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Alt a 1 Allergen Homologs from Alternaria and Related Taxa: Analysis of Phylogenetic Content and Secondary Structure

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Alt a 1 Allergen Homologs from Alternaria and Related Taxa: Analysis of Phylogenetic Content and Secondary Structure Fungal Genetics and Biology 42 (2005) 119–129 www.elsevier.com/locate/yfgbi Alt a 1 allergen homologs from Alternaria and related taxa: analysis of phylogenetic content and secondary structure Soon Gyu Honga, Robert A. Cramerb, Christopher B. Lawrenceb,1, Barry M. Pryora,¤ a Division of Plant Pathology and Microbiology, Department of Plant Sciences, College of Agriculture, University of Arizona, Tucson, AZ 85721, USA b Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177, USA Received 31 March 2004; accepted 9 October 2004 Available online 25 November 2004 Abstract A gene for the Alternaria major allergen, Alt a 1, was ampliWed from 52 species of Alternaria and related genera, and sequence information was used for phylogenetic study. Alt a 1 gene sequences evolved 3.8 times faster and contained 3.5 times more parsi- mony-informative sites than glyceraldehyde-3-phosphate dehydrogenase (gpd) sequences. Analyses of Alt a 1 gene and gpd exon sequences strongly supported grouping of Alternaria spp. and related taxa into several species-groups described in previous studies, especially the infectoria, alternata, porri, brassicicola, and radicina species-groups and the Embellisia group. The sonchi species- group was newly suggested in this study. Monophyly of the Nimbya group was moderately supported, and monophyly of the Ulocla- dium group was weakly supported. Relationships among species-groups and among closely related species of the same species-group were not fully resolved. However, higher resolution could be obtained using Alt a 1 sequences or a combined dataset than using gpd sequences alone. Despite high levels of variation in amino acid sequences, results of in silico prediction of protein secondary structure for Alt a 1 demonstrated a high degree of structural similarity for most of the species suggesting a conservation of function. 2004 Elsevier Inc. All rights reserved. Keywords: Alternaria; Phylogenetics; Alt a 1 allergen; Secondary structute; gpd 1. Introduction known function in fungal metabolism or ecology (Bar- nes et al., 1996; De Vouge et al., 1996). Recently, a homo- Alternaria alternata is considered one of the most pro- log of the gene was found to be highly up-regulated liWc producers of fungal allergens. Many allergens pro- during the infection process of Alternaria brassicicola on duced are proteins such as enolase, ribosomal proteins, Arabidopsis thaliana, suggesting the gene may be nuclear transport factor, and aldehyde dehydrogenase, involved in plant pathogenicity (Cramer and Lawrence, which induce allergenic responses in humans (Achatz 2003, 2004). A comparison between Alt a 1 homologs of et al., 1995; Simon-Nobbe et al., 2000; Weichel et al., A. alternata and A. brassicicola revealed greater 2003). However, the biological functions of many other sequence divergence than that found in similar compari- allergenic proteins are unknown (Achatz et al., 1995; De sons of other ribosomal and protein-coding genes such Vouge et al., 1996). For example, the major allergen as the internal transcribed spacer (ITS) and mitochon- produced by A. alternata, Alt a 1, is a protein with no drial small subunit (mt SSU) rDNA, and glyceralde- hyde-3-phosphate dehydrogenase (gpd) for the same two species (92% similarity vs. 96, 99, and 97%, respectively) * Corresponding author. Fax: +1 520 621 9290. E-mail address: [email protected] (B.M. Pryor). (Cramer and Lawrence, 2003; Pryor and Bigelow, 2003). 1 Present address: Virginia Bioinformatics Institute, 1180 Pratt This level of sequence variation is worth noting, given Drive, Research Building XV, Blacksburg, VA 24061, USA. the role the corresponding protein may play in human 1087-1845/$ - see front matter 2004 Elsevier Inc. All rights reserved. doi:10.1016/j.fgb.2004.10.009 120 S.G. Hong et al. / Fungal Genetics and Biology 42 (2005) 119–129 allergenic responses as well as potential roles in fungal Table 1 pathogenicity. If Alt a 1 homologs are present in other Isolates used in this study, their sources, and GenBank accession num- related species, the gene may be useful in reconstructing bers for sequences used in phylogenetic analyses phylogenetic relationships among Alternaria and related Species name Source GenBank accession taxa. Furthermore, an analysis of nucleotide and amino Alt-a1 gpd acid conservation of Alt a 1 homologs might be valuable A. alternata EGS 34-016 AY563301 AY278808 in understanding the evolution of this gene and its A. arborescens EGS 39-128 AY563303 AY278810 potential role in fungal biology. A. argyranthemi EGS 43-033 AY563280 AY562400 Phylogenetic relationships among Alternaria and A. blumeae EGS 40-149 AY563291 AY562405 A. brassicae BMP 0322 AY563309 AY562414 related species of Ulocladium, Embellisia, and Nimbya A. brassicicola EEB 2232 AY563311 AY278813 have been established based on analysis of ITS, mt SSU, A. capsici EGS 45-075 AY563298 AY562408 and gpd sequences (Chou and