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Tang J, Hu Z, Zhang J, Daroch M. Genome-scale identification and comparative analysis of transcription factors in thermophilic cyanobacteria. BMC Genomics 2024; 25:44. [PMID: 38195395 PMCID: PMC10775510 DOI: 10.1186/s12864-024-09969-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 01/03/2024] [Indexed: 01/11/2024] Open
Abstract
BACKGROUND The transcription factors (TFs) in thermophilic cyanobacteria might represent a uniquely evolved gene repertoire in light of the strong selective pressure caused by hostile habitats. Understanding the molecular composition of the TF genes in thermophilic cyanobacteria will facilitate further studies regarding verifying their exact biochemical functions and genetic engineering. However, limited information is available on the TFs of thermophilic cyanobacteria. Herein, a thorough investigation and comparative analysis were performed to gain insights into the molecular composition of the TFs in 22 thermophilic cyanobacteria. RESULTS The results suggested a fascinating diversity of the TFs among these thermophiles. The abundance and type of TF genes were diversified in these genomes. The identified TFs are speculated to play various roles in biological regulations. Further comparative and evolutionary genomic analyses revealed that HGT may be associated with the genomic plasticity of TF genes in Thermostichus and Thermosynechococcus strains. Comparative analyses also indicated different pattern of TF composition between thermophiles and corresponding mesophilic reference cyanobacteria. Moreover, the identified unique TFs of thermophiles are putatively involved in various biological regulations, mainly as responses to ambient changes, may facilitating the thermophiles to survive in hot springs. CONCLUSION The findings herein shed light on the TFs of thermophilic cyanobacteria and fundamental knowledge for further research regarding thermophilic cyanobacteria with a broad potential for transcription regulations in responses to environmental fluctuations.
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Affiliation(s)
- Jie Tang
- School of Pharmacy and Bioengineering, Chengdu University, Chengdu, 610106, China
| | - Zhe Hu
- School of Pharmacy and Bioengineering, Chengdu University, Chengdu, 610106, China
| | - Jing Zhang
- Food Safety Detection Key Laboratory of Sichuan, Technical Center of Chengdu Customs, Chengdu, 610041, China.
| | - Maurycy Daroch
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
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2
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Omics-Inferred Partitioning and Expression of Diverse Biogeochemical Functions in a Low-O 2 Cyanobacterial Mat Community. mSystems 2021; 6:e0104221. [PMID: 34874776 PMCID: PMC8651085 DOI: 10.1128/msystems.01042-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cyanobacterial mats profoundly influenced Earth’s biological and geochemical evolution and still play important ecological roles in the modern world. However, the biogeochemical functioning of cyanobacterial mats under persistent low-O2 conditions, which dominated their evolutionary history, is not well understood. To investigate how different metabolic and biogeochemical functions are partitioned among community members, we conducted metagenomics and metatranscriptomics on cyanobacterial mats in the low-O2, sulfidic Middle Island sinkhole (MIS) in Lake Huron. Metagenomic assembly and binning yielded 144 draft metagenome assembled genomes, including 61 of medium quality or better, and the dominant cyanobacteria and numerous Proteobacteria involved in sulfur cycling. Strains of a Phormidium autumnale-like cyanobacterium dominated the metagenome and metatranscriptome. Transcripts for the photosynthetic reaction core genes psaA and psbA were abundant in both day and night. Multiple types of psbA genes were expressed from each cyanobacterium, and the dominant psbA transcripts were from an atypical microaerobic type of D1 protein from Phormidium. Further, cyanobacterial transcripts for photosystem I genes were more abundant than those for photosystem II, and two types of Phormidium sulfide quinone reductase were recovered, consistent with anoxygenic photosynthesis via photosystem I in the presence of sulfide. Transcripts indicate active sulfur oxidation and reduction within the cyanobacterial mat, predominately by Gammaproteobacteria and Deltaproteobacteria, respectively. Overall, these genomic and transcriptomic results link specific microbial groups to metabolic processes that underpin primary production and biogeochemical cycling in a low-O2 cyanobacterial mat and suggest mechanisms for tightly coupled cycling of oxygen and sulfur compounds in the mat ecosystem. IMPORTANCE Cyanobacterial mats are dense communities of microorganisms that contain photosynthetic cyanobacteria along with a host of other bacterial species that play important yet still poorly understood roles in this ecosystem. Although such cyanobacterial mats were critical agents of Earth’s biological and chemical evolution through geological time, little is known about how they function under the low-oxygen conditions that characterized most of their natural history. Here, we performed sequencing of the DNA and RNA of modern cyanobacterial mat communities under low-oxygen and sulfur-rich conditions from the Middle Island sinkhole in Lake Huron. The results reveal the organisms and metabolic pathways that are responsible for both oxygen-producing and non-oxygen-producing photosynthesis as well as interconversions of sulfur that likely shape how much O2 is produced in such ecosystems. These findings indicate tight metabolic reactions between community members that help to explain the limited the amount of O2 produced in cyanobacterial mat ecosystems.
