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Wagner AD, Ahmed MMA, Starks V, Boudreau PD. Using Repeated Lysis Steps Fractionates Between Heterotrophic and Cyanobacterial DNA Extracted from Xenic Cyanobacterial Cultures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.22.609136. [PMID: 39229059 PMCID: PMC11370537 DOI: 10.1101/2024.08.22.609136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Extracting DNA from cyanobacteria can be a challenge because of their diverse morphologies, challenging cellular structure, and the heterotrophic microbiome often present within cyanobacterial cultures. As such, even when our DNA yields are sufficient for sequencing, the percentage of reads coming from the cyanobacterial host can be low, leading to incomplete genomes spread across several scaffolds. In this research, we optimized a DNA isolation protocol using three iterative cell lysis steps to enrich the portion of DNA isolated coming from the cyanobacterial host rather than the heterotrophic microbiome. In order to utilize in-house nanopore sequencing, we faced a challenge in that our lysis protocol led to DNA shearing and a lower molecular weight DNA extract than is suitable for this sequencing technology. As such we used two bead-based size selection steps to remove shorter molecules of DNA before nanopore sequencing. EPI2ME analysis of the processed reads from the iterative lysis steps showed that in the first lysis the heterotrophic microbiome could make up more than half of all reads, but with each lysis the proportion of reads coming from these other species decreased. Using our iterative lysis protocol, we were able to sequence the genomes of two cyanobacteria isolated from fresh water sources around northern Mississippi, namely Leptolyngbya sp. BL-A-14 and Limnothrix sp. BL-A-16. The genomes of these isolates were assembled as closed chromosomes of 7.2 and 4.5 Mb for Leptolyngbya sp. BL-A-14 and Limnothrix sp. BL-A-16, respectively. Because some cyanobacteria have symbioses with their heterotrophic microbiome it is not always possible to prepare axenic cultures of these organisms, we hope our approach will be useful for sequencing xenic cultures of cyanobacteria, but we can also imagine applications in studying this microbiome specifically by focusing sequencing efforts on the first fraction.
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Affiliation(s)
- Alexis D Wagner
- Department of BioMolecular Science, School of Pharmacy, University of Mississippi, University, Mississippi, 38677, United States of America
| | | | - Victoria Starks
- Department of BioMolecular Science, School of Pharmacy, University of Mississippi, University, Mississippi, 38677, United States of America
| | - Paul D Boudreau
- Department of BioMolecular Science, School of Pharmacy, University of Mississippi, University, Mississippi, 38677, United States of America
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2
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Zhang Y, Wu F, Gu JD, He K, Fang Z, Liu X, He D, Ding X, Li J, Han Z, Zhang Q, Feng H. Dominance by cyanobacteria in the newly formed biofilms on stone monuments under a protective shade at the Beishiku Temple in China. ENVIRONMENTAL RESEARCH 2024; 251:118576. [PMID: 38432571 DOI: 10.1016/j.envres.2024.118576] [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: 01/04/2024] [Revised: 02/17/2024] [Accepted: 02/26/2024] [Indexed: 03/05/2024]
Abstract
Following the installation of a protective shade, rapid propagation of microorganisms showing in black and grey colors occurred at Beishiku Temple in Gansu Province of China. This study employed a combination of high-throughput sequencing technology, morphological examinations, and an assessment of the surrounding environmental condition to analyze newly formed microbial disease spots. The investigation unveiled the responsible microorganisms and the instigating factors of the microbial outbreak that subsequently to the erection of the shade. Through comparison of bioinformatics, the ASV method surpasses the OTU method in characterizing community compositional changes by the dominant microbial groups, the phylum Cyanobacteria emerged as the most dominant ones in the microbial community accountable for the post-shade microbial deterioration. The black spot and grey spot are predominantly composed of Mastigocladopsis and Scytonema, respectively. Validation analysis, based on the active RNA-level community results, supported and validated these conclusions. Comparative scrutiny of the microbial community before shade installation and the background environmental data disclosed that the erection of the shade prompted a decrease in temperatures and an increase in humidity within the protected area. Consequently, this spurred the exponential proliferation of indigenous cyanobacteria in the spots observed. The outcomes of this study carry considerable significance in devising preventive conservation strategies for cultural heritage and in managing the process of biodeterioration.
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Affiliation(s)
- Yong Zhang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, P.R. China
| | - Fasi Wu
- National Research Center for Conservation of Ancient Wall Paintings and Earthen Sites, Department of Conservation Research, Dunhuang Academy, Dunhuang, Gansu, 736200, P.R. China; Gansu Provincial Research Center for Conservation of Dunhuang Cultural Heritage, Dunhuang, Gansu, 736200, P.R. China.
| | - Ji-Dong Gu
- Environmental Science and Engineering Group, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, P.R. China; Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion - Israel Institute of Technology, 241 Daxue Road, Shantou, Guangdong, 515063, P.R. China
| | - Kun He
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, P.R. China
| | - Zhou Fang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, P.R. China
| | - Xiaobo Liu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing, 210094, Jiangsu, P.R. China
| | - Dongpeng He
- National Research Center for Conservation of Ancient Wall Paintings and Earthen Sites, Department of Conservation Research, Dunhuang Academy, Dunhuang, Gansu, 736200, P.R. China; Gansu Provincial Research Center for Conservation of Dunhuang Cultural Heritage, Dunhuang, Gansu, 736200, P.R. China
| | - Xinghua Ding
- School of History and Culture, Hunan Normal University, 36 Lushan Road, Changsha, 410000, Hunan, P.R. China
| | - Jie Li
- National Research Center for Conservation of Ancient Wall Paintings and Earthen Sites, Department of Conservation Research, Dunhuang Academy, Dunhuang, Gansu, 736200, P.R. China; Gansu Provincial Research Center for Conservation of Dunhuang Cultural Heritage, Dunhuang, Gansu, 736200, P.R. China
| | - Zengyang Han
- National Research Center for Conservation of Ancient Wall Paintings and Earthen Sites, Department of Conservation Research, Dunhuang Academy, Dunhuang, Gansu, 736200, P.R. China; Gansu Provincial Research Center for Conservation of Dunhuang Cultural Heritage, Dunhuang, Gansu, 736200, P.R. China
| | - Qi Zhang
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, P.R. China
| | - Huyuan Feng
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, P.R. China.
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3
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Espinoza-Corral R, Iwai M, Zavřel T, Lechno-Yossef S, Sutter M, Červený J, Niyogi KK, Kerfeld CA. Phycobilisome protein ApcG interacts with PSII and regulates energy transfer in Synechocystis. PLANT PHYSIOLOGY 2024; 194:1383-1396. [PMID: 37972281 PMCID: PMC10904348 DOI: 10.1093/plphys/kiad615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/25/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023]
Abstract
Photosynthetic organisms harvest light using pigment-protein complexes. In cyanobacteria, these are water-soluble antennae known as phycobilisomes (PBSs). The light absorbed by PBS is transferred to the photosystems in the thylakoid membrane to drive photosynthesis. The energy transfer between these complexes implies that protein-protein interactions allow the association of PBS with the photosystems. However, the specific proteins involved in the interaction of PBS with the photosystems are not fully characterized. Here, we show in Synechocystis sp. PCC 6803 that the recently discovered PBS linker protein ApcG (sll1873) interacts specifically with PSII through its N-terminal region. Growth of cyanobacteria is impaired in apcG deletion strains under light-limiting conditions. Furthermore, complementation of these strains using a phospho-mimicking version of ApcG causes reduced growth under normal growth conditions. Interestingly, the interaction of ApcG with PSII is affected when a phospho-mimicking version of ApcG is used, targeting the positively charged residues interacting with the thylakoid membrane, suggesting a regulatory role mediated by phosphorylation of ApcG. Low-temperature fluorescence measurements showed decreased PSI fluorescence in apcG deletion and complementation strains. The PSI fluorescence was the lowest in the phospho-mimicking complementation strain, while the pull-down experiment showed no interaction of ApcG with PSI under any tested condition. Our results highlight the importance of ApcG for selectively directing energy harvested by the PBS and imply that the phosphorylation status of ApcG plays a role in regulating energy transfer from PSII to PSI.
