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Genome-wide identification and characterization of seed storage proteins (SSPs) of foxtail millet (Setaria italica (L.) P. Beauv.)

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Abstract

We report the identification of 47 foxtail millet (Setaria italica (L.) P. Beauv.) seed storage proteins (SSPs) consisting of 14 albumins, 12 prolamins, 18 globulins and 3 glutelins using computational approaches and compared their essential amino acid composition with 225 SSPs of rice, barley, sorghum and maize. Comparative analysis revealed several unique foxtail millet SSPs containing high amounts of essential amino acids. These include three 2s-albumin proteins containing 11.9%, 10.9%, 9.82% lysine, one 10-kDa prolamin containing 20% methionine residues and one each 7S-globulin, 10-kDa prolamin, alpha-zein proteins containing 9.2% threonine, 9.35% phenylalanine and 2.5% tryptophan, respectively. High lysine containing albumins and high methionine containing prolamins were also detected in other cereals indicating that these SSPs are widespread in cereals. Phylogenetic studies revealed that the foxtail millet SSPs are closer to sorghum and maize. The lysine-rich albumins and the methionine-rich prolamins formed a separate cluster. Motif analysis of lysine-rich albumins displayed several lysine containing conserved motifs across cereals including foxtail millet. The 10-kDa prolamin protein containing 20% methionine was unique as it lacked the characteristic repeat motifs of methionine found in the high methionine containing zeins and kafirins. The motif “NPAAFWQQQQLL” was uniquely repeated in the foxtail millet high tryptophan prolamin protein. The findings of the present study provide new insights in foxtail millet seed storage protein characterization and their nutritional importance in terms of essential amino acid composition.

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Abbreviations

SSP:

Seed storage proteins

kDa:

Kilo Dalton

HMM:

Hidden Markov models

MEME:

Multiple Em for motif elicitation

RGAPD:

Rice Genome Annotation Project Database

Myr:

Million year

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Authors and Affiliations

  1. College of Agriculture, Waraseoni, Balaghat, JNKVV, Jabalpur, 481331, India

    Vikram Singh Gaur

  2. Division of Crop Improvement, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India

    Salej Sood

  3. Department of Plant Breeding and Genetics, JNKVV, Jabalpur, 482004, India

    Sharad Tiwari

  4. Department of Molecular Biology and Biotechnology, GB Pant University of Agriculture and Technology, Pantnagar, 263145, India

    Anil Kumar

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  1. Vikram Singh Gaur
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  2. Salej Sood
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  3. Sharad Tiwari
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  4. Anil Kumar
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Correspondence to Vikram Singh Gaur.

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Gaur, V.S., Sood, S., Tiwari, S. et al. Genome-wide identification and characterization of seed storage proteins (SSPs) of foxtail millet (Setaria italica (L.) P. Beauv.). 3 Biotech 8, 415 (2018). https://doi.org/10.1007/s13205-018-1431-8

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