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Cameron ES, Sanchez S, Goldman N, Blaxter ML, Finn RD. Diversity and specificity of molecular functions in cyanobacterial symbionts. Sci Rep 2024; 14:18658. [PMID: 39134591 PMCID: PMC11319675 DOI: 10.1038/s41598-024-69215-8] [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: 04/13/2024] [Accepted: 08/01/2024] [Indexed: 08/15/2024] Open
Abstract
Cyanobacteria are globally occurring photosynthetic bacteria notable for their contribution to primary production and production of toxins which have detrimental ecosystem impacts. Furthermore, cyanobacteria can form mutualistic symbiotic relationships with a diverse set of eukaryotes, including land plants, aquatic plankton and fungi. Nevertheless, not all cyanobacteria are found in symbiotic associations suggesting symbiotic cyanobacteria have evolved specializations that facilitate host-interactions. Photosynthetic capabilities, nitrogen fixation, and the production of complex biochemicals are key functions provided by host-associated cyanobacterial symbionts. To explore if additional specializations are associated with such lifestyles in cyanobacteria, we have conducted comparative phylogenomics of molecular functions and of biosynthetic gene clusters (BGCs) in 984 cyanobacterial genomes. Cyanobacteria with host-associated and symbiotic lifestyles were concentrated in the family Nostocaceae, where eight monophyletic clades correspond to specific host taxa. In agreement with previous studies, symbionts are likely to provide fixed nitrogen to their eukaryotic partners, through multiple different nitrogen fixation pathways. Additionally, our analyses identified chitin metabolising pathways in cyanobacteria associated with specific host groups, while obligate symbionts had fewer BGCs. The conservation of molecular functions and BGCs between closely related symbiotic and free-living cyanobacteria suggests the potential for additional cyanobacteria to form symbiotic relationships than is currently known.
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Affiliation(s)
- Ellen S Cameron
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, UK
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Santiago Sanchez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, UK
| | - Nick Goldman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, UK
| | - Mark L Blaxter
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, UK.
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2
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Dhabalia Ashok A, de Vries S, Darienko T, Irisarri I, de Vries J. Evolutionary assembly of the plant terrestrialization toolkit from protein domains. Proc Biol Sci 2024; 291:20240985. [PMID: 39081174 PMCID: PMC11289646 DOI: 10.1098/rspb.2024.0985] [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: 08/15/2023] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 08/02/2024] Open
Abstract
Land plants (embryophytes) came about in a momentous evolutionary singularity: plant terrestrialization. This event marks not only the conquest of land by plants but also the massive radiation of embryophytes into a diverse array of novel forms and functions. The unique suite of traits present in the earliest land plants is thought to have been ushered in by a burst in genomic novelty. Here, we asked the question of how these bursts were possible. For this, we explored: (i) the initial emergence and (ii) the reshuffling of domains to give rise to hallmark environmental response genes of land plants. We pinpoint that a quarter of the embryophytic genes for stress physiology are specific to the lineage, yet a significant portion of this novelty arises not de novo but from reshuffling and recombining of pre-existing domains. Our data suggest that novel combinations of old genomic substrate shaped the plant terrestrialization toolkit, including hallmark processes in signalling, biotic interactions and specialized metabolism.
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Affiliation(s)
- Amra Dhabalia Ashok
- Department of Applied Bioinformatics, University of Goettingen, Institute for Microbiology and Genetics, Goldschmidtstr. 1, Goettingen37077, Germany
| | - Sophie de Vries
- Department of Applied Bioinformatics, University of Goettingen, Institute for Microbiology and Genetics, Goldschmidtstr. 1, Goettingen37077, Germany
| | - Tatyana Darienko
- Department of Applied Bioinformatics, University of Goettingen, Institute for Microbiology and Genetics, Goldschmidtstr. 1, Goettingen37077, Germany
| | - Iker Irisarri
- Department of Applied Bioinformatics, University of Goettingen, Institute for Microbiology and Genetics, Goldschmidtstr. 1, Goettingen37077, Germany
- University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, Goettingen37077, Germany
- Section Phylogenomics, Centre for Molecular biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature Hamburg, Martin-Luther-King-Platz 3, Hamburg20146, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, University of Goettingen, Institute for Microbiology and Genetics, Goldschmidtstr. 1, Goettingen37077, Germany
- University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, Goettingen37077, Germany
- Department of Applied Bioinformatics, University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Goldschmidtstr. 1, Goettingen37077, Germany
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3
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Stadnichuk IN, Krasilnikov PM. Relationship between non-photochemical quenching efficiency and the energy transfer rate from phycobilisomes to photosystem II. PHOTOSYNTHESIS RESEARCH 2024; 159:177-189. [PMID: 37328680 DOI: 10.1007/s11120-023-01031-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/02/2023] [Indexed: 06/18/2023]
Abstract
The chromophorylated PBLcm domain of the ApcE linker protein in the cyanobacterial phycobilisome (PBS) serves as a bottleneck for Förster resonance energy transfer (FRET) from the PBS to the antennal chlorophyll of photosystem II (PS II) and as a redirection point for energy distribution to the orange protein ketocarotenoid (OCP), which is excitonically coupled to the PBLcm chromophore in the process of non-photochemical quenching (NPQ) under high light conditions. The involvement of PBLcm in the quenching process was first directly demonstrated by measuring steady-state fluorescence spectra of cyanobacterial cells at different stages of NPQ development. The time required to transfer energy from the PBLcm to the OCP is several times shorter than the time it takes to transfer energy from the PBLcm to the PS II, ensuring quenching efficiency. The data obtained provide an explanation for the different rates of PBS quenching in vivo and in vitro according to the half ratio of OCP/PBS in the cyanobacterial cell, which is tens of times lower than that realized for an effective NPQ process in solution.
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Affiliation(s)
- Igor N Stadnichuk
- K.A. Timiryazev Institute of Plant Physiology, RAS, Botanicheskaya 35, 127726, Moscow, Russia.
| | - Pavel M Krasilnikov
- Biological Faculty of M.V., Lomonosov State University, Lenin Hills 12, 119991, Moscow, Russia
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4
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Dhabalia Ashok A, Freitag JN, Irisarri I, de Vries S, de Vries J. Sequence similarity networks bear out hierarchical relationships of green cytochrome P450. PHYSIOLOGIA PLANTARUM 2024; 176:e14244. [PMID: 38480467 DOI: 10.1111/ppl.14244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/24/2024]
Abstract
Land plants have diversified enzyme families. One of the most prominent is the cytochrome P450 (CYP or CYP450) family. With over 443,000 CYP proteins sequenced across the tree of life, CYPs are ubiquitous in archaea, bacteria, and eukaryotes. Here, we focused on land plants and algae to study the role of CYP diversification. CYPs, acting as monooxygenases, catalyze hydroxylation reactions crucial for specialized plant metabolic pathways, including detoxification and phytohormone production; the CYPome consists of one enormous superfamily that is divided into clans and families. Their evolutionary history speaks of high substrate promiscuity; radiation and functional diversification have yielded numerous CYP families. To understand the evolutionary relationships within the CYPs, we employed sequence similarity network analyses. We recovered distinct clusters representing different CYP families, reflecting their diversified sequences that we link to the prediction of functionalities. Hierarchical clustering and phylogenetic analysis further elucidated relationships between CYP clans, uncovering their shared deep evolutionary history. We explored the distribution and diversification of CYP subfamilies across plant and algal lineages, uncovering novel candidates and providing insights into the evolution of these enzyme families. This identified unexpected relationships between CYP families, such as the link between CYP82 and CYP74, shedding light on their roles in plant defense signaling pathways. Our approach provides a methodology that brings insights into the emergence of new functions within the CYP450 family, contributing to the evolutionary history of plants and algae. These insights can be further validated and implemented via experimental setups under various external conditions.
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Affiliation(s)
- Amra Dhabalia Ashok
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Jella N Freitag
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Iker Irisarri
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
- Section Phylogenomics, Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change (LIB), Museum of Nature, Hamburg, Germany
| | - Sophie de Vries
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
| | - Jan de Vries
- Institute of Microbiology and Genetics, Department of Applied Bioinformatics, University of Goettingen, Goettingen, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Goettingen, Germany
- Goettingen Center for Molecular Biosciences (GZMB), Department of Applied Bioinformatics, University of Goettinzgen, Goettingen, Germany
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5
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Glasser NR, Cui D, Risser DD, Okafor CD, Balskus EP. Accelerating the discovery of alkyl halide-derived natural products using halide depletion. Nat Chem 2024; 16:173-182. [PMID: 38216751 PMCID: PMC10849952 DOI: 10.1038/s41557-023-01390-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/30/2023] [Indexed: 01/14/2024]
Abstract
Even in the genomic era, microbial natural product discovery workflows can be laborious and limited in their ability to target molecules with specific structural features. Here we leverage an understanding of biosynthesis to develop a workflow that targets the discovery of alkyl halide-derived natural products by depleting halide anions, a key biosynthetic substrate for enzymatic halogenation, from microbial growth media. By comparing the metabolomes of bacterial cultures grown in halide-replete and deficient media, we rapidly discovered the nostochlorosides, the products of an orphan halogenase-encoding gene cluster from Nostoc punctiforme ATCC 29133. We further found that these products, a family of unusual chlorinated glycolipids featuring the rare sugar gulose, are polymerized via an unprecedented enzymatic etherification reaction. Together, our results highlight the power of leveraging an understanding of biosynthetic logic to streamline natural product discovery.
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Affiliation(s)
- Nathaniel R Glasser
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Dongtao Cui
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Douglas D Risser
- Department of Biology, University of the Pacific, Stockton, CA, USA
| | - C Denise Okafor
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Emily P Balskus
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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6
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Irit N, Hana B, Laura R, Arielle K, Mariela P, Esti KW, Guadalupe P, Katja S, Ariel K. Trichocoleus desertorum isolated from Negev desert petroglyphs: Characterization, adaptation and bioerosion potential. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 904:166739. [PMID: 37673239 DOI: 10.1016/j.scitotenv.2023.166739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 08/23/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023]
Abstract
The Negev petroglyphs are considered valuable cultural heritage sites, but unfortunately, they are exposed to deterioration processes caused by anthropogenic and natural forces. Despite the many studies that have already pointed to the role of cyanobacteria in biogenic rock weathering, the knowledge involved in the process is still lacking. In this study, a cyanobacterial strain was isolated from the Negev Desert petroglyphs aiming to reveal its involvement in geochemical cycles and in the weathering processes of the rock substrate. The strain was characterized using morphological, molecular, and microscopic studies. The morphological research revealed a green-bluish, bundle-forming filamentous strain characterized by trichomes embedded in a common sheath. A combination of Nanopore and Illumina sequencing technologies facilitated the assembly of a near-complete genome containing 5,458,034 base pairs. A total of 5027 coding sequences were revealed by implementing PROKKA software. Annotation of five replicas of the 16S ribosomal RNA genes revealed that the Negev cyanobacteria isolate is closely (99.73 %) related to Trichocoleus desertorum LSB90_MW403957 isolated from the Sahara Desert, Algeria. The local strain was thus named Trichocoleus desertorum NBK24 CP116619. Several gene sequences that code for possible environmental adaptation mechanisms were found. Our study also identified genes for membrane transporters involved in the exchange of chemical elements, suggesting a possible interaction with rock minerals. Microscopic observations of T. desertorum NBK24 CP116619 infected onto calcareous stone slabs under laboratory conditions demonstrated the effect of the isolated cyanobacteria on stone surface degradation. In conclusion, the findings of this study further our understanding of terrestrial cyanobacterial genomes and functions and highlight the role of T. desertorum NBK24 CP116619 in stone weathering processes. This information may contribute to the creation of efficient restoration strategies for stone monuments affected by cyanobacteria.
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Affiliation(s)
- Nir Irit
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Barak Hana
- Department of Civil and Environmental Engineering, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Rabbachin Laura
- Institute of Natural Sciences and Technology in the Arts (INTK), Academy of Fine Arts Vienna, Vienna, Austria
| | - Kahn Arielle
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Pavan Mariela
- The Ilse Katz Center for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Kramarsky-Winter Esti
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel
| | - Piñar Guadalupe
- Institute of Natural Sciences and Technology in the Arts (INTK), Academy of Fine Arts Vienna, Vienna, Austria
| | - Sterflinger Katja
- Institute of Natural Sciences and Technology in the Arts (INTK), Academy of Fine Arts Vienna, Vienna, Austria
| | - Kushmaro Ariel
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel; The Ilse Katz Center for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva 8410501, Israel; School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
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7
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Risser DD. Hormogonium Development and Motility in Filamentous Cyanobacteria. Appl Environ Microbiol 2023; 89:e0039223. [PMID: 37199640 PMCID: PMC10304961 DOI: 10.1128/aem.00392-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023] Open
Abstract
Filamentous cyanobacteria exhibit some of the greatest developmental complexity observed in the prokaryotic domain. This includes the ability to differentiate nitrogen-fixing cells known as heterocysts, spore-like akinetes, and hormogonia, which are specialized motile filaments capable of gliding on solid surfaces. Hormogonia and motility play critical roles in several aspects of the biology of filamentous cyanobacteria, including dispersal, phototaxis, the formation of supracellular structures, and the establishment of nitrogen-fixing symbioses with plants. While heterocyst development has been investigated extensively at the molecular level, much less is known about akinete or hormogonium development and motility. This is due, in part, to the loss of developmental complexity during prolonged laboratory culture in commonly employed model filamentous cyanobacteria. In this review, recent progress in understanding the molecular level regulation of hormogonium development and motility in filamentous cyanobacteria is discussed, with a focus on experiments performed using the genetically tractable model filamentous cyanobacterium Nostoc punctiforme, which retains the developmental complexity of field isolates.