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Affiliation(s)
- Roberto Espinoza-Corral
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Masakazu Iwai
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Tomáš Zavřel
- Department of Adaptive Biotechnologies, Global Change Research Institute of the Czech Academy of Sciences, Drásov 470, CZ-66424 Drásov, Czech Republic
| | - Sigal Lechno-Yossef
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jan Červený
- Department of Adaptive Biotechnologies, Global Change Research Institute of the Czech Academy of Sciences, Drásov 470, CZ-66424 Drásov, Czech Republic
| | - Krishna K Niyogi
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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4
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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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5
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Saleem F, Jiang JL, Atrache R, Paschos A, Edge TA, Schellhorn HE. Cyanobacterial Algal Bloom Monitoring: Molecular Methods and Technologies for Freshwater Ecosystems. Microorganisms 2023; 11:851. [PMID: 37110273 PMCID: PMC10144707 DOI: 10.3390/microorganisms11040851] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/15/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Cyanobacteria (blue-green algae) can accumulate to form harmful algal blooms (HABs) on the surface of freshwater ecosystems under eutrophic conditions. Extensive HAB events can threaten local wildlife, public health, and the utilization of recreational waters. For the detection/quantification of cyanobacteria and cyanotoxins, both the United States Environmental Protection Agency (USEPA) and Health Canada increasingly indicate that molecular methods can be useful. However, each molecular detection method has specific advantages and limitations for monitoring HABs in recreational water ecosystems. Rapidly developing modern technologies, including satellite imaging, biosensors, and machine learning/artificial intelligence, can be integrated with standard/conventional methods to overcome the limitations associated with traditional cyanobacterial detection methodology. We examine advances in cyanobacterial cell lysis methodology and conventional/modern molecular detection methods, including imaging techniques, polymerase chain reaction (PCR)/DNA sequencing, enzyme-linked immunosorbent assays (ELISA), mass spectrometry, remote sensing, and machine learning/AI-based prediction models. This review focuses specifically on methodologies likely to be employed for recreational water ecosystems, especially in the Great Lakes region of North America.
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Affiliation(s)
| | | | | | | | | | - Herb E. Schellhorn
- Department of Biology, McMaster University, Hamilton, ON L8S 4L8, Canada
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6
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Janisch N, Levendosky K, Budell WC, Quadri LEN. Genetic Underpinnings of Carotenogenesis and Light-Induced Transcriptome Remodeling in the Opportunistic Pathogen Mycobacterium kansasii. Pathogens 2023; 12:86. [PMID: 36678434 PMCID: PMC9861118 DOI: 10.3390/pathogens12010086] [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: 11/19/2022] [Revised: 12/24/2022] [Accepted: 12/28/2022] [Indexed: 01/06/2023] Open
Abstract
Mycobacterium kansasii (Mk) causes opportunistic pulmonary infections with tuberculosis-like features. The bacterium is well known for its photochromogenicity, i.e., the production of carotenoid pigments in response to light. The genetics defining the photochromogenic phenotype of Mk has not been investigated and defined pigmentation mutants to facilitate studies on the role of carotenes in the bacterium's biology are not available thus far. In this study, we set out to identify genetic determinants involved in Mk photochromogenicity. We screened a library of ~150,000 transposon mutants for colonies with pigmentation abnormalities. The screen rendered a collection of ~200 mutants. Each of these mutants could be assigned to one of four distinct phenotypic groups. The insertion sites in the mutant collection clustered in three chromosomal regions. A combination of phenotypic analysis, sequence bioinformatics, and gene expression studies linked these regions to carotene biosynthesis, carotene degradation, and monounsaturated fatty acid biosynthesis. Furthermore, introduction of the identified carotenoid biosynthetic gene cluster into non-pigmented Mycobacterium smegmatis endowed the bacterium with photochromogenicity. The studies also led to identification of MarR-type and TetR/AcrR-type regulators controlling photochromogenicity and carotenoid breakdown, respectively. Lastly, the work presented also provides a first insight into the Mk transcriptome changes in response to light.
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Affiliation(s)
- Niklas Janisch
- Department of Biology, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Biology Program, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Keith Levendosky
- Department of Biology, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Biology Program, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - William C. Budell
- Department of Biology, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Biology Program, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
| | - Luis E. N. Quadri
- Department of Biology, Brooklyn College, City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA
- Biology Program, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
- Biochemistry Program, Graduate Center, City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
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7
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Napoli A, Micheletti D, Pindo M, Larger S, Cestaro A, de Vera JP, Billi D. Absence of increased genomic variants in the cyanobacterium Chroococcidiopsis exposed to Mars-like conditions outside the space station. Sci Rep 2022; 12:8437. [PMID: 35589950 PMCID: PMC9120168 DOI: 10.1038/s41598-022-12631-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 05/06/2022] [Indexed: 11/08/2022] Open
Abstract
Despite the increasing interest in using microbial-based technologies to support human space exploration, many unknowns remain not only on bioprocesses but also on microbial survivability and genetic stability under non-Earth conditions. Here the desert cyanobacterium Chroococcidiopsis sp. CCMEE 029 was investigated for robustness of the repair capability of DNA lesions accumulated under Mars-like conditions (UV radiation and atmosphere) simulated in low Earth orbit using the EXPOSE-R2 facility installed outside the International Space Station. Genomic alterations were determined in a space-derivate of Chroococcidiopsis sp. CCMEE 029 obtained upon reactivation on Earth of the space-exposed cells. Comparative analysis of whole-genome sequences showed no increased variant numbers in the space-derivate compared to triplicates of the reference strain maintained on the ground. This result advanced cyanobacteria-based technologies to support human space exploration.
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Affiliation(s)
- Alessandro Napoli
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica snc, 00133, Rome, Italy
- PhD Program in Cellular and Molecular Biology, Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Diego Micheletti
- Edmund Mach Foundation, via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Massimo Pindo
- Edmund Mach Foundation, via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Simone Larger
- Edmund Mach Foundation, via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Alessandro Cestaro
- Edmund Mach Foundation, via E. Mach 1, 38010, San Michele all'Adige, Italy
| | - Jean-Pierre de Vera
- German Aerospace Center (DLR), Microgravity User Support Center, Linder Höhe, 51147, Cologne, Germany
| | - Daniela Billi
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica snc, 00133, Rome, Italy.
