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Vo NNT, Yang A, Leesutthiphonchai W, Liu Y, Hughes TR, Judelson HS. Transcription factor binding specificities of the oomycete Phytophthora infestans reflect conserved and divergent evolutionary patterns and predict function. BMC Genomics 2024; 25:710. [PMID: 39044130 PMCID: PMC11267843 DOI: 10.1186/s12864-024-10630-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 07/17/2024] [Indexed: 07/25/2024] Open
Abstract
BACKGROUND Identifying the DNA-binding specificities of transcription factors (TF) is central to understanding gene networks that regulate growth and development. Such knowledge is lacking in oomycetes, a microbial eukaryotic lineage within the stramenopile group. Oomycetes include many important plant and animal pathogens such as the potato and tomato blight agent Phytophthora infestans, which is a tractable model for studying life-stage differentiation within the group. RESULTS Mining of the P. infestans genome identified 197 genes encoding proteins belonging to 22 TF families. Their chromosomal distribution was consistent with family expansions through unequal crossing-over, which were likely ancient since each family had similar sizes in most oomycetes. Most TFs exhibited dynamic changes in RNA levels through the P. infestans life cycle. The DNA-binding preferences of 123 proteins were assayed using protein-binding oligonucleotide microarrays, which succeeded with 73 proteins from 14 families. Binding sites predicted for representatives of the families were validated by electrophoretic mobility shift or chromatin immunoprecipitation assays. Consistent with the substantial evolutionary distance of oomycetes from traditional model organisms, only a subset of the DNA-binding preferences resembled those of human or plant orthologs. Phylogenetic analyses of the TF families within P. infestans often discriminated clades with canonical and novel DNA targets. Paralogs with similar binding preferences frequently had distinct patterns of expression suggestive of functional divergence. TFs were predicted to either drive life stage-specific expression or serve as general activators based on the representation of their binding sites within total or developmentally-regulated promoters. This projection was confirmed for one TF using synthetic and mutated promoters fused to reporter genes in vivo. CONCLUSIONS We established a large dataset of binding specificities for P. infestans TFs, representing the first in the stramenopile group. This resource provides a basis for understanding transcriptional regulation by linking TFs with their targets, which should help delineate the molecular components of processes such as sporulation and host infection. Our work also yielded insight into TF evolution during the eukaryotic radiation, revealing both functional conservation as well as diversification across kingdoms.
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Affiliation(s)
- Nguyen N T Vo
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Ally Yang
- Department of Molecular Genetics and Donnelly Center, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Wiphawee Leesutthiphonchai
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA
- Current address: Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand
| | - Yulong Liu
- Department of Molecular Genetics and Donnelly Center, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Timothy R Hughes
- Department of Molecular Genetics and Donnelly Center, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Howard S Judelson
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA, 92521, USA.
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Waheed A, Shen L, Nkurikiyimfura O, Fang H, Wang Y, Andersson B, Zhan J, Yang L. Evaluating the contribution of historical and contemporary temperature to the oospore production of self-fertile Phytophthora infestans. Evol Appl 2024; 17:e13643. [PMID: 38293269 PMCID: PMC10824702 DOI: 10.1111/eva.13643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/27/2023] [Accepted: 01/03/2024] [Indexed: 02/01/2024] Open
Abstract
Reproductive systems play an important role in the ecological function of species, but little is known about how climate change, such as global warming, may affect the reproductive systems of microbes. In this study, 116 Phytophthora infestans isolates sampled from five different altitudes along a mountain were evaluated under five temperature regimes to determine the effects of historical and experimental temperature on the reproductive system of the pathogen. Both altitude, a proxy for historical pathogen adaptation to temperature, and temperature used in the experiment affected the sexual reproduction of the pathogen, with experimental temperature, that is, contemporary temperature, playing a role several times more important than historical temperature. Furthermore, the potential of sexual reproduction, measured by the number of oospores quantified, increased with the temperature breadth (i.e., difference between the highest and lowest temperature at which sexual reproduction takes place) of the pathogen and reached the maximum at the experimental temperature of 21°C, which is higher than the annual average temperature in many potato-producing areas. The results suggest that rising air temperature associated with global warming may increase the potential of sexual reproduction in P. infestans. Given the importance of sexuality in pathogenicity and ecological adaptation of pathogens, these results suggest that global warming may increase the threat of P. infestans to agricultural production and other ecological services and highlight that new epidemiological strategies may need to be implemented for future food security and ecological resilience.