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Meier DV, Greve AJ, Chennu A, van Erk MR, Muthukrishnan T, Abed RMM, Woebken D, de Beer D. Limitation of Microbial Processes at Saturation-Level Salinities in a Microbial Mat Covering a Coastal Salt Flat. Appl Environ Microbiol 2021; 87:e0069821. [PMID: 34160273 PMCID: PMC8357274 DOI: 10.1128/aem.00698-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/16/2021] [Indexed: 12/18/2022] Open
Abstract
Hypersaline microbial mats are dense microbial ecosystems capable of performing complete element cycling and are considered analogs of early Earth and hypothetical extraterrestrial ecosystems. We studied the functionality and limits of key biogeochemical processes, such as photosynthesis, aerobic respiration, and sulfur cycling, in salt crust-covered microbial mats from a tidal flat at the coast of Oman. We measured light, oxygen, and sulfide microprofiles as well as sulfate reduction rates at salt saturation and in flood conditions and determined fine-scale stratification of pigments, biomass, and microbial taxa in the resident microbial community. The salt crust did not protect the mats against irradiation or evaporation. Although some oxygen production was measurable at salinities of ≤30% (wt/vol) in situ, at saturation-level salinity (40%), oxygenic photosynthesis was completely inhibited and only resumed 2 days after reducing the porewater salinity to 12%. Aerobic respiration and active sulfur cycling occurred at low rates under salt saturation and increased strongly upon salinity reduction. Apart from high relative abundances of Chloroflexi, photoheterotrophic Alphaproteobacteria, Bacteroidetes, and Archaea, the mat contained a distinct layer harboring filamentous Cyanobacteria, which is unusual for such high salinities. Our results show that the diverse microbial community inhabiting this salt flat mat ultimately depends on periodic salt dilution to be self-sustaining and is rather adapted to merely survive salt saturation than to thrive under the salt crust. IMPORTANCE Due to their abilities to survive intense radiation and low water availability, hypersaline microbial mats are often suggested to be analogs of potential extraterrestrial life. However, even the limitations imposed on microbial processes by saturation-level salinity found on Earth have rarely been studied in situ. While abundance and diversity of microbial life in salt-saturated environments are well documented, most of our knowledge on process limitations stems from culture-based studies, few in situ studies, and theoretical calculations. In particular, oxygenic photosynthesis has barely been explored beyond 5 M NaCl (28% wt/vol). By applying a variety of biogeochemical and molecular methods, we show that despite abundance of photoautotrophic microorganisms, oxygenic photosynthesis is inhibited in salt-crust-covered microbial mats at saturation salinities, while rates of other energy generation processes are decreased several-fold. Hence, the complete element cycling required for self-sustaining microbial communities only occurs at lower salt concentrations.
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Affiliation(s)
- Dimitri V. Meier
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | - Arjun Chennu
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Leibniz Centre for Tropical Marine Research, Bremen, Germany
| | | | | | - Raeid M. M. Abed
- Biology Department, College of Science, Sultan Qaboos University, Muscat, Sultanate of Oman
| | - Dagmar Woebken
- Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Dirk de Beer
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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4
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Nagy C, Thiel K, Mulaku E, Mustila H, Tamagnini P, Aro EM, Pacheco CC, Kallio P. Comparison of alternative integration sites in the chromosome and the native plasmids of the cyanobacterium Synechocystis sp. PCC 6803 in respect to expression efficiency and copy number. Microb Cell Fact 2021; 20:130. [PMID: 34246263 PMCID: PMC8272380 DOI: 10.1186/s12934-021-01622-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 06/29/2021] [Indexed: 11/10/2022] Open
Abstract
Background Synechocystis sp. PCC 6803 provides a well-established reference point to cyanobacterial metabolic engineering as part of basic photosynthesis research, as well as in the development of next-generation biotechnological production systems. This study focused on expanding the current knowledge on genomic integration of expression constructs in Synechocystis, targeting a range of novel sites in the chromosome and in the native plasmids, together with established loci used in literature. The key objective was to obtain quantitative information on site-specific expression in reference to replicon copy numbers, which has been speculated but never compared side by side in this host. Results An optimized sYFP2 expression cassette was successfully integrated in two novel sites in Synechocystis chromosome (slr0944; sll0058) and in all four endogenous megaplasmids (pSYSM/slr5037-slr5038; pSYSX/slr6037; pSYSA/slr7023; pSYSG/slr8030) that have not been previously evaluated for the purpose. Fluorescent analysis of the segregated strains revealed that the expression levels between the megaplasmids and chromosomal constructs were very similar, and reinforced the view that highest expression in Synechocystis can be obtained using RSF1010-derived replicative vectors or the native small plasmid pCA2.4 evaluated in comparison. Parallel replicon copy number analysis by RT-qPCR showed that the expression from the alternative loci is largely determined by the gene dosage in Synechocystis, thereby confirming the dependence formerly proposed based on literature. Conclusions This study brings together nine different integrative loci in the genome of Synechocystis to demonstrate quantitative differences between target sites in the chromosome, the native plasmids, and a RSF1010-based replicative expression vector. To date, this is the most comprehensive comparison of alternative integrative sites in Synechocystis, and provides the first direct reference between expression efficiency and replicon gene dosage in the context. In the light of existing literature, the findings support the view that the small native plasmids can be notably more difficult to target than the chromosome or the megaplasmids, and that the RSF1010-derived vectors may be surprisingly well maintained under non-selective culture conditions in this cyanobacterial host. Altogether, the work broadens our views on genomic integration and the rational use of different integrative loci versus replicative plasmids, when aiming at expressing heterologous genes in Synechocystis. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01622-2.
