A family of small cyclic amphipathic peptides (SCAmpPs) genes in citrus

Authors: Belknap, William; McCue, Kent; Harden, Leslie - Les; Vensel, William; Bausher, Michael; Stover, Eddie

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/25/2015
Publication Date: 4/16/2015
Citation: Belknap, W.R., Mc Cue, K.F., Harden, L.A., Vensel, W.H., Bausher, M.G., Stover, E.W. 2015. A family of small cyclic amphipathic peptides (SCAmpPs) genes in citrus. Genome. 16:303-313.

Interpretive Summary: There is an ongoing need to identify potential resistance genes to combat newly emerging diseases that threaten crop plants, and this is especially true of citrus which is currently being devastated by a bacterial disease (Huanglongbing, HLB). Towards this goal, we have identified a family of genes in citrus that code for small cyclic peptides called SCAmpPs. These genes have all the properties of many other plant defensive genes. They exist in duplicated clusters on the chromosome, they change very rapidly, they are turned on in response to stress, and they are associated with other disease-resistance gene types. The SCAmpPs genes code for a small peptide with only 50 amino acids and this peptide is further processed down to a 5-10 amino acid cyclic peptide product. The portion of the gene coding for the cyclic peptide is evolutionarily extremely unstable; it is hypervariable. Thus, the approximately 50 very different cyclic peptides currently encoded by this gene family can quickly (relative to other genes and proteins) change. We analyzed one cyclic product that accumulates to very high levels in the citrus phloem. This cyclic peptide (SCAmpPs-4) has properties very like the valinomycin class of antibiotics in that it is capable of shuttling potassium ions across a membrane. Thus, the SCAmpPs appear to encode a number of novel antibiotics that can be mobilized in response to wounding or infection to protect the plant. This research identifies a never before described class of potential resistance genes that can be utilized by citrus breeders and molecular biologists to improve the commodity.

Technical Abstract: A gene family of Small Cyclic Amphipathic Peptides (SCAmpPs) in citrus is described. The citrus genomes contain 100-150 SCAmpPs genes, approximately 50 of which are represented in the citrus EST database. These genes encode small '50 residue precursor proteins that are post-translationally processed, releasing 5-10 residue cyclic peptides. The structures of the SCAmpPs genes are highly conserved, with relatively extended untranslated regions and short coding domains interrupted by single introns. Some family members are very highly transcribed in specific citrus tissues, as determined by representation in tissue-specific cDNA libraries. Comparisons among ESTs of related SCAmpPs revealed an unexpected evolutionary profile suggestive of targeted mutagenesis of the cyclic peptide domain. The SCAmpPs genes are displayed in clusters on the citrus chromosomes, with apparent association with receptor leucine-rich repeat protein gene arrays. This study focuses on three SCAmpPs family members with high constitutive expression in citrus phloem. Unexpectedly high sequence conservation was observed in the promoter region of two phloem-expressed SCAmpPs that encode very distinct cyclic products. The processed cyclic product of one of these phloem peptides, SCAmpPs-4, was characterized by LC-MS analysis of phloem tissue, revealing properties of a K+ ionophore. The SCAmpPs amino acid composition, protein structure, expression patterns, evolutionary profile and chromosomal distribution are consistent with their proposed designation as ribosomally synthesized antimicrobial peptides. The discovery of a whole new class of potential resistance genes offers promise for combating pathogens that threaten the viability of the citrus industry.