Pearls

Indifferent, Affectionate, or Deceitful: Lifestyles and

Secretomes of Fungi
Rohan G. T. Lowe, Barbara J. Howlett*
School of Botany, The University of Melbourne, Victoria, Australia

Introduction from complex molecules in the environment. Insect and plant

pathogens that have to breach the host surface to gain entry also
Fungi occupy a myriad of niches. They can be free-living have large numbers, as do necrotrophs, which feed from tissue after
(indifferent) as saprophytes recycling nutrients in the natural they kill it. In contrast, biotrophs have few such families, as
environment and/or have a range of relationships (affectionate previously noted for mycorrhizae [5]; consequently, there is
and deceitful) with insect, animal, or plant hosts. Interactions with minimal release of pathogen-associated molecular patterns (PAMPs)
plants can be a continuum and range from obligate biotrophy from the plant cell wall. Accordingly, basal innate immunity, a
where fungi cannot be cultured outside living hosts to necrotrophy mechanism common to animals and plants, is not triggered.
where fungi kill and live on released nutrients. Biotrophic fungi Another class is effectors, which facilitate infection and/or induce
need to avoid or suppress defence responses. They include defence responses [6]. Effectors are generally ,300 amino acids,
symbionts, which confer a benefit to the host, and pathogens, cysteine-rich, and lack transmembrane domains. They are often
which can cause devastating diseases such as stem rust, which species-specific, polymorphic between isolates, and highly tran-
threatens production of wheat worldwide [1]. Mycorrhizae scribed in planta. They can be avirulence proteins, which are
colonise roots of .80% of land plants and are symbiotic, complementary to plant resistance proteins in ‘‘gene for gene’’
increasing nitrogen and phosphorus uptake from the soil, while
interactions, host-specific toxins, or interfere with innate immunity
feeding on sugars from the host photosynthate. Secreted proteins
by dampening or strengthening defence responses. Many proteins
are on the front line of host–fungal interactions, and a particular
with effector-like properties have unknown functions.
class, effectors, is a hot topic. Here, we examine a range of fungi
and consider their complement of secreted proteins (secretome)
and roles of effectors in fungal lifestyles. Effectors of Biotrophic Fungi Modulate Plant
Responses
For Some Fungi, There Is a Relationship between There are few genome sequences of biotrophic fungi, and as
Lifestyle and Secretome Size gene knockouts are difficult to carry out in such fungi, few effectors
have been functionally analysed. Three that elicit plant responses
The Fungal Secretome Database (FSD) [2] predicts secreted
have been characterized recently, two from symbionts and one
proteins using SignalP, which identifies secretion signal peptides
from a pathogen. MISS7 from L. bicolor is the most highly
within proteins. We applied SignalP to several recently completed
upregulated gene during symbiosis with poplar. The encoded
genomes and examined whether the ratio of secretome size to total
protein, which is crucial for successful symbiosis, moves to the
gene number reflects the predominant lifestyles (Figure 1). The
nucleus where it modulates expression of poplar genes, including
total gene number ranges from 4,000 to 20,000, and the
proportion of secreted proteins from 4% to 14%. Fungi with ones that alter root architecture [7]. A highly expressed effector
biphasic lifestyles have a large proportion of secreted proteins. from the mycorrhiza Glomus intraradices, SP7, moves to the plant
These include the hemibiotrophic rice blast fungus Magnaporthe nucleus where it interacts with pathogenesis-related transcription
oryzae, the corn smut fungus Ustilago maydis, and Piriformospora indica, factor ERF19 and helps establish symbiosis, probably by
which colonizes dead roots saprophytically and live roots as a dampening host defence [8]. A third effector that modulates plant
biotrophic symbiont [3]. Its biphasic lifestyle is reflected in its responses is a chorismate mutase from U. maydis. This enzyme
transcriptome; many genes induced during growth on living roots dimerises with a chorismate mutase from corn, and suppresses the
are similar to those of the symbiont Laccaria bicolor, whereas genes
induced during saprophytic growth are similar to those of the
saprophyte Coprinus cinereus. The insect pathogens Metarhizium Citation: Lowe RGT, Howlett BJ (2012) Indifferent, Affectionate, or Deceitful:
anisopliae and Metarhizium acridum also have large secretomes [4]. Lifestyles and Secretomes of Fungi. PLoS Pathog 8(3): e1002515. doi:10.1371/
journal.ppat.1002515
Many saprophytes have similarly sized secretomes as necrotrophs,
Editor: Joseph Heitman, Duke University Medical Center, United States of
as noted previously [2], which may reflect the fact that necrotrophs America
often have an extended saprophytic phase as part of their life cycle.
Published March 1, 2012
Animal pathogens have fewer genes than saprophytes or plant-
interacting fungi do, and a lower proportion of predicted secreted Copyright: ß 2012 Lowe, Howlett. This is an open-access article distributed
under the terms of the Creative Commons Attribution License, which permits
proteins. unrestricted use, distribution, and reproduction in any medium, provided the
original author and source are credited.
The Fungal Secretome Includes Carbohydrate- Funding: The Australian Grains Research and Development Corporation funds
Degrading Enzymes and Effectors our research. The funders had no role in study design, data collection and
analysis, decision to publish, or preparation of the manuscript.
Within the secretome there are different classes of proteins. Below Competing Interests: The authors have declared that no competing interests
we discuss two of them. Carbohydrate-degrading enzymes encoded exist.
by multigene families are secreted copiously by saprophytes to feed * E-mail: bhowlett@unimelb.edu.au