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Affiliation(s)
- Csaba Nagy
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Kati Thiel
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Edita Mulaku
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Henna Mustila
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Paula Tamagnini
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Edifício FC4, 4169-007, Porto, Portugal
| | - Eva-Mari Aro
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Catarina C Pacheco
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Pauli Kallio
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland.
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5
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Aulitto M, Gallo G, Puopolo R, Mormone A, Limauro D, Contursi P, Piochi M, Bartolucci S, Fiorentino G. Genomic Insight of Alicyclobacillus mali FL18 Isolated From an Arsenic-Rich Hot Spring. Front Microbiol 2021; 12:639697. [PMID: 33897644 PMCID: PMC8060452 DOI: 10.3389/fmicb.2021.639697] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/05/2021] [Indexed: 12/24/2022] Open
Abstract
Extreme environments are excellent places to find microorganisms capable of tolerating extreme temperature, pH, salinity pressure, and elevated concentration of heavy metals and other toxic compounds. In the last decades, extremophilic microorganisms have been extensively studied since they can be applied in several fields of biotechnology along with their enzymes. In this context, the characterization of heavy metal resistance determinants in thermophilic microorganisms is the starting point for the development of new biosystems and bioprocesses for environmental monitoring and remediation. This work focuses on the isolation and the genomic exploration of a new arsenic-tolerant microorganism, classified as Alicyclobacillus mali FL18. The bacterium was isolated from a hot mud pool of the solfataric terrains in Pisciarelli, a well-known hydrothermally active zone of the Campi Flegrei volcano near Naples in Italy. A. mali FL18 showed a good tolerance to arsenite (MIC value of 41 mM), as well as to other metals such as nickel (MIC 30 mM), cobalt, and mercury (MIC 3 mM and 17 μM, respectively). Signatures of arsenic resistance genes (one arsenate reductase, one arsenite methyltransferase, and several arsenite exporters) were found interspersed in the genome as well as several multidrug resistance efflux transporters that could be involved in the export of drugs and heavy metal ions. Moreover, the strain showed a high resistance to bacitracin and ciprofloxacin, suggesting that the extreme environment has positively selected multiple resistances to different toxic compounds. This work provides, for the first time, insights into the heavy metal tolerance and antibiotic susceptibility of an Alicyclobacillus strain and highlights its putative molecular determinants.