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8
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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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9
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Urrejola C, Alcorta J, Salas L, Vásquez M, Polz MF, Vicuña R, Díez B. Genomic Features for Desiccation Tolerance and Sugar Biosynthesis in the Extremophile Gloeocapsopsis sp. UTEX B3054. Front Microbiol 2019; 10:950. [PMID: 31134010 PMCID: PMC6513891 DOI: 10.3389/fmicb.2019.00950] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 04/15/2019] [Indexed: 01/06/2023] Open
Abstract
For tolerating extreme desiccation, cyanobacteria are known to produce both compatible solutes at intracellular level and a copious amount of exopolysaccharides as a protective coat. However, these molecules make cyanobacterial cells refractory to a broad spectrum of cell disruption methods, hindering genome sequencing, and molecular studies. In fact, few genomes are already available from cyanobacteria from extremely desiccated environments such as deserts. In this work, we report the 5.4 Mbp draft genome (with 100% of completeness in 105 contigs) of Gloeocapsopsis sp. UTEX B3054 (subsection I; Order Chroococcales), a cultivable sugar-rich and hardly breakable hypolithic cyanobacterium from the Atacama Desert. Our in silico analyses focused on genomic features related to sugar-biosynthesis and adaptation to dryness. Among other findings, screening of Gloeocapsopsis genome revealed a unique genetic potential related to the biosynthesis and regulation of compatible solutes and polysaccharides. For instance, our findings showed for the first time a novel genomic arrangement exclusive of Chroococcaceae cyanobacteria associated with the recycling of trehalose, a compatible solute involved in desiccation tolerance. Additionally, we performed a comparative genome survey and analyses to entirely predict the highly diverse pool of glycosyltransferases enzymes, key players in polysaccharide biosynthesis and the formation of a protective coat to dryness. We expect that this work will set the fundamental genomic framework for further research on microbial tolerance to desiccation and to a wide range of other extreme environmental conditions. The study of microorganisms like Gloeocapsopsis sp. UTEX B3054 will contribute to expand our limited understanding regarding water optimization and molecular mechanisms allowing extremophiles to thrive in xeric environments such as the Atacama Desert.
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Affiliation(s)
- Catalina Urrejola
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jaime Alcorta
- Laboratorio de Ecología Microbiana de Sistemas Extremos, Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Loreto Salas
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Mónica Vásquez
- Laboratorio de Ecología Microbiana y Toxicología Ambiental, Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Martin F Polz
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Rafael Vicuña
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Beatriz Díez
- Laboratorio de Ecología Microbiana de Sistemas Extremos, Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
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10
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Billi D, Verseux C, Fagliarone C, Napoli A, Baqué M, de Vera JP. A Desert Cyanobacterium under Simulated Mars-like Conditions in Low Earth Orbit: Implications for the Habitability of Mars. ASTROBIOLOGY 2019; 19:158-169. [PMID: 30742497 DOI: 10.1089/ast.2017.1807] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In the ESA space experiment BIOMEX (BIOlogy and Mars EXperiment), dried Chroococcidiopsis cells were exposed to Mars-like conditions during the EXPOSE-R2 mission on the International Space Station. The samples were exposed to UV radiation for 469 days and to a Mars-like atmosphere for 722 days, approaching the conditions that could be faced on the surface of Mars. Once back on Earth, cell survival was tested by growth-dependent assays, while confocal laser scanning microscopy and PCR-based assay were used to analyze the accumulated damage in photosynthetic pigments (chlorophyll a and phycobiliproteins) and genomic DNA, respectively. Survival occurred only for dried cells (4-5 cell layers thick) mixed with the martian soil simulants P-MRS (phyllosilicatic martian regolith simulant) and S-MRS (sulfatic martian regolith simulant), and viability was only maintained for a few hours after space exposure to a total UV (wavelength from 200 to 400 nm) radiation dose of 492 MJ/m2 (attenuated by 0.1% neutral density filters) and 0.5 Gy of ionizing radiation. These results have implications for the hypothesis that, during Mars's climatic history, desiccation- and radiation-tolerant life-forms could have survived in habitable niches and protected niches while transported.
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Affiliation(s)
- Daniela Billi
- 1 University of Rome Tor Vergata, Department of Biology, Rome, Italy
| | - Cyprien Verseux
- 1 University of Rome Tor Vergata, Department of Biology, Rome, Italy
| | | | - Alessandro Napoli
- 1 University of Rome Tor Vergata, Department of Biology, Rome, Italy
| | - Mickael Baqué
- 2 German Aerospace Center, Institute of Planetary Research, Management and Infrastructure, Astrobiological Laboratories, Berlin, Germany
| | - Jean-Pierre de Vera
- 2 German Aerospace Center, Institute of Planetary Research, Management and Infrastructure, Astrobiological Laboratories, Berlin, Germany
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Avoidance of protein oxidation correlates with the desiccation and radiation resistance of hot and cold desert strains of the cyanobacterium Chroococcidiopsis. Extremophiles 2017; 21:981-991. [DOI: 10.1007/s00792-017-0957-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 08/21/2017] [Indexed: 12/29/2022]
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12
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Verseux C, Baqué M, Cifariello R, Fagliarone C, Raguse M, Moeller R, Billi D. Evaluation of the Resistance of Chroococcidiopsis spp. to Sparsely and Densely Ionizing Irradiation. ASTROBIOLOGY 2017; 17:118-125. [PMID: 28151689 DOI: 10.1089/ast.2015.1450] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Studying the resistance of cyanobacteria to ionizing radiation provides relevant information regarding astrobiology-related topics including the search for life on Mars, lithopanspermia, and biological life-support systems. Here, we report on the resistance of desert cyanobacteria of the genus Chroococcidiopsis, which were exposed (as part of the STARLIFE series of experiments) in both hydrated and dried states to ionizing radiation with different linear energy transfer values (0.2 to 200 keV/μm). Irradiation with up to 1 kGy of He or Si ions, 2 kGy of Fe ions, 5 kGy of X-rays, or 11.59 kGy of γ rays (60Co) did not eradicate Chroococcidiopsis populations, nor did it induce detectable damage to DNA or plasma membranes. The relevance of these results for astrobiology is briefly discussed. Key Words: Ionizing radiation-Linear energy transfer-Lithopanspermia-Cyanobacterial radioresistance-Chroococcidiopsis-Mars. Astrobiology 17, 118-125.
