Phakopsora pachyrhizi
CLASSIFICATION
Domain: Eukaryota
Kingdom: Fungi
Phylum: Basidiomycota
Class: Pucciniomycetes
Order: Pucciniales
Family: Phakopsoraceae
Species: Phakopsora pachyrhizi
|
NCBI: [1] |
DESCRIPTION AND SIGNIFICANCE
Phakopsora pachyrhizi is an obligate plant pathogen, famously known for causing soybean rust disease (SBR). However, it is capable of infecting 158 species of plants including lima beans, kudzu, and green beans [1]. P. pachyrhizi was first described in 1902 in Japan and first appeared as SBR disease in North American state of Louisiana in 2004 [1]. The fungus is a biotrophic plant pathogen, meaning it invades the host without killing and lives a parasitic lifestyle, draining nutrients away from the plant tissue [2]. Urediniospores are the primary dispersal method of the fungi, where the wind carries the spores to host tissues [3]. There are three main methods of controlling the pathogen: use of fungicides, soybean off seasons, and genetic breeding of resistant soybean [1]. Fungicides have been an expensive method of controlling SBR, thus much of current scientific investigation focuses on elucidating the genes that may confer soybean plant resistance to P. pachyrhizi infection.
Soybean rust disease has threatened the production of soybean food supply in Eastern Asia since its discovery in 1902 in Japan, and most recently destroying soybean crops in Bolivia, Brazil and Paraguay [4]. In 2003, Brazilian farmers have spent two billion USD on fungicidal management of the disease caused by P. pachyrhizind [4]. In 2004, the plant pathogen was discovered in the U.S. state of Louisiana, posing a major threat to U.S. soybean agriculture and economy [5]. According to American Soybean Association, the total value of U.S. soybean crop was approximately $18 million in 2004, and $34 million in 2015. The rust causing pathogen remains a large threat to soybean production, and its management costly. In 2002, P. pachyrhizi was included as a select agent in the U.S. Bioterrorism Act, meaning that the pathogen is a bioweapon and poses a high level national threat [6].
GENOME STRUCTURE
It has been difficult to sequence the complete genome of P. pachyrhizi, partially due to its large size and the fact that it consists of more than 45% transposable elements [7]. The size of the genome is estimated to range from 300 to 950 Mb depending on the sequencing methods used [7]. Almost 19,000 transcripts not found in other rust fungi have been discovered in the P. pachyrhizi transcriptome, which indicates that it has more genes than other rust fungi [7]. While the whole genome has not been effectively sequenced yet, the mitochondrial genome has been. The mt genome is circular with 31835 bp. Similar to P. meibomiae, another fungus in the Phakopsoracaea family, and many other fungal mt genomes, there is a strong bias towards A + T content, which constitutes 65.1% of the P. pachyrhizi mt genome. G + C content comprises 34.6% [8]. Of the chromosomal genome that has been sequenced, researchers detected 189 genes, with 28.6 % coding for proteins displaying similarity to proteins found in yeast. Additionally, 50.8% of the genes exhibit similarity to protein sequences found in other fungi [3]. The remaining genes are similar to genes found in bacteria, plants, mammals, insects, nematodes and other invertebrates. However, a majority of the identified genes are of unknown function. Over 52% of the gene sequences entered in the public protein database showed no similarity to other known proteins [3]. Nevertheless, most of these genes are speculated to be involved in metabolism and in protein and gene expression. P. pachyrhizi Pp1147 and Pp1420 ribosomal proteins show a high degree of similarity to those in Neurospora Crassa and Saccharomyces cerevisiae, which are also filamentous fungi [3]. Additionally, the internal transcribed spacer region of the rRNA genes demonstrate 80% likeness to those in P. meibomiae [3].