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Affiliation(s)
- Martina Aulitto
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Naples, Italy
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Giovanni Gallo
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Naples, Italy
- Institute of Polymers, Composites and Biomaterials (IPCB), Consiglio Nazionale delle Ricerche CNR, Pozzuoli, Italy
| | - Rosanna Puopolo
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Angela Mormone
- Istituto Nazionale di Geofisica e Vulcanologia, Sezione di Napoli Osservatorio Vesuviano, Naples, Italy
| | - Danila Limauro
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Patrizia Contursi
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Monica Piochi
- Istituto Nazionale di Geofisica e Vulcanologia, Sezione di Napoli Osservatorio Vesuviano, Naples, Italy
| | - Simonetta Bartolucci
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Naples, Italy
| | - Gabriella Fiorentino
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, Naples, Italy
- Institute of Polymers, Composites and Biomaterials (IPCB), Consiglio Nazionale delle Ricerche CNR, Pozzuoli, Italy
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6
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Lumian JE, Jungblut AD, Dillion ML, Hawes I, Doran PT, Mackey TJ, Dick GJ, Grettenberger CL, Sumner DY. Metabolic Capacity of the Antarctic Cyanobacterium Phormidium pseudopriestleyi That Sustains Oxygenic Photosynthesis in the Presence of Hydrogen Sulfide. Genes (Basel) 2021; 12:genes12030426. [PMID: 33809699 PMCID: PMC8002359 DOI: 10.3390/genes12030426] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/05/2021] [Accepted: 03/12/2021] [Indexed: 01/11/2023] Open
Abstract
Sulfide inhibits oxygenic photosynthesis by blocking electron transfer between H2O and the oxygen-evolving complex in the D1 protein of Photosystem II. The ability of cyanobacteria to counter this effect has implications for understanding the productivity of benthic microbial mats in sulfidic environments throughout Earth history. In Lake Fryxell, Antarctica, the benthic, filamentous cyanobacterium Phormidium pseudopriestleyi creates a 1–2 mm thick layer of 50 µmol L−1 O2 in otherwise sulfidic water, demonstrating that it sustains oxygenic photosynthesis in the presence of sulfide. A metagenome-assembled genome of P. pseudopriestleyi indicates a genetic capacity for oxygenic photosynthesis, including multiple copies of psbA (encoding the D1 protein of Photosystem II), and anoxygenic photosynthesis with a copy of sqr (encoding the sulfide quinone reductase protein that oxidizes sulfide). The genomic content of P. pseudopriestleyi is consistent with sulfide tolerance mechanisms including increasing psbA expression or directly oxidizing sulfide with sulfide quinone reductase. However, the ability of the organism to reduce Photosystem I via sulfide quinone reductase while Photosystem II is sulfide-inhibited, thereby performing anoxygenic photosynthesis in the presence of sulfide, has yet to be demonstrated.
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Affiliation(s)
- Jessica E. Lumian
- Microbiology Graduate Group, University of California, Davis, CA 95616, USA;
| | - Anne D. Jungblut
- Life Sciences Department, The Natural History Museum, London SW7 5BD, UK;
| | - Megan L. Dillion
- Genomics and Bioinformatics, Novozymes, Inc., Davis, CA 95616, USA;
| | - Ian Hawes
- Coastal Marine Field Station, University of Waikato, Tauranga 3110, New Zealand;
| | - Peter T. Doran
- Geology and Geophysics, Louisiana State University, Baton Rouge, LA 70803, USA;
| | - Tyler J. Mackey
- Department of Earth and Planetary Sciences, University of New Mexico, Albuquerque, NM 87131, USA;
| | - Gregory J. Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann Arbor, MI 48109, USA;
| | | | - Dawn Y. Sumner
- Department of Earth and Planetary Sciences, University of California, Davis, CA 95616, USA;
- Correspondence: ; Tel.: +1-530-752-5353
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7
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Yoshimura KM, Todorova S, Biddle JF. Mercury geochemistry and microbial diversity in meromictic Glacier Lake, Jamesville, NY. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:195-202. [PMID: 32036624 DOI: 10.1111/1758-2229.12823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/06/2020] [Accepted: 01/22/2020] [Indexed: 06/10/2023]
Abstract
Meromictic lakes are stratified lakes that typically stimulate phototrophic anoxic microbial metabolism, including the transformation of sulphur. Less studied are the transformations of mercury in these environments, and the microorganisms, which mediate these reactions. In order to further an understanding of redox species, mercury and microbial populations in meromictic lakes, we examined the geochemistry and microbiology of Glacier Lake in Jamesville, NY. We found an anoxic transition at a depth of 6 m, followed by active nitrate and sulphate utilization. A chlorophyll a maximum was located at 11 m, coinciding with peaks of several photoautotrophic microbial lineages and total mercury and methyl mercury. Via amplicon sequencing, the microbial population showed pronounced peaks of cyanobacteria at 10 m, Chlorobi at 12 m and Chloroflexi at 14 m. Sulphate-reducing bacteria were also most abundant between 10 and 14 m depth. A functional gene indicating the potential for the production of methyl mercury, hgcA, was detected at several depths in the lake. Our work suggests that in addition to the sulphur cycle, the cycling of mercury may be indirectly coupled with phototrophic processes in Glacier Lake.