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Affiliation(s)
- Cyprien Verseux
- 1 Department of Biology, Laboratory of Astrobiology and Molecular Biology of Cyanobacteria from Extreme Environments, University of Rome Tor Vergata , Rome, Italy
| | - Mickael Baqué
- 1 Department of Biology, Laboratory of Astrobiology and Molecular Biology of Cyanobacteria from Extreme Environments, University of Rome Tor Vergata , Rome, Italy
- 2 Astrobiological Laboratories Research Group, Institute of Planetary Research , Management and Infrastructure, German Aerospace Center (DLR), Berlin, Germany
| | - Riccardo Cifariello
- 1 Department of Biology, Laboratory of Astrobiology and Molecular Biology of Cyanobacteria from Extreme Environments, University of Rome Tor Vergata , Rome, Italy
| | - Claudia Fagliarone
- 1 Department of Biology, Laboratory of Astrobiology and Molecular Biology of Cyanobacteria from Extreme Environments, University of Rome Tor Vergata , Rome, Italy
| | - Marina Raguse
- 3 Space Microbiology Research Group, Radiation Biology Department, Institute of Aerospace Medicine , German Aerospace Center (DLR), Cologne, Germany
| | - Ralf Moeller
- 3 Space Microbiology Research Group, Radiation Biology Department, Institute of Aerospace Medicine , German Aerospace Center (DLR), Cologne, Germany
| | - Daniela Billi
- 1 Department of Biology, Laboratory of Astrobiology and Molecular Biology of Cyanobacteria from Extreme Environments, University of Rome Tor Vergata , Rome, Italy
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Mareš J, Lara Y, Dadáková I, Hauer T, Uher B, Wilmotte A, Kaštovský J. Phylogenetic analysis of cultivation-resistant terrestrial cyanobacteria with massive sheaths (Stigonema spp. and Petalonema alatum, Nostocales, Cyanobacteria) using single-cell and filament sequencing of environmental samples. JOURNAL OF PHYCOLOGY 2015; 51:288-297. [PMID: 26986524 DOI: 10.1111/jpy.12273] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 11/22/2014] [Indexed: 06/05/2023]
Abstract
Molecular assessment of a large portion of traditional cyanobacterial taxa has been hindered by the failure to isolate and grow them in culture. In this study, we developed an optimized protocol for single cell/filament isolation and 16S rRNA gene sequencing of terrestrial cyanobacteria with large mucilaginous sheaths, and applied it to determine the phylogenetic position of typical members of the genera Petalonema and Stigonema. A methodology based on a glass-capillary isolation technique and a semi-nested PCR protocol enabled reliable sequencing of the 16S rRNA gene from all samples analyzed. Ten samples covering seven species of Stigonema from Europe, North and Central America, and Hawaii, and the type species of Petalonema from Slovakia were sequenced. Contrary to some previous studies, which proposed a relationship with heteropolar nostocalean cyanobacteria, Petalonema appeared to belong to the family Scytonemataceae. Analysis of Stigonema specimens recovered a unique coherent phylogenetic cluster, substantially broadening our knowledge of the molecular diversity within this genus. Neither the uni- to biseriate species nor the multiseriate species formed monophyletic subclusters within the genus. Typical multiseriate species of Stigonema clustered in a phylogenetic branch derived from uni- to biseriate S. ocellatum Thuret ex Bornet & Flahault in our analysis, suggesting that species with more complex thalli may have evolved from the more simple ones. We propose the technique tested in this study as a promising tool for a future revision of the molecular taxonomy in cyanobacteria.
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Affiliation(s)
- Jan Mareš
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-37005, Czech Republic
- Centre for Phycology, Institute of Botany ASCR, v.v.i., Dukelská 135, Třeboň, CZ-379 82, Czech Republic
| | - Yannick Lara
- Center for Protein Engineering, University of Liège, Liège, 4000, Belgium
| | - Iva Dadáková
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno, CZ-61137, Czech Republic
| | - Tomáš Hauer
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-37005, Czech Republic
- Centre for Phycology, Institute of Botany ASCR, v.v.i., Dukelská 135, Třeboň, CZ-379 82, Czech Republic
| | - Bohuslav Uher
- Department of Limnology and Bio-Oceanography, Faculty of Life Sciences, University of Vienna, Althanstrasse 14, Vienna, A-1090, Austria
| | - Annick Wilmotte
- Center for Protein Engineering, University of Liège, Liège, 4000, Belgium
| | - Jan Kaštovský
- Department of Botany, Faculty of Science, University of South Bohemia, Branišovská 1760, České Budějovice, CZ-37005, Czech Republic
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Cumbers J, Rothschild LJ. Salt tolerance and polyphyly in the cyanobacterium Chroococcidiopsis (Pleurocapsales). JOURNAL OF PHYCOLOGY 2014; 50:472-82. [PMID: 26988320 DOI: 10.1111/jpy.12169] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 12/16/2013] [Indexed: 05/19/2023]
Abstract
Chroococcidiopsis Geitler (Geitler 1933) is a genus of cyanobacteria containing desiccation and radiation resistant strains. Members of the genus live in habitats ranging from hot and cold deserts to fresh and saltwater environments. Morphology and cell division pattern have historically been used to define the genus. To better understand the evolution and ability of the Chroococcidiopsis genus to survive in diverse environments we investigated how salt tolerance varies among 15 strains previously isolated from different locations, and if salt tolerant strains are monophyletic to those isolated from freshwater and land environments. Four markers were sequenced from these 15 strains, the 16S rRNA, rbcL, desC1, and gltX genes. Phylogenetic trees were generated which identified a distinct clade of salt-tolerant strains. This study demonstrates that the genus is polyphyletic based on saltwater and freshwater phenotypes. To understand the resistance to salt in more details, the strains were grown on a range of sea salt concentrations which demonstrated that the freshwater strains were salt-intolerant whilst the saltwater strains required salt for growth. This study shows an increased resolution of the phylogeny of Chroococcidiopsis and provides further evidence that the genus is polyphyletic and should be reclassified to improve clarity in the literature.
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Affiliation(s)
- John Cumbers
- NASA Ames Space Portal/SynBioBeta, NASA Ames Research Center, Mail Stop 555-2, P.O. Box 1, Moffett Field, California, 94035, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Box G-W, Providence, Rhode Island, 02912, USA
| | - Lynn J Rothschild
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Box G-W, Providence, Rhode Island, 02912, USA
- Biospheric Science Branch, NASA Ames Research Center, Mail Stop 239-20, P.O. Box 1, Moffett Field, California, 94035, USA
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15
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Li M, Semchonok DA, Boekema EJ, Bruce BD. Characterization and evolution of tetrameric photosystem I from the thermophilic cyanobacterium Chroococcidiopsis sp TS-821. THE PLANT CELL 2014; 26:1230-45. [PMID: 24681621 PMCID: PMC4001380 DOI: 10.1105/tpc.113.120782] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 03/09/2014] [Accepted: 03/13/2014] [Indexed: 05/20/2023]
Abstract
Photosystem I (PSI) is a reaction center associated with oxygenic photosynthesis. Unlike the monomeric reaction centers in green and purple bacteria, PSI forms trimeric complexes in most cyanobacteria with a 3-fold rotational symmetry that is primarily stabilized via adjacent PsaL subunits; however, in plants/algae, PSI is monomeric. In this study, we discovered a tetrameric form of PSI in the thermophilic cyanobacterium Chroococcidiopsis sp TS-821 (TS-821). In TS-821, PSI forms tetrameric and dimeric species. We investigated these species by Blue Native PAGE, Suc density gradient centrifugation, 77K fluorescence, circular dichroism, and single-particle analysis. Transmission electron microscopy analysis of native membranes confirms the presence of the tetrameric PSI structure prior to detergent solubilization. To investigate why TS-821 forms tetramers instead of trimers, we cloned and analyzed its psaL gene. Interestingly, this gene product contains a short insert between the second and third predicted transmembrane helices. Phylogenetic analysis based on PsaL protein sequences shows that TS-821 is closely related to heterocyst-forming cyanobacteria, some of which also have a tetrameric form of PSI. These results are discussed in light of chloroplast evolution, and we propose that PSI evolved stepwise from a trimeric form to tetrameric oligomer en route to becoming monomeric in plants/algae.
