Are high-lysine cereal crops still a challenge?

The essential amino acids lysine and threonine are synthesized in higher plants via a pathway starting with aspartate that also leads to the formation of methionine and isoleucine. Lysine is one of most limiting amino acids in plants consumed by humans and livestock. Recent genetic, molecular, and biochemical evidence suggests that lysine synthesis and catabolism are regulated by complex mechanisms. Early kinetic studies utilizing mutants and transgenic plants that over-accumulate lysine have indicated that the major step for the regulation of lysine biosynthesis is at the enzyme dihydrodipicolinate synthase. Despite this tight regulation, recent strong evidence indicates that lysine catabolism is also subject to control, particularly in cereal seeds. The challenge of producing crops with a high-lysine concentration in the seeds appeared to be in sight a few years ago. However, apart from the quality protein maize lines currently commercially available, the release of high-lysine crops has not yet occurred. We are left with the question, is the production of high-lysine crops still a challenge?98599

Genome And Secretome Analysis Of The Hemibiotrophic Fungal Pathogen, Moniliophthora Roreri, Which Causes Frosty Pod Rot Disease Of Cacao: Mechanisms Of The Biotrophic And Necrotrophic Phases

Background: The basidiomycete Moniliophthora roreri is the causal agent of Frosty pod rot (FPR) disease of cacao (Theobroma cacao), the source of chocolate, and FPR is one of the most destructive diseases of this important perennial crop in the Americas. This hemibiotroph infects only cacao pods and has an extended biotrophic phase lasting up to sixty days, culminating in plant necrosis and sporulation of the fungus without the formation of a basidiocarp.Results: We sequenced and assembled 52.3 Mb into 3,298 contigs that represent the M. roreri genome. Of the 17,920 predicted open reading frames (OFRs), 13,760 were validated by RNA-Seq. Using read count data from RNA sequencing of cacao pods at 30 and 60 days post infection, differential gene expression was estimated for the biotrophic and necrotrophic phases of this plant-pathogen interaction. The sequencing data were used to develop a genome based secretome for the infected pods. Of the 1,535 genes encoding putative secreted proteins, 1,355 were expressed in the biotrophic and necrotrophic phases. Analysis of the data revealed secretome gene expression that correlated with infection and intercellular growth in the biotrophic phase and invasive growth and plant cellular death in the necrotrophic phase.Conclusions: Genome sequencing and RNA-Seq was used to determine and validate the Moniliophthora roreri genome and secretome. High sequence identity between Moniliophthora roreri genes and Moniliophthora perniciosa genes supports the taxonomic relationship with Moniliophthora perniciosa and the relatedness of this fungus to other basidiomycetes. Analysis of RNA-Seq data from infected plant tissues revealed differentially expressed genes in the biotrophic and necrotrophic phases. The secreted protein genes that were upregulated in the biotrophic phase are primarily associated with breakdown of the intercellular matrix and modification of the fungal mycelia, possibly to mask the fungus from plant defenses. Based on the transcriptome data, the upregulated secreted proteins in the necrotrophic phase are hypothesized to be actively attacking the plant cell walls and plant cellular components resulting in necrosis. These genes are being used to develop a new understanding of how this disease interaction progresses and to identify potential targets to reduce the impact of this devastating disease. © 2014 Meinhardt et al.; licensee BioMed Central Ltd.151USDA; U.S. Department of AgricultureLatunde-Dada, A.O., Colletotrichum: tales of forcible entry, stealth, transient confinement and breakout (2001) Mol Plant Pathol, 2 (4), pp. 187-198. , 10.1046/j.1464-6722.2001.00069.x, 20573006Oliver, R.P., Ipcho, S.V.S., Arabidopsis pathology breathes new life into the necrotrophs-vs.-biotrophs classification of fungal pathogens (2004) Mol Plant Pathol, 5 (4), pp. 347-352. , 10.1111/j.1364-3703.2004.00228.x, 20565602Catanzariti, A.M., Dodds, P.N., Lawrence, G.J., Ayliffe, M.A., Ellis, J.G., Haustorially expressed secreted proteins from flax rust are highly enriched for avirulence elicitors (2006) Plant Cell, 18 (1), pp. 243-256. , 10.1105/tpc.105.035980, 1323496, 16326930Link, T.I., Voegele, R.T., Secreted proteins of Uromyces fabae: similarities and stage specificity (2008) Mol Plant Pathol, 9 (1), pp. 59-66Brown, N.A., Antoniw, J., Hammond-Kosack, K.E., The predicted secretome of the plant pathogenic fungus Fusarium graminearum: a refined comparative analysis (2012) Plos One, 7 (4), pp. e33731. , 10.1371/journal.pone.0033731, 3320895, 22493673Thomma, B.P., Alternaria spp.: from general saprophyte to specific parasite (2003) Mol Plant Pathol, 4 (4), pp. 225-236. , 10.1046/j.1364-3703.2003.00173.x, 20569383Evans, H.C., Stalpers, J.A., Samson, R.A., Benny, G.L., Taxonomy of Monilia-Roreri, an important pathogen of theobroma-cacao in South-America (1978) Can J Bot, 56 (20), pp. 2528-2532Aime, M.C., Phillips-Mora, W., The causal agents of witches' broom and frosty pod rot of cacao (chocolate, Theobroma cacao) form a new lineage of Marasmiaceae (2005) Mycologia, 97 (5), pp. 1012-1022. , 10.3852/mycologia.97.5.1012, 16596953Phillips-Mora, W., Wilkinson, M.J., Frosty pod of cacao: a disease with a limited geographic range but unlimited potential for damage (2007) Phytopathology, 97 (12), pp. 1644-1647. , 10.1094/PHYTO-97-12-1644, 18943726Meinhardt, L.W., Rincones, J., Bailey, B.A., Aime, M.C., Griffith, G.W., Zhang, D.P., Pereira, G.A.G., Moniliophthora perniciosa, the causal agent of witches' broom disease of cacao: what's new from this old foe? (2008) Mol Plant Pathol, 9 (5), pp. 577-588. , 10.1111/j.1364-3703.2008.00496.x, 19018989Ferreira, L.F.R., Duarte, K.M.R., Gomes, L.H., Carvalho, R.S., Leal, G.A., Aguiar, M.M., Armas, R.D., Tavares, F.C.A., Genetic diversity of polysporic isolates of Moniliophthora perniciosa (Tricholomataceae) (2012) Genet Mol Res, 11 (3), pp. 2559-2568. , 10.4238/2012.July.10.11, 22869076Phillips-Mora, W., Wilkinson, M.J., Frosty pod: a disease of limited geographic distribution but unlimited potential for damage (2006) Phytopathology, 96 (6), pp. S138-S138Evans, H.C., (1981) Pod Rot of Cacao caused by Moniliophthora (Monilia) roreri, , London: Commonwealth Agricultural Bureau, 24Joosten, M., de Wit, P., THE TOMATO-CLADOSPORIUM FULVUM INTERACTION: a versatile experimental system to study plant-pathogen interactions (1999) Annu Rev Phytopathol, 37, pp. 335-367. , 10.1146/annurev.phyto.37.1.335, 11701827Perfect, S.E., Green, J.R., Infection structures of biotrophic and hemibiotrophic fungal plant pathogens (2001) Mol Plant Pathol, 2 (2), pp. 101-108. , 10.1046/j.1364-3703.2001.00055.x, 20572997Scarpari, L.M., Meinhardt, L.W., Mazzafera, P., Pomella, A.W.V., Schiavinato, M.A., Cascardo, J.C.M., Pereira, G.A.G., Biochemical changes during the development of witches' broom: the most important disease of cocoa in Brazil caused by Crinipellis perniciosa (2005) J Exp Bot, 56 (413), pp. 865-877. , 10.1093/jxb/eri079, 15642708Melnick, R.L., Marelli, J., Bailey, B.A., The molecular interaction of Theobroma cacao and Moniliophthora perniciosa, causal agent of witches' broom, during infection of young pods (2011) Phytopathology, 101 (6), pp. S274-S274Melnick, R.L., Marelli, J.P., Sicher, R.C., Strem, M.D., Bailey, B.A., The interaction of Theobroma cacao and Moniliophthora perniciosa, the causal agent of witches' broom disease, during parthenocarpy (2012) Tree Genet Genomes, 8 (6), pp. 1261-1279Thomazella, D.P., Teixeira, P.J., Oliveira, H.C., Saviani, E.E., Rincones, J., Toni, I.M., Reis, O., Pereira, G.A., The hemibiotrophic cacao pathogen Moniliophthora perniciosa depends on a mitochondrial alternative oxidase for biotrophic development (2012) New Phytol, 194 (4), pp. 1025-1034. , 10.1111/j.1469-8137.2012.04119.x, 3415677, 22443281Mondego, J.M., Carazzolle, M.F., Costa, G.G., Formighieri, E.F., Parizzi, L.P., Rincones, J., Cotomacci, C., Pereira, G.A.G., A genome survey of Moniliophthora perniciosa gives new insights into Witches' Broom disease of cacao (2008) Bmc Genomics, 9, p. 548. , 10.1186/1471-2164-9-548, 2644716, 19019209Bailey, B.A., Crozier, J., Sicher, R.C., Strem, M.D., Melnick, R., Carazzolle, M.F., Costa, G.G.L., Meinhardt, L., Dynamic changes in pod and fungal physiology associated with the shift from biotrophy to necrotrophy during the infection of Theobroma cacao by Moniliophthora roreri (2013) Physiol Mol Plant P, 81, pp. 84-96Henrissat, B., A classification of glycosyl hydrolases based on amino acid sequence similarities (1991) Biochem J, 280 (PART 2), pp. 309-316. , 1130547, 1747104Dias, F.M., Vincent, F., Pell, G., Prates, J.A., Centeno, M.S., Tailford, L.E., Ferreira, L.M., Gilbert, H.J., Insights into the molecular determinants of substrate specificity in glycoside hydrolase family 5 revealed by the crystal structure and kinetics of Cellvibrio mixtus mannosidase 5A (2004) J Biol Chem, 279 (24), pp. 25517-25526. , 10.1074/jbc.M401647200, 15014076Fibriansah, G., Masuda, S., Koizumi, N., Nakamura, S., Kumasaka, T., The 1.3 A crystal structure of a novel endo-beta-1,3-glucanase of glycoside hydrolase family 16 from alkaliphilic Nocardiopsis sp. strain F96 (2007) Proteins, 69 (3), pp. 683-690. , 10.1002/prot.21589, 17879342Markovic, O., Janecek, S., Pectin degrading glycoside hydrolases of family 28: sequence-structural features, specificities and evolution (2001) Protein Eng, 14 (9), pp. 615-631. , 10.1093/protein/14.9.615, 11707607Vandermarliere, E., Bourgois, T.M., Winn, M.D., van Campenhout, S., Volckaert, G., Delcour, J.A., Strelkov, S.V., Courtin, C.M., Structural analysis of a glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase in complex with xylotetraose reveals a different binding mechanism compared with other members of the same family (2009) Biochem J, 418 (1), pp. 39-47. , 10.1042/BJ20081256, 18980579Tiels, P., Baranova, E., Piens, K., De Visscher, C., Pynaert, G., Nerinckx, W., Stout, J., Callewaert, N., A bacterial glycosidase enables mannose-6-phosphate modification and improved cellular uptake of yeast-produced recombinant human lysosomal enzymes (2012) Nat Biotechnol, 30 (12), pp. 1225-1231. , 10.1038/nbt.2427, 23159880Ferreira, P., Hernandez-Ortega, A., Herguedas, B., Martinez, A.T., Medina, M., Aryl-alcohol oxidase involved in lignin degradation: a mechanistic study based on steady and pre-steady state kinetics and primary and solvent isotope effects with two alcohol substrates (2009) J Biol Chem, 284 (37), pp. 24840-24847. , 10.1074/jbc.M109.011593, 2757187, 19574215Mayer, A.M., Staples, R.C., Laccase: new functions for an old enzyme (2002) Phytochemistry, 60 (6), pp. 551-565. , 10.1016/S0031-9422(02)00171-1, 12126701Kersten, P.J., Glyoxal oxidase of Phanerochaete chrysosporium: its characterization and activation by lignin peroxidase (1990) Proc Natl Acad Sci U S A, 87 (8), pp. 2936-2940. , 10.1073/pnas.87.8.2936, 53808, 11607073Henrissat, B., Callebaut, I., Fabrega, S., Lehn, P., Mornon, J.P., Davies, G., Conserved catalytic machinery and the prediction of a common fold for several families of glycosyl hydrolases (1995) Proc Natl Acad Sci U S A, 92 (15), pp. 7090-7094. , 10.1073/pnas.92.15.7090, 41477, 7624375Wostemeyer, J., Kreibich, A., Repetitive DNA elements in fungi (Mycota): impact on genomic architecture and evolution (2002) Curr Genet, 41 (4), pp. 189-198. , 10.1007/s00294-002-0306-y, 12172959Goffeau, A., Barrell, B.G., Bussey, H., Davis, R.W., Dujon, B., Feldmann, H., Galibert, F., Oliver, S.G., Life with 6000 genes (1996) Science, 274 (5287), pp. 546-563. , 547, 10.1126/science.274.5287.546, 8849441Dean, R.A., Talbot, N.J., Ebbole, D.J., Farman, M.L., Mitchell, T.K., Orbach, M.J., Thon, M., Nicol, R., The genome sequence of the rice blast fungus Magnaporthe grisea (2005) Nature, 434 (7036), pp. 980-986. , 10.1038/nature03449, 15846337Labbe, J., Murat, C., Morin, E., Tuskan, G.A., Le Tacon, F., Martin, F., Characterization of transposable elements in the ectomycorrhizal fungus Laccaria bicolor (2012) Plos One, 7 (8), pp. e40197. , 10.1371/journal.pone.0040197, 3411680, 22870194Adomako, D., Cocoa pod husk pectin (1972) Phytochemistry, 11 (3), p. 1145Gan, P., Ikeda, K., Irieda, H., Narusaka, M., O'Connell, R.J., Narusaka, Y., Takano, Y., Shirasu, K., Comparative genomic and transcriptomic analyses reveal the hemibiotrophic stage shift of Colletotrichum fungi (2013) New Phytol, 197 (4), pp. 1236-1249. , 10.1111/nph.12085, 23252678Garcia, O., Macedo, J.A.N., Tiburcio, R., Zaparoli, G., Rincones, J., Bittencourt, L.M.C., Ceita, G.O., Cascardo, J.C., Characterization of necrosis and ethylene-inducing proteins (NEP) in the basidiomycete Moniliophthora perniciosa, the causal agent of witches' broom in Theobroma cacao (2007) Mycol Res, 111, pp. 443-455. , 10.1016/j.mycres.2007.01.017, 17512713Pemberton, C.L., Salmond, G.P., The Nep1-like proteins-a growing family of microbial elicitors of plant necrosis (2004) Mol Plant Pathol, 5 (4), pp. 353-359. , 10.1111/j.1364-3703.2004.00235.x, 20565603Zaparoli, G., Barsottini, M.R., de Oliveira, J.F., Dyszy, F., Teixeira, P.J., Barau, J.G., Garcia, O., Dias, S.M., The