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Figure 1. Relationship between predicted secreted protein number and total gene content of fungi. Data are from [3], or by applying
SignalP to genome releases (indicated by *). Dashed lines discriminate between fungi with high (.10) or low (,6) % secreted proteins. Animal
pathogens: Batrachochytrium dendrobatidis, Candida albicans, Coccidioides immitis, C. posadasii, Cryptococcus neoformans, Histoplasma capsulatum,
Malassezia globosa, Microsporum gypseum, Paracoccidioides brasiliensis, Penicillium marneffei, Trichophyton equinum. Hemibiotrophs: Grosmania
clavigera*, Leptosphaeria maculans* [14], Magnaporthe oryzae*, Mycosphaerella fijiensis, M. graminicola, Moniliophthora perniciosa, Ustilago maydis.
Entomopathogen: Metarhizium anisopliae* [4]. Necrotrophs: Botrytis cinerea, Cochliobolus heterostrophus, Fusarium graminearum, F. oxysporum, F.
solani, Pyrenophora tritici-repentis, Stagonospora nodorum*, Sclerotinia sclerotiorum, Verticillium albo-atrum, V. dahliae. Biotrophs: Melampsora laricis-
populina* [15], Puccinia graminis f.sp. tritici. Saprophytes: Aspergillus flavus, A. nidulans, A. niger, Coprinus cinereus, Neurospora crassa, Neosartorya
fischeri, Podospora anserina, Penicillium chrysogenum, Phanerochaete chrysosporium, Pleurotus ostreatus, Postia placenta, Sporotrichum thermophile,
Trichoderma reesei, T. virens. Symbionts: Laccaria bicolor, Piriformospora indica* [3], Tuber melanosporum* [16].
doi:10.1371/journal.ppat.1002515.g001

production of salicylic acid, a key molecule in plant defence transfer (HGT) on co-infected wheat leaves about 50 years ago.
signaling [9]. Genes not only move between fungal genera, but also across
kingdoms. Phylogenetic analyses have revealed transfer of effector
Effector Genes Can Move within and between genes from fungi to oomycetes with 8% of the secretome of the
Kingdoms sudden oak death oomycete Phytophthora ramorum proposed to be
derived by HGT from fungi [12].
Effector genes are often located within repeat-rich regions, near
telomeres, or even on lineage-specific chromosomes; as a result, Animal Pathogens May Not Need Many Effectors
these genes are readily lost, gained, or mutated [10]. The gene
encoding the host-specific toxin ToxA of Stagonospora nodorum is Generally, there are few barriers for a fungus to overcome when
located near a transposase and is present in another wheat infecting animals. In many cases a fungus needs to be small
pathogen, Pyrenophora tritici-repentis [11]. Transfer of ToxA from S. enough to enter the host, survive at 37uC (in the case of
nodorum to P. tritici-repentis probably occurred by horizontal gene mammalian pathogens), and evade immune responses [13].