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Affiliation(s)
| | - Svetoslava Todorova
- Department of Civil and Environmental Engineering, Syracuse University, Syracuse, NY, USA
| | - Jennifer F Biddle
- School of Marine Science and Policy, University of Delaware, Lewes, DE, USA
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8
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Momper L, Hu E, Moore KR, Skoog EJ, Tyler M, Evans AJ, Bosak T. Metabolic versatility in a modern lineage of cyanobacteria from terrestrial hot springs. Free Radic Biol Med 2019; 140:224-232. [PMID: 31163257 DOI: 10.1016/j.freeradbiomed.2019.05.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 05/14/2019] [Accepted: 05/31/2019] [Indexed: 01/23/2023]
Abstract
The extent of oxygenated environments on the early Earth was much lower than today, and cyanobacteria were critical players in Earth's shift from widespread anoxia to oxygenated surface environments. Extant cyanobacteria that aggregate into cones, tufts and ridges are used to understand the long record of photosynthesis and microbe-mineral interactions during times when oxygen was much lower, i.e., the Archean and the Proterozoic. To better understand the metabolic versatility and physiological properties of these organisms, we examined publicly available genomes of cyanobacteria from modern terrestrial hydrothermal systems and a newly sequenced genome of a cyanobacterium isolated from conical and ridged microbialites that grow in occasionally sulfidic hydrothermal springs in Yellowstone National Park, USA. Phylogenomic analyses reveal that cyanobacteria from globally distributed terrestrial and shallow marine hydrothermal systems form a monophyletic clade within the Cyanobacteria phylum. Comparative genomics of this clade reveals the genetic capacity for oxygenic photosynthesis that uses photosystems I and II, and anoxygenic photosynthesis that uses a putative sulfide quinone reductase to oxidize sulfide and bypass photosystem II. Surprisingly large proportions of the newly sequenced genome from Yellowstone National Park are also dedicated to secondary metabolite production (15.1-15.6%), of which ∼6% can be attributed to antibiotic production and resistance genes. All this may be advantageous to benthic, mat-forming photosynthesizers that have to compete for light and nutrients in sporadically or permanently sulfidic environments, and may have also improved the tolerance of ancient counterparts of these cyanobacteria to sulfidic conditions in benthic communities that colonized the coastal margins in the Archean and the Proterozoic.
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Affiliation(s)
- Lily Momper
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Eileen Hu
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Kelsey R Moore
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Emilie J Skoog
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Madeline Tyler
- College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA
| | - Alexander J Evans
- Department of Earth, Environmental and Planetary Sciences, Brown University, Providence, RI, USA
| | - Tanja Bosak
- Department of Earth, Atmospheric & Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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9
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Ahn AC, Cavalca L, Colombo M, Schuurmans JM, Sorokin DY, Muyzer G. Transcriptomic Analysis of Two Thioalkalivibrio Species Under Arsenite Stress Revealed a Potential Candidate Gene for an Alternative Arsenite Oxidation Pathway. Front Microbiol 2019; 10:1514. [PMID: 31333619 PMCID: PMC6620896 DOI: 10.3389/fmicb.2019.01514] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 06/17/2019] [Indexed: 11/30/2022] Open
Abstract
The genus Thioalkalivibrio includes haloalkaliphilic chemolithoautotrophic sulfur-oxidizing bacteria isolated from various soda lakes worldwide. Some of these lakes possess in addition to their extreme haloalkaline environment also other harsh conditions, to which Thioalkalivibrio needs to adapt. An example is arsenic in soda lakes in eastern California, which is found there in concentrations up to 3000 μM. Arsenic is a widespread element that can be an environmental issue, as it is highly toxic to most organisms. However, resistance mechanisms in the form of detoxification are widespread and some prokaryotes can even use arsenic as an energy source. We first screened the genomes of 76 Thioalkalivibrio strains for the presence of known arsenic oxidoreductases and found 15 putative ArxA (arsenite oxidase) and two putative ArrA (arsenate reductase). Subsequently, we studied the resistance to arsenite in detail in Thioalkalivibrio jannaschii ALM2T, and Thioalkalivibrio thiocyanoxidans ARh2T by comparative genomics and by growing them at different arsenite concentrations followed by arsenic species and transcriptomic analysis. Tv. jannaschii ALM2T, which has been isolated from Mono Lake, an arsenic-rich soda lake, could resist up to 5 mM arsenite, whereas Tv. thiocyanoxidans ARh2T, which was isolated from a Kenyan soda lake, could only grow up to 0.1 mM arsenite. Interestingly, both species oxidized arsenite to arsenate under aerobic conditions, although Tv. thiocyanoxidans ARh2T does not contain any known arsenite oxidases, and in Tv. jannaschii ALM2T, only arxB2 was clearly upregulated. However, we found the expression of a SoeABC-like gene, which we assume might have been involved in arsenite oxidation. Other arsenite stress responses for both strains were the upregulation of the vitamin B12 synthesis pathway, which can be linked to antioxidant activity, and the up- and downregulation of different DsrE/F-like genes whose roles are still unclear. Moreover, Tv. jannaschii ALM2T induced the ars gene operon and the Pst system, and Tv. thiocanoxidans ARh2T upregulated the sox and apr genes as well as different heat shock proteins. Our findings for Thioalkalivibrio confirm previously observed adaptations to arsenic, but also provide new insights into the arsenic stress response and the connection between the arsenic and the sulfur cycle.