crystal structure of necrosis-and ethylene-inducing protein 2 from the causal agent of cacao's Witches' Broom disease reveals key elements for its activity (2011) Biochemistry-Us, 50 (45), pp. 9901-9910Cabral, A., Oome, S., Sander, N., Kufner, I., Nurnberger, T., Van den Ackerveken, G., Nontoxic Nep1-like proteins of the downy mildew pathogen Hyaloperonospora arabidopsidis: repression of necrosis-inducing activity by a surface-exposed region (2012) Mol Plant Microbe Interact, 25 (5), pp. 697-708. , 10.1094/MPMI-10-11-0269, 22235872Mosquera, G., Giraldo, M.C., Khang, C.H., Coughlan, S., Valent, B., Interaction transcriptome analysis identifies magnaporthe oryzae BAS1-4 as Biotrophy-associated secreted proteins in rice blast disease (2009) Plant Cell, 21 (4), pp. 1273-1290. , 10.1105/tpc.107.055228, 2685627, 19357089Paper, J.M., Scott-Craig, J.S., Adhikari, N.D., Cuomo, C.A., Walton, J.D., Comparative proteomics of extracellular proteins in vitro and in planta from the pathogenic fungus Fusarium graminearum (2007) Proteomics, 7 (17), pp. 3171-3183. , 10.1002/pmic.200700184, 17676664van den Burg, H.A., Harrison, S.J., Joosten, M.H., Vervoort, J., de Wit, P.J., Cladosporium fulvum Avr4 protects fungal cell walls against hydrolysis by plant chitinases accumulating during infection (2006) Mol Plant Microbe Interact, 19 (12), pp. 1420-1430. , 10.1094/MPMI-19-1420, 17153926Roby, D., Gadelle, A., Toppan, A., Chitin oligosaccharides as elicitors of chitinase activity in melon plants (1987) Biochem Biophys Res Commun, 143 (3), pp. 885-892. , 10.1016/0006-291X(87)90332-9, 3566760Deising, H., Siegrist, J., Chitin deacetylase activity of the rust uromyces-viciae-fabae is controlled by fungal morphogenesis (1995) Fems Microbiol Lett, 127 (3), pp. 207-211Teixeira, P.J.P.L., Thomazella, D.P.T., Vidal, R.O., Do Prado, P.F.V., Reis, O., Baroni, R.M., Franco, S.F., Mondego, J.M.C., The fungal pathogen moniliophthora perniciosa has genes similar to plant PR-1 that are highly expressed during its interaction with cacao (2012) Plos One, 7 (9)Riviere, M.P., Marais, A., Ponchet, M., Willats, W., Galiana, E., Silencing of acidic pathogenesis-related PR-1 genes increases extracellular beta-(1→ 3)-glucanase activity at the onset of tobacco defence reactions (2008) J Exp Bot, 59 (6), pp. 1225-1239. , 10.1093/jxb/ern044, 18390849Levy, A., Guenoune-Gelbart, D., Epel, B.L., Beta-1,3-Glucanases: plasmodesmal gate keepers for intercellular communication (2007) Plant Signal Behav, 2 (5), pp. 404-407. , 10.4161/psb.2.5.4334, 2634228, 19704615Prados-Rosales, R.C., Roldan-Rodriguez, R., Serena, C., Lopez-Berges, M.S., Guarro, J., Martinez-del-Pozo, A., Di Pietro, A., A PR-1-like protein of fusarium oxysporum functions in virulence on mammalian hosts (2012) J Biol Chem, 287 (26), pp. 21970-21979. , 10.1074/jbc.M112.364034, 3381157, 22553200Kershaw, M.J., Talbot, N.J., Hydrophobins and repellents: proteins with fundamental roles in fungal morphogenesis (1998) Fungal Genet Biol, 23 (1), pp. 18-33. , 10.1006/fgbi.1997.1022, 9501475Zelena, K., Takenberg, M., Lunkenbein, S., Woche, S.K., Nimtz, M., Berger, R.G., PfaH2: a novel hydrophobin from the ascomycete Paecilomyces farinosus (2013) Biotechnol Appl Biochem, 60 (2), pp. 147-154. , 10.1002/bab.1077, 23600571Wosten, H.A., Hydrophobins: multipurpose proteins (2001) Annu Rev Microbiol, 55, pp. 625-646. , 10.1146/annurev.micro.55.1.625, 11544369Bayry, J., Aimanianda, V., Guijarro, J.I., Sunde, M., Latge, J.P., Hydrophobins-unique fungal proteins (2012) PLoS Pathog, 8 (5), pp. e1002700. , 10.1371/journal.ppat.1002700, 3364958, 22693445De Oliveira, A.L., Gallo, M., Pazzagli, L., Benedetti, C.E., Cappugi, G., Scala, A., Pantera, B., Cicero, D.O., The structure of the elicitor cerato-platanin (CP), the first member of the CP fungal protein family, reveals a double psi beta-barrel fold and carbohydrate binding (2011) J Biol Chem, 286 (20), pp. 17560-17568. , 10.1074/jbc.M111.223644, 3093830, 21454637Baccelli, I., Comparini, C., Bettini, P.P., Martellini, F., Ruocco, M., Pazzagli, L., Bernardi, R., Scala, A., The expression of the cerato-platanin gene is related to hyphal growth and chlamydospores formation in Ceratocystis platani (2012) Fems Microbiol Lett, 327 (2), pp. 155-163. , 10.1111/j.1574-6968.2011.02475.x, 22136757Zaparoli, G., Cabrera, O.G., Medrano, F.J., Tiburcio, R., Lacerda, G., Pereira, G.G., Identification of a second family of genes in Moniliophthora perniciosa, the causal agent of witches' broom disease in cacao, encoding necrosis-inducing proteins similar to cerato-platanins (2009) Mycol Res, 113, pp. 61-72. , 10.1016/j.mycres.2008.08.004, 18796332Lombardi, L., Faoro, F., Luti, S., Baccelli, I., Martellini, F., Bernardi, R., Picciarelli, P., Pazzagli, L., Differential timing of defense-related responses induced by cerato-platanin and cerato-populin, two non-catalytic fungal elicitors (2013) Physiol Plant, 149, pp. 408-421Yang, Y., Zhang, H., Li, G., Li, W., Wang, X., Song, F., Ectopic expression of MgSM1, a Cerato-platanin family protein from Magnaporthe grisea, confers broad-spectrum disease resistance in Arabidopsis (2009) Plant Biotechnol J, 7 (8), pp. 763-777. , 10.1111/j.1467-7652.2009.00442.x, 19754836Bhadauria, V., Banniza, S., Vandenberg, A., Selvaraj, G., Wei, Y., EST mining identifies proteins putatively secreted by the anthracnose pathogen Colletotrichum truncatum (2011) Bmc Genomics, 12, p. 327. , 10.1186/1471-2164-12-327, 3149586, 21699715Frischmann, A., Neudl, S., Gaderer, R., Bonazza, K., Zach, S., Gruber, S., Spadiut, O., Seidl-Seiboth, V., Self-assembly at air/water interfaces and carbohydrate binding properties of the small secreted protein EPL1 from the fungus trichoderma atroviride (2013) J Biol Chem, 288 (6), pp. 4278-4287. , 10.1074/jbc.M112.427633, 3567679, 23250741Jeong, J.S., Mitchell, T.K., Dean, R.A., The magnaporthe grisea snodprot1 homolog, MSP1, is required for virulence (2007) Fems Microbiol Lett, 273 (2), pp. 157-165. , 10.1111/j.1574-6968.2007.00796.x, 17590228Peter, M., Courty, P.E., Kohler, A., Delaruelle, C., Martin, D., Tagu, D., Frey-Klett, P., Martin, F., Analysis of expressed sequence tags from the ectomycorrhizal basidiomycetes Laccaria bicolor and Pisolithus microcarpus (2003) New Phytol, 159 (1), pp. 117-129Cosgrove, D.J., Loosening of plant cell walls by expansins (2000) Nature, 407 (6802), pp. 321-326. , 10.1038/35030000, 11014181Quiroz-Castaneda, R.E., Martinez-Anaya, C., Cuervo-Soto, L.I., Segovia, L., Folch-Mallol, J.L., Loosenin, a novel protein with cellulose-disrupting activity from Bjerkandera adusta (2011) Microb Cell Fact, 10, p. 8. , 10.1186/1475-2859-10-8, 3050684, 