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Buivydaitė Ž, Aryal L, Corrêa FB, Chen T, Langlois V, Elberg CL, Netherway T, Wang R, Zhao T, Acharya B, Emerson JB, Hillary L, Khadka RB, Mason-Jones K, Sapkota R, Sutela S, Trubl G, White RA, Winding A, Carreira C. Meeting report: The first soil viral workshop 2022. Virus Res 2023; 331:199121. [PMID: 37086855 PMCID: PMC10457523 DOI: 10.1016/j.virusres.2023.199121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/20/2023] [Accepted: 04/20/2023] [Indexed: 04/24/2023]
Abstract
Soil viral ecology is a growing research field; however, the state of knowledge still lags behind that of aquatic systems. Therefore, to facilitate progress, the first Soil Viral Workshop was held to encourage international scientific discussion and collaboration, suggest guidelines for future research, and establish soil viral research as a concrete research area. The workshop took place at Søminestationen, Denmark, between 15 and 17th of June 2022. The meeting was primarily held in person, but the sessions were also streamed online. The workshop was attended by 23 researchers from ten different countries and from a wide range of subfields and career stages. Eleven talks were presented, followed by discussions revolving around three major topics: viral genomics, virus-host interactions, and viruses in the soil food web. The main take-home messages and suggestions from the discussions are summarized in this report.
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Affiliation(s)
- Živilė Buivydaitė
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark.
| | - Laxman Aryal
- Nepal National Plant Pathology Research Center, Nepal Agricultural Research Council, Khumaltar, Lalitpur, Nepal
| | - Felipe Borim Corrêa
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Tingting Chen
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Valérie Langlois
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, G1V 0A6 Québec, QC, Canada
| | - Christine Lorenzen Elberg
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Tarquin Netherway
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51 Uppsala, Sweden
| | - Ruiqi Wang
- Department of Environmental Biology, Institute of Environmental Sciences (CML), Leiden University, Einsteinweg 2, 2333 CC Leiden, the Netherlands
| | - Tianci Zhao
- Microbial Ecology Cluster, Genomics Research in Ecology and Evolution in Nature (Green), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, 9747AG Groningen, the Netherlands
| | - Basistha Acharya
- Nepal National Plant Pathology Research Center, Nepal Agricultural Research Council, Khumaltar, Lalitpur, Nepal
| | - Joanne B Emerson
- Department of Plant Pathology, University of California, 1 Shields Ave., Davis, CA, USA
| | - Luke Hillary
- Department of Plant Pathology, University of California, 1 Shields Ave., Davis, CA, USA
| | - Ram B Khadka
- Nepal National Plant Pathology Research Center, Nepal Agricultural Research Council, Khumaltar, Lalitpur, Nepal
| | - Kyle Mason-Jones
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, the Netherlands
| | - Rumakanta Sapkota
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Suvi Sutela
- Forest Health and Biodiversity Group, Natural Resources Institute Finland, Helsinki, Finland
| | - Gareth Trubl
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Richard Allen White
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Kannapolis, NC, USA
| | - Anne Winding
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Cátia Carreira
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
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2
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Raco M, Vainio EJ, Sutela S, Eichmeier A, Hakalová E, Jung T, Botella L. High Diversity of Novel Viruses in the Tree Pathogen Phytophthora castaneae Revealed by High-Throughput Sequencing of Total and Small RNA. Front Microbiol 2022; 13:911474. [PMID: 35783401 PMCID: PMC9244493 DOI: 10.3389/fmicb.2022.911474] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 04/21/2022] [Indexed: 12/11/2022] Open
Abstract
Phytophthora castaneae, an oomycete pathogen causing root and trunk rot of different tree species in Asia, was shown to harbor a rich diversity of novel viruses from different families. Four P. castaneae isolates collected from Chamaecyparis hodginsii in a semi-natural montane forest site in Vietnam were investigated for viral presence by traditional and next-generation sequencing (NGS) techniques, i.e., double-stranded RNA (dsRNA) extraction and high-throughput sequencing (HTS) of small RNAs (sRNAs) and total RNA. Genome organization, sequence similarity, and phylogenetic analyses indicated that the viruses were related to members of the order Bunyavirales and families Endornaviridae, Megabirnaviridae, Narnaviridae, Totiviridae, and the proposed family “Fusagraviridae.” The study describes six novel viruses: Phytophthora castaneae RNA virus 1–5 (PcaRV1-5) and Phytophthora castaneae negative-stranded RNA virus 1 (PcaNSRV1). All six viruses were detected by sRNA sequencing, which demonstrates an active RNA interference (RNAi) system targeting viruses in P. castaneae. To our knowledge, this is the first report of viruses in P. castaneae and the whole Phytophthora major Clade 5, as well as of the activity of an RNAi mechanism targeting viral genomes among Clade 5 species. PcaRV1 is the first megabirnavirus described in oomycetes and the genus Phytophthora.
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Affiliation(s)
- Milica Raco
- Phytophthora Research Centre, Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czechia
- *Correspondence: Milica Raco,
| | - Eeva J. Vainio
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Suvi Sutela
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Aleš Eichmeier
- Mendeleum-Institute of Genetics, Faculty of Horticulture, Mendel University in Brno, Brno, Czechia
| | - Eliška Hakalová
- Mendeleum-Institute of Genetics, Faculty of Horticulture, Mendel University in Brno, Brno, Czechia
| | - Thomas Jung
- Phytophthora Research Centre, Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czechia
| | - Leticia Botella
- Phytophthora Research Centre, Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czechia
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Sutela S, Piri T, Vainio EJ. Discovery and Community Dynamics of Novel ssRNA Mycoviruses in the Conifer Pathogen Heterobasidion parviporum. Front Microbiol 2021; 12:770787. [PMID: 34899655 PMCID: PMC8652122 DOI: 10.3389/fmicb.2021.770787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 10/11/2021] [Indexed: 11/24/2022] Open
Abstract
Heterobasidion species are highly destructive basidiomycetous conifer pathogens of the Boreal forest region. Earlier studies have revealed dsRNA virus infections of families Curvulaviridae and Partitiviridae in Heterobasidion strains, and small RNA deep sequencing has also identified infections of Mitoviridae members in these fungi. In this study, the virome of Heterobasidion parviporum was examined for the first time by RNA-Seq using total RNA depleted of rRNA. This method successfully revealed new viruses representing two established (+)ssRNA virus families not found earlier in Heterobasidion: Narnaviridae and Botourmiaviridae. In addition, we identified the presence of a recently described virus group tentatively named “ambiviruses” in H. parviporum. The H. parviporum isolates included in the study originated from experimental forest sites located within 0.7 km range from each other, and a population analysis including 43 isolates was conducted at one of the experimental plots to establish the prevalence of the newly identified viruses in clonally spreading H. parviporum individuals. Our results indicate that viral infections are considerably more diverse and common among Heterobasidion isolates than known earlier and include ssRNA viruses with high prevalence and interspecies variation.
