1
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Baunach M, Guljamow A, Miguel-Gordo M, Dittmann E. Harnessing the potential: advances in cyanobacterial natural product research and biotechnology. Nat Prod Rep 2024; 41:347-369. [PMID: 38088806 DOI: 10.1039/d3np00045a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
Covering: 2000 to 2023Cyanobacteria produce a variety of bioactive natural products that can pose a threat to humans and animals as environmental toxins, but also have potential for or inspire pharmaceutical use. As oxygenic phototrophs, cyanobacteria furthermore hold great promise for sustainable biotechnology. Yet, the necessary tools for exploiting their biotechnological potential have so far been established only for a few model strains of cyanobacteria, while large untapped biosynthetic resources are hidden in slow-growing cyanobacterial genera that are difficult to access by genetic techniques. In recent years, several approaches have been developed to circumvent the bottlenecks in cyanobacterial natural product research. Here, we summarize current progress that has been made in unlocking or characterizing cryptic metabolic pathways using integrated omics techniques, orphan gene cluster activation, use of genetic approaches in original producers, heterologous expression and chemo-enzymatic techniques. We are mainly highlighting genomic mining concepts and strategies towards high-titer production of cyanobacterial natural products from the last 10 years and discuss the need for further research developments in this field.
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Affiliation(s)
- Martin Baunach
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
- University of Bonn, Institute of Pharmaceutical Biology, Nußallee 6, 53115 Bonn, Germany
| | - Arthur Guljamow
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
| | - María Miguel-Gordo
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
| | - Elke Dittmann
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24/25, 14476 Potsdam, Germany.
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2
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Bustos-Diaz ED, Cruz-Perez A, Garfias-Gallegos D, D'Agostino PM, Gehringer MM, Cibrian-Jaramillo A, Barona-Gomez F. Phylometagenomics of cycad coralloid roots reveals shared symbiotic signals. Microb Genom 2024; 10:001207. [PMID: 38451250 PMCID: PMC10999742 DOI: 10.1099/mgen.0.001207] [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: 09/27/2023] [Accepted: 02/09/2024] [Indexed: 03/08/2024] Open
Abstract
Cycads are known to host symbiotic cyanobacteria, including Nostocales species, as well as other sympatric bacterial taxa within their specialized coralloid roots. Yet, it is unknown if these bacteria share a phylogenetic origin and/or common genomic functions that allow them to engage in facultative symbiosis with cycad roots. To address this, we obtained metagenomic sequences from 39 coralloid roots sampled from diverse cycad species and origins in Australia and Mexico. Culture-independent shotgun metagenomic sequencing was used to validate sub-community co-cultures as an efficient approach for functional and taxonomic analysis. Our metanalysis shows a host-independent microbiome core consisting of seven bacterial orders with high species diversity within the identified taxa. Moreover, we recovered 43 cyanobacterial metagenome-assembled genomes, and in addition to Nostoc spp., symbiotic cyanobacteria of the genus Aulosira were identified for the first time. Using this robust dataset, we used phylometagenomic analysis to reveal three monophyletic cyanobiont clades, two host-generalist and one cycad-specific that includes Aulosira spp. Although the symbiotic clades have independently arisen, they are enriched in certain functional genes, such as those related to secondary metabolism. Furthermore, the taxonomic composition of associated sympatric bacterial taxa remained constant. Our research quadruples the number of cycad cyanobiont genomes and provides a robust framework to decipher cyanobacterial symbioses, with the potential of improving our understanding of symbiotic communities. This study lays a solid foundation to harness cyanobionts for agriculture and bioprospection, and assist in conservation of critically endangered cycads.
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Affiliation(s)
- Edder D. Bustos-Diaz
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav, Irapuato, Guanajuato, Mexico
- Institute of Biology, Leiden University, Netherlands, 2333 BE, Leiden
| | - Arely Cruz-Perez
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav, Irapuato, Guanajuato, Mexico
| | - Diego Garfias-Gallegos
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav, Irapuato, Guanajuato, Mexico
| | - Paul M. D'Agostino
- Chair of Technical Biochemistry, Technical University of Dresden, Bergstraße 66, 01069 Dresden, Germany
| | - Michelle M. Gehringer
- Department of Microbiology, University of Kaiserslautern-Landau (RPTU), 67663 Kaiserslautern, Germany
| | - Angelica Cibrian-Jaramillo
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav, Irapuato, Guanajuato, Mexico
- Naturalis Biodiversity Center, Leiden 2333 CR, Netherlands
| | - Francisco Barona-Gomez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav, Irapuato, Guanajuato, Mexico
- Institute of Biology, Leiden University, Netherlands, 2333 BE, Leiden
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3
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D'Agostino PM. Highlights of biosynthetic enzymes and natural products from symbiotic cyanobacteria. Nat Prod Rep 2023; 40:1701-1717. [PMID: 37233731 DOI: 10.1039/d3np00011g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Covering: up to 2023Cyanobacteria have long been known for their intriguing repertoire of natural product scaffolds, which are often distinct from other phyla. Cyanobacteria are ecologically significant organisms that form a myriad of different symbioses including with sponges and ascidians in the marine environment or with plants and fungi, in the form of lichens, in terrestrial environments. Whilst there have been several high-profile discoveries of symbiotic cyanobacterial natural products, genomic data is scarce and discovery efforts have remained limited. However, the rise of (meta-)genomic sequencing has improved these efforts, emphasized by a steep increase in publications in recent years. This highlight focuses on selected examples of symbiotic cyanobacterial-derived natural products and their biosyntheses to link chemistry with corresponding biosynthetic logic. Further highlighted are remaining gaps in knowledge for the formation of characteristic structural motifs. It is anticipated that the continued rise of (meta-)genomic next-generation sequencing of symbiontic cyanobacterial systems will lead to many exciting discoveries in the future.
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Affiliation(s)
- Paul M D'Agostino
- Technical University of Dresden, Chair of Technical Biochemistry, Bergstraβe 66, 01069 Dresden, Germany.
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4
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Bechteler J, Peñaloza-Bojacá G, Bell D, Gordon Burleigh J, McDaniel SF, Christine Davis E, Sessa EB, Bippus A, Christine Cargill D, Chantanoarrapint S, Draper I, Endara L, Forrest LL, Garilleti R, Graham SW, Huttunen S, Lazo JJ, Lara F, Larraín J, Lewis LR, Long DG, Quandt D, Renzaglia K, Schäfer-Verwimp A, Lee GE, Sierra AM, von Konrat M, Zartman CE, Pereira MR, Goffinet B, Villarreal A JC. Comprehensive phylogenomic time tree of bryophytes reveals deep relationships and uncovers gene incongruences in the last 500 million years of diversification. AMERICAN JOURNAL OF BOTANY 2023; 110:e16249. [PMID: 37792319 DOI: 10.1002/ajb2.16249] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/28/2023] [Accepted: 09/29/2023] [Indexed: 10/05/2023]
Abstract
PREMISE Bryophytes form a major component of terrestrial plant biomass, structuring ecological communities in all biomes. Our understanding of the evolutionary history of hornworts, liverworts, and mosses has been significantly reshaped by inferences from molecular data, which have highlighted extensive homoplasy in various traits and repeated bursts of diversification. However, the timing of key events in the phylogeny, patterns, and processes of diversification across bryophytes remain unclear. METHODS Using the GoFlag probe set, we sequenced 405 exons representing 228 nuclear genes for 531 species from 52 of the 54 orders of bryophytes. We inferred the species phylogeny from gene tree analyses using concatenated and coalescence approaches, assessed gene conflict, and estimated the timing of divergences based on 29 fossil calibrations. RESULTS The phylogeny resolves many relationships across the bryophytes, enabling us to resurrect five liverwort orders and recognize three more and propose 10 new orders of mosses. Most orders originated in the Jurassic and diversified in the Cretaceous or later. The phylogenomic data also highlight topological conflict in parts of the tree, suggesting complex processes of diversification that cannot be adequately captured in a single gene-tree topology. CONCLUSIONS We sampled hundreds of loci across a broad phylogenetic spectrum spanning at least 450 Ma of evolution; these data resolved many of the critical nodes of the diversification of bryophytes. The data also highlight the need to explore the mechanisms underlying the phylogenetic ambiguity at specific nodes. The phylogenomic data provide an expandable framework toward reconstructing a comprehensive phylogeny of this important group of plants.