21314954Brotman, Y., Briff, E., Viterbo, A., Chet, I., Role of swollenin, an expansin-like protein from Trichoderma, in plant root colonization (2008) Plant Physiol, 147 (2), pp. 779-789. , 10.1104/pp.108.116293, 2409044, 18400936Yamada, M., Sakuraba, S., Shibata, K., Taguchi, G., Inatomi, S., Okazaki, M., Shimosaka, M., Isolation and analysis of genes specifically expressed during fruiting body development in the basidiomycete Flammulina velutipes by fluorescence differential display (2006) Fems Microbiol Lett, 254 (1), pp. 165-172. , 10.1111/j.1574-6968.2005.00023.x, 16451195Rincones, J., Scarpari, L.M., Carazzolle, M.F., Mondego, J.M.C., Formighieri, E.F., Barau, J.G., Costa, G.G.L., Pereira, G.A., Differential gene expression between the biotrophic-like and saprotrophic mycelia of the witches' broom pathogen Moniliophthora perniciosa (2008) Mol Plant Microbe In, 21 (7), pp. 891-908Zerbino, D.R., Birney, E., Velvet: algorithms for de novo short read assembly using de Bruijn graphs (2008) Genome Res, 18 (5), pp. 821-829. , 10.1101/gr.074492.107, 2336801, 18349386Sommer, D.D., Delcher, A.L., Salzberg, S.L., Pop, M., Minimus: a fast, lightweight genome assembler (2007) BMC Bioinforma, 8, p. 64Ter-Hovhannisyan, V., Lomsadze, A., Chernoff, Y.O., Borodovsky, M., Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training (2008) Genome Res, 18 (12), pp. 1979-1990. , 10.1101/gr.081612.108, 2593577, 18757608Stanke, M., Keller, O., Gunduz, I., Hayes, A., Waack, S., Morgenstern, B., AUGUSTUS: ab initio prediction of alternative transcripts (2006) Nucleic Acids Res, 34, pp. W435-W439. , Web Server issue, 1538822, 16845043Stanke, M., Tzvetkova, A., Morgenstern, B., AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome (2006) Genome Biol, 7 (SUPPL. 1), pp. S11 11-18Slater, G.S., Birney, E., Automated generation of heuristics for biological sequence comparison (2005) BMC Bioinforma, 6, p. 31Borodovsky, M., Lomsadze, A., Ivanov, N., Mills, R., Eukaryotic gene prediction using GeneMark.hmm (2003) Curr Protoc Bioinformatics, , Chapter 4, Unit4 6Haas, B.J., Salzberg, S.L., Zhu, W., Pertea, M., Allen, J.E., Orvis, J., White, O., Wortman, J.R., Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments (2008) Genome Biol, 9 (1), pp. R7. , 10.1186/gb-2008-9-1-r7, 2395244, 18190707Koski, L.B., Gray, M.W., Lang, B.F., Burger, G., AutoFACT: an automatic functional annotation and classification tool (2005) BMC Bioinforma, 6, p. 151Suzek, B.E., Huang, H., McGarvey, P., Mazumder, R., Wu, C.H., UniRef: comprehensive and non-redundant UniProt reference clusters (2007) Bioinformatics, 23 (10), pp. 1282-1288. , 10.1093/bioinformatics/btm098, 17379688Bateman, A., Birney, E., Cerruti, L., Durbin, R., Etwiller, L., Eddy, S.R., Griffiths-Jones, S., Sonnhammer, E.L., The Pfam protein families database (2002) Nucleic Acids Res, 30 (1), pp. 276-280. , 10.1093/nar/30.1.276, 99071,

Are high-lysine cereal crops still a challenge?

The essential amino acids lysine and threonine are synthesized in higher plants via a pathway starting with aspartate that also leads to the formation of methionine and isoleucine. Lysine is one of most limiting amino acids in plants consumed by humans and livestock. Recent genetic, molecular, and biochemical evidence suggests that lysine synthesis and catabolism are regulated by complex mechanisms. Early kinetic studies utilizing mutants and transgenic plants that over-accumulate lysine have indicated that the major step for the regulation of lysine biosynthesis is at the enzyme dihydrodipicolinate synthase. Despite this tight regulation, recent strong evidence indicates that lysine catabolism is also subject to control, particularly in cereal seeds. The challenge of producing crops with a high-lysine concentration in the seeds appeared to be in sight a few years ago. However, apart from the quality protein maize lines currently commercially available, the release of high-lysine crops has not yet occurred. We are left with the question, is the production of high-lysine crops still a challenge

The Hemibiotrophic Cacao Pathogen Moniliophthora Perniciosa Depends On A Mitochondrial Alternative Oxidase For Biotrophic Development

The tropical pathogen Moniliophthora perniciosa causes witches' broom disease in cacao. As a hemibiotrophic fungus, it initially colonizes the living host tissues (biotrophic phase), and later grows over the dead plant (necrotrophic phase). Little is known about the mechanisms that promote these distinct fungal phases or mediate the transition between them. An alternative oxidase gene (Mp-aox) was identified in the M. perniciosa genome and its expression was analyzed througout the fungal life cycle. In addition, the effects of inhibitors of the cytochrome-dependent respiratory chain (CRC) and alternative oxidase (AOX) were evaluated on the invitro development of M. perniciosa. Larger numbers of Mp-aox transcripts were observed in the biotrophic hyphae, which accordingly showed elevated sensitivity to AOX inhibitors. More importantly, the inhibition of CRC prevented the transition from the biotrophic to the necrotrophic phase, and the combined use of a CRC and AOX inhibitor completely halted fungal growth. On the basis of these results, a novel mechanism is presented in which AOX plays a role in the biotrophic development of M. perniciosa and regulates the transition to its necrotrophic stage. Strikingly, this model correlates well with the infection strategy of animal pathogens, particularly Trypanosoma brucei, which uses AOX as a strategy for pathogenicity. © 2012 The Authors New Phytologist. © 2012 New Phytologist Trust.194410251034Avila-Adame, C., Koller, W., Disruption of the alternative oxidase gene in Magnaporthe grisea and its impact on host infection (2002) Molecular Plant-Microbe Interactions, 15, pp. 493-500Affourtit, C., Albury, M.S., Krab, K., Moore, A.L., Functional expression of the plant alternative oxidase affects growth of the yeast Schizosaccharomyces pombe (1999) Journal of Biological Chemistry, 274, pp. 6212-6218Affourtit, C., Heaney, S.P., Moore, A.L., Mitochondrial electron transfer in the wheat pathogenic fungus Septoria tritici: on the role of alternative respiratory enzymes in fungicide resistance (2000) Biochimica et Biophysica Acta, 1459, pp. 291-298Aime, M.C., Phillips-Mora, W., The causal agents of witches' broom and frosty pod rot of cacao (chocolate, Theobroma cacao) form a new lineage of Marasmiaceae (2005) Mycologia, 97, pp. 1012-1022Akhter, S., McDade, H.C., Gorlach, J.M., Heinrich, G., Cox, G.M., Perfect, J.R., Role of alternative oxidase gene in pathogenesis of Cryptococcus neoformans (2003) Infection and Immunology, 71, pp. 5794-5802Albury, M.S., Elliott, C., Moore, A.L., Towards