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Genome-Wide Analyses of Subtilisin-Like Serine Proteases on Solanum tuberosum

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Abstract

Plant subtilisin-like serine proteases or subtilases constitute a large expanded gene subfamily in potato. We identified 82 potato subtilases encoded by 74 genes. All subtilases present a characteristic S08 domain, and the majority of them have an association protein domain, an inhibition_I9 domain and a signal peptide that consists of a signal sequence for targeting to the secretory pathway. Phylogenetic studies revealed five subtilase groups named StSBT1 to StSBT5. A genome expansion of potato subtilase subfamily was reflected in two phylogenetic clusters, StSBT1 and StSBT4 both characterized by intronless genes in tandem arrays mainly in chromosome I and VIII. Twenty nine of the identified subtilases co-localize with six out of 24 metaQTLs related to late blight resistance previously described in potato. These metaQTLs includes subtilase genes up regulated in detached potato leaves inoculated with P. infestans, some of which are homologous to p69 subtilases genes from tomato.

Resumen

Las serin proteasas tipo subtilisinas o subtilasas constituyen una gran subfamilia de genes en papa. En este trabajo se identificaron 82 subtilasas codificadas por 74 genes. Todas las subtilasas presentan un dominio S08 característico, y la mayoría de ellas poseen un dominio asociado a proteasa, un dominio inhibidor I9 y un péptido señal que consiste en una señal que conduce a la vía secretora. En los estudios filogenéticos se describen cinco grupos de subtilasas nombrados de StSBT1 a StSBT5. La expansión en la subfamilia de subtilasas se ve reflejada en dos grupos,  StSBT1 y StSBT4, caracterizados por la presencia de genes sin intrones con disposición en tándem localizados en el cromosoma I y VIII. Veintinueve de las subtilasas identificadas co-localizan con seis de los 24 metaQTLs de resistencia a tizón tardío previamente descriptos en papa. Estos metaQTLs incluyen genes de subtilasas con regulación positiva en ensayos de hojas de papa desprendidas inoculadas con P. infestans, algunos de los cuáles son  homologos a genes de subtilasas p69 descriptos en tomate.

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Acknowledgments

This paper is submitted in partial fulfillment of Natalia Norero Doctoral degree at Facultad de Ciencias Agrarias, Universidad Nacional de Mar del Plata, Argentina. We thanks Gabriela Massa for fruitful discussions while working in the paper. This work was financed by the Instituto Nacional de Tecnología Agropecuaria (INTA), Ministerio de Tecnología e Innovación Productiva, Agencia Nacional de Promoción Científica y Tecnológica, PICT-2010-2037 and NN doctoral fellowship from Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET).

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  1. Laboratorio de Agrobiotecnología, Instituto Nacional de Tecnología Agropecuaria (INTA) EEA - Balcarce, Ruta 226, Km 73,5. C.C. 276, (7620), Balcarce, Argentina

    Natalia Sigrid Norero, Martin Alfredo Castellote & Sergio Enrique Feingold

  2. Instituto de Investigaciones Biológicas (IIB), Universidad Nacional de Mar del Plata (UNMdP), Dean Funes 3350. C.C. 722, (7600), Mar del Plata, Argentina

    Laura de la Canal

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  1. Natalia Sigrid Norero
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  2. Martin Alfredo Castellote
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  3. Laura de la Canal
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  4. Sergio Enrique Feingold
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Correspondence to Natalia Sigrid Norero or Sergio Enrique Feingold.

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ESM 1

HMMER2.3.2. profile (DOCX 28 kb)

ESM 2

Figure 1: HMMER logo used for potato subtilases identification. It was built with LogoMat-M (Schuster-Böckler et al. 2004) (PPT 412 kb)

ESM 3

HMMER2.3.2. output file. Subtilases identification on PGSC database. (DOC 117 kb)

ESM 4

HMMER2.3.2. output file. Subtilases identification on TAIR database. (XLS 33 kb)

ESM 5

Table 1: Specificity determining positions of StSBT groups. The table was obtained with SDPfox software (Mazin et al. 2010). (XLS 28 kb)

ESM 6

Table 2: Subcellular localization predictions of subtilases (DOC 175 kb)

ESM 7

Table 3: Potato subtilases and metaQTLs of late blight resistance localization in potato genome (PGSC V4.0, 2011). (DOC 110 kb)

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Norero, N.S., Castellote, M.A., de la Canal, L. et al. Genome-Wide Analyses of Subtilisin-Like Serine Proteases on Solanum tuberosum . Am. J. Potato Res. 93, 485–496 (2016). https://doi.org/10.1007/s12230-016-9525-5

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