Gene Expression Profiling During Asexual Development of the Late Blight Pathogen Phytophthora infestans Reveals a Highly Dynamic Transcriptome

Abstract

Much of the pathogenic success of Phytophthora infestans, the potato and tomato late blight agent, relies on its ability to generate from mycelia large amounts of sporangia, which release zoospores that encyst and form infection structures. To better understand these stages, Affymetrix GeneChips based on 15,650 unigenes were designed and used to profile the life cycle. Approximately half of P. infestans genes were found to exhibit significant differential expression between developmental transitions, with approximately (1)/(10) being stage-specific and most changes occurring during zoosporogenesis. Quantitative reverse-transcription polymerase chain reaction assays confirmed the robustness of the array results and showed that similar patterns of differential expression were obtained regardless of whether hyphae were from laboratory media or infected tomato. Differentially expressed genes encode potential cellular regulators, especially protein kinases; metabolic enzymes such as those involved in glycolysis, gluconeogenesis, or the biosynthesis of amino acids or lipids; regulators of DNA synthesis; structural proteins, including predicted flagellar proteins; and pathogenicity factors, including cell-wall-degrading enzymes, RXLR effector proteins, and enzymes protecting against plant defense responses. Curiously, some stage-specific transcripts do not appear to encode functional proteins. These findings reveal many new aspects of oomycete biology, as well as potential targets for crop protection chemicals.

bZIP Transcription Factors in the Oomycete Phytophthora infestans with Novel DNA-Binding Domains Are Involved in Defense against Oxidative Stress

“…The data presented in Fig. 4 combine results from RT-qPCR (19 genes, from this study) and microarray analysis (22 genes, mined from the data described by Judelson et al [15]). Seven genes were measured by both methods, which yielded similar results (correlation coefficient [R] ϭ 0.85).…”

“…Amplifications were performed using the Dynamo SYBR green qPCR kit (Thermo) with the following program: 95°C for 15 min, followed by 40 cycles of 94°C for 30 s, 58°C for 30 s, and 72°C for 30 s. At the end of the run, melting curves were generated to evaluate the fidelity of amplification. Expression levels were calculated using the ⌬⌬C T method, using a constitutive gene (ribosomal protein S3a, PITG_11766) as a control; prior studies demonstrated that this gene is expressed at similar levels during the life cycles of both P. infestans and Phytophthora parasitica (15,37).…”

“…P. infestans is classified as an oomycete, a group that belongs to the stramenopile kingdom (13). Dynamic changes in transcription occur during the life cycle, which involves several spore stages that are important to pathogenicity (14,15). Sporangia develop from hyphae and are important for movement to new hosts.…”

Dynamics and Innovations within Oomycete Genomes: Insights into Biology, Pathology, and Evolution

“…mRNA profiles exhibit dynamic changes throughout these developmental transitions, with many genes expressed specifically in spore or infection stages. In P. infestans, mRNA levels for nearly one-half of genes change Ͼ2-fold during life stage changes, with about 14% being expressed exclusively in one stage or another (35). Studies in P. infestans, the lima bean pathogen Phytophthora phaseoli, and the cucumber downy mildew agent Pseudoperonospora cubensis also documented changes during different stages of growth (31,49).…”

“…Others, however, such as new isoforms of metabolic enzymes, have roles that are more challenging to discern. Many transcription factors also show strong differential expression, especially those in the bZIP and Myb families which have patterns suggestive of a transcription factor cascade (35,71,92).…”