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Affiliation(s)
- Suvi Sutela
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Tuula Piri
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Eeva J Vainio
- Natural Resources Institute Finland (Luke), Helsinki, Finland
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Sutela S, Forgia M, Vainio EJ, Chiapello M, Daghino S, Vallino M, Martino E, Girlanda M, Perotto S, Turina M. The virome from a collection of endomycorrhizal fungi reveals new viral taxa with unprecedented genome organization. Virus Evol 2020; 6:veaa076. [PMID: 33324490 PMCID: PMC7724248 DOI: 10.1093/ve/veaa076] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mutualistic plant-associated fungi are recognized as important drivers in plant evolution, diversity, and health. The discovery that mycoviruses can take part and play important roles in symbiotic tripartite interactions has prompted us to study the viromes associated with a collection of ericoid and orchid mycorrhizal (ERM and ORM, respectively) fungi. Our study, based on high-throughput sequencing of transcriptomes (RNAseq) from fungal isolates grown in axenic cultures, revealed in both ERM and ORM fungi the presence of new mycoviruses closely related to already classified virus taxa, but also new viruses that expand the boundaries of characterized RNA virus diversity to previously undescribed evolutionary trajectories. In ERM fungi, we provide first evidence of a bipartite virus, distantly related to narnaviruses, that splits the RNA-dependent RNA polymerase (RdRP) palm domain into two distinct proteins, encoded by each of the two segments. Furthermore, in one isolate of the ORM fungus Tulasnella spp. we detected a 12 kb genomic fragment coding for an RdRP with features of bunyavirus-like RdRPs. However, this 12 kb genomic RNA has the unique features, for Bunyavirales members, of being tri-cistronic and carrying ORFs for the putative RdRP and putative nucleocapsid in ambisense orientation on the same genomic RNA. Finally, a number of ORM fungal isolates harbored a group of ambisense bicistronic viruses with a genomic size of around 5 kb, where we could identify a putative RdRP palm domain that has some features of plus strand RNA viruses; these new viruses may represent a new lineage in the Riboviria, as they could not be reliably assigned to any of the branches in the recently derived monophyletic tree that includes most viruses with an RNA genome.
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Affiliation(s)
- Suvi Sutela
- Natural Resources Institute Finland (Luke), Forest Health and Biodiversity Group, Latokartanonkaari 9, Helsinki FI-00790, Finland
| | - Marco Forgia
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, Torino 10135, Italy
| | - Eeva J Vainio
- Natural Resources Institute Finland (Luke), Forest Health and Biodiversity Group, Latokartanonkaari 9, Helsinki FI-00790, Finland
| | - Marco Chiapello
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, Torino 10135, Italy
| | - Stefania Daghino
- Department of Life Science and Systems Biology, University of Torino, Viale Mattioli 25, Torino 10125, Italy
| | - Marta Vallino
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, Torino 10135, Italy
| | - Elena Martino
- Department of Life Science and Systems Biology, University of Torino, Viale Mattioli 25, Torino 10125, Italy
| | - Mariangela Girlanda
- Department of Life Science and Systems Biology, University of Torino, Viale Mattioli 25, Torino 10125, Italy
| | - Silvia Perotto
- Department of Life Science and Systems Biology, University of Torino, Viale Mattioli 25, Torino 10125, Italy
| | - Massimo Turina
- Institute for Sustainable Plant Protection, CNR, Strada delle Cacce 73, Torino 10135, Italy
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Vainio EJ, Sutela S. Mixed infection by a partitivirus and a negative-sense RNA virus related to mymonaviruses in the polypore fungus Bondarzewia berkeleyi. Virus Res 2020; 286:198079. [PMID: 32599089 DOI: 10.1016/j.virusres.2020.198079] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 11/30/2022]
Abstract
Virus communities of forest fungi remain poorly characterized. In this study, we detected two new viruses co-infecting an isolate of the polypore fungus Bondarzewia berkeleyi using high-throughput sequencing. One of them was a putative new partitivirus designated as Bondarzewia berkeleyi partitivirus 1 (BbPV1), with two linear dsRNA genome segments of 1928 and 1863 bp encoding a putative RNA-dependent RNA polymerase (RdRP) of 591 aa and a putative capsid protein of 538 aa. The other virus, designated as Bondarzewia berkeleyi negative-strand RNA virus 1 (BbNSRV1), had a non-segmented negative-sense RNA genome of 10,983 nt and was related to members of family Mymonaviridae. The BbNSRV1 genome includes six predicted open reading frames (ORFs) of 279, 425, 230, 174, 200 and 1970 aa. The longest ORF contained conserved regions corresponding to Mononegavirales RdRP and mRNA-capping enzyme region V constituting the mononegavirus Large protein. In addition, a low level of sequence identity was detected between the putative nucleocapsid protein-coding ORF2 of Lentinula edodes negative-strand RNA virus 1 and BbNSRV1. The viruses characterized in this study are the first ones described in Bondarzewia spp., and BbNSRV1 is the second mymona-like virus described in a basidiomycete host.
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Affiliation(s)
- Eeva J Vainio
- Natural Resources Institute Finland, Latokartanonkaari 9, 00790, Helsinki, Finland.
| | - Suvi Sutela
- Natural Resources Institute Finland, Latokartanonkaari 9, 00790, Helsinki, Finland
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6
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Sutela S, Vainio EJ. Virus population structure in the ectomycorrhizal fungi Lactarius rufus and L. tabidus at two forest sites in Southern Finland. Virus Res 2020; 285:197993. [PMID: 32360299 DOI: 10.1016/j.virusres.2020.197993] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/25/2020] [Accepted: 04/25/2020] [Indexed: 01/27/2023]
Abstract
Lactarius fungi belong to the Russulaceae family and have an important ecological role as ectomycorrhizal symbionts of coniferous and deciduous trees. Two Lactarius species, L. tabidus and L. rufus have been shown to harbor bisegmented dsRNA viruses belonging to an unclassified virus group including the mutualistic Curvularia thermal tolerance virus (CThTV). In this study, we characterized the first complete genome sequences of these viruses designated as Lactarius tabidus RNA virus 1 (LtRV1) and Lactarius rufus RNA virus 1 (LrRV1), both of which included two genome segments of 2241 and 2049 bp. We also analyzed spatial distribution and sequence diversity of the viruses in sixty host strains at two forest sites, and showed that the viruses are species-specific at sites where both host species co-occur. We also found that single virus isolates inhabited several different conspecific host strains, and were involved in persistent infections during up to eight years.