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Affiliation(s)
- Julia Bechteler
- Nees-Institute for Plant Biodiversity, University of Bonn, Meckenheimer Allee 170, 53115, Bonn, Germany
- Plant Biodiversity and Ecology, iES Landau, Institute for Environmental Sciences, RPTU University of Kaiserslautern-Landau, Fortstraße 7, 76829, Landau, Germany
| | - Gabriel Peñaloza-Bojacá
- Laboratório de Sistemática Vegetal, Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Brazil
| | - David Bell
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - J Gordon Burleigh
- Department of Biological Sciences, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
| | - Stuart F McDaniel
- Department of Biological Sciences, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
| | - E Christine Davis
- Department of Biological Sciences, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
| | - Emily B Sessa
- Department of Biological Sciences, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
| | - Alexander Bippus
- California State Polytechnic University, Humboldt, Arcata, CA, 95521, USA
| | - D Christine Cargill
- Australian National Herbarium, Centre for Australian National Biodiversity Research, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Sahut Chantanoarrapint
- PSU Herbarium, Division of Biological Science, Faculty of Science Prince of Songkla University, Hat Yai, Songkhla, 90110, Thailand
| | - Isabel Draper
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain/Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Lorena Endara
- Department of Biological Sciences, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
| | - Laura L Forrest
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Ricardo Garilleti
- Departamento de Botánica y Geología. Universidad de Valencia, Avda. Vicente Andrés Estelles s/n, 46100, Burjassot, Spain
| | - Sean W Graham
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Sanna Huttunen
- Herbarium (TUR), Biodiversity Unit, 20014 University of Turku, Finland
| | - Javier Jauregui Lazo
- Department of Plant Biology and Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA, 95616, USA
| | - Francisco Lara
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain/Centro de Investigación en Biodiversidad y Cambio Global, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Juan Larraín
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O'Higgins, Avenida Viel 1497, Santiago, Chile
| | - Lily R Lewis
- Department of Biological Sciences, University of Florida, 220 Bartram Hall, Gainesville, FL, 32611, USA
| | - David G Long
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Dietmar Quandt
- Nees-Institute for Plant Biodiversity, University of Bonn, Meckenheimer Allee 170, 53115, Bonn, Germany
| | - Karen Renzaglia
- Department of Plant Biology, Southern Illinois University, Carbondale, IL, 62901, USA
| | | | - Gaik Ee Lee
- Faculty of Science and Marine Environment/Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21020 Kuala Nerus, Terengganu, Malaysia
| | - Adriel M Sierra
- Département de Biologie, Université Laval, Québec, Québec, G1V 0A6, Canada
| | - Matt von Konrat
- Gantz Family Collections Center, Field Museum, 1400 S. DuSable Lake Shore Drive, Chicago, IL, 60605, USA
| | - Charles E Zartman
- Instituto Nacional de Pesquisas da Amazônia, Departamento de Biodiversidade, Avenida André Araújo, 2936, Aleixo, CEP 69060-001, Manaus, AM, Brazil
| | - Marta Regina Pereira
- Universidade do Estado do Amazonas, Av. Djalma Batista, 2470, Chapada, Manaus, 69050-010, Amazonas, Brazil
| | - Bernard Goffinet
- Ecology and Evolutionary Biology, University of Connecticut, 75 North Eagleville Road, Storrs, CT, 06269-3043, USA
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5
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Álvarez C, Jiménez-Ríos L, Iniesta-Pallarés M, Jurado-Flores A, Molina-Heredia FP, Ng CKY, Mariscal V. Symbiosis between cyanobacteria and plants: from molecular studies to agronomic applications. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6145-6157. [PMID: 37422707 PMCID: PMC10575698 DOI: 10.1093/jxb/erad261] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 07/06/2023] [Indexed: 07/10/2023]
Abstract
Nitrogen-fixing cyanobacteria from the order Nostocales are able to establish symbiotic relationships with diverse plant species. They are promiscuous symbionts, as the same strain of cyanobacterium is able to form symbiotic biological nitrogen-fixing relationships with different plants species. This review will focus on the different types of cyanobacterial-plant associations, both endophytic and epiphytic, and provide insights from a structural viewpoint, as well as our current understanding of the mechanisms involved in the symbiotic crosstalk. In all these symbioses, the benefit for the plant is clear; it obtains from the cyanobacterium fixed nitrogen and other bioactive compounds, such as phytohormones, polysaccharides, siderophores, or vitamins, leading to enhanced plant growth and productivity. Additionally, there is increasing use of different cyanobacterial species as bio-inoculants for biological nitrogen fixation to improve soil fertility and crop production, thus providing an eco-friendly, alternative, and sustainable approach to reduce the over-reliance on synthetic chemical fertilizers.
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Affiliation(s)
- Consolación Álvarez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, 41092 Sevilla, Spain
| | - Lucía Jiménez-Ríos
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, 41092 Sevilla, Spain
| | - Macarena Iniesta-Pallarés
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, 41092 Sevilla, Spain
| | - Ana Jurado-Flores
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, 41092 Sevilla, Spain
| | - Fernando P Molina-Heredia
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, 41092 Sevilla, Spain
| | - Carl K Y Ng
- UCD School of Biology and Environmental Science, University College Dublin, Belfield, Dublin, Ireland
- UCD Centre for Plant Science, University College Dublin, Belfield, Dublin, Ireland
- UCD Earth Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Vicente Mariscal
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, Américo Vespucio 49, 41092 Sevilla, Spain
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6
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Liu J, Xu H, Wang Z, Liu J, Gong X. Core Endophytic Bacteria and Their Roles in the Coralloid Roots of Cultivated Cycas revoluta (Cycadaceae). Microorganisms 2023; 11:2364. [PMID: 37764208 PMCID: PMC10537169 DOI: 10.3390/microorganisms11092364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 09/10/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
As a gymnosperm group, cycads are known for their ancient origin and specialized coralloid root, which can be used as an ideal system to explore the interaction between host and associated microorganisms. Previous studies have revealed that some nitrogen-fixing cyanobacteria contribute greatly to the composition of the endophytic microorganisms in cycad coralloid roots. However, the roles of host and environment in shaping the composition of endophytic bacteria during the recruitment process remain unclear. Here, we determined the diversity, composition, and function prediction of endophytic bacteria from the coralloid roots of a widely cultivated cycad, Cycas revoluta Thunb. Using next-generation sequencing techniques, we comprehensively investigated the diversity and community structure of the bacteria in coralloid roots and bulk soils sampled from 11 sites in China, aiming to explore the variations in core endophytic bacteria and to predict their potential functions. We found a higher microbe diversity in bulk soils than in coralloid roots. Meanwhile, there was no significant difference in the diversity and composition of endophytic bacteria across different localities, and the same result was found after removing cyanobacteria. Desmonostoc was the most dominant in coralloid roots, followed by Nostoc, yet these two cyanobacteria were not shared by all samples. Rhodococcus, Edaphobacter, Niastella, Nordella, SH-PL14, and Virgisporangium were defined as the core microorganisms in coralloid roots. A function prediction analysis revealed that endophytic bacteria majorly participated in the plant uptake of phosphorus and metal ions and in disease resistance. These results indicate that the community composition of the bacteria in coralloid roots is affected by both the host and environment, in which the host is more decisive. Despite the very small proportion of core microbes, their interactions are significant and likely contribute to functions related to host survival. Our study contributes to an understanding of microbial diversity and composition in cycads, and it expands the knowledge on the association between hosts and symbiotic microbes.
