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Duduk B, Ćurčić Ž, Stepanović J, Böhm JW, Kosovac A, Rekanović E, Kube M. Prevalence of a ' Candidatus Phytoplasma solani'-Related Strain Designated as New 16SrXII-P Subgroup over ' Candidatus Arsenophonus phytopathogenicus' in Sugar Beet in Eastern Germany. PLANT DISEASE 2023; 107:3792-3800. [PMID: 37189042 DOI: 10.1094/pdis-04-23-0613-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Two phloem-limited pathogens, 'Candidatus Arsenophonus phytopathogenicus' and 'Candidatus Phytoplasma solani', threaten sugar beet production in France, Switzerland, and Germany. Previous studies of these pathogens in Germany had focused on its western and southern regions, leaving a knowledge gap about eastern Germany. Despite their importance, this study is the first to investigate phytoplasmas in sugar beet in Saxony-Anhalt, Germany. A phytoplasma strain related to 'Ca. P. solani' is found predominant in Saxony-Anhalt, unlike in France, where 'Ca. P. solani' has a minor role compared with 'Ca. A. phytopathogenicus'. The phytoplasma strain infecting sugar beet in Saxony-Anhalt was classified into a new subgroup designated as 16SrXII-P. The multilocus sequence analysis (MLSA) of nonribosomal genes of the novel phytoplasma strain showed that it is significantly different from the reference and all previously reported 'Ca. P. solani' strains including the strain from western Germany. Analyses of sugar beet samples from previous years confirmed the presence of the 16SrXII-P strain in sugar beet as early as 2020 and also in Bavaria in southern Germany. Based on 16S rDNA analysis, 'Ca. A. phytopathogenicus' in Saxony-Anhalt is identical to strains in sugar beet in other parts of Germany and France, as well as to a strain in potato from Germany. The presence and prevalence of two phytoplasmas in sugar beet in Germany suggest that more attention should be directed toward understanding phytoplasma infection in sugar beet in this country.
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Affiliation(s)
- Bojan Duduk
- Institute of Pesticides and Environmental Protection, Belgrade 11080, Serbia
| | - Živko Ćurčić
- Institute of Field and Vegetable Crops, Novi Sad 21000, Serbia
| | - Jelena Stepanović
- Institute of Pesticides and Environmental Protection, Belgrade 11080, Serbia
| | | | - Andrea Kosovac
- Institute of Pesticides and Environmental Protection, Belgrade 11080, Serbia
| | - Emil Rekanović
- Institute of Pesticides and Environmental Protection, Belgrade 11080, Serbia
| | - Michael Kube
- University of Hohenheim, Stuttgart 70599, Germany
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2
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Dermastia M, Tomaž Š, Strah R, Lukan T, Coll A, Dušak B, Anžič B, Čepin T, Wienkoop S, Kladnik A, Zagorščak M, Riedle-Bauer M, Schönhuber C, Weckwerth W, Gruden K, Roitsch T, Pompe Novak M, Brader G. Candidate pathogenicity factor/effector proteins of ' Candidatus Phytoplasma solani' modulate plant carbohydrate metabolism, accelerate the ascorbate-glutathione cycle, and induce autophagosomes. FRONTIERS IN PLANT SCIENCE 2023; 14:1232367. [PMID: 37662165 PMCID: PMC10471893 DOI: 10.3389/fpls.2023.1232367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023]
Abstract
The pathogenicity of intracellular plant pathogenic bacteria is associated with the action of pathogenicity factors/effectors, but their physiological roles for most phytoplasma species, including 'Candidiatus Phytoplasma solani' are unknown. Six putative pathogenicity factors/effectors from six different strains of 'Ca. P. solani' were selected by bioinformatic analysis. The way in which they manipulate the host cellular machinery was elucidated by analyzing Nicotiana benthamiana leaves after Agrobacterium-mediated transient transformation with the pathogenicity factor/effector constructs using confocal microscopy, pull-down, and co-immunoprecipitation, and enzyme assays. Candidate pathogenicity factors/effectors were shown to modulate plant carbohydrate metabolism and the ascorbate-glutathione cycle and to induce autophagosomes. PoStoSP06, PoStoSP13, and PoStoSP28 were localized in the nucleus and cytosol. The most active effector in the processes studied was PoStoSP06. PoStoSP18 was associated with an increase in phosphoglucomutase activity, whereas PoStoSP28, previously annotated as an antigenic membrane protein StAMP, specifically interacted with phosphoglucomutase. PoStoSP04 induced only the ascorbate-glutathione cycle along with other pathogenicity factors/effectors. Candidate pathogenicity factors/effectors were involved in reprogramming host carbohydrate metabolism in favor of phytoplasma own growth and infection. They were specifically associated with three distinct metabolic pathways leading to fructose-6-phosphate as an input substrate for glycolysis. The possible significance of autophagosome induction by PoStoSP28 is discussed.
