1
|
Casero MC, Herrero MÁ, De la Roche JP, Quesada A, Velázquez D, Cirés S. Effect of salinity on scytonemin yield in endolithic cyanobacteria from the Atacama Desert. Sci Rep 2024; 14:9731. [PMID: 38679613 PMCID: PMC11056366 DOI: 10.1038/s41598-024-60499-4] [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: 01/26/2024] [Accepted: 04/23/2024] [Indexed: 05/01/2024] Open
Abstract
Cyanobacteria inhabiting extreme environments constitute a promising source for natural products with biotechnological applications. However, they have not been studied in-depth for this purpose due to the difficulties in their isolation and mass culturing. The Atacama Desert suffers one of the highest solar irradiances that limits the presence of life on its hyperarid core to endolithic microbial communities supported by cyanobacteria as primary producers. Some of these cyanobacteria are known to produce scytonemin, a UV-screening liposoluble pigment with varied biotechnological applications in cosmetics and other industries. In this work we carried out a strain selection based on growth performance among 8 endolithic cyanobacteria of the genera Chroococcidiopsis, Gloeocapsa and Gloeocapsopsis isolated from non-saline rocks of the Atacama Desert. Then we investigated the influence of NaCl exposure on scytonemin production yield. Results in the selected strain (Chroococcidiopsis sp. UAM571) showed that rising concentrations of NaCl lead to a growth decrease while triggering a remarkable increase in the scytonemin content, reaching maximum values at 20 g L-1 of NaCl over 50-fold higher scytonemin contents than those obtained without NaCl. Altogether, these findings point out to cyanobacteria from the Atacama Desert as potentially suitable candidates for pilot-scale cultivation with biotechnological purposes, particularly to obtain scytonemin.
Collapse
Affiliation(s)
| | | | | | - Antonio Quesada
- Departamento de Biología, Universidad Autónoma de Madrid, 28014, Madrid, Spain
| | - David Velázquez
- Departamento de Biología, Universidad Autónoma de Madrid, 28014, Madrid, Spain
| | - Samuel Cirés
- Departamento de Biología, Universidad Autónoma de Madrid, 28014, Madrid, Spain.
| |
Collapse
|
2
|
Thøgersen MS, Zervas A, Stougaard P, Ellegaard-Jensen L. Investigating eukaryotic and prokaryotic diversity and functional potential in the cold and alkaline ikaite columns in Greenland. Front Microbiol 2024; 15:1358787. [PMID: 38655082 PMCID: PMC11035741 DOI: 10.3389/fmicb.2024.1358787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/08/2024] [Indexed: 04/26/2024] Open
Abstract
The ikaite columns in the Ikka Fjord, SW Greenland, represent a permanently cold and alkaline environment known to contain a rich bacterial diversity. 16S and 18S rRNA gene amplicon and metagenomic sequencing was used to investigate the microbial diversity in the columns and for the first time, the eukaryotic and archaeal diversity in ikaite columns were analyzed. The results showed a rich prokaryotic diversity that varied across columns as well as within each column. Seven different archaeal phyla were documented in multiple locations inside the columns. The columns also contained a rich eukaryotic diversity with 27 phyla representing microalgae, protists, fungi, and small animals. Based on metagenomic sequencing, 25 high-quality MAGs were assembled and analyzed for the presence of genes involved in cycling of nitrogen, sulfur, and phosphorous as well as genes encoding carbohydrate-active enzymes (CAZymes), showing a potentially very bioactive microbial community.
Collapse
|
3
|
Santoro M, Hassenrück C, Labrenz M, Hagemann M. Acclimation of Nodularia spumigena CCY9414 to inorganic phosphate limitation - Identification of the P-limitation stimulon via RNA-seq. Front Microbiol 2023; 13:1082763. [PMID: 36687591 PMCID: PMC9846622 DOI: 10.3389/fmicb.2022.1082763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/05/2022] [Indexed: 01/06/2023] Open
Abstract
Nodularia spumigena is a toxic, filamentous cyanobacterium capable of fixing atmospheric N2, which is often dominating cyanobacterial bloom events in the Baltic Sea and other brackish water systems worldwide. Increasing phosphate limitation has been considered as one environmental factor promoting cyanobacterial mass developments. In the present study, we analyzed the response of N. spumigena strain CCY9414 toward strong phosphate limitation. Growth of the strain was diminished under P-deplete conditions; however, filaments contained more polyphosphate under P-deplete compared to P-replete conditions. Using RNA-seq, gene expression was compared in N. spumigena CCY9414 after 7 and 14 days in P-deplete and P-replete conditions, respectively. After 7 days, 112 genes were significantly up-regulated in P-deplete filaments, among them was a high proportion of genes encoding proteins related to P-homeostasis such as transport systems for different P species. Many of these genes became also up-regulated after 14 days compared to 7 days in filaments grown under P-replete conditions, which was consistent with the almost complete consumption of dissolved P in these cultures after 14 days. In addition to genes directly related to P starvation, genes encoding proteins for bioactive compound synthesis, gas vesicles formation, or sugar catabolism were stimulated under P-deplete conditions. Collectively, our data describe an experimentally validated P-stimulon in N. spumigena CCY9414 and provide the indication that severe P limitation could indeed support bloom formation by this filamentous strain.
Collapse
Affiliation(s)
- Mariano Santoro
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research, Warnemünde (IOW), Rostock, Germany,Department of Plant Physiology, Institute for Biosciences, University of Rostock, Rostock, Germany
| | - Christiane Hassenrück
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research, Warnemünde (IOW), Rostock, Germany
| | - Matthias Labrenz
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research, Warnemünde (IOW), Rostock, Germany
| | - Martin Hagemann
- Department of Plant Physiology, Institute for Biosciences, University of Rostock, Rostock, Germany,*Correspondence: Martin Hagemann,
| |
Collapse
|
4
|
Liepina-Leimane I, Barda I, Jurgensone I, Labucis A, Suhareva N, Kozlova V, Maderniece A, Aigars J. Seasonal dynamic of diazotrophic activity and environmental variables affecting it in the Gulf of Riga, Baltic Sea. FEMS Microbiol Ecol 2022; 98:6819948. [PMID: 36354101 PMCID: PMC9712029 DOI: 10.1093/femsec/fiac132] [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] [Received: 04/29/2022] [Revised: 10/30/2022] [Accepted: 11/07/2022] [Indexed: 11/11/2022] Open
Abstract
The semi-enclosed Baltic Sea experiences regular summer blooms of diazotrophic cyanobacteria. Previously, it has been conclusively demonstrated that in open nitrogen-limited parts of the Baltic Sea, cyanobacteria successfully fix atmospheric N2. At the same time, diazotrophic activity is still poorly understood in Baltic Sea sub-regions where nitrogen and phosphorus are co-limiting primary production. To address this gap in research, we used the15 N tracer method for in situ incubations and measured the N2-fixation rate of heterocyst-forming cyanobacteria and picocyanobacteria in the Gulf of Riga, Baltic Sea, from April to September. Physicochemical variables and phytoplankton community composition were also determined. Our results show that the dominant species of cyanobacteria for this region (Aphanizomenon flosaquae) was present in the phytoplankton community during most of the study period. We also establish that the N2-fixation rate has a strong correlation with the proportion of A. flosaquae biomass containing heterocysts (r = 0.80). Our findings highlight the importance of a heterocyst-focused approach for an accurate diazotrophic activity evaluation that is one of the foundations for future management and protection of the Baltic Sea.
Collapse
Affiliation(s)
| | - Ieva Barda
- Latvian Institute of Aquatic Ecology, Agency of Daugavpils University, Voleru Street 4, Riga, Latvia, LV-1007
| | - Iveta Jurgensone
- Latvian Institute of Aquatic Ecology, Agency of Daugavpils University, Voleru Street 4, Riga, Latvia, LV-1007
| | - Atis Labucis
- Latvian Institute of Aquatic Ecology, Agency of Daugavpils University, Voleru Street 4, Riga, Latvia, LV-1007
| | - Natalija Suhareva
- Latvian Institute of Aquatic Ecology, Agency of Daugavpils University, Voleru Street 4, Riga, Latvia, LV-1007
| | - Vendija Kozlova
- Latvian Institute of Aquatic Ecology, Agency of Daugavpils University, Voleru Street 4, Riga, Latvia, LV-1007
| | - Agita Maderniece
- Latvian Institute of Aquatic Ecology, Agency of Daugavpils University, Voleru Street 4, Riga, Latvia, LV-1007
| | - Juris Aigars
- Latvian Institute of Aquatic Ecology, Agency of Daugavpils University, Voleru Street 4, Riga, Latvia, LV-1007
| |
Collapse
|
5
|
Kramer BJ, Jankowiak JG, Nanjappa D, Harke MJ, Gobler CJ. Nitrogen and phosphorus significantly alter growth, nitrogen fixation, anatoxin-a content, and the transcriptome of the bloom-forming cyanobacterium, Dolichospermum. Front Microbiol 2022; 13:955032. [PMID: 36160233 PMCID: PMC9490380 DOI: 10.3389/fmicb.2022.955032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/19/2022] [Indexed: 11/27/2022] Open
Abstract
While freshwater cyanobacteria are traditionally thought to be limited by the availability of phosphorus (P), fixed nitrogen (N) supply can promote the growth and/or toxin production of some genera. This study characterizes how growth on N2 (control), nitrate (NO3 -), ammonium (NH4 +), and urea as well as P limitation altered the growth, toxin production, N2 fixation, and gene expression of an anatoxin-a (ATX-A) - producing strain of Dolichospermum sp. 54. The transcriptomes of fixed N and P-limited cultures differed significantly from those of fixed N-deplete, P-replete (control) cultures, while the transcriptomes of P-replete cultures amended with either NH4 + or NO3 - were not significantly different relative to those of the control. Growth rates of Dolichospermum (sp. 54) were significantly higher when grown on fixed N relative to without fixed N; growth on NH4 + was also significantly greater than growth on NO3 -. NH4 + and urea significantly lowered N2 fixation and nifD gene transcript abundance relative to the control while cultures amended with NO3 - exhibited N2 fixation and nifD gene transcript abundance that was not different from the control. Cultures grown on NH4 + exhibited the lowest ATX-A content per cell and lower transcript abundance of genes associated ATX-A synthesis (ana), while the abundance of transcripts of several ana genes were highest under fixed N and P - limited conditions. The significant negative correlation between growth rate and cellular anatoxin quota as well as the significantly higher number of transcripts of ana genes in cultures deprived of fixed N and P relative to P-replete cultures amended with NH4 + suggests ATX-A was being actively synthesized under P limitation. Collectively, these findings indicate that management strategies that do not regulate fixed N loading will leave eutrophic water bodies vulnerable to more intense and toxic (due to increased biomass) blooms of Dolichospermum.
Collapse
Affiliation(s)
- Benjamin J. Kramer
- School of Marine and Atmospheric Sciences, Stony Brook University, Southampton, NY, United States
| | | | - Deepak Nanjappa
- School of Marine and Atmospheric Sciences, Stony Brook University, Southampton, NY, United States
| | - Matthew J. Harke
- Gloucester Marine Genomics Institute, Gloucester, MA, United States
| | - Christopher J. Gobler
- School of Marine and Atmospheric Sciences, Stony Brook University, Southampton, NY, United States
| |
Collapse
|
6
|
Phan CS, Mehjabin JJ, Anas ARJ, Hayasaka M, Onoki R, Wang J, Umezawa T, Washio K, Morikawa M, Okino T. Nostosin G and Spiroidesin B from the Cyanobacterium Dolichospermum sp. NIES-1697. JOURNAL OF NATURAL PRODUCTS 2022; 85:2000-2005. [PMID: 35948062 DOI: 10.1021/acs.jnatprod.2c00382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Chemical investigation of the cyanobacterium Dolichospermum sp. NIES-1697 afforded nostosin G (1), a linear tripeptide, spiroidesin B (2), and two known compounds, anabaenopeptins I (3) and J (4). Planar structures and absolute configurations for 1 and 2 were determined by 2D NMR, HRMS, Marfey's methodology, chiral-phase HPLC, and enzymatic degradation. Nostosin G (1) is a unique example of a linear peptide containing three subunits, 4-hydroxyphenyllactic acid (Hpla), homotyrosine (Hty), and argininal, with potent trypsin inhibitory properties. The biosynthetic gene clusters for nostosin G (1) and spiroidesin B (2) were investigated based on the genome sequence of Dolichospermum sp. NIES-1697.