a structural elucidation of the alternative oxidase in plants (2009) Physiologia Plantarum, 137, pp. 316-327Berruyer, R., Poussier, S., Kankanala, P., Mosquera, G., Valent, B., Quantitative and qualitative influence of inoculation methods on inplanta growth of rice blast fungus (2006) Phytopathology, 96, pp. 346-355Bradford, M.M., A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding (1976) Analytical Biochemistry, 72, pp. 248-254Brown, G.C., Nitric oxide and mitochondrial respiration (1999) Biochimica et Biophysica Acta, 1411, pp. 351-369Brown, G.C., Borutaite, V., Nitric oxide inhibition of mitochondrial respiration and its role in cell death (2002) Free Radical Biology and Medicine, 33, pp. 1440-1450Ceita, G.O., Macêdo, J.N.A., Santos, T.B., Alemanno, L., Da Silva Gesteira, A., Micheli, F., Mariano, A.C., Meinhardt, L.W., Involvement of calcium oxalate degradation during programmed cell death in Theobroma cacao tissues triggered by the hemibiotrophic fungus Moniliophthora perniciosa (2007) Plant Science, 173, pp. 106-117Chaudhuri, M., Ott, R.D., Hill, G.C., Trypanosome alternative oxidase: from molecule to function (2006) Trends in Parasitology, 22, pp. 484-491Day, P.R., Anagnostakis, S.L., Corn smut dikaryon in culture (1971) Nature: New Biology, 231, pp. 19-20Dean, R.A., Talbot, N.J., Ebbole, D.J., Farman, M.L., Mitchell, T.K., Orbach, M.J., Thon, M., Pan, H., The genome sequence of the rice blast fungus Magnaporthe grisea (2005) Nature, 434, pp. 980-986Delledonne, M., Xia, Y., Dixon, R.A., Lamb, C., Nitric oxide functions as a signal in plant disease resistance (1998) Nature, 394, pp. 585-588Dufresne, M., Perfect, S., Pellier, A.L., Bailey, J.A., Langin, T., A GAL4-like protein is involved in the switch between biotrophic and necrotrophic phases of the infection process of Colletotrichum lindemuthianum on common bean (2000) Plant Cell, 12, pp. 1579-1590Elthon, T.E., McIntosh, L., Identification of the alternative terminal oxidase of higher plant mitochondria (1987) Proceedings of the National Academy of Sciences, USA, 84, pp. 8399-8403Elthon, T.E., Nickels, R.L., McIntosh, L., Monoclonal antibodies to the alternative oxidase of higher plant mitochondria (1989) Plant Physiology, 89, pp. 1311-1317Evans, H.C., Pleomorphism in Crinipellis perniciosa, causal agent of Witches' broom disease of cocoa (1980) Transactions of the British Mycological Society, 74, pp. 515-526Fang, J., Beattie, D.S., Alternative oxidase present in procyclic Trypanosoma brucei may act to lower the mitochondrial production of superoxide (2003) Archives of Biochemistry and Biophysics, 414, pp. 294-302Frias, G., Purdy, L.H., Schmidt, R.A., An inoculation method for evaluating resistance of cacao to Crinipellis perniciosa (1995) Plant Disease, 79, pp. 787-791Glazebrook, J., Contrasting mechanisms of defense against biotrophic and necrotrophic pathogens (2005) Annual Review of Phytopathology, 43, pp. 205-227Gredilla, R., Grief, J., Osiewacz, H.D., Mitochondrial free radical generation and lifespan control in the fungal aging model Podospora anserina (2006) Experimental Gerontology, 41, pp. 439-447Griffith, G.W., Hedger, J.N., A novel method for producing basidiocarps of the cocoa pathogen Crinipellis perniciosa using a bran-vermiculite medium (1993) European Journal of Plant Pathology, 99, pp. 227-230Griffith, G.W., Hedger, J.N., Dual culture of Crinipellis perniciosa and potato callus (1994) European Journal of Plant Pathology, 100, pp. 371-379Hernandez, R.O., Gonzalez, A., Almeida, A.J., Tamayo, D., Garcia, A.M., Restrepo, A., McEwen, J.G., Alternative oxidase mediates pathogen resistance in Paracoccidioides brasiliensis infection (2011) PLoS Neglected Tropical Diseases, 5, pp. e1353Ishii, H., Fountaine, J., Chung, W.H., Kansako, M., Nishimura, K., Takahashi, K., Oshima, M., Characterization of QoI-resistant field isolates of Botrytis cinerea from citrus and strawberry (2009) Pest Management Science, 65, pp. 916-922Joseph-Horne, T., Hollomon, D.W., Wood, P.M., Fungal respiration: a fusion of standard and alternative components (2001) Biochimica et Biophysica Acta, 1504, pp. 179-195Livak, K.J., Schmittgen, T.D., Analysis of relative gene expression data using real-time quantitative PCR and the method (2001) Methods, 25, pp. 402-408Magnani, T., Soriani, F.M., Martins, V., Policarpo, A.C., Sorgi, C.A., Faccioli, L.H., Curti, C., Uyemura, S.A., Silencing of mitochondrial alternative oxidase gene of Aspergillus fumigatus enhances reactive oxygen species production and killing of the fungus by macrophages (2008) Journal of Bioenergetics and Biomembranes, 40, pp. 631-636Maxwell, D.P., Wang, Y., McIntosh, L., The alternative oxidase lowers mitochondrial reactive oxygen production in plant cells (1999) Proceedings of the National Academy of Sciences, USA, 96, pp. 8271-8276McDonald, A.E., Alternative oxidase: what information can protein sequence comparisons give us? (2009) Physiologia Plantarum, 137, pp. 328-341McDonald, A.E., Vanlerberghe, G.C., Taples, J.F., Alternative oxidase in animals: unique characteristics and taxonomic distribution (2009) Journal of Experimental Biology, 212, pp. 2627-2634Meinhardt, L.W., Bellato, C.M., Rincones, J., Azevedo, R.A., Cascardo, J.C., Pereira, G.A.G., Invitro production of biotrophic-like cultures of Crinipellis perniciosa, the causal agent of witches' broom disease of Theobroma cacao (2006) Current Microbiology, 52, pp. 191-196Meinhardt, L.W., Rincones, J., Bailey, B.A., Aime, M.C., Griffith, G.W., Zhang, D., Pereira, G.A.G., Moniliophthora perniciosa, the causal agent of witches' broom disease of cacao: what's new from this old foe? (2008) Molecular Plant Pathology, 9, pp. 577-588Miguez, M., Reeve, C., Wood, P.M., Hollomon, D.W., Alternative oxidase reduces the sensitivity of Mycosphaerella graminicola to QOI fungicides (2004) Pest Management Science, 60, pp. 3-7Minagawa, N., Koga, S., Nakano, M., Sakajo, S., Yoshimoto, A., Possible involvement of superoxide anion in the induction of cyanide-resistant respiration in Hansenula anomala (1992) FEBS Letters, 302, pp. 217-219Mondego, J.M., Carazzolle, M.F., Costa, G.G., Formighieri, E.F., Parizzi, L.P., Rincones, J., Cotomacci, C., Carrer, H., A genome survey of Moniliophthora perniciosa gives new insights into witches' broom disease of cacao (2008) BMC Genomics, 9, p. 548Munch, S., Lingner, U., Floss, D.S., Ludwig, N., Sauer, N., Deising, H.B., The hemibiotrophic lifestyle of Colletotrichum species (2008) Journal of Plant Physiology, 165, pp. 41-51Niella, G., Resende, M.L., Castro, H.A., de Carvalho, G.A., Silva, L.H.C.P., Improving the methodology of artificial production of basidiomata of Crinipellis perniciosa/Aperfeiçoamento