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Affiliation(s)
- Marina Dermastia
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Špela Tomaž
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Rebeka Strah
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Tjaša Lukan
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Anna Coll
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Barbara Dušak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- Department of Plant and Environmental Sciences, University of Copenhagen, Taastrup, Denmark
| | - Barbara Anžič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Timotej Čepin
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Stefanie Wienkoop
- Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Aleš Kladnik
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Zagorščak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Monika Riedle-Bauer
- Federal College and Research Institute for Viticulture and Pomology Klosterneuburg, Klosterneuburg, Austria
| | - Christina Schönhuber
- Bioresources Unit, Health & Environment Department, Austrian Institute of Technology, Tulln, Austria
| | - Wolfram Weckwerth
- Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Thomas Roitsch
- Department of Plant and Environmental Sciences, University of Copenhagen, Taastrup, Denmark
| | - Maruša Pompe Novak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
- Faculty of Viticulture and Enology, University of Nova Gorica, Vipava, Slovenia
| | - Günter Brader
- Bioresources Unit, Health & Environment Department, Austrian Institute of Technology, Tulln, Austria
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3
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Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates. Mar Drugs 2023; 21:md21030165. [PMID: 36976214 PMCID: PMC10054348 DOI: 10.3390/md21030165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/21/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Marine invertebrate microbiomes have been a rich source of bioactive compounds and interesting genomic features. In cases where the achievable amounts of metagenomic DNA are too low for direct sequencing, multiple displacement amplification (MDA) can be used for whole genome amplification. However, MDA has known limitations which can affect the quality of the resulting genomes and metagenomes. In this study, we evaluated the conservation of biosynthetic gene clusters (BGCs) and enzymes in MDA products from low numbers of prokaryotic cells (estimated 2–850). Marine invertebrate microbiomes collected from Arctic and sub-Arctic areas served as source material. The cells were separated from the host tissue, lysed, and directly subjected to MDA. The MDA products were sequenced by Illumina sequencing. Corresponding numbers of bacteria from a set of three reference strains were treated the same way. The study demonstrated that useful information on taxonomic, BGC, and enzyme diversities was obtainable from such marginal quantities of metagenomic material. Although high levels of assembly fragmentation resulted in most BGCs being incomplete, we conclude that this genome mining approach has the potential to reveal interesting BGCs and genes from hard-to-reach biological sources.
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Duduk N, Vico I, Kosovac A, Stepanović J, Ćurčić Ž, Vučković N, Rekanović E, Duduk B. A biotroph sets the stage for a necrotroph to play: ' Candidatus Phytoplasma solani' infection of sugar beet facilitated Macrophomina phaseolina root rot. Front Microbiol 2023; 14:1164035. [PMID: 37152751 PMCID: PMC10158981 DOI: 10.3389/fmicb.2023.1164035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 03/31/2023] [Indexed: 05/09/2023] Open
Abstract
'Candidatus Phytoplasma solani' (stolbur phytoplasma) is associated with rubbery taproot disease (RTD) of sugar beet (Beta vulgaris L.), while Macrophomina phaseolina is considered the most important root rot pathogen of this plant in Serbia. The high prevalence of M. phaseolina root rot reported on sugar beet in Serbia, unmatched elsewhere in the world, coupled with the notorious tendency of RTD-affected sugar beet to rot, has prompted research into the relationship between the two diseases. This study investigates the correlation between the occurrence of sugar beet RTD and the presence of root rot fungal pathogens in a semi-field 'Ca. P. solani' transmission experiment with the cixiid vector Reptalus quinquecostatus (Dufour), in addition to naturally infected sugar beet in the open field. Our results showed that: (i) Reptalus quinquecostatus transmitted 'Ca. P. solani' to sugar beet which induced typical RTD root symptoms; (ii) Macrophomina phaseolina root rot was exclusively present in 'Ca. P. solani'-infected sugar beet in both the semi-field experiment and naturally infected sugar beet; and that (iii) even under environmental conditions favorable to the pathogen, M. phaseolina did not infect sugar beet, unless the plants had been previously infected with phytoplasma.
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Affiliation(s)
- Nataša Duduk
- Faculty of Agriculture, University of Belgrade, Belgrade, Serbia
- *Correspondence: Nataša Duduk,
| | - Ivana Vico
- Faculty of Agriculture, University of Belgrade, Belgrade, Serbia
| | - Andrea Kosovac
- Institute of Pesticides and Environmental Protection, Belgrade, Serbia
| | - Jelena Stepanović
- Institute of Pesticides and Environmental Protection, Belgrade, Serbia
| | - Živko Ćurčić
- Institute of Field and Vegetable Crops, Novi Sad, Serbia
| | - Nina Vučković
- Faculty of Agriculture, University of Belgrade, Belgrade, Serbia
| | - Emil Rekanović
- Institute of Pesticides and Environmental Protection, Belgrade, Serbia
| | - Bojan Duduk
- Institute of Pesticides and Environmental Protection, Belgrade, Serbia
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Wei W, Zhao Y. Phytoplasma Taxonomy: Nomenclature, Classification, and Identification. BIOLOGY 2022; 11:biology11081119. [PMID: 35892975 PMCID: PMC9394401 DOI: 10.3390/biology11081119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 11/30/2022]
Abstract
Simple Summary Phytoplasmas are vector-borne and graft-transmissible bacteria that cause various plant diseases, leading to severe economic losses. Since phytoplasmas cannot be cultured in cell-free media, their identification and taxonomy rely on molecular techniques and gene sequences. In this article, we summarize the recent advances in phytoplasma taxonomy from three different aspects, including (i) nomenclature (naming Candidatus Phytoplasma species); (ii) classification (group and subgroup assignment based on 16S rRNA gene sequences); and (iii) identification (fine differentiation of phytoplasma strains). In addition, some important issues, especially those related to recognizing new ‘Candidatus Phytoplasma’ species, are discussed. This information will be helpful for rapid diagnosis of phytoplasma diseases and accurate taxonomic identification of both emerging and known phytoplasma strains. Abstract Phytoplasmas are pleomorphic, wall-less intracellular bacteria that can cause devastating diseases in a wide variety of plant species. Rapid diagnosis and precise identification of phytoplasmas responsible for emerging plant diseases are crucial to preventing further spread of the diseases and reducing economic losses. Phytoplasma taxonomy (identification, nomenclature, and classification) has lagged in comparison to culturable bacteria, largely due to lack of axenic phytoplasma culture and consequent inaccessibility of phenotypic characteristics. However, the rapid expansion of molecular techniques and the advent of high throughput genome sequencing have tremendously enhanced the nucleotide sequence-based phytoplasma taxonomy. In this article, the key events and milestones that shaped the current phytoplasma taxonomy are highlighted. In addition, the distinctions and relatedness of two parallel systems of ‘Candidatus phytoplasma’ species/nomenclature system and group/subgroup classification system are clarified. Both systems are indispensable as they serve different purposes. Furthermore, some hot button issues in phytoplasma nomenclature are also discussed, especially those pertinent to the implementation of newly revised guidelines for ‘Candidatus Phytoplasma’ species description. To conclude, the challenges and future perspectives of phytoplasma taxonomy are briefly outlined.