Collapse
|
7
|
Chow GK, Chavan AG, Heisler J, Chang YG, Zhang N, LiWang A, Britt RD. A Night-Time Edge Site Intermediate in the Cyanobacterial Circadian Clock Identified by EPR Spectroscopy. J Am Chem Soc 2022; 144:184-194. [PMID: 34979080 DOI: 10.1021/jacs.1c08103] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As the only circadian oscillator that can be reconstituted in vitro with its constituent proteins KaiA, KaiB, and KaiC using ATP as an energy source, the cyanobacterial circadian oscillator serves as a model system for detailed mechanistic studies of day-night transitions of circadian clocks in general. The day-to-night transition occurs when KaiB forms a night-time complex with KaiC to sequester KaiA, the latter of which interacts with KaiC during the day to promote KaiC autophosphorylation. However, how KaiB forms the complex with KaiC remains poorly understood, despite the available structures of KaiB bound to hexameric KaiC. It has been postulated that KaiB-KaiC binding is regulated by inter-KaiB cooperativity. Here, using spin labeling continuous-wave electron paramagnetic resonance spectroscopy, we identified and quantified two subpopulations of KaiC-bound KaiB, corresponding to the "bulk" and "edge" KaiBC sites in stoichiometric and substoichiometric KaiBiC6 complexes (i = 1-5). We provide kinetic evidence to support the intermediacy of the "edge" KaiBC sites as bridges and nucleation sites between free KaiB and the "bulk" KaiBC sites. Furthermore, we show that the relative abundance of "edge" and "bulk" sites is dependent on both KaiC phosphostate and KaiA, supporting the notion of phosphorylation-state controlled inter-KaiB cooperativity. Finally, we demonstrate that the interconversion between the two subpopulations of KaiC-bound KaiB is intimately linked to the KaiC phosphorylation cycle. These findings enrich our mechanistic understanding of the cyanobacterial clock and demonstrate the utility of EPR in elucidating circadian clock mechanisms.
Collapse
Affiliation(s)
- Gary K Chow
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Archana G Chavan
- School of Natural Sciences, University of California, Merced, California 95343, United States
| | - Joel Heisler
- Chemistry and Chemical Biology, University of California, Merced, California 95343, United States
| | - Yong-Gang Chang
- School of Natural Sciences, University of California, Merced, California 95343, United States
| | - Ning Zhang
- School of Natural Sciences, University of California, Merced, California 95343, United States
| | - Andy LiWang
- School of Natural Sciences, Chemistry and Biochemistry, Health Sciences Research Institute, and Center for Cellular and Biomolecular Machines, University of California, Merced, California 95343, United States.,Center for Circadian Biology, University of California, San Diego, La Jolla, California 92093, United States
| | - R David Britt
- Department of Chemistry, University of California, Davis, California 95616, United States
| |
Collapse
|
8
|
Lage S, Mazur-Marzec H, Gorokhova E. Competitive interactions as a mechanism for chemical diversity maintenance in Nodularia spumigena. Sci Rep 2021; 11:8970. [PMID: 33903638 PMCID: PMC8076297 DOI: 10.1038/s41598-021-88361-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/12/2021] [Indexed: 02/06/2023] Open
Abstract
Nodularia spumigena is a bloom-forming diazotrophic cyanobacterium inhabiting brackish waters worldwide. This species produces non-ribosomal peptides (NRPs), including the hepatotoxin nodularin, often referred to as cyanotoxin. Several known classes of NRPs have various biological activities, although their modes of action are poorly understood. In the Baltic N. spumigena, there is a high NRP chemodiversity among strains, allowing their grouping in specific chemotypes and subgroups. Therefore, it is relevant to ask whether the NRP production is affected by intraspecific interactions between the co-existing strains. Using a novel approach that combines culture technique and liquid chromatography-tandem mass spectrometry for the NRP analysis, we examined N. spumigena strains under mono- and co-culture conditions. The test strains were selected to represent N. spumigena belonging to the same or different chemotype subgroups. In this setup, we observed physiological and metabolic responses in the test strains grown without cell contact. The changes in NRP levels to co-culture conditions were conserved within a chemotype subgroup but different between the subgroups. Our results suggest that intraspecific interactions may promote a chemical diversity in N. spumigena population, with higher NRP production compared to a single-strain population. Studying allelochemical signalling in this cyanobacterium is crucial for understanding toxicity mechanisms and plankton community interactions in the Baltic Sea and other aquatic systems experiencing regular blooms.
Collapse
Affiliation(s)
- Sandra Lage
- grid.10548.380000 0004 1936 9377Department of Environmental Science, Stockholm University, Stockholm, Sweden ,grid.8585.00000 0001 2370 4076Division of Marine Biotechnology, Institute of Oceanography, University of Gdańsk, Gdynia, Poland
| | - Hanna Mazur-Marzec
- grid.8585.00000 0001 2370 4076Division of Marine Biotechnology, Institute of Oceanography, University of Gdańsk, Gdynia, Poland
| | - Elena Gorokhova
- grid.10548.380000 0004 1936 9377Department of Environmental Science, Stockholm University, Stockholm, Sweden
| |
Collapse
|
9
|
16S rRNA gene and 18S rRNA gene diversity in microbial mat communities in meltwater ponds on the McMurdo Ice Shelf, Antarctica. Polar Biol 2021. [DOI: 10.1007/s00300-021-02843-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
AbstractThe undulating ice of the McMurdo Ice Shelf, Southern Victoria Land, supports one of the largest networks of ice-based, multiyear meltwater pond habitats in Antarctica, where microbial mats are abundant and contribute most of the biomass and biodiversity. We used 16S rRNA and 18S rRNA gene high-throughput sequencing to compare variance of the community structure in microbial mats within and between ponds with different salinities and pH. Proteobacteria and Cyanobacteria were the most abundant phyla, and composition at OTU level was highly specific for the meltwater ponds with strong community sorting along the salinity gradient. Our study provides the first detailed evaluation of eukaryote communities for the McMurdo Ice Shelf using the 18S rRNA gene. They were dominated by Ochrophyta, Chlorophyta and Ciliophora, consistent with previous microscopic analyses, but many OTUs belonging to less well-described heterotrophic protists from Antarctic ice shelves were also identified including Amoebozoa, Rhizaria and Labyrinthulea. Comparison of 16S and 18S rRNA gene communities showed that the Eukaryotes had lower richness and greater similarity between ponds in comparison with Bacteria and Archaea communities on the McMurdo Ice shelf. While there was a weak correlation between community dissimilarity and geographic distance, the congruity of microbial assemblages within ponds, especially for Bacteria and Archaea, implies strong habitat filtering in ice shelf meltwater pond ecosystems, especially due to salinity. These findings help to understand processes that are important in sustaining biodiversity and the impact of climate change on ice-based aquatic habitats in Antarctica.
Collapse
|
10
|
Cornet L, Magain N, Baurain D, Lutzoni F. Exploring syntenic conservation across genomes for phylogenetic studies of organisms subjected to horizontal gene transfers: A case study with Cyanobacteria and cyanolichens. Mol Phylogenet Evol 2021; 162:107100. [PMID: 33592234 DOI: 10.1016/j.ympev.2021.107100] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 01/22/2021] [Accepted: 02/01/2021] [Indexed: 11/16/2022]
Abstract
Understanding the evolutionary history of symbiotic Cyanobacteria at a fine scale is essential to unveil patterns of associations with their hosts and factors driving their spatiotemporal interactions. As for bacteria in general, Horizontal Gene Transfers (HGT) are expected to be rampant throughout their evolution, which justified the use of single-locus phylogenies in macroevolutionary studies of these photoautotrophic bacteria. Genomic approaches have greatly increased the amount of molecular data available, but the selection of orthologous, congruent genes that are more likely to reflect bacterial macroevolutionary histories remains problematic. In this study, we developed a synteny-based approach and searched for Collinear Orthologous Regions (COR), under the assumption that genes that are present in the same order and orientation across a wide monophyletic clade are less likely to have undergone HGT. We searched sixteen reference Nostocales genomes and identified 99 genes, part of 28 COR comprising three to eight genes each. We then developed a bioinformatic pipeline, designed to minimize inter-genome contamination and processed twelve Nostoc-associated lichen metagenomes. This reduced our original dataset to 90 genes representing 25 COR, which were used to infer phylogenetic relationships within Nostocales and among lichenized Cyanobacteria. This dataset was narrowed down further to 71 genes representing 22 COR by selecting only genes part of one (largest) operon per COR. We found a relatively high level of congruence among trees derived from the 90-gene dataset, but congruence was only slightly higher among genes within a COR compared to genes across COR. However, topological congruence was significantly higher among the 71 genes part of one operon per COR. Nostocales phylogenies resulting from concatenation and species tree approaches based on the 90- and 71-gene datasets were highly congruent, but the most highly supported result was obtained when using synteny, collinearity, and operon information (i.e., 71-gene dataset) as gene selection criteria, which outperformed larger datasets with more genes.
Collapse
Affiliation(s)
- Luc Cornet
- InBioS - PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
| | - Nicolas Magain
- Department of Biology, Duke University, Durham, NC, USA; Evolution and Conservation Biology, InBioS, University of Liège, Liège, Belgium
| | - Denis Baurain
- InBioS - PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium.
| | | |
Collapse
|
11
|
Vallota-Eastman A, Arrington EC, Meeken S, Roux S, Dasari K, Rosen S, Miller JF, Valentine DL, Paul BG. Role of diversity-generating retroelements for regulatory pathway tuning in cyanobacteria. BMC Genomics 2020; 21:664. [PMID: 32977771 PMCID: PMC7517822 DOI: 10.1186/s12864-020-07052-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/03/2020] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Cyanobacteria maintain extensive repertoires of regulatory genes that are vital for adaptation to environmental stress. Some cyanobacterial genomes have been noted to encode diversity-generating retroelements (DGRs), which promote protein hypervariation through localized retrohoming and codon rewriting in target genes. Past research has shown DGRs to mainly diversify proteins involved in cell-cell attachment or viral-host attachment within viral, bacterial, and archaeal lineages. However, these elements may be critical in driving variation for proteins involved in other core cellular processes. RESULTS Members of 31 cyanobacterial genera encode at least one DGR, and together, their retroelements form a monophyletic clade of closely-related reverse transcriptases. This class of retroelements diversifies target proteins with unique domain architectures: modular ligand-binding domains often paired with a second domain that is linked to signal response or regulation. Comparative analysis indicates recent intragenomic duplication of DGR targets as paralogs, but also apparent intergenomic exchange of DGR components. The prevalence of DGRs and the paralogs of their targets is disproportionately high among colonial and filamentous strains of cyanobacteria. CONCLUSION We find that colonial and filamentous cyanobacteria have recruited DGRs to optimize a ligand-binding module for apparent function in signal response or regulation. These represent a unique class of hypervariable proteins, which might offer cyanobacteria a form of plasticity to adapt to environmental stress. This analysis supports the hypothesis that DGR-driven mutation modulates signaling and regulatory networks in cyanobacteria, suggestive of a new framework for the utility of localized genetic hypervariation.
Collapse
Affiliation(s)
- Alec Vallota-Eastman
- Interdepartmental Graduate Program for Marine Science, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Eleanor C Arrington
- Interdepartmental Graduate Program for Marine Science, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Siobhan Meeken
- Josephine Bay Paul Center, Marine Biological Laboratory, 7 MBL St, Woods Hole, MA, 02543, USA
| | - Simon Roux
- DOE Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Krishna Dasari
- Research Mentorship Program (RMP), University of California, Santa Barbara, CA, 93106, USA
| | - Sydney Rosen
- Research Mentorship Program (RMP), University of California, Santa Barbara, CA, 93106, USA
| | - Jeff F Miller
- Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, 90095, USA
- California NanoSystems Institute, University of California, Los Angeles, CA, 90095, USA
| | - David L Valentine
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
- Department of Earth Science, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Blair G Paul
- Josephine Bay Paul Center, Marine Biological Laboratory, 7 MBL St, Woods Hole, MA, 02543, USA.
| |
Collapse
|
12
|
Cervantes-Rivera R, Puhar A. Whole-genome Identification of Transcriptional Start Sites by Differential RNA-seq in Bacteria. Bio Protoc 2020; 10:e3757. [PMID: 33659416 PMCID: PMC7842792 DOI: 10.21769/bioprotoc.3757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/25/2020] [Accepted: 07/23/2020] [Indexed: 11/02/2022] Open
Abstract
Gene transcription in bacteria often starts some nucleotides upstream of the start codon. Identifying the specific Transcriptional Start Site (TSS) is essential for genetic manipulation, as in many cases upstream of the start codon there are sequence elements that are involved in gene expression regulation. Taken into account the classical gene structure, we are able to identify two kinds of transcriptional start site: primary and secondary. A primary transcriptional start site is located some nucleotides upstream of the translational start site, while a secondary transcriptional start site is located within the gene encoding sequence. Here, we present a step by step protocol for genome-wide transcriptional start sites determination by differential RNA-sequencing (dRNA-seq) using the enteric pathogen Shigella flexneri serotype 5a strain M90T as model. However, this method can be employed in any other bacterial species of choice. In the first steps, total RNA is purified from bacterial cultures using the hot phenol method. Ribosomal RNA (rRNA) is specifically depleted via hybridization probes using a commercial kit. A 5'-monophosphate-dependent exonuclease (TEX)-treated RNA library enriched in primary transcripts is then prepared for comparison with a library that has not undergone TEX-treatment, followed by ligation of an RNA linker adaptor of known sequence allowing the determination of TSS with single nucleotide precision. Finally, the RNA is processed for Illumina sequencing library preparation and sequenced as purchased service. TSS are identified by in-house bioinformatic analysis. Our protocol is cost-effective as it minimizes the use of commercial kits and employs freely available software.
