Two RNA binding proteins, HEN4 and HUA1, act in the processing of AGAMOUS pre-mRNA in Arabidopsis thaliana

Abstract

AGAMOUS, a key player in floral morphogenesis, specifies reproductive organ identities and regulates the timely termination of stem cell fates in the floral meristem. Here, we report that strains carrying mutations in three genes, HUA1, HUA2, and HUA ENHANCER4 (HEN4), exhibit floral defects similar to those in agamous mutants: reproductive-to-perianth organ transformation and loss of floral determinacy. HEN4 codes for a K homology (KH) domain-containing, putative RNA binding protein that interacts with HUA1, a CCCH zinc finger RNA binding protein in the nucleus. We show that HUA1 binds AGAMOUS pre-mRNA in vitro and that HEN4, HUA1, and HUA2 act in floral morphogenesis by specifically promoting the processing of AGAMOUS pre-mRNA. Our studies underscore the importance of RNA processing in modulating plant development.

Figure 1. Floral Phenotypes Caused by hua1, hua2, and hen4 Mutations

(A–G) Floral phenotypes of various genotypes. Arrows indicate third whorl organs. (A) An Ler flower. (B) A hua1 hua2 flower. (C–E) An early, an intermediate, and a late flower, respectively, from a hua1 hua2 hen4-1 plant. Note petaloid stamens or petals in the third whorl. The black and white arrows in (C) indicate lateral and medial third whorl organs, respectively. (F) An early-arising flower from a hua1 hua2 hen4-2 plant. Note stamen-to-petal transformation in the third whorl. (G) A hua1 hen4-1 flower. (H) Gynoecia dissected out from stage 14 flowers. From left to right are gynoecia from a hua1 hua2 flower, an early-arising hua1 hua2 hen4-1 flower, a late-arising hua1 hua2 hen4-1 flower, and an early-arising hua1 hua2 hen4-2 flower. The latter two gynoecia are found on gynophores (arrowheads), indicating that the gynoecia have partial floral character. (I and J) Scanning electron micrographs of stage 7 flowers of the hua1 hua2 and hua1 hua2 hen4-2 genotypes, respectively. Two sepals from each flower were dissected away to reveal the third whorl organs. The second whorl organs are small (purple arrows). The third whorl organs in the hua1 hua2 flower have begun to differentiate into anthers (arrowhead) and filaments (black arrow), whereas those (black arrows) in the hua1 hua2 hen4-2 flower show no sign of such differentiation. (K–N) Scanning electron micrographs of ovary epidermal cells of various genotypes. (K and L) The top and bottom regions of a hua1 hua2 ovary. Some cells in the top lateral region show epicuticular thickenings (K), whereas all cells in the bottom half of the ovary have a smooth surface (L). (M and N) The bottom region of a hua1 hua2 hen4-1 and a hua1 hua2 hen4-2 ovary, respectively. All cells show epiculticular striation. The scale bars represent 50 μm in (I) and (J) and 10 μm in (K)–(N). (O–V) Floral phenotypes of quadruple mutants and transgenic lines. (O) hua1 hua2 hen4-1 ap1-1. Note stamens in the third whorl. (P) hua1 hua2 hen4-1 ap2-2. Leaf-like organs are found in all four whorls. (Q) hua1 hua2 hen4-1 ag-4, which resembles ag-1. (R) hua1 hua2 hen4-1 ag-1, which is similar to ag-1. (S and T) Flowers of hua1 hua2 hen4-1 plants transformed with the vector alone or HEN4 genomic DNA, respectively. Note the difference in the morphology of the third whorl organs (arrows). (U) Gynoecia of stage 14 flowers from hua1 hua2 (left), hua1 hua2 hen4-1 transformed with HEN4 genomic DNA (middle), and hua1 hua2 hen4-1 (right). (V) hua1 hua2 hen4-1 35S∷AG. Note stamens in the second and third whorls (arrow).

Figure 2. RNA Accumulation Patterns of AP1, AG, WUS, and HEN4 as Determined by In Situ Hybridization

(A–E) AP1 RNA accumulation patterns. (A) A stage 3 hua1 hua2 flower, with no AP1 RNA in the center of the flower. (B) A stage 3 hua1 hua2 hen4-2 flower, with a low level of AP1 RNA in the center of the flower. (C and D) Stage 8 hua1 hua2 and hua1 hua2 hen4-2 flowers, respectively. The arrow indicates a patch of third whorl cells expressing AP1. Ectopic AP1 RNA accumulation in the inner two whorls is more extensive in the triple mutant than in the double mutant. (E) A stage 14 hua1 hua2 hen4-2 flower. Note internal flower (arrowhead) and strong AP1 expression in the fourth whorl. (F) AG RNA accumulation in hua1 hua2 hen4-2 stage 3 (s3) and stage 6 (s6) flowers. The onset and the domain of AG RNA accumulation are normal. (G and H) AG RNA accumulation in stage 9 hua1 hua2 hen4-2 and hua1 hua2 flowers, respectively. In hua1 hua2 hen4-2, the domain of AG RNA accumulation is normal but the level is reduced. (I) In situ hybridization using a probe specific for the larger AG RNAs on a stage 7 hua1 hua2 hen4-2 flower. (J and K) WUS RNA accumulation in a hua1 hua2 (J) and a hua1 hua2 hen4-2 (K) flower. The arrow in (K) marks the WUS-expressing cells. (L and M) HEN4 RNA accumulation patterns. (L) Hybridization with a HEN4 sense probe. (M) Hybridization with a HEN4 antisense probe. HEN4 RNA is found throughout the stage 4 flower. The scale bars represent 50 μm. Numbers in (A)–(E) and (G)–(I) indicate floral whorls.