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Affiliation(s)
- Jiating Liu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haiyan Xu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
| | - Zhaochun Wang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
| | - Jian Liu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
| | - Xun Gong
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; (J.L.); (H.X.); (Z.W.)
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7
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Schneider YKH, Liaimer A, Isaksson J, Wilhelmsen OSB, Andersen JH, Hansen KØ, Hansen EH. Four new suomilides isolated from the cyanobacterium Nostoc sp. KVJ20 and proposal of their biosynthetic origin. Front Microbiol 2023; 14:1130018. [PMID: 37152725 PMCID: PMC10157211 DOI: 10.3389/fmicb.2023.1130018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/24/2023] [Indexed: 05/09/2023] Open
Abstract
The suomilide and the banyasides are highly modified and functionalized non-ribosomal peptides produced by cyanobacteria of the order Nostocales. These compound classes share several substructures, including a complex azabicyclononane core, which was previously assumed to be derived from the amino acid tyrosine. In our study we were able to isolate and determine the structures of four suomilides, named suomilide B - E (1-4). The compounds differ from the previously isolated suomilide A by the functionalization of the glycosyl group. Compounds 1-4 were assayed for anti-proliferative, anti-biofilm and anti-bacterial activities, but no significant activity was detected. The sequenced genome of the producer organism Nostoc sp. KVJ20 enabled us to propose a biosynthetic gene cluster for suomilides. Our findings indicated that the azabicyclononane core of the suomilides is derived from prephenate and is most likely incorporated by a proline specific non-ribosomal peptide synthetase-unit.
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Affiliation(s)
- Yannik K.-H. Schneider
- Marbio, Faculty of Biosciences, Fisheries and Economics, UiT—The Arctic University of Norway, Tromsø, Norway
- *Correspondence: Yannik K.-H. Schneider,
| | - Anton Liaimer
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT—The Arctic University of Norway, Tromsø, Norway
| | - Johan Isaksson
- Department of Chemistry, Faculty of Natural Sciences, UiT—The Arctic University of Norway, Tromsø, Norway
| | - Oda S. B. Wilhelmsen
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT—The Arctic University of Norway, Tromsø, Norway
| | - Jeanette H. Andersen
- Marbio, Faculty of Biosciences, Fisheries and Economics, UiT—The Arctic University of Norway, Tromsø, Norway
| | - Kine Ø. Hansen
- Marbio, Faculty of Biosciences, Fisheries and Economics, UiT—The Arctic University of Norway, Tromsø, Norway
| | - Espen H. Hansen
- Marbio, Faculty of Biosciences, Fisheries and Economics, UiT—The Arctic University of Norway, Tromsø, Norway
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8
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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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9
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Freitas S, Castelo-Branco R, Wenzel-Storjohann A, Vasconcelos VM, Tasdemir D, Leão PN. Structure and Biosynthesis of Desmamides A-C, Lipoglycopeptides from the Endophytic Cyanobacterium Desmonostoc muscorum LEGE 12446. JOURNAL OF NATURAL PRODUCTS 2022; 85:1704-1714. [PMID: 35793792 PMCID: PMC9315949 DOI: 10.1021/acs.jnatprod.2c00162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Certain cyanobacteria of the secondary metabolite-rich order Nostocales can establish permanent symbioses with a large number of cycads, by accumulating in their coralloid roots and shifting their metabolism to dinitrogen fixation. Here, we report the discovery of two new lipoglycopeptides, desmamides A (1) and B (2), together with their aglycone desmamide C (3), from the nostocalean cyanobacterium Desmonostoc muscorum LEGE 12446 isolated from a cycad (Cycas revoluta) coralloid root. The chemical structures of the compounds were elucidated using a combination of 1D and 2D NMR spectroscopy and mass spectrometry. The desmamides are decapeptides featuring O-glycosylation of tyrosine (in 1 and 2) and an unusual 3,5-dihydroxy-2-methyldecanoic acid residue. The biosynthesis of the desmamides was studied by substrate incubation experiments and bioinformatics. We describe herein the dsm biosynthetic gene cluster and propose it to be associated with desmamide production. The discovery of this class of very abundant (>1.5% d.w.) bacterial lipoglycopeptides paves the way for exploration of their potential role in root endosymbiosis.
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Affiliation(s)
- Sara Freitas
- Interdisciplinary
Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal
- Department
of Biology, Faculty of Sciences, University
of Porto Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Raquel Castelo-Branco
- Interdisciplinary
Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal
| | - Arlette Wenzel-Storjohann
- GEOMAR
Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz
Centre for Ocean Research Kiel, Am Kiel Kanal 44, 24106 Kiel, Germany
| | - Vitor M. Vasconcelos
- Interdisciplinary
Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal
- Department
of Biology, Faculty of Sciences, University
of Porto Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Deniz Tasdemir
- GEOMAR
Centre for Marine Biotechnology (GEOMAR-Biotech), Research Unit Marine Natural Product Chemistry, GEOMAR Helmholtz
Centre for Ocean Research Kiel, Am Kiel Kanal 44, 24106 Kiel, Germany
- Kiel
University, Christian-Albrechts-Platz
4, 24118 Kiel, Germany
| | - Pedro N. Leão
- Interdisciplinary
Centre of Marine and Environmental Research (CIIMAR/CIMAR), University of Porto, Avenida General Norton de Matos, s/n, 4450-208 Matosinhos, Portugal
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10
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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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11
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Bouaïcha N, Metcalf JS, Porzani SJ, Konur O. Plant-cyanobacteria interactions: Beneficial and harmful effects of cyanobacterial bioactive compounds on soil-plant systems and subsequent risk to animal and human health. PHYTOCHEMISTRY 2021; 192:112959. [PMID: 34649057 DOI: 10.1016/j.phytochem.2021.112959] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 09/10/2021] [Accepted: 09/15/2021] [Indexed: 05/17/2023]
Abstract
Plant-cyanobacteria interactions occur in different ways and at many different levels, both beneficial and harmful. Plant-cyanobacteria interactions, as a beneficial symbiosis, have long been demonstrated in rice-growing areas (Poaceae) where the most efficient nitrogen-fixing cyanobacteria are present in paddies. Moreover, cyanobacteria may in turn produce and/or secrete numerous bioactive compounds that have plant growth-promoting abilities or that may make the plant more resistant to abiotic or biotic stress. In recent years, there has been a growing worldwide interest in the use of cyanobacterial biomass as biofertilizers to replace chemical fertilizers, in part to overcome increasing organic-farming demands. However, the potential presence of harmful cyanotoxins has delayed the use of such cyanobacterial biomass, which can be found in large quantities in freshwater ecosystems around the world. In this review, we describe the existing evidence for the positive benefit of plant-cyanobacteria interactions and discuss the use of cyanobacterial biomass as biofertilizers and its growing worldwide interest. Although mass cyanobacterial blooms and scums are a current and emerging threat to the degradation of ecosystems and to animal and human health, they may serve as a source of numerous bioactive compounds with multiple positive effects that could be of use as an alternative to chemical fertilizers in the context of sustainable development.