Collapse
Affiliation(s)
- Ramón Cervantes-Rivera
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, 90 187 Umeå, Sweden
- Department of Molecular Biology, Umeå University, 90 187 Umeå, Sweden
| | - Andrea Puhar
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, 90 187 Umeå, Sweden
- Department of Molecular Biology, Umeå University, 90 187 Umeå, Sweden
| |
Collapse
|
13
|
Álvarez-Escribano I, Brenes-Álvarez M, Olmedo-Verd E, Georg J, Hess WR, Vioque A, Muro-Pastor AM. NsiR3, a nitrogen stress-inducible small RNA, regulates proline oxidase expression in the cyanobacterium Nostoc sp. PCC 7120. FEBS J 2020; 288:1614-1629. [PMID: 32799414 DOI: 10.1111/febs.15516] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/17/2020] [Accepted: 08/10/2020] [Indexed: 11/30/2022]
Abstract
NsiR3 (nitrogen stress-inducible RNA 3) is a small noncoding RNA strongly conserved in heterocyst-forming cyanobacteria. In Nostoc sp. PCC 7120, transcription of NsiR3 is induced by nitrogen starvation and depends on the global nitrogen regulator NtcA. A conserved NtcA-binding site is centered around position -42.5 with respect to the transcription start site of NsiR3 homologs, and NtcA binds in vitro to a DNA fragment containing this sequence. In the absence of combined nitrogen, NsiR3 expression is induced in all cells along the Nostoc filament but much more strongly in heterocysts, differentiated cells devoted to nitrogen fixation. Co-expression analysis of transcriptomic data obtained from microarrays hybridized with RNA obtained from Nostoc wild-type or mutant strains grown in the presence of ammonium or in the absence of combined nitrogen revealed that the expression profile of gene putA (proline oxidase) correlates negatively with that of NsiR3. Using a heterologous system in Escherichia coli, we show that NsiR3 binds to the 5'-UTR of putA mRNA, resulting in reduced expression of a reporter gene. Overexpression of NsiR3 in Nostoc resulted in strong reduction of putA mRNA accumulation, further supporting the negative regulation of putA by NsiR3. The higher expression of NsiR3 in heterocysts versus vegetative cells of the N2 -fixing filament could contribute to the previously described absence of putA mRNA and of the catabolic pathway to produce glutamate from arginine via proline specifically in heterocysts. Post-transcriptional regulation by NsiR3 represents an indirect NtcA-operated regulatory mechanism of putA expression. DATABASE: Microarray data are available in GEO database under accession numbers GSE120377 and GSE150191.
Collapse
Affiliation(s)
- Isidro Álvarez-Escribano
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Sevilla, Spain
| | - Manuel Brenes-Álvarez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Sevilla, Spain
| | - Elvira Olmedo-Verd
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Sevilla, Spain
| | - Jens Georg
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Agustín Vioque
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Sevilla, Spain
| | - Alicia M Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Sevilla, Spain
| |
Collapse
|
14
|
Transcriptome Analysis Reveals IsiA-Regulatory Mechanisms Underlying Iron Depletion and Oxidative-Stress Acclimation in Synechocystis sp. Strain PCC 6803. Appl Environ Microbiol 2020; 86:AEM.00517-20. [PMID: 32332138 DOI: 10.1128/aem.00517-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/19/2020] [Indexed: 12/22/2022] Open
Abstract
Microorganisms in nature are commonly exposed to various stresses in parallel. The isiA gene encodes an iron stress-induced chlorophyll-binding protein which is significantly induced under iron starvation and oxidative stress. Acclimation of oxidative stress and iron deficiency was investigated using a regulatory mutant of the Synechocystis sp. strain PCC 6803. In this study, the ΔisiA mutant grew more slowly in oxidative-stress and iron depletion conditions compared to the wild-type (WT) counterpart under the same conditions. Thus, we performed transcriptome sequencing (RNA-seq) analysis of the WT strain and the ΔisiA mutant under double-stress conditions to obtain a comprehensive view of isiA-regulated genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed significant differences between the WT strain and ΔisiA mutant, mainly related to photosynthesis and the iron-sulfur cluster. The deletion of isiA affects the expression of various genes that are involved in cellular processes and structures, such as photosynthesis, phycobilisome, and the proton-transporting ATPase complex. Weighted gene coexpression network analysis (WGCNA) demonstrated three functional modules in which the turquoise module was negatively correlated with superoxide dismutase (SOD) activity. Coexpression network analysis identified several hub genes of each module. Cotranscriptional PCR and reads coverage using the Integrative Genomics Viewer demonstrated that isiA, isiB, isiC, ssl0461, and dfp belonged to the isi operon. Three sRNAs related to oxidative stress were identified. This study enriches our knowledge of IsiA-regulatory mechanisms under iron deficiency and oxidative stress.IMPORTANCE This study analyzed the impact of isiA deletion on the transcriptomic profile of Synechocystis The isiA gene encodes an iron stress-induced chlorophyll-binding protein, which is significantly induced under iron starvation. The deletion of isiA affects the expression of various genes that are involved in photosynthesis and ABC transporters. WGCNA revealed three functional modules in which the blue module was correlated with oxidative stress. We further demonstrated that the isi operon contained the following five genes: isiA, isiB, isiC, ssl0461, and dfp by cotranscriptional PCR. Three sRNAs were identified that were related to oxidative stress. This study enhances our knowledge of IsiA-regulatory mechanisms under iron deficiency and oxidative stress.
Collapse
|
15
|
Popin RV, Delbaje E, de Abreu VAC, Rigonato J, Dörr FA, Pinto E, Sivonen K, Fiore MF. Genomic and Metabolomic Analyses of Natural Products in Nodularia spumigena Isolated from a Shrimp Culture Pond. Toxins (Basel) 2020; 12:toxins12030141. [PMID: 32106513 PMCID: PMC7150779 DOI: 10.3390/toxins12030141] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/13/2020] [Accepted: 02/21/2020] [Indexed: 11/16/2022] Open
Abstract
The bloom-forming cyanobacterium Nodularia spumigena CENA596 encodes the biosynthetic gene clusters (BGCs) of the known natural products nodularins, spumigins, anabaenopeptins/namalides, aeruginosins, mycosporin-like amino acids, and scytonemin, along with the terpenoid geosmin. Targeted metabolomics confirmed the production of these metabolic compounds, except for the alkaloid scytonemin. Genome mining of N. spumigena CENA596 and its three closely related Nodularia strains—two planktonic strains from the Baltic Sea and one benthic strain from Japanese marine sediment—revealed that the number of BGCs in planktonic strains was higher than in benthic one. Geosmin—a volatile compound with unpleasant taste and odor—was unique to the Brazilian strain CENA596. Automatic annotation of the genomes using subsystems technology revealed a related number of coding sequences and functional roles. Orthologs from the Nodularia genomes are involved in the primary and secondary metabolisms. Phylogenomic analysis of N. spumigena CENA596 based on 120 conserved protein sequences positioned this strain close to the Baltic Nodularia. Phylogeny of the 16S rRNA genes separated the Brazilian CENA596 strain from those of the Baltic Sea, despite their high sequence identities (99% identity, 100% coverage). The comparative analysis among planktic Nodularia strains showed that their genomes were considerably similar despite their geographically distant origin.
Collapse
Affiliation(s)
- Rafael Vicentini Popin
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba 13400-970, São Paulo, Brazil; (R.V.P.); (E.D.); (V.A.C.d.A.); (J.R.); (E.P.)
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland;
| | - Endrews Delbaje
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba 13400-970, São Paulo, Brazil; (R.V.P.); (E.D.); (V.A.C.d.A.); (J.R.); (E.P.)
| | - Vinicius Augusto Carvalho de Abreu
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba 13400-970, São Paulo, Brazil; (R.V.P.); (E.D.); (V.A.C.d.A.); (J.R.); (E.P.)
- Institute of Exact and Natural Sciences, Federal University of Pará, Rua Augusto Corrêa 1, Belém 66075-10, Pará, Brazil
| | - Janaina Rigonato
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba 13400-970, São Paulo, Brazil; (R.V.P.); (E.D.); (V.A.C.d.A.); (J.R.); (E.P.)
| | - Felipe Augusto Dörr
- Faculty of Pharmaceutical Sciences, University of São Paulo, Avenida Professor Lineu Prestes, São Paulo 05508-000, São Paulo, Brazil;
| | - Ernani Pinto
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba 13400-970, São Paulo, Brazil; (R.V.P.); (E.D.); (V.A.C.d.A.); (J.R.); (E.P.)
- Faculty of Pharmaceutical Sciences, University of São Paulo, Avenida Professor Lineu Prestes, São Paulo 05508-000, São Paulo, Brazil;
| | - Kaarina Sivonen
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland;
| | - Marli Fatima Fiore
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba 13400-970, São Paulo, Brazil; (R.V.P.); (E.D.); (V.A.C.d.A.); (J.R.); (E.P.)
- Correspondence:
| |
Collapse
|
16
|
Hennon GMM, Dyhrman ST. Progress and promise of omics for predicting the impacts of climate change on harmful algal blooms. HARMFUL ALGAE 2020; 91:101587. [PMID: 32057337 DOI: 10.1016/j.hal.2019.03.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 03/10/2019] [Indexed: 06/10/2023]
Abstract
Climate change is predicted to increase the severity and prevalence of harmful algal blooms (HABs). In the past twenty years, omics techniques such as genomics, transcriptomics, proteomics and metabolomics have transformed that data landscape of many fields including the study of HABs. Advances in technology have facilitated the creation of many publicly available omics datasets that are complementary and shed new light on the mechanisms of HAB formation and toxin production. Genomics have been used to reveal differences in toxicity and nutritional requirements, while transcriptomics and proteomics have been used to explore HAB species responses to environmental stressors, and metabolomics can reveal mechanisms of allelopathy and toxicity. In this review, we explore how omics data may be leveraged to improve predictions of how climate change will impact HAB dynamics. We also highlight important gaps in our knowledge of HAB prediction, which include swimming behaviors, microbial interactions and evolution that can be addressed by future studies with omics tools. Lastly, we discuss approaches to incorporate current omics datasets into predictive numerical models that may enhance HAB prediction in a changing world. With the ever-increasing omics databases, leveraging these data for understanding climate-driven HAB dynamics will be increasingly powerful.
Collapse
Affiliation(s)
- Gwenn M M Hennon
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States; College of Fisheries and Ocean Sciences University of Alaska Fairbanks Fairbanks, AK, United States
| | - Sonya T Dyhrman
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States; Department of Earth and Environmental Sciences, Columbia University, New York, NY, United States.
| |
Collapse
|
17
|
Muro-Pastor AM, Hess WR. Regulatory RNA at the crossroads of carbon and nitrogen metabolism in photosynthetic cyanobacteria. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1863:194477. [PMID: 31884117 DOI: 10.1016/j.bbagrm.2019.194477] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 12/16/2019] [Accepted: 12/22/2019] [Indexed: 12/17/2022]
Abstract
Cyanobacteria are photosynthetic bacteria that populate widely different habitats. Accordingly, cyanobacteria exhibit a wide spectrum of lifestyles, physiologies, and morphologies and possess genome sizes and gene numbers which may vary by up to a factor of ten within the phylum. Consequently, large differences exist between individual species in the size and complexity of their regulatory networks. Several non-coding RNAs have been identified that play crucial roles in the acclimation responses of cyanobacteria to changes in the environment. Some of these regulatory RNAs are conserved throughout the cyanobacterial phylum, while others exist only in a few taxa. Here we give an overview on characterized regulatory RNAs in cyanobacteria, with a focus on regulators of photosynthesis, carbon and nitrogen metabolism. However, chances are high that these regulators represent just the tip of the iceberg.
Collapse
Affiliation(s)
- Alicia M Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, E-41092 Sevilla, Spain
| | - Wolfgang R Hess
- University of Freiburg, Faculty of Biology, Genetics and Experimental Bioinformatics, Schänzlestr. 1, D-79104 Freiburg, Germany; University of Freiburg, Freiburg Institute for Advanced Studies, Albertstr. 19, D-79104 Freiburg, Germany.
| |
Collapse
|
18
|
Olmedo-Verd E, Brenes-Álvarez M, Vioque A, Muro-Pastor AM. A Heterocyst-Specific Antisense RNA Contributes to Metabolic Reprogramming in Nostoc sp. PCC 7120. PLANT & CELL PHYSIOLOGY 2019; 60:1646-1655. [PMID: 31093664 DOI: 10.1093/pcp/pcz087] [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] [Received: 03/26/2019] [Accepted: 04/28/2019] [Indexed: 06/09/2023]
Abstract
Upon nitrogen deficiency, some filamentous cyanobacteria differentiate specialized cells, called heterocysts, devoted to N2 fixation. Heterocysts appear regularly spaced along the filaments and exhibit structural and metabolic adaptations, such as loss of photosynthetic CO2 fixation or increased respiration, to provide a proper microaerobic environment for its specialized function. Heterocyst development is under transcriptional control of the global nitrogen regulator NtcA and the specific regulator HetR. Transcription of a large number of genes is induced or repressed upon nitrogen deficiency specifically in cells undergoing differentiation. In recent years, the HetR regulon has been described to include heterocyst-specific trans-acting small RNAs and antisense RNAs (asRNAs), suggesting that there is an additional layer of post-transcriptional regulation involved in heterocyst development. Here, we characterize in the cyanobacterium Nostoc (Anabaena) sp. PCC 7120 an asRNA, that we call as_glpX, transcribed within the glpX gene encoding the Calvin cycle bifunctional enzyme sedoheptulose-1,7-bisphosphatase/fructose-1,6-bisphosphatase (SBPase). Transcription of as_glpX is restricted to heterocysts and is induced very early during the process of differentiation. Expression of as_glpX RNA promotes the cleavage of the glpX mRNA by RNase III, resulting in a reduced amount of SBPase. Therefore, the early expression of this asRNA could contribute to the quick shut-down of CO2 fixation in those cells in the filament that are undergoing differentiation into heterocysts. In summary, as_glpX is the first naturally occurring asRNA shown to rapidly and dynamically regulate metabolic transformation in Nostoc heterocysts. The use of antisense transcripts to manipulate gene expression specifically in heterocysts could became a useful tool for metabolic engineering in cyanobacteria.
