Christopher D. Rock

Abscisic Acid Signaling in Seeds and Seedlings

Abscisic acid (ABA) regulates many agronomically important aspects of plant development, including the synthesis of seed storage proteins and lipids, the promotion of seed desiccation tolerance and dormancy, and the inhibition of the phase transitions from embryonic to germinative growth and from

Modulation of Abscisic Acid Signal Transduction and Biosynthesis by an Sm-like Protein in Arabidopsis

The phytohormone abscisic acid (ABA) regulates plant growth and development as well as stress tolerance. The Arabidopsis sad1 (supersensitive to ABA and drought) mutation increases plant sensitivity to drought stress and ABA in seed germination, root growth, and the expression of some stress-responsive genes. sad1 plants are also defective in the positive feedback regulation of ABA biosynthesis genes by ABA and are impaired in drought stress induction of ABA biosynthesis. SAD1 encodes a polypeptide similar to multifunctional Sm-like snRNP proteins that are required for mRNA splicing, export, and degradation. These results suggest a critical role for mRNA metabolism in the control of ABA signaling as well as in the regulation of ABA homeostasis.

Abscisic Acid Biosynthesis and Response

Abscisic acid (ABA) is an optically active 15-C weak acid that was first identified in the early 1960s as a growth inhibitor accumulating in abscising cotton fruit (“abscisin II”) and leaves of sycamore trees photoperiodically induced to become dormant (“dormin”) (reviewed in Addicott, 1983). It has since been shown to regulate many aspects of plant growth and development including embryo maturation, seed dormancy, germination, cell division and elongation, and responses to environmental stresses such as drought, salinity, cold, pathogen attack and UV radiation (reviewed in Leung and Giraudat, 1998; Rock, 2000). However, despite the name, it does not appear to control abscission directly; the presence of ABA in abscising organs reflects its role in promoting senescence and/or stress responses, the processes preceding abscission. Although ABA has historically been thought of as a growth inhibitor, young tissues have high ABA levels, and ABA-deficient mutant plants are severely stunted (Figure 1) because their ability to reduce transpiration and establish turgor is impaired. Exogenous ABA treatment of mutants restores normal cell expansion and growth. Figure 1. Exogenous ABA suppresses growth inhibition of ABA-deficient mutants. Plants with one of three mutant alleles of aba1 were grown with (bottom) or without (top) ABA treatment (spraying twice weekly with 10 µM ABA for 8 weeks). (Photograph courtesy ... ABA is ubiquitous in lower and higher plants. It is also produced by some phytopathogenic fungi (Assante et al., 1977; Neill et al., 1982; Kitagawa et al., 1995) and has even been found in mammalian brain tissue (Le Page-Degivry et al., 1986). As a sesquiterpenoid, it was long thought to be synthesized directly from farnesyl pyrophosphate, as in fungi (reviewed in Zeevaart and Creelman, 1988). However, it is actually synthesized indirectly from carotenoids. As a weak acid (pKa=4.8), ABA is mostly uncharged when present in the relatively acidic apoplastic compartment of plants and can easily enter cells across the plasma membrane. The major control of ABA distribution among plant cell compartments follows the “anion trap” concept: the dissociated (anion) form of this weak acid accumulates in alkaline compartments (e.g. illuminated chloroplasts) and may redistribute according to the steepness of the pH gradients across membranes. In addition to partitioning according to the relative pH of compartments, specific uptake carriers contribute to maintaining a low apoplastic ABA concentration in unstressed plants. Despite the ease with which ABA can enter cells, there is evidence for extracellular as well as intracellular perception of ABA (reviewed in Leung and Giraudat, 1998; Rock, 2000). Multiple receptor types are also implicated by the variation in stereospecificity among ABA responses. Genetic studies, especially in Arabidopsis, have identified many loci involved in ABA synthesis and response and analyzed their functional roles in ABA physiology (reviewed in Leung and Giraudat, 1998; Rock, 2000). Many likely signaling intermediates correlated with ABA response (e.g. ABA-activated or -induced kinases and DNA-binding proteins that specifically bind ABA-responsive promoter elements) have also been identified by molecular and biochemical studies, but the relationships among these proteins are unclear. Cell biological studies have identified secondary messengers involved in ABA response. Ongoing studies combine these approaches in efforts to determine coherent models of ABA signaling mechanism(s).