CELL STRUCTURE
P. pachyrhizi is generally hypophyllus, growing on the undersurface of leaves. It grows in circular, powdery patches, white and becoming light brown, in scattered groups [9]. P. pachyrhizi have a cell wall, about 1-1.5 µm thick which is densely packed with spines. The fungus grows out of the host plant, cone-like and about 1-2 mm in diameter, surrounded by club-shaped, yellowish-brown filaments [9]. P. pachyrhizi spreads by forming uredospores which remain dormant until encountering a favorable host [10]. These spores form an appressorium which contains hyphae that are used to penetrate and then further invade the soybean leaf [11]. After several days of infection P. pachyrhizi will then form haustoria, a specialized hyphae that that draws nutrients from mesophyll cells [12].
METABOLIC PROCESSES
Deep sequencing of P. pachyrhizi RNA transcripts at various stages of infection was performed in 2013 and provides descriptive analysis of potential P. pachyrhizi metabolic pathways. During infection, energy production is high in uredospores as indicated by high level of transcripts found encoding oxidative phosphorylation enzymatic complex I (an NADH dehydrogenase), complex IV (cytochrome oxidase), and complex V (ATP synthase), all of which participate in the electron transport chain [13]. Transcripts encoding glycolysis components such as fructose 1-6 bisphosphatase were also detected. During germination, energy production transcripts were downregulated while transcripts of enzymes involved in nucleotide metabolism and protein synthesis were upregulated [13]. Enzymes involved in carbohydrate and lipid metabolism were also present, suggesting a possible role in expansion and synthesis of hyphal components. Lastly, toward the end of infection, transcripts encoding enzymes involved in fatty acid and carbohydrate metabolism were upregulated [13]. Additionally, a DAHP synthase homolog was identified in P. pachyrhizi, which catalyzes the first step in the shikimate aromatic amino acid synthesis pathway [3]. P. pachyrhizi penetrates the host tissue by mechanical force through the leaf cuticle, followed by enzymatic digestion of the epidermal cell wall [2]. Penetration of the cuticle occurs at the earliest after 7 hours of inoculation in dew chambers [5]. The exact role of digestive enzymes during the infection process remains to be investigated, and may be a potential target for breeding resistant soybean strains [2].
ECOLOGY
The fungal species P. pachyrhizi is an obligate pathogen and thus, exists as a dormant uredospore until it latches onto a host and germinates under ideal conditions. Spore growth occurs at temperatures between 10°C and 28.5°C, with an optimal growth range of 15-25°C. Spore germination is inhibited at temperatures below 9°C and greater than 28°C [10]. The rate at which soy rust disease develops is dependent upon two factors, temperature and moisture [14]. Maximal infection by P. pachyrhizi occurs at 20-25°C with 10-12 hours of dew, or at 15-17.5°C with 16-18 hours of dew [10]. The importance of moisture for growth and infection is demonstrated by the fact that P. pachyrhizi can grow in areas of expected drought if local micro-climates are humid. Whereas in dry seasons, with low humidity, growth is limited [15] . Excessive humidity, can also hinder germination. Exposure at a very high humidity of 92.5% decreases P. pachyrhizi germination. Reports show that 91% to 100% humidity causes the spore to take on a greater reserve of water, which reduces food storage availability in the protoplasm, reducing cell viability [16]. P. pachyrhizi can persist in most tropical and subtropical climates around the world. First originating in the Eastern hemisphere, in countries such as Japan, Southern China and eastern Australia and Indonesia, soybean rust has spread [15]. The microbe is now found in South America, which saw an epidemic in Brazil in Paraguay from 2001 to 2003. Additionally, Bolivia also experienced an outbreak in 2003 due to a cool winter with sufficient moisture for prolonged dew periods [4]. Soybean rust disease has also become prevalent in Southeastern United States, where winters are mild. However, Southeastern U.S. did not experience as great of a crop loss as expected because of diurnal temperature highs of 29, 33 and 37°C, which causes a delay in urediniospore development [14].