Collapse
Affiliation(s)
- Elvira Olmedo-Verd
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and CSIC, Américo Vespucio 49, 41092 Sevilla, Spain
| | - Manuel Brenes-Álvarez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and CSIC, Américo Vespucio 49, 41092 Sevilla, Spain
| | - Agustín Vioque
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and CSIC, Américo Vespucio 49, 41092 Sevilla, Spain
| | - Alicia M Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and CSIC, Américo Vespucio 49, 41092 Sevilla, Spain
| |
Collapse
|
19
|
Phosphate availability affects fixed nitrogen transfer from diazotrophs to their epibionts. ISME JOURNAL 2019; 13:2701-2713. [PMID: 31249392 PMCID: PMC6794295 DOI: 10.1038/s41396-019-0453-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 03/20/2019] [Accepted: 05/17/2019] [Indexed: 12/02/2022]
Abstract
Dinitrogen (N2) fixation is a major source of external nitrogen (N) to aquatic ecosystems and therefore exerts control over productivity. Studies have shown that N2 -fixers release freshly fixed N into the environment, but the causes for this N release are largely unclear. Here, we show that the availability of phosphate can directly affect the transfer of freshly fixed N to epibionts in filamentous, diazotrophic cyanobacteria. Stable-isotope incubations coupled to single-cell analyses showed that <1% and ~15% of freshly fixed N was transferred to epibionts of Aphanizomenon and Nodularia, respectively, at phosphate scarcity during a summer bloom in the Baltic Sea. When phosphate was added, the transfer of freshly fixed N to epibionts dropped to about half for Nodularia, whereas the release from Aphanizomenon increased slightly. At the same time, the growth rate of Nodularia roughly doubled, indicating that less freshly fixed N was released and was used for biomass production instead. Phosphate scarcity and the resulting release of freshly fixed N could explain the heavy colonization of Nodularia filaments by microorganisms during summer blooms. As such, the availability of phosphate may directly affect the partitioning of fixed N2 in colonies of diazotrophic cyanobacteria and may impact the interactions with their microbiome.
Collapse
|
20
|
Brenes‐Álvarez M, Mitschke J, Olmedo‐Verd E, Georg J, Hess WR, Vioque A, Muro‐Pastor AM. Elements of the heterocyst‐specific transcriptome unravelled by co‐expression analysis inNostocsp. PCC 7120. Environ Microbiol 2019; 21:2544-2558. [DOI: 10.1111/1462-2920.14647] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/06/2019] [Accepted: 05/01/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Manuel Brenes‐Álvarez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla E‐41092 Sevilla Spain
| | - Jan Mitschke
- Genetics and Experimental Bioinformatics, Faculty of BiologyUniversity of Freiburg D‐79104 Freiburg Germany
| | - Elvira Olmedo‐Verd
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla E‐41092 Sevilla Spain
| | - Jens Georg
- Genetics and Experimental Bioinformatics, Faculty of BiologyUniversity of Freiburg D‐79104 Freiburg Germany
| | - Wolfgang R. Hess
- Genetics and Experimental Bioinformatics, Faculty of BiologyUniversity of Freiburg D‐79104 Freiburg Germany
- Freiburg Institute for Advanced Studies, University of Freiburg D‐79104 Freiburg Germany
| | - Agustín Vioque
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla E‐41092 Sevilla Spain
| | - Alicia M. Muro‐Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla E‐41092 Sevilla Spain
| |
Collapse
|
21
|
Schoffelen NJ, Mohr W, Ferdelman TG, Littmann S, Duerschlag J, Zubkov MV, Ploug H, Kuypers MMM. Single-cell imaging of phosphorus uptake shows that key harmful algae rely on different phosphorus sources for growth. Sci Rep 2018; 8:17182. [PMID: 30464246 PMCID: PMC6249326 DOI: 10.1038/s41598-018-35310-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 11/02/2018] [Indexed: 12/04/2022] Open
Abstract
Single-cell measurements of biochemical processes have advanced our understanding of cellular physiology in individual microbes and microbial populations. Due to methodological limitations, little is known about single-cell phosphorus (P) uptake and its importance for microbial growth within mixed field populations. Here, we developed a nanometer-scale secondary ion mass spectrometry (nanoSIMS)-based approach to quantify single-cell P uptake in combination with cellular CO2 and N2 fixation. Applying this approach during a harmful algal bloom (HAB), we found that the toxin-producer Nodularia almost exclusively used phosphate for growth at very low phosphate concentrations in the Baltic Sea. In contrast, the non-toxic Aphanizomenon acquired only 15% of its cellular P-demand from phosphate and ~85% from organic P. When phosphate concentrations were raised, Nodularia thrived indicating that this toxin-producer directly benefits from phosphate inputs. The phosphate availability in the Baltic Sea is projected to rise and therefore might foster more frequent and intense Nodularia blooms with a concomitant rise in the overall toxicity of HABs in the Baltic Sea. With a projected increase in HABs worldwide, the capability to use organic P may be a critical factor that not only determines the microbial community structure, but the overall harmfulness and associated costs of algal blooms.
Collapse
Affiliation(s)
- Niels J Schoffelen
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Wiebke Mohr
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.
| | - Timothy G Ferdelman
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Sten Littmann
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Julia Duerschlag
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Mikhail V Zubkov
- Ocean Biogeochemistry and Ecosystems, National Oceanography Centre Southampton, European Way, Southampton, SO14 3ZH, United Kingdom.,Scottish Association for Marine Science, Oban, Argyll PA37 1QA, Scotland, United Kingdom
| | - Helle Ploug
- Department of Marine Sciences, University of Gothenburg, Carl Skottsbergs Gata 22B, 41319, Gothenburg, Sweden
| | - Marcel M M Kuypers
- Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| |
Collapse
|
22
|
Elhai J, Khudyakov I. Ancient association of cyanobacterial multicellularity with the regulator HetR and an RGSGR pentapeptide-containing protein (PatX). Mol Microbiol 2018; 110:931-954. [PMID: 29885033 DOI: 10.1111/mmi.14003] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2018] [Indexed: 12/14/2022]
Abstract
One simple model to explain biological pattern postulates the existence of a stationary regulator of differentiation that positively affects its own expression, coupled with a diffusible suppressor of differentiation that inhibits the regulator's expression. The first has been identified in the filamentous, heterocyst-forming cyanobacterium, Anabaena PCC 7120 as the transcriptional regulator, HetR and the second as the small protein, PatS, which contains a critical RGSGR motif that binds to HetR. HetR is present in almost all filamentous cyanobacteria, but only a subset of heterocyst-forming strains carry proteins similar to PatS. We identified a third protein, PatX that also carries the RGSGR motif and is coextensive with HetR. Amino acid sequences of PatX contain two conserved regions: the RGSGR motif and a hydrophobic N-terminus. Within 69 nt upstream from all instances of the gene is a DIF1 motif correlated in Anabaena with promoter induction in developing heterocysts, preceded in heterocyst-forming strains by an apparent NtcA-binding site, associated with regulation by nitrogen-status. Consistent with a role in the simple model, PatX is expressed dependent on HetR and acts to inhibit differentiation. The acquisition of the PatX/HetR pair preceded the appearance of both PatS and heterocysts, dating back to the beginnings of multicellularity.
Collapse
Affiliation(s)
- Jeff Elhai
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Ivan Khudyakov
- All-Russia Research Institute for Agricultural Microbiology, Saint-Petersburg, 196608, Russia
| |
Collapse
|
23
|
Abstract
ABSTRACT
Although bacterial genomes are usually densely protein-coding, genome-wide mapping approaches of transcriptional start sites revealed that a significant fraction of the identified promoters drive the transcription of noncoding RNAs. These can be
trans
-acting RNAs, mainly originating from intergenic regions and, in many studied examples, possessing regulatory functions. However, a significant fraction of these noncoding RNAs consist of natural antisense transcripts (asRNAs), which overlap other transcriptional units. Naturally occurring asRNAs were first observed to play a role in bacterial plasmid replication and in bacteriophage λ more than 30 years ago. Today’s view is that asRNAs abound in all three domains of life. There are several examples of asRNAs in bacteria with clearly defined functions. Nevertheless, many asRNAs appear to result from pervasive initiation of transcription, and some data point toward global functions of such widespread transcriptional activity, explaining why the search for a specific regulatory role is sometimes futile. In this review, we give an overview about the occurrence of antisense transcription in bacteria, highlight particular examples of functionally characterized asRNAs, and discuss recent evidence pointing at global relevance in RNA processing and transcription-coupled DNA repair.
Collapse
|
24
|
Driscoll CB, Meyer KA, Šulčius S, Brown NM, Dick GJ, Cao H, Gasiūnas G, Timinskas A, Yin Y, Landry ZC, Otten TG, Davis TW, Watson SB, Dreher TW. A closely-related clade of globally distributed bloom-forming cyanobacteria within the Nostocales. HARMFUL ALGAE 2018; 77:93-107. [PMID: 30005805 DOI: 10.1016/j.hal.2018.05.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/18/2018] [Accepted: 05/24/2018] [Indexed: 06/08/2023]
Abstract
In order to better understand the relationships among current Nostocales cyanobacterial blooms, eight genomes were sequenced from cultured isolates or from environmental metagenomes of recent planktonic Nostocales blooms. Phylogenomic analysis of publicly available sequences placed the new genomes among a group of 15 genomes from four continents in a distinct ADA clade (Anabaena/Dolichospermum/Aphanizomenon) within the Nostocales. This clade contains four species-level groups, two of which include members with both Anabaena-like and Aphanizomenon flos-aquae-like morphology. The genomes contain many repetitive genetic elements and a sizable pangenome, in which ABC-type transporters are highly represented. Alongside common core genes for photosynthesis, the differentiation of N2-fixing heterocysts, and the uptake and incorporation of the major nutrients P, N and S, we identified several gene pathways in the pangenome that may contribute to niche partitioning. Genes for problematic secondary metabolites-cyanotoxins and taste-and-odor compounds-were sporadically present, as were other polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) gene clusters. By contrast, genes predicted to encode the ribosomally generated bacteriocin peptides were found in all genomes.
Collapse
Affiliation(s)
- Connor B Driscoll
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA
| | - Kevin A Meyer
- Department of Earth & Environmental Sciences, University of Michigan, Ann Arbor, MI 48109-1005, USA; Cooperative Institute for Great Lakes Research (CIGLR), University of Michigan, Ann Arbor, MI 48109-1005, USA
| | - Sigitas Šulčius
- Laboratory of Algology and Microbial Ecology, Akademijos Str. 2, LT-08412, Vilnius, Lithuania
| | - Nathan M Brown
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA
| | - Gregory J Dick
- Department of Earth & Environmental Sciences, University of Michigan, Ann Arbor, MI 48109-1005, USA
| | - Huansheng Cao
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, 427 E Tyler Mall, Tempe, AZ 85287, USA
| | - Giedrius Gasiūnas
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, LT-10257, Vilnius, Lithuania
| | - Albertas Timinskas
- Department of Bioinformatics, Institute of Biotechnology, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania
| | - Yanbin Yin
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL, USA
| | - Zachary C Landry
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA
| | - Timothy G Otten
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA
| | - Timothy W Davis
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43402, USA
| | - Susan B Watson
- Environment and Climate Change Canada, Canada Centre for Inland Waters, Burlington, ON L7S 1A1, Canada
| | - Theo W Dreher
- Department of Microbiology, Oregon State University, 226 Nash Hall, Corvallis, OR, 97331, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA.
| |
Collapse
|
25
|
Teikari JE, Fewer DP, Shrestha R, Hou S, Leikoski N, Mäkelä M, Simojoki A, Hess WR, Sivonen K. Strains of the toxic and bloom-forming Nodularia spumigena (cyanobacteria) can degrade methylphosphonate and release methane. THE ISME JOURNAL 2018; 12:1619-1630. [PMID: 29445131 PMCID: PMC5955973 DOI: 10.1038/s41396-018-0056-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 11/10/2022]
Abstract
Nodularia spumigena is a nitrogen-fixing cyanobacterium that forms toxic blooms in the Baltic Sea each summer and the availability of phosphorous is an important factor limiting the formation of these blooms. Bioinformatic analysis identified a phosphonate degrading (phn) gene cluster in the genome of N. spumigena suggesting that this bacterium may use phosphonates as a phosphorus source. Our results show that strains of N. spumigena could grow in medium containing methylphosphonic acid (MPn) as the sole source of phosphorous and released methane when growing in medium containing MPn. We analyzed the total transcriptomes of N. spumigena UHCC 0039 grown using MPn and compared them with cultures growing in Pi-replete medium. The phnJ, phosphonate lyase gene, was upregulated when MPn was the sole source of phosphorus, suggesting that the expression of this gene could be used to indicate the presence of bioavailable phosphonates. Otherwise, growth on MPn resulted in only a minor reconstruction of the transcriptome and enabled good growth. However, N. spumigena strains were not able to utilize any of the anthropogenic phosphonates tested. The phosphonate utilizing pathway may offer N. spumigena a competitive advantage in the Pi-limited cyanobacterial blooms of the Baltic Sea.