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Affiliation(s)
- Suvi Sutela
- Natural Resources Institute Finland, Latokartanonkaari 9, 00790 Helsinki, Finland.
| | - Eeva J Vainio
- Natural Resources Institute Finland, Latokartanonkaari 9, 00790 Helsinki, Finland
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7
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Abstract
Programmed cell death (PCD) processes are essential in the plant embryogenesis. To understand how PCD operates in a developing seed, the dying cells need to be identified in relation to their surviving neighbors. This can be accomplished by the means of in situ visualization of fragmented DNA-a well-known hallmark of PCD. In the developing Scots pine (Pinus sylvestris L.) seed, several tissues die via morphologically different PCD processes during the embryogenesis. Here, we describe the protocols for the characterization of Scots pine seeds at the early and late developmental stages and, further, the localization of nucleic acids and DNA fragmentation by the acridine orange staining and TUNEL (terminal deoxynucleotidyl transferase (TdT)-mediated deoxyuridine triphosphate (dUTP) nick end labeling) assay in the dying seed tissues.
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Affiliation(s)
- Jaana Vuosku
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland.
| | - Suvi Sutela
- Natural Resources Institute Finland (Luke), Helsinki, Finland
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8
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Sutela S, Poimala A, Vainio EJ. Viruses of fungi and oomycetes in the soil environment. FEMS Microbiol Ecol 2019; 95:5542194. [DOI: 10.1093/femsec/fiz119] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/30/2019] [Indexed: 12/17/2022] Open
Abstract
ABSTRACTSoils support a myriad of organisms hosting highly diverse viromes. In this minireview, we focus on viruses hosted by true fungi and oomycetes (members of Stamenopila, Chromalveolata) inhabiting bulk soil, rhizosphere and litter layer, and representing different ecological guilds, including fungal saprotrophs, mycorrhizal fungi, mutualistic endophytes and pathogens. Viruses infecting fungi and oomycetes are characterized by persistent intracellular nonlytic lifestyles and transmission via spores and/or hyphal contacts. Almost all fungal and oomycete viruses have genomes composed of single-stranded or double-stranded RNA, and recent studies have revealed numerous novel viruses representing yet unclassified family-level groups. Depending on the virus–host combination, infections can be asymptomatic, beneficial or detrimental to the host. Thus, mycovirus infections may contribute to the multiplex interactions of hosts, therefore likely affecting the dynamics of fungal communities required for the functioning of soil ecosystems. However, the effects of fungal and oomycete viruses on soil ecological processes are still mostly unknown. Interestingly, new metagenomics data suggest an extensive level of horizontal virus transfer between plants, fungi and insects.
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Affiliation(s)
- Suvi Sutela
- Forest Health and Biodiversity, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, 00790 Helsinki, Finland
| | - Anna Poimala
- Forest Health and Biodiversity, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, 00790 Helsinki, Finland
| | - Eeva J Vainio
- Forest Health and Biodiversity, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, 00790 Helsinki, Finland
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9
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Salojärvi J, Smolander OP, Nieminen K, Rajaraman S, Safronov O, Safdari P, Lamminmäki A, Immanen J, Lan T, Tanskanen J, Rastas P, Amiryousefi A, Jayaprakash B, Kammonen JI, Hagqvist R, Eswaran G, Ahonen VH, Serra JA, Asiegbu FO, de Dios Barajas-Lopez J, Blande D, Blokhina O, Blomster T, Broholm S, Brosché M, Cui F, Dardick C, Ehonen SE, Elomaa P, Escamez S, Fagerstedt KV, Fujii H, Gauthier A, Gollan PJ, Halimaa P, Heino PI, Himanen K, Hollender C, Kangasjärvi S, Kauppinen L, Kelleher CT, Kontunen-Soppela S, Koskinen JP, Kovalchuk A, Kärenlampi SO, Kärkönen AK, Lim KJ, Leppälä J, Macpherson L, Mikola J, Mouhu K, Mähönen AP, Niinemets Ü, Oksanen E, Overmyer K, Palva ET, Pazouki L, Pennanen V, Puhakainen T, Poczai P, Possen BJHM, Punkkinen M, Rahikainen MM, Rousi M, Ruonala R, van der Schoot C, Shapiguzov A, Sierla M, Sipilä TP, Sutela S, Teeri TH, Tervahauta AI, Vaattovaara A, Vahala J, Vetchinnikova L, Welling A, Wrzaczek M, Xu E, Paulin LG, Schulman AH, Lascoux M, Albert VA, Auvinen P, Helariutta Y, Kangasjärvi J. Author Correction: Genome sequencing and population genomic analyses provide insights into the adaptive landscape of silver birch. Nat Genet 2019; 51:1187-1189. [PMID: 31197270 PMCID: PMC8076037 DOI: 10.1038/s41588-019-0442-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jarkko Salojärvi
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | | | - Kaisa Nieminen
- Green Technology, Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Sitaram Rajaraman
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Omid Safronov
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Pezhman Safdari
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Airi Lamminmäki
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Juha Immanen
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Tianying Lan
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA
| | - Jaakko Tanskanen
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Green Technology, Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Pasi Rastas
- Department of Zoology, University of Cambridge, Cambridge, UK.,Ecological Genetics Research Unit, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Ali Amiryousefi
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Balamuralikrishna Jayaprakash
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,National Institute of Health and Welfare (THL), Kuopio, Finland
| | - Juhana I Kammonen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Risto Hagqvist
- Green Technology, Natural Resources Institute Finland (Luke), Haapastensyrjä, Läyliäinen, Finland
| | - Gugan Eswaran
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Viivi Helena Ahonen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland.,Finnish Institute of Occupational Health, Work Environment Laboratories, Kuopio, Finland
| | - Juan Alonso Serra
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Fred O Asiegbu
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | | | - Daniel Blande
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Olga Blokhina
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Tiina Blomster
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Suvi Broholm
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland, and Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Mikael Brosché
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Institute of Technology, University of Tartu, Tartu, Estonia
| | - Fuqiang Cui
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,School of Forest Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, China
| | - Chris Dardick
- Appalachian Fruit Research Station, Agricultural Research Service, United States Department of Agriculture, Kearnysville, West Virginia, USA
| | - Sanna E Ehonen
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Paula Elomaa
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Sacha Escamez
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Kurt V Fagerstedt
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Hiroaki Fujii
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Adrien Gauthier
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Unité AGRI'TERR, UniLaSalle, Campus de Rouen, Mont-Saint-Aignan, France
| | - Peter J Gollan
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Pauliina Halimaa
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Pekka I Heino
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Division of Genetics, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Kristiina Himanen
