title: The chloroplast RNA helicase ISE2 is required for multiple chloroplast RNA processing steps in Arabidopsis thaliana.
abstract: INCREASED SIZE EXCLUSION LIMIT2 (ISE2) is a chloroplast-localized RNA helicase that is indispensable for proper plant development. Chloroplasts in leaves with reduced ISE2 expression have previously been shown to exhibit reduced thylakoid contents and increased stromal volume, indicative of defective development. It has recently been reported that ISE2 is required for the splicing of group II introns from chloroplast transcripts. The current study extends these findings, and presents evidence for ISE2's role in multiple aspects of chloroplast RNA processing beyond group II intron splicing. Loss of ISE2 from Arabidopsis thaliana leaves resulted in defects in C-to-U RNA editing, altered accumulation of chloroplast transcripts and chloroplast-encoded proteins, and defective processing of chloroplast ribosomal RNAs. Potential ISE2 substrates were identified by RNA immunoprecipitation followed by next-generation sequencing (RIP-seq), and the diversity of RNA species identified supports ISE2's involvement in multiple aspects of chloroplast RNA metabolism. Comprehensive phylogenetic analyses revealed that ISE2 is a non-canonical Ski2-like RNA helicase that represents a separate sub-clade unique to green photosynthetic organisms, consistent with its function as an essential protein. Thus ISE2's evolutionary conservation may be explained by its numerous roles in regulating chloroplast gene expression.
authors.affiliation: Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA.
authors.forename: Krzysztof
authors.initials: K
authors.lastname: Bobik
authors.affiliation: School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA.
authors.forename: Tyra N
authors.initials: TN
authors.lastname: McCray
authors.affiliation: School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA.
authors.forename: Ben
authors.initials: B
authors.lastname: Ernest
authors.affiliation: Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA.
authors.forename: Jessica C
authors.initials: JC
authors.lastname: Fernandez
authors.affiliation: Plant Energy Biology, ARC Center of Excellence, University of Western Australia, Perth, Australia.
authors.forename: Katharine A
authors.identifier: http://orcid.org/0000-0002-5044-0034
authors.initials: KA
authors.lastname: Howell
authors.affiliation: Department of Entomology and Plant Pathology, University of Tennessee Institute of Agriculture, Knoxville, TN, 37996, USA.
authors.forename: Thomas
authors.initials: T
authors.lastname: Lane
authors.affiliation: School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA.|Department of Entomology and Plant Pathology, University of Tennessee Institute of Agriculture, Knoxville, TN, 37996, USA.
authors.forename: Margaret
authors.initials: M
authors.lastname: Staton
authors.affiliation: Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA.|School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA.
authors.forename: Tessa M
authors.identifier: http://orcid.org/0000-0002-5994-4343
authors.initials: TM
authors.lastname: Burch-Smith
mesh_terms: D017360:Arabidopsis / Q000201:enzymology* / Q000235:genetics / Q000378:metabolism*; D002736:Chloroplasts / Q000235:genetics / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D007438:Introns / Q000235:genetics; D031425:Plasmodesmata / Q000378:metabolism; D017393:RNA Editing / Q000235:genetics; D020365:RNA Helicases / Q000235:genetics / Q000378:metabolism*; D018747:RNA, Chloroplast / Q000378:metabolism*
chemical_list: D018747:RNA, Chloroplast; D020365:RNA Helicases
keywords: Arabidopsis thaliana; ISE2, group II intron; RNA editing; RNA helicase; chloroplast; plasmodesmata; ribosome; splicing