Collapse
Affiliation(s)
- Jonna E Teikari
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, FI-00014, Finland
| | - David P Fewer
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, FI-00014, Finland
| | - Rashmi Shrestha
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, FI-00014, Finland
| | - Shengwei Hou
- Genetics and Experimental Bioinformatics, Institute of Biology III, University Freiburg, Schänzlestraße 1, Freiburg, D-79104, Germany
| | - Niina Leikoski
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, FI-00014, Finland
| | - Minna Mäkelä
- Department of Agricultural Sciences, University of Helsinki, Viikinkaari 9, Helsinki, FI-00014, Finland
| | - Asko Simojoki
- Department of Agricultural Sciences, University of Helsinki, Viikinkaari 9, Helsinki, FI-00014, Finland
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Institute of Biology III, University Freiburg, Schänzlestraße 1, Freiburg, D-79104, Germany
| | - Kaarina Sivonen
- Department of Microbiology, University of Helsinki, Viikinkaari 9, Helsinki, FI-00014, Finland.
| |
Collapse
|
26
|
Teikari JE, Hou S, Wahlsten M, Hess WR, Sivonen K. Comparative Genomics of the Baltic Sea Toxic Cyanobacteria Nodularia spumigena UHCC 0039 and Its Response to Varying Salinity. Front Microbiol 2018; 9:356. [PMID: 29568283 PMCID: PMC5853447 DOI: 10.3389/fmicb.2018.00356] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 02/14/2018] [Indexed: 11/13/2022] Open
Abstract
Salinity is an important abiotic factor controlling the distribution and abundance of Nodularia spumigena, the dominating diazotrophic and toxic phototroph, in the brackish water cyanobacterial blooms of the Baltic Sea. To expand the available genomic information for brackish water cyanobacteria, we sequenced the isolate Nodularia spumigena UHCC 0039 using an Illumina-SMRT hybrid sequencing approach, revealing a chromosome of 5,294,286 base pairs (bp) and a single plasmid of 92,326 bp. Comparative genomics in Nostocales showed pronounced genetic similarity among Nodularia spumigena strains evidencing their short evolutionary history. The studied Baltic Sea strains share similar sets of CRISPR-Cas cassettes and a higher number of insertion sequence (IS) elements compared to Nodularia spumigena CENA596 isolated from a shrimp production pond in Brazil. Nodularia spumigena UHCC 0039 proliferated similarly at three tested salinities, whereas the lack of salt inhibited its growth and triggered transcriptome remodeling, including the up-regulation of five sigma factors and the down-regulation of two other sigma factors, one of which is specific for strain UHCC 0039. Down-regulated genes additionally included a large genetic region for the synthesis of two yet unidentified natural products. Our results indicate a remarkable plasticity of the Nodularia salinity acclimation, and thus salinity strongly impacts the intensity and distribution of cyanobacterial blooms in the Baltic Sea.
Collapse
Affiliation(s)
- Jonna E Teikari
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Shengwei Hou
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - Matti Wahlsten
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Institute of Biology III, University of Freiburg, Freiburg, Germany.,Freiburg Institute for Advanced Studies, University of Freiburg, Freiburg, Germany
| | - Kaarina Sivonen
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| |
Collapse
|
27
|
Grand Challenges in Marine Biotechnology: Overview of Recent EU-Funded Projects. GRAND CHALLENGES IN MARINE BIOTECHNOLOGY 2018. [DOI: 10.1007/978-3-319-69075-9_11] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
28
|
Lott SC, Wolfien M, Riege K, Bagnacani A, Wolkenhauer O, Hoffmann S, Hess WR. Customized workflow development and data modularization concepts for RNA-Sequencing and metatranscriptome experiments. J Biotechnol 2017; 261:85-96. [DOI: 10.1016/j.jbiotec.2017.06.1203] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/22/2017] [Accepted: 06/26/2017] [Indexed: 12/14/2022]
|
29
|
Jokela J, Heinilä LMP, Shishido TK, Wahlsten M, Fewer DP, Fiore MF, Wang H, Haapaniemi E, Permi P, Sivonen K. Production of High Amounts of Hepatotoxin Nodularin and New Protease Inhibitors Pseudospumigins by the Brazilian Benthic Nostoc sp. CENA543. Front Microbiol 2017; 8:1963. [PMID: 29062311 PMCID: PMC5640712 DOI: 10.3389/fmicb.2017.01963] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 09/25/2017] [Indexed: 01/26/2023] Open
Abstract
Nostoc is a cyanobacterial genus, common in soils and a prolific producer of natural products. This research project aimed to explore and characterize Brazilian cyanobacteria for new bioactive compounds. Here we report the production of hepatotoxins and new protease inhibitors from benthic Nostoc sp. CENA543 isolated from a small, shallow, saline-alkaline lake in the Nhecolândia, Pantanal wetland area in Brazil. Nostoc sp. CENA543 produces exceptionally high amounts of nodularin-R. This is the first free-living Nostoc that produces nodularin at comparable levels as the toxic, bloom-forming, Nodularia spumigena. We also characterized pseudospumigins A-F, which are a novel family of linear tetrapeptides. Pseudospumigins are structurally related to linear tetrapeptide spumigins and aeruginosins both present in N. spumigena but differ in respect to their diagnostic amino acid, which is Ile/Leu/Val in pseudospumigins, Pro/mPro in spumigins, and Choi in aeruginosins. The pseudospumigin gene cluster is more similar to the spumigin biosynthetic gene cluster than the aeruginosin gene cluster. Pseudospumigin A inhibited trypsin (IC50 4.5 μM after 1 h) in a similar manner as spumigin E from N. spumigena but was almost two orders of magnitude less potent. This study identifies another location and environment where the hepatotoxic nodularin has the potential to cause the death of eukaryotic organisms.
Collapse
Affiliation(s)
- Jouni Jokela
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Lassi M P Heinilä
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Tânia K Shishido
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Matti Wahlsten
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - David P Fewer
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Marli F Fiore
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Hao Wang
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Esa Haapaniemi
- Department of Chemistry, University of Jyväskylä, Helsinki, Finland
| | - Perttu Permi
- Department of Chemistry, University of Jyväskylä, Helsinki, Finland.,Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Helsinki, Finland
| | - Kaarina Sivonen
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| |
Collapse
|
30
|
Kerfeld CA, Melnicki MR, Sutter M, Dominguez-Martin MA. Structure, function and evolution of the cyanobacterial orange carotenoid protein and its homologs. THE NEW PHYTOLOGIST 2017; 215:937-951. [PMID: 28675536 DOI: 10.1111/nph.14670] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/09/2017] [Indexed: 06/07/2023]
Abstract
Contents 937 I. 937 II. 938 III. 939 IV. 943 V. 947 VI. 948 948 References 949 SUMMARY: The orange carotenoid protein (OCP) is a water-soluble, photoactive protein involved in thermal dissipation of excess energy absorbed by the light-harvesting phycobilisomes (PBS) in cyanobacteria. The OCP is structurally and functionally modular, consisting of a sensor domain, an effector domain and a keto-carotenoid. On photoactivation, the OCP converts from a stable orange form, OCPO , to a red form, OCPR . Activation is accompanied by a translocation of the carotenoid deeper into the effector domain. The increasing availability of cyanobacterial genomes has enabled the identification of new OCP families (OCP1, OCP2, OCPX). The fluorescence recovery protein (FRP) detaches OCP1 from the PBS core, accelerating its back-conversion to OCPO ; by contrast, other OCP families are not regulated by FRP. N-terminal domain homologs, the helical carotenoid proteins (HCPs), have been found among diverse cyanobacteria, occurring as multiple paralogous groups, with two representatives exhibiting strong singlet oxygen (1 O2 ) quenching (HCP2, HCP3) and another capable of dissipating PBS excitation (HCP4). Crystal structures are presently available for OCP1 and HCP1, and models of other HCP subtypes can be readily produced as a result of strong sequence conservation, providing new insights into the determinants of carotenoid binding and 1 O2 quenching.
Collapse
Affiliation(s)
- Cheryl A Kerfeld
- 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
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Matthew R Melnicki
- 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
| | - 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
| | | |
Collapse
|
31
|
Lima ST, Alvarenga DO, Etchegaray A, Fewer DP, Jokela J, Varani AM, Sanz M, Dörr FA, Pinto E, Sivonen K, Fiore MF. Genetic Organization of Anabaenopeptin and Spumigin Biosynthetic Gene Clusters in the Cyanobacterium Sphaerospermopsis torques-reginae ITEP-024. ACS Chem Biol 2017; 12:769-778. [PMID: 28085246 DOI: 10.1021/acschembio.6b00948] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyanobacteria produce a broad range of natural products, many of which are potent protease inhibitors. Biosynthetic gene clusters encoding the production of novel protease inhibitors belonging to the spumigin and anabaenopeptin family of nonribosomal peptides were identified in the genome of the bloom-forming cyanobacterium Sphaerospermopsis torques-reginae ITEP-024. The genetic architecture and gene organization of both nonribosomal peptide biosynthetic clusters were compared in parallel with their chemical structure variations obtained by liquid chromatography (LC-MS/MS). The spumigin (spu) and anabaenopeptin (apt) gene clusters are colocated in the genomes of S. torques-reginae ITEP-024 and Nodularia spumigena CCY9414 and separated by a 12 kb region containing genes encoding a patatin-like phospholipase, l-homophenylalanine (l-Hph) biosynthetic enzymes, and four hypothetical proteins. hphABCD gene cluster encoding the production of l-Hph was linked to all eight apt gene clusters investigated here. We suggest that while the HphABCD enzymes are an integral part of the anabaenopeptin biosynthetic pathway, they provide substrates for the biosynthesis of both anabaenopeptins and spumigins. The organization of the spu and apt suggests a plausible model for the biosynthesis of the 4-(4-hydroxyphenyl)-2-acid (Hpoba) precursor of spumigin variants in S. torques-reginae ITEP-024 based on the acceptable substrates of HphABCD enzymes.
Collapse
Affiliation(s)
- Stella T. Lima
- University of São Paulo, Center for Nuclear
Energy in Agriculture, Piracicaba-SP, Brazil
| | - Danillo O. Alvarenga
- University of São Paulo, Center for Nuclear
Energy in Agriculture, Piracicaba-SP, Brazil
| | - Augusto Etchegaray
- Pontifical Catholic University of Campinas, Faculty
of Chemistry, Campinas-SP, Brazil
| | - David P. Fewer
- University of Helsinki, Department of Food and Environmental
Sciences, Division of Microbiology and Biotechnology, Helsinki, Finland
| | - Jouni Jokela
- University of Helsinki, Department of Food and Environmental
Sciences, Division of Microbiology and Biotechnology, Helsinki, Finland
| | - Alessandro M. Varani
- São Paulo State University, College of Agricultural
and Veterinary Sciences, Department of Technology, Jaboticabal-SP, Brazil
| | - Miriam Sanz
- University of São Paulo, School of Pharmaceutical
Sciences, São Paulo-SP, Brazil
| | - Felipe A. Dörr
- University of São Paulo, School of Pharmaceutical
Sciences, São Paulo-SP, Brazil
| | - Ernani Pinto
- University of São Paulo, School of Pharmaceutical
Sciences, São Paulo-SP, Brazil
| | - Kaarina Sivonen
- University of Helsinki, Department of Food and Environmental
Sciences, Division of Microbiology and Biotechnology, Helsinki, Finland
| | - Marli F. Fiore
- University of São Paulo, Center for Nuclear
Energy in Agriculture, Piracicaba-SP, Brazil
| |
Collapse
|
32
|
The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses. mSystems 2017; 2:mSystems00125-16. [PMID: 28217745 PMCID: PMC5309335 DOI: 10.1128/msystems.00125-16] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 12/27/2016] [Indexed: 11/20/2022] Open
Abstract
Inferred virus-host relationships, community structures of ubiquitous ecologically relevant groups, and identification of transcriptionally active populations have been achieved with our Baltic Sea study. Further, these data, highlighting the transcriptional activity of viruses, represent one of the more powerful uses of omics concerning ecosystem health. The use of omics-related data to assess ecosystem health holds great promise for rapid and relatively inexpensive determination of perturbations and risk, explicitly with regard to viral assemblages, as no single marker gene is suitable for widespread taxonomic coverage. Metagenomic and metatranscriptomic data were generated from size-fractionated samples from 11 sites within the Baltic Sea and adjacent marine waters of Kattegat and freshwater Lake Torneträsk in order to investigate the diversity, distribution, and transcriptional activity of virioplankton. Such a transect, spanning a salinity gradient from freshwater to the open sea, facilitated a broad genome-enabled investigation of natural as well as impacted aspects of Baltic Sea viral communities. Taxonomic signatures representative of phages within the widely distributed order Caudovirales were identified with enrichments in lesser-known families such as Podoviridae and Siphoviridae. The distribution of phage reported to infect diverse and ubiquitous heterotrophic bacteria (SAR11 clades) and cyanobacteria (Synechococcus sp.) displayed population-level shifts in diversity. Samples from higher-salinity conditions (>14 practical salinity units [PSU]) had increased abundances of viruses for picoeukaryotes, i.e., Ostreococcus. These data, combined with host diversity estimates, suggest viral modulation of diversity on the whole-community scale, as well as in specific prokaryotic and eukaryotic lineages. RNA libraries revealed single-stranded DNA (ssDNA) and RNA viral populations throughout the Baltic Sea, with ssDNA phage highly represented in Lake Torneträsk. Further, our data suggest relatively high transcriptional activity of fish viruses within diverse families known to have broad host ranges, such as Nodoviridae (RNA), Iridoviridae (DNA), and predicted zoonotic viruses that can cause ecological and economic damage as well as impact human health. IMPORTANCE Inferred virus-host relationships, community structures of ubiquitous ecologically relevant groups, and identification of transcriptionally active populations have been achieved with our Baltic Sea study. Further, these data, highlighting the transcriptional activity of viruses, represent one of the more powerful uses of omics concerning ecosystem health. The use of omics-related data to assess ecosystem health holds great promise for rapid and relatively inexpensive determination of perturbations and risk, explicitly with regard to viral assemblages, as no single marker gene is suitable for widespread taxonomic coverage.