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Affiliation(s)
- Noureddine Bouaïcha
- Laboratory Ecology, Systematic and Evolution, UMR 8079 Univ. Paris-Sud, CNRS, AgroParisTech, University Paris-Saclay, 91405, Orsay, France
| | | | - Samaneh Jafari Porzani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Ozcan Konur
- Formerly, Ankara Yildirim Beyazit University, Ankara, Turkey
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12
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Fidor A, Cekała K, Wieczerzak E, Cegłowska M, Kasprzykowski F, Edwards C, Mazur-Marzec H. Nostocyclopeptides as New Inhibitors of 20S Proteasome. Biomolecules 2021; 11:biom11101483. [PMID: 34680116 PMCID: PMC8533403 DOI: 10.3390/biom11101483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/29/2021] [Accepted: 10/05/2021] [Indexed: 11/16/2022] Open
Abstract
Nostocyclopeptides (Ncps) are a small class of bioactive nonribosomal peptides produced solely by cyanobacteria of the genus Nostoc. In the current work, six Ncps were isolated from Nostoc edaphicum strain CCNP1411. The bioactivity of these compounds was tested in vitro against 20S proteasome, a proteolytic complex that plays an important role in maintaining cellular proteostasis. Dysfunction of the complex leads to many pathological disorders. The assays indicated selective activity of specific Ncp variants. For two linear peptide aldehydes, Ncp-A2-L and Ncp-E2-L, the inhibitory effects on chymotrypsin-like activity were revealed, while the cyclic variant, Ncp-A2, inactivated the trypsin-like site of this enzymatic complex. The aldehyde group was confirmed to be an important element of the chymotrypsin-like activity inhibitors. The nostocyclopeptides, as novel inhibitors of 20S proteasome, increased the number of natural products that can be considered potential regulators of cellular processes.
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Affiliation(s)
- Anna Fidor
- Division of Marine Biotechnology, Institute of Oceanography, University of Gdańsk, Marszałka Józefa Piłsudskiego 46, PL-81378 Gdynia, Poland;
| | - Katarzyna Cekała
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, PL-80308 Gdańsk, Poland; (K.C.); (E.W.); (F.K.)
| | - Ewa Wieczerzak
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, PL-80308 Gdańsk, Poland; (K.C.); (E.W.); (F.K.)
| | - Marta Cegłowska
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, PL-81712 Sopot, Poland;
| | - Franciszek Kasprzykowski
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, PL-80308 Gdańsk, Poland; (K.C.); (E.W.); (F.K.)
| | - Christine Edwards
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen AB10 7GJ, UK;
| | - Hanna Mazur-Marzec
- Division of Marine Biotechnology, Institute of Oceanography, University of Gdańsk, Marszałka Józefa Piłsudskiego 46, PL-81378 Gdynia, Poland;
- Correspondence:
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13
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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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14
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Nelson JM, Hauser DA, Li FW. The diversity and community structure of symbiotic cyanobacteria in hornworts inferred from long-read amplicon sequencing. AMERICAN JOURNAL OF BOTANY 2021; 108:1731-1744. [PMID: 34533221 DOI: 10.1002/ajb2.1729] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 05/16/2021] [Accepted: 05/17/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Nitrogen-fixing endosymbioses with cyanobacteria have evolved independently in five very different plant lineages. Expanding knowledge of these symbioses promises to improve the understanding of symbiosis evolution and broaden the toolkit for agricultural engineering to reduce artificial fertilizer use. Here we focused on hornworts, a bryophyte lineage in which all members host cyanobacteria, and investigated factors shaping the diversity of their cyanobiont communities. METHODS We sampled hornworts and adjacent soils in upstate New York throughout the hornwort growing season. We included all three sympatric hornwort species in the area, allowing us to directly compare partner selectivity. To profile cyanobacteria communities, we established a metabarcoding protocol targeting rbcL-X with PacBio long reads. RESULTS The hornwort cyanobionts detected were phylogenetically diverse, including clades that do not contain other known plant symbionts. We found significant overlap between hornwort cyanobionts and soil cyanobacteria, a pattern not previously reported in other plant-cyanobacteria symbioses. Cyanobiont communities differed between host plants only centimeters apart, but we did not detect an effect of sampling time or host species on the cyanobacterial community structure. CONCLUSIONS This study expands the phylogenetic diversity of known symbiotic cyanobacteria. Our analyses suggest that hornwort cyanobionts have a tight connection to the soil background, and we found no evidence that time within growing season, host species, or distance at the scale of meters strongly govern cyanobacteria community assembly. This study provides a critical foundation for further study of the ecology, evolution, and interaction dynamics of plant-cyanobacteria symbiosis.
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Affiliation(s)
| | | | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, Cornell University, Ithaca, NY, USA
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15
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Satjarak A, Graham LE, Piotrowski MJ, Trest MT, Wilcox LW, Cook ME, Knack JJ, Arancibia-Avila P. Shotgun metagenomics and microscopy indicate diverse cyanophytes, other bacteria, and microeukaryotes in the epimicrobiota of a northern Chilean wetland Nostoc (Cyanobacteria). JOURNAL OF PHYCOLOGY 2021; 57:39-50. [PMID: 33070358 DOI: 10.1111/jpy.13084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 09/01/2020] [Accepted: 09/19/2020] [Indexed: 06/11/2023]
Abstract
Prokaryotic Nostoc, one of the world's most conspicuous and widespread algal genera (similar to eukaryotic algae, plants, and animals) is known to support a microbiome that influences host ecological roles. Past taxonomic characterizations of surface microbiota (epimicrobiota) of free-living Nostoc sampled from freshwater systems employed 16S rRNA genes, typically amplicons. We compared taxa identified from 16S, 18S, 23S, and 28S rRNA gene sequences filtered from shotgun metagenomic sequence and used microscopy to illuminate epimicrobiota diversity for Nostoc sampled from a wetland in the northern Chilean Altiplano. Phylogenetic analysis and rRNA gene sequence abundance estimates indicated that the host was related to Nostoc punctiforme PCC 73102. Epimicrobiota were inferred to include 18 epicyanobacterial genera or uncultured taxa, six epieukaryotic algal genera, and 66 anoxygenic bacterial genera, all having average genomic coverage ≥90X. The epicyanobacteria Geitlerinemia, Oscillatoria, Phormidium, and an uncultured taxon were detected only by 16S rRNA gene; Gloeobacter and Pseudanabaena were detected using 16S and 23S; and Phormididesmis, Neosynechococcus, Symphothece, Aphanizomenon, Nodularia, Spirulina, Nodosilinea, Synechococcus, Cyanobium, and Anabaena (the latter corroborated by microscopy), plus two uncultured cyanobacterial taxa (JSC12, O77) were detected only by 23S rRNA gene sequences. Three chlamydomonad and two heterotrophic stramenopiles genera were inferred from 18S; the streptophyte green alga Chaetosphaeridium globosum was detected by microscopy and 28S rRNA genes, but not 18S rRNA genes. Overall, >60% of epimicrobial taxa were detected by markers other than 16S rRNA genes. Some algal taxa observed microscopically were not detected from sequence data. Results indicate that multiple taxonomic markers derived from metagenomic sequence data and microscopy increase epimicrobiota detection.
