to identify compounds produced in anabolism that are suitable to be coupled to growth by deletion of their re-utilization pathway(s), and computes their respective biomass and product formation rates. When applied to Synechocystis sp. PCC6803, a model cyanobacterium explored for sustainable bioproduction, a total of nine target metabolites were identified. We tested our approach for one of these compounds, acetate, which is used in a wide range of industrial applications. The model-guided engineered strain shows an obligatory coupling between acetate production and photoautotrophic growth as predicted. Furthermore, the stability of acetate productivity in this strain was confirmed by performing prolonged turbidostat cultivations. CONCLUSIONS This work demonstrates a novel approach to stabilize the production of target compounds in cyanobacteria that culminated in the first report of a photoautotrophic growth-coupled cell factory. The method developed is generic and can easily be extended to any other modeled microbial production system.
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Affiliation(s)
- Wei Du
- Molecular Microbial Physiology Group, Faculty of Science, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Joeri A. Jongbloets
- Molecular Microbial Physiology Group, Faculty of Science, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Coco van Boxtel
- Systems Bioinformatics/Amsterdam Institute for Molecules, Medicines and Systems (AIMMS)/Netherlands Institute for Systems Biology, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
| | - Hugo Pineda Hernández
- Molecular Microbial Physiology Group, Faculty of Science, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - David Lips
- Molecular Microbial Physiology Group, Faculty of Science, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Brett G. Oliver
- Systems Bioinformatics/Amsterdam Institute for Molecules, Medicines and Systems (AIMMS)/Netherlands Institute for Systems Biology, VU University Amsterdam, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
- Modelling of Biological Process, BioQuant, Heidelberg University, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Klaas J. Hellingwerf
- Molecular Microbial Physiology Group, Faculty of Science, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Filipe Branco dos Santos
- Molecular Microbial Physiology Group, Faculty of Science, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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Kim Y, Jeon J, Kwak MS, Kim GH, Koh I, Rho M. Photosynthetic functions of Synechococcus in the ocean microbiomes of diverse salinity and seasons. PLoS One 2018; 13:e0190266. [PMID: 29293601 PMCID: PMC5749766 DOI: 10.1371/journal.pone.0190266] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 12/11/2017] [Indexed: 12/27/2022] Open
Abstract
Synechococcus is an important photosynthetic picoplankton in the temperate to tropical oceans. As a photosynthetic bacterium, Synechococcus has an efficient mechanism to adapt to the changes in salinity and light intensity. The analysis of the distributions and functions of such microorganisms in the ever changing river mouth environment, where freshwater and seawater mix, should help better understand their roles in the ecosystem. Toward this objective, we have collected and sequenced the ocean microbiome in the river mouth of Kwangyang Bay, Korea, as a function of salinity and temperature. In conjunction with comparative genomics approaches using the sequenced genomes of a wide phylogeny of Synechococcus, the ocean microbiome was analyzed in terms of their composition and clade-specific functions. The results showed significant differences in the compositions of Synechococcus sampled in different seasons. The photosynthetic functions in such enhanced Synechococcus strains were also observed in the microbiomes in summer, which is significantly different from those in other seasons.