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Affiliation(s)
- Meng Li
- Department of Biochemistry, Cellular, and Molecular
Biology, University of Tennessee, Knoxville, Tennessee 37996
- The Bredesen Center for Interdisciplinary Research and
Graduate Education, University of Tennessee, Knoxville, Tennessee 37996
| | - Dmitry A. Semchonok
- Department of Electron Microscopy, Groningen Biomolecular
Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The
Netherlands
| | - Egbert J. Boekema
- Department of Electron Microscopy, Groningen Biomolecular
Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The
Netherlands
| | - Barry D. Bruce
- Department of Biochemistry, Cellular, and Molecular
Biology, University of Tennessee, Knoxville, Tennessee 37996
- The Bredesen Center for Interdisciplinary Research and
Graduate Education, University of Tennessee, Knoxville, Tennessee 37996
- Department of Microbiology, University of Tennessee,
Knoxville, Tennessee 37996
- Sustainable Energy and Education Research Center,
University of Tennessee, Knoxville, Tennessee 37996
- Address correspondence to
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16
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Gloeocapsopsis AAB1, an extremely desiccation-tolerant cyanobacterium isolated from the Atacama Desert. Extremophiles 2013; 18:61-74. [DOI: 10.1007/s00792-013-0592-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 10/07/2013] [Indexed: 10/26/2022]
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17
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Baqué M, Scalzi G, Rabbow E, Rettberg P, Billi D. Biofilm and planktonic lifestyles differently support the resistance of the desert cyanobacterium Chroococcidiopsis under space and Martian simulations. ORIGINS LIFE EVOL B 2013; 43:377-89. [PMID: 23955666 DOI: 10.1007/s11084-013-9341-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Accepted: 07/12/2013] [Indexed: 01/10/2023]
Abstract
When Chroococcidiopsis sp. strain CCMEE 057 from the Sinai Desert and strain CCMEE 029 from the Negev Desert were exposed to space and Martian simulations in the dried status as biofilms or multilayered planktonic samples, the biofilms exhibited an enhanced rate of survival. Compared to strain CCMEE 029, biofilms of strain CCME 057 better tolerated UV polychromatic radiation (5 × 10(5) kJ/m(2) attenuated with a 0.1% neutral density filter) combined with space vacuum or Martian atmosphere of 780 Pa. CCMEE 029, on the other hand, failed to survive UV polychromatic doses higher than 1.5 × 10(3) kJ/m(2). The induced damage to genomic DNA, plasma membranes and photosynthetic apparatus was quantified and visualized by means of PCR-based assays and CLSM imaging. Planktonic samples of both strains accumulated a higher amount of damage than did the biofilms after exposure to each simulation; CLSM imaging showed that photosynthetic pigment bleaching, DNA fragmentation and damaged plasma membranes occurred in the top 3-4 cell layers of both biofilms and of multilayered planktonic samples. Differences in the EPS composition were revealed by molecular probe staining as contributing to the enhanced endurance of biofilms compared to that of planktonic samples. Our results suggest that compared to strain CCMEE 029, biofilms of strain CCMEE 057 might better tolerate 1 year's exposure in space during the next EXPOSE-R2 mission.
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Affiliation(s)
- Mickael Baqué
- Dipartimento di Biologia, Università di Roma "Tor Vergata", Rome, Italy
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18
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Baqué M, Viaggiu E, Scalzi G, Billi D. Endurance of the endolithic desert cyanobacterium Chroococcidiopsis under UVC radiation. Extremophiles 2012; 17:161-9. [DOI: 10.1007/s00792-012-0505-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 11/29/2012] [Indexed: 11/28/2022]
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Stivaletta N, Barbieri R, Billi D. Microbial colonization of the salt deposits in the driest place of the Atacama Desert (Chile). ORIGINS LIFE EVOL B 2012; 42:187-200. [PMID: 22661023 DOI: 10.1007/s11084-012-9289-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Accepted: 02/13/2012] [Indexed: 11/27/2022]
Abstract
The Atacama Desert (Chile), one of the most arid places on Earth, shows hostile conditions for the development of epilithic microbial communities. In this study, we report the association of cyanobacteria (Chroococcidiopsis sp.) and bacteria belonging to Actinobacteria and Beta-Gammaproteobacteria and Firmicutes phyla inhabiting the near surface of salt (halite) deposits of the Salar Grande Basin, Atacama Desert (Chile). The halite deposits were investigated by using optical, confocal and field emission scanning electron microscopes, whereas culture-independent molecular techniques, 16S rDNA clone library, alongside RFLP analysis and 16S rRNA gene sequencing were applied to investigate the bacterial diversity. These microbial communities are an example of life that has adapted to extreme environmental conditions caused by dryness, high irradiation, and metal concentrations. Their adaptation is, therefore, important in the investigation of the environmental conditions that might be expected for life outside of Earth.
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Affiliation(s)
- Nunzia Stivaletta
- Dipartimento di Scienze della Terra e Geologico-Ambientali, Università di Bologna, Via Zamboni 67, 40126, Bologna, Italy.
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Billi D. Plasmid stability in dried cells of the desert cyanobacterium Chroococcidiopsis and its potential for GFP imaging of survivors on Earth and in space. ORIGINS LIFE EVOL B 2012; 42:235-45. [PMID: 22638838 DOI: 10.1007/s11084-012-9277-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 02/09/2012] [Indexed: 10/27/2022]
Abstract
Two GFP-based plasmids, namely pTTQ18-GFP-pDU1(mini) and pDUCA7-GFP, of about 7 kbp and 15 kbp respectively, able to replicate in Chroococcidiopsis sp. CCMEE 029 and CCMEE 123, were developed. Both plasmids were maintained in Chroococcidiopsis cells after 18 months of dry storage as demonstrated by colony PCR, plasmid restriction analysis, GFP imaging and colony-forming ability under selection of dried transformants; thus suggesting that strategies employed by this cyanobacterium to stabilize dried chromosomal DNA, must have protected plasmid DNA. The suitability of pDU1(mini)-plasmid for GFP tagging in Chroococcidiopsis was investigated by using the RecA homolog of Synechocystis sp. PCC 6803. After 2 months of dry storage, the presence of dried cells with a GFP-RecA(Syn) distribution resembling that of hydrated cells, supported its capability of preventing desiccation-induced genome damage, whereas the rewetted cells with filamentous GFP-RecA(Syn) structures revealed sub-lethal DNA damage. The long-term stability of plasmid DNA in dried Chroococcidiopsis has implication for space research, for example when investigating the recovery of dried cells after Martian and space simulations or when developing life support systems based on phototrophs with genetically enhanced stress tolerance and stored in the dry state for prolonged periods.
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Affiliation(s)
- Daniela Billi
- Dipartimento di Biologia, Università di Roma Tor Vergata, Via della Ricerca Scientifica s.n.c, 00133, Rome, Italy.
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Highly sensitive direct detection and quantification of Burkholderia pseudomallei bacteria in environmental soil samples by using real-time PCR. Appl Environ Microbiol 2011; 77:6486-94. [PMID: 21803915 DOI: 10.1128/aem.00735-11] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The soil bacterium and potential biothreat agent Burkholderia pseudomallei causes the infectious disease melioidosis, which is naturally acquired through environmental contact with the bacterium. Environmental detection of B. pseudomallei represents the basis for the development of a geographical risk map for humans and livestock. The aim of the present study was to develop a highly sensitive, culture-independent, DNA-based method that allows direct quantification of B. pseudomallei from soil. We established a protocol for B. pseudomallei soil DNA isolation, purification, and quantification by quantitative PCR (qPCR) targeting a type three secretion system 1 single-copy gene. This assay was validated using 40 soil samples from Northeast Thailand that underwent parallel bacteriological culture. All 26 samples that were B. pseudomallei positive by direct culture were B. pseudomallei qPCR positive, with a median of 1.84 × 10(4) genome equivalents (range, 3.65 × 10(2) to 7.85 × 10(5)) per gram of soil, assuming complete recovery of DNA. This was 10.6-fold (geometric mean; range, 1.1- to 151.3-fold) higher than the bacterial count defined by direct culture. Moreover, the qPCR detected B. pseudomallei in seven samples (median, 36.9 genome equivalents per g of soil; range, 9.4 to 47.3) which were negative by direct culture. These seven positive results were reproduced using a nested PCR targeting a second, independent B. pseudomallei-specific sequence. Two samples were direct culture and qPCR negative but nested PCR positive. Five samples were negative by both PCR methods and culture. In conclusion, our PCR-based system provides a highly specific and sensitive tool for the quantitative environmental surveillance of B. pseudomallei.