Redundant and distinct functions of the ABA response loci ABA- INSENSITIVE(ABI)5 and ABRE-BINDING FACTOR (ABF)3

Abscisic acid-responsive gene expression is regulated by numerous transcription factors, including a subgroup of basic leucine zipper factors that bind to the conserved cis-acting sequences known as ABA-responsive elements. Although one of these factors, ABA-insensitive 5 (ABI5), was identified genetically, the paucity of genetic data for the other family members has left it unclear whether they perform unique functions or act redundantly to ABI5 or each other. To test for potential redundancy with ABI5, we identified the family members with most similar effects and interactions in transient expression systems (ABF3 and ABF1), then characterized loss-of-function lines for those loci. The abf1 and abf3 monogenic mutant lines had at most minimal effects on germination or seed-specific gene expression, but the enhanced ABA- and stress-resistance of abf3 abi5 double mutants revealed redundant action of these genes in multiple stress responses of seeds and seedlings. Although ABI5, ABF3, and ABF1 have some overlapping effects, they appear to antagonistically regulate each other’s expression at specific stages. Consequently, loss of any one factor may be partially compensated by increased expression of other family members.

Hydrogen peroxide is a common signal for darkness- and ABA-induced stomatal closure in Pisum sativum

The requirement for hydrogen peroxide (H2O2) generation and action during stomatal closure induced by darkness and abscisic acid (ABA) was investigated in pea (Pisum sativum L.). Stomatal closure induced by darkness or ABA was inhibited by the H2O2-scavenging enzyme catalase or the antioxidant N-acetyl cysteine (NAC), or by diphenylene iodonium (DPI), an inhibitor of the H2O2-generating enzyme NADPH oxidase. Exogenous H2O2 induced stomatal closure in a dose- and time-dependent manner, and H2O2 was also required for ABA-inhibition of stomatal opening in the light. H2O2 accumulation in guard cells was increased by darkness or ABA, as assessed with the fluorescent dye dichlorodihydrofluorescein diacetate (H2-DCFDA) and confocal microscopy. Such increases were inhibited by catalase, NAC or DPI, consistent with the effects of these compounds on stomatal apertures. Employing polymerase chain reaction (PCR) with degenerate oligonucleotide primers, several NADPH oxidase homologues were identified from pea genomic DNA that had substantial identity to the Arabidopsis thaliana (L.) Heynh. rboh (respiratory burst oxidase homologue) genes. Furthermore, an antibody raised against the tomato rboh identified immunoreactive proteins in epidermal, mesophyll and guard cells.

An autoregulatory feedback loop involving PAP1 and TAS4 in response to sugars in Arabidopsis

AbstractmiR828 in Arabidopsis triggers the cleavage of Trans-Acting SiRNA Gene 4 (TAS4) transcripts and production of small interfering RNAs (ta-siRNAs). One siRNA, TAS4-siRNA81(−), targets a set of MYB transcription factors including PAP1, PAP2, and MYB113 which regulate the anthocyanin biosynthesis pathway. Interestingly, miR828 also targets MYB113, suggesting a close relationship between these MYBs, miR828, and TAS4, but their evolutionary origins are unknown. We found that PAP1, PAP2, and TAS4 expression is induced specifically by exogenous treatment with sucrose and glucose in seedlings. The induction is attenuated in abscisic acid (ABA) pathway mutants, especially in abi3-1 and abi5-1 for PAP1 or PAP2, while no such effect is observed for TAS4. PAP1 is under regulation by TAS4, demonstrated by the accumulation of PAP1 transcripts and anthocyanin in ta-siRNA biogenesis pathway mutants. TAS4-siR81(−) expression is induced by physiological concentrations of Suc and Glc and in pap1-D, an activation-tagged line, indicating a feedback regulatory loop exists between PAP1 and TAS4. Bioinformatic analysis revealed MIR828 homologues in dicots and gymnosperms, but only in one basal monocot, whereas TAS4 is only found in dicots. Consistent with this observation, PAP1, PAP2, and MYB113 dicot paralogs show peptide and nucleotide footprints for the TAS4-siR81(−) binding site, providing evidence for purifying selection in contrast to monocots. Extended sequence similarities between MIR828, MYBs, and TAS4 support an inverted duplication model for the evolution of MIR828 from an ancestral gymnosperm MYB gene and subsequent formation of TAS4 by duplication of the miR828* arm. We obtained evidence by modified 5′-RACE for a MYB mRNA cleavage product guided by miR828 in Pinus resinosa. Taken together, our results suggest that regulation of anthocyanin biosynthesis by TAS4 and miR828 in higher plants is evolutionarily significant and consistent with the evolution of TAS4 since the dicot—monocot divergence.