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Affiliation(s)
- Anchittha Satjarak
- Plants of Thailand Research Unit, Department of Botany, Faculty of Science, Chulalongkorn University, Bangkok, 103330, Thailand
| | - Linda E Graham
- Department of Botany, University of Wisconsin, Madison, Wisconsin, 53706, USA
| | | | - Marie T Trest
- Department of Botany, University of Wisconsin, Madison, Wisconsin, 53706, USA
| | - Lee W Wilcox
- Department of Botany, University of Wisconsin, Madison, Wisconsin, 53706, USA
| | - Martha E Cook
- School of Biological Sciences, Illinois State University, Normal, Illinois, 61790, USA
| | - Jennifer J Knack
- Department of Biology, University of Minnesota, Duluth, Minnesota, 55812, USA
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16
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Fidor A, Grabski M, Gawor J, Gromadka R, Węgrzyn G, Mazur-Marzec H. Nostoc edaphicum CCNP1411 from the Baltic Sea-A New Producer of Nostocyclopeptides. Mar Drugs 2020; 18:E442. [PMID: 32858999 PMCID: PMC7551626 DOI: 10.3390/md18090442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/21/2020] [Accepted: 08/25/2020] [Indexed: 12/17/2022] Open
Abstract
Nostocyclopeptides (Ncps) constitute a small class of nonribosomal peptides, exclusively produced by cyanobacteria of the genus Nostoc. The peptides inhibit the organic anion transporters, OATP1B3 and OATP1B1, and prevent the transport of the toxic microcystins and nodularin into hepatocytes. So far, only three structural analogues, Ncp-A1, Ncp-A2 and Ncp-M1, and their linear forms were identified in Nostoc strains as naturally produced cyanometabolites. In the current work, the whole genome sequence of the new Ncps producer, N. edaphicum CCNP1411 from the Baltic Sea, has been determined. The genome consists of the circular chromosome (7,733,505 bps) and five circular plasmids (from 44.5 kb to 264.8 kb). The nostocyclopeptide biosynthetic gene cluster (located between positions 7,609,981-7,643,289 bps of the chromosome) has been identified and characterized in silico. The LC-MS/MS analyzes of N. edaphicum CCNP1411 cell extracts prepared in aqueous methanol revealed several products of the genes. Besides the known peptides, Ncp-A1 and Ncp-A2, six other compounds putatively characterized as new noctocyclopeptide analogues were detected. This includes Ncp-E1 and E2 and their linear forms (Ncp-E1-L and E2-L), a cyclic Ncp-E3 and a linear Ncp-E4-L. Regardless of the extraction conditions, the cell contents of the linear nostocyclopeptides were found to be higher than the cyclic ones, suggesting a slow rate of the macrocyclization process.
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Affiliation(s)
- Anna Fidor
- Division of Marine Biotechnology, Faculty of Oceanography and Geography, University of Gdańsk, Marszałka J. Piłsudskiego 46, PL-81378 Gdynia, Poland;
| | - Michał Grabski
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.G.); (G.W.)
| | - Jan Gawor
- DNA Sequencing and Oligonucleotide Synthesis Laboratory, Polish Academy of Sciences, Institute of Biochemistry and Biophysics, 02-106 Warsaw, Poland; (J.G.); (R.G.)
| | - Robert Gromadka
- DNA Sequencing and Oligonucleotide Synthesis Laboratory, Polish Academy of Sciences, Institute of Biochemistry and Biophysics, 02-106 Warsaw, Poland; (J.G.); (R.G.)
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland; (M.G.); (G.W.)
| | - Hanna Mazur-Marzec
- Division of Marine Biotechnology, Faculty of Oceanography and Geography, University of Gdańsk, Marszałka J. Piłsudskiego 46, PL-81378 Gdynia, Poland;
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17
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A novel cyanobacterial geosmin producer, revising GeoA distribution and dispersion patterns in Bacteria. Sci Rep 2020; 10:8679. [PMID: 32457360 PMCID: PMC7251104 DOI: 10.1038/s41598-020-64774-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 04/21/2020] [Indexed: 11/08/2022] Open
Abstract
Cyanobacteria are ubiquitous organisms with a relevant contribution to primary production in all range of habitats. Cyanobacteria are well known for their part in worldwide occurrence of aquatic blooms while producing a myriad of natural compounds, some with toxic potential, but others of high economical impact, as geosmin. We performed an environmental survey of cyanobacterial soil colonies to identify interesting metabolic pathways and adaptation strategies used by these microorganisms and isolated, sequenced and assembled the genome of a cyanobacterium that displayed a distinctive earthy/musty smell, typical of geosmin, confirmed by GC-MS analysis of the culture's volatile extract. Morphological studies pointed to a new Oscillatoriales soil ecotype confirmed by phylogenetic analysis, which we named Microcoleus asticus sp. nov. Our studies of geosmin gene presence in Bacteria, revealed a scattered distribution among Cyanobacteria, Actinobacteria, Delta and Gammaproteobacteria, covering different niches. Careful analysis of the bacterial geosmin gene and gene tree suggests an ancient bacterial origin of the gene, that was probably successively lost in different time frames. The high sequence similarities in the cyanobacterial geosmin gene amidst freshwater and soil strains, reinforce the idea of an evolutionary history of geosmin, that is intimately connected to niche adaptation.
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18
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Riba M, Kiss-Szikszai A, Gonda S, Parizsa P, Deák B, Török P, Valkó O, Felföldi T, Vasas G. Chemotyping of terrestrial Nostoc-like isolates from alkali grassland areas by non-targeted peptide analysis. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101798] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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19
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Shishido TK, Popin RV, Jokela J, Wahlsten M, Fiore MF, Fewer DP, Herfindal L, Sivonen K. Dereplication of Natural Products with Antimicrobial and Anticancer Activity from Brazilian Cyanobacteria. Toxins (Basel) 2019; 12:E12. [PMID: 31878347 PMCID: PMC7020483 DOI: 10.3390/toxins12010012] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/20/2019] [Accepted: 12/21/2019] [Indexed: 12/19/2022] Open
Abstract
Cyanobacteria are photosynthetic organisms that produce a large diversity of natural products with interesting bioactivities for biotechnological and pharmaceutical applications. Cyanobacterial extracts exhibit toxicity towards other microorganisms and cancer cells and, therefore, represent a source of potentially novel natural products for drug discovery. We tested 62 cyanobacterial strains isolated from various Brazilian biomes for antileukemic and antimicrobial activities. Extracts from 39 strains induced selective apoptosis in acute myeloid leukemia (AML) cancer cell lines. Five of these extracts also exhibited antifungal and antibacterial activities. Chemical and dereplication analyses revealed the production of nine known natural products. Natural products possibly responsible for the observed bioactivities and five unknown, chemically related chlorinated compounds present only in Brazilian cyanobacteria were illustrated in a molecular network. Our results provide new information on the vast biosynthetic potential of cyanobacteria isolated from Brazilian environments.