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Billi D, Viaggiu E, Cockell CS, Rabbow E, Horneck G, Onofri S. Damage escape and repair in dried Chroococcidiopsis spp. from hot and cold deserts exposed to simulated space and martian conditions. ASTROBIOLOGY 2011; 11:65-73. [PMID: 21294638 DOI: 10.1089/ast.2009.0430] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The cyanobacterium Chroococcidiopsis, overlain by 3 mm of Antarctic sandstone, was exposed as dried multilayers to simulated space and martian conditions. Ground-based experiments were conducted in the context of Lichens and Fungi Experiments (EXPOSE-E mission, European Space Agency), which were performed to evaluate, after 1.5 years on the International Space Station, the survival of cyanobacteria (Chroococcidiopsis), lichens, and fungi colonized on Antarctic rock. The survival potential and the role played by protection and repair mechanisms in the response of dried Chroococcidiopsis cells to ground-based experiments were both investigated. Different methods were employed, including evaluation of the colony-forming ability, single-cell analysis of subcellular integrities based on membrane integrity molecular and redox probes, evaluation of the photosynthetic pigment autofluorescence, and assessment of the genomic DNA integrity with a PCR-based assay. Desiccation survivors of strain CCMEE 123 (coastal desert, Chile) were better suited than CCMEE 134 (Beacon Valley, Antarctica) to withstand cellular damage imposed by simulated space and martian conditions. Exposed dried cells of strain CCMEE 123 formed colonies, maintained subcellular integrities, and, depending on the exposure conditions, also escaped DNA damage or repaired the induced damage upon rewetting.
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Affiliation(s)
- Daniela Billi
- Dipartimento di Biologia, Università di Roma "Tor Vergata ," Roma, Italy.
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23
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Morin N, Vallaeys T, Hendrickx L, Natalie L, Wilmotte A. An efficient DNA isolation protocol for filamentous cyanobacteria of the genus Arthrospira. J Microbiol Methods 2009; 80:148-54. [PMID: 20004220 DOI: 10.1016/j.mimet.2009.11.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2009] [Revised: 11/24/2009] [Accepted: 11/29/2009] [Indexed: 11/26/2022]
Abstract
Thanks to their photosynthetic and nutritive properties, cyanobacteria of the Arthrospira genus are of interest as food supplements, as efficient oxygen producing life support system organisms for manned space flight, and for the production of biofuels. Despite these potential valuable applications, full genome sequences and genetic information in general on Arthrospira remain scarce. This is mainly due to the difficulty to extract sufficient high molecular weight nucleic acids from these filamentous cyanobacteria. In this article, an efficient and reproducible DNA extraction procedure for cyanobacteria of the genus Arthrospira was developed. The method is based on the combination of a soft mechanical lysis with enzymatic disruption of the cell wall. The comparison with other extraction protocols clearly indicates that this optimised method allows the recovery of a larger amount of DNA. Furthermore, the extracted DNA presents a high molecular weight, a reduced degradation and an excellent overall quality. It can be directly used for molecular biology purposes such as PCR, and clone library construction.
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Affiliation(s)
- Nicolas Morin
- Expert group for Molecular and Cellular Biology, Belgian Nuclear Research Center SCK*CEN, 2400 Mol, Belgium.
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Loss of topological relationships in a Pleurocapsalean cyanobacterium (Chroococcidiopsis sp.) with partially inactivatedftsZ. ANN MICROBIOL 2009. [DOI: 10.1007/bf03178322] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Kido H, Micic M, Smith D, Zoval J, Norton J, Madou M. A novel, compact disk-like centrifugal microfluidics system for cell lysis and sample homogenization. Colloids Surf B Biointerfaces 2007; 58:44-51. [PMID: 17499489 DOI: 10.1016/j.colsurfb.2007.03.015] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2007] [Accepted: 03/19/2007] [Indexed: 11/29/2022]
Abstract
In this paper, we present the design and characterization of a novel platform for mechanical cell lysis of even the most difficult to lyse cell types on a micro or nanoscale (maximum 70 microL total volume). The system incorporates a machined plastic circular disk assembly, magnetic field actuated microfluidics, centrifugal cells and tissue homogenizer and centrifugation system. The mechanism of tissue disruption of this novel cell homogenization apparatus derives from the relative motion of ferromagnetic metal disks and grinding matrices in a liquid medium within individual chambers of the disk in the presence of an oscillating magnetic field. The oscillation of the ferromagnetic disks or blades produces mechanical impaction and shear forces capable of disrupting cells within the chamber both by direct action of the blade and by the motion of the surrounding lysis matrix, and by motion induced vortexing of buffer fluid. Glass beads or other grinding media are integrated into each lysis chamber within the disk to enhance the transfer of energy from the oscillating metal blade to the cells. The system also achieves the centrifugal elimination of solids from each liquid sample and allows the elution of clarified supernatants via siphoning into a collection chamber fabricated into the plastic disk assembly. This article describes system design, implementation and validation of proof of concept on two samples--Escherichia coli and Saccharomyces cerevisiae representing model systems for cells that are easy and difficult to lyse, respectively.
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Affiliation(s)
- Horacio Kido
- Department of Mechanical and Aerospace Engineering, University of California, Irvine, Irvine, CA 92697-3975, USA.
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26
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Lee YC, Chien HCR, Hsu WH. Production of N-acetyl-D-neuraminic acid by recombinant whole cells expressing Anabaena sp. CH1 N-acetyl-D-glucosamine 2-epimerase and Escherichia coli N-acetyl-D-neuraminic acid lyase. J Biotechnol 2007; 129:453-60. [PMID: 17349707 DOI: 10.1016/j.jbiotec.2007.01.027] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2006] [Revised: 01/17/2007] [Accepted: 01/29/2007] [Indexed: 10/23/2022]
Abstract
N-acetyl-d-neuraminic acid (NeuAc; sialic acid) is a precursor for the manufacture of many pharmaceutical drugs, such as anti-influenza virus agents. To develop a whole cell process for NeuAc production, genes of Anabaena sp. CH1 N-acetyl-d-glucosamine 2-epimerase (bage) and Escherichia coli N-acetyl-d-neuraminic acid lyase (nanA) were cloned and expressed in E. coli BL21 (DE3). The expressed bGlcNAc 2-epimerase was purified from the crude cell extract of IPTG-induced E. coli BL21 (DE3) (pET-bage) to homogeneity by nickel-chelate chromatography. The molecular mass of the purified bGlcNAc 2-epimerase was determined to be 42kDa by SDS-PAGE. The pH and temperature optima of the recombinant bGlcNAc 2-epimerase were pH 7.0 and 50 degrees C, respectively, and only needs 20mum ATP for maximal activity. The specific activity of bGlcNAc 2-epimerase (124Umg(-1) protein) for the conversion of N-acetyl-d-glucosamine to N-acetyl-d-manosamine was about four-fold higher than that of porcine N-acetyl-d-glucosamine 2-epimerase. A stirred glass vessel containing transformed E. coli cells expressing age gene from Anabaena sp. CH1 and NeuAc lyase gene from E. coli NovaBlue separately was used for the conversion of GlcNAc and pyruvate to NeuAc. A maximal productivity of 10.2gNeuAcl(-1)h(-1) with 33.3% conversion yield from GlcNAc could be obtained in a 12-h reaction. The recombinant E. coli cells can be reused for more than eight cycles with a productivity of >8.0gNeuAcL(-1)h(-1). In this process, the expensive activator, ATP, necessary for maximal activity of GlcNAc 2-epimerase in free enzyme system can be omitted.