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Courtney Hollender
- Appalachian Fruit Research Station, Agricultural Research Service, United States Department of Agriculture, Kearnysville, West Virginia, USA
| | - Saijaliisa Kangasjärvi
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Leila Kauppinen
- Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Colin T Kelleher
- DBN Plant Molecular Laboratory, National Botanic Gardens of Ireland, Dublin, Ireland
| | - Sari Kontunen-Soppela
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - J Patrik Koskinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Blueprint Genetics, Helsinki, Finland
| | - Andriy Kovalchuk
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Department of Forest Sciences, University of Helsinki, Helsinki, Finland
| | - Sirpa O Kärenlampi
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Anna K Kärkönen
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.,Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Kean-Jin Lim
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Johanna Leppälä
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Lee Macpherson
- Department of Haemato-oncology, King's College London, London, UK
| | - Juha Mikola
- Department of Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Katriina Mouhu
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Ari Pekka Mähönen
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Ülo Niinemets
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Elina Oksanen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Kirk Overmyer
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - E Tapio Palva
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Division of Genetics, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Leila Pazouki
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Ville Pennanen
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Division of Genetics, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Tuula Puhakainen
- Division of Genetics, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Institute of Botany, The Chinese Academy of Sciences, Beijing, China
| | - Péter Poczai
- Finnish Museum of Natural History (Botany), University of Helsinki, Helsinki, Finland
| | - Boy J H M Possen
- Management and Production of Renewable Resources, Natural Resources Institute Finland (Luke), Helsinki, Finland.,Green Technology, Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Matleena Punkkinen
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Moona M Rahikainen
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Matti Rousi
- Management and Production of Renewable Resources, Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Raili Ruonala
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Agricultural and Food Science/Scientific Agricultural Society of Finland, Lemu, Finland
| | | | - Alexey Shapiguzov
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Institute of Plant Physiology, Russian Academy of Sciences, Moscow, Russia
| | - Maija Sierla
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Timo P Sipilä
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Suvi Sutela
- Genetics and Physiology Unit, University of Oulu, Oulu, Finland
| | - Teemu H Teeri
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Arja I Tervahauta
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Aleksia Vaattovaara
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Jorma Vahala
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Lidia Vetchinnikova
- Forest Research Institute Karelian Research Centre Russian Academy of Sciences, Petrozavodsk, Russia
| | - Annikki Welling
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Royal Haskoning DHV, Maastricht Airport, Beek, the Netherlands
| | - Michael Wrzaczek
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | - Enjun Xu
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Chemistry and Toxicology Research Unit, Finnish Food Safety Authority Evira, Helsinki, Finland
| | - Lars G Paulin
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Alan H Schulman
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Green Technology, Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Martin Lascoux
- Department of Ecology and Genetics, Evolutionary Biology Center and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, New York, USA.
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
| | - Ykä Helariutta
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland. .,Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland. .,Institute of Biotechnology, University of Helsinki, Helsinki, Finland. .,Sainsbury Laboratory, University of Cambridge, Cambridge, UK.
| | - Jaakko Kangasjärvi
- Division of Plant Biology, Department of Biosciences, University of Helsinki, Helsinki, Finland. .,Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
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10
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Vuosku J, Sutela S, Kestilä J, Jokela A, Sarjala T, Häggman H. Expression of catalase and retinoblastoma-related protein genes associates with cell death processes in Scots pine zygotic embryogenesis. BMC Plant Biol 2015; 15:88. [PMID: 25887788 PMCID: PMC4396594 DOI: 10.1186/s12870-015-0462-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 02/18/2015] [Indexed: 05/02/2023]
Abstract
BACKGROUND The cell cycle and cellular oxidative stress responses are tightly controlled for proper growth and development of Scots pine (Pinus sylvestris L.) seed. Programmed cell death (PCD) is an integral part of the embryogenesis during which megagametophyte cells in the embryo surrounding region (ESR) and cells in the nucellar layers face death. In the present study, we show both the tissue and developmental stage specific expression of the genes encoding the autophagy related ATG5, catalase (CAT), and retinoblastoma related protein (RBR) as well as the connection between the gene expressions and cell death programs. RESULTS We found strong CAT expression in the cells of the developing embryo throughout the embryogenesis as well as in the cells of the megagametophyte and the nucellar layers at the early embryogeny. The CAT expression was found to overlap with both the ATG5 expression and hydrogen peroxide localization. At the late embryogeny, CAT expression diminished in the dying cells of the nucellar layers as well as in megagametophyte cells, showing the first signs of incipient cell death. Accumulation of starch and minor RBR expression were characteristic of megagametophyte cells in the ESR, whereas strong RBR expression was found in the cells of the nucellar layers at the late embryogeny. CONCLUSIONS Our results suggest that ATG5, CAT, and RBR are involved in the Scots pine embryogenesis and cell death processes. CAT seems to protect cells against hydrogen peroxide accumulation and oxidative stress related cell death especially during active metabolism. The opposite expression of RBR in the ESR and nucellar layers alongside morphological characteristics emphasizes the different type of the cell death processes in these tissues. Furthermore, the changes in ATG5 and RBR expressions specifically in the megagametophyte cells dying by necrotic cell death suggest the genetic regulation of developmental necrosis in Scots pine embryogenesis.
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Affiliation(s)
- Jaana Vuosku
- Genetics and Physiology Unit, University of Oulu, P.O. Box 3000, FI-90014, Oulu, Finland.
- Current address: Natural Resources Institute Finland (Luke), Rovaniemi Unit, FI-96301, Rovaniemi, Finland.
| | - Suvi Sutela
- Genetics and Physiology Unit, University of Oulu, P.O. Box 3000, FI-90014, Oulu, Finland.
| | - Johanna Kestilä
- Genetics and Physiology Unit, University of Oulu, P.O. Box 3000, FI-90014, Oulu, Finland.
| | - Anne Jokela
- Genetics and Physiology Unit, University of Oulu, P.O. Box 3000, FI-90014, Oulu, Finland.
| | - Tytti Sarjala
- Natural Resources Institute Finland (Luke), Parkano Unit, Kaironiementie 15, FI-39700, Parkano, Finland.
| | - Hely Häggman
- Genetics and Physiology Unit, University of Oulu, P.O. Box 3000, FI-90014, Oulu, Finland.