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Affiliation(s)
- Tania Keiko Shishido
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland; (T.K.S.); (R.V.P.); (J.J.); (M.W.); (D.P.F.)
- Institute of Biotechnology, University of Helsinki, Viikinkaari 5D, FI-00014 Helsinki, Finland
| | - Rafael Vicentini Popin
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland; (T.K.S.); (R.V.P.); (J.J.); (M.W.); (D.P.F.)
| | - Jouni Jokela
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland; (T.K.S.); (R.V.P.); (J.J.); (M.W.); (D.P.F.)
| | - Matti Wahlsten
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland; (T.K.S.); (R.V.P.); (J.J.); (M.W.); (D.P.F.)
| | - Marli Fatima Fiore
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, 13400-970 Piracicaba, São Paulo, Brazil;
| | - David P. Fewer
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland; (T.K.S.); (R.V.P.); (J.J.); (M.W.); (D.P.F.)
| | - Lars Herfindal
- Centre for Pharmacy, Department of Clinical Science, University of Bergen, P.O. Box 7804, 5020 Bergen, Norway;
| | - Kaarina Sivonen
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland; (T.K.S.); (R.V.P.); (J.J.); (M.W.); (D.P.F.)
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20
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Halsør MJH, Liaimer A, Pandur S, Ræder ILU, Smalås AO, Altermark B. Draft Genome Sequence of the Symbiotically Competent Cyanobacterium Nostoc sp. Strain KVJ20. Microbiol Resour Announc 2019; 8:e01190-19. [PMID: 31699770 PMCID: PMC6838628 DOI: 10.1128/mra.01190-19] [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: 09/23/2019] [Accepted: 10/04/2019] [Indexed: 11/20/2022] Open
Abstract
Nostoc sp. strain KVJ20 was isolated from the symbiotic organs of the liverwort Blasia pusilla This cyanobacterium has been shown to have broad symbiotic competence, and bacterial extracts have inhibitory effects on cancer cell lines and microbes. An array of genes for the production of secondary metabolites is present.
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Affiliation(s)
- Marie-Josée H Halsør
- NorStruct, Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Anton Liaimer
- Department of Arctic and Marine Biology, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Tromsø, Norway
| | - Seila Pandur
- NorStruct, Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Inger L U Ræder
- NorStruct, Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Arne O Smalås
- NorStruct, Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Bjørn Altermark
- NorStruct, Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø, Norway
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21
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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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22
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Halsør MJH, Rothweiler U, Altermark B, Raeder ILU. The crystal structure of the N-acetylglucosamine 2-epimerase from Nostoc sp. KVJ10 reveals the true dimer. Acta Crystallogr D Struct Biol 2019; 75:90-100. [PMID: 30644848 PMCID: PMC6333288 DOI: 10.1107/s2059798318017047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/30/2018] [Indexed: 11/12/2022] Open
Abstract
N-Acetylglucosamine 2-epimerases (AGEs) catalyze the interconversion of N-acetylglucosamine and N-acetylmannosamine. They can be used to perform the first step in the synthesis of sialic acid from N-acetylglucosamine, which makes the need for efficient AGEs a priority. This study presents the structure of the AGE from Nostoc sp. KVJ10 collected in northern Norway, referred to as nAGE10. It is the third AGE structure to be published to date, and the first one in space group P42212. The nAGE10 monomer folds as an (α/α)6 barrel in a similar manner to that of the previously published AGEs, but the crystal did not contain the dimers that have previously been reported. The previously proposed `back-to-back' assembly involved the face of the AGE monomer where the barrel helices are connected by small loops. Instead, a `front-to-front' dimer was found in nAGE10 involving the long loops that connect the barrel helices at this end. This assembly is also present in the other AGE structures, but was attributed to crystal packing, even though the `front' interface areas are larger and are more conserved than the `back' interface areas. In addition, the front-to-front association allows a better explanation of the previously reported observations considering surface cysteines. Together, these results indicate that the `front-to-front' dimer is the most probable biological assembly for AGEs.
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Affiliation(s)
- Marie-Josée Haglund Halsør
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT – The Arctic University of Norway, 9037 Tromsø, Norway
| | - Ulli Rothweiler
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT – The Arctic University of Norway, 9037 Tromsø, Norway
| | - Bjørn Altermark
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT – The Arctic University of Norway, 9037 Tromsø, Norway
| | - Inger Lin Uttakleiv Raeder
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT – The Arctic University of Norway, 9037 Tromsø, Norway
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23
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Gutiérrez-García K, Bustos-Díaz ED, Corona-Gómez JA, Ramos-Aboites HE, Sélem-Mojica N, Cruz-Morales P, Pérez-Farrera MA, Barona-Gómez F, Cibrián-Jaramillo A. Cycad Coralloid Roots Contain Bacterial Communities Including Cyanobacteria and Caulobacter spp. That Encode Niche-Specific Biosynthetic Gene Clusters. Genome Biol Evol 2019; 11:319-334. [PMID: 30534962 PMCID: PMC6350856 DOI: 10.1093/gbe/evy266] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2018] [Indexed: 12/29/2022] Open
Abstract
Cycads are the only early seed plants that have evolved a specialized root to host endophytic bacteria that fix nitrogen. To provide evolutionary and functional insights into this million-year old symbiosis, we investigate endophytic bacterial sub-communities isolated from coralloid roots of species from Dioon (Zamiaceae) sampled from their natural habitats. We employed a sub-community co-culture experimental strategy to reveal both predominant and rare bacteria, which were characterized using phylogenomics and detailed metabolic annotation. Diazotrophic plant endophytes, including Bradyrhizobium, Burkholderia, Mesorhizobium, Rhizobium, and Nostoc species, dominated the epiphyte-free sub-communities. Draft genomes of six cyanobacteria species were obtained after shotgun metagenomics of selected sub-communities. These data were used for whole-genome inferences that suggest two Dioon-specific monophyletic groups, and a level of specialization characteristic of co-evolved symbiotic relationships. Furthermore, the genomes of these cyanobacteria were found to encode unique biosynthetic gene clusters, predicted to direct the synthesis of specialized metabolites, mainly involving peptides. After combining genome mining with detection of pigment emissions using multiphoton excitation fluorescence microscopy, we also show that Caulobacter species co-exist with cyanobacteria, and may interact with them by means of a novel indigoidine-like specialized metabolite. We provide an unprecedented view of the composition of the cycad coralloid root, including phylogenetic and functional patterns mediated by specialized metabolites that may be important for the evolution of ancient symbiotic adaptations.