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Affiliation(s)
- Wei Wei
- Correspondence: ; Tel.: +1-301-504-0786
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Wang XY, Zhang RY, Li J, Li YH, Shan HL, Li WF, Huang YK. The Diversity, Distribution and Status of Phytoplasma Diseases in China. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.943080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Phytoplasmas are important prokaryotic pathogenic bacteria without cell walls, which were formerly known as mycoplasma-like organisms, and belong to the Mollicutes class, Candidatus Phytoplasma genus. They are widely distributed in plants and insects, and can cause serious diseases in important food crops, vegetables, fruit trees, ornamental plants and trees, resulting in huge economic losses. To date, more than 100 phytoplasma diseases have been reported in China, which are distributed throughout the country. Jujube witches'-broom, paulownia witches'-broom, wheat blue dwarf, banana bunchy top, sugarcane white leaf, rice orange leaf and mulberry dwarf represent the phytoplasma diseases causing the most serious damage in China. New phytoplasma diseases and their strains are being reported continuously, indicating that phytoplasmas are more diverse than previously thought. Phytoplasmas are mainly transmitted by insect vectors, such as leafhopper and planthopper, and can also be spread by grafting or Cuscuta australis (known as dodder). Mixed infections of phytoplasmas and viruses, bacteria, and spiroplasmas have also become a serious problem in several crops and are responsible for more synergistic losses. With the continuous development and improvement of technology, molecular biological detection has become the main technique for phytoplasma detection and identification. Currently, research on phytoplasma diseases in China mainly focuses on pathogen identification and classification, and insect vector and host diversity; however, there is less focus on pathogenicity, comparative genomics, and effect factors. More research attention has been paid to wheat blue dwarf phytoplasma, paulownia witches'-broom phytoplasma, jujube witches'-broom phytoplasma, and sugarcane white leaf phytoplasma. Other phytoplasma diseases have been reported; however, there have been no in-depth studies. In this paper, the history and present situation of phytoplasma research, and the status, distribution, and diversity of phytoplasma diseases are summarized, and some possible research directions of phytoplasma in the future in China are proposed.
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7
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Ćurčić Ž, Stepanović J, Zübert C, Taški-Ajduković K, Kosovac A, Rekanović E, Kube M, Duduk B. Rubbery Taproot Disease of Sugar Beet in Serbia Associated with ' Candidatus Phytoplasma solani'. PLANT DISEASE 2021; 105:255-263. [PMID: 33021915 DOI: 10.1094/pdis-07-20-1602-re] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Rubbery taproot disease (RTD) of sugar beet was observed in Serbia for the first time in the 1960s. The disease was already described in neighboring Bulgaria and Romania at the time but it was associated with abiotic factors. In this study on RTD of sugar beet in its main growing area of Serbia, we provide evidence of the association between 'Candidatus Phytoplasma solani' (stolbur phytoplasma) infection and the occurrence of typical RTD symptomatology. 'Ca. P. solani' was identified by PCR and the sequence analyses of 16S ribosomal RNA, tuf, secY, and stamp genes. In contrast, the causative agent of the syndrome "basses richesses" of sugar beet-namely, 'Ca. Arsenophonus phytopathogenicus'-was not detected. Sequence analysis of the stolbur strain's tuf gene confirmed a previously reported and a new, distinct tuf stolbur genotype (named 'tuf d') that is prevalent in sugar beet. The sequence signatures of the tuf gene as well as the one of stamp both correlate with the epidemiological cycle and reservoir plant host. This study provides knowledge that, for the first time, enables the differentiation of stolbur strains associated with RTD of sugar beet from closely related strains, thereby providing necessary information for further epidemiological work seeking to identify insect vectors and reservoir plant hosts. The results of this study indicate that there are differences in hybrid susceptibility. Clarifying the etiology of RTD as a long-known and economically important disease is certainly the first step toward disease management in Serbia and neighboring countries.
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Affiliation(s)
- Živko Ćurčić
- Institute of Field and Vegetable Crops, Novi Sad 21000, Serbia
| | - Jelena Stepanović
- Institute of Pesticides and Environmental Protection, Belgrade 11080, Serbia
| | - Christina Zübert
- University of Hohenheim, Integrative Infection Biology Crops-Livestock, Stuttgart 70599, Germany
| | | | - Andrea Kosovac
- Institute of Pesticides and Environmental Protection, Belgrade 11080, Serbia
| | - Emil Rekanović
- Institute of Pesticides and Environmental Protection, Belgrade 11080, Serbia
| | - Michael Kube
- University of Hohenheim, Integrative Infection Biology Crops-Livestock, Stuttgart 70599, Germany
| | - Bojan Duduk
- Institute of Pesticides and Environmental Protection, Belgrade 11080, Serbia
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8
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Multilocus Genotyping Reveals New Molecular Markers for Differentiating Distinct Genetic Lineages among " Candidatus Phytoplasma Solani" Strains Associated with Grapevine Bois Noir. Pathogens 2020; 9:pathogens9110970. [PMID: 33233322 PMCID: PMC7700334 DOI: 10.3390/pathogens9110970] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 11/16/2022] Open
Abstract
Grapevine Bois noir (BN) is associated with infection by “Candidatus Phytoplasma solani” (CaPsol). In this study, an array of CaPsol strains was identified from 142 symptomatic grapevines in vineyards of northern, central, and southern Italy and North Macedonia. Molecular typing of the CaPsol strains was carried out by analysis of genes encoding 16S rRNA and translation elongation factor EF-Tu, as well as eight other previously uncharacterized genomic fragments. Strains of tuf-type a and b were found to be differentially distributed in the examined geographic regions in correlation with the prevalence of nettle and bindweed. Two sequence variants were identified in each of the four genomic segments harboring hlyC, cbiQ-glyA, trxA-truB-rsuA, and rplS-tyrS-csdB, respectively. Fifteen CaPsol lineages were identified based on distinct combinations of sequence variations within these genetic loci. Each CaPsol lineage exhibited a unique collective restriction fragment length polymorphism (RFLP) pattern and differed from each other in geographic distribution, probably in relation to the diverse ecological complexity of vineyards and their surroundings. This RFLP-based typing method could be a useful tool for investigating the ecology of CaPsol and the epidemiology of its associated diseases. Phylogenetic analyses highlighted that the sequence variants of the gene hlyC, which encodes a hemolysin III-like protein, separated into two clusters consistent with the separation of two distinct lineages on the basis of tufB gene sequences. Alignments of deduced full protein sequences of elongation factor-Tu (tufB gene) and hemolysin III-like protein (hlyC gene) revealed the presence of critical amino acid substitutions distinguishing CaPsol strains of tuf-type a and b. Findings from the present study provide new insights into the genetic diversity and ecology of CaPsol populations in vineyards.