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Affiliation(s)
- Anne-Catherine Ahn
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Lucia Cavalca
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Milena Colombo
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - J Merijn Schuurmans
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Dimitry Y Sorokin
- Research Centre of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia.,Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Gerard Muyzer
- Microbial Systems Ecology, Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
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10
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Hughes AR, Sulesky A, Andersson B, Peers G. Sulfate amendment improves the growth and bioremediation capacity of a cyanobacteria cultured on municipal wastewater centrate. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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11
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Gutekunst K. Hypothesis on the Synchronistic Evolution of Autotrophy and Heterotrophy. Trends Biochem Sci 2018; 43:402-411. [DOI: 10.1016/j.tibs.2018.03.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 03/05/2018] [Accepted: 03/20/2018] [Indexed: 10/17/2022]
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Duzs Á, Tóth A, Németh B, Balogh T, Kós PB, Rákhely G. A novel enzyme of type VI sulfide:quinone oxidoreductases in purple sulfur photosynthetic bacteria. Appl Microbiol Biotechnol 2018; 102:5133-5147. [PMID: 29680900 DOI: 10.1007/s00253-018-8973-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 02/23/2018] [Accepted: 03/28/2018] [Indexed: 11/24/2022]
Abstract
Sulfide detoxification can be catalyzed by ancient membrane-bound flavoproteins, sulfide:quinone oxidoreductases (Sqr), which have important roles in sulfide homeostasis and sulfide-dependent energy conservation processes by transferring electrons from sulfide to respiratory or photosynthetic membrane electron flow. Sqr enzymes have been categorized into six groups. Several members of the groups I, II, III, and V are well-known, but type IV and VI Sqrs are, as yet, uncharacterized or hardly characterized at all. Here, we report detailed characterization of a type VI sulfide:quinone oxidoreductase (TrSqrF) from a purple sulfur bacterium, Thiocapsa roseopersicina. Phylogenetic analysis classified this enzyme in a special group composed of SqrFs of endosymbionts, while a weaker relationship could be observed with SqrF of Chlorobaculum tepidum which is the only type VI enzyme characterized so far. Directed mutagenesis experiments showed that TrSqrF contributed substantially to the sulfide:quinone oxidoreductase activity of the membranes. Expression of the sqrF gene could be induced by sulfide. Homologous recombinant TrSqrF protein was expressed and purified from the membranes of a SqrF-deleted T. roseopersicina strain. The purified protein contains redox-active covalently bound FAD cofactor. The recombinant TrSqrF enzyme catalyzes sulfur-dependent quinone reduction and prefers ubiquinone-type quinone compounds. Kinetic parameters of TrSqrF show that the affinity of the enzyme is similar to duroquinone and decylubiquinone, but the reaction has substantially lower activation energy with decylubiquinone, indicating that the quinone structure has an effect on the catalytic process. TrSqrF enzyme affinity for sulfide is low, therefore, in agreement with the gene expressional analyis, SqrF could play a role in energy-conserving sulfide oxidation at high sulfide concentrations. TrSqrF is a good model enzyme for the subgroup of type VI Sqrs of endosymbionts and its characterization might provide deeper insight into the molecular details of the ancient, anoxic, energy-gaining processes using sulfide as an electron donor.
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Affiliation(s)
- Ágnes Duzs
- Department of Biotechnology, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary.,Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt 62, Szeged, 6726, Hungary
| | - András Tóth
- Department of Biotechnology, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary.,Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt 62, Szeged, 6726, Hungary
| | - Brigitta Németh
- Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt 62, Szeged, 6726, Hungary
| | - Tímea Balogh
- Department of Biotechnology, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary
| | - Péter B Kós
- Department of Biotechnology, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary.,Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt 62, Szeged, 6726, Hungary
| | - Gábor Rákhely
- Department of Biotechnology, University of Szeged, Közép fasor 52, Szeged, 6726, Hungary. .,Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt 62, Szeged, 6726, Hungary.