Wu, 2002; de Hoog and A. carontiincultae EGS 26-010 AY563287 AY278798 Horre, 2002; Pryor and Bigelow, 2003; Pryor and Gilb- A. cetera EGS 41-072 AY563278 AY562398 ertson, 2000). In these studies, it was revealed that the A. cheiranthi EGS 41-188 AY563290 AY278802 A. cinerariae EGS 33-169 AY563308 AY562413 four genera composed a large monophyletic Alternaria- A. conjuncta EGS 37-139 AY563281 AY562401 Nimbya-Embellisia-Ulocladium clade with Stemphylium A. crassa DDG Acr1 AY563293 AY278804 as the sister taxon. It was also revealed that Alternaria, A. cucumerina BMP 0188 AY563300 AY562409 Embellisia, and Ulocladium are polyphyletic, and eight A. dauci ATCC 36613 AY563292 AY278803 species-groups were proposed based on monophyletic A. dumosa EGS 45-007 AY563305 AY562410 A. eryngii EGS 41-005 AY563313 AY562416 relationships. Most of the species-groups were supported A. ethzedia EGS 37-143 AY563284 AY278795 by high bootstrap values, especially the alternata, infec- A. euphorbiicola EGS 42-049 AY563314 AY562417 toria, porri, and radicina species-groups. However, rela- A. japonica ATCC 13618 AY563312 AY278814 tionships among species-group and among closely A. limoniasperae EGS 45-100 AY563306 AY562411 related species were not clearly resolved. To develop a A. longipes EGS 30-033 AY563304 AY278811 A. macrospora DDG Am1 AY563294 AY278805 more robust phylogeny of Alternaria and related taxa, A. metachromatica EGS 38-132 AY563285 AY562404 additional analyses incorporating more variable genetic A. mimicula EGS 01-056 AY563310 AY562415 loci are required. A. mouchaccae EGS 31-061 AY563279 AY562399 The objectives of this study were to determine if Alt a A. oregonensis EGS 29-194 AY563283 AY562403 1 gene homologs are present in other Alternaria spp. and A. petroselini EGS 09-159 AY563288 AY278799 A. photistica EGS 35-172 AY563282 AY562402 related taxa, and to assess their potential phylogenetic A. porri ATCC 58175 AY563296 AY278806 content. In addition, the secondary structure of Alt a 1 A. pseudorostrata EGS 42-060 AY563295 AY562406 homologs was predicted in silico to assess structural con- A. radicina ATCC 96831 AY563286 AY278797 servation, which may provide additional clues for assess- A. solani ATCC 58177 AY563299 AY278807 ing biological function and stimulation of allergenic A. sonchi EGS 46-051 AY563307 AY562412 A. smyrniii EGS 37-093 AY563289 AY278801 response. A. tagetica EGS 44-044 AY563297 Y562407 A. tenuissima EGS 34-015 AY563302 AY278809 E. allii EGS 38-073 AY563322 AY278827 2. Materials and methods E. indefessa EGS 30-195 AY563323 AY278828 E. novae-zelandiae EGS 39-099 AY563324 AY278831 2.1. Fungal strains, DNA extraction, PCR ampliWcation, E. telluster EGS 33-026 AY563325 AY562419 sequencing, and alignment N. caricis EGS 13-094 AY563321 AY278826 N. scirpicola EGS 19-016 AY563320 AY278825 P. herbarum ATCC 11681 AY563277 AY278823 Thirty-seven species of Alternaria, four species of S. botryosum ATCC 42170 AY563274 AY278820 Embellisia, two species of Nimbya, Wve species of Ulocla- S. callistephi EEB 1055 AY563276 AY278822 dium, three species of Stemphylium, and Pleospora herba- S. vesicarium ATCC 18521 AY563275 AY278821 rum (a teleomorph of Stemphylium) were used in this U. alternariae BMP 0352 AY563316 AY278815 U. atrum ATCC 18040 AY563318 AY278818 study (Table 1). All isolates were cultured on 0.05£ U. botrytis ATCC 18043 AY563317 AY278817 potato dextrose agar (PDA, Pryor and Michailides, U. chartarum ATCC 18044 AY563319 AY278819 2002) and diagnostic morphology was conWrmed. U. cucurbitae EGS 31-021 AY563315 AY562418 DNA extraction and puriWcations were conducted Abbreviations for source: ATCC, American Type Culture Collection, according to the previously described protocols (Pryor Manassas, VA 20108; BMP, B. M. Pryor, Division of Plant Pathology and Gilbertson, 2000). AmpliWcation of gpd genes was and Microbiology, Department of Plant Sciences, University of Ari- conducted according to previously described protocols zona, Tucson, AZ 85721; DGG, D. G. Gilchrist, Department of Plant W Pathology, University of California, Davis, CA 95616; EEB, E. E. But- (Berbee et al., 1999). Ampli cation of Alt a 1 genes was ler, Department of Plant Pathology, University of California, Davis, conducted using primers Alt-for (5Ј-ATGCAGTTCAC CA 95616; EGS, E. G. Simmons, Mycological Services, Crawfords- CACCATCGC-3Ј) and Alt-rev (5Ј-ACGAGGGTGAY ville, IN 47933. S.G. Hong et al. / Fungal Genetics and Biology 42 (2005) 119–129 121 using the TrN + I + G model, which was deduced as the best Wt for the data by the likelihood ratio test using MODELTEST ver3.06 (Posada and Crandall, 1998). Distance-based trees were reconstructed by the neigh- Fig. 1. Alt a 1 gene structure of Alternaria alternata (534 bp) and posi- bor-joining method (Saitou and Nei, 1987) from data tion of primers used in PCR ampliWcation. Alt-for and Alt-rev primers matrixes calculated using Kimura’s 2-parameter model were located at 1–20 and 493–512 nt positions, respectively. (Kimura, 1980). Sequence of Stemphylium spp. and P. herbarum were used as outgroups based on results from GTAGGCGTC-3Ј), which were designed based on the previous studies (Pryor and Bigelow, 2003; Pryor and conserved regions of A.
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