PATHOLOGY
P. pachyrhizi is a unique type of fungal pathogen in that it infects soybean plants, causing Soybean rust disease. Infection occurs via urediniospore penetration of the leaf cuticle, rather than entering the stomates [2]. Essentially, the fungal spores disperse through the air, landing on the surface of the leaf. Once the spore latches, germination begins within 24 hours [13]. Upon development, the spore grows a single germ tube from which an appressorium develops, penetrating through the cuticle and invasively growing within the host plant [3]. An appressorium, also known as a hyphal “pressing” organ, is a specialized infection hyphae common to fungal plant pathogens [17]. The pathogen must first establish itself within the epidermal cell before it can begin invading the mesophyll tissue [5]. To effectively penetrate the cuticle, P. pachyrhizi employs mechanical force, via the grown appressorium, piercing through the plant cuticle. The appressorium is able to pervade through the cell wall by swelling at its tips and accumulating turgor pressure, independent of melanin accumulation, which is usually common for appressoria [11]. The host plant epidermal cell wall responds to such penetration by forming papilla below the breached site. After the appressorium presses through the outer epidermal cell wall, within the intracellular space, a primary hypha develops. This hypha breaks through the inner epidermal cell wall using digestive enzymes rather than mechanical force. The primary hypha proceeds to grow in the mesophyll tissue, penetrating mesophyll cells by forming a small penetrating peg and digesting a hole through the cell wall [2]. Within 12 days, secondary haustoria form [1]. Haustoria are specialized hyphae that invade mesophyll cells and draw nutrients, such as sugars and amino acids, from the plant cell into the fungus [12]. Additionally, dome-shaped eruption of uredinia, the fruiting body that produces urediospores, appears on the host plant epidermal surface. The uredinia is rusty in appearance and is what gives the pathogenesis its characteristic name, soybean rust disease. Uredinia can develop on the plant for up to 3 weeks, with a single lesion can keep sporulating urediniospores for as long as 15 weeks [1]. In the United States alone, P. pachyrhizi infects coral bean, Flordia beggarweed, green bean, kudzu, lima bean, scarlett runner bean, and soybean. Currently, there are 158 known species in danger of potential P. pachyrhizi infiltration [1].
CURRENT RESEARCH
- Scientists are investigating how n-hexane crude extracts of Amaranthus Spinosus inhibit spore germination in P. pachyrhizi. Since the presence of flavonoids, tannins, terpenoids, alkaloids, and saponins in the extract show inhibitory properties toward P. pachyrhizi , further research may allow scientists to develop an effective fungicide to prevent spread of soybean rust [17].
- Since turgor pressure accumulation of P. pachyrizi appessoria is independent of melanin, scientists know that the ability to disrupt the infection process by manipulating turgor pressure is invalid. This could explain why current methods of some pesticide solutions are not effective, and illustrates that more research into other differences between the appressoria of plant-pathogenic fungi and P. pachyrhizi can yield critical knowledge in preventing SBR [16].
- Fungicides are currently the most effective way to control SBR. However, due to the high cost of fungicides and the likelihood of P. pachyrhizi becoming insensitive to the effects of fungicides in the near future (REF), current research looks toward transcription utilization, engineering resistance genes, and developing biocontrols as alternate and effective means of controlling SBR. An experiment involving biocontrols with beneficial microbes found that Simplicillium Lanosoniveum reduces growth of SBR [18]. Another study in the early 2000s that investigated colonies of P. pachyrhizi uredospores with Trichothecium rosae observed both extreme cell growth and shrinkage of the fungus [18]. Finding a way to apply the correlation between Trichothecium rosae and shrinking of P. pachyrhizi uredospores may provide at least a temporary solution to SBR control [18].
REFERENCES
It is required that you add at least five primary research articles (in same format as the sample reference below) that corresponds to the info that you added to this page.
[Sample reference] Faller, A., and Schleifer, K. "Modified Oxidase and Benzidine Tests for Separation of Staphylococci from Micrococci". Journal of Clinical Microbiology. 1981. Volume 13. p. 1031-1035.