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Affiliation(s)
- Douglas D. Risser
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, Colorado, USA
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8
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Becker B, Pushkareva E. Metagenomics Provides a Deeper Assessment of the Diversity of Bacterial Communities in Polar Soils Than Metabarcoding. Genes (Basel) 2023; 14:genes14040812. [PMID: 37107570 PMCID: PMC10138292 DOI: 10.3390/genes14040812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/23/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023] Open
Abstract
The diversity of soil bacteria was analyzed via metabarcoding and metagenomic approaches using DNA samples isolated from the biocrusts of 12 different Arctic and Antarctic sites. For the metabarcoding approach, the V3-4 region of the 16S rRNA was targeted. Our results showed that nearly all operational taxonomic units (OTUs = taxa) found in metabarcoding analyses were recovered in metagenomic analyses. In contrast, metagenomics identified a large number of additional OTUs absent in metabarcoding analyses. In addition, we found huge differences in the abundance of OTUs between the two methods. The reasons for these differences seem to be (1) the higher sequencing depth in metagenomics studies, which allows the detection of low-abundance community members in metagenomics, and (2) bias of primer pairs used to amplify the targeted sequence in metabarcoding, which can change the community composition dramatically even at the lower taxonomic levels. We strongly recommend using only metagenomic approaches when establishing the taxonomic profiles of whole biological communities.
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9
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Christian R, Labbancz J, Usadel B, Dhingra A. Understanding protein import in diverse non-green plastids. Front Genet 2023; 14:969931. [PMID: 37007964 PMCID: PMC10063809 DOI: 10.3389/fgene.2023.969931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 02/24/2023] [Indexed: 03/19/2023] Open
Abstract
The spectacular diversity of plastids in non-green organs such as flowers, fruits, roots, tubers, and senescing leaves represents a Universe of metabolic processes in higher plants that remain to be completely characterized. The endosymbiosis of the plastid and the subsequent export of the ancestral cyanobacterial genome to the nuclear genome, and adaptation of the plants to all types of environments has resulted in the emergence of diverse and a highly orchestrated metabolism across the plant kingdom that is entirely reliant on a complex protein import and translocation system. The TOC and TIC translocons, critical for importing nuclear-encoded proteins into the plastid stroma, remain poorly resolved, especially in the case of TIC. From the stroma, three core pathways (cpTat, cpSec, and cpSRP) may localize imported proteins to the thylakoid. Non-canonical routes only utilizing TOC also exist for the insertion of many inner and outer membrane proteins, or in the case of some modified proteins, a vesicular import route. Understanding this complex protein import system is further compounded by the highly heterogeneous nature of transit peptides, and the varying transit peptide specificity of plastids depending on species and the developmental and trophic stage of the plant organs. Computational tools provide an increasingly sophisticated means of predicting protein import into highly diverse non-green plastids across higher plants, which need to be validated using proteomics and metabolic approaches. The myriad plastid functions enable higher plants to interact and respond to all kinds of environments. Unraveling the diversity of non-green plastid functions across the higher plants has the potential to provide knowledge that will help in developing climate resilient crops.
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Affiliation(s)
- Ryan Christian
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - June Labbancz
- Department of Horticulture, Washington State University, Pullman, WA, United States
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
| | | | - Amit Dhingra
- Department of Horticulture, Washington State University, Pullman, WA, United States
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, United States
- *Correspondence: Amit Dhingra,
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10
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Rieseberg TP, Dadras A, Fürst-Jansen JMR, Dhabalia Ashok A, Darienko T, de Vries S, Irisarri I, de Vries J. Crossroads in the evolution of plant specialized metabolism. Semin Cell Dev Biol 2023; 134:37-58. [PMID: 35292191 DOI: 10.1016/j.semcdb.2022.03.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 02/17/2022] [Accepted: 03/04/2022] [Indexed: 12/25/2022]
Abstract
The monophyletic group of embryophytes (land plants) stands out among photosynthetic eukaryotes: they are the sole constituents of the macroscopic flora on land. In their entirety, embryophytes account for the majority of the biomass on land and constitute an astounding biodiversity. What allowed for the massive radiation of this particular lineage? One of the defining features of all land plants is the production of an array of specialized metabolites. The compounds that the specialized metabolic pathways of embryophytes produce have diverse functions, ranging from superabundant structural polymers and compounds that ward off abiotic and biotic challenges, to signaling molecules whose abundance is measured at the nanomolar scale. These specialized metabolites govern the growth, development, and physiology of land plants-including their response to the environment. Hence, specialized metabolites define the biology of land plants as we know it. And they were likely a foundation for their success. It is thus intriguing to find that the closest algal relatives of land plants, freshwater organisms from the grade of streptophyte algae, possess homologs for key enzymes of specialized metabolic pathways known from land plants. Indeed, some studies suggest that signature metabolites emerging from these pathways can be found in streptophyte algae. Here we synthesize the current understanding of which routes of the specialized metabolism of embryophytes can be traced to a time before plants had conquered land.
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Affiliation(s)
- Tim P Rieseberg
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Armin Dadras
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Janine M R Fürst-Jansen
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Amra Dhabalia Ashok
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Tatyana Darienko
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Sophie de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany
| | - Iker Irisarri
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany; University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany
| | - Jan de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goldschmidtstr. 1, 37077 Goettingen, Germany; University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077 Goettingen, Germany; University of Goettingen, Goettingen Center for Molecular Biosciences (GZMB), Department of Applied Bioinformatics, Goldschmidtsr. 1, 37077 Goettingen, Germany.
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11
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Álvarez C, Brenes-Álvarez M, Molina-Heredia FP, Mariscal V. Quantitative Proteomics at Early Stages of the Symbiotic Interaction Between Oryza sativa and Nostoc punctiforme Reveals Novel Proteins Involved in the Symbiotic Crosstalk. PLANT & CELL PHYSIOLOGY 2022; 63:1433-1445. [PMID: 35373828 PMCID: PMC9620832 DOI: 10.1093/pcp/pcac043] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/22/2022] [Accepted: 04/09/2022] [Indexed: 06/14/2023]
Abstract
Symbiosis between cyanobacteria and plants is considered pivotal for biological nitrogen deposition in terrestrial ecosystems. Despite extensive knowledge of the ecology of plant-cyanobacterium symbioses, little is known about the molecular mechanisms involved in recognition between partners. Here, we conducted a quantitative sequential window acquisition of all theoretical fragment ion spectra mass spectrometry pipeline to analyze protein changes in Oryza sativa and Nostoc punctiforme during early events of symbiosis. We found differentially expressed proteins in both organisms linked to several biological functions, including signal transduction, adhesion, defense-related proteins and cell wall modification. In N. punctiforme we found increased expression of 62 proteins that have been previously described in other Nostoc-plant symbioses, reinforcing the robustness of our study. Our findings reveal new proteins activated in the early stages of the Nostoc-Oryza symbiosis that might be important for the recognition between the plant and the host. Oryza mutants in genes in the common symbiosis signaling pathway (CSSP) show reduced colonization efficiency, providing first insights on the involvement of the CSSP for the accommodation of N. punctiforme inside the plant cells. This information may have long-term implications for a greater understanding of the symbiotic interaction between Nostoc and land plants.
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Affiliation(s)
- Consolación Álvarez
- *Corresponding authors: Vicente Mariscal, E-mail, ; Consolación Álvarez, E-mail,
| | - Manuel Brenes-Álvarez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, cicCartuja, Américo Vespucio 49, Seville 41092, Spain
| | - Fernando P Molina-Heredia
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, cicCartuja, Américo Vespucio 49, Seville 41092, Spain
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes s/n, Seville 41012, Spain
| | - Vicente Mariscal
- *Corresponding authors: Vicente Mariscal, E-mail, ; Consolación Álvarez, E-mail,
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12
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Multiple Photolyases Protect the Marine Cyanobacterium Synechococcus from Ultraviolet Radiation. mBio 2022; 13:e0151122. [PMID: 35856560 PMCID: PMC9426592 DOI: 10.1128/mbio.01511-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine cyanobacteria depend on light for photosynthesis, restricting their growth to the photic zone. The upper part of this layer is exposed to strong UV radiation (UVR), a DNA mutagen that can harm these microorganisms. To thrive in UVR-rich waters, marine cyanobacteria employ photoprotection strategies that are still not well defined. Among these are photolyases, light-activated enzymes that repair DNA dimers generated by UVR. Our analysis of genomes of 81 strains of Synechococcus, Cyanobium, and Prochlorococcus isolated from the world’s oceans shows that they possess up to five genes encoding different members of the photolyase/cryptochrome family, including a photolyase with a novel domain arrangement encoded by either one or two separate genes. We disrupted the putative photolyase-encoding genes in Synechococcus sp. strain RS9916 and discovered that each gene contributes to the overall capacity of this organism to survive UVR. Additionally, each conferred increased survival after UVR exposure when transformed into Escherichia coli lacking its photolyase and SOS response. Our results provide the first evidence that this large set of photolyases endows Synechococcus with UVR resistance that is far superior to that of E. coli, but that, unlike for E. coli, these photolyases provide Synechococcus with the vast majority of its UVR tolerance.
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Klicki K, Ferreira D, Risser D, Garcia-Pichel F. A Regulatory Linkage Between Scytonemin Production and Hormogonia Differentiation in Nostoc punctiforme. iScience 2022; 25:104361. [PMID: 35620423 PMCID: PMC9127174 DOI: 10.1016/j.isci.2022.104361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 01/17/2022] [Accepted: 05/02/2022] [Indexed: 11/16/2022] Open
Abstract
Bacteria sometimes hedge their survival bets by concurrently activating response circuits leading to different phenotypes in isogenic populations. We show that the cyanobacterium Nostoc punctiforme responds to UV-A by concurrently producing the sunscreen scytonemin and differentiating into motile hormogonia but segregating the responses at the filament level. Mutational studies show that a four-gene partner-switching regulatory system (hcyA-D) orchestrates the cross-talk between the respective regulatory circuitries. Transcription of hormogonium genes and hcyA-D is upregulated by UVA through the scytonemin two-component regulator (scyTCR), hcyA-D being directly involved in signal transduction into the hormogonium response and its modulation by visible light. The sigma factor cascade that regulates developmental commitment to hormogonia also upregulates hcyA-D transcription and strongly suppresses scytonemin synthesis through downregulation of the scyTCR itself. Through this complex bidirectional mechanism, Nostoc can concurrently deploy two fundamentally different UV stress mitigation strategies, either hunker down or flee, in a single population. Nostoc responds to UV-A by both producing sunscreen and differentiating hormogonia The responses are, however, mutually exclusive at the single filament level A novel 4-gene system (hcyA-D) orchestrates the regulation between the two responses This affords Nostoc a bet-hedging means to both hunker down and flee UV-A stress
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Affiliation(s)
- Kevin Klicki
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
- School of Life Sciences, Arizona State University, AZ 95281, USA
| | - Daniela Ferreira
- School of Life Sciences, Arizona State University, AZ 95281, USA
| | - Douglas Risser
- Department of Biological Sciences, University of the Pacific, Stockton, CA 95211, USA
| | - Ferran Garcia-Pichel
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
- School of Life Sciences, Arizona State University, AZ 95281, USA
- Corresponding author
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Peng F, Engel U, Aliyu H, Rudat J. Origin and Evolution of Enzymes with MIO Prosthetic Group: Microbial Coevolution After the Mass Extinction Event. Front Genet 2022; 13:851738. [PMID: 35422843 PMCID: PMC9002059 DOI: 10.3389/fgene.2022.851738] [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: 01/10/2022] [Accepted: 02/16/2022] [Indexed: 11/20/2022] Open
Abstract
After major mass extinction events, ancient plants and terrestrial vertebrates were faced with various challenges, especially ultraviolet (UV) light. These stresses probably resulted in changes in the biosynthetic pathways, which employed the MIO (3,5-dihydro-5-methylidene-4H-imidazole-4-one)-dependent enzymes (ammonia-lyase and aminomutase), leading to enhanced accumulation of metabolites for defense against UV radiation, pathogens, and microorganisms. Up to now, the origin and evolution of genes from this superfamily have not been extensively studied. In this report, we perform an analysis of the phylogenetic relations between the members of the aromatic amino acid MIO-dependent enzymes (AAM), which demonstrate that they most probably have a common evolutionary origin from ancient bacteria. In early soil environments, numerous bacterial species with tyrosine ammonia-lyase genes (TAL; EC 4.3.1.23) developed tyrosine aminomutase (TAM; EC 5.4.3.6) activity as a side reaction for competing with their neighbors in the community. These genes also evolved into other TAL-like enzymes, such as histidine ammonia-lyase (HAL, EC 4.3.1.3) and phenylalanine ammonia-lyase (PAL; EC 4.3.1.24), in different bacterial species for metabolite production and accumulation for adaptation to adverse terrestrial environmental conditions. On the other hand, the existence of phenylalanine aminomutase (PAM; EC 5.4.3.10) and phenylalanine/tyrosine ammonia-lyase (PTAL; EC 4.3.1.25) strongly indicates the horizontal gene transfer (HGT) between bacteria, fungi, and plants in symbiotic association after acquiring the PAL gene from their ancestor.