Figure 3. Map-Based Cloning of HEN4 and Features of the HEN4 Gene and Protein

(A) HEN4 was mapped to a 48 kb region on chromosome V covered by the P1 clone MSJ1 and the BAC T12B11. The numbers under the BAC or P1 clones indicate the numbers of recombination breakpoints between markers in the clones and HEN4 in 684 chromosomes. The structure of the HEN4 gene is shown with the rectangles representing exons and the lines representing introns. The hatched rectangle represents a region that is part of an exon in transcript 2 but is spliced out of transcript 1. The position and nature of the two hen4 mutations are indicated. (B) Diagrams of the two putative HEN4 protein forms with the KH domains and the potential nuclear localization signal (NLS) as indicated. Note that proteins 1 and 2 are from the short (1) and the long (2) HEN4 transcripts, respectively. The hen4 mutations would terminate the proteins at the indicated positions. (C) A clustalW alignment of the five KH domains from HEN4 and the KH domains from three animal proteins, MEX-3 from C. elegans, and αCP1 and Nova-2 from humans. If six or more amino acids are identical at one position, the amino acids are in dark shade. Amino acids that are similar in nature at one position are lightly shaded.

Figure 4. HEN4 RNA Accumulation in Inflorescences from Various Genotypes

Both HEN4 transcripts are present in wild-type, ag-2, and hua1 hua2 inflorescences. HEN4 transcript 2 is absent in hen4 genotypes. Transcripts 1 and 2 correspond to HEN4 cDNAs 1 and 2, respectively. UBQ5 was the loading control.

Figure 5. Interaction of HEN4 and HUA1 in Tobacco Nuclei

(A–D and G–J) Low-magnification fluorescence images collected with the CFP or YFP filter sets as indicated from tobacco leaves infiltrated with Agrobacteria containing 35S∷HUA1-ECFP (A and G), HEN4p∷HEN4-EYFP (B and H), 35S∷HUA1-ECFP and HEN4p∷HEN4-EYFP (C and I), or 35S∷GAL4-ECFP and HEN4p∷HEN4-EYFP (D and J). The bright dots represent multiple nuclei showing CFP orYFP fluorescence. (E, F, K, and L) High-magnification images collected with the CFP or YFP filter sets as indicated showing single nuclei from tobacco cells infiltrated with Agrobacteria containing 35S∷HUA1-ECFP and HEN4p∷HEN4-EYFP (E and K) or 35S∷HUA1-ECFP and 35S∷EYFP-TGA5 (F and L). The dots represent CFP or YFP fluorescence in nuclear speckles. HUA1 and HEN4 are concentrated in the same speckles (arrows and arrowheads in [E] and [K]). TGA5 appears to be more uniform throughout the nucleus. (M and N) cFRET images as displayed using quantitative pseudocolor to show the interaction between HEN4 and HUA1. cFRET values, in arbitrary linear units of fluorescence intensity (a.l.u.f.i.), were calculated by subtracting the crossover fluorescence from the fluorescence collected with the FRET filter set (see Supplemental Data for details). The reason why only some nuclear speckles appear to be cFRET positive is that cFRET values are proportional to fluorescence intensity. In fact, the most accurate measure of FRET is cFRETN/Y/C (see Table 1), which is normalized against EYFP and ECFP fluorescence intensity. The scale bar represents 10 μm. Magnification in (E), (F), and (K)-(N) is the same.

Figure 6. AG Pre-mRNA Processing Defects in Various Genotypes

(A) RNA filter hybridization using probes corresponding to the entire AG genomic region or part of the second intron (probes 1 and 4, respectively; see [B]) on 50 μg of total RNA isolated from various genotypes. The corresponding UBQ5 control hybridization is shown below the AG hybridization. The abundance of the three larger bands (1–3) and AG mRNA in various genotypes is indicated by the numbers below the gel images, with wild-type levels arbitrarily set to 1.0. (B) A summary of various RNA filter hybridization experiments aimed to determine the nature of the large transcripts in bands 1 and 2. The AG genomic region is diagrammed on top, with rectangles and lines representing exons and introns, respectively. The lines numbered 1 to 7 represent various probes used for RNA filter hybridization. Line 8 represents the region corresponding to AG RNA III used for in vitro binding assays. Results from various hybridization experiments are shown in the table below. Positive and negative hybridization signals are represented by “+” and “−,” respectively. “+?” indicates a weak signal that may or may not be real. (C) Diagrams of the nucleotide composition of large transcripts represented by bands 1 and 2. The ends of the transcripts are represented by small, black rectangles or the dot in (B). The ends represented by the rectangles may belong to transcripts in band 2, whereas the one represented by the dot may belong to a transcript in band 1. All large transcripts contain the first two exons and are polyadenylated.

Figure 7. Binding of HUA1 to AG RNA In Vitro

(A) In vitro-synthesized and ³²P-labeled AG RNA I or II, which corresponds to fragments 4 or 5 in Figure 6B, respectively, was incubated with purified GST-αCP1 or GST-HUA1. After washing, the bound transcripts were eluted and resolved on a polyacrylamide gel. (B) One sixtieth of the two proteins used for the binding assay was run on an SDS-polyacrylamide gel to show that near equal amounts of the two proteins were used in the binding assay. The arrowheads indicate the full-length GST fusion proteins. The lower bands were likely truncated proteins.