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Affiliation(s)
- Karina Gutiérrez-García
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Acanzada (Langebio), Irapuato, Guanajuato, México
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genómica Avanzada (Langebio), Irapuato, Guanajuato, México
| | - Edder D Bustos-Díaz
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Acanzada (Langebio), Irapuato, Guanajuato, México
| | - José Antonio Corona-Gómez
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genómica Avanzada (Langebio), Irapuato, Guanajuato, México
| | - Hilda E Ramos-Aboites
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Acanzada (Langebio), Irapuato, Guanajuato, México
| | - Nelly Sélem-Mojica
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Acanzada (Langebio), Irapuato, Guanajuato, México
| | - Pablo Cruz-Morales
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Acanzada (Langebio), Irapuato, Guanajuato, México
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genómica Avanzada (Langebio), Irapuato, Guanajuato, México
| | - Miguel A Pérez-Farrera
- Herbario Eizi Matuda, Laboratorio de Ecología Evolutiva, Instituto de Ciencias Biológicas, Universidad de Ciencias y Artes del Estado de Chiapas, Tuxtla Gutiérrez, Chiapas, México
| | - Francisco Barona-Gómez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Acanzada (Langebio), Irapuato, Guanajuato, México
| | - Angélica Cibrián-Jaramillo
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genómica Avanzada (Langebio), Irapuato, Guanajuato, México
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24
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Gagunashvili AN, Andrésson ÓS. Distinctive characters of Nostoc genomes in cyanolichens. BMC Genomics 2018; 19:434. [PMID: 29866043 PMCID: PMC5987646 DOI: 10.1186/s12864-018-4743-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 04/30/2018] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Cyanobacteria of the genus Nostoc are capable of forming symbioses with a wide range of organism, including a diverse assemblage of cyanolichens. Only certain lineages of Nostoc appear to be able to form a close, stable symbiosis, raising the question whether symbiotic competence is determined by specific sets of genes and functionalities. RESULTS We present the complete genome sequencing, annotation and analysis of two lichen Nostoc strains. Comparison with other Nostoc genomes allowed identification of genes potentially involved in symbioses with a broad range of partners including lichen mycobionts. The presence of additional genes necessary for symbiotic competence is likely reflected in larger genome sizes of symbiotic Nostoc strains. Some of the identified genes are presumably involved in the initial recognition and establishment of the symbiotic association, while others may confer advantage to cyanobionts during cohabitation with a mycobiont in the lichen symbiosis. CONCLUSIONS Our study presents the first genome sequencing and genome-scale analysis of lichen-associated Nostoc strains. These data provide insight into the molecular nature of the cyanolichen symbiosis and pinpoint candidate genes for further studies aimed at deciphering the genetic mechanisms behind the symbiotic competence of Nostoc. Since many phylogenetic studies have shown that Nostoc is a polyphyletic group that includes several lineages, this work also provides an improved molecular basis for demarcation of a Nostoc clade with symbiotic competence.
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Affiliation(s)
- Andrey N. Gagunashvili
- Faculty of Life and Environmental Sciences, University of Iceland, Sturlugata 7, Reykjavík, 101 Iceland
| | - Ólafur S. Andrésson
- Faculty of Life and Environmental Sciences, University of Iceland, Sturlugata 7, Reykjavík, 101 Iceland
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25
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Kust A, Mareš J, Jokela J, Urajová P, Hájek J, Saurav K, Voráčová K, Fewer DP, Haapaniemi E, Permi P, Řeháková K, Sivonen K, Hrouzek P. Discovery of a Pederin Family Compound in a Nonsymbiotic Bloom-Forming Cyanobacterium. ACS Chem Biol 2018; 13:1123-1129. [PMID: 29570981 DOI: 10.1021/acschembio.7b01048] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The pederin family includes a number of bioactive compounds isolated from symbiotic organisms of diverse evolutionary origin. Pederin is linked to beetle-induced dermatitis in humans, and pederin family members possess potent antitumor activity caused by selective inhibition of the eukaryotic ribosome. Their biosynthesis is accomplished by a polyketide/nonribosomal peptide synthetase machinery employing an unusual trans-acyltransferase mechanism. Here, we report a novel pederin type compound, cusperin, from the free-living cyanobacterium Cuspidothrix issatschenkoi (earlier Aphanizomenon). The chemical structure of cusperin is similar to that of nosperin recently isolated from the lichen cyanobiont Nostoc sharing the tehrahydropyran moiety and major part of the linear backbone. However, the cusperin molecule is extended by a glycine residue and lacks one hydroxyl substituent. Pederins were previously thought to be exclusive to symbiotic relationships. However, C. issatschenkoi is a nonsymbiotic planktonic organism and a frequent component of toxic water blooms. Cusperin is devoid of the cytotoxic activity reported for other pederin family members. Hence, our findings raise questions about the role of pederin analogues in cyanobacteria and broaden the knowledge of ecological distribution of this group of polyketides.
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Affiliation(s)
- Andreja Kust
- Institute of Microbiology CAS, Center Algatech, Třeboň, Czech Republic
- The Czech Academy of Sciences, Biology Centre, Institute of Hydrobiology, České Budějovice, Czech Republic
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
| | - Jan Mareš
- Institute of Microbiology CAS, Center Algatech, Třeboň, Czech Republic
- The Czech Academy of Sciences, Biology Centre, Institute of Hydrobiology, České Budějovice, Czech Republic
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
| | - Jouni Jokela
- Department of Microbiology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Petra Urajová
- Institute of Microbiology CAS, Center Algatech, Třeboň, Czech Republic
| | - Jan Hájek
- Institute of Microbiology CAS, Center Algatech, Třeboň, Czech Republic
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
| | - Kumar Saurav
- Institute of Microbiology CAS, Center Algatech, Třeboň, Czech Republic
| | - Kateřina Voráčová
- Institute of Microbiology CAS, Center Algatech, Třeboň, Czech Republic
| | - David P. Fewer
- Department of Microbiology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Esa Haapaniemi
- Department of Chemistry, University of Jyväskylä, FI-40010 Jyväskylä, Finland
| | - Perttu Permi
- Department of Chemistry, University of Jyväskylä, FI-40010 Jyväskylä, Finland
- Department of Biology and Environmental Science, Nanoscience Center, University of Jyväskylä, FI-40010 Jyväskylä, Finland
| | - Klára Řeháková
- The Czech Academy of Sciences, Biology Centre, Institute of Hydrobiology, České Budějovice, Czech Republic
| | | | - Pavel Hrouzek
- Institute of Microbiology CAS, Center Algatech, Třeboň, Czech Republic
- University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
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26
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Highly diverse endophytes in roots of Cycas bifida (Cycadaceae), an ancient but endangered gymnosperm. J Microbiol 2018; 56:337-345. [PMID: 29721831 DOI: 10.1007/s12275-018-7438-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 02/11/2018] [Accepted: 02/27/2018] [Indexed: 10/17/2022]
Abstract
As an ancient seed plant, cycads are one of the few gymnosperms that develop a root symbiosis with cyanobacteria, which has allowed cycads to cope with harsh geologic and climatic conditions during the evolutionary process. However, the endophytic microbes in cycad roots remain poorly identified. In this study, using next-generation sequencing techniques, we investigated the microbial diversity and composition of both the coralloid and regular roots of Cycas bifida (Dyer) K.D. Hill. Highly diverse endophytic communities were observed in both the coralloid and regular roots. Of the associated bacteria, the top five families were the Nostocaceae, Sinobacteraceae, Bradyrhizobiaceae, Bacillaceae, and Hyphomicrobiaceae. The Nectriaceae, Trichocomaceae, and Incertae sedis were the predominant fungal families in all root samples. A significant difference in the endophytic bacterial community was detected between coralloid roots and regular roots, but no difference was observed between the fungal communities in the two root types. Cyanobacteria were more dominant in coralloid roots than in regular roots. The divergence of cycad root structures and the modified physiological processes may have contributed to the abundance of cyanobionts in coralloid roots. Consequently, the colonization of cyanobacteria inhibits the assemblage of other endophytes. Our results contribute to an understanding of the species diversity and composition of the cycad-endophyte microbiome and provide an abbreviated list of potential ecological roles of the core microbes present.