Collapse
|
33
|
Colgan AM, Cameron AD, Kröger C. If it transcribes, we can sequence it: mining the complexities of host-pathogen-environment interactions using RNA-seq. Curr Opin Microbiol 2017; 36:37-46. [PMID: 28189909 DOI: 10.1016/j.mib.2017.01.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 01/23/2017] [Accepted: 01/24/2017] [Indexed: 02/07/2023]
Abstract
Host-pathogen interactions are exceedingly complex because they involve multiple host tissues, often occur in the context of normal microflora, and can span diverse microenvironments. Although decades of gene expression studies have provided detailed insights into infection processes, technical challenges have restricted experiments to single pathogenic species or host tissues. RNA-sequencing (RNA-seq) has revolutionized the study of gene expression because in addition to quantifying transcriptional output, it allows detection and characterization of all transcripts in a genome. Here, we review how refined approaches to RNA-seq are used to map the transcriptional networks that control host-pathogen interactions. These enhanced techniques include dRNA-seq and term-seq for the fine-scale mapping of transcriptional start and termination sites, and dual RNA-seq for simultaneous sequencing of host and bacterial pathogen transcriptomes. Dual RNA-seq experiments are currently limited to in vitro infection systems that do not fully reflect the complexities of the in vivo environment, thus a challenge is to develop in vivo model systems and experimental approaches that address the biological heterogeneity of host environments, followed by the integration of RNA-seq with other genome-scale datasets to identify the transcriptional networks that mediate host-pathogen interactions.
Collapse
Affiliation(s)
- Aoife M Colgan
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland
| | - Andrew Ds Cameron
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
| | - Carsten Kröger
- Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin, Ireland.
| |
Collapse
|
34
|
Buratti FM, Manganelli M, Vichi S, Stefanelli M, Scardala S, Testai E, Funari E. Cyanotoxins: producing organisms, occurrence, toxicity, mechanism of action and human health toxicological risk evaluation. Arch Toxicol 2017; 91:1049-1130. [DOI: 10.1007/s00204-016-1913-6] [Citation(s) in RCA: 258] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 12/13/2016] [Indexed: 12/11/2022]
|
35
|
Mazur-Marzec H, Bertos-Fortis M, Toruńska-Sitarz A, Fidor A, Legrand C. Chemical and Genetic Diversity of Nodularia spumigena from the Baltic Sea. Mar Drugs 2016; 14:md14110209. [PMID: 27834904 PMCID: PMC5128752 DOI: 10.3390/md14110209] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 10/26/2016] [Accepted: 11/02/2016] [Indexed: 12/31/2022] Open
Abstract
Nodularia spumigena is a toxic, filamentous cyanobacterium occurring in brackish waters worldwide, yet forms extensive recurrent blooms in the Baltic Sea. N. spumigena produces several classes of non-ribosomal peptides (NRPs) that are active against several key metabolic enzymes. Previously, strains from geographically distant regions showed distinct NRP metabolic profiles. In this work, conspecific diversity in N. spumigena was studied using chemical and genetic approaches. NRP profiles were determined in 25 N. spumigena strains isolated in different years and from different locations in the Baltic Sea using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Genetic diversity was assessed by targeting the phycocyanin intergenic spacer and flanking regions (cpcBA-IGS). Overall, 14 spumigins, 5 aeruginosins, 2 pseudaeruginosins, 2 nodularins, 36 anabaenopeptins, and one new cyanopeptolin-like peptide were identified among the strains. Seven anabaenopeptins were new structures; one cyanopeptolin-like peptide was discovered in N. spumigena for the first time. Based on NRP profiles and cpcBA-IGS sequences, the strains were grouped into two main clusters without apparent influence of year and location, indicating persistent presence of these two subpopulations in the Baltic Sea. This study is a major step in using chemical profiling to explore conspecific diversity with a higher resolution than with a sole genetic approach.
Collapse
Affiliation(s)
- Hanna Mazur-Marzec
- Department of Marine Biotechnology, University of Gdansk, Marszałka J. Piłusudskiego 46, 81378 Gdynia, Poland.
| | - Mireia Bertos-Fortis
- Department of Biology and Environmental Science, Center of Ecology and Evolution in Microbial Model Systems, Linnaeus University, 39182 Kalmar, Sweden.
| | - Anna Toruńska-Sitarz
- Department of Marine Biotechnology, University of Gdansk, Marszałka J. Piłusudskiego 46, 81378 Gdynia, Poland.
| | - Anna Fidor
- Department of Marine Biotechnology, University of Gdansk, Marszałka J. Piłusudskiego 46, 81378 Gdynia, Poland.
| | - Catherine Legrand
- Department of Biology and Environmental Science, Center of Ecology and Evolution in Microbial Model Systems, Linnaeus University, 39182 Kalmar, Sweden.
| |
Collapse
|
36
|
Melnicki MR, Leverenz RL, Sutter M, López-Igual R, Wilson A, Pawlowski EG, Perreau F, Kirilovsky D, Kerfeld CA. Structure, Diversity, and Evolution of a New Family of Soluble Carotenoid-Binding Proteins in Cyanobacteria. MOLECULAR PLANT 2016; 9:1379-1394. [PMID: 27392608 DOI: 10.1016/j.molp.2016.06.009] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/25/2016] [Accepted: 06/20/2016] [Indexed: 05/15/2023]
Abstract
Using a phylogenomic approach, we have identified and subclassified a new family of carotenoid-binding proteins. These proteins have sequence homology to the N-terminal domain (NTD) of the Orange Carotenoid Protein (OCP), and are referred to as Helical Carotenoid Proteins (HCPs). These proteins comprise at least nine distinct clades and are found in diverse organisms, frequently as multiple paralogs representing the distinct clades. These seem to be out-paralogs maintained from ancient duplications associated with subfunctionalization. All of the HCPs share conservation of the residues for carotenoid binding, and we confirm that carotenoid binding is a fundamental property of HCPs. We solved two crystal structures of the Nostoc sp. PCC 7120 HCP1 protein, each binding a different carotenoid, suggesting that the proteins flexibly bind a range of carotenoids. Based on a comprehensive phylogenetic analysis, we propose that one of the HCP subtypes is likely the evolutionary ancestor of the NTD of the OCP, which arose following a domain fusion event. However, we predict that the majority of HCPs have functions distinct from the NTD of the OCP. Our results demonstrate that the HCPs are a new family of functionally diverse carotenoid-binding proteins found among ecophysiologically diverse cyanobacteria.
Collapse
Affiliation(s)
- Matthew R Melnicki
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ryan L Leverenz
- MSU-DOE Plant Research Laboratory, Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Markus Sutter
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; MSU-DOE Plant Research Laboratory, Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Rocío López-Igual
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France; Commissariat à l'Energie Atomique (CEA), Institut de Biologie et Technologies de Saclay (iBiTec-S), 91191 Gif-sur-Yvette, France
| | - Adjélé Wilson
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France; Commissariat à l'Energie Atomique (CEA), Institut de Biologie et Technologies de Saclay (iBiTec-S), 91191 Gif-sur-Yvette, France
| | - Emily G Pawlowski
- MSU-DOE Plant Research Laboratory, Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - François Perreau
- INRA, Institut Jean-Pierre Bourgin, UMR 1318, ERL CNRS 3559, Saclay Plant Sciences, RD10, 78026 Versailles, France
| | - Diana Kirilovsky
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 91198 Gif-sur-Yvette, France; Commissariat à l'Energie Atomique (CEA), Institut de Biologie et Technologies de Saclay (iBiTec-S), 91191 Gif-sur-Yvette, France
| | - Cheryl A Kerfeld
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; MSU-DOE Plant Research Laboratory, Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA.
| |
Collapse
|
37
|
Asplund-Samuelsson J, Sundh J, Dupont CL, Allen AE, McCrow JP, Celepli NA, Bergman B, Ininbergs K, Ekman M. Diversity and Expression of Bacterial Metacaspases in an Aquatic Ecosystem. Front Microbiol 2016; 7:1043. [PMID: 27458440 PMCID: PMC4933709 DOI: 10.3389/fmicb.2016.01043] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/22/2016] [Indexed: 11/13/2022] Open
Abstract
Metacaspases are distant homologs of metazoan caspase proteases, implicated in stress response, and programmed cell death (PCD) in bacteria and phytoplankton. While the few previous studies on metacaspases have relied on cultured organisms and sequenced genomes, no studies have focused on metacaspases in a natural setting. We here present data from the first microbial community-wide metacaspase survey; performed by querying metagenomic and metatranscriptomic datasets from the brackish Baltic Sea, a water body characterized by pronounced environmental gradients and periods of massive cyanobacterial blooms. Metacaspase genes were restricted to ~4% of the bacteria, taxonomically affiliated mainly to Bacteroidetes, Alpha- and Betaproteobacteria and Cyanobacteria. The gene abundance was significantly higher in larger or particle-associated bacteria (>0.8 μm), and filamentous Cyanobacteria dominated metacaspase gene expression throughout the bloom season. Distinct seasonal expression patterns were detected for the three metacaspase genes in Nodularia spumigena, one of the main bloom-formers. Clustering of normalized gene expression in combination with analyses of genomic and assembly data suggest functional diversification of these genes, and possible roles of the metacaspase genes related to stress responses, i.e., sulfur metabolism in connection to oxidative stress, and nutrient stress induced cellular differentiation. Co-expression of genes encoding metacaspases and nodularin toxin synthesis enzymes was also observed in Nodularia spumigena. The study shows that metacaspases represent an adaptation of potentially high importance for several key organisms in the Baltic Sea, most prominently Cyanobacteria, and open up for further exploration of their physiological roles in microbes and assessment of their ecological impact in aquatic habitats.
Collapse
Affiliation(s)
- Johannes Asplund-Samuelsson
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm UniversitySolna, Sweden
| | - John Sundh
- Science for Life Laboratory, Department of Biology and Environmental Science, Linnaeus UniversitySolna, Sweden
| | - Chris L. Dupont
- Microbial and Environmental Genomics, J. Craig Venter InstituteSan Diego, CA, USA
| | - Andrew E. Allen
- Microbial and Environmental Genomics, J. Craig Venter InstituteSan Diego, CA, USA
| | - John P. McCrow
- Microbial and Environmental Genomics, J. Craig Venter InstituteSan Diego, CA, USA
| | - Narin A. Celepli
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm UniversitySolna, Sweden
| | - Birgitta Bergman
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm UniversitySolna, Sweden
| | - Karolina Ininbergs
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm UniversitySolna, Sweden
| | - Martin Ekman
- Science for Life Laboratory, Department of Ecology, Environment and Plant Sciences, Stockholm UniversitySolna, Sweden
| |
Collapse
|
38
|
D'Arrigo I, Bojanovič K, Yang X, Holm Rau M, Long KS. Genome-wide mapping of transcription start sites yields novel insights into the primary transcriptome ofPseudomonas putida. Environ Microbiol 2016; 18:3466-3481. [DOI: 10.1111/1462-2920.13326] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/01/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Isotta D'Arrigo
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; Kogle Allé 6 DK-2970 Hørsholm Denmark
| | - Klara Bojanovič
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; Kogle Allé 6 DK-2970 Hørsholm Denmark
| | - Xiaochen Yang
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; Kogle Allé 6 DK-2970 Hørsholm Denmark
| | - Martin Holm Rau
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; Kogle Allé 6 DK-2970 Hørsholm Denmark
| | - Katherine S. Long
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; Kogle Allé 6 DK-2970 Hørsholm Denmark
| |
Collapse
|
39
|
Dittmann E, Gugger M, Sivonen K, Fewer DP. Natural Product Biosynthetic Diversity and Comparative Genomics of the Cyanobacteria. Trends Microbiol 2016; 23:642-652. [PMID: 26433696 DOI: 10.1016/j.tim.2015.07.008] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 07/07/2015] [Accepted: 07/17/2015] [Indexed: 10/23/2022]
Abstract
Cyanobacteria are an ancient lineage of slow-growing photosynthetic bacteria and a prolific source of natural products with intricate chemical structures and potent biological activities. The bulk of these natural products are known from just a handful of genera. Recent efforts have elucidated the mechanisms underpinning the biosynthesis of a diverse array of natural products from cyanobacteria. Many of the biosynthetic mechanisms are unique to cyanobacteria or rarely described from other organisms. Advances in genome sequence technology have precipitated a deluge of genome sequences for cyanobacteria. This makes it possible to link known natural products to biosynthetic gene clusters but also accelerates the discovery of new natural products through genome mining. These studies demonstrate that cyanobacteria encode a huge variety of cryptic gene clusters for the production of natural products, and the known chemical diversity is likely to be just a fraction of the true biosynthetic capabilities of this fascinating and ancient group of organisms.