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11
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Sutela S, Hahl T, Tiimonen H, Aronen T, Ylioja T, Laakso T, Saranpää P, Chiang V, Julkunen-Tiitto R, Häggman H. Phenolic compounds and expression of 4CL genes in silver birch clones and Pt4CL1a lines. PLoS One 2014; 9:e114434. [PMID: 25502441 PMCID: PMC4263613 DOI: 10.1371/journal.pone.0114434] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 11/10/2014] [Indexed: 01/09/2023] Open
Abstract
A small multigene family encodes 4-coumarate:CoA ligases (4CLs) catalyzing the CoA ligation of hydroxycinnamic acids, a branch point step directing metabolites to a flavonoid or monolignol pathway. In the present study, we examined the effect of antisense Populus tremuloides 4CL (Pt4CL1) to the lignin and soluble phenolic compound composition of silver birch (Betula pendula) Pt4CL1a lines in comparison with non-transgenic silver birch clones. The endogenous expression of silver birch 4CL genes was recorded in the stems and leaves and also in leaves that were mechanically injured. In one of the transgenic Pt4CL1a lines, the ratio of syringyl (S) and guaiacyl (G) lignin units was increased. Moreover, the transcript levels of putative silver birch 4CL gene (Bp4CL1) were reduced and contents of cinnamic acid derivatives altered. In the other two Pt4CL1a lines changes were detected in the level of individual phenolic compounds. However, considerable variation was found in the transcript levels of silver birch 4CLs as well as in the concentration of phenolic compounds among the transgenic lines and non-transgenic clones. Wounding induced the expression of Bp4CL1 and Bp4CL2 in leaves in all clones and transgenic lines, whereas the transcript levels of Bp4CL3 and Bp4CL4 remained unchanged. Moreover, minor changes were detected in the concentrations of phenolic compounds caused by wounding. As an overall trend the wounding decreased the flavonoid content in silver birches and increased the content of soluble condensed tannins. The results indicate that by reducing the Bp4CL1 transcript levels lignin composition could be modified. However, the alterations found among the Pt4CL1a lines and the non-transgenic clones were within the natural variation of silver birches, as shown in the present study by the clonal differences in the transcripts levels of 4CL genes, soluble phenolic compounds and condensed tannins.
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Affiliation(s)
- Suvi Sutela
- Department of Biology, University of Oulu, Oulu, Finland
| | - Terhi Hahl
- Department of Biology, University of Oulu, Oulu, Finland
| | - Heidi Tiimonen
- The Finnish Border Guard, Border and Coast Guard Academy, Imatra, Finland
| | - Tuija Aronen
- Finnish Forest Research Institute, Eastern Finland Regional Unit (Punkaharju Unit), Punkaharju, Finland
| | - Tiina Ylioja
- Finnish Forest Research Institute, Southern Finland Regional Unit (Vantaa Unit), Vantaa, Finland
| | - Tapio Laakso
- Finnish Forest Research Institute, Southern Finland Regional Unit (Vantaa Unit), Vantaa, Finland
| | - Pekka Saranpää
- Finnish Forest Research Institute, Southern Finland Regional Unit (Vantaa Unit), Vantaa, Finland
| | - Vincent Chiang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, United States of America
| | | | - Hely Häggman
- Department of Biology, University of Oulu, Oulu, Finland
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12
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Pohjanen J, Koskimäki JJ, Sutela S, Ardanov P, Suorsa M, Niemi K, Sarjala T, Häggman H, Pirttilä AM. Interaction with ectomycorrhizal fungi and endophytic Methylobacterium affects nutrient uptake and growth of pine seedlings in vitro. Tree Physiol 2014; 34:993-1005. [PMID: 25149086 DOI: 10.1093/treephys/tpu062] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Tissues of Scots pine (Pinus sylvestris L.) contain several endophytic microorganisms of which Methylobacterium extorquens DSM13060 is a dominant species throughout the year. Similar to other endophytic bacteria, M. extorquens is able to colonize host plant tissues without causing any symptoms of disease. In addition to endophytic bacteria, plants associate simultaneously with a diverse set of microorganisms. Furthermore, plant-colonizing microorganisms interact with each other in a species- or strain-specific manner. Several studies on beneficial microorganisms interacting with plants have been carried out, but few deal with interactions between different symbiotic organisms and specifically, how these interactions affect the growth and development of the host plant. Our aim was to study how the pine endophyte M. extorquens DSM13060 affects pine seedlings and how the co-inoculation with ectomycorrhizal (ECM) fungi [Suillus variegatus (SV) or Pisolithus tinctorius (PT)] alters the response of Scots pine. We determined the growth, polyamine and nutrient contents of inoculated and non-inoculated Scots pine seedlings in vitro. Our results show that M. extorquens is able to improve the growth of seedlings at the same level as the ECM fungi SV and PT do. The effect of co-inoculation using different symbiotic organisms was seen in terms of changes in growth and nutrient uptake. Inoculation using M. extorquens together with ECM fungi improved the growth of the host plant even more than single ECM inoculation. Symbiotic organisms also had a strong effect on the potassium content of the seedling. The results indicate that interaction between endophyte and ECM fungus is species dependent, leading to increased or decreased nutrient content and growth of pine seedlings.
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Affiliation(s)
- Johanna Pohjanen
- Department of Biology, University of Oulu, PO Box 3000, FIN-90014 Oulu, Finland
| | - Janne J Koskimäki
- Department of Biology, University of Oulu, PO Box 3000, FIN-90014 Oulu, Finland
| | - Suvi Sutela
- Department of Biology, University of Oulu, PO Box 3000, FIN-90014 Oulu, Finland
| | - Pavlo Ardanov
- Department of Biology, University of Oulu, PO Box 3000, FIN-90014 Oulu, Finland
| | - Marja Suorsa
- Department of Biology, University of Oulu, PO Box 3000, FIN-90014 Oulu, Finland
| | - Karoliina Niemi
- Finnish Forest Industries Federation, PO Box 336, FIN-00171 Helsinki, Finland
| | - Tytti Sarjala
- Finnish Forest Research Institute, Parkano Research Unit, FIN-39700 Parkano, Finland
| | - Hely Häggman
- Department of Biology, University of Oulu, PO Box 3000, FIN-90014 Oulu, Finland
| | - Anna Maria Pirttilä
- Department of Biology, University of Oulu, PO Box 3000, FIN-90014 Oulu, Finland
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13
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Dumont E, Jokipii-Lukkari S, Parkash V, Vuosku J, Sundström R, Nymalm Y, Sutela S, Taskinen K, Kallio PT, Salminen TA, Häggman H. Evolution, three-dimensional model and localization of truncated hemoglobin PttTrHb of hybrid aspen. PLoS One 2014; 9:e88573. [PMID: 24520401 PMCID: PMC3919811 DOI: 10.1371/journal.pone.0088573] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 01/09/2014] [Indexed: 11/19/2022] Open
Abstract
Thus far, research on plant hemoglobins (Hbs) has mainly concentrated on symbiotic and non-symbiotic Hbs, and information on truncated Hbs (TrHbs) is scarce. The aim of this study was to examine the origin, structure and localization of the truncated Hb (PttTrHb) of hybrid aspen (Populus tremula L. × tremuloides Michx.), the model system of tree biology. Additionally, we studied the PttTrHb expression in relation to non-symbiotic class1 Hb gene (PttHb1) using RNAi-silenced hybrid aspen lines. Both the phylogenetic analysis and the three-dimensional (3D) model of PttTrHb supported the view that plant TrHbs evolved vertically from a bacterial TrHb. The 3D model suggested that PttTrHb adopts a 2-on-2 sandwich of α-helices and has a Bacillus subtilis -like ligand-binding pocket in which E11Gln and B10Tyr form hydrogen bonds to a ligand. However, due to differences in tunnel cavity and gate residue (E7Ala), it might not show similar ligand-binding kinetics as in Bs-HbO (E7Thr). The immunolocalization showed that PttTrHb protein was present in roots, stems as well as leaves of in vitro -grown hybrid aspens. In mature organs, PttTrHb was predominantly found in the vascular bundles and specifically at the site of lateral root formation, overlapping consistently with areas of nitric oxide (NO) production in plants. Furthermore, the NO donor sodium nitroprusside treatment increased the amount of PttTrHb in stems. The observed PttTrHb localization suggests that PttTrHb plays a role in the NO metabolism.