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Iwabuchi N, Kitazawa Y, Maejima K, Koinuma H, Miyazaki A, Matsumoto O, Suzuki T, Nijo T, Oshima K, Namba S, Yamaji Y. Functional variation in phyllogen, a phyllody-inducing phytoplasma effector family, attributable to a single amino acid polymorphism. MOLECULAR PLANT PATHOLOGY 2020; 21:1322-1336. [PMID: 32813310 PMCID: PMC7488466 DOI: 10.1111/mpp.12981] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/25/2020] [Accepted: 07/05/2020] [Indexed: 05/08/2023]
Abstract
Flower malformation represented by phyllody is a common symptom of phytoplasma infection induced by a novel family of phytoplasma effectors called phyllogens. Despite the accumulation of functional and structural phyllogen information, the molecular mechanisms of phyllody have not yet been integrated with their evolutionary aspects due to the limited data on their homologs across diverse phytoplasma lineages. Here, we developed a novel universal PCR-based approach to identify 25 phytoplasma phyllogens related to nine "Candidatus Phytoplasma" species, including four species whose phyllogens have not yet been identified. Phylogenetic analyses showed that the phyllogen family consists of four groups (phyl-A, -B, -C, and -D) and that the evolutionary relationships of phyllogens were significantly distinct from those of phytoplasmas, suggesting that phyllogens were transferred horizontally among phytoplasma strains and species. Although phyllogens belonging to the phyl-A, -C, and -D groups induced phyllody, the phyl-B group lacked the ability to induce phyllody. Comparative functional analyses of phyllogens revealed that a single amino acid polymorphism in phyl-B group phyllogens prevented interactions between phyllogens and A- and E-class MADS domain transcription factors (MTFs), resulting in the inability to degrade several MTFs and induce phyllody. Our finding of natural variation in the function of phytoplasma effectors provides new insights into molecular mechanisms underlying the aetiology of phytoplasma diseases.
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Affiliation(s)
- Nozomu Iwabuchi
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Yugo Kitazawa
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Kensaku Maejima
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Hiroaki Koinuma
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Akio Miyazaki
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Ouki Matsumoto
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Takumi Suzuki
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Takamichi Nijo
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | | | - Shigetou Namba
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Yasuyuki Yamaji
- Department of Agricultural and Environmental BiologyGraduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
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Polano C, Firrao G. Assembly of Phytoplasma Genome Drafts from Illumina Reads Using Phytoassembly. Methods Mol Biol 2019; 1875:203-211. [PMID: 30362006 DOI: 10.1007/978-1-4939-8837-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Genome drafts for the phytoplasmas may be rapidly and efficiently assembled from NGS sequence data alone exploiting the proper bioinformatic tools and starting from properly collected samples. Here, we describe the use of the Phytoassembly pipeline ( https://github.com/cpolano/phytoassembly ), a fully automated tool that accepts as input row Illumina data from two samples (a phytoplasma infected sample and a healthy reference sample) to produce a phytoplasma genome draft, using the healthy plant host genome as a filter and profiting from the difference in reads coverage between the genome of the pathogen and that of the host. For phytoplasma infected samples containing >2% of pathogen DNA and an isogenic healthy reference sequence the resulting assemblies span the almost entire genomes.
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Affiliation(s)
- Cesare Polano
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Udine, Italy
| | - Giuseppe Firrao
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Udine, Italy.
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11
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Music MS, Samarzija I, Hogenhout SA, Haryono M, Cho ST, Kuo CH. The genome of 'Candidatus Phytoplasma solani' strain SA-1 is highly dynamic and prone to adopting foreign sequences. Syst Appl Microbiol 2018; 42:117-127. [PMID: 30455068 DOI: 10.1016/j.syapm.2018.10.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 10/15/2018] [Accepted: 10/25/2018] [Indexed: 11/15/2022]
Abstract
Bacteria of the genus 'Candidatus Phytoplasma' are uncultivated intracellular plant pathogens transmitted by phloem-feeding insects. They have small genomes lacking genes for essential metabolites, which they acquire from either plant or insect hosts. Nonetheless, some phytoplasmas, such as 'Ca. P. solani', have broad plant host range and are transmitted by several polyphagous insect species. To understand better how these obligate symbionts can colonize such a wide range of hosts, the genome of 'Ca. P. solani' strain SA-1 was sequenced from infected periwinkle via a metagenomics approach. The de novo assembly generated a draft genome with 19 contigs totalling 821,322bp, which corresponded to more than 80% of the estimated genome size. Further completion of the genome was challenging due to the high occurrence of repetitive sequences. The majority of repeats consisted of gene arrangements characteristic of phytoplasma potential mobile units (PMUs). These regions showed variation in gene orders intermixed with genes of unknown functions and lack of similarity to other phytoplasma genes, suggesting that they were prone to rearrangements and acquisition of new sequences via recombination. The availability of this high-quality draft genome also provided a foundation for genome-scale genotypic analysis (e.g., average nucleotide identity and average amino acid identity) and molecular phylogenetic analysis. Phylogenetic analyses provided evidence of horizontal transfer for PMU-like elements from various phytoplasmas, including distantly related ones. The 'Ca. P. solani' SA-1 genome also contained putative secreted protein/effector genes, including a homologue of SAP11, found in many other phytoplasma species.