Collapse
Affiliation(s)
- Elke Dittmann
- Department of Microbiology, Institute of Biochemistry and Biology, University of Potsdam, Golm, Germany
| | - Muriel Gugger
- Institut Pasteur, Collection des Cyanobactéries, Paris, France
| | - Kaarina Sivonen
- Microbiology and Biotechnology Division, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - David P Fewer
- Microbiology and Biotechnology Division, Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland.
| |
Collapse
|
40
|
D'Agostino PM, Woodhouse JN, Makower AK, Yeung ACY, Ongley SE, Micallef ML, Moffitt MC, Neilan BA. Advances in genomics, transcriptomics and proteomics of toxin-producing cyanobacteria. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:3-13. [PMID: 26663762 DOI: 10.1111/1758-2229.12366] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 11/10/2015] [Accepted: 12/05/2015] [Indexed: 06/05/2023]
Abstract
A common misconception persists that the genomes of toxic and non-toxic cyanobacterial strains are largely conserved with the exception of the presence or absence of the genes responsible for toxin production. Implementation of -omics era technologies has challenged this paradigm, with comparative analyses providing increased insight into the differences between strains of the same species. The implementation of genomic, transcriptomic and proteomic approaches has revealed distinct profiles between toxin-producing and non-toxic strains. Further, metagenomics and metaproteomics highlight the genomic potential and functional state of toxic bloom events over time. In this review, we highlight how these technologies have shaped our understanding of the complex relationship between these molecules, their producers and the environment at large within which they persist.
Collapse
Affiliation(s)
- Paul M D'Agostino
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Biological Sciences Building D26, Sydney, NSW, 2052, Australia
| | - Jason N Woodhouse
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Biological Sciences Building D26, Sydney, NSW, 2052, Australia
| | - A Katharina Makower
- Department of Microbiology, Institute for Biochemistry and Biology, University of Potsdam, Potsdam-Golm, 14476, Germany
| | - Anna C Y Yeung
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Biological Sciences Building D26, Sydney, NSW, 2052, Australia
| | - Sarah E Ongley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Biological Sciences Building D26, Sydney, NSW, 2052, Australia
| | - Melinda L Micallef
- School of Science and Health, University of Western Sydney, Sydney, NSW, 2571, Australia
| | - Michelle C Moffitt
- School of Science and Health, University of Western Sydney, Sydney, NSW, 2571, Australia
| | - Brett A Neilan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Biological Sciences Building D26, Sydney, NSW, 2052, Australia
| |
Collapse
|
41
|
Brenes-Álvarez M, Olmedo-Verd E, Vioque A, Muro-Pastor AM. Identification of Conserved and Potentially Regulatory Small RNAs in Heterocystous Cyanobacteria. Front Microbiol 2016; 7:48. [PMID: 26870012 PMCID: PMC4734099 DOI: 10.3389/fmicb.2016.00048] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 01/12/2016] [Indexed: 12/13/2022] Open
Abstract
Small RNAs (sRNAs) are a growing class of non-protein-coding transcripts that participate in the regulation of virtually every aspect of bacterial physiology. Heterocystous cyanobacteria are a group of photosynthetic organisms that exhibit multicellular behavior and developmental alternatives involving specific transcriptomes exclusive of a given physiological condition or even a cell type. In the context of our ongoing effort to understand developmental decisions in these organisms we have undertaken an approach to the global identification of sRNAs. Using differential RNA-Seq we have previously identified transcriptional start sites for the model heterocystous cyanobacterium Nostoc sp. PCC 7120. Here we combine this dataset with a prediction of Rho-independent transcriptional terminators and an analysis of phylogenetic conservation of potential sRNAs among 89 available cyanobacterial genomes. In contrast to predictive genome-wide approaches, the use of an experimental dataset comprising all active transcriptional start sites (differential RNA-Seq) facilitates the identification of bona fide sRNAs. The output of our approach is a dataset of predicted potential sRNAs in Nostoc sp. PCC 7120, with different degrees of phylogenetic conservation across the 89 cyanobacterial genomes analyzed. Previously described sRNAs appear among the predicted sRNAs, demonstrating the performance of the algorithm. In addition, new predicted sRNAs are now identified that can be involved in regulation of different aspects of cyanobacterial physiology, including adaptation to nitrogen stress, the condition that triggers differentiation of heterocysts (specialized nitrogen-fixing cells). Transcription of several predicted sRNAs that appear exclusively in the genomes of heterocystous cyanobacteria is experimentally verified by Northern blot. Cell-specific transcription of one of these sRNAs, NsiR8 (nitrogen stress-induced RNA 8), in developing heterocysts is also demonstrated.
Collapse
Affiliation(s)
- Manuel Brenes-Álvarez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla Sevilla, Spain
| | - Elvira Olmedo-Verd
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla Sevilla, Spain
| | - Agustín Vioque
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla Sevilla, Spain
| | - Alicia M Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla Sevilla, Spain
| |
Collapse
|
42
|
Transcriptomic and Proteomic Profiling of Anabaena sp. Strain 90 under Inorganic Phosphorus Stress. Appl Environ Microbiol 2015; 81:5212-22. [PMID: 26025890 DOI: 10.1128/aem.01062-15] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 05/18/2015] [Indexed: 01/06/2023] Open
Abstract
Inorganic phosphorus (Pi) is one of the main growth-limiting factors of diazotrophic cyanobacteria. Due to human activity, the availability of Pi has increased in water bodies, resulting in eutrophication and the formation of massive cyanobacterial blooms. In this study, we examined the molecular responses of the cyanobacterium Anabaena sp. strain 90 to phosphorus deprivation, aiming at the identification of candidate genes to monitor the Pi status in cyanobacteria. Furthermore, this study increased the basic understanding of how phosphorus affects diazotrophic and bloom-forming cyanobacteria as a major growth-limiting factor. Based on RNA sequencing data, we identified 246 differentially expressed genes after phosphorus starvation and 823 differentially expressed genes after prolonged Pi limitation, most of them related to central metabolism and cellular growth. The transcripts of the genes related to phosphorus transport and assimilation (pho regulon) were most upregulated during phosphorus depletion. One of the most increased transcripts encodes a giant protein of 1,869 amino acid residues, which contains, among others, a phytase-like domain. Our findings predict its crucial role in phosphorus starvation, but future studies are still needed. Using two-dimensional difference in gel electrophoresis (2D-DIGE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), we found 43 proteins that were differentially expressed after prolonged phosphorus stress. However, correlation analysis unraveled an association only to some extent between the transcriptomic and proteomic abundances. Based on the present results, we suggest that the method used for monitoring the Pi status in cyanobacterial bloom should contain wider combinations of pho regulon genes (e.g., PstABCS transport systems) in addition to the commonly used alkaline phosphatase gene alone.
Collapse
|
43
|
Abstract
Regulatory RNAs play versatile roles in bacteria in the coordination of gene expression
during various physiological processes, especially during stress adaptation.
Photosynthetic bacteria use sunlight as their major energy source. Therefore, they are
particularly vulnerable to the damaging effects of excess light or UV irradiation. In
addition, like all bacteria, photosynthetic bacteria must adapt to limiting nutrient
concentrations and abiotic and biotic stress factors. Transcriptome analyses have
identified hundreds of potential regulatory small RNAs (sRNAs) in model cyanobacteria such
as Synechocystis sp. PCC 6803 or Anabaena sp. PCC 7120,
and in environmentally relevant genera such as Trichodesmium,
Synechococcus and Prochlorococcus. Some sRNAs have
been shown to actually contain μORFs and encode short proteins. Examples include the
40-amino-acid product of the sml0013 gene, which encodes the NdhP subunit
of the NDH1 complex. In contrast, the functional characterization of the non-coding sRNA
PsrR1 revealed that the 131 nt long sRNA controls photosynthetic functions by targeting
multiple mRNAs, providing a paradigm for sRNA functions in photosynthetic bacteria. We
suggest that actuatons comprise a new class of genetic elements in which an sRNA gene is
inserted upstream of a coding region to modify or enable transcription of that region. Hundreds of potentially regulatory small RNAs (sRNAs) have been identified in model
cyanobacteria and, despite recent significant progress, their functional characterization
is substantial work and continues to provide surprising insights of general interest.
Collapse
Affiliation(s)
- Matthias Kopf
- Faculty of Biology, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany
| | - Wolfgang R Hess
- Faculty of Biology, Institute of Biology III, University of Freiburg, D-79104 Freiburg, Germany
| |
Collapse
|
44
|
Liu L, Budnjo A, Jokela J, Haug BE, Fewer DP, Wahlsten M, Rouhiainen L, Permi P, Fossen T, Sivonen K. Pseudoaeruginosins, nonribosomal peptides in Nodularia spumigena. ACS Chem Biol 2015; 10:725-33. [PMID: 25419633 DOI: 10.1021/cb5004306] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nodularia spumigena is a filamentous cyanobacterium that forms toxic blooms in brackish waters around the world through the production of the pentapeptide toxin nodularin. This cyanobacterium also produces large amounts of protease inhibitors belonging to the aeruginosin and spumigin families. Here we report the discovery of previously unknown protease inhibitors, pseudoaeruginosins NS1 (1) and NS2 (2), from 33 strains of N. spumigena isolated from the Baltic Sea. Pseudoaeruginosin NS1 (1) and NS2 (2) contain hexanoic acid, tyrosine, 4-methylproline, and argininal/argininol. The chemical structure of the two pseudoaeruginosins was verified by thorough comparison of the liquid chromatography-mass spectrometry (LC-MS) analyses of the extracts from the N. spumigena strains with synthetic peptides. The structures of the synthetic pseudoaeruginosins were confirmed using nuclear magnetic resonance spectroscopy. Surprisingly, the structure of pseudoaeruginosin NS1 (1) and NS2 (2) combines features of both aeruginosins and spumigins, suggesting that they have been produced through the joint action of both the spumigin and aeruginosin biosynthesis pathways. We screened with polymerase chain reaction and LC-MS 68 N. spumigena strains from the Baltic Sea and Australia. Pseudoaeruginosins were present in half of the Baltic Sea strains but were not found from the Australian strains. The production of pseudoaeruginosin seems to be coupled to the production of aeruginosins and 4-methylproline-containing spumigins. Pseudoaeruginosin NS1 was found to be as potent trypsin inhibitor as the most potent aeruginosins and spumigins with an IC50 of 0.19 ± 0.04 μM. This finding suggests that cooperation between the spumigin and aeruginosin biosynthetic pathways results in hybrid pseudoaeruginosin peptides.
Collapse
Affiliation(s)
- Liwei Liu
- Food and
Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, P.O. Box 56, Viikki Biocenter, Viikinkaari 9, FI-00014 Helsinki, Finland
| | - Adnan Budnjo
- Department of Chemistry and Centre for Pharmacy, University of Bergen, Allégaten 41, 5007 Bergen, Norway
| | - Jouni Jokela
- Food and
Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, P.O. Box 56, Viikki Biocenter, Viikinkaari 9, FI-00014 Helsinki, Finland
| | - Bengt Erik Haug
- Department of Chemistry and Centre for Pharmacy, University of Bergen, Allégaten 41, 5007 Bergen, Norway
| | - David P. Fewer
- Food and
Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, P.O. Box 56, Viikki Biocenter, Viikinkaari 9, FI-00014 Helsinki, Finland
| | - Matti Wahlsten
- Food and
Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, P.O. Box 56, Viikki Biocenter, Viikinkaari 9, FI-00014 Helsinki, Finland
| | - Leo Rouhiainen
- Food and
Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, P.O. Box 56, Viikki Biocenter, Viikinkaari 9, FI-00014 Helsinki, Finland
| | - Perttu Permi
- Program in Structural
Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, FI-00014 Helsinki, Finland
| | - Torgils Fossen
- Department of Chemistry and Centre for Pharmacy, University of Bergen, Allégaten 41, 5007 Bergen, Norway
| | - Kaarina Sivonen
- Food and
Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki, P.O. Box 56, Viikki Biocenter, Viikinkaari 9, FI-00014 Helsinki, Finland
| |
Collapse
|
45
|
Kopf M, Möke F, Bauwe H, Hess WR, Hagemann M. Expression profiling of the bloom-forming cyanobacterium Nodularia CCY9414 under light and oxidative stress conditions. ISME JOURNAL 2015; 9:2139-52. [PMID: 25689027 DOI: 10.1038/ismej.2015.16] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2014] [Accepted: 01/08/2015] [Indexed: 11/10/2022]
Abstract
Massive blooms of toxic cyanobacteria frequently occur in the central Baltic Sea during the summer. In the surface scum, cyanobacterial cells are exposed to high light (HL) intensity, high oxygen partial pressure and other stresses. To mimic these conditions, cultures of Nodularia spumigena CCY9414, which is a strain isolated from a cyanobacterial summer bloom in the Baltic Sea, were incubated at a HL intensity of 1200 μmol photons m(-2) s(-1) or a combination of HL and increased oxygen partial pressure. Using differential RNA sequencing, we compared the global primary transcriptomes of control and stressed cells. The combination of oxidative and light stresses induced the expression of twofold more genes compared with HL stress alone. In addition to the induction of known stress-responsive genes, such as psbA, ocp and sodB, Nodularia cells activated the expression of genes coding for many previously unknown light- and oxidative stress-related proteins. In addition, the expression of non-protein-coding RNAs was found to be stimulated by these stresses. Among them was an antisense RNA to the phycocyanin-encoding mRNA cpcBAC and the trans-encoded regulator of photosystem I, PsrR1. The large genome capacity allowed Nodularia to harbor more copies of stress-relevant genes such as psbA and small chlorophyll-binding protein genes, combined with the coordinated induction of these and many additional genes for stress acclimation. Our data provide a first insight on how N. spumigena became adapted to conditions relevant for a cyanobacterial bloom in the Baltic Sea.