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Affiliation(s)
- Estelle Dumont
- Department of Biology, University of Oulu, Oulu, Finland
- UMR-MD1, Transporteurs Membranaires, Chimiorésistance et Drug-Design, Aix-Marseille Université, Marseille, France
| | | | - Vimal Parkash
- Structural Bioinformatics Laboratory, Department of Biosciences, Åbo Akademi University, Turku, Finland
| | - Jaana Vuosku
- Department of Biology, University of Oulu, Oulu, Finland
| | - Robin Sundström
- Structural Bioinformatics Laboratory, Department of Biosciences, Åbo Akademi University, Turku, Finland
| | - Yvonne Nymalm
- Structural Bioinformatics Laboratory, Department of Biosciences, Åbo Akademi University, Turku, Finland
| | - Suvi Sutela
- Department of Biology, University of Oulu, Oulu, Finland
| | | | | | - Tiina A. Salminen
- Structural Bioinformatics Laboratory, Department of Biosciences, Åbo Akademi University, Turku, Finland
| | - Hely Häggman
- Department of Biology, University of Oulu, Oulu, Finland
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14
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Sutela S, Ylioja T, Jokipii-Lukkari S, Anttila AK, Julkunen-Tiitto R, Niemi K, Mölläri T, Kallio PT, Häggman H. The responses of Vitreoscilla hemoglobin-expressing hybrid aspen (Populus tremula × tremuloides) exposed to 24-h herbivory: expression of hemoglobin and stress-related genes in exposed and nonorthostichous leaves. J Plant Res 2013; 126:795-809. [PMID: 23744275 DOI: 10.1007/s10265-013-0569-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Accepted: 04/17/2013] [Indexed: 06/02/2023]
Abstract
The responses of transcriptome and phenolic compounds were determined with Populus tremula L. × Populus tremuloides Michx. expressing the hemoglobin (Hb) of Vitreoscilla (VHb) and non-transformant (wt) line. After 24-h exposure of leaves to Conistra vaccinii L., the transcript levels of endogenous non-symbiotic class 1 Hb (PttHb1) and truncated Hb (PttTrHb) genes were modestly reduced and increased, respectively, in both wt and VHb-expressing line. Besides the herbivory exposed leaves showing the most significant transcriptome changes, alterations were also detected in the transcriptome of nonorthostichous leaves positioned directly above the exposed leaves. Both wt and VHb-expressing line displayed similar herbivory-induced effects on gene expression, although the extent of responses was more pronounced in the wt than in the VHb-expressing line. The contents of phenolic compounds were not altered due to herbivory and they were alike in the wt and VHb-expressing line. In addition, we determined the relative growth rates (RGRs) of Orthosia gothica L., Ectropis crepuscularia Denis & Schiff. and Orgyia antiqua L. larvae, and found no variation in the RGRs between the lines. Thus, VHb-expressing P. tremula × tremuloides lines showed to be comparable with wt in regards to the food quality of leaves.
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Affiliation(s)
- Suvi Sutela
- Department of Biology, University of Oulu, P.O. Box 3000, 90014, Oulu, Finland,
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15
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Vuosku J, Suorsa M, Ruottinen M, Sutela S, Muilu-Mäkelä R, Julkunen-Tiitto R, Sarjala T, Neubauer P, Häggman H. Polyamine metabolism during exponential growth transition in Scots pine embryogenic cell culture. Tree Physiol 2012; 32:1274-87. [PMID: 23022686 DOI: 10.1093/treephys/tps088] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Polyamine (PA) metabolism was studied in liquid cultures of Scots pine (Pinus sylvestris L.) embryogenic cells. The focus of the study was on the metabolic changes at the interphase between the initial lag phase and the exponential growth phase. PA concentrations fluctuated in the liquid cultures as follows. Putrescine (Put) concentrations increased, whereas spermidine (Spd) concentrations decreased in both free and soluble conjugated PA fractions. The concentrations of free and soluble conjugated spermine (Spm) remained low, and small amounts of excreted PAs were also found in the culture medium. The minor production of secondary metabolites reflected the undifferentiated stage of the embryogenic cell culture. Put was produced via the arginine decarboxylase (ADC) pathway. Futhermore, the gene expression data suggested that the accumulation of Put was caused neither by an increase in Put biosynthesis nor by a decrease in Put catabolism, but resulted mainly from the decrease in the biosynthesis of Spd and Spm. Put seemed to play an important role in cell proliferation in Scots pine embryogenic cells, but the low pH of the culture medium could also, at least partially, be the reason for the accumulation of endogenous Put. High Spd concentrations at the initiation of the culture, when cells were exposed to stress and cell death, suggested that Spd may act not only as a protector against stress but also as a growth suppressor, when proliferative growth is not promoted. All in all, Scots pine embryogenic cell culture was proved to be a favourable experimental platform to study PA metabolism and, furthermore, the developed system may also be beneficial in experiments where, e.g., the effect of specific stressors on PA metabolism is addressed.
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Affiliation(s)
- Jaana Vuosku
- Department of Biology, University of Oulu, 90014 Oulu, Finland.