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Affiliation(s)
- Fei Peng
- Institute of Process Engineering in Life Sciences, II, Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Ulrike Engel
- Institute of Process Engineering in Life Sciences, II, Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Habibu Aliyu
- Institute of Process Engineering in Life Sciences, II, Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Jens Rudat
- Institute of Process Engineering in Life Sciences, II, Technical Biology, Karlsruhe Institute of Technology, Karlsruhe, Germany
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Xu HF, Dai GZ, Wang YJ, Cheng C, Shang JL, Li RH, Liu K, Duanmu D, Qiu BS. Expansion of bilin-based red light sensors in the subaerial desert cyanobacterium Nostoc flagelliforme. Environ Microbiol 2022; 24:2047-2058. [PMID: 35172392 DOI: 10.1111/1462-2920.15932] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/29/2022] [Accepted: 02/03/2022] [Indexed: 11/27/2022]
Abstract
Light is the crucial environmental signal for desiccation-tolerant cyanobacteria to activate photosynthesis and prepare for desiccation at dawn. However, the photobiological characteristics of desert cyanobacteria adaptation to one of the harshest habitats on Earth remain unresolved. In this study, we surveyed the genome of a subaerial desert cyanobacterium Nostoc flagelliforme and identified two phytochromes and seven cyanobacteriochromes (CBCRs) with one or more bilin-binding GAF (cGMP phosphodiesterase/adenylyl cyclase/FhlA) domains. Biochemical and spectroscopic analyses of 69 purified GAF-containing proteins from recombinant phycocyanobilin (PCB), biliverdin or phycoerythrobilin-producing Escherichia coli indicated that nine of these proteins bind chromophores. Further investigation revealed that 11 GAFs form covalent adducts responsive to near-UV and visible light: eight GAFs contained PCB chromophores, three GAFs contained biliverdin chromophores and one contained the PCB isomer, phycoviolobilin. Interestingly, COO91_03972 is the first-ever reported GAF-only CBCR capable of sensing five wavelengths of light. Bioinformatics and biochemical analyses revealed that residue P132 of COO91_03972 is essential for chromophore binding to dual-cysteine CBCRs. Furthermore, the complement of N. flagelliforme CBCRs is enriched in red light sensors. We hypothesize that these sensors are critical for the acclimatization of N. flagelliforme to weak light environments at dawn.
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Affiliation(s)
- Hai-Feng Xu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Guo-Zheng Dai
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Yu-Jie Wang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Chao Cheng
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Jin-Long Shang
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Ren-Han Li
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Ke Liu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Deqiang Duanmu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Bao-Sheng Qiu
- School of Life Sciences, and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
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Belton S, Lamari N, Jermiin LS, Mariscal V, Flores E, McCabe PF, Ng CKY. Genetic and lipidomic analyses suggest that Nostoc punctiforme, a plant-symbiotic cyanobacterium, does not produce sphingolipids. Access Microbiol 2022; 4:000306. [PMID: 35252750 PMCID: PMC8895605 DOI: 10.1099/acmi.0.000306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 11/23/2021] [Indexed: 11/21/2022] Open
Abstract
Sphingolipids, a class of amino-alcohol-based lipids, are well characterized in eukaryotes and in some anaerobic bacteria. However, the only sphingolipids so far identified in cyanobacteria are two ceramides (i.e., an acetylsphingomyelin and a cerebroside), both based on unbranched, long-chain base (LCB) sphingolipids in Scytonema julianum and Moorea producens, respectively. The first step in de novo sphingolipid biosynthesis is the condensation of l-serine with palmitoyl-CoA to produce 3-keto-diyhydrosphingosine (KDS). This reaction is catalyzed by serine palmitoyltransferase (SPT), which belongs to a small family of pyridoxal phosphate-dependent α-oxoamine synthase (AOS) enzymes. Based on sequence similarity to molecularly characterized bacterial SPT peptides, we identified a putative SPT (Npun_R3567) from the model nitrogen-fixing, plant-symbiotic cyanobacterium, Nostoc punctiforme strain PCC 73102 (ATCC 29133). Gene expression analysis revealed that Npun_R3567 is induced during late-stage diazotrophic growth in N. punctiforme. However, Npun_R3567 could not produce the SPT reaction product, 3-keto-diyhydrosphingosine (KDS), when heterologously expressed in Escherichia coli. This agreed with a sphingolipidomic analysis of N. punctiforme cells, which revealed that no LCBs or ceramides were present. To gain a better understanding of Npun_R3567, we inferred the phylogenetic position of Npun_R3567 relative to other bacterial AOS peptides. Rather than clustering with other bacterial SPTs, Npun_R3567 and the other cyanobacterial BioF homologues formed a separate, monophyletic group. Given that N. punctiforme does not appear to possess any other gene encoding an AOS enzyme, it is altogether unlikely that N. punctiforme is capable of synthesizing sphingolipids. In the context of cross-kingdom symbiosis signalling in which sphingolipids are emerging as important regulators, it appears unlikely that sphingolipids from N. punctiforme play a regulatory role during its symbiotic association with plants.
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Affiliation(s)
- Samuel Belton
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin D4, Ireland
- Present address: DBN Plant Molecular Biology Lab, National Botanic Gardens of Ireland, Dublin, Ireland
| | - Nadia Lamari
- Present address: Philip Morris International, Quai Jeanrenaud 3, 2000, Neuchâtel, Switzerland
- UCD Earth Institute, O’Brien Centre for Science, University College Dublin, Belfield, Dublin D4, Ireland
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin D4, Ireland
| | - Lars S. Jermiin
- Research School of Biology, Australian National University, Canberra, ACT 2600, Australia
- UCD Earth Institute, O’Brien Centre for Science, University College Dublin, Belfield, Dublin D4, Ireland
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin D4, Ireland
| | - Vicente Mariscal
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, cicCartuja, Avda. Américo Vespucio 49, 41092 Seville, Spain
| | - Enrique Flores
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, cicCartuja, Avda. Américo Vespucio 49, 41092 Seville, Spain
| | - Paul F. McCabe
- UCD Earth Institute, O’Brien Centre for Science, University College Dublin, Belfield, Dublin D4, Ireland
- UCD Centre for Plant Science, University College Dublin, Belfield, Dublin D4, Ireland
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin D4, Ireland
| | - Carl K. Y. Ng
- UCD Earth Institute, O’Brien Centre for Science, University College Dublin, Belfield, Dublin D4, Ireland
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin D4, Ireland
- UCD Centre for Plant Science, University College Dublin, Belfield, Dublin D4, Ireland
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17
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Samanta L, Stensjö K, Lindblad P, Bhattacharya J. Differential catalase activity and tolerance to hydrogen peroxide in the filamentous cyanobacteria Nostoc punctiforme ATCC 29133 and Anabaena sp. PCC 7120. Arch Microbiol 2022; 204:121. [PMID: 34993618 DOI: 10.1007/s00203-021-02643-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 10/03/2021] [Accepted: 10/29/2021] [Indexed: 11/28/2022]
Abstract
Photoautotrophic cyanobacteria often confront hydrogen peroxide (H2O2), a reactive oxygen species potentially toxic to cells when present in sufficiently high concentrations. In this study, H2O2 tolerance ability of filamentous cyanobacteria Nostoc punctiforme ATCC 29133 (Nostoc 29133) and Anabaena sp. PCC 7120 (Anabaena 7120) was investigated at increasing concentrations of H2O2 (0-0.5 mM). In Nostoc 29133, 0.25 and 0.5 mM H2O2 caused a reduction in chlorophyll a content by 12 and 20%, respectively, whereas with similar treatments, a total loss of chlorophyll a was detected in Anabaena 7120. Further, Nostoc 29133 was able to maintain its photosystem II performance in the presence of H2O2 up to a concentration of 0.5 mM, whereas in Anabaena 7120, 0.25 mM H2O2 caused a complete reduction of photosystem II performance. The intracellular hydroperoxide level (indicator of oxidative status) did not increase to the same high level in Nostoc 29133, as compared to in Anabaena 7120 after H2O2 treatment. This might be explained by that Nostoc 29133 showed a 20-fold higher intrinsic constitutive catalase activity than Anabaena 7120, thus indicating that the superior tolerance of Nostoc 29133 to H2O2 stems from its higher ability to decompose H2O2. It is suggested that difference in H2O2 tolerance between closely related filamentous cyanobacteria, as revealed in this study, may be taken into account for judicious selection and effective use of strains in biotechnological applications.
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Affiliation(s)
- Loknath Samanta
- Department of Biotechnology, Mizoram University, PB No. 190, Aizawl, 796004, Mizoram, India
| | - Karin Stensjö
- Microbial Chemistry-Ångström Laboratory, Uppsala University, Box 523, 751 20, Uppsala, Sweden
| | - Peter Lindblad
- Microbial Chemistry-Ångström Laboratory, Uppsala University, Box 523, 751 20, Uppsala, Sweden
| | - Jyotirmoy Bhattacharya
- Department of Biotechnology, Mizoram University, PB No. 190, Aizawl, 796004, Mizoram, India.
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de Vries S, de Vries J. Evolutionary genomic insights into cyanobacterial symbioses in plants. QUANTITATIVE PLANT BIOLOGY 2022; 3:e16. [PMID: 37077989 PMCID: PMC10095879 DOI: 10.1017/qpb.2022.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 05/03/2023]
Abstract
Photosynthesis, the ability to fix atmospheric carbon dioxide, was acquired by eukaryotes through symbiosis: the plastids of plants and algae resulted from a cyanobacterial symbiosis that commenced more than 1.5 billion years ago and has chartered a unique evolutionary path. This resulted in the evolutionary origin of plants and algae. Some extant land plants have recruited additional biochemical aid from symbiotic cyanobacteria; these plants associate with filamentous cyanobacteria that fix atmospheric nitrogen. Examples of such interactions can be found in select species from across all major lineages of land plants. The recent rise in genomic and transcriptomic data has provided new insights into the molecular foundation of these interactions. Furthermore, the hornwort Anthoceros has emerged as a model system for the molecular biology of cyanobacteria-plant interactions. Here, we review these developments driven by high-throughput data and pinpoint their power to yield general patterns across these diverse symbioses.
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Affiliation(s)
- Sophie de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
- Authors for correspondence: Sophie de Vries E-mail: Jan de Vries E-mail:
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goettingen, Germany
- Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany
- Campus Institute Data Science (CIDAS), University of Goettingen, Goettingen, Germany
- Authors for correspondence: Sophie de Vries E-mail: Jan de Vries E-mail:
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Huo D, Li H, Cai F, Guo X, Qiao Z, Wang W, Yu G, Li R. Genome Evolution of Filamentous Cyanobacterium Nostoc Species: From Facultative Symbiosis to Free Living. Microorganisms 2021; 9:microorganisms9102015. [PMID: 34683336 PMCID: PMC8539589 DOI: 10.3390/microorganisms9102015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/15/2021] [Accepted: 09/19/2021] [Indexed: 11/16/2022] Open
Abstract
In contrast to obligate bacteria, facultative symbiotic bacteria are mainly characterized by genome enlargement. However, the underlying relationship of this feature with adaptations to various habitats remains unclear. In this study, we used the global genome data of Nostoc strains, including 10 novel genomes sequenced in this study and 26 genomes available from public databases, and analyzed their evolutionary history. The evolutionary boundary of the real clade of Nostoc species was identified and was found to be consistent with the results of polyphasic taxonomy. The initial ancestral species of Nostoc was demonstrated to be consistent with a facultative symbiotic population. Further analyses revealed that Nostoc strains tended to shift from facultative symbiosis to a free-living one, along with an increase in genome sizes during the dispersal of each exterior branch. Intracellular symbiosis was proved to be essentially related to Nostoc evolution, and the adaptation of its members to free-living environments was coupled with a large preference for gene acquisition involved in gene repair and recombination. These findings provided unique evidence of genomic mechanisms by which homologous microbes adapt to distinct life manners and external environments.