Collapse
Affiliation(s)
- Matthias Kopf
- Albert-Ludwigs-Universität Freiburg, Fakultät für Biologie, Genetik und Experimentelle Bioinformatik, Freiburg, Germany
| | - Fred Möke
- Universität Rostock, Institut für Biowissenschaften, Pflanzenphysiologie, Rostock, Germany
| | - Hermann Bauwe
- Universität Rostock, Institut für Biowissenschaften, Pflanzenphysiologie, Rostock, Germany
| | - Wolfgang R Hess
- Albert-Ludwigs-Universität Freiburg, Fakultät für Biologie, Genetik und Experimentelle Bioinformatik, Freiburg, Germany
| | - Martin Hagemann
- Universität Rostock, Institut für Biowissenschaften, Pflanzenphysiologie, Rostock, Germany
| |
Collapse
|
46
|
Li X, Sandh G, Nenninger A, Muro-Pastor AM, Stensjö K. Differential transcriptional regulation of orthologous dps genes from two closely related heterocyst-forming cyanobacteria. FEMS Microbiol Lett 2015; 362:fnv017. [PMID: 25663155 DOI: 10.1093/femsle/fnv017] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
In cyanobacteria, DNA-binding proteins from starved cells (Dps) play an important role in the cellular response to oxidative and nutritional stresses. In this study, we have characterized the cell-type specificity and the promoter regions of two orthologous dps genes, Npun_R5799 in Nostoc punctiforme and alr3808 in Anabaena sp. PCC 7120. A transcriptional start site (TSS), identical in location to the previously identified proximal TSS of alr3808, was identified for Npun_R5799 under both combined nitrogen supplemented and N2-fixing growth conditions. However, only alr3808 was also transcribed from a second distal TSS. Sequence homologies suggest that the promoter region containing the distal TSS is not conserved upstream of orthologous genes among heterocyst-forming cyanobacteria. The analysis of promoter GFP-reporter strains showed a different role in governing cell-type specificity between the proximal and distal promoter of alr3808. We here confirmed the heterocyst specificity of the distal promoter of alr3808 and described a very early induction of its expression during proheterocyst differentiation. In contrast, the complete promoters of both genes were active in all cells. Even though Npun_R5799 and alr3808 are orthologs, the regulation of their respective expression differs, indicating distinctions in the function of these cyanobacterial Dps proteins depending on the strain and cell type.
Collapse
Affiliation(s)
- Xin Li
- Microbial Chemistry, Department of Chemistry - Ångström Laboratory, Science for Life Laboratory, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
| | - Gustaf Sandh
- Microbial Chemistry, Department of Chemistry - Ångström Laboratory, Science for Life Laboratory, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
| | - Anja Nenninger
- Microbial Chemistry, Department of Chemistry - Ångström Laboratory, Science for Life Laboratory, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
| | - Alicia M Muro-Pastor
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, E-41092 Seville, Spain
| | - Karin Stensjö
- Microbial Chemistry, Department of Chemistry - Ångström Laboratory, Science for Life Laboratory, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
| |
Collapse
|
47
|
Loera-Quezada MM, Leyva-González MA, López-Arredondo D, Herrera-Estrella L. Phosphite cannot be used as a phosphorus source but is non-toxic for microalgae. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 231:124-30. [PMID: 25575997 DOI: 10.1016/j.plantsci.2014.11.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 11/28/2014] [Accepted: 11/29/2014] [Indexed: 05/16/2023]
Abstract
Phosphorous (P) plays a critical role for all living organisms as a structural component of RNA, DNA and phospholipids. Microalgae are autotrophs organisms that have been reported to only assimilate the fully oxidized phosphate (Pi) as P source. However, there are microorganisms capable of utilizing P reduced compounds (i.e. phosphite (Phi) and hypophosphite) as a sole P source, such as bacteria and cyanobacteria. In this study, we evaluated whether microalgae, such as Chlamydomonas reinhardtii, Botryococcus braunii and Ettlia oleoabundans, are capable of using Phi as a sole P source. Our studies revealed that these three microalgae are unable to use Phi as a sole P source. We also found that when Phi is present at concentrations equal or higher than that of Pi, Phi has an inhibitory effect on C. reinhardtii growth. However, since C. reinhardtii was able to survive for a long period of cultivation in the presence of high concentrations of Phi and to recover cell division capacity after transfer to media containing Pi, we noticed that Phi is not toxic for this microalga. We propose that the inhibitory effect of Phi on C. reinhardtii growth might be caused, at least in part, by a competition between the transport of Pi and Phi.
Collapse
Affiliation(s)
- Maribel M Loera-Quezada
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada del Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km 9.6 carretera Irapuato León, 36500 Irapuato, Guanajuato, Mexico
| | | | - Damar López-Arredondo
- StelaGenomics México, S de RL de CV, Av. Camino Real de Guanajuato s/n, 36821 Irapuato, Guanajuato, Mexico.
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada del Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km 9.6 carretera Irapuato León, 36500 Irapuato, Guanajuato, Mexico.
| |
Collapse
|
48
|
Abstract
Microbes produce a huge array of secondary metabolites endowed with important ecological functions. These molecules, which can be catalogued as natural products, have long been exploited in medical fields as antibiotics, anticancer and anti-infective agents. Recent years have seen considerable advances in elucidating natural-product biosynthesis and many drugs used today are natural products or natural-product derivatives. The major contribution to recent knowledge came from application of genomics to secondary metabolism and was facilitated by all relevant genes being organised in a contiguous DNA segment known as gene cluster. Clustering of genes regulating biosynthesis in bacteria is virtually universal. Modular gene clusters can be mixed and matched during evolution to generate structural diversity in natural products. Biosynthesis of many natural products requires the participation of complex molecular machines known as polyketide synthases and non-ribosomal peptide synthetases. Discovery of new evolutionary links between the polyketide synthase and fatty acid synthase pathways may help to understand the selective advantages that led to evolution of secondary-metabolite biosynthesis within bacteria. Secondary metabolites confer selective advantages, either as antibiotics or by providing a chemical language that allows communication among species, with other organisms and their environment. Herewith, we discuss these aspects focusing on the most clinically relevant bioactive molecules, the thiotemplated modular systems that include polyketide synthases, non-ribosomal peptide synthetases and fatty acid synthases. We begin by describing the evolutionary and physiological role of marine natural products, their structural/functional features, mechanisms of action and biosynthesis, then turn to genomic and metagenomic approaches, highlighting how the growing body of information on microbial natural products can be used to address fundamental problems in environmental evolution and biotechnology.
Collapse
|
49
|
Micallef ML, D'Agostino PM, Al-Sinawi B, Neilan BA, Moffitt MC. Exploring cyanobacterial genomes for natural product biosynthesis pathways. Mar Genomics 2014; 21:1-12. [PMID: 25482899 DOI: 10.1016/j.margen.2014.11.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 11/22/2014] [Accepted: 11/23/2014] [Indexed: 11/26/2022]
Abstract
Cyanobacteria produce a vast array of natural products, some of which are toxic to human health, while others possess potential pharmaceutical activities. Genome mining enables the identification and characterisation of natural product gene clusters; however, the current number of cyanobacterial genomes remains low compared to other phyla. There has been a recent effort to rectify this issue by increasing the number of sequenced cyanobacterial genomes. This has enabled the identification of biosynthetic gene clusters for structurally diverse metabolites, including non-ribosomal peptides, polyketides, ribosomal peptides, UV-absorbing compounds, alkaloids, terpenes and fatty acids. While some of the identified biosynthetic gene clusters correlate with known metabolites, genome mining also highlights the number and diversity of clusters for which the product is unknown (referred to as orphan gene clusters). A number of bioinformatic tools have recently been developed in order to predict the products of orphan gene clusters; however, in some cases the complexity of the cyanobacterial pathways makes the prediction problematic. This can be overcome by the use of mass spectrometry-guided natural product genome mining, or heterologous expression. Application of these techniques to cyanobacterial natural product gene clusters will be explored.
Collapse
Affiliation(s)
- Melinda L Micallef
- School of Science and Health, University of Western Sydney, Campbelltown, NSW 2560, Australia
| | - Paul M D'Agostino
- School of Science and Health, University of Western Sydney, Campbelltown, NSW 2560, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia
| | - Bakir Al-Sinawi
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia
| | - Brett A Neilan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia
| | - Michelle C Moffitt
- School of Science and Health, University of Western Sydney, Campbelltown, NSW 2560, Australia.
| |
Collapse
|
50
|
Klähn S, Baumgartner D, Pfreundt U, Voigt K, Schön V, Steglich C, Hess WR. Alkane Biosynthesis Genes in Cyanobacteria and Their Transcriptional Organization. Front Bioeng Biotechnol 2014; 2:24. [PMID: 25022427 PMCID: PMC4094844 DOI: 10.3389/fbioe.2014.00024] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 06/26/2014] [Indexed: 12/26/2022] Open
Abstract
In cyanobacteria, alkanes are synthesized from a fatty acyl-ACP by two enzymes, acyl–acyl carrier protein reductase and aldehyde deformylating oxygenase. Despite the great interest in the exploitation for biofuel production, nothing is known about the transcriptional organization of their genes or the physiological function of alkane synthesis. The comparison of 115 microarray datasets indicates the relatively constitutive expression of aar and ado genes. The analysis of 181 available genomes showed that in 90% of the genomes both genes are present, likely indicating their physiological relevance. In 61% of them they cluster together with genes encoding acetyl-CoA carboxyl transferase and a short-chain dehydrogenase, strengthening the link to fatty acid metabolism and in 76% of the genomes they are located in tandem, suggesting constraints on the gene arrangement. However, contrary to the expectations for an operon, we found in Synechocystis sp. PCC 6803 specific promoters for the two genes, sll0208 (ado) and sll0209 (aar), which give rise to monocistronic transcripts. Moreover, the upstream located ado gene is driven by a proximal as well as a second, distal, promoter, from which a third transcript, the ~160 nt sRNA SyR9 is transcribed. Thus, the transcriptional organization of the alkane biosynthesis genes in Synechocystis sp. PCC 6803 is of substantial complexity. We verified all three promoters to function independently from each other and show a similar promoter arrangement also in the more distant Nodularia spumigena, Trichodesmium erythraeum, Anabaena sp. PCC 7120, Prochlorococcus MIT9313, and MED4. The presence of separate regulatory elements and the dominance of monocistronic mRNAs suggest the possible autonomous regulation of ado and aar. The complex transcriptional organization of the alkane synthesis gene cluster has possible metabolic implications and should be considered when manipulating the expression of these genes in cyanobacteria.
Collapse
Affiliation(s)
- Stephan Klähn
- Genetics and Experimental Bioinformatics, Institute of Biology 3, Faculty of Biology, University of Freiburg , Freiburg , Germany
| | - Desirée Baumgartner
- Genetics and Experimental Bioinformatics, Institute of Biology 3, Faculty of Biology, University of Freiburg , Freiburg , Germany
| | - Ulrike Pfreundt
- Genetics and Experimental Bioinformatics, Institute of Biology 3, Faculty of Biology, University of Freiburg , Freiburg , Germany
| | - Karsten Voigt
- Genetics and Experimental Bioinformatics, Institute of Biology 3, Faculty of Biology, University of Freiburg , Freiburg , Germany
| | - Verena Schön
- Genetics and Experimental Bioinformatics, Institute of Biology 3, Faculty of Biology, University of Freiburg , Freiburg , Germany
| | - Claudia Steglich
- Genetics and Experimental Bioinformatics, Institute of Biology 3, Faculty of Biology, University of Freiburg , Freiburg , Germany
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Institute of Biology 3, Faculty of Biology, University of Freiburg , Freiburg , Germany
| |
Collapse
|