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16
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Häggman H, Sutela S, Jokipii-Lukkari S, Ylioja T, Kasanen R, Anttila AK, Suokas M, Dumont E, Kallio PT. The effect of heterologous VHb expression to the functioning of stress-related genes in hybrid aspen lines exposured to biotic stress. BMC Proc 2011. [PMCID: PMC3240113 DOI: 10.1186/1753-6561-5-s7-p88] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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17
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Krajňáková J, Sutela S, Aronen T, Gömöry D, Vianello A, Häggman H. Long-term cryopreservation of Greek fir embryogenic cell lines: recovery, maturation and genetic fidelity. Cryobiology 2011; 63:17-25. [PMID: 21521636 DOI: 10.1016/j.cryobiol.2011.04.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Revised: 04/01/2011] [Accepted: 04/12/2011] [Indexed: 11/19/2022]
Abstract
In coniferous species, including Greek fir (Abies cephalonica Loud), the involvement of somatic embryo plants in breeding and reforestation programs is dependent on the success of long-term cryostorage of embryogenic cultures during clonal field testing. In the present study on Greek fir, we assayed the recovery, morphological characteristics and genetic fidelity of embryogenic cell lines 6 and 8 during proliferation and maturation after long-term cryostorage. Our results indicate successful recovery of both cell lines after 6 years in cryostorage. In the maturation phase, both cell lines were capable of producing somatic embryos although some differences were detected among experiments. However, these changes were more dependent on the differences in the components of the maturation media or in the experimental set-up than on the long-term cryostorage. During both proliferation and maturation phases, the morphological fidelity of the embryogenic cultures as well as of the somatic embryos were alike before and after cryopreservation. The genetic fidelity of the cryopreserved cell line 6 that was assayed by random amplified polymorphic DNA (i.e. RAPD) markers demonstrated some changes in the RAPD profiles. The results indicate possible genetic aberrations caused by long-term cryopreservation or somaclonal variation during the proliferation stage. However, in spite of these changes the embryogenic cultures did not lose their proliferation or maturation abilities.
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18
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Vuosku J, Sutela S, Sääskilahti M, Kestilä J, Jokela A, Sarjala T, Häggman H. Dealing with the problem of non-specific in situ mRNA hybridization signals associated with plant tissues undergoing programmed cell death. Plant Methods 2010; 6:7. [PMID: 20181098 PMCID: PMC2829549 DOI: 10.1186/1746-4811-6-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2009] [Accepted: 02/05/2010] [Indexed: 05/02/2023]
Abstract
BACKGROUND In situ hybridization is a general molecular method typically used for the localization of mRNA transcripts in plants. The method provides a valuable tool to unravel the connection between gene expression and anatomy, especially in species such as pines which show large genome size and shortage of sequence information. RESULTS In the present study, expression of the catalase gene (CAT) related to the scavenging of reactive oxygen species (ROS) and the polyamine metabolism related genes, diamine oxidase (DAO) and arginine decarboxylase (ADC), were localized in developing Scots pine (Pinus sylvestris L.) seeds. In addition to specific signals from target mRNAs, the probes continually hybridized non-specifically in the embryo surrounding region (ESR) of the megagametophyte tissue, in the remnants of the degenerated suspensors as well as in the cells of the nucellar layers, i.e. tissues exposed to cell death processes and extensive nucleic acid fragmentation during Scots pine seed development. CONCLUSIONS In plants, cell death is an integral part of both development and defence, and hence it is a common phenomenon in all stages of the life cycle. Our results suggest that extensive nucleic acid fragmentation during cell death processes can be a considerable source of non-specific signals in traditional in situ mRNA hybridization. Thus, the visualization of potential nucleic acid fragmentation simultaneously with the in situ mRNA hybridization assay may be necessary to ensure the correct interpretation of the signals in the case of non-specific hybridization of probes in plant tissues.
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Affiliation(s)
- Jaana Vuosku
- Department of Biology, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland
- Finnish Forest Research Institute, Parkano Research Unit, 39700 Parkano, Finland
| | - Suvi Sutela
- Department of Biology, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland
| | - Mira Sääskilahti
- Department of Biology, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland
| | - Johanna Kestilä
- Department of Biology, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland
| | - Anne Jokela
- Department of Biology, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland
| | - Tytti Sarjala
- Finnish Forest Research Institute, Parkano Research Unit, 39700 Parkano, Finland
| | - Hely Häggman
- Department of Biology, University of Oulu, P.O. Box 3000, 90014 Oulu, Finland
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Vuosku J, Sutela S, Tillman-Sutela E, Kauppi A, Jokela A, Sarjala T, Häggman H. Pine embryogenesis: many licences to kill for a new life. Plant Signal Behav 2009; 4:928-32. [PMID: 19826239 PMCID: PMC2801355 DOI: 10.4161/psb.4.10.9535] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
In plants, programmed cell death (PCD) is an important mechanism that controls normal growth and development as well as many defence responses. At present, research on PCD in different plant species is actively carried out due to the possibilities offered by modern methods in molecular biology and the increasing amount of genome data. The pine seed provides a favourable model for PCD because it represents an interesting inheritance of seed tissues as well as an anatomically well-described embryogenesis during which several tissues die via morphologically different PCD processes.
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Affiliation(s)
- Jaana Vuosku
- Department of Biology, University of Oulu, Oulu, Finland.
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Sutela S, Niemi K, Edesi J, Laakso T, Saranpää P, Vuosku J, Mäkelä R, Tiimonen H, Chiang VL, Koskimäki J, Suorsa M, Julkunen-Tiitto R, Häggman H. Phenolic compounds in ectomycorrhizal interaction of lignin modified silver birch. BMC Plant Biol 2009; 9:124. [PMID: 19788757 PMCID: PMC2763875 DOI: 10.1186/1471-2229-9-124] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Accepted: 09/29/2009] [Indexed: 05/28/2023]
Abstract
BACKGROUND The monolignol biosynthetic pathway interconnects with the biosynthesis of other secondary phenolic metabolites, such as cinnamic acid derivatives, flavonoids and condensed tannins. The objective of this study is to evaluate whether genetic modification of the monolignol pathway in silver birch (Betula pendula Roth.) would alter the metabolism of these phenolic compounds and how such alterations, if exist, would affect the ectomycorrhizal symbiosis. RESULTS Silver birch lines expressing quaking aspen (Populus tremuloides L.) caffeate/5-hydroxyferulate O-methyltransferase (PtCOMT) under the 35S cauliflower mosaic virus (CaMV) promoter showed a reduction in the relative expression of a putative silver birch COMT (BpCOMT) gene and, consequently, a decrease in the lignin syringyl/guaiacyl composition ratio. Alterations were also detected in concentrations of certain phenolic compounds. All PtCOMT silver birch lines produced normal ectomycorrhizas with the ectomycorrhizal fungus Paxillus involutus (Batsch: Fr.), and the formation of symbiosis enhanced the growth of the transgenic plants. CONCLUSION The down-regulation of BpCOMT in the 35S-PtCOMT lines caused a reduction in the syringyl/guaiacyl ratio of lignin, but no significant effect was seen in the composition or quantity of phenolic compounds that would have been caused by the expression of PtCOMT under the 35S or UbB1 promoter. Moreover, the detected alterations in the composition of lignin and secondary phenolic compounds had no effect on the interaction between silver birch and P. involutus.