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13
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Grim SL, Dick GJ. Photosynthetic Versatility in the Genome of Geitlerinema sp. PCC 9228 (Formerly Oscillatoria limnetica 'Solar Lake'), a Model Anoxygenic Photosynthetic Cyanobacterium. Front Microbiol 2016; 7:1546. [PMID: 27790189 PMCID: PMC5061849 DOI: 10.3389/fmicb.2016.01546] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 09/15/2016] [Indexed: 12/27/2022] Open
Abstract
Anoxygenic cyanobacteria that use sulfide as the electron donor for photosynthesis are a potentially influential but poorly constrained force on Earth's biogeochemistry. Their versatile metabolism may have boosted primary production and nitrogen cycling in euxinic coastal margins in the Proterozoic. In addition, they represent a biological mechanism for limiting the accumulation of atmospheric oxygen, especially before the Great Oxidation Event and in the low-oxygen conditions of the Proterozoic. In this study, we describe the draft genome sequence of Geitlerinema sp. PCC 9228, formerly Oscillatoria limnetica 'Solar Lake', a mat-forming diazotrophic cyanobacterium that can switch between oxygenic photosynthesis and sulfide-based anoxygenic photosynthesis (AP). Geitlerinema possesses three variants of psbA, which encodes protein D1, a core component of the photosystem II reaction center. Phylogenetic analyses indicate that one variant is closely affiliated with cyanobacterial psbA genes that code for a D1 protein used for oxygen-sensitive processes. Another version is phylogenetically similar to cyanobacterial psbA genes that encode D1 proteins used under microaerobic conditions, and the third variant may be cued to high light and/or elevated oxygen concentrations. Geitlerinema has the canonical gene for sulfide quinone reductase (SQR) used in cyanobacterial AP and a putative transcriptional regulatory gene in the same operon. Another operon with a second, distinct sqr and regulatory gene is present, and is phylogenetically related to sqr genes used for high sulfide concentrations. The genome has a comprehensive nif gene suite for nitrogen fixation, supporting previous observations of nitrogenase activity. Geitlerinema possesses a bidirectional hydrogenase rather than the uptake hydrogenase typically used by cyanobacteria in diazotrophy. Overall, the genome sequence of Geitlerinema sp. PCC 9228 highlights potential cyanobacterial strategies to cope with fluctuating redox gradients and nitrogen availability that occur in benthic mats over a diel cycle. Such dynamic geochemical conditions likely also challenged Proterozoic cyanobacteria, modulating oxygen production. The genetic repertoire that underpins flexible oxygenic/anoxygenic photosynthesis in cyanobacteria provides a foundation to explore the regulation, evolutionary context, and biogeochemical implications of these co-occurring metabolisms in Earth history.
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Affiliation(s)
- Sharon L. Grim
- Department of Earth and Environmental Sciences, University of Michigan, Ann ArborMI, USA
| | - Gregory J. Dick
- Department of Earth and Environmental Sciences, University of Michigan, Ann ArborMI, USA
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14
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Sure S, Ackland ML, Gaur A, Gupta P, Adholeya A, Kochar M. Probing Synechocystis-Arsenic Interactions through Extracellular Nanowires. Front Microbiol 2016; 7:1134. [PMID: 27486454 PMCID: PMC4949250 DOI: 10.3389/fmicb.2016.01134] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/07/2016] [Indexed: 11/13/2022] Open
Abstract
Microbial nanowires (MNWs) can play an important role in the transformation and mobility of toxic metals/metalloids in environment. The potential role of MNWs in cell-arsenic (As) interactions has not been reported in microorganisms and thus we explored this interaction using Synechocystis PCC 6803 as a model system. The effect of half maximal inhibitory concentration (IC50) [~300 mM As (V) and ~4 mM As (III)] and non-inhibitory [4X lower than IC50, i.e., 75 mM As (V) and 1 mM As (III)] of As was studied on Synechocystis cells in relation to its effect on Chlorophyll (Chl) a, type IV pili (TFP)-As interaction and intracellular/extracellular presence of As. In silico analysis showed that subunit PilA1 of electrically conductive TFP, i.e., microbial nanowires of Synechocystis have putative binding sites for As. In agreement with in silico analysis, transmission electron microscopy analysis showed that As was deposited on Synechocystis nanowires at all tested concentrations. The potential of Synechocystis nanowires to immobilize As can be further enhanced and evaluated on a large scale and thus can be applied for bioremediation studies.