da metodologia de produção artificial de basidiocarpos de Crinipellis perniciosa (1999) Fitopatologia Brasileira, 24, pp. 523-527Nittler, M.P., Hocking-Murray, D., Foo, C.K., Sil, A., Identification of Histoplasma capsulatum transcripts induced in response to reactive nitrogen species (2005) Molecular Biology of the Cell, 16, pp. 4792-4813Pellier, A.L., Lauge, R., Veneault-Fourrey, C., Langin, T., CLNR1, the AREA/NIT2-like global nitrogen regulator of the plant fungal pathogen Colletotrichum lindemuthianum is required for the infection cycle (2003) Molecular Microbiology, 48, pp. 639-655Purdy, L.H., Schmidt, R.A., Status of cacao witches' broom: biology, epidemiology, and management (1996) Annual Review of Phytopathology, 34, pp. 573-594Ribot, C., Hirsch, J., Balzergue, S., Tharreau, D., Notteghem, J.L., Lebrun, M.H., Morel, J.B., Susceptibility of rice to the blast fungus, Magnaporthe grisea (2008) Journal of Plant Physiology, 165, pp. 114-124Rincones, J., Scarpari, L.M., Carazzolle, M.F., Mondego, J.M., Formighieri, E.F., Barau, J.G., Costa, G.G., Vilas-Boas, L.A., Differential gene expression between the biotrophic-like and saprotrophic mycelia of the witches' broom pathogen Moniliophthora perniciosa (2008) Molecular Plant-Microbe Interactions, 21, pp. 891-908Romero-Puertas, M.C., Perazzolli, M., Zago, E.D., Delledonne, M., Nitric oxide signalling functions in plant-pathogen interactions (2004) Cellular Microbiology, 6, pp. 795-803Ruy, F., Vercesi, A.E., Kowaltowski, A.J., Inhibition of specific electron transport pathways leads to oxidative stress and decreased Candida albicans proliferation (2006) Journal of Bioenergetics and Biomembranes, 38, pp. 129-135Sakajo, S., Minagawa, N., Yoshimoto, A., Characterization of the alternative oxidase protein in the yeast Hansenula anomala (1993) FEBS Letters, 318, pp. 310-312Scarpari, L.M., Meinhardt, L.W., Mazzafera, P., Pomella, A.W., Schiavinato, M.A., Cascardo, J.C., Pereira, G.A.G., Biochemical changes during the development of witches' broom: the most important disease of cocoa in Brazil caused by Crinipellis perniciosa (2005) Journal of Experimental Botany, 56, pp. 865-877Seligman, K., Saviani, E.E., Oliveira, H.C., Pinto-Maglio, C.A., Salgado, I., Floral transition and nitric oxide emission during flower development in Arabidopsis thaliana is affected in nitrate reductase-deficient plants (2008) Plant and Cell Physiology, 49, pp. 1112-1121Siedow, J.N., Umbach, A.L., The mitochondrial cyanide-resistant oxidase: structural conservation amid regulatory diversity (2000) Biochimica et Biophysica Acta, 1459, pp. 432-439Spanu, P., Kamper, J., Genomics of biotrophy in fungi and oomycetes - emerging patterns (2010) Current Opinion in Plant Biology, 13, pp. 409-414Stenmark, P., Nordlund, P., A prokaryotic alternative oxidase present in the bacterium Novosphingobium aromaticivorans (2003) FEBS Letters, 552, pp. 189-192Tanton, L.L., Nargang, C.E., Kessler, K.E., Li, Q.H., Nargang, F.E., Alternative oxidase expression in Neurospora crassa (2003) Fungal Genetics and Biology, 39, pp. 176-190Van Aken, O., Giraud, E., Clifton, R., Whelan, J., Alternative oxidase: a target and regulator of stress responses (2009) Physiologia Plantarum, 137, pp. 354-361Vanlerberghe, G.C., Cvetkovska, M., Wang, J., Is the maintenance of homeostatic mitochondrial signaling during stress a physiological role for alternative oxidase? (2009) Physiologia Plantarum, 137, pp. 392-406Vanlerberghe, G.C., McIntosh, L., Mitochondrial electron transport regulation of nuclear gene expression. Studies with the alternative oxidase gene of tobacco (1994) Plant Physiology, 105, pp. 867-874Vanlerberghe, G.C., McIntosh, L., Alternative oxidase: from gene to function (1997) Annual Review of Plant Physiology and Plant Molecular Biology, 48, pp. 703-734Wagner, A.M., Krab, K., Wagner, M.J., Moore, A.L., Regulation of thermogenesis in flowering Araceae: the role of the alternative oxidase (2008) Biochimica et Biophysica Acta, 1777, pp. 993-1000Wilson, R.A., Talbot, N.J., Under pressure: investigating the biology of plant infection by Magnaporthe oryzae (2009) Nature Reviews: Microbiology, 7, pp. 185-195Yukioka, H., Inagaki, S., Tanaka, R., Katoh, K., Miki, N., Mizutani, A., Masuko, M., Transcriptional activation of the alternative oxidase gene of the fungus Magnaporthe grisea by a respiratory-inhibiting fungicide and hydrogen peroxide (1998) Biochimica et Biophysica Acta, 1442, pp. 161-16

A Potential Role For An Extracellular Methanol Oxidase Secreted By Moniliophthora Perniciosa In Witches' Broom Disease In Cacao

The hemibiotrophic basidiomycete fungus Moniliophthora perniciosa, the causal agent of Witches' broom disease (WBD) in cacao, is able to grow on methanol as the sole carbon source. In plants, one of the main sources of methanol is the pectin present in the structure of cell walls. Pectin is composed of highly methylesterified chains of galacturonic acid. The hydrolysis between the methyl radicals and galacturonic acid in esterified pectin, mediated by a pectin methylesterase (PME), releases methanol, which may be decomposed by a methanol oxidase (MOX). The analysis of the M. pernciosa genome revealed putative mox and pme genes. Real-time quantitative RT-PCR performed with RNA from mycelia grown in the presence of methanol or pectin as the sole carbon source and with RNA from infected cacao seedlings in different stages of the progression of WBD indicate that the two genes are coregulated, suggesting that the fungus may be metabolizing the methanol released from pectin. Moreover, immunolocalization of homogalacturonan, the main pectic domain that constitutes the primary cell wall matrix, shows a reduction in the level of pectin methyl esterification in infected cacao seedlings. Although MOX has been classically classified as a peroxisomal enzyme, M. perniciosa presents an extracellular methanol oxidase. Its activity was detected in the fungus culture supernatants, and mass spectrometry analysis indicated the presence of this enzyme in the fungus secretome. Because M. pernciosa possesses all genes classically related to methanol metabolism, we propose a peroxisome-independent model for the utilization of methanol by this fungus, which begins with the extracellular oxidation of methanol derived from the demethylation of pectin and finishes in the cytosol. © 2012 Elsevier Inc.4911922932Aime, M.C., Phillips-Mora, W., The causal agents of Witches' broom and frosty pod rot of cacao (chocolate, Theobroma cacao) form a new lineage of Marasmiaceae (2005) Mycologia, 97, pp. 1012-1022Buckeridge, M.S., Reid, J.S., Purification and properties of a novel beta-galactosidase or exo-(1→4)-beta-d-galactanase