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27
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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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28
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The Swinholide Biosynthesis Gene Cluster from a Terrestrial Cyanobacterium, Nostoc sp. Strain UHCC 0450. Appl Environ Microbiol 2018; 84:AEM.02321-17. [PMID: 29150506 PMCID: PMC5772238 DOI: 10.1128/aem.02321-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 11/03/2017] [Indexed: 12/02/2022] Open
Abstract
Swinholides are 42-carbon ring polyketides with a 2-fold axis of symmetry. They are potent cytotoxins that disrupt the actin cytoskeleton. Swinholides were discovered from the marine sponge Theonella sp. and were long suspected to be produced by symbiotic bacteria. Misakinolide, a structural variant of swinholide, was recently demonstrated to be the product of a symbiotic heterotrophic proteobacterium. Here, we report the production of swinholide A by an axenic strain of the terrestrial cyanobacterium Nostoc sp. strain UHCC 0450. We located the 85-kb trans-AT polyketide synthase (PKS) swinholide biosynthesis gene cluster from a draft genome of Nostoc sp. UHCC 0450. The swinholide and misakinolide biosynthesis gene clusters share an almost identical order of catalytic domains, with 85% nucleotide sequence identity, and they group together in phylogenetic analysis. Our results resolve speculation around the true producer of swinholides and demonstrate that bacteria belonging to two distantly related phyla both produce structural variants of the same natural product. In addition, we described a biosynthesis cluster from Anabaena sp. strain UHCC 0451 for the synthesis of the cytotoxic and antifungal scytophycin. All of these biosynthesis gene clusters were closely related to each other and created a group of cytotoxic macrolide compounds produced by trans-AT PKSs of cyanobacteria and proteobacteria. IMPORTANCE Many of the drugs in use today originate from natural products. New candidate compounds for drug development are needed due to increased drug resistance. An increased knowledge of the biosynthesis of bioactive compounds can be used to aid chemical synthesis to produce novel drugs. Here, we show that a terrestrial axenic culture of Nostoc cyanobacterium produces swinholides, which have been previously found only from marine sponge or samples related to them. Swinholides are polyketides with a 2-fold axis of symmetry, and they are potent cytotoxins that disrupt the actin cytoskeleton. We describe the biosynthesis gene clusters of swinholide from Nostoc cyanobacteria, as well as the related cytotoxic and antifungal scytophycin from Anabaena cyanobacteria, and we study the evolution of their trans-AT polyketide synthases. Interestingly, swinholide is closely related to misakinolide produced by a symbiotic heterotrophic proteobacterium, demonstrating that bacteria belonging to two distantly related phyla and different habitats can produce similar natural products.
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29
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High-Density Cultivation of Terrestrial Nostoc Strains Leads to Reprogramming of Secondary Metabolome. Appl Environ Microbiol 2017; 83:AEM.01510-17. [PMID: 28939609 DOI: 10.1128/aem.01510-17] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 09/18/2017] [Indexed: 11/20/2022] Open
Abstract
Terrestrial symbiotic cyanobacteria of the genus Nostoc exhibit a large potential for the production of bioactive natural products of the nonribosomal peptide, polyketide, and ribosomal peptide classes, and yet most of the biosynthetic gene clusters are silent under conventional cultivation conditions. In the present study, we utilized a high-density cultivation approach recently developed for phototrophic bacteria to rapidly generate biomass of the filamentous bacteria up to a density of 400 g (wet weight)/liter. Unexpectedly, integrated transcriptional and metabolomics studies uncovered a major reprogramming of the secondary metabolome of two Nostoc strains at high culture density and a governing effect of extracellular signals in this process. The holistic approach enabled capturing and structural elucidation of novel variants of anabaenopeptin, including one congener with potent allelopathic activity against a strain isolated from the same habitat. The study provides a snapshot on the role of cell-type-specific expression for the formation of natural products in cyanobacteria.IMPORTANCE Terrestrial filamentous cyanobacteria are a largely untapped source of small-molecule natural products. Exploitation of the phototrophic organisms is hampered by their slow growth and the requirement of photobioreactors. The present study not only demonstrates the suitability of a recently developed two-tier vessel cultivation approach for the rapid generation of biomass of Nostoc strains but also demonstrates a pronounced upregulation of high value natural products at ultrahigh culture densities. The study provides new guidelines for high-throughput screening and exploitation of small-molecule natural products and can facilitate the discovery new bioactive products from terrestrial cyanobacteria.
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30
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Jokela J, Heinilä LMP, Shishido TK, Wahlsten M, Fewer DP, Fiore MF, Wang H, Haapaniemi E, Permi P, Sivonen K. Production of High Amounts of Hepatotoxin Nodularin and New Protease Inhibitors Pseudospumigins by the Brazilian Benthic Nostoc sp. CENA543. Front Microbiol 2017; 8:1963. [PMID: 29062311 PMCID: PMC5640712 DOI: 10.3389/fmicb.2017.01963] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 09/25/2017] [Indexed: 01/26/2023] Open
Abstract
Nostoc is a cyanobacterial genus, common in soils and a prolific producer of natural products. This research project aimed to explore and characterize Brazilian cyanobacteria for new bioactive compounds. Here we report the production of hepatotoxins and new protease inhibitors from benthic Nostoc sp. CENA543 isolated from a small, shallow, saline-alkaline lake in the Nhecolândia, Pantanal wetland area in Brazil. Nostoc sp. CENA543 produces exceptionally high amounts of nodularin-R. This is the first free-living Nostoc that produces nodularin at comparable levels as the toxic, bloom-forming, Nodularia spumigena. We also characterized pseudospumigins A-F, which are a novel family of linear tetrapeptides. Pseudospumigins are structurally related to linear tetrapeptide spumigins and aeruginosins both present in N. spumigena but differ in respect to their diagnostic amino acid, which is Ile/Leu/Val in pseudospumigins, Pro/mPro in spumigins, and Choi in aeruginosins. The pseudospumigin gene cluster is more similar to the spumigin biosynthetic gene cluster than the aeruginosin gene cluster. Pseudospumigin A inhibited trypsin (IC50 4.5 μM after 1 h) in a similar manner as spumigin E from N. spumigena but was almost two orders of magnitude less potent. This study identifies another location and environment where the hepatotoxic nodularin has the potential to cause the death of eukaryotic organisms.
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Affiliation(s)
- Jouni Jokela
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Lassi M P Heinilä
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Tânia K Shishido
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Matti Wahlsten
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - David P Fewer
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Marli F Fiore
- Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Hao Wang
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Esa Haapaniemi
- Department of Chemistry, University of Jyväskylä, Helsinki, Finland
| | - Perttu Permi
- Department of Chemistry, University of Jyväskylä, Helsinki, Finland.,Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Helsinki, Finland
| | - Kaarina Sivonen
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
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