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Affiliation(s)
- Sandeep Sure
- TERI-Deakin Nano biotechnology Centre, The Energy and Resources Institute Gurgaon, India
| | - M L Ackland
- Centre for Cellular & Molecular Biology, Deakin University, Melbourne VIC, Australia
| | - Aditya Gaur
- TERI-Deakin Nano biotechnology Centre, The Energy and Resources Institute Gurgaon, India
| | - Priyanka Gupta
- TERI-Deakin Nano biotechnology Centre, The Energy and Resources Institute Gurgaon, India
| | - Alok Adholeya
- TERI-Deakin Nano biotechnology Centre, The Energy and Resources Institute Gurgaon, India
| | - Mandira Kochar
- TERI-Deakin Nano biotechnology Centre, The Energy and Resources Institute Gurgaon, India
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Unraveling the Physiological Roles of the Cyanobacterium Geitlerinema sp. BBD and Other Black Band Disease Community Members through Genomic Analysis of a Mixed Culture. PLoS One 2016; 11:e0157953. [PMID: 27336619 PMCID: PMC4918915 DOI: 10.1371/journal.pone.0157953] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 06/07/2016] [Indexed: 11/19/2022] Open
Abstract
Black band disease (BBD) is a cyanobacterial-dominated polymicrobial mat that propagates on and migrates across coral surfaces, necrotizing coral tissue. Culture-based laboratory studies have investigated cyanobacteria and heterotrophic bacteria isolated from BBD, but the metabolic potential of various BBD microbial community members and interactions between them remain poorly understood. Here we report genomic insights into the physiological and metabolic potential of the BBD-associated cyanobacterium Geitlerinema sp. BBD 1991 and six associated bacteria that were also present in the non-axenic culture. The essentially complete genome of Geitlerinema sp. BBD 1991 contains a sulfide quinone oxidoreductase gene for oxidation of sulfide, suggesting a mechanism for tolerating the sulfidic conditions of BBD mats. Although the operon for biosynthesis of the cyanotoxin microcystin was surprisingly absent, potential relics were identified. Genomic evidence for mixed-acid fermentation indicates a strategy for energy metabolism under the anaerobic conditions present in BBD during darkness. Fermentation products may supply carbon to BBD heterotrophic bacteria. Among the six associated bacteria in the culture, two are closely related to organisms found in culture-independent studies of diseased corals. Their metabolic pathways for carbon and sulfur cycling, energy metabolism, and mechanisms for resisting coral defenses suggest adaptations to the coral surface environment and biogeochemical roles within the BBD mat. Polysulfide reductases were identified in a Flammeovirgaceae genome (Bacteroidetes) and the sox pathway for sulfur oxidation was found in the genome of a Rhodospirillales bacterium (Alphaproteobacteria), revealing mechanisms for sulfur cycling, which influences virulence of BBD. Each genomic bin possessed a pathway for conserving energy from glycerol degradation, reflecting adaptations to the glycerol-rich coral environment. The presence of genes for detoxification of reactive oxygen species and resistance to antibiotics suggest mechanisms for combating coral defense strategies. This study builds upon previous research on BBD and provides new insights into BBD disease etiology.
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Bradley RW, Wang B. Designer cell signal processing circuits for biotechnology. N Biotechnol 2015; 32:635-43. [PMID: 25579192 PMCID: PMC4571992 DOI: 10.1016/j.nbt.2014.12.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/02/2014] [Accepted: 12/31/2014] [Indexed: 01/13/2023]
Abstract
Microorganisms are able to respond effectively to diverse signals from their environment and internal metabolism owing to their inherent sophisticated information processing capacity. A central aim of synthetic biology is to control and reprogramme the signal processing pathways within living cells so as to realise repurposed, beneficial applications ranging from disease diagnosis and environmental sensing to chemical bioproduction. To date most examples of synthetic biological signal processing have been built based on digital information flow, though analogue computing is being developed to cope with more complex operations and larger sets of variables. Great progress has been made in expanding the categories of characterised biological components that can be used for cellular signal manipulation, thereby allowing synthetic biologists to more rationally programme increasingly complex behaviours into living cells. Here we present a current overview of the components and strategies that exist for designer cell signal processing and decision making, discuss how these have been implemented in prototype systems for therapeutic, environmental, and industrial biotechnological applications, and examine emerging challenges in this promising field.
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Affiliation(s)
- Robert W Bradley
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK; Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, UK
| | - Baojun Wang
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, UK.
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Responses to oxidative and heavy metal stresses in cyanobacteria: recent advances. Int J Mol Sci 2014; 16:871-86. [PMID: 25561236 PMCID: PMC4307280 DOI: 10.3390/ijms16010871] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 12/24/2014] [Indexed: 12/24/2022] Open
Abstract
Cyanobacteria, the only known prokaryotes that perform oxygen-evolving photosynthesis, are receiving strong attention in basic and applied research. In using solar energy, water, CO2 and mineral salts to produce a large amount of biomass for the food chain, cyanobacteria constitute the first biological barrier against the entry of toxics into the food chain. In addition, cyanobacteria have the potential for the solar-driven carbon-neutral production of biofuels. However, cyanobacteria are often challenged by toxic reactive oxygen species generated under intense illumination, i.e., when their production of photosynthetic electrons exceeds what they need for the assimilation of inorganic nutrients. Furthermore, in requiring high amounts of various metals for growth, cyanobacteria are also frequently affected by drastic changes in metal availabilities. They are often challenged by heavy metals, which are increasingly spread out in the environment through human activities, and constitute persistent pollutants because they cannot be degraded. Consequently, it is important to analyze the protection against oxidative and metal stresses in cyanobacteria because these ancient organisms have developed most of these processes, a large number of which have been conserved during evolution. This review summarizes what is known regarding these mechanisms, emphasizing on their crosstalk.
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