from the cotyledons of germinated Lupinus angustifolius L. seeds (1994) Planta, 192, pp. 502-511Daniel, G., Volc, J., Filonova, L., Plihal, O., Kubatova, E., Halada, P., Characteristics of Gloeophyllum trabeum alcohol oxidase, an extracellular source of H2O2 in brown rot decay of wood (2007) Appl. Environ. Microbiol., 73, pp. 6241-6253de Hoop, M.J., Ab, G., Import of proteins into peroxisomes and other microbodies (1992) Biochem. J., 286 (PART 3), pp. 657-669de Souza, T.A., Soprano, A.S., de Lira, N.P., Quaresma, A.J., Pauletti, B.A., Paes Leme, A.F., Benedetti, C.E., The TAL effector PthA4 interacts with nuclear factors involved in RNA-dependent processes including a HMG protein that selectively binds poly(U) RNA (2012) PLoS One, 7, pp. e32305Delgado, J.C., Cook, A.A., Nuclear condition of basidia, basidiospores, and mycelium of Marasmius-Perniciosus (1976) Can. J. Bot. - Rev. Can. Bot., 54, pp. 66-72Evans, H.C., Witches broom disease of cocoa (Crinipellis-Perniciosa) in Ecuador 1. Fungus (1978) Ann. Appl. Biol., 89, pp. 185-192Evans, H.C., Pleomorphism in Crinipellis-Perniciosa, causal agent of Witches broom disease of cocoa (1980) Trans. Brit. Mycol. Soc., 74, pp. 515-523Evans, H.C., Bastos, C.N., Basidiospore germination as a means of assessing resistance to Crinipellis-Perniciosa (Witches broom disease) in cocoa cultivars (1980) Trans. Brit. Mycol. Soc., 74, pp. 525-536Frias, G.A., Purdy, L.H., Schmidt, R.A., Infection biology of Crinipellis-Perniciosa on vegetative flushes of cacao (1991) Plant Dis., 75, pp. 552-556Giuseppin, M.L., Van Eijk, H.M., Bes, B.C., Molecular regulation of methanol oxidase activity in continuous cultures of Hansenula polymorpha (1988) Biotechnol. Bioeng., 32, pp. 577-583Gould, S.G., Keller, G.A., Subramani, S., Identification of a peroxisomal targeting signal at the carboxy terminus of firefly luciferase (1987) J. Cell Biol., 105, pp. 2923-2931Griffith, G.W., Hedger, J.N., The breeding biology of biotypes of the Witches-broom pathogen of cocoa Crinipellis-Perniciosa (1994) Heredity., 72, pp. 278-289Griffith, G.W., Nicholson, J., Nenninger, A., Birch, R.N., Hedger, J.N., Witches' brooms and frosty pods: two major pathogens of cacao (2003) NZ J. Bot., 41, pp. 423-435Guimaraes, R.L., Stotz, H.U., Oxalate production by Sclerotinia sclerotiorum deregulates guard cells during infection (2004) Plant Physiol., 136, pp. 3703-3711Gunkel, K., van Dijk, R., Veenhuis, M., van der Klei, I.J., Routing of Hansenula polymorpha alcohol oxidase: an alternative peroxisomal protein-sorting machinery (2004) Mol. Biol. Cell, 15, pp. 1347-1355Han, Y., Joosten, H.J., Niu, W., Zhao, Z., Mariano, P.S., McCalman, M., van Kan, J., Dunaway-Mariano, D., Oxaloacetate hydrolase, the C-C bond lyase of oxalate secreting fungi (2007) J. Biol. Chem., 282, pp. 9581-9590Hanna, S.L., Sherman, N.E., Kinter, M.T., Goldberg, J.B., Comparison of proteins expressed by Pseudomonas aeruginosa strains representing initial and chronic isolates from a cystic fibrosis patient: an analysis by 2-D gel electrophoresis and capillary column liquid chromatography-tandem mass spectrometry (2000) Microbiology, 146 (PSRT 10), pp. 2495-2508Karnovsky, M.J., A formaldehyde-glutaraldehyde fixative of high osmolarity for use in electron microscopy (1965) J. Cell Biol., 27, p. 137Kaszycki, P., Koloczek, H., Formaldehyde and methanol biodegradation with the methylotrophic yeast Hansenula polymorpha in a model wastewater system (2000) Microbiol. Res., 154, pp. 289-296Langmead, B., Aligning short sequencing reads with Bowtie (2010) Curr. Protoc. Bioinfor, , Unit 11 7 (Chapter 11)Lazarow, P.B., The import receptor Pex7p and the PTS2 targeting sequence (2006) Biochim. Biophys. Acta, 1763, pp. 1599-1604Martinez, D., Challacombe, J., Morgenstern, I., Hibbett, D., Schmoll, M., Kubicek, C.P., Ferreira, P., Cullen, D., Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion (2009) Proc. Natl. Acad. Sci. USA, 106, pp. 1954-1959Meinhardt, L.W., Bellato Cde, M., Rincones, J., Azevedo, R.A., Cascardo, J.C., Pereira, G.A., In vitro production of biotrophic-like cultures of Crinipellis perniciosa, the causal agent of Witches' broom disease of Theobroma cacao (2006) Curr. Microbiol., 52, pp. 191-196Mondego, J.M., Carazzolle, M.F., Costa, G.G., Formighieri, E.F., Parizzi, L.P., Rincones, J., Cotomacci, C., Pereira, G.A., A genome survey of Moniliophthora perniciosa gives new insights into Witches' broom disease of cacao (2008) BMC Genom., 9, p. 548Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L., Wold, B., Mapping and quantifying mammalian transcriptomes by RNA-Seq (2008) Nat. Methods, 5, pp. 621-628Nakagawa, T., Miyaji, T., Yurimoto, H., Sakai, Y., Kato, N., Tomizuka, N., A methylotrophic pathway participates in pectin utilization by Candida boidinii (2000) Appl. Environ. Microbiol., 66, pp. 4253-4257Nakagawa, T., Yamada, K., Fujimura, S., Ito, T., Miyaji, T., Tomizuka, N., Pectin utilization by the methylotrophic yeast Pichia methanolica (2005) Microbiology, 151, pp. 2047-2052Nemecek-Marshall, M., MacDonald, R.C., Franzen, J.J., Wojciechowski, C.L., Fall, R., Methanol emission from leaves (enzymatic detection of gas-phase methanol and relation of methanol fluxes to stomatal conductance and leaf development) (1995) Plant Physiol., 108, pp. 1359-1368Orfila, C., Knox, J.P., Spatial regulation of pectic polysaccharides in relation to pit fields in cell walls of tomato fruit pericarp (2000) Plant Physiol., 122, pp. 775-781Ozimek, P., Kotter, P., Veenhuis, M., van der Klei, I.J., Hansenula polymorpha and Saccharomyces cerevisiae Pex5p's recognize different, independent peroxisomal targeting signals in alcohol oxidase (2006) FEBS Lett., 580, pp. 46-50Ozimek, P., Veenhuis, M., van der Klei, I.J., Alcohol oxidase: a complex peroxisomal, oligomeric flavoprotein (2005) FEMS Yeast Res., 5, pp. 975-983Pelloux, J., Rusterucci, C., Mellerowicz, E.J., New insights into pectin methylesterase structure and function (2007) Trends Plant Sci., 12, pp. 267-277Penman, D., Britton, G., Hardwick, K., Collin, H.A., Isaac, S., Chitin as a measure of biomass of Crinipellis perniciosa, causal agent of witches' broom disease of Theobroma cacao (2000) Mycol. Res., 104, pp. 671-675Pereira, J.L., Ram, A., Figuereido, J.M., de Almeida, L.C., La primera aparición de la " Escoba de Bruja" en la principal región productora de cacao del Brasil (1989) Turrialba, 36, pp. 459-461Pfaffl, M.W., A new mathematical model for relative quantification in real-time RT-PCR (2001) Nucl. Acids Res., 29, pp. e45Rincones, J., Scarpari, L.M., Carazzolle, M.F., Mondego, J.M., Formighieri, E.F., Barau, J.G., Costa, G.G., Pereira, G.A., Differential gene expression between the biotrophic-like and