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Affiliation(s)
- Yen-Chung Lee
- Institute of Molecular Biology, National Chung Hsing University, Taichung 402, Taiwan
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Chroococcidiopsis from Desert to Mars. CELLULAR ORIGIN, LIFE IN EXTREME HABITATS AND ASTROBIOLOGY 2007. [DOI: 10.1007/978-1-4020-6112-7_30] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Boison G, Mergel A, Jolkver H, Bothe H. Bacterial life and dinitrogen fixation at a gypsum rock. Appl Environ Microbiol 2005; 70:7070-7. [PMID: 15574902 PMCID: PMC535155 DOI: 10.1128/aem.70.12.7070-7077.2004] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The organisms of a bluish-green layer beneath the shards of a gypsum rock were characterized by molecular techniques. The cyanobacterial consortium consisted almost exclusively of Chroococcidiopsis spp. The organisms of the shards expressed nitrogenase activity (C2H2 reduction) aerobically and in light. After a prolonged period of drought at the rock, the cells were inactive, but they resumed nitrogenase activity 2 to 3 days after the addition of water. In a suspension culture of Chroococcidiopsis sp. strain PCC7203, C2H2 reduction required microaerobic conditions and was strictly dependent on low light intensities. Sequencing of a segment of the nitrogenase reductase gene (nifH) indicated that Chroococcidiopsis possesses the alternative molybdenum nitrogenase 2, expressed in Anabaena variabilis only under reduced O2 tensions, rather than the widespread, common molybdenum nitrogenase. The shards apparently provide microsites with reduced light intensities and reduced O2 tension that allow N2 fixation to proceed in the unicellular Chroococcidiopsis at the gypsum rock, unless the activity is due to minute amounts of other, very active cyanobacteria. Phylogenetic analysis of nifH sequences tends to suggest that molybdenum nitrogenase 2 is characteristic of those unicellular or filamentous, nonheterocystous cyanobacteria fixing N2 under microaerobic conditions only.
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Affiliation(s)
- Gudrun Boison
- Botanical Institute, The University of Cologne, Gyrhofstr. 15, D-50923 Cologne, Germany
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Crispim CA, Gaylarde CC. Cyanobacteria and biodeterioration of cultural heritage: a review. MICROBIAL ECOLOGY 2005; 49:1-9. [PMID: 15883863 DOI: 10.1007/s00248-003-1052-5] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2003] [Accepted: 10/09/2003] [Indexed: 05/02/2023]
Abstract
Growing concern for the preservation of cultural heritage has led to a greater interest in the biological attack on these buildings. The importance of cyanobacteria as deteriogens is emphasized and the traditional and more modern molecular methods used to detect these microorganisms are discussed. The development of molecular techniques for the rapid identification of cyanobacteria without need for culture and isolation is fundamental if our knowledge of these communities in biofilms on the surfaces of historic buildings is to be extended.
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Affiliation(s)
- C A Crispim
- Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.
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Gaylarde C, Gaylarde P, Copp J, Neilan B. Polyphasic detection of cyanobacteria in terrestrial biofilms. BIOFOULING 2004; 20:71-79. [PMID: 15203960 DOI: 10.1080/08927010410001681237] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cyanobacterial populations detected on buildings by traditional methods are mainly filamentous, whereas direct microscopy shows that they are principally coccoid morphotypes that often cannot be isolated in culture, but may grow on artificial media when the spatial biofilm relationships are maintained. The polyphasic strategy described here was to select morphologically distinct colonies from rehydrated biofilms for direct DNA amplification, allowing uncultured organisms to be sequenced and their morphology to be characterized by microscopy. DNA data banks currently contain many entries for cyanobacteria of unrecorded morphology, which does not facilitate identification, although genetic variability in a population may be assessed. The sequence homologies of the present biofilm organisms (EMBL accession numbers AJ619681 to 619690) with those in DNA databanks were low, indicating differences between xerophytic cyanobacteria on walls and aquatic species comprising the majority in the databases. Further development of databases for the populations found in this environment, subject to temperature extremes, repeated desiccation and high UV and salt levels, is required.
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Affiliation(s)
- Christine Gaylarde
- Department of Biophysics Federal University of Rio Grande do Sul (UFRGS) Avenue Bento Gonçalves 9500 Porto Alegre--RS 91501-970 Brazil.
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Dillon JG, Castenholz RW. The synthesis of the UV-screening pigment, scytonemin, and photosynthetic performance in isolates from closely related natural populations of cyanobacteria (Calothrix sp.). Environ Microbiol 2003; 5:484-91. [PMID: 12755715 DOI: 10.1046/j.1462-2920.2003.00436.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Two populations of the cyanobacterium Calothrix sp. found in Yellowstone thermal spring outflows differ greatly in their contents of scytonemin, a UV-screening pigment, and in their photosynthetic carbon assimilation rates. Clonal isolates from both populations were used to investigate these phenotypic differences. Identical partial 16S rDNA sequences ( approximately 900 bp) suggest a very close relationship between the two Calothrix populations and indicate that environmental differences may, in part, explain the field observations. The effects of native spring water on scytonemin synthesis and photosynthesis were tested during experiments using plated cells. Results show differences in the spring water environment were at least partly responsible for the differences in scytonemin content observed in the field. Furthermore, spring water effects on photosynthetic performance suggest adaptation in these strains to their spring of origin. Controlled experiments performed using cultures grown in artificial liquid medium showed no significant difference in photosynthetic carbon uptake between strains. However, significant differences were detected in their ability to synthesize scytonemin indicating genetic differences between populations. These findings suggest that both genetic and environmental differences are responsible for the naturally occurring variation in scytonemin content and photosynthetic ability in these two closely related populations.
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Affiliation(s)
- Jesse G Dillon
- University of Washington, Department of Civil and Environmental Engineering, 201 More Hall, Seattle, WA 98195, USA
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Holtzendorff J, Marie D, Post AF, Partensky F, Rivlin A, Hess WR. Synchronized expression of ftsZ in natural Prochlorococcus populations of the Red Sea. Environ Microbiol 2002; 4:644-53. [PMID: 12460272 DOI: 10.1046/j.1462-2920.2002.00347.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The expression of ftsZ, encoding the initiating protein of the prokaryotic cell division was analysed in natural Prochlorococcus populations in the Gulf of Aqaba, northern Red Sea. During the seasonal Prochlorococcus bloom in September 2000, picoplankton was collected from the deep chlorophyll maximum (DCM) at 2-4 h intervals over 3 consecutive days. Flow cytometric measurements as well as DNA sequence analyses showed that Prochlorococcus was the dominant photosynthetic organism. Cell densities peaked as high as 1.4 x 10(5) cells ml(-1). This DCM population mainly consisted of brightly red fluorescing Prochlorococcus cells, corresponding to low light-adapted 'ecotypes' (sensu Moore et al., 1998, Nature 393: 464-467). Prochlorococcus populations grew in a highly synchronized fashion with DNA replication in the afternoon and cell division during the night. The ftsZ mRNA level reached maximum values within the replication phase between 14.00 and 16.00 hours, and minimum values between 02.00 and 06.00 hours. Thus, the transcriptional regulation of ftsZ could be a major factor triggering the synchronized cell division of Prochlorococcus populations. This is the first application of quantitative reverse transcriptase-coupled real-time polymerase chain reaction (PCR) to natural populations of an environmentally relevant marine organism.