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Animal pathogens are often soil saprophytes that infect opportu- intimate cellular relationship between fungus and animal as exists
nistically, but, unlike most plant pathogens, some mammalian for obligate biotrophs or symbionts, which are enveloped in fungal
pathogens are not highly adapted to their hosts. Perhaps because and plant plasmalemmas. Thus, effectors may not be necessary to
of this, many animal fungal pathogens, in contrast to most plant mediate deceit in all fungal–animal interactions, but are likely to
fungal pathogens, do not display host specificity. An obvious be crucial for interactions that deceitful and affectionate fungi have
exception to this is the insect pathogenic genus Metarhizium, which with plants.
displays species specificity [4]. Furthermore, there is generally no

References
1. Singh RP, Hodson DP, Huerta-Espino J, Jin Y, Bhavani S, et al. (2011) The 9. Djamei A, Schipper K, Rabe F, Ghosh A, Vincon V, et al. (2011) Metabolic
emergence of Ug99 races of the stem rust fungus is a threat to world wheat priming by a secreted fungal effector. Nature 478: 395–398.
production. Ann Rev Phytopathol 49: 465–481. 10. Rep M, Kistler HC (2010) The genomic organization of plant pathogenicity in
2. Choi J, Park J, Kim D, Jung K, Kang S, et al. (2010) Fungal Secretome Fusarium species. Curr Opin Plant Biol 13: 420–426.
Database: integrated platform for annotation of fungal secretomes. BMC 11. Friesen TL, Stukenbrock EH, Liu Z, Meinhardt S, Ling H, et al. (2006)
Genomics 11: 105. Emergence of a new disease as a result of interspecific virulence gene transfer.
3. Zuccaro A, Lahrmann U, Güldener U, Langen G, Pfiffi S, et al. (2011) Nat Genet 38: 953–956.
Endophytic life strategies decoded by genome and transcriptome analyses of the 12. Richards TA, Soanes DM, Jones MDM, Vasieva O, Leonard G, et al. (2011)
mutualistic root symbiont Piriformospora indica. PLoS Pathog 7: e1002290. Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms
doi:10.1371/journal.ppat.1002290. in the oomycetes. Proc Nat Acad Sci U S A 108: 15258–15263.
4. Gao Q, Jin K, Ying S-H, Zhang Y, Xiao G, et al. (2011) Genome sequencing 13. Howlett BJ (2011) Fungal pathogenesis in plants and animals; similarities and
and comparative transcriptomics of the model entomopathogenic fungi differences. In: Fungal diseases: an emerging challenge to human, animal and
Metarhizium anisopliae and M. acridum. PLoS Genet 7: e1001264. doi:10.1371/ plant health Choffnes ER, Relman DA, eds. Washington (D.C.): National
journal.pgen.1001264. Academies Press. pp 264–273.
5. Plett JM, Martin F (2011) Blurred boundaries: lifestyle lessons from ectomycor- 14. Rouxel T, Grandaubert J, Hane JK, Hoede C, van de Wouw AP, et al. (2011)
rhizal fungal genomes. Trends Genet 27: 14–22. Effector diversification within compartments of the Leptosphaeria maculans genome
6. De Wit PJ, Mehrabi R, Van den Burg HA, Stergiopoulos I (2009) Fungal affected by Repeat-Induced Point mutations. Nature Commun 2: 202.
effector proteins: past, present and future. Mol Plant Pathol 10: 735–747. 15. Duplessis S, Cuomo CA, Lin Y-C, Aerts A, Tisserant E, et al. (2011) Obligate
7. Plett JM, Kemppainen M, Kale SD, Kohler A, Legue V, et al. (2011) A secreted biotrophy features unraveled by the genomic analysis of rust fungi. Proc Natl
effector protein of Laccaria bicolor is required for symbiosis development. Curr Acad Sci U S A 108: 9166–9171.
Biol 21: 1197–1203. 16. Martin F, Kohler A, Murat C, Balestrini R, Coutinho PM, et al. (2010) Perigord
8. Kloppholz S, Kuhn H, Requena N (2011) A secreted fungal effector of Glomus black truffle genome uncovers evolutionary origins and mechanisms of
intraradices promotes symbiotic biotrophy. Curr Biol 21: 1204–1209. symbiosis. Nature 464: 1033–1038.

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