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Affiliation(s)
- Yihwan Kim
- Department of Computer Science and Engineering, Hanyang University, Seoul, Korea
| | - Jehyun Jeon
- Department of Computer Science and Engineering, Hanyang University, Seoul, Korea
| | - Min Seok Kwak
- Department of Biology, Kongju National University, Kongju, Korea
| | - Gwang Hoon Kim
- Department of Biology, Kongju National University, Kongju, Korea
| | - InSong Koh
- Department of Biomedical Informatics, Hanyang University, Seoul, Korea
| | - Mina Rho
- Department of Computer Science and Engineering, Hanyang University, Seoul, Korea
- Department of Biomedical Informatics, Hanyang University, Seoul, Korea
- * E-mail:
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Du W, Burbano PC, Hellingwerf KJ, Branco Dos Santos F. Challenges in the Application of Synthetic Biology Toward Synthesis of Commodity Products by Cyanobacteria via "Direct Conversion". ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1080:3-26. [PMID: 30091089 DOI: 10.1007/978-981-13-0854-3_1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Cyanobacterial direct conversion of CO2 to several commodity chemicals has been recognized as a potential contributor to support the much-needed sustainable development of human societies. However, the feasibility of this "green conversion" hinders on our ability to overcome the hurdles presented by the natural evolvability of microbes. The latter may result in the genetic instability of engineered cyanobacterial strains leading to impaired productivity. This challenge is general to any "cell factory" approach in which the cells grow for multiple generations, and based on several studies carried out in different microbial hosts, we could identify that three distinct strategies have been proposed to tackle it. These are (1) to reduce microbial evolvability by decreasing the native mutation rate, (2) to align product formation with cell growth/fitness, and, paradoxically, (3) to efficiently reallocate cellular resources to product formation by uncoupling it from growth. The implementation of either of these strategies requires an advanced synthetic biology toolkit. Here, we review the existing methods available for cyanobacteria and identify areas of focus in which specific developments are still needed. Furthermore, we discuss how potentially stabilizing strategies may be used in combination leading to further increases of productivity while ensuring the stability of the cyanobacterial-based direct conversion process.
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Affiliation(s)
- Wei Du
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, Faculty of Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Patricia Caicedo Burbano
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, Faculty of Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Klaas J Hellingwerf
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, Faculty of Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Filipe Branco Dos Santos
- Molecular Microbial Physiology Group, Swammerdam Institute for Life Sciences, Faculty of Sciences, University of Amsterdam, Amsterdam, The Netherlands.
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Santos-Merino M, Garcillán-Barcia MP, de la Cruz F. Engineering the fatty acid synthesis pathway in Synechococcus elongatus PCC 7942 improves omega-3 fatty acid production. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:239. [PMID: 30202434 PMCID: PMC6123915 DOI: 10.1186/s13068-018-1243-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 08/27/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND The microbial production of fatty acids has received great attention in the last few years as feedstock for the production of renewable energy. The main advantage of using cyanobacteria over other organisms is their ability to capture energy from sunlight and to transform CO2 into products of interest by photosynthesis, such as fatty acids. Fatty acid synthesis is a ubiquitous and well-characterized pathway in most bacteria. However, the activity of the enzymes involved in this pathway in cyanobacteria remains poorly explored. RESULTS To characterize the function of some enzymes involved in the saturated fatty acid synthesis in cyanobacteria, we genetically engineered Synechococcus elongatus PCC 7942 by overexpressing or deleting genes encoding enzymes of the fatty acid synthase system and tested the lipid profile of the mutants. These modifications were in turn used to improve alpha-linolenic acid production in this cyanobacterium. The mutant resulting from fabF overexpression and fadD deletion, combined with the overexpression of desA and desB desaturase genes from Synechococcus sp. PCC 7002, produced the highest levels of this omega-3 fatty acid. CONCLUSIONS The fatty acid composition of S. elongatus PCC 7942 can be significantly modified by genetically engineering the expression of genes coding for the enzymes involved in the first reactions of fatty acid synthesis pathway. Variations in fatty acid composition of S. elongatus PCC 7942 mutants did not follow the pattern observed in Escherichia coli derivatives. Some of these modifications can be used to improve omega-3 fatty acid production. This work provides new insights into the saturated fatty acid synthesis pathway and new strategies that might be used to manipulate the fatty acid content of cyanobacteria.
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Affiliation(s)
- María Santos-Merino
- Instituto de Biomedicina y Biotecnología de Cantabria (Universidad de Cantabria—Consejo Superior de Investigaciones Científicas), Santander, Cantabria Spain
| | - M. Pilar Garcillán-Barcia
- Instituto de Biomedicina y Biotecnología de Cantabria (Universidad de Cantabria—Consejo Superior de Investigaciones Científicas), Santander, Cantabria Spain
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria (Universidad de Cantabria—Consejo Superior de Investigaciones Científicas), Santander, Cantabria Spain
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