Crosstalk between ABA and auxin signaling pathways in roots of Arabidopsis thaliana (L.) Heynh.

Studies of abscisic acid (ABA) and auxin have revealed that these pathways impinge on each other. The Daucus carota (L.) Dc3 promoter: uidA (β-glucuronidase: GUS) chimaeric reporter (ProDc3:GUS) is induced by ABA, osmoticum, and the auxin indole-3-acetic acid (IAA) in vegetative tissues of transgenic Arabidopsis thaliana (L.) Heynh. Here, we describe the root tissue-specific expression of ProDc3:GUS in the ABA-insensitive-2 (abi2-1), auxin-insensitive-1 (aux1), auxin-resistant-4 (axr4), and rooty (rty1) mutants of Arabidopsis in response to ABA, IAA and synthetic auxins naphthalene acetic acid (NAA), and 2, 4-(dichlorophenoxy) acetic acid. Quantitative analysis of ProDc3:GUS expression showed that the abi2-1 mutant had reduced GUS activity in response to ABA, IAA, or 2, 4-d, but not to NAA. Similarly, chromogenic staining of ProDc3:GUS activity showed that the aux1 and axr4 mutants gave predictable hypomorphic ProDc3:GUS expression phenotypes in roots treated with IAA or 2, 4-d, but not the diffusible auxin NAA. Likewise the rty mutant, which accumulates auxin, showed elevated ProDc3:GUS expression in the absence or presence of hormones relative to wild type. Interestingly, the aux1 and axr4 mutants showed a hypomorphic effect on ABA-inducible ProDc3:GUS expression, demonstrating that ABA and IAA signaling pathways interact in roots. Possible mechanisms of crosstalk between ABA and auxin signaling are discussed.

The genes ABI1 and ABI2 are involved in abscisic acid- and drought-inducible expression of the Daucus carota L. Dc3 promoter in guard cells of transgenic Arabidopsis thaliana (L.) Heynh.

Abstract. The ABA INSENSITIVE1 (ABI1) and ABI2 genes encode homologous type-2C protein phosphatases with redundant yet distinct functions in abscisic acid (ABA) responses. Results from Northern blot analysis showed that ABA- and mannitol-inducible expression of the COR47 and COR78/LTI78/RD29A (COR78) genes was more impaired in the abi2 mutant of Arabidopsis thaliana (L.) Heynh than in the abi1 mutant. Furthermore, ABA-plus-mannitol treatments were additive towards COR47 gene expression; however, the ABA-deficient aba1 mutant showed reduced COR expression relative to the wild type in response to mannitol and ABA-plus-mannitol treatments. These results support the notion that drought- and ABA-signalling pathways are separate yet overlapping. To facilitate quantitative analysis of the genetic control of tissue-specific ABA- and desiccation-response pathways, we analyzed ABA- and mannitol-inducible expression of a carrot (Daucus carota L.) Dc3 promoter:uidA (β-glucuronidase; GUS) chimaeric reporter (Dc3-GUS) in transgenic wild-type, ABA-deficient aba1, and ABA-insensitive abi1 and abi2 mutants. The Dc3 promoter directed ABA- and mannitol-inducible GUS expression in Arabidopsis guard cells and the two treatments were additive. The aba1, abi1, and abi2 mutant genotypes had reduced GUS expression in guard cells of cotyledons in response to mannitol, whereas abi1 and abi2 mutants were reduced in ABA-inducible GUS expression, consistent with overlapping ABA- and drought-response pathways. Quantitative fluorometric GUS assays of leaf extracts showed that abi2 mutants responded less to exogenous ABA than did abi1 mutants, and abi2 mutants responded more to mannitol than did abi1 mutants. We conclude that Dc3-GUSArabidopsis is a tractable system in which to study tissue-specific ABA and drought signalling and suggest that ABI2 functions predominantly over ABI1 in COR78 and COR47 gene expression and guard-cell Dc3-GUS expression.