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Affiliation(s)
- Da Huo
- CAS Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (D.H.); (H.L.); (F.C.); (X.G.)
| | - Hua Li
- CAS Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (D.H.); (H.L.); (F.C.); (X.G.)
- Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining 810016, China
| | - Fangfang Cai
- CAS Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (D.H.); (H.L.); (F.C.); (X.G.)
- School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan 430023, China
| | - Xiaoyu Guo
- CAS Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (D.H.); (H.L.); (F.C.); (X.G.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiyi Qiao
- Tianjin Key Laboratory of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin 300384, China;
| | - Weibo Wang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China;
| | - Gongliang Yu
- CAS Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (D.H.); (H.L.); (F.C.); (X.G.)
- Correspondence: (G.Y.); (R.L.); Tel.: +86-027-68780067 (G.Y.); +86-027-68780080 (R.L.); Fax: +86-027-68780123 (G.Y.)
| | - Renhui Li
- College of Life and Environmental Sciences, Wenzhou University, Wenzhou 325000, China
- Correspondence: (G.Y.); (R.L.); Tel.: +86-027-68780067 (G.Y.); +86-027-68780080 (R.L.); Fax: +86-027-68780123 (G.Y.)
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Ghosh A, Bhadury P. Genome description of Nostoc ellipsosporum strain NOK (Nostocales, Cyanobacteria) isolated from an arsenic contaminated paddy field of the Bengal Delta Plains. IOP SCINOTES 2021. [DOI: 10.1088/2633-1357/ac202f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
A diazotrophic cyanobacterium, Nostoc ellipsosporum strain NOK, was isolated from an arsenic contaminated paddy field of the Bengal Delta Plains (BDP). Located across India and Bangladesh, BDP, is one of the worst arsenic (As)-affected regions of the world. Previous studies have shown this isolate to be tolerant to high concentration of arsenic (≦400 μM). The genome of this isolate was sequenced to identify the genes involved in various metabolic pathways including arsenic resistance and biofilm formation. Whole genome analyses showed Nostoc ellipsosporum strain NOK to be closely related to N. punctiforme strain PCC73102. The genome is about 10.9 Mbp which assembled into 694 contigs. Genome annotation identified 10120 genes out of which 10000 were CDSs. There are a total of 9927 protein coding genes in addition to 120 RNA coding genes. The genome codes three 5S rRNA, four 16S rRNA and three 23S rRNA genes along with 103 tRNAs, 7 ncRNAs and 73 pseudo-genes. The G + C% of the genome is 54.28. The genome codes for crucial genes involved in biofilm formation in response to stress conditions including arsenic stress. The arsBHC operon is present within the genome which makes this tolerant to high concentration of arsenic which might lead to biofilm formation. A number of ABC transporters including cysUW and sbp (sulfate/thiosulfate), nrtABC (nitrate/nitrite/cyanate), cmpABCD (bicarbonate), ssuABC (alkane sulfonate), modABCF (molybdate; 2 copies), afuAC (iron), pstA (phosphate; 2 copies), pstBC, pstS (4 copies), cbiOQ (cobalt and nickel) and opuBC, opuBB and opuBA (osmoprotectants) were identified.
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Abstract
Species of the floating, freshwater fern Azolla form a well-characterized symbiotic association with the non-culturable cyanobacterium Nostoc azollae, which fixes nitrogen for the plant. However, several cyanobacterial strains have over the years been isolated and cultured from Azolla from all over the world. The genomes of 10 of these strains were sequenced and compared with each other, with other symbiotic cyanobacterial strains, and with similar strains that were not isolated from a symbiotic association. The 10 strains fell into three distinct groups: six strains were nearly identical to the non-symbiotic strain, Nostoc (Anabaena) variabilis ATCC 29413; three were similar to the symbiotic strain, Nostoc punctiforme, and one, Nostoc sp. 2RC, was most similar to non-symbiotic strains of Nostoc linckia. However, Nostoc sp. 2RC was unusual because it has three sets of nitrogenase genes; it has complete gene clusters for two distinct Mo-nitrogenases and an alternative V-nitrogenase. Genes for Mo-nitrogenase, sugar transport, chemotaxis and pili characterized all the symbiotic strains. Several of the strains infected the liverwort Blasia, including N. variabilis ATCC 29413, which did not originate from Azolla but rather from a sewage pond. However, only Nostoc sp. 2RC, which produced highly motile hormogonia, was capable of high-frequency infection of Blasia. Thus, some of these strains, which grow readily in the laboratory, may be useful in establishing novel symbiotic associations with other plants.
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Affiliation(s)
- Brenda S. Pratte
- Department of Biology, University of Missouri–St. Louis, One University Blvd, St. Louis, MO 63121, USA
| | - Teresa Thiel
- Department of Biology, University of Missouri–St. Louis, One University Blvd, St. Louis, MO 63121, USA
- *Correspondence: Teresa Thiel,
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22
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Soule T, Ferreira D, Lothamer J, Garcia-Pichel F. The Independent and Shared Transcriptomic Response to UVA, UVB and Oxidative Stress in the Cyanobacterium Nostoc punctiforme ATCC 29133. Photochem Photobiol 2021; 97:1063-1071. [PMID: 33955032 DOI: 10.1111/php.13444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 05/01/2021] [Indexed: 11/27/2022]
Abstract
Research on the UVA, UVB and oxidative (as reactive oxygen species, ROS) stress response in cyanobacteria has typically focused on each individual stress condition, with limited studies addressing the intersection. Here, we evaluated the transcriptomic responses of the model cyanobacterium Nostoc punctiforme after exposure to each of these conditions. Overall, response to UVA was characterized by more gene down-regulation than the UVB or ROS response, although UVB affected over fourfold more genes than UVA or ROS. Regarding expression patterns, responses to UVA and ROS were more similar and differentiated from those to UVB. For example, genes involved in ROS metabolism were up-regulated under both UVA and ROS. However, when it came to RNA and protein metabolism, there were more up-regulated genes under UVB and ROS compared to UVA. This suggests that the response to UVB and ROS is more active than the response to UVA, which stimulated more genes in secondary metabolism. Histidine kinases and response regulators were often differentially expressed, demonstrating that regulatory systems were at the base of the patterns. This study provides background for future studies targeting different genes, proteins and systems sensitive to these conditions. It also highlights the significance of considering multiple stress conditions.
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Affiliation(s)
- Tanya Soule
- Department of Biology, Purdue University Fort Wayne, Fort Wayne, IN, USA
| | - Daniela Ferreira
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Justin Lothamer
- Department of Biology, Purdue University Fort Wayne, Fort Wayne, IN, USA
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Chen Z, Shang JL, Hou S, Li T, Li Q, Yang YW, Hess WR, Qiu BS. Genomic and transcriptomic insights into the habitat adaptation of the diazotrophic paddy-field cyanobacterium Nostoc sphaeroides. Environ Microbiol 2021; 23:5802-5822. [PMID: 33848055 DOI: 10.1111/1462-2920.15521] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 03/25/2021] [Accepted: 04/08/2021] [Indexed: 12/13/2022]
Abstract
Nitrogen-fixing cyanobacteria are common in paddy fields, one of the most productive wetland ecosystems. Here, we present the complete genome of Nostoc sphaeroides, a paddy-field diazotroph used for food and medicine for more than 1700 years and deciphered the transcriptional regulation during the developmental transition from hormogonia to vegetative filaments with heterocysts. The genome of N. sphaeroides consists of one circular chromosome (6.48 Mb), one of the largest ever reported megaplasmids (2.34 Mb), and seven plasmids. Multiple gene families involved in the adaption to high solar radiation and water fluctuation conditions were found expanded, while genes involved in anoxic adaptation and phosphonate utilization are located on the megaplasmid, suggesting its indispensable role in environmental adaptation. Distinct gene expression patterns were observed during the light-intensity-regulated transition from hormogonia to vegetative filaments, specifically, genes encoding proteins involved in photosynthetic light reaction, carbon fixation, nitrogen metabolism and heterocyst differentiation were significantly upregulated, whereas genes related to cell motility were down-regulated. Our results provide genomic and transcriptomic insights into the adaptation of a filamentous nitrogen-fixing cyanobacterium to the highly dynamic paddy-field habitat, suggesting N. sphaeroides as an excellent system to understand the transition from aquatic to terrestrial habitats and to support sustainable rice production.
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Affiliation(s)
- Zhen Chen
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China.,Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Huangshi, Hubei, 435002, China
| | - Jin-Long Shang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Shengwei Hou
- Department of Biological Sciences, University of Southern California, CA, Los Angeles, 90089, USA
| | - Tao Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Science, Wuhan, Hubei, 430072, China
| | - Qi Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Science, Wuhan, Hubei, 430072, China
| | - Yi-Wen Yang
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Wolfgang R Hess
- Genetics and Experimental Bioinformatics, Institute of Biology III, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - Bao-Sheng Qiu
- School of Life Sciences, Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan, Hubei, 430079, China
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24
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Bradley JM, Svistunenko DA, Wilson MT, Hemmings AM, Moore GR, Le Brun NE. Bacterial iron detoxification at the molecular level. J Biol Chem 2021; 295:17602-17623. [PMID: 33454001 PMCID: PMC7762939 DOI: 10.1074/jbc.rev120.007746] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 10/07/2020] [Indexed: 01/18/2023] Open
Abstract
Iron is an essential micronutrient, and, in the case of bacteria, its availability is commonly a growth-limiting factor. However, correct functioning of cells requires that the labile pool of chelatable "free" iron be tightly regulated. Correct metalation of proteins requiring iron as a cofactor demands that such a readily accessible source of iron exist, but overaccumulation results in an oxidative burden that, if unchecked, would lead to cell death. The toxicity of iron stems from its potential to catalyze formation of reactive oxygen species that, in addition to causing damage to biological molecules, can also lead to the formation of reactive nitrogen species. To avoid iron-mediated oxidative stress, bacteria utilize iron-dependent global regulators to sense the iron status of the cell and regulate the expression of proteins involved in the acquisition, storage, and efflux of iron accordingly. Here, we survey the current understanding of the structure and mechanism of the important members of each of these classes of protein. Diversity in the details of iron homeostasis mechanisms reflect the differing nutritional stresses resulting from the wide variety of ecological niches that bacteria inhabit. However, in this review, we seek to highlight the similarities of iron homeostasis between different bacteria, while acknowledging important variations. In this way, we hope to illustrate how bacteria have evolved common approaches to overcome the dual problems of the insolubility and potential toxicity of iron.
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Affiliation(s)
- Justin M Bradley
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, United Kingdom.
| | | | - Michael T Wilson
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Andrew M Hemmings
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, United Kingdom; Centre for Molecular and Structural Biochemistry, School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Geoffrey R Moore
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, United Kingdom
| | - Nick E Le Brun
- Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich, United Kingdom.
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Aguilera A, Klemenčič M, Sueldo DJ, Rzymski P, Giannuzzi L, Martin MV. Cell Death in Cyanobacteria: Current Understanding and Recommendations for a Consensus on Its Nomenclature. Front Microbiol 2021; 12:631654. [PMID: 33746925 PMCID: PMC7965980 DOI: 10.3389/fmicb.2021.631654] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 02/11/2021] [Indexed: 01/31/2023] Open
Abstract
Cyanobacteria are globally widespread photosynthetic prokaryotes and are major contributors to global biogeochemical cycles. One of the most critical processes determining cyanobacterial eco-physiology is cellular death. Evidence supports the existence of controlled cellular demise in cyanobacteria, and various forms of cell death have been described as a response to biotic and abiotic stresses. However, cell death research in this phylogenetic group is a relatively young field and understanding of the underlying mechanisms and molecular machinery underpinning this fundamental process remains largely elusive. Furthermore, no systematic classification of modes of cell death has yet been established for cyanobacteria. In this work, we analyzed the state of knowledge in the field of cyanobacterial cell death. Based on that, we propose unified criterion for the definition of accidental, regulated, and programmed forms of cell death in cyanobacteria based on molecular, biochemical, and morphologic aspects following the directions of the Nomenclature Committee on Cell Death (NCCD). With this, we aim to provide a guide to standardize the nomenclature related to this topic in a precise and consistent manner, which will facilitate further ecological, evolutionary, and applied research in the field of cyanobacterial cell death.