saprotrophic mycelia of the Witches' broom pathogen Moniliophthora perniciosa (2008) Mol. Plant-Microbe Interact., 21, pp. 891-908Rio, M.C., de Oliveira, B.V., de Tomazella, D.P., Silva, J.A., Pereira, G.A., Production of calcium oxalate crystals by the basidiomycete Moniliophthora perniciosa, the causal agent of witches' broom disease of cacao (2008) Curr. Microbiol., 56, pp. 363-370Roggenkamp, R., Janowicz, Z., Stanikowski, B., Hollenberg, C.P., Biosynthesis and regulation of the peroxisomal methanol oxidase from the methylotrophic yeast Hansenula polymorpha (1984) Mol. Gen. Genet., 194, pp. 489-493Rozen, S., Skaletsky, H., Primer3 on the WWW for general users and for biologist programmers (2000) Methods Mol. Biol., 132, pp. 365-386Sahm, H., Wagner, F., Microbial assimilation of methanol. The ethanol- and methanol-oxidizing enzymes of the yeast Candida boidinii (1973) Eur. J. Biochem., 36, pp. 250-256Sakai, T., Sakamoto, T., Hallaert, J., Vandamme, E.J., Pectin, pectinase and protopectinase: production, properties, and applications (1993) Adv. Appl. Microbiol., 39, pp. 213-294Scarpari, L.M., Meinhardt, L.W., Mazzafera, P., Pomella, A.W., Schiavinato, M.A., Cascardo, J.C., Pereira, G.A., Biochemical changes during the development of Witches' broom: the most important disease of cocoa in Brazil caused by Crinipellis perniciosa (2005) J. Exp. Bot., 56, pp. 865-877Schlosser, D., Fahr, K., Karl, W., Wetzstein, H.G., Hydroxylated metabolites of 2,4-dichlorophenol imply a Fenton-type reaction in Gloeophyllum striatum (2000) Appl. Environ. Microbiol., 66, pp. 2479-2483Segers, G., Bradshaw, N., Archer, D., Blissett, K., Oliver, R.P., Alcohol oxidase is a novel pathogenicity factor for Cladosporium fulvum, but aldehyde dehydrogenase is dispensable (2001) Mol. Plant-Microbe Interact., 14, pp. 367-377Silva, S., Histologia da Interação Crinipellis perniciosa em Cacaueiros Suscetível e Resistente à Vassoura-de-Bruxa (1999) Fitopatol. Bras., 24, pp. 54-59Teixeira, P.J.P.L., Mondego, J.M.C., Pereira, G.A.G., A method for production of Moniliophthora perniciosa basidiospores in vitro Manuscript in preparationThomazella, D.P., Teixeira, P.J., Oliveira, H.C., Saviani, E.E., Rincones, J., Toni, I.M., Reis, O., Pereira, G.A., The hemibiotrophic cacao pathogen Moniliophthora perniciosa depends on a mitochondrial alternative oxidase for biotrophic development (2012) New PhytolTiburcio, R.A., Costa, G.G., Carazzolle, M.F., Mondego, J.M., Schuster, S.C., Carlson, J.E., Guiltinan, M.J., Pereira, G.A., Genes acquired by horizontal transfer are potentially involved in the evolution of phytopathogenicity in Moniliophthora perniciosa and Moniliophthora roreri, two of the major pathogens of cacao (2010) J. Mol. Evol., 70, pp. 85-97Valette-Collet, O., Cimerman, A., Reignault, P., Levis, C., Boccara, M., Disruption of Botrytis cinerea pectin methylesterase gene Bcpme1 reduces virulence on several host plants (2003) Mol. Plant-Microbe Interact., 16, pp. 360-367Van der Klei, I.J., Bystrykh, L.V., Harder, W., Alcohol oxidase from Hansenula polymorpha CBS 4732 (1990) Methods Enzymol., 188, pp. 420-427Veenhuis, M., Van Dijken, J.P., Harder, W., The significance of peroxisomes in the metabolism of one-carbon compounds in yeasts (1983) Adv. Microb. Physiol., 24, pp. 1-82Vidal, R.O., Mondego, J.M., Pot, D., Ambrosio, A.B., Andrade, A.C., Pereira, L.F., Colombo, C.A., Pereira, G.A., A high-throughput data mining of single nucleotide polymorphisms in Coffea species expressed sequence tags suggests differential homeologous gene expression in the allotetraploid Coffea arabica (2010) Plant Physiol., 154, pp. 1053-1066Waterham, H.R., Russell, K.A., Vries, Y., Cregg, J.M., Peroxisomal targeting, import, and assembly of alcohol oxidase in Pichia pastoris (1997) J. Cell Biol., 139, pp. 1419-1431Wierenga, R.K., Terpstra, P., Hol, W.G.J., Prediction of the occurrence of the ADP-binding βαβ-fold in proteins, using an amino acid sequence fingerprint (1986) J. Mol. Biol., 187, pp. 101-107Willats, W.G., Limberg, G., Buchholt, H.C., van Alebeek, G.J., Benen, J., Christensen, T.M., Visser, J., Knox, J.P., Analysis of pectic epitopes recognised by hybridoma and phage display monoclonal antibodies using defined oligosaccharides, polysaccharides, and enzymatic degradation (2000) Carbohydrate Res., 327, pp. 309-320Willats, W.G., McCartney, L., Mackie, W., Knox, J.P., Pectin: cell biology and prospects for functional analysis (2001) Plant Mol. Biol., 47, pp. 9-27Wymelenberg, A.V., Gaskell, J., Mozuch, M., Sabat, G., Ralph, J., Skyba, O., Mansfield, S.D., Cullen, D., Comparative transcriptome and secretome analysis of wood decay fungi Postia placenta and Phanerochaete chrysosporium (2010) Appl. Environ. Microbiol., 76, pp. 3599-3610Yurimoto, H., Komeda, T., Lim, C.R., Nakagawa, T., Kondo, K., Kato, N., Sakai, Y., Regulation and evaluation of five methanol-inducible promoters in the methylotrophic yeast Candida boidinii (2000) Biochim. Biophys. Acta, 1493, pp. 56-63Yurimoto, H., Oku, M., Sakai, Y., Yeast methylotrophy: metabolism, gene regulation and peroxisome homeostasis (2011) Int. J. Microbiol., 2011, p. 10129

Colletotrichum : tales of forcible entry, stealth, transient confinement and breakout

Taxonomy: Imperfect, anamorphic fungus (subdivision Deuteromycotina, form-class Deuteromycetes, form-subclass Coelomycetidae, form-order Melanconiales, form-family Melanconiaceae) with 39 'accepted' species [Sutton, B. C. (1992) The genus Glom-erella and its anamorph Colletotrichum. In: Colletotrichum: Biology, Pathology and Control (Bailey, J. A. and Leger, M. J., eds). Wallingford, UK: CAB International, pp. 1-26.] which continue to be revised and clarified by molecular taxonomic techniques. Species complexes and subspecific groups have been proposed. Host range: Species of Colletotrichum attack a large number of important tropical and sub-tropical crop species and cause economically significant diseases of cereals, grain legumes, vegetables, forage legumes, fruit crops and perennial crops. Tropical and sub-tropical fruit production is significantly affected by postharvest anthracnose. Disease symptoms: Symptoms of the attack are commonly known as anthracnose and comprise dark, sunken, lenticular necrotic lesions containing the acervuli of the pathogen. Key attractions: A model fungus for research on host specificity, mycoherbicides, appressorial melanization, appressorial function, quiescent infection, fungal lifestyles, intracellular hemibiotrophy and the determinants of the switch from biotrophy to necrotrophy among others. Useful websites: http://www.uark.edu/depts/plant/, http://www.sorghumanthracnose.org/, http:// www.iacr.bbscr.ac.uk/ppi/staff/roc_rc.htm