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Affiliation(s)
- Julia Holtzendorff
- Humboldt-University, Institute of Biology/Genetics, Chausseestr. 117, D-10115 Berlin, Germany
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Billi D, Friedmann EI, Helm RF, Potts M. Gene transfer to the desiccation-tolerant cyanobacterium Chroococcidiopsis. J Bacteriol 2001; 183:2298-305. [PMID: 11244070 PMCID: PMC95137 DOI: 10.1128/jb.183.7.2298-2305.2001] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The coccoid cyanobacterium Chroococcidiopsis dominates microbial communities in the most extreme arid hot and cold deserts. These communities withstand constraints that result from multiple cycles of drying and wetting and/or prolonged desiccation, through mechanisms which remain poorly understood. Here we describe the first system for genetic manipulation of Chroococcidiopsis. Plasmids pDUCA7 and pRL489, based on the pDU1 replicon of Nostoc sp. strain PCC 7524, were transferred to different isolates of Chroococcidiopsis via conjugation and electroporation. This report provides the first evidence that pDU1 replicons can be maintained in cyanobacteria other than Nostoc and Anabaena. Following conjugation, both plasmids replicated in Chroococcidiopsis sp. strains 029, 057, and 123 but not in strains 171 and 584. Both plasmids were electroporated into strains 029 and 123 but not into strains 057, 171, and 584. Expression of P(psbA)-luxAB on pRL489 was visualized through in vivo luminescence. Efficiencies of conjugative transfer for pDUCA7 and pRL489 into Chroococcidiopsis sp. strain 029 were approximately 10(-2) and 10(-4) transconjugants per recipient cell, respectively. Conjugative transfer occurred with a lower efficiency into strains 057 and 123. Electrotransformation efficiencies of about 10(-4) electrotransformants per recipient cell were achieved with strains 029 and 123, using either pDUCA7 or pRL489. Extracellular deoxyribonucleases were associated with each of the five strains. Phylogenetic analysis, based upon the V6 to V8 variable regions of 16S rRNA, suggests that desert strains 057, 123, 171, and 029 are distinct from the type species strain Chroococcidiopsis thermalis PCC 7203. The high efficiency of conjugative transfer of Chroococcidiopsis sp. strain 029, from the Negev Desert, Israel, makes this a suitable experimental strain for genetic studies on desiccation tolerance.
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Affiliation(s)
- D Billi
- Virginia Tech Center for Genomics (VIGEN), Fralin Biotechnology Center, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0001
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Holtzendorff J, Partensky F, Jacquet S, Bruyant F, Marie D, Garczarek L, Mary I, Vaulot D, Hess WR. Diel expression of cell cycle-related genes in synchronized cultures of Prochlorococcus sp. strain PCC 9511. J Bacteriol 2001; 183:915-20. [PMID: 11208789 PMCID: PMC94958 DOI: 10.1128/jb.183.3.915-920.2001] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2000] [Accepted: 11/07/2000] [Indexed: 11/20/2022] Open
Abstract
The cell cycle of the chlorophyll b-possessing marine cyanobacterium Prochlorococcus is highly synchronized under natural conditions. To understand the underlying molecular mechanisms we cloned and sequenced dnaA and ftsZ, two key cell cycle-associated genes, and studied their expression. An axenic culture of Prochlorococcus sp. strain PCC 9511 was grown in a turbidostat with a 12 h-12 h light-dark cycle for 2 weeks. During the light periods, a dynamic light regimen was used in order to simulate the natural conditions found in the upper layers of the world's oceans. This treatment resulted in strong cell cycle synchronization that was monitored by flow cytometry. The steady-state mRNA levels of dnaA and ftsZ were monitored at 4-h intervals during four consecutive division cycles. Both genes exhibited clear diel expression patterns with mRNA maxima during the replication (S) phase. Western blot experiments indicated that the peak of FtsZ concentration occurred at night, i.e., at the time of cell division. Thus, the transcript accumulation of genes involved in replication and division is coordinated in Prochlorococcus sp. strain PCC 9511 and might be crucial for determining the timing of DNA replication and cell division.
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Affiliation(s)
- J Holtzendorff
- Institute of Biology/Genetics, Humboldt-University, D-10115 Berlin, Germany
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Billi D, Friedmann EI, Hofer KG, Caiola MG, Ocampo-Friedmann R. Ionizing-radiation resistance in the desiccation-tolerant cyanobacterium Chroococcidiopsis. Appl Environ Microbiol 2000; 66:1489-92. [PMID: 10742231 PMCID: PMC92012 DOI: 10.1128/aem.66.4.1489-1492.2000] [Citation(s) in RCA: 182] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The effect of X-ray irradiation on cell survival, induction, and repair of DNA damage was studied by using 10 Chroococcidiopsis strains isolated from desert and hypersaline environments. After exposure to 2.5 kGy, the percentages of survival for the strains ranged from 80 to 35%. In the four most resistant strains, the levels of survival were reduced by 1 or 2 orders of magnitude after irradiation with 5 kGy; viable cells were recovered after exposure to 15 kGy but not after exposure to 20 kGy. The severe DNA damage evident after exposure to 2.5 kGy was repaired within 3 h, and the severe DNA damage evident after exposure to 5 kGy was repaired within 24 h. The increase in trichloroacetic acid-precipitable radioactivity in the culture supernatant after irradiation with 2.5 kGy might have been due to cell lysis and/or an excision process involved in DNA repair. The radiation resistance of Chroococcidiopsis strains may reflect the ability of these cyanobacteria to survive prolonged desiccation through efficient repair of the DNA damage that accumulates during dehydration.
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Affiliation(s)
- D Billi
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-1100, USA.
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Life Without Water: Responses of Prokaryotes to Desiccation. CELL AND MOLECULAR RESPONSE TO STRESS 2000. [DOI: 10.1016/s1568-1254(00)80015-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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Abstract
A hybrid assay, based on the properties of the lambda repressor, was developed to detect FtsZ dimerization in Escherichia coli in vivo. A gene fusion comprising the N-terminal end of the lambda cI repressor gene and the complete E. coli ftsZ gene was constructed. The fused protein resulted in a functional lambda repressor and was able to complement the thermosensitive mutant ftsZ84. Using the same strategy, a series of 10 novel mutants of FtsZ that are unable to dimerize was selected, and a deletion analysis of the protein was carried out. Characterization of these mutants allowed the identification of three separate FtsZ portions: the N-terminal of about 150 amino acids; the C-terminal of about 60 amino acids, which corresponds to the less conserved portion of the protein; and a central region of about 150 residues. Mutants belonging to this region would define the dimerization domain of FtsZ.
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Affiliation(s)
- G Di Lallo
- Dipartimento di Biologia, Università di Roma 'Tor Vergata', via della Ricerca Scientifica, La Romanina, Rome, Italy
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