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Rapid sequence and functional diversification of a miRNA superfamily targeting calcium signaling components in seed plants
Author(s) -
Attri Komal,
Zhang Zijie,
Singh Atinder,
Sharrock Robert A.,
Xie Zhixin
Publication year - 2022
Publication title -
new phytologist
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.742
H-Index - 244
eISSN - 1469-8137
pISSN - 0028-646X
DOI - 10.1111/nph.18185
Subject(s) - biology , arabidopsis , genetics , gene silencing , microrna , conserved sequence , gene , mutant , computational biology , peptide sequence
Summary MicroRNA (miRNA)‐directed posttranscriptional gene silencing (miR‐PTGS) is an integral component of gene regulatory networks governing plant development and responses to the environment. The sequence homology between Sly‐miR4376, a miRNA common to Solanaceae and reported to target autoinhibited Ca 2+ ‐ATPase 10 ( ACA10 ) messenger RNA (mRNA) in tomato, and Arabidopsis miR391 (Ath‐miR391), previously annotated as a nonconserved member of the deeply conserved miR390 family, has prompted us to revisit the function of Ath‐miR391, as well as its regulatory conservation. A combination of genetic, molecular, and bioinformatic analyses revealed a hidden conservation for miR‐PTGS of ACA10 homologs in spermatophytes. We found that the Arabidopsis ACA10 mRNA undergoes miR391‐directed cleavage in vivo . Furthermore, transgenic overexpression of miR391 recapitulated the compact inflorescence ( cif ) phenotypes characteristic of ACA10 loss‐of‐function mutants, due to miR391‐directed PTGS of ACA10 . Significantly, comprehensive data mining revealed robust evidence for widespread PTGS of ACA10 homologs directed by a superfamily of related miRNAs sharing a conserved sequence core. Intriguingly, the ACA‐targeting miRNAs in Poaceae also direct PTGS for calmodulin‐like proteins which are putative Ca 2+ sensors. The PTGS of ACA10 homologs is therefore directed by a miRNA superfamily that is of ancient origin and has undergone rapid sequence diversification associated with functional innovation.