Identification of SFBB-containing canonical and noncanonical SCF complexes in pollen of apple (Malus × domestica)

Analyses of Cullin1 homologs reveal functional redundancy in S-RNase-based self-incompatibility and evolutionary relationships in eudicots

In Petunia (Solanaceae family), self-incompatibility (SI) is regulated by the polymorphic S-locus, which contains the pistil-specific S-RNase and multiple pollen-specific S-Locus F-box (SLF) genes. SLFs assemble into E3 ubiquitin ligase complexes known as Skp1-Cullin1-F-box complexes (SCFSLF). In pollen tubes, these complexes collectively mediate ubiquitination and degradation of all nonself S-RNases, but not self S-RNase, resulting in cross-compatible, but self-incompatible, pollination. Using Petunia inflata, we show that two pollen-expressed Cullin1 (CUL1) proteins, PiCUL1-P and PiCUL1-B, function redundantly in SI. This redundancy is lost in Petunia hybrida, not because of the inability of PhCUL1-B to interact with SSK1, but due to a reduction in the PhCUL1-B transcript level. This is possibly caused by the presence of a DNA transposon in the PhCUL1-B promoter region, which was inherited from Petunia axillaris, one of the parental species of Pe. hybrida. Phylogenetic and syntenic analyses of Cullin genes in various eudicots show that three Solanaceae-specific CUL1 genes share a common origin, with CUL1-P dedicated to S-RNase-related reproductive processes. However, CUL1-B is a dispersed duplicate of CUL1-P present only in Petunia, and not in the other species of the Solanaceae family examined. We suggest that the CUL1s involved (or potentially involved) in the SI response in eudicots share a common origin.

Genome-wide identification of members of the Skp1 family in almond (Prunus dulcis), cloning and expression characterization of PsdSSK1

Skp1 (S-phase kinase-associated protein 1) is the core gene of SCF ubiquitin ligase, which mediates protein degradation, thereby regulating biological processes such as cell cycle progression, transcriptional regulation, and signal transduction. A variety of plant Skp1 gene family studies have been reported. However, the almond Skp1 gene family has not yet been studied. In this study, we identified 18 members of the Prunus dulcis PdSkp1 family that were unevenly distributed across six chromosomes of the almond genome. Phylogenetic tree analysis revealed that the PdSkp1 members can be divided into three groups: I, II, and III. PdSkp1 members in each subfamily have relatively conserved motif types and exon/intron numbers. There were three pairs of fragment duplication genes and one pair of tandem repeat genes, and their functions were highly evolutionarily conserved. Transcriptome data showed that PdSkp1 is expressed in almond flower tissues, and that its expression shows significant change during cross-pollination. Fluorescence quantitative results showed that eight PdSkp1 genes had different expression levels in five tissues of almond, i.e., branches, leaves, flower buds, flesh, and cores. In addition, we cloned a PsdSSK1 gene based on PdSkp1. The cloned PsdSSK1 showed the same protein sequence as PdSkp1-12. Results of qPCR and western blot analysis showed high expression of PsdSSK1 in almond pollen. In conclusion, we report the first clone of the key gene SSK1 that controls self-incompatibility in almonds. Our research lays a foundation for future functional research on PdSkp1 members, especially for exploring the mechanism of almond self-incompatibility.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01278-9.

Ubiquitination of S4-RNase by S-LOCUS F-BOX LIKE2 Contributes to Self-Compatibility of Sweet Cherry