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Affiliation(s)
- Anabella Aguilera
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
| | - Marina Klemenčič
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Daniela J. Sueldo
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Piotr Rzymski
- Department of Environmental Medicine, Poznan University of Medical Sciences, Poznan´, Poland
- Integrated Science Association (ISA), Universal Scientific Education and Research Network (USERN), Poznan´, Poland
| | - Leda Giannuzzi
- Centro de Investigación y Desarrollo en Criotecnología de Alimentos, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Universidad Nacional de La Plata, La Plata, Argentina
- Área de Toxicología General, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - María Victoria Martin
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET), Fundación para Investigaciones Biológicas Aplicadas (CIB-FIBA), Mar del Plata, Argentina
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26
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Nieves-Morión M, Flores E, Foster RA. Predicting substrate exchange in marine diatom-heterocystous cyanobacteria symbioses. Environ Microbiol 2020; 22:2027-2052. [PMID: 32281201 DOI: 10.1111/1462-2920.15013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 11/27/2022]
Abstract
In the open ocean, some phytoplankton establish symbiosis with cyanobacteria. Some partnerships involve diatoms as hosts and heterocystous cyanobacteria as symbionts. Heterocysts are specialized cells for nitrogen fixation, and a function of the symbiotic cyanobacteria is to provide the host with nitrogen. However, both partners are photosynthetic and capable of carbon fixation, and the possible metabolites exchanged and mechanisms of transfer are poorly understood. The symbiont cellular location varies from internal to partial to fully external, and this is reflected in the symbiont genome size and content. In order to identify the membrane transporters potentially involved in metabolite exchange, we compare the draft genomes of three differently located symbionts with known transporters mainly from model free-living heterocystous cyanobacteria. The types and numbers of transporters are directly related to the symbiont cellular location: restricted in the endosymbionts and wider in the external symbiont. Three proposed models of metabolite exchange are suggested which take into account the type of transporters in the symbionts and the influence of their cellular location on the available nutrient pools. These models provide a basis for several hypotheses that given the importance of these symbioses in global N and C budgets, warrant future testing.
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Affiliation(s)
- Mercedes Nieves-Morión
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden
| | - Enrique Flores
- Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad de Sevilla, Américo Vespucio 49, Seville, E-41092, Spain
| | - Rachel A Foster
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden
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Singh P, Šnokhousová J, Saraf A, Suradkar A, Elster J. Phylogenetic evaluation of the genus Nostoc and description of Nostoc neudorfense sp. nov., from the Czech Republic. Int J Syst Evol Microbiol 2020; 70:2740-2749. [DOI: 10.1099/ijsem.0.004102] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Cyanobacterial strain ARC8 was isolated from seepage coming into the river Dračice, Františkov, Czech Republic, and was characterized using a polyphasic approach. Strain ARC8 showed a typical
Nostoc
-like morphology and in-depth morphological characterization indicated that it is a member of the genus
Nostoc
. Furthermore, in the 16S rRNA gene phylogeny inferred using Bayesian inference, maximum likelihood and neighbour joining methods, strain ARC8 clustered within the Nostoc sensu stricto clade. The phylogenetic distance and the positioning of strain ARC8 also indicated that it is a member of the genus
Nostoc
. Furthermore, the rbcL gene phylogeny along with the 16S–23S ITS secondary structure analysis also supported the findings from the 16S rRNA gene tree. In accordance with the International Code of Nomenclature for Algae, Fungi and Plants we describe a novel species of
Nostoc
with the name Nostoc neudorfense sp. nov.
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Affiliation(s)
- Prashant Singh
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, India
- Laboratory of Cyanobacterial Systematics and Stress Biology, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Jana Šnokhousová
- Phycology Centre, Institute of Botany, Academy of Science CR, Třeboň, Czechia
| | - Aniket Saraf
- Ramniranjan Jhunjhunwala College, Ghatkopar, Mumbai, India
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, India
| | - Archana Suradkar
- National Centre for Microbial Resource (NCMR), National Centre for Cell Science (NCCS), Pune, India
| | - Josef Elster
- Phycology Centre, Institute of Botany, Academy of Science CR, Třeboň, Czechia
- Centre for Polar Ecology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
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28
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The Hybrid Histidine Kinase HrmK Is an Early-Acting Factor in the Hormogonium Gene Regulatory Network. J Bacteriol 2020; 202:JB.00675-19. [PMID: 31792014 DOI: 10.1128/jb.00675-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/27/2019] [Indexed: 01/15/2023] Open
Abstract
Filamentous, heterocyst-forming cyanobacteria belonging to taxonomic subsections IV and V are developmentally complex multicellular organisms capable of differentiating an array of cell and filament types, including motile hormogonia. Hormogonia exhibit gliding motility that facilitates dispersal, phototaxis, and the establishment of nitrogen-fixing symbioses. The gene regulatory network (GRN) governing hormogonium development involves a hierarchical sigma factor cascade, but the factors governing the activation of this cascade are currently undefined. Here, using a forward genetic approach, we identified hrmK, a gene encoding a putative hybrid histidine kinase that functions upstream of the sigma factor cascade. The deletion of hrmK produced nonmotile filaments that failed to display hormogonium morphology or accumulate hormogonium-specific proteins or polysaccharide. Targeted transcriptional analyses using reverse transcription-quantitative PCR (RT-qPCR) demonstrated that hormogonium-specific genes both within and outside the sigma factor cascade are drastically downregulated in the absence of hrmK and that hrmK may be subject to indirect, positive autoregulation via sigJ and sigC Orthologs of HrmK are ubiquitous among, and exclusive to, heterocyst-forming cyanobacteria. Collectively, these results indicate that hrmK functions upstream of the sigma factor cascade to initiate hormogonium development, likely by modulating the phosphorylation state of an unknown protein that may serve as the master regulator of hormogonium development in heterocyst-forming cyanobacteria.IMPORTANCE Filamentous cyanobacteria are morphologically complex, with several representative species amenable to routine genetic manipulation, making them excellent model organisms for the study of development. Furthermore, two of the developmental alternatives, nitrogen-fixing heterocysts and motile hormogonia, are essential to establish nitrogen-fixing symbioses with plant partners. These symbioses are integral to global nitrogen cycles and could be artificially recreated with crop plants to serve as biofertilizers, but to achieve this goal, detailed understanding and manipulation of the hormogonium and heterocyst gene regulatory networks may be necessary. Here, using the model organism Nostoc punctiforme, we identify a previously uncharacterized hybrid histidine kinase that is confined to heterocyst-forming cyanobacteria as the earliest known participant in hormogonium development.
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29
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Wiltbank LB, Kehoe DM. Diverse light responses of cyanobacteria mediated by phytochrome superfamily photoreceptors. Nat Rev Microbiol 2020; 17:37-50. [PMID: 30410070 DOI: 10.1038/s41579-018-0110-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Cyanobacteria are an evolutionarily and ecologically important group of prokaryotes. They exist in diverse habitats, ranging from hot springs and deserts to glaciers and the open ocean. The range of environments that they inhabit can be attributed in part to their ability to sense and respond to changing environmental conditions. As photosynthetic organisms, one of the most crucial parameters for cyanobacteria to monitor is light. Cyanobacteria can sense various wavelengths of light and many possess a range of bilin-binding photoreceptors belonging to the phytochrome superfamily. Vital cellular processes including growth, phototaxis, cell aggregation and photosynthesis are tuned to environmental light conditions by these photoreceptors. In this Review, we examine the physiological responses that are controlled by members of this diverse family of photoreceptors and discuss the signal transduction pathways through which these photoreceptors operate. We highlight specific examples where the activities of multiple photoreceptors function together to fine-tune light responses. We also discuss the potential application of these photosensing systems in optogenetics and synthetic biology.
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Affiliation(s)
- Lisa B Wiltbank
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - David M Kehoe
- Department of Biology, Indiana University, Bloomington, IN, USA.
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30
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Li X, Mustila H, Magnuson A, Stensjö K. Homologous overexpression of NpDps2 and NpDps5 increases the tolerance for oxidative stress in the multicellular cyanobacterium Nostoc punctiforme. FEMS Microbiol Lett 2019; 365:5071947. [PMID: 30107525 PMCID: PMC6116882 DOI: 10.1093/femsle/fny198] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 08/10/2018] [Indexed: 12/30/2022] Open
Abstract
The filamentous cyanobacterium Nostoc punctiforme has several oxidative stress-managing systems, including Dps proteins. Dps proteins belong to the ferritin superfamily and are involved in abiotic stress management in prokaryotes. Previously, we found that one of the five Dps proteins in N. punctiforme, NpDps2, was critical for H2O2 tolerance. Stress induced by high light intensities is aggravated in N. punctiforme strains deficient of either NpDps2, or the bacterioferritin-like NpDps5. Here, we have investigated the capacity of NpDps2 and NpDps5 to enhance stress tolerance by homologous overexpression of these two proteins in N. punctiforme. Both overexpression strains were found to tolerate twice as high concentrations of added H2O2 as the control strain, indicating that overexpression of either NpDps2 or NpDps5 will enhance the capacity for H2O2 tolerance. Under high light intensities, the overexpression of the two NpDps did not enhance the tolerance against general light-induced stress. However, overexpression of the heterocyst-specific NpDps5 in all cells of the filament led to a higher amount of chlorophyll-binding proteins per cell during diazotrophic growth. The OENpDps5 strain also showed an increased tolerance to ammonium-induced oxidative stress. Our results provide information of how Dps proteins may be utilised for engineering of cyanobacteria with enhanced stress tolerance.
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Affiliation(s)
- Xin Li
- Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, SE 75120 Uppsala, Swedens
| | - Henna Mustila
- Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, SE 75120 Uppsala, Swedens
| | - Ann Magnuson
- Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, SE 75120 Uppsala, Swedens
| | - Karin Stensjö
- Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, SE 75120 Uppsala, Swedens
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31
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Chang ACG, Chen T, Li N, Duan J. Perspectives on Endosymbiosis in Coralloid Roots: Association of Cycads and Cyanobacteria. Front Microbiol 2019; 10:1888. [PMID: 31474965 PMCID: PMC6702271 DOI: 10.3389/fmicb.2019.01888] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 07/30/2019] [Indexed: 12/30/2022] Open
Abstract
Past endosymbiotic events allowed photosynthetic organisms to flourish and evolve in terrestrial areas. The precursor of chloroplasts was an ancient photosynthetic cyanobacterium. Presently, cyanobacteria are still capable of establishing successful symbioses in a wide range of hosts. One particular host plant among the gymnosperms is cycads (Order Cycadales) in which a special type of root system, referred to as coralloid roots, develops to house symbiotic cyanobacteria. A number of studies have explained coralloid root formation and cyanobiont invasion but the questions on mechanisms of this host-microbe association remains vague. Most researches focus on diversity of symbionts in coralloid roots but equally important is to explore the underlying mechanisms of cycads-Nostoc symbiosis as well. Besides providing an overview of relevant areas presently known about this association and citing putative genes involved in cycad-cyanobacteria symbioses, this paper aims to identify the limitations that hamper attempts to get to the root of the matter and suggests future research directions that may prove useful.
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Affiliation(s)
- Aimee Caye G. Chang
- University of Chinese Academy of Sciences, Beijing, China
- Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen, China
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Tao Chen
- Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen, China
| | - Nan Li
- Fairy Lake Botanical Garden, Chinese Academy of Sciences, Shenzhen, China
| | - Jun Duan
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
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32
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Structural diffusion properties of two atypical Dps from the cyanobacterium Nostoc punctiforme disclose interactions with ferredoxins and DNA. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:148063. [PMID: 31419396 DOI: 10.1016/j.bbabio.2019.148063] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 08/06/2019] [Accepted: 08/10/2019] [Indexed: 12/14/2022]
Abstract
Ferritin-like proteins, Dps (DNA-binding protein from starved cells), store iron and play a key role in the iron homeostasis in bacteria, yet their iron releasing machinery remains largely unexplored. The electron donor proteins that may interact with Dps and promote the mobilization of the stored iron have hitherto not been identified. Here, we investigate the binding capacity of the two atypical Dps proteins NpDps4 and NpDps5 from Nostoc punctiforme to isolated ferredoxins. We report NpDps-ferredoxin interactions by fluorescence correlation spectroscopy (FCS) and fluorescence resonance energy transfer (FRET) methods. Dynamic light scattering, size exclusion chromatography and native gel electrophoresis results show that NpDps4 forms a dodecamer at both pH 6.0 and pH 8.0, while NpDps5 forms a dodecamer only at pH 6.0. In addition, FCS data clearly reveal that the non-canonical NpDps5 interacts with DNA at pH 6.0. Our spectroscopic analysis shows that [FeS] centers of the three recombinantly expressed and isolated ferredoxins are properly incorporated and are consistent with their respective native states. The results support our hypothesis that ferredoxins could be involved in cellular iron homeostasis by interacting with Dps and assisting the release of stored iron.
