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Amplification of prolamin storage protein genes in different subfamilies of the Poaceae

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Abstract

Prolamins are seed storage proteins in cereals and represent an important source of essential amino acids for feed and food. Genes encoding these proteins resulted from dispersed and tandem amplification. While previous studies have concentrated on protein sequences from different grass species, we now can add a new perspective to their relationships by asking how their genes are shared by ancestry and copied in different lineages of the same family of species. These differences are derived from alignment of chromosomal regions, where collinearity is used to identify prolamin genes in syntenic positions, also called orthologous gene copies. New or paralogous gene copies are inserted in tandem or new locations of the same genome. More importantly, one can detect the loss of older genes. We analyzed chromosomal intervals containing prolamin genes from rice, sorghum, wheat, barley, and Brachypodium, representing different subfamilies of the Poaceae. The Poaceae commonly known as the grasses includes three major subfamilies, the Ehrhartoideae (rice), Pooideae (wheat, barley, and Brachypodium), and Panicoideae (millets, maize, sorghum, and switchgrass). Based on chromosomal position and sequence divergence, it becomes possible to infer the order of gene amplification events. Furthermore, the loss of older genes in different subfamilies seems to permit a faster pace of divergence of paralogous genes. Change in protein structure affects their physical properties, subcellular location, and amino acid composition. On the other hand, regulatory sequence elements and corresponding transcriptional activators of new gene copies are more conserved than coding sequences, consistent with the tissue-specific expression of these genes.

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Acknowledgments

The research described in this manuscript was supported by the Selman A. Waksman Chair in Molecular Genetics and a grant from the DOE (# DE-FG05-95ER20194) to JM. The Brachypodium sequence data was produced by the US Department of Energy Joint Genome Institute http://www.jgi.doe.gov/.

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  1. Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ, 08854, USA

    Jian-Hong Xu & Joachim Messing

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  1. Jian-Hong Xu
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Correspondence to Joachim Messing.

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Communicated by J. Snape.

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Supplemental Figure 1.

Sequence alignments of orthologous regions of prolamins Ory10 (A, B), Ory13a (C), and Ory16 (D) between rice and sorghum. Prolamins are showed in red colors, and conserved genes in black colors (PDF 198 kb)

Supplemental Figure 2.

Amino acid sequence alignment of all prolamins from rice, sorghum, maize, wheat, barley, rye, Brachypodium with MAFFT program (Katoh and Toh 2008) with manually modified, repetitive domains of all prolamins are deleted, and S-poor prolamins (omega-gliadin, omega-secalin and B-hordein) are removed for analysis because of their most totally repetitive DNA. See Fig. 4 for details (PDF 169 kb)

Supplemental Figure 3.

Amino acid sequence alignment of HMW-like prolamin genes and related protein genes with MAFFT program (Katoh and Toh 2008) (PDF 55 kb)

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Xu, JH., Messing, J. Amplification of prolamin storage protein genes in different subfamilies of the Poaceae . Theor Appl Genet 119, 1397–1412 (2009). https://doi.org/10.1007/s00122-009-1143-x

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