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Affiliation(s)
- Martina Seruga Music
- Department of Biology, Faculty of Science, University of Zagreb, Marulicev trg 9A, HR-10000 Zagreb, Croatia.
| | - Ivana Samarzija
- Department of Biology, Faculty of Science, University of Zagreb, Marulicev trg 9A, HR-10000 Zagreb, Croatia.
| | - Saskia A Hogenhout
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney Ln, Norwich NR4 7UH, UK.
| | - Mindia Haryono
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd., Taipei 11529, Taiwan.
| | - Shu-Ting Cho
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd., Taipei 11529, Taiwan.
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd., Taipei 11529, Taiwan.
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Comparative genome analysis of jujube witches'-broom Phytoplasma, an obligate pathogen that causes jujube witches'-broom disease. BMC Genomics 2018; 19:689. [PMID: 30231900 PMCID: PMC6148798 DOI: 10.1186/s12864-018-5075-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 09/13/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND JWB phytoplasma is a kind of insect-transmitted and uncultivable bacterial plant pathogen causeing a destructive Jujube disease. To date, no genome information about JWB phytoplasma has been published, which hindered its characterization at genomic level. To understand its pathogenicity and ecology, the genome of a JWB phytoplasma isolate jwb-nky was sequenced and compared with other phytoplasmas enabled us to explore the mechanisms of genomic rearrangement. RESULTS The complete genome sequence of JWB phytoplasma (jwb-nky) was determined, which consisting of one circular chromosome of 750,803 bp with a GC content of 23.3%. 694 protein-encoding genes, 2 operons for rRNA genes and 31 tRNA genes as well as 4 potential mobile units (PMUs) containing clusters of DNA repeats were identified. Based on PHIbaes analysis, a large number of genes were genome-specific and approximately 13% of JWB phytoplasma genes were predicted to be associated with virulence. Although transporters for maltose, dipeptides/oligopeptides, spermidine/putrescine, cobalt, Mn/Zn and methionine were identified, KEGG pathway analysis revealed the reduced metabolic capabilities of JWB phytoplasma. Comparative genome analyses between JWB phytoplasma and other phytoplasmas shows the occurrence of large-scale gene rearrangements. The low synteny with other phytoplasmas indicated that the expansion of multiple gene families/duplication probably occurred separately after differentiation. CONCLUSIONS In this study, the complete genome sequence of a JWB phytoplasma isolate jwb-nky that causing JWB disease was reported for the first time and a number of species-specific genes were identified in the genome. The study enhanced our understandings about genomic basis and the pathogenicity mechanism of this pathogen, which will aid in the development of improved strategies for efficient management of JWB diseases.
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Sparks ME, Bottner-Parker KD, Gundersen-Rindal DE, Lee IM. Draft genome sequence of the New Jersey aster yellows strain of 'Candidatus Phytoplasma asteris'. PLoS One 2018; 13:e0192379. [PMID: 29408883 PMCID: PMC5800598 DOI: 10.1371/journal.pone.0192379] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/20/2018] [Indexed: 01/21/2023] Open
Abstract
The NJAY (New Jersey aster yellows) strain of ‘Candidatus Phytoplasma asteris’ is a significant plant pathogen responsible for causing severe lettuce yellows in the U.S. state of New Jersey. A draft genome sequence was prepared for this organism. A total of 177,847 reads were assembled into 75 contigs > 518 bp with a total base value of 652,092 and an overall [G+C] content of 27.1%. A total of 733 protein coding genes were identified. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession MAPF00000000. This draft genome was used for genome- and gene-based comparative phylogenetic analyses with other phytoplasmas, including the closely related ‘Ca. Phytoplasma asteris’ strain, aster yellows witches’- broom (AY-WB). NJAY and AY-WB exhibit approximately 0.5% dissimilarity at the nucleotide level among their shared genomic segments. Evidence indicated that NJAY harbors four plasmids homologous to those known to encode pathogenicity determinants in AY-WB, as well as a chromosome-encoded mobile unit. Apparent NJAY orthologs to the important AY-WB virulence factors, SAP11 and SAP54, were identified. A number of secreted proteins, both membrane-bound and soluble, were encoded, with many bearing similarity to known AY-WB effector molecules and others representing possible secreted proteins that may be novel to the NJAY lineage.