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Nelson JM, Hauser DA, Gudiño JA, Guadalupe YA, Meeks JC, Salazar Allen N, Villarreal JC, Li FW. Complete Genomes of Symbiotic Cyanobacteria Clarify the Evolution of Vanadium-Nitrogenase. Genome Biol Evol 2019; 11:1959-1964. [PMID: 31243438 PMCID: PMC6645180 DOI: 10.1093/gbe/evz137] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2019] [Indexed: 02/07/2023] Open
Abstract
Plant endosymbiosis with nitrogen-fixing cyanobacteria has independently evolved in diverse plant lineages, offering a unique window to study the evolution and genetics of plant-microbe interaction. However, very few complete genomes exist for plant cyanobionts, and therefore little is known about their genomic and functional diversity. Here, we present four complete genomes of cyanobacteria isolated from bryophytes. Nanopore long-read sequencing allowed us to obtain circular contigs for all the main chromosomes and most of the plasmids. We found that despite having a low 16S rRNA sequence divergence, the four isolates exhibit considerable genome reorganizations and variation in gene content. Furthermore, three of the four isolates possess genes encoding vanadium (V)-nitrogenase (vnf), which is uncommon among diazotrophs and has not been previously reported in plant cyanobionts. In two cases, the vnf genes were found on plasmids, implying possible plasmid-mediated horizontal gene transfers. Comparative genomic analysis of vnf-containing cyanobacteria further identified a conserved gene cluster. Many genes in this cluster have not been functionally characterized and would be promising candidates for future studies to elucidate V-nitrogenase function and regulation.
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Affiliation(s)
- Jessica M Nelson
- Boyce Thompson Institute, Ithaca, New York
- Plant Biology Section, Cornell University, Ithaca, New York
| | - Duncan A Hauser
- Boyce Thompson Institute, Ithaca, New York
- Plant Biology Section, Cornell University, Ithaca, New York
| | - José A Gudiño
- Smithsonian Tropical Research Institute, Panama City, Panama
| | | | - John C Meeks
- Department of Microbiology and Molecular Genetics, University of California, Davis, California
| | | | - Juan Carlos Villarreal
- Smithsonian Tropical Research Institute, Panama City, Panama
- Department of Biology, Laval University, Quebec City, Quebec, Canada
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, New York
- Plant Biology Section, Cornell University, Ithaca, New York
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Dehm D, Krumbholz J, Baunach M, Wiebach V, Hinrichs K, Guljamow A, Tabuchi T, Jenke-Kodama H, Süssmuth RD, Dittmann E. Unlocking the Spatial Control of Secondary Metabolism Uncovers Hidden Natural Product Diversity in Nostoc punctiforme. ACS Chem Biol 2019; 14:1271-1279. [PMID: 31091070 DOI: 10.1021/acschembio.9b00240] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Filamentous cyanobacteria belong to the most prolific producers of structurally unique and biologically active natural products, yet the majority of biosynthetic gene clusters predicted for these multicellular collectives are currently orphan. Here, we present a systems analysis of secondary metabolite gene expression in the model strain Nostoc punctiforme PCC73102 using RNA-seq and fluorescence reporter analysis. Our data demonstrate that the majority of the cryptic gene clusters are not silent but are expressed with regular or sporadic pattern. Cultivation of N. punctiforme using high-density fermentation overrules the spatial control and leads to a pronounced upregulation of more than 50% of biosynthetic gene clusters. Our data suggest that a combination of autocrine factors, a high CO2 level, and high light account for the upregulation of individual pathways. Our overarching study not only sheds light on the strategies of filamentous cyanobacteria to share the enormous metabolic burden connected with the production of specialized molecules but provides an avenue for the genome-based discovery of natural products in multicellular cyanobacteria as exemplified by the discovery of highly unusual variants of the tricyclic peptide microviridin.
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Affiliation(s)
- Daniel Dehm
- University of Potsdam , Institute for Biochemistry and Biology , Karl-Liebknecht-Str. 24/25 , 14476 Potsdam-Golm , Germany
| | - Julia Krumbholz
- University of Potsdam , Institute for Biochemistry and Biology , Karl-Liebknecht-Str. 24/25 , 14476 Potsdam-Golm , Germany
| | - Martin Baunach
- University of Potsdam , Institute for Biochemistry and Biology , Karl-Liebknecht-Str. 24/25 , 14476 Potsdam-Golm , Germany
| | - Vincent Wiebach
- Fakultät II - Institut für Chemie , Technische Universität Berlin , Straße des 17. Juni 124 , 10623 Berlin , Germany
| | - Katrin Hinrichs
- University of Potsdam , Institute for Biochemistry and Biology , Karl-Liebknecht-Str. 24/25 , 14476 Potsdam-Golm , Germany
| | - Arthur Guljamow
- University of Potsdam , Institute for Biochemistry and Biology , Karl-Liebknecht-Str. 24/25 , 14476 Potsdam-Golm , Germany
| | - Takeshi Tabuchi
- Microbiology and Biochemistry of Secondary Metabolites Unit . Okinawa Institute of Science and Technology , Tancha 1919-1 , Onna-son , 904-0495 Okinawa , Japan
| | - Holger Jenke-Kodama
- Microbiology and Biochemistry of Secondary Metabolites Unit . Okinawa Institute of Science and Technology , Tancha 1919-1 , Onna-son , 904-0495 Okinawa , Japan
| | - Roderich D Süssmuth
- Fakultät II - Institut für Chemie , Technische Universität Berlin , Straße des 17. Juni 124 , 10623 Berlin , Germany
| | - Elke Dittmann
- University of Potsdam , Institute for Biochemistry and Biology , Karl-Liebknecht-Str. 24/25 , 14476 Potsdam-Golm , Germany
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Gonzalez A, Riley KW, Harwood TV, Zuniga EG, Risser DD. A Tripartite, Hierarchical Sigma Factor Cascade Promotes Hormogonium Development in the Filamentous Cyanobacterium Nostoc punctiforme. mSphere 2019; 4:e00231-19. [PMID: 31043519 PMCID: PMC6495340 DOI: 10.1128/msphere.00231-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 04/12/2019] [Indexed: 11/24/2022] Open
Abstract
Cyanobacteria are prokaryotes capable of oxygenic photosynthesis, and frequently, nitrogen fixation as well. As a result, they contribute substantially to global primary production and nitrogen cycles. Furthermore, the multicellular filamentous cyanobacteria in taxonomic subsections IV and V are developmentally complex, exhibiting an array of differentiated cell types and filaments, including motile hormogonia, making them valuable model organisms for studying development. To investigate the role of sigma factors in the gene regulatory network (GRN) controlling hormogonium development, a combination of genetic, immunological, and time-resolved transcriptomic analyses were conducted in the model filamentous cyanobacterium Nostoc punctiforme, which, unlike other common model cyanobacteria, retains the developmental complexity of field isolates. The results support a model where the hormogonium GRN is driven by a hierarchal sigma factor cascade, with sigJ activating the expression of both sigC and sigF, as well as a substantial portion of additional hormogonium-specific genes, including those driving changes to cellular architecture. In turn, sigC regulates smaller subsets of genes for several processes, plays a dominant role in promoting reductive cell division, and may also both positively and negatively regulate sigJ to reinforce the developmental program and coordinate the timing of gene expression, respectively. In contrast, the sigF regulon is extremely limited. Among genes with characterized roles in hormogonium development, only pilA shows stringent sigF dependence. For sigJ-dependent genes, a putative consensus promoter was also identified, consisting primarily of a highly conserved extended -10 region, here designated a J-Box, which is widely distributed among diverse members of the cyanobacterial lineage.IMPORTANCE Cyanobacteria are integral to global carbon and nitrogen cycles, and their metabolic capacity coupled with their ease of genetic manipulation make them attractive platforms for applications such as biomaterial and biofertilizer production. Achieving these goals will likely require a detailed understanding and precise rewiring of these organisms' GRNs. The complex phenotypic plasticity of filamentous cyanobacteria has also made them valuable models of prokaryotic development. However, current research has been limited by focusing primarily on a handful of model strains which fail to reflect the phenotypes of field counterparts, potentially limiting biotechnological advances and a more comprehensive understanding of developmental complexity. Here, using Nostoc punctiforme, a model filamentous cyanobacterium that retains the developmental range of wild isolates, we define previously unknown definitive roles for a trio of sigma factors during hormogonium development. These findings substantially advance our understanding of cyanobacterial development and gene regulation and could be leveraged for future applications.
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Affiliation(s)
- Alfonso Gonzalez
- Department of Biology, University of the Pacific, Stockton, California, USA
| | - Kelsey W Riley
- Department of Biology, University of the Pacific, Stockton, California, USA
| | - Thomas V Harwood
- Department of Biology, University of the Pacific, Stockton, California, USA
| | - Esthefani G Zuniga
- Department of Biology, University of the Pacific, Stockton, California, USA
| | - Douglas D Risser
- Department of Biology, University of the Pacific, Stockton, California, USA
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Inoue-Sakamoto K, Nazifi E, Tsuji C, Asano T, Nishiuchi T, Matsugo S, Ishihara K, Kanesaki Y, Yoshikawa H, Sakamoto T. Characterization of mycosporine-like amino acids in the cyanobacterium Nostoc verrucosum. J GEN APPL MICROBIOL 2018; 64:203-211. [PMID: 29709901 DOI: 10.2323/jgam.2017.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The aquatic cyanobacterium Nostoc verrucosum forms macroscopic colonies in streams, and its appearance is superficially similar to that of the terrestrial cyanobacterium Nostoc commune. N. verrucosum is sensitive to desiccation, unlike N. commune, although these Nostoc cyanobacterial species share physiological features, including massive extracellular polysaccharide production and trehalose accumulation capability. In this study, water-soluble sunscreen pigments of mycosporine-like amino acids (MAAs) were characterized in N. verrucosum, and the mysABCD genes responsible for MAA biosynthesis in N. verrucosum and N. commune were compared. N. verrucosum produced porphyra-334 and shinorine, with porphyra-334 accounting for >90% of the total MAAs. Interestingly, porphyra-334 is an atypical cyanobacteial MAA, whereas shinorine is known as a common and dominant MAA in cyanobacteria. Porphyra-334 from N. verrucosum showed little or no radical scavenging activity in vitro, although the glycosylated derivatives of porphyra-334 from N. commune are potent radical scavengers. The presence of the mysABCD gene cluster in N. commune strain KU002 (genotype A) supported its porphyra-334 producing capability via the Nostoc-type mechanism, although the genotype A of N. commune mainly produces the arabinose-bound porphyra-334. The mysABC gene cluster was conserved in N. verrucosum, but the mysD gene was not included in the cluster. These results suggest that the mysABCD gene products are involved in the biosynthesis of porphyra-334 commonly in these Nostoc species, and that the genotype A of N. commune additionally acquired the glycosylation of porphyra-334.
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Affiliation(s)
- Kaori Inoue-Sakamoto
- Department of Applied Bioscience, College of Bioscience and Chemistry, Kanazawa Institute of Technology
| | - Ehsan Nazifi
- Division of Life Science, Graduate School of Natural Science and Technology, Kanazawa University
| | - Chieri Tsuji
- Division of Biological Sciences, Graduate School of Natural Science and Technology, Kanazawa University
| | - Tomoya Asano
- Division of Functional Genomics, Advanced Science Research Center, Kanazawa University
| | - Takumi Nishiuchi
- Division of Functional Genomics, Advanced Science Research Center, Kanazawa University
| | - Seiichi Matsugo
- School of Natural System, College of Science and Engineering, Kanazawa University
| | - Kenji Ishihara
- Marine Biochemistry Division, National Research Institute of Fisheries Science
| | - Yu Kanesaki
- NODAI Genome Research Center, Tokyo University of Agriculture
| | | | - Toshio Sakamoto
- Division of Life Science, Graduate School of Natural Science and Technology, Kanazawa University.,Division of Biological Sciences, Graduate School of Natural Science and Technology, Kanazawa University.,School of Natural System, College of Science and Engineering, Kanazawa University
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37
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Pokharel R, Gerrits R, Schuessler JA, Frings PJ, Sobotka R, Gorbushina AA, von Blanckenburg F. Magnesium Stable Isotope Fractionation on a Cellular Level Explored by Cyanobacteria and Black Fungi with Implications for Higher Plants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:12216-12224. [PMID: 30351034 DOI: 10.1021/acs.est.8b02238] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In a controlled growth experiment we found that the cyanobacterium Nostoc punctiforme has a bulk cell 26Mg/24Mg ratio (expressed as δ26Mg) that is -0.27‰ lower than the growth solution at a pH of ca. 5.9. This contrasts with a recently published δ26Mg value that was 0.65‰ higher than growth solution for the black fungus Knufia petricola at similar laboratory conditions, interpreted to reflect loss of 24Mg during cell growth. By a mass balance model constrained by δ26Mg in chlorophyll extract we inferred the δ26 Mg value of the main Mg compartments in a cyanobacteria cell: free cytosolic Mg (-2.64‰), chlorophyll (1.85‰), and the nonchlorophyll-bonded Mg compartments like ATP and ribosomes (-0.64‰). The lower δ26Mg found in Nostoc punctiforme would thus result from the absence of significant Mg efflux during cell growth in combination with either (a) discrimination against 26Mg during uptake by desolvation of Mg or transport across protein channels or (b) discrimination against 24Mg in the membrane transporter during efflux. The model predicts the preferential incorporation of 26Mg in cells and plant organs low in Mg and the absence of isotope fractionation in those high in Mg, corroborated by a compilation of Mg isotope ratios from fungi, bacteria, and higher plants.