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Affiliation(s)
- Abdul Waheed
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of OceanographyMinjiang UniversityFuzhouChina
| | - Lin‐Lin Shen
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of OceanographyMinjiang UniversityFuzhouChina
| | | | - Han‐Mei Fang
- Institute of Plant PathologyFujian Agriculture and Forestry UniversityFuzhouChina
| | - Yan‐Ping Wang
- College of Chemistry and Life SciencesChengdu Normal UniversityChengduChina
| | - Björn Andersson
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | - Jiasui Zhan
- Department of Forest Mycology and Plant PathologySwedish University of Agricultural SciencesUppsalaSweden
| | - Li‐Na Yang
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of OceanographyMinjiang UniversityFuzhouChina
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Matson MEH, Liang Q, Lonardi S, Judelson HS. Karyotype variation, spontaneous genome rearrangements affecting chemical insensitivity, and expression level polymorphisms in the plant pathogen Phytophthora infestans revealed using its first chromosome-scale assembly. PLoS Pathog 2022; 18:e1010869. [PMID: 36215336 PMCID: PMC9584435 DOI: 10.1371/journal.ppat.1010869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/20/2022] [Accepted: 09/09/2022] [Indexed: 11/18/2022] Open
Abstract
Natural isolates of the potato and tomato pathogen Phytophthora infestans exhibit substantial variation in virulence, chemical sensitivity, ploidy, and other traits. A chromosome-scale assembly was developed to expand genomic resources for this oomyceteous microbe, and used to explore the basis of variation. Using PacBio and Illumina data, a long-range linking library, and an optical map, an assembly was created and coalesced into 15 pseudochromosomes spanning 219 Mb using SNP-based genetic linkage data. De novo gene prediction combined with transcript evidence identified 19,981 protein-coding genes, plus about eight thousand tRNA genes. The chromosomes were comprised of a mosaic of gene-rich and gene-sparse regions plus very long centromeres. Genes exhibited a biased distribution across chromosomes, especially members of families encoding RXLR and CRN effectors which clustered on certain chromosomes. Strikingly, half of F1 progeny of diploid parents were polyploid or aneuploid. Substantial expression level polymorphisms between strains were identified, much of which could be attributed to differences in chromosome dosage, transposable element insertions, and adjacency to repetitive DNA. QTL analysis identified a locus on the right arm of chromosome 3 governing sensitivity to the crop protection chemical metalaxyl. Strains heterozygous for resistance often experienced megabase-sized deletions of that part of the chromosome when cultured on metalaxyl, increasing resistance due to loss of the sensitive allele. This study sheds light on diverse phenomena affecting variation in P. infestans and relatives, helps explain the prevalence of polyploidy in natural populations, and provides a new foundation for biologic and genetic investigations.
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Affiliation(s)
- Michael E. H. Matson
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Qihua Liang
- Department of Computer Science and Engineering, University of California, Riverside, California, United States of America
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, California, United States of America
| | - Howard S. Judelson
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
- * E-mail:
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4
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Zhang C, Cai M, Chen S, Zhang F, Cui T, Xue Z, Wang W, Zhang B, Liu X. The consensus N glyco -X-S/T motif and a previously unknown N glyco -N-linked glycosylation are necessary for growth and pathogenicity of Phytophthora. Environ Microbiol 2021; 23:5147-5163. [PMID: 33728790 DOI: 10.1111/1462-2920.15468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/10/2021] [Accepted: 03/15/2021] [Indexed: 11/26/2022]
Abstract
Asparagine (Asn, N)-linked glycosylation within Nglyco -X-S/T; X ≠ P motif is a ubiquitously distributed post-translational modification that participates in diverse cellular processes. In this work, N-glycosylation inhibitor was shown to prevent Phytophthora sojae growth, suggesting that N-glycosylation is necessary for oomycete development. We conducted a glycoproteomic analysis of P. sojae to identify and map N-glycosylated proteins and to quantify differentially expressed glycoproteins associated with mycelia, asexual cyst, and sexual oospore developmental stages. A total of 355 N-glycosylated proteins was found, containing 496 glycosites, potentially involved in glycan degradation, carbon metabolism, glycolysis, or other metabolic pathways. Through PNGase F deglycosylation assays and site-directed mutagenesis of a GPI transamidase protein (GPI16) upregulated in cysts and a heat shock protein 70 (HSP70) upregulated in oospores, we demonstrated that both proteins were N-glycosylated and that the Nglyco -N motif is a target site for asparagine - oligosaccharide linkage. Glycosite mutations of Asn 94 Nglyco -X-S/T in the GPI16 led to impaired cyst germination and pathogenicity, while mutation of the previously unknown Asn 270 Nglyco -N motif in HSP70 led to decreased oospore production. In addition to providing a map of the oomycete N-glycoproteome, this work confirms that P. sojae has evolved multiple N-glycosylation motifs essential for growth.