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Affiliation(s)
- Michael E. Sparks
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, Maryland, United States of America
| | | | - Dawn E. Gundersen-Rindal
- USDA-ARS Invasive Insect Biocontrol and Behavior Laboratory, Beltsville, Maryland, United States of America
| | - Ing-Ming Lee
- USDA-ARS Molecular Plant Pathology Laboratory, Beltsville, Maryland, United States of America
- * E-mail:
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Orlovskis Z, Canale MC, Haryono M, Lopes JRS, Kuo CH, Hogenhout SA. A few sequence polymorphisms among isolates of Maize bushy stunt phytoplasma associate with organ proliferation symptoms of infected maize plants. ANNALS OF BOTANY 2017; 119:869-884. [PMID: 28069632 PMCID: PMC5379588 DOI: 10.1093/aob/mcw213] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 08/16/2016] [Indexed: 05/18/2023]
Abstract
Background and Aims Maize bushy stunt phytoplasma (MBSP) is a bacterial pathogen of maize ( Zea mays L.) across Latin America. MBSP belongs to the 16SrI-B sub-group within the genus ' Candidatus Phytoplasma'. MBSP and its insect vector Dalbulus maidis (Hemiptera: Cicadellidae) are restricted to maize; both are thought to have coevolved with maize during its domestication from a teosinte-like ancestor. MBSP-infected maize plants show a diversity of symptoms. and it is likely that MBSP is under strong selection for increased virulence and insect transmission on maize hybrids that are widely grown in Brazil. In this study it was investigated whether the differences in genome sequences of MBSP isolates from two maize-growing regions in South-east Brazil explain variations in symptom severity of the MBSP isolates on various maize genotypes. Methods MBSP isolates were collected from maize production fields in Guaíra and Piracicaba in South-east Brazil for infection assays. One representative isolate was chosen for de novo whole-genome assembly and for the alignment of sequence reads from the genomes of other phytoplasma isolates to detect polymorphisms. Statistical methods were applied to investigate the correlation between variations in disease symptoms of infected maize plants and MBSP sequence polymorphisms. Key Results MBSP isolates contributed consistently to organ proliferation symptoms and maize genotype to leaf necrosis, reddening and yellowing of infected maize plants. The symptom differences are associated with polymorphisms in a phase-variable lipoprotein, which is a candidate effector, and an ATP-dependent lipoprotein ABC export protein, whereas no polymorphisms were observed in other candidate effector genes. Lipoproteins and ABC export proteins activate host defence responses, regulate pathogen attachment to host cells and activate effector secretion systems in other pathogens. Conclusions Polymorphisms in two putative virulence genes among MBSP isolates from maize-growing regions in South-east Brazil are associated with variations in organ proliferation symptoms of MBSP-infected maize plants.
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Affiliation(s)
- Zigmunds Orlovskis
- John Innes Centre, Department of Cell and Developmental Biology, Norwich Research Park, Norwich NR4 7UH, UK
| | - Maria Cristina Canale
- John Innes Centre, Department of Cell and Developmental Biology, Norwich Research Park, Norwich NR4 7UH, UK
- Luiz de Queiroz College of Agriculture, University of São Paulo, Department of Entomology and Acarology, Piracicaba 13·418-900, Brazil
| | - Mindia Haryono
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - João Roberto Spotti Lopes
- Luiz de Queiroz College of Agriculture, University of São Paulo, Department of Entomology and Acarology, Piracicaba 13·418-900, Brazil
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Saskia A. Hogenhout
- John Innes Centre, Department of Cell and Developmental Biology, Norwich Research Park, Norwich NR4 7UH, UK
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Seward EA, Kelly S. Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms. Genome Biol 2016; 17:226. [PMID: 27842572 PMCID: PMC5109750 DOI: 10.1186/s13059-016-1087-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/12/2016] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Genomes are composed of long strings of nucleotide monomers (A, C, G and T) that are either scavenged from the organism's environment or built from metabolic precursors. The biosynthesis of each nucleotide differs in atomic requirements with different nucleotides requiring different quantities of nitrogen atoms. However, the impact of the relative availability of dietary nitrogen on genome composition and codon bias is poorly understood. RESULTS Here we show that differential nitrogen availability, due to differences in environment and dietary inputs, is a major determinant of genome nucleotide composition and synonymous codon use in both bacterial and eukaryotic microorganisms. Specifically, low nitrogen availability species use nucleotides that require fewer nitrogen atoms to encode the same genes compared to high nitrogen availability species. Furthermore, we provide a novel selection-mutation framework for the evaluation of the impact of metabolism on gene sequence evolution and show that it is possible to predict the metabolic inputs of related organisms from an analysis of the raw nucleotide sequence of their genes. CONCLUSIONS Taken together, these results reveal a previously hidden relationship between cellular metabolism and genome evolution and provide new insight into how genome sequence evolution can be influenced by adaptation to different diets and environments.
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Affiliation(s)
- Emily A Seward
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
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16
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Siampour M, Izadpanah K, Marzachi C, Salehi Abarkoohi M. Identification and characterization of conserved and variable regions of lime witches' broom phytoplasma genome. MICROBIOLOGY-SGM 2015; 161:1741-1751. [PMID: 26296664 DOI: 10.1099/mic.0.000133] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Several segments (∼20 kbp) of the lime witches' broom (LWB) phytoplasma genome (16SrII group) were sequenced and analysed. A 5.7 kbp segment (LWB-C) included conserved genes whose phylogenetic tree was consistent with that generated using 16S rRNA genes. Another 6.4 kbp LWB phytoplasma genome segment (LWB-NC) was structurally similar to the putative mobile unit or sequence variable mosaic genomic region of phytoplasmas, although it represented a new arrangement of genes or pseudogenes such as phage-related protein genes and tra5 insertion sequences. Sequence- and phylogenetic-based evidence suggested that LWB-NC is a genomic region which includes horizontally transferred genes and could be regarded as a hot region to incorporate more foreign genes into the genome of LWB phytoplasma. The presence of phylogenetically related fragments of retroelements was also verified in the LWB phytoplasma genome. Putative intragenomic retrotransposition or retrohoming of these elements might have been determinant in shaping and manipulating the LWB phytoplasma genome. Altogether, the results of this study suggested that the genome of LWB phytoplasma is colonized by a variety of genes that have been acquired through horizontal gene transfer events, which may have further affected the genome through intragenomic mobility and insertion at cognate or incognate sites. Some of these genes are expected to have been involved in the development of features specific to LWB phytoplasma.
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Affiliation(s)
- Majid Siampour
- Department of Plant Protection, College of Agriculture, Shahrekord University, Shahrekord, Iran
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17
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Quaglino F, Kube M, Jawhari M, Abou-Jawdah Y, Siewert C, Choueiri E, Sobh H, Casati P, Tedeschi R, Lova MM, Alma A, Bianco PA. 'Candidatus Phytoplasma phoenicium' associated with almond witches'-broom disease: from draft genome to genetic diversity among strain populations. BMC Microbiol 2015; 15:148. [PMID: 26223451 PMCID: PMC4518686 DOI: 10.1186/s12866-015-0487-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 07/16/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Almond witches'-broom (AlmWB), a devastating disease of almond, peach and nectarine in Lebanon, is associated with 'Candidatus Phytoplasma phoenicium'. In the present study, we generated a draft genome sequence of 'Ca. P. phoenicium' strain SA213, representative of phytoplasma strain populations from different host plants, and determined the genetic diversity among phytoplasma strain populations by phylogenetic analyses of 16S rRNA, groEL, tufB and inmp gene sequences. RESULTS Sequence-based typing and phylogenetic analysis of the gene inmp, coding an integral membrane protein, distinguished AlmWB-associated phytoplasma strains originating from diverse host plants, whereas their 16S rRNA, tufB and groEL genes shared 100 % sequence identity. Moreover, dN/dS analysis indicated positive selection acting on inmp gene. Additionally, the analysis of 'Ca. P. phoenicium' draft genome revealed the presence of integral membrane proteins and effector-like proteins and potential candidates for interaction with hosts. One of the integral membrane proteins was predicted as BI-1, an inhibitor of apoptosis-promoting Bax factor. Bioinformatics analyses revealed the presence of putative BI-1 in draft and complete genomes of other 'Ca. Phytoplasma' species. CONCLUSION The genetic diversity within 'Ca. P. phoenicium' strain populations in Lebanon suggested that AlmWB disease could be associated with phytoplasma strains derived from the adaptation of an original strain to diverse hosts. Moreover, the identification of a putative inhibitor of apoptosis-promoting Bax factor (BI-1) in 'Ca. P. phoenicium' draft genome and within genomes of other 'Ca. Phytoplasma' species suggested its potential role as a phytoplasma fitness-increasing factor by modification of the host-defense response.
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Affiliation(s)
- Fabio Quaglino
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, via Celoria 2, 20133, Milan, Italy.
| | - Michael Kube
- Division Phytomedicine, Thaer-Institute, Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Maan Jawhari
- Faculty of Agricultural and Food Sciences, American University of Beirut, Beirut, Lebanon.
| | - Yusuf Abou-Jawdah
- Faculty of Agricultural and Food Sciences, American University of Beirut, Beirut, Lebanon.
| | - Christin Siewert
- Division Phytomedicine, Thaer-Institute, Humboldt-Universität zu Berlin, Berlin, Germany.
| | - Elia Choueiri
- Department of Plant Protection, Lebanese Agricultural Research Institute, Tal Amara, Lebanon.
| | - Hana Sobh
- Faculty of Agricultural and Food Sciences, American University of Beirut, Beirut, Lebanon.
| | - Paola Casati
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, via Celoria 2, 20133, Milan, Italy.
| | - Rosemarie Tedeschi
- Department of Agricultural, Forest and Food Sciences, Università degli Studi di Torino, Grugliasco (TO), Italy.
| | | | - Alberto Alma
- Department of Agricultural, Forest and Food Sciences, Università degli Studi di Torino, Grugliasco (TO), Italy.
| | - Piero Attilio Bianco
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, via Celoria 2, 20133, Milan, Italy.
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Siewert C, Hess WR, Duduk B, Huettel B, Reinhardt R, Büttner C, Kube M. Complete genome determination and analysis of Acholeplasma oculi strain 19L, highlighting the loss of basic genetic features in the Acholeplasmataceae. BMC Genomics 2014; 15:931. [PMID: 25344468 PMCID: PMC4221730 DOI: 10.1186/1471-2164-15-931] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 09/25/2014] [Indexed: 11/17/2022] Open
Abstract
Background Acholeplasma oculi belongs to the Acholeplasmataceae family, comprising the genera Acholeplasma and ‘Candidatus Phytoplasma’. Acholeplasmas are ubiquitous saprophytic bacteria. Several isolates are derived from plants or animals, whereas phytoplasmas are characterised as intracellular parasitic pathogens of plant phloem and depend on insect vectors for their spread. The complete genome sequences for eight strains of this family have been resolved so far, all of which were determined depending on clone-based sequencing. Results The A. oculi strain 19L chromosome was sequenced using two independent approaches. The first approach comprised sequencing by synthesis (Illumina) in combination with Sanger sequencing, while single molecule real time sequencing (PacBio) was used in the second. The genome was determined to be 1,587,120 bp in size. Sequencing by synthesis resulted in six large genome fragments, while the single molecule real time sequencing approach yielded one circular chromosome sequence. High-quality sequences were obtained by both strategies differing in six positions, which are interpreted as reliable variations present in the culture population. Our genome analysis revealed 1,471 protein-coding genes and highlighted the absence of the F1FO-type Na+ ATPase system and GroEL/ES chaperone. Comparison of the four available Acholeplasma sequences revealed a core-genome encoding 703 proteins and a pan-genome of 2,867 proteins. Conclusions The application of two state-of-the-art sequencing technologies highlights the potential of single molecule real time sequencing for complete genome determination. Comparative genome analyses revealed that the process of losing particular basic genetic features during genome reduction occurs in both genera, as indicated for several phytoplasma strains and at least A. oculi. The loss of the F1FO-type Na+ ATPase system may separate Acholeplasmataceae from other Mollicutes, while the loss of those genes encoding the chaperone GroEL/ES is not a rare exception in this bacterial class. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-931) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Michael Kube
- Humboldt-Universität zu Berlin, Faculty of Life Science, Thaer-Institute, Division Phytomedicine, Lentzeallee 55/57, 14195 Berlin, Germany.
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Aryan A, Brader G, Mörtel J, Pastar M, Riedle-Bauer M. An abundant ' Candidatus Phytoplasma solani' tuf b strain is associated with grapevine, stinging nettle and Hyalesthes obsoletus.. EUROPEAN JOURNAL OF PLANT PATHOLOGY 2014; 140:213-227. [PMID: 25309042 PMCID: PMC4188982 DOI: 10.1007/s10658-014-0455-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/08/2014] [Indexed: 05/24/2023]
Abstract
Bois noir (BN) associated with 'Candidatus Phytoplasma solani' (Stolbur) is regularly found in Austrian vine growing regions. Investigations between 2003 and 2008 indicated sporadic presence of the confirmed disease vector Hyalesthes obsoletus and frequent infections of bindweed and grapevine. Infections of nettles were rare. In contrast present investigations revealed a mass occurrence of H. obsoletus almost exclusively on stinging nettle. The high population densities of H. obsoletus on Urtica dioica were accompanied by frequent occurrence of 'Ca. P. solani' in nettles and planthoppers. Sequence analysis of the molecular markers secY, stamp, tuf and vmp1 of stolbur revealed a single genotype named CPsM4_At1 in stinging nettles and more than 64 and 90 % abundance in grapevine and H. obsoletus, respectively. Interestingly, this genotype showed tuf b type restriction pattern previously attributed to bindweed associated 'Ca. P. solani' strains, but a different sequence assigned as tuf b2 compared to reference tuf b strains. All other marker genes of CPsM4_At1 clustered with tuf a and nettle derived genotypes verifying distinct nettle phytoplasma genotypes. Transmission experiments with H. obsoletus and Anaceratagallia ribauti resulted in successful transmission of five different strains including the major genotype to Catharanthus roseus and in transmission of the major genotype to U. dioica. Altogether, five nettle and nine bindweed associated genotypes were described. Bindweed types were verified in 34 % of grapevine samples, in few positive Reptalus panzeri, rarely in bindweeds and occasionally in Catharanthus roseus infected by H. obsoletus or A. ribauti. 'Candidatus Phytoplasma convolvuli' (bindweed yellows) was ascertained in nettle and bindweed samples.
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Affiliation(s)
- A. Aryan
- Austrian Institute of Technology, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
| | - G. Brader
- Austrian Institute of Technology, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
| | - J. Mörtel
- Höhere Bundeslehranstalt und Bundesamt für Wein- und Obstbau Klosterneuburg, Wienerstraße 74, 3400 Klosterneuburg, Austria
| | - M. Pastar
- Austrian Institute of Technology, Konrad-Lorenz-Straße 24, 3430 Tulln, Austria
| | - M. Riedle-Bauer
- Höhere Bundeslehranstalt und Bundesamt für Wein- und Obstbau Klosterneuburg, Wienerstraße 74, 3400 Klosterneuburg, Austria
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20
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Siewert C, Luge T, Duduk B, Seemüller E, Büttner C, Sauer S, Kube M. Analysis of expressed genes of the bacterium 'Candidatus phytoplasma Mali' highlights key features of virulence and metabolism. PLoS One 2014; 9:e94391. [PMID: 24728201 PMCID: PMC3984173 DOI: 10.1371/journal.pone.0094391] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 03/14/2014] [Indexed: 11/19/2022] Open
Abstract
'Candidatus Phytoplasma mali' is a phytopathogenic bacterium of the family Acholeplasmataceae assigned to the class Mollicutes. This causative agent of the apple proliferation colonizes in Malus domestica the sieve tubes of the plant phloem resulting in a range of symptoms such as witches'--broom formation, reduced vigor and affecting size and quality of the crop. The disease is responsible for strong economical losses in Europe. Although the genome sequence of the pathogen is available, there is only limited information on expression of selected genes and metabolic key features that have not been examined on the transcriptomic or proteomic level so far. This situation is similar to many other phytoplasmas. In the work presented here, RNA-Seq and mass spectrometry shotgun techniques were applied on tissue samples from Nicotiana occidentalis infected by 'Ca. P. mali' strain AT providing insights into transcriptome and proteome of the pathogen. Data analysis highlights expression of 208 genes including 14 proteins located in the terminal inverted repeats of the linear chromosome. Beside a high portion of house keeping genes, the recently discussed chaperone GroES/GroEL is expressed. Furthermore, gene expression involved in formation of a type IVB and of the Sec-dependent secretion system was identified as well as the highly expressed putative pathogenicity-related SAP11-like effector protein. Metabolism of phytoplasmas depends on the uptake of spermidine/putescine, amino acids, co-factors, carbohydrates and in particular malate/citrate. The expression of these transporters was confirmed and the analysis of the carbohydrate cycle supports the suggested alternative energy-providing pathway for phytoplasmas releasing acetate and providing ATP. The phylogenetic analyses of malate dehydrogenase and acetate kinase in phytoplasmas show a closer relatedness to the Firmicutes in comparison to Mycoplasma species indicating an early divergence of the Acholeplasmataceae from the Mollicutes.
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Affiliation(s)
- Christin Siewert
- Division Phytomedicine, Department of Crop and Animal Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Toni Luge
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bojan Duduk
- Institute of Pesticides and Environmental Protection, Belgrade, Serbia
| | - Erich Seemüller
- Julius Kuehn Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, Dossenheim, Germany
| | - Carmen Büttner
- Division Phytomedicine, Department of Crop and Animal Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sascha Sauer
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Michael Kube
- Division Phytomedicine, Department of Crop and Animal Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
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