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Affiliation(s)
- Rasesh Pokharel
- GFZ German Research Centre for Geosciences , Section 3.3, Earth Surface Geochemistry, Telegrafenberg, 14473 Potsdam , Germany
- Institute of Geological Sciences , Freie Universität Berlin , 12249 Berlin , Germany
| | - Ruben Gerrits
- Department 4, Materials & Environment , BAM Federal Institute for Materials Research & Testing , 12205 Berlin , Germany
- Department of Biology, Chemistry and Pharmacy , Freie Universität Berlin , 14195 Berlin , Germany
| | - Jan A Schuessler
- GFZ German Research Centre for Geosciences , Section 3.3, Earth Surface Geochemistry, Telegrafenberg, 14473 Potsdam , Germany
| | - Patrick J Frings
- GFZ German Research Centre for Geosciences , Section 3.3, Earth Surface Geochemistry, Telegrafenberg, 14473 Potsdam , Germany
| | - Roman Sobotka
- Institute of Microbiology , Centre Algatech , 379 81 Třebon , Czech Republic
| | - Anna A Gorbushina
- Institute of Geological Sciences , Freie Universität Berlin , 12249 Berlin , Germany
- Department 4, Materials & Environment , BAM Federal Institute for Materials Research & Testing , 12205 Berlin , Germany
- Department of Biology, Chemistry and Pharmacy , Freie Universität Berlin , 14195 Berlin , Germany
| | - Friedhelm von Blanckenburg
- GFZ German Research Centre for Geosciences , Section 3.3, Earth Surface Geochemistry, Telegrafenberg, 14473 Potsdam , Germany
- Institute of Geological Sciences , Freie Universität Berlin , 12249 Berlin , Germany
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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.
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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
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Riley KW, Gonzalez A, Risser DD. A partner-switching regulatory system controls hormogonium development in the filamentous cyanobacterium Nostoc punctiforme. Mol Microbiol 2018; 109:555-569. [PMID: 29995991 DOI: 10.1111/mmi.14061] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2018] [Indexed: 11/29/2022]
Abstract
Filamentous cyanobacteria exhibit developmental complexity, including the transient differentiation of motile hormogonia in many species. Using a forward genetic approach, a trio of genes unique to filamentous cyanobacteria encoding a putative Rsb-like partner-switching regulatory system (PSRS) was implicated in regulating hormogonium development in the model filamentous cyanobacterium Nostoc punctiforme. Analysis of in-frame deletion strains indicated that HmpU (putative serine phosphatase) and HmpV (STAS domain) enhance, while HmpW (putative serine kinase) represses motility and persistence of the hormogonium state. Protein-protein interaction studies demonstrated specificity between HmpW and HmpV. Epistasis analysis between hmpW and hmpV was consistent with HmpV acting as the downstream effector of the system, rather than regulation of a sigma factor by HmpW. Deletion of hmpU or hmpV reduced accumulation of extracellular PilA and hormogonium polysaccharide (HPS), and expression of type IV pilus- and HPS-specific genes was reduced in the ΔhmpV strain. Expression of the Hmp PSRS is induced in hormogonia, and the cytoplasmic localization of HmpV-GFPuv implies that its downstream target is probably cytoplasmic as well. Collectively, these results support a model where HmpU and HmpW antagonistically regulate the phosphorylation state of HmpV, and subsequently, unphosphorylated HmpV positively regulates an undefined downstream target to affect hormogonium-specific gene expression.
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Affiliation(s)
- Kelsey W Riley
- Department of Biology, University of the Pacific, Stockton, CA, 95211, USA
| | - Alfonso Gonzalez
- Department of Biology, University of the Pacific, Stockton, CA, 95211, USA
| | - Douglas D Risser
- Department of Biology, University of the Pacific, Stockton, CA, 95211, USA
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40
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Hu L, Xiao P, Jiang Y, Dong M, Chen Z, Li H, Hu Z, Lei A, Wang J. Transgenerational Epigenetic Inheritance Under Environmental Stress by Genome-Wide DNA Methylation Profiling in Cyanobacterium. Front Microbiol 2018; 9:1479. [PMID: 30022974 PMCID: PMC6039552 DOI: 10.3389/fmicb.2018.01479] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/13/2018] [Indexed: 11/19/2022] Open
Abstract
Epigenetic modifications such as DNA methylation are well known as connected with many important biological processes. Rapid accumulating evidence shows environmental stress can generate particular defense epigenetic changes across generations in eukaryotes. This transgenerational epigenetic inheritance in animals and plants has gained interest over the last years. Cyanobacteria play very crucial role in the earth, and as the primary producer they can adapt to nearly all diverse environments. However, few knowledge about the genome wide epigenetic information such as methylome information in cyanobacteria, especially under any environment stress, was reported so far. In this study we profiled the genome-wide cytosine methylation from a model cyanobacterium Synechocystis sp. PCC 6803, and explored the possibility of transgenerational epigenetic process in this ancient single-celled prokaryote by comparing the DNA methylomes among normal nitrogen medium cultivation, nitrogen starvation for 72 h and nitrogen recovery for about 12 generations. Our results shows that DNA methylation patterns in nitrogen starvation and nitrogen recovery are much more similar with each other, significantly different from that of the normal nitrogen. This study reveals the difference in global DNA methylation pattern of cyanobacteria between normal and nutrient stress conditions and reports the evidence of transgenerational epigenetic process in cyanobacteria. The results of this study may contribute to a better understanding of epigenetic regulation in prokaryotic adaptation to and survive in the ever changing environment.
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Affiliation(s)
- Lang Hu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Nanshan District Key Lab for Biopolymers and Safety Evaluation, College of Materials Science and Engineering, Shenzhen University, Shenzhen, China
| | - Peng Xiao
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Yongguang Jiang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Mingjie Dong
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Zixi Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Hui Li
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Zhangli Hu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Anping Lei
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Jiangxin Wang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Shenzhen Engineering Laboratory for Marine Algal Biotechnology, Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Nanshan District Key Lab for Biopolymers and Safety Evaluation, College of Materials Science and Engineering, Shenzhen University, Shenzhen, China
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41
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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.
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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.
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Warshan D, Liaimer A, Pederson E, Kim SY, Shapiro N, Woyke T, Altermark B, Pawlowski K, Weyman PD, Dupont CL, Rasmussen U. Genomic Changes Associated with the Evolutionary Transitions of Nostoc to a Plant Symbiont. Mol Biol Evol 2018; 35:1160-1175. [PMID: 29554291 PMCID: PMC5913679 DOI: 10.1093/molbev/msy029] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Cyanobacteria belonging to the genus Nostoc comprise free-living strains and also facultative plant symbionts. Symbiotic strains can enter into symbiosis with taxonomically diverse range of host plants. Little is known about genomic changes associated with evolutionary transition of Nostoc from free-living to plant symbiont. Here, we compared the genomes derived from 11 symbiotic Nostoc strains isolated from different host plants and infer phylogenetic relationships between strains. Phylogenetic reconstructions of 89 Nostocales showed that symbiotic Nostoc strains with a broad host range, entering epiphytic and intracellular or extracellular endophytic interactions, form a monophyletic clade indicating a common evolutionary history. A polyphyletic origin was found for Nostoc strains which enter only extracellular symbioses, and inference of transfer events implied that this trait was likely acquired several times in the evolution of the Nostocales. Symbiotic Nostoc strains showed enriched functions in transport and metabolism of organic sulfur, chemotaxis and motility, as well as the uptake of phosphate, branched-chain amino acids, and ammonium. The genomes of the intracellular clade differ from that of other Nostoc strains, with a gain/enrichment of genes encoding proteins to generate l-methionine from sulfite and pathways for the degradation of the plant metabolites vanillin and vanillate, and of the macromolecule xylan present in plant cell walls. These compounds could function as C-sources for members of the intracellular clade. Molecular clock analysis indicated that the intracellular clade emerged ca. 600 Ma, suggesting that intracellular Nostoc symbioses predate the origin of land plants and the emergence of their extant hosts.
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Affiliation(s)
- Denis Warshan
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Anton Liaimer
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Eric Pederson
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Sea-Yong Kim
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Nicole Shapiro
- US Department of Energy Joint Genome Institute, Walnut Creek, CA
| | - Tanja Woyke
- US Department of Energy Joint Genome Institute, Walnut Creek, CA
| | - Bjørn Altermark
- Department of Chemistry, Faculty of Science and Technology, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Philip D Weyman
- Department of Synthetic Biology and Bioenergy, J. Craig Venter Institute, La Jolla, CA
| | - Christopher L Dupont
- Department of Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA
| | - Ulla Rasmussen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
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43
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Nishizuka H, Hashidoko Y. Comparison of Nostocean hormogonium induction and its motility on solid plates between agar and gellan gum at varying gel matrix concentrations. Biosci Biotechnol Biochem 2018; 82:525-531. [PMID: 29375025 DOI: 10.1080/09168451.2017.1420464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
To establish a sensitive bioassay for Nostocean hormogonium induction, we compared the effectiveness of the morpho-differentiation induction on two gelled plates, agar and gellan gum, for anacardic acid C15:1-Δ8 decyl ester (1) (100 nmol/disc). On BG-110 (nitrogen-free) medium-based 0.6 and 0.8% agar plates, Nostoc sp. strain Yaku-1 isolated from a coralloid root of Cycas revoluta in Yakushima Island showed clear morpho-differentiation from filamentous aggregates into hormogonia, and the induced hormogonia dispersed within 24 h; however, similar hormogonium formation was not observed at agar concentrations of 1.0% or higher. Conversely, hormogonium induction was considerably more pronounced on gellan gum plates than those on agar plates through concentrations ranging from 0.6 to 1.6% even after 12 h of incubation, particularly active on the 0.8-1.0% gellan gum plates. Thus, gellan gum plates can achieve clear results within 12 h and are thus highly useful for primary screening for hormogonium-inducing factors (HIFs).
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Affiliation(s)
- Hiroaki Nishizuka
- a Graduate School of Agriculture , Hokkaido University , Sapporo , Japan
| | - Yasuyuki Hashidoko
- a Graduate School of Agriculture , Hokkaido University , Sapporo , Japan.,b Research Faculty of Agriculture , Hokkaido University , Sapporo , Japan
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44
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Inoue-Sakamoto K, Tanji Y, Yamaba M, Natsume T, Masaura T, Asano T, Nishiuchi T, Sakamoto T. Characterization of extracellular matrix components from the desiccation-tolerant cyanobacterium Nostoc commune. J GEN APPL MICROBIOL 2018; 64:15-25. [DOI: 10.2323/jgam.2017.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Kaori Inoue-Sakamoto
- Department of Applied Bioscience, College of Bioscience and Chemistry, Kanazawa Institute of Technology
| | - Yasunori Tanji
- Division of Biological Sciences, Graduate School of Natural Science and Technology, Kanazawa University
| | - Minami Yamaba
- Division of Biological Sciences, Graduate School of Natural Science and Technology, Kanazawa University
| | - Takumi Natsume
- School of Natural System, College of Science and Engineering, Kanazawa University
| | - Takuya Masaura
- Division of Biological Sciences, Graduate School of Natural Science and Technology, Kanazawa University
| | - Tomoya Asano
- Division of Functional Genomics, Advanced Science Research Center, Kanazawa University
| | - Takumi Nishiuchi
- Division of Functional Genomics, Advanced Science Research Center, Kanazawa University
| | - Toshio Sakamoto
- Division of Biological Sciences, Graduate School of Natural Science and Technology, Kanazawa University
- School of Natural System, College of Science and Engineering, Kanazawa University
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45
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Gomes MP, Garcia QS, Barreto LC, Pimenta LPS, Matheus MT, Figueredo CC. Allelopathy: An overview from micro- to macroscopic organisms, from cells to environments, and the perspectives in a climate-changing world. Biologia (Bratisl) 2017. [DOI: 10.1515/biolog-2017-0019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Moraes LE, Blow MJ, Hawley ER, Piao H, Kuo R, Chiniquy J, Shapiro N, Woyke T, Fadel JG, Hess M. Resequencing and annotation of the Nostoc punctiforme ATTC 29133 genome: facilitating biofuel and high-value chemical production. AMB Express 2017; 7:42. [PMID: 28211005 PMCID: PMC5313495 DOI: 10.1186/s13568-017-0338-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 02/03/2017] [Indexed: 01/13/2023] Open
Abstract
Cyanobacteria have the potential to produce bulk and fine chemicals and members belonging to Nostoc sp. have received particular attention due to their relatively fast growth rate and the relative ease with which they can be harvested. Nostoc punctiforme is an aerobic, motile, Gram-negative, filamentous cyanobacterium that has been studied intensively to enhance our understanding of microbial carbon and nitrogen fixation. The genome of the type strain N. punctiforme ATCC 29133 was sequenced in 2001 and the scientific community has used these genome data extensively since then. Advances in bioinformatics tools for sequence annotation and the importance of this organism prompted us to resequence and reanalyze its genome and to make both, the initial and improved annotation, available to the scientific community. The new draft genome has a total size of 9.1 Mbp and consists of 65 contiguous pieces of DNA with a GC content of 41.38% and 7664 protein-coding genes. Furthermore, the resequenced genome is slightly (5152 bp) larger and contains 987 more genes with functional prediction when compared to the previously published version. We deposited the annotation of both genomes in the Department of Energy's IMG database to facilitate easy genome exploration by the scientific community without the need of in-depth bioinformatics skills. We expect that an facilitated access and ability to search the N. punctiforme ATCC 29133 for genes of interest will significantly facilitate metabolic engineering and genome prospecting efforts and ultimately the synthesis of biofuels and natural products from this keystone organism and closely related cyanobacteria.