MIR846 and MIR842 comprise a cistronic MIRNA pair that is regulated by abscisic acid by alternative splicing in roots of Arabidopsis

MicroRNAs (miRNAs) are ~21-nucleotide long endogenous small RNAs that regulate gene expression through post-transcriptional or transcriptional gene silencing and/or translational inhibition. miRNAs can arise from the “exon” of a MIRNA gene, from an intron (e.g. mirtrons in animals), or from the antisense strand of a protein coding gene (natural antisense microRNAs, nat-miRNAs). Here we demonstrate that two functionally related miRNAs, miR842 and miR846, arise from the same transcription unit but from alternate splicing isoforms. miR846 is expressed only from Isoform1 while in Isoforms2 and -3, a part of pre-miR846 containing the miRNA* sequence is included in the intron. The splicing of the intron truncates the pre-MIRNA and disrupts the expression of the mature miR846. We name this novel phenomenon splicing-regulated miRNA. Abscisic acid (ABA) is shown to mediate the alternative splicing event by reducing the functional Isoform1 and increasing the non-functional Isoform3, thus repressing the expression of miR846 concomitant with accumulation of an ABA-inducible target jacalin At5g28520 mRNA, whose cleavage was shown by modified 5′-RACE. This regulation shows the functional importance of splicing-regulated miRNA and suggests possible mechanisms for altered ABA response phenotypes of miRNA biogenesis mutants. Arabidopsis lyrata-MIR842 and Aly-MIR846 have conserved genomic arrangements with A. thaliana and candidate target jacalins, similar primary transcript structures and intron processing, and better miRNA–miRNA* pairings, suggesting that the interactions between ABA, MIR842, MIR846 and jacalins are similar in A. lyrata. Together, splicing-regulated miRNAs, nat-miRNAs/inc-miRNAs and mirtrons illustrate the complexity of MIRNA genes, the importance of introns in the biogenesis and regulation of miRNAs, and raise questions about the processes and molecular mechanisms that drive MIRNA evolution.

Evidence for antisense transcription associated with microRNA target mRNAs in arabidopsis

Antisense transcription is a pervasive phenomenon, but its source and functional significance is largely unknown. We took an expression-based approach to explore microRNA (miRNA)-related antisense transcription by computational analyses of published whole-genome tiling microarray transcriptome and deep sequencing small RNA (smRNA) data. Statistical support for greater abundance of antisense transcription signatures and smRNAs was observed for miRNA targets than for paralogous genes with no miRNA cleavage site. Antisense smRNAs were also found associated with MIRNA genes. This suggests that miRNA-associated “transitivity” (production of small interfering RNAs through antisense transcription) is more common than previously reported. High-resolution (3 nt) custom tiling microarray transcriptome analysis was performed with probes 400 bp 5′ upstream and 3′ downstream of the miRNA cleavage sites (direction relative to the mRNA) for 22 select miRNA target genes. We hybridized RNAs labeled from the smRNA pathway mutants, including hen1-1, dcl1-7, hyl1-2, rdr6-15, and sgs3-14. Results showed that antisense transcripts associated with miRNA targets were mainly elevated in hen1-1 and sgs3-14 to a lesser extent, and somewhat reduced in dcl11-7, hyl11-2, or rdr6-15 mutants. This was corroborated by semi-quantitative reverse transcription PCR; however, a direct correlation of antisense transcript abundance in MIR164 gene knockouts was not observed. Our overall analysis reveals a more widespread role for miRNA-associated transitivity with implications for functions of antisense transcription in gene regulation. HEN1 and SGS3 may be links for miRNA target entry into different RNA processing pathways.