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Affiliation(s)
- Suvi Sutela
- Department of Biology, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Karoliina Niemi
- Department of Applied Biology, University of Helsinki, PO Box 27, 00014 Helsinki, Finland
| | - Jaanika Edesi
- Department of Biology, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Tapio Laakso
- Finnish Forest Research Institute, Vantaa Research Unit, Jokiniemenkuja 1, 01301 Vantaa, Finland
| | - Pekka Saranpää
- Finnish Forest Research Institute, Vantaa Research Unit, Jokiniemenkuja 1, 01301 Vantaa, Finland
| | - Jaana Vuosku
- Department of Biology, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Riina Mäkelä
- Department of Biology, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Heidi Tiimonen
- Finnish Forest Research Institute, Punkaharju Research Unit, Finlandiantie 18, 58450 Punkaharju, Finland
| | - Vincent L Chiang
- Forest Biotechnology Research Group, Department of Forestry and Environmental Resources, College of Natural Resources, North Carolina State University, Campus Box 7247, 2500, Partners II Building, Raleigh, NC 27695-7247, USA
| | - Janne Koskimäki
- Department of Biology, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Marja Suorsa
- Department of Biology, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | | | - Hely Häggman
- Department of Biology, University of Oulu, PO Box 3000, 90014 Oulu, Finland
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Vuosku J, Sarjala T, Jokela A, Sutela S, Sääskilahti M, Suorsa M, Läärä E, Häggman H. One tissue, two fates: different roles of megagametophyte cells during Scots pine embryogenesis. J Exp Bot 2009; 60:1375-86. [PMID: 19246593 PMCID: PMC2657542 DOI: 10.1093/jxb/erp020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
In the Scots pine (Pinus sylvestris L.) seed, embryos grow and develop within the corrosion cavity of the megagametophyte, a maternally derived haploid tissue, which houses the majority of the storage reserves of the seed. In the present study, histochemical methods and quantification of the expression levels of the programmed cell death (PCD) and DNA repair processes related genes (MCA, TAT-D, RAD51, KU80, and LIG) were used to investigate the physiological events occurring in the megagametophyte tissue during embryo development. It was found that the megagametophyte was viable from the early phases of embryo development until the early germination of mature seeds. However, the megagametophyte cells in the narrow embryo surrounding region (ESR) were destroyed by cell death with morphologically necrotic features. Their cell wall, plasma membrane, and nuclear envelope broke down with the release of cell debris and nucleic acids into the corrosion cavity. The occurrence of necrotic-like cell death in gymnosperm embryogenesis provides a favourable model for the study of developmental cell death with necrotic-like morphology and suggests that the mechanism underlying necrotic cell death is evolutionary conserved.
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Affiliation(s)
- Jaana Vuosku
- Department of Biology, University of Oulu, PO Box 3000, 90014 Oulu, Finland.
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Vuosku J, Jokela A, Läärä E, Sääskilahti M, Muilu R, Sutela S, Altabella T, Sarjala T, Häggman H. Consistency of polyamine profiles and expression of arginine decarboxylase in mitosis during zygotic embryogenesis of Scots pine. Plant Physiol 2006; 142:1027-38. [PMID: 16963525 PMCID: PMC1630739 DOI: 10.1104/pp.106.083030] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2006] [Accepted: 09/05/2006] [Indexed: 05/11/2023]
Abstract
In this study, we show that both arginine decarboxylase (ADC) protein and mRNA transcript are present at different phases of mitosis in Scots pine (Pinus sylvestris) zygotic embryogenesis. We also examined the consistency of polyamine (PA) profiles with the effective temperature sum, the latter indicating the developmental stage of the embryos. PA metabolism was analyzed by fitting statistical regression models to the data of free and soluble conjugated PAs, to the enzyme activities of ADC and ornithine decarboxylase (ODC), as well as to the gene expression of ADC. According to the fitted models, PAs typically had the tendency to increase at the early stages but decrease at the late stages of embryogenesis. Only the free putrescine fraction remained stable during embryo development. The PA biosynthesis strongly preferred the ADC pathway. Both ADC gene expression and ADC enzyme activity were substantially higher than putative ODC gene expression or ODC enzyme activity, respectively. ADC gene expression and enzyme activity increased during embryogenesis, which suggests the involvement of transcriptional regulation in the expression of ADC. Both ADC mRNA and ADC protein localized in dividing cells of embryo meristems and more specifically within the mitotic spindle apparatus and close to the chromosomes, respectively. The results suggest the essential role of ADC in the mitosis of plant cells.
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Affiliation(s)
- Jaana Vuosku
- Department of Biology , University of Oulu, 90014 Oulu, Finland.
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Niemi K, Sutela S, Häggman H, Scagel C, Vuosku J, Jokela A, Sarjala T. Changes in polyamine content and localization of Pinus sylvestris ADC and Suillus variegatus ODC mRNA transcripts during the formation of mycorrhizal interaction in an in vitro cultivation system. J Exp Bot 2006; 57:2795-804. [PMID: 16868043 DOI: 10.1093/jxb/erl049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The involvement of polyamines (PAs) in the interaction between Pinus sylvestris L. seedlings and an ectomycorrhizal fungus Suillus variegatus (Swatz: Fr.) O. Kunze was studied in an in vitro cultivation system. PA concentrations in seedlings were analysed after 1, 3, and 5 weeks in dual culture with S. variegatus, and changes in PA pools were compared with the growth of the seedlings. Pinus sylvestris arginine decarboxylase (ADC) and S. variegatus ornithine decarboxylase (ODC) mRNA transcripts were localized during the formation of mycorrhizas. During mycorrhiza formation, Suillus variegatus ODC transcripts were found in developing hyphal mantle and Hartig net, and P. sylvestris ADC transcripts in specific root parenchyma cells adjacent to tracheids and in mitotic cells of the root apical meristem. However, no unambiguous difference in ADC transcript localization between inoculated and non-inoculated roots was observed. Regardless of the unchanged distribution of ADC transcripts, inoculation with S. variegatus increased free putrescine, spermidine, and spermine concentrations in roots within the first week in dual culture. The concentration of free and conjugated putrescine and conjugated spermidine also increased in the needles due to the fungus. The fungus-induced lateral root formation and main root elongation were greatest between the first and third week in dual culture, coinciding with retarded accumulation or a decrease of free PAs. These results show that accumulation of PAs in the host plant is one of the first indicators of the establishment of ectomycorrhizal interaction between P. sylvestris and S. variegatus in the in vitro system.
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Affiliation(s)
- Karoliina Niemi
- Department of Applied Biology, University of Helsinki, PO Box 27, 00014 University of Helsinki, Finland.
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