WHIRLY1 Acts Upstream of ABA-Related Reprogramming of Drought-Induced Gene Expression in Barley and Affects Stress-Related Histone Modifications

Abstract

WHIRLY1, a small plant-specific ssDNA-binding protein, dually located in chloroplasts and the nucleus, is discussed to act as a retrograde signal transmitting a stress signal from the chloroplast to the nucleus and triggering there a stress-related gene expression. In this work, we investigated the function of WHIRLY1 in the drought stress response of barley, employing two overexpression lines (oeW1-2 and oeW1-15). The overexpression of WHIRLY1 delayed the drought-stress-related onset of senescence in primary leaves. Two abscisic acid (ABA)-dependent marker genes of drought stress, HvNCED1 and HvS40, whose expression in the wild type was induced during drought treatment, were not induced in overexpression lines. In addition, a drought-related increase in ABA concentration in the leaves was suppressed in WHIRLY1 overexpression lines. To analyze the impact of the gain-of-function of WHIRLY1 on the drought-related reprogramming of nuclear gene expression, RNAseq was performed comparing the wild type and an overexpression line. Cluster analyses revealed a set of genes highly up-regulated in response to drought in the wild type but not in the WHIRLY1 overexpression lines. Among these genes were many stress- and abscisic acid (ABA)-related ones. Another cluster comprised genes up-regulated in the oeW1 lines compared to the wild type. These were related to primary metabolism, chloroplast function and growth. Our results indicate that WHIRLY1 acts as a hub, balancing trade-off between stress-related and developmental pathways. To test whether the gain-of-function of WHIRLY1 affects the epigenetic control of stress-related gene expression, we analyzed drought-related histone modifications in different regions of the promoter and at the transcriptional start sites of HvNCED1 and HvS40. Interestingly, the level of euchromatic marks (H3K4me3 and H3K9ac) was clearly decreased in both genes in a WHIRLY1 overexpression line. Our results indicate that WHIRLY1, which is discussed to act as a retrograde signal, affects the ABA-related reprogramming of nuclear gene expression during drought via differential histone modifications.

Drought-Stress-Related Reprogramming of Gene Expression in Barley Involves Differential Histone Modifications at ABA-Related Genes

“…For barley, the levels of H3K4me3 are increased at the heat shock protein 17 (HSP17), whereas H3K9me2 is reduced [57]. Recently, overexpression analyses of the WHIRLY1 protein in drought-stressed barley leading to a decrease in H3K9ac and H3K4me3 levels at the ABA-related genes HvNCED1 and HvS40 revealed its possible regulatory role toward drought stress responses by interacting with epigenetic regulators [58]. There are further indications that the regulation of drought-stress-related genes is under epigenetic control.…”

Investigation of the morphological, physiological, biochemical, and catabolic characteristics and gene expression under drought stress in tolerant and sensitive genotypes of wild barley [Hordeum vulgare subsp. spontaneum (K. Koch) Asch. & Graebn.]

“…Several studies have identified differentially expressed genes in barley under drought stress [ 12 ]. Manh et al [ 13 ]found that overexpression of the WHIRLY1 gene in barley delayed the onset of senescence and suppressed expression of drought-related marker genes. Alamholo and Tarinejad [ 14 ] performed a meta-analysis of microarray data and identified numerous upregulated and downregulated genes related to drought tolerance in barley.…”

WHIRLY1 regulates aliphatic glucosinolate biosynthesis in early seedling development of Arabidopsis

“…Both genes function in leaf senescence (HUMBECK et al, 1996; Miao et al, 2004) and are proposed to be negatively regulated by WHIRLY1. In addition to functions in pathogen response and leaf senescence, WHIRLY proteins are involved in abiotic stress responses, e.g., drought, possibly acting via histone marker modulation at the promoter of stress-related genes including HvNCED1 (Janack et al, 2016a; Manh et al, 2023).…”