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Affiliation(s)
- Luis E. Moraes
- Department of Animal Science, University of California, Davis, 2251 Meyer Hall, Davis, CA 95616 USA
| | - Matthew J. Blow
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598 USA
| | | | - Hailan Piao
- Washington State University, Richland, WA 99354 USA
| | - Rita Kuo
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Jennifer Chiniquy
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Nicole Shapiro
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - James G. Fadel
- Department of Animal Science, University of California, Davis, 2251 Meyer Hall, Davis, CA 95616 USA
| | - Matthias Hess
- Department of Animal Science, University of California, Davis, 2251 Meyer Hall, Davis, CA 95616 USA
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598 USA
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Genome Sequence and Composition of a Tolyporphin-Producing Cyanobacterium-Microbial Community. Appl Environ Microbiol 2017; 83:AEM.01068-17. [PMID: 28754701 DOI: 10.1128/aem.01068-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 07/19/2017] [Indexed: 11/20/2022] Open
Abstract
The cyanobacterial culture HT-58-2 was originally described as a strain of Tolypothrix nodosa with the ability to produce tolyporphins, which comprise a family of distinct tetrapyrrole macrocycles with reported efflux pump inhibition properties. Upon reviving the culture from what was thought to be a nonextant collection, studies of culture conditions, strain characterization, phylogeny, and genomics have been undertaken. Here, HT-58-2 was shown by 16S rRNA analysis to closely align with Brasilonema strains and not with Tolypothrix isolates. Light, fluorescence, and scanning electron microscopy revealed cyanobacterium filaments that are decorated with attached bacteria and associated with free bacteria. Metagenomic surveys of HT-58-2 cultures revealed a diversity of bacteria dominated by Erythrobacteraceae, 97% of which are Porphyrobacter species. A dimethyl sulfoxide washing procedure was found to yield enriched cyanobacterial DNA (presumably by removing community bacteria) and sequence data sufficient for genome assembly. The finished, closed HT-58-2Cyano genome consists of 7.85 Mbp (42.6% G+C) and contains 6,581 genes. All genes for biosynthesis of tetrapyrroles (e.g., heme, chlorophyll a, and phycocyanobilin) and almost all for cobalamin were identified dispersed throughout the chromosome. Among the 6,177 protein-encoding genes, coding sequences (CDSs) for all but two of the eight enzymes for conversion of glutamic acid to protoporphyrinogen IX also were found within one major gene cluster. The cluster also includes 10 putative genes (and one hypothetical gene) encoding proteins with domains for a glycosyltransferase, two cytochrome P450 enzymes, and a flavin adenine dinucleotide (FAD)-binding protein. The composition of the gene cluster suggests a possible role in tolyporphin biosynthesis.IMPORTANCE A worldwide search more than 25 years ago for cyanobacterial natural products with anticancer activity identified a culture (HT-58-2) from Micronesia that produces tolyporphins. Tolyporphins are tetrapyrroles, like chlorophylls, but have several profound structural differences that reside outside the bounds of known biosynthetic pathways. To begin probing the biosynthetic origin and biological function of tolyporphins, our research has focused on studying the cyanobacterial strain, about which almost nothing has been previously reported. We find that the HT-58-2 culture is composed of the cyanobacterium and a community of associated bacteria, complicating the question of which organisms make tolyporphins. Elucidation of the cyanobacterial genome revealed an intriguing gene cluster that contains tetrapyrrole biosynthesis genes and a collection of unknown genes, suggesting that the cluster may be responsible for tolyporphin production. Knowledge of the genome and the gene cluster sharply focuses research to identify related cyanobacterial producers of tolyporphins and delineate the tolyporphin biosynthetic pathway.
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Lack of Methylated Hopanoids Renders the Cyanobacterium Nostoc punctiforme Sensitive to Osmotic and pH Stress. Appl Environ Microbiol 2017; 83:AEM.00777-17. [PMID: 28455341 DOI: 10.1128/aem.00777-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 04/26/2017] [Indexed: 11/20/2022] Open
Abstract
To investigate the function of 2-methylhopanoids in modern cyanobacteria, the hpnP gene coding for the radical S-adenosyl methionine (SAM) methylase protein that acts on the C-2 position of hopanoids was deleted from the filamentous cyanobacterium Nostoc punctiforme ATCC 29133S. The resulting ΔhpnP mutant lacked all 2-methylhopanoids but was found to produce much higher levels of two bacteriohopanepentol isomers than the wild type. Growth rates of the ΔhpnP mutant cultures were not significantly different from those of the wild type under standard growth conditions. Akinete formation was also not impeded by the absence of 2-methylhopanoids. The relative abundances of the different hopanoid structures in akinete-dominated cultures of the wild-type and ΔhpnP mutant strains were similar to those of vegetative cell-dominated cultures. However, the ΔhpnP mutant was found to have decreased growth rates under both pH and osmotic stress, confirming a role for 2-methylhopanoids in stress tolerance. Evidence of elevated photosystem II yield and NAD(P)H-dependent oxidoreductase activity in the ΔhpnP mutant under stress conditions, compared to the wild type, suggested that the absence of 2-methylhopanoids increases cellular metabolic rates under stress conditions.IMPORTANCE As the first group of organisms to develop oxygenic photosynthesis, Cyanobacteria are central to the evolutionary history of life on Earth and the subsequent oxygenation of the atmosphere. To investigate the origin of cyanobacteria and the emergence of oxygenic photosynthesis, geobiologists use biomarkers, the remnants of lipids produced by different organisms that are found in geologic sediments. 2-Methylhopanes have been considered indicative of cyanobacteria in some environmental settings, with the parent lipids 2-methylhopanoids being present in many contemporary cyanobacteria. We have created a Nostoc punctiforme ΔhpnP mutant strain that does not produce 2-methylhopanoids to assess the influence of 2-methylhopanoids on stress tolerance. Increased metabolic activity in the mutant under stress indicates compensatory alterations in metabolism in the absence of 2-methylhopanoids.
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Suradkar A, Villanueva C, Gaysina LA, Casamatta DA, Saraf A, Dighe G, Mergu R, Singh P. Nostoc thermotolerans sp. nov., a soil-dwelling species of Nostoc (Cyanobacteria). Int J Syst Evol Microbiol 2017; 67:1296-1305. [PMID: 28109209 DOI: 10.1099/ijsem.0.001800] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A filamentous, soil-dwelling cyanobacterial strain (9C-PST) was isolated from Mandsaur, Madhya Pradesh, India, and is described as a new species of the genus Nostoc. Extensive morphological and molecular characterization along with a thorough assessment of ecology was performed. The style of filament orientation, type and nature of the sheath (e.g. distribution and visibility across the trichome), and vegetative and heterocyte cell dimensions and shape were assessed for over one year using both the laboratory grown culture and the naturally occurring samples. Sequencing of the 16S rRNA gene showed 94 % similarity with Nostocpiscinale CENA21 while analyses of the secondary structures of the 16S-23S ITS region showed unique folding patterns that differentiated this strain from other species of Nostoc. The level of rbcl and rpoC1 gene sequence similarity was 91 and 94 % to Nostocsp. PCC 7524 and Nostocpiscinale CENA21, respectively, while the nifD gene sequence similarity was found to be 99 % with Nostocpiscinale CENA21. The phenotypic, ecological, genetic and phylogenetic observations indicate that the strain 9C-PST represents a novel species of the genus Nostoc with the name proposed being Nostoc thermotolerans sp. nov. according to the International Code of Nomenclature for Algae, Fungi, and Plants.
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Affiliation(s)
- Archana Suradkar
- Microbial Culture Collection (MCC), National Centre for Cell Science (NCCS), Pune, India
| | - Chelsea Villanueva
- Department of Biology, University of North Florida, Jacksonville, FL 32224, USA
| | - Lira A Gaysina
- Department of Bioecology and Biological Education, M. Akmullah Bashkir State Pedagogical University, Ufa 450000, Russian Federation.,All-Russian Research Institute of Phytopathology, Moscow Region, Odintsovo district, B.Vyazyomy, Institute street, 5, Russian Federation
| | - Dale A Casamatta
- Department of Biology, University of North Florida, Jacksonville, FL 32224, USA
| | - Aniket Saraf
- Microbial Culture Collection (MCC), National Centre for Cell Science (NCCS), Pune, India
| | - Gandhali Dighe
- Microbial Culture Collection (MCC), National Centre for Cell Science (NCCS), Pune, India
| | - Ratnaprabha Mergu
- Microbial Culture Collection (MCC), National Centre for Cell Science (NCCS), Pune, India
| | - Prashant Singh
- Microbial Culture Collection (MCC), National Centre for Cell Science (NCCS), Pune, India
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Quantitative Proteomics Shows Extensive Remodeling Induced by Nitrogen Limitation in Prochlorococcusmarinus SS120. mSystems 2017; 2:mSystems00008-17. [PMID: 28593196 PMCID: PMC5451487 DOI: 10.1128/msystems.00008-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 04/26/2017] [Indexed: 12/27/2022] Open
Abstract
Prochlorococcus requires the capability to accommodate to environmental changes in order to proliferate in oligotrophic oceans, in particular regarding nitrogen availability. A precise knowledge of the composition and changes in the proteome can yield fundamental insights into such a response. Here we report a detailed proteome analysis of the important model cyanobacterium Prochlorococcus marinus SS120 after treatment with azaserine, an inhibitor of ferredoxin-dependent glutamate synthase (GOGAT), to simulate extreme nitrogen starvation. In total, 1,072 proteins, corresponding to 57% of the theoretical proteome, were identified-the maximum proteome coverage obtained for any Prochlorococcus strain thus far. Spectral intensity, calibrated quantification by the Hi3 method, was obtained for 1,007 proteins. Statistically significant changes (P value of <0.05) were observed for 408 proteins, with the majority of proteins (92.4%) downregulated after 8 h of treatment. There was a strong decrease in ribosomal proteins upon azaserine addition, while many transporters were increased. The regulatory proteins PII and PipX were decreased, and the global nitrogen regulator NtcA was upregulated. Furthermore, our data for Prochlorococcus indicate that NtcA also participates in the regulation of photosynthesis. Prochlorococcus responds to the lack of nitrogen by slowing down translation, while inducing photosynthetic cyclic electron flow and biosynthesis of proteins involved in nitrogen uptake and assimilation. IMPORTANCEProchlorococcus is the most abundant photosynthetic organism on Earth, contributing significantly to global primary production and playing a prominent role in biogeochemical cycles. Here we study the effects of extreme nitrogen limitation, a feature of the oligotrophic oceans inhabited by this organism. Quantitative proteomics allowed an accurate quantification of the Prochlorococcus proteome, finding three main responses to nitrogen limitation: upregulation of nitrogen assimilation-related proteins, including transporters; downregulation of ribosome proteins; and induction of the photosystem II cyclic electron flow. This suggests that nitrogen limitation affects a range of metabolic processes far wider than initially believed, with the ultimate goal of saving nitrogen and maximizing the nitrogen uptake and assimilation capabilities of the cell.
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