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Affiliation(s)
- Can Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Meng Cai
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Shanshan Chen
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Fan Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Tongshan Cui
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Zhaolin Xue
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Weizhen Wang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Borui Zhang
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China
| | - Xili Liu
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, China.,State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, China
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5
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Can Anaerobic Soil Disinfestation (ASD) be a Game Changer in Tropical Agriculture? Pathogens 2021; 10:pathogens10020133. [PMID: 33525615 PMCID: PMC7911048 DOI: 10.3390/pathogens10020133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/23/2021] [Accepted: 01/25/2021] [Indexed: 11/17/2022] Open
Abstract
Anaerobic soil disinfection (ASD) has been identified as an alternative soil-borne pathogen control strategy to chemical fumigation. ASD involves the application of an easily liable carbon source followed by irrigation to field capacity and maintenance of an anaerobic condition for a certain period. A literature search undertaken on ASD found that more than 50 comprehensive research projects have been conducted since its first discovery in 2000. Most of these studies were conducted in the USA and in the Netherlands. Though the exact mechanism of ASD in pathogen control is unknown, promising results have been reported against a wide range of pathogens such as fungi, nematodes, protists, and oomycetes. However, it is interesting to note that, except for a few studies, ASD research in the developing world and in the tropical countries has lagged behind. Nevertheless, with soil quality depletion, reduction in arable lands, and exponential population growth, a drastic change to the current agricultural practices should be adapted since yield gain has reached a plateau for major staple crops. Under such circumstances, we identified the gaps and the potentials of ASD in tropical agricultural systems and proposed promising biodegradable materials.
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Invertases in Phytophthora infestans Localize to Haustoria and Are Programmed for Infection-Specific Expression. mBio 2020; 11:mBio.01251-20. [PMID: 33051363 PMCID: PMC7554665 DOI: 10.1128/mbio.01251-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The oomycete Phytophthora infestans, the causal agent of potato and tomato blight, expresses two extracellular invertases. Unlike typical fungal invertases, the P. infestans genes are not sucrose induced or glucose repressed but instead appear to be under developmental control. Transcript levels of both genes were very low in mycelia harvested from artificial medium but high in preinfection stages (sporangia, zoospores, and germinated cysts), high during biotrophic growth in leaves and tubers, and low during necrotrophy. Genome-wide analyses of metabolic enzymes and effectors indicated that this expression profile was fairly unusual, matched only by a few other enzymes, such as carbonic anhydrases and a few RXLR effectors. Genes for other metabolic enzymes were typically downregulated in the preinfection stages. Overall metabolic gene expression during the necrotrophic stage of infection clustered with artificial medium, while the biotrophic phase formed a separate cluster. Confocal microscopy of transformants expressing green fluorescent protein (GFP) fusions indicated that invertase protein resided primarily in haustoria during infection. This localization was not attributable to haustorium-specific promoter activity. Instead, the N-terminal regions of proteins containing signal peptides were sufficient to deliver proteins to haustoria. Invertase expression during leaf infection was linked to a decline in apoplastic sucrose, consistent with a role of the enzymes in plant pathogenesis. This was also suggested by the discovery that invertase genes occur across multiple orders of oomycetes but not in most animal pathogens or a mycoparasite.IMPORTANCE Oomycetes cause hundreds of diseases in economically and environmentally significant plants. How these microbes acquire host nutrients is not well understood. Many oomycetes insert specialized hyphae called haustoria into plant cells, but unlike their fungal counterparts, a role in nutrition has remained unproven. The discovery that Phytophthora invertases localize to haustoria provides the first strong evidence that these structures participate in feeding. Since regions of proteins containing signal peptides targeted proteins to the haustorium-plant interface, haustoria appear to be the primary machinery for secreting proteins during biotrophic pathogenesis. Although oomycete invertases were acquired laterally from fungi, their expression patterns have adapted to the Phytophthora lifestyle by abandoning substrate-level regulation in favor of developmental control, allowing the enzymes to be produced in anticipation of plant colonization. This study highlights how a widely distributed hydrolytic enzyme has evolved new behaviors in oomycetes.
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7
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Zhang C, Cui T, Zhang F, Xue Z, Miao J, Wang W, Liu X. Identification of differentially activated pathways in Phytophthora sojae at the mycelial, cyst, and oospore stages by TMT-based quantitative proteomics analysis. J Proteomics 2020; 221:103776. [PMID: 32268220 DOI: 10.1016/j.jprot.2020.103776] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/25/2020] [Accepted: 04/02/2020] [Indexed: 01/24/2023]
Abstract
Phytophthora sojae is a widely distributed, destructive oomycete plant pathogen that has been developed as a model for oomycete biology. Given the important but limited reports on the comparison of the sexual and asexual stages in Phytophthora, we performed a large-scale quantitative proteomics study on two key asexual life stages of P. sojae-the mycelium and cyst-as well as on the oospore, which is a key sexual stage. Over 29,631 peptides from 4688 proteins were analyzed. Briefly, 445 proteins, 624 proteins, and 579 proteins were defined as differentially quantified proteins in cyst vs mycelium, oospore vs cyst, and oospore vs mycelium comparisons, respectively (|log2 fold change| > 1 and P < 0.05). Compared to the mycelium and oospore, fatty acid and nitrogen metabolism were specifically induced in cysts. In oospores, the up-regulated proteins focused on RNA transport and protein processing in endoplasmic reticulum, indicating translation, folding, and the secretion of core cellular or stage-specific proteins active in oospores, which might be used for oospore germination. The data presented expand our knowledge of pathways specifically linked to asexual and sexual stages of this pathogen. BIOLOGICAL SIGNIFICANCE: The sexual spores (oospores) in oomycetes have thick cell walls and can survive in the soil for years, thus providing a primary source and allowing the reinfection of their host plant in subsequent growing seasons. However, the proteomic study on oospores remains very limited as they are generally considered to be dormant. In the present study, we successfully isolated oospores, and performed a large-scale comparative quantitative proteomics study on this key sexual stage and two representative asexual stages of P. sojae. The results provide an improved understanding of P. sojae biology and suggest potential metabolic targets for disease control at the three different developmental stages in oomycetes.
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Affiliation(s)
- Can Zhang
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Tongshan Cui
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Fan Zhang
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Zhaolin Xue
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Jianqiang Miao
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling 712100, China
| | - Weizhen Wang
- Department of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Xili Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling 712100, China.
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8
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Tzelepis G, Hodén KP, Fogelqvist J, Åsman AKM, Vetukuri RR, Dixelius C. Dominance of Mating Type A1 and Indication of Epigenetic Effects During Early Stages of Mating in Phytophthora infestans. Front Microbiol 2020; 11:252. [PMID: 32153537 PMCID: PMC7046690 DOI: 10.3389/fmicb.2020.00252] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 02/03/2020] [Indexed: 12/21/2022] Open
Abstract
The potato late blight pathogen Phytophthora infestans has both an asexual and a sexual mode of reproduction. In Scandinavia, the pathogen is reproducing sexually on a regular basis, whereas clonal lineages dominate in other geographical regions. This study aimed at elucidating events or key genes underlying this difference in sexual behavior. First, the transcriptomes of eight strains, known as either clonal or sexual, were compared during early stages of mating. Principal component analysis (PCA) divided the samples in two clusters A and B and a clear grouping of the mating samples together with the A1 mating type parents was observed. Induction of genes encoding DNA adenine N6-methylation (6mA) methyl-transferases clearly showed a bias toward the cluster A. In contrast, the Avrblb2 effector gene family was highly induced in most of the mating samples and was associated with cluster B in the PCA, similarly to genes coding for acetyl-transferases, which play an important role in RXLR modification prior to secretion. Avrblb2 knock-down strains displayed a reduction in virulence and oospore formation, suggesting a role during the mating process. In conclusion, a number of gene candidates important for the reproductive processes were revealed. The results suggest a possible epigenetic influence and involvement of specific RXLR effectors in mating-related processes.
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Affiliation(s)
- Georgios Tzelepis
- Department of Plant Biology, Uppsala Biocenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Kristian Persson Hodén
- Department of Plant Biology, Uppsala Biocenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Johan Fogelqvist
- Department of Plant Biology, Uppsala Biocenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anna K M Åsman
- Department of Plant Biology, Uppsala Biocenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ramesh R Vetukuri
- Department of Plant Biology, Uppsala Biocenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Christina Dixelius
- Department of Plant Biology, Uppsala Biocenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Vu AL, Leesutthiphonchai W, Ah-Fong AMV, Judelson HS. Defining Transgene Insertion Sites and Off-Target Effects of Homology-Based Gene Silencing Informs the Application of Functional Genomics Tools in Phytophthora infestans. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:915-927. [PMID: 30811313 DOI: 10.1094/mpmi-09-18-0265-ta] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
DNA transformation and homology-based transcriptional silencing are frequently used to assess gene function in Phytophthora spp. Since unplanned side-effects of these tools are not well-characterized, we used P. infestans to study plasmid integration sites and whether knockdowns caused by homology-dependent silencing spread to other genes. Insertions occurred both in gene-dense and gene-sparse regions but disproportionately near the 5' ends of genes, which disrupted native coding sequences. Microhomology at the recombination site between plasmid and chromosome was common. Studies of transformants silenced for 12 different gene targets indicated that neighbors within 500 nt were often cosilenced, regardless of whether hairpin or sense constructs were employed and the direction of transcription of the target. However, this cis spreading of silencing did not occur in all transformants obtained with the same plasmid. Genome-wide studies indicated that unlinked genes with partial complementarity with the silencing-inducing transgene were not usually down-regulated. We learned that hairpin or sense transgenes were not cosilenced with the target in all transformants, which informs how screens for silencing should be performed. We conclude that transformation and gene silencing can be reliable tools for functional genomics in Phytophthora spp. but must be used carefully, especially by testing for the spread of silencing to genes flanking the target.
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Affiliation(s)
- Andrea L Vu
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A
| | | | - Audrey M V Ah-Fong
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A
| | - Howard S Judelson
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A
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10
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Rodenburg SYA, Seidl MF, Judelson HS, Vu AL, Govers F, de Ridder D. Metabolic Model of the Phytophthora infestans-Tomato Interaction Reveals Metabolic Switches during Host Colonization. mBio 2019; 10:e00454-19. [PMID: 31289172 PMCID: PMC6747730 DOI: 10.1128/mbio.00454-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 06/03/2019] [Indexed: 01/01/2023] Open
Abstract
The oomycete pathogen Phytophthora infestans causes potato and tomato late blight, a disease that is a serious threat to agriculture. P. infestans is a hemibiotrophic pathogen, and during infection, it scavenges nutrients from living host cells for its own proliferation. To date, the nutrient flux from host to pathogen during infection has hardly been studied, and the interlinked metabolisms of the pathogen and host remain poorly understood. Here, we reconstructed an integrated metabolic model of P. infestans and tomato (Solanum lycopersicum) by integrating two previously published models for both species. We used this integrated model to simulate metabolic fluxes from host to pathogen and explored the topology of the model to study the dependencies of the metabolism of P. infestans on that of tomato. This showed, for example, that P. infestans, a thiamine auxotroph, depends on certain metabolic reactions of the tomato thiamine biosynthesis. We also exploited dual-transcriptome data of a time course of a full late blight infection cycle on tomato leaves and integrated the expression of metabolic enzymes in the model. This revealed profound changes in pathogen-host metabolism during infection. As infection progresses, P. infestans performs less de novo synthesis of metabolites and scavenges more metabolites from tomato. This integrated metabolic model for the P. infestans-tomato interaction provides a framework to integrate data and generate hypotheses about in planta nutrition of P. infestans throughout its infection cycle.IMPORTANCE Late blight disease caused by the oomycete pathogen Phytophthora infestans leads to extensive yield losses in tomato and potato cultivation worldwide. To effectively control this pathogen, a thorough understanding of the mechanisms shaping the interaction with its hosts is paramount. While considerable work has focused on exploring host defense mechanisms and identifying P. infestans proteins contributing to virulence and pathogenicity, the nutritional strategies of the pathogen are mostly unresolved. Genome-scale metabolic models (GEMs) can be used to simulate metabolic fluxes and help in unravelling the complex nature of metabolism. We integrated a GEM of tomato with a GEM of P. infestans to simulate the metabolic fluxes that occur during infection. This yields insights into the nutrients that P. infestans obtains during different phases of the infection cycle and helps in generating hypotheses about nutrition in planta.
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Affiliation(s)
- Sander Y A Rodenburg
- Laboratory of Phytopathology, Wageningen University, Wageningen, the Netherlands
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
| | - Michael F Seidl
- Laboratory of Phytopathology, Wageningen University, Wageningen, the Netherlands
| | - Howard S Judelson
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, California, USA
| | - Andrea L Vu
- Department of Microbiology and Plant Pathology, University of California Riverside, Riverside, California, USA
| | - Francine Govers
- Laboratory of Phytopathology, Wageningen University, Wageningen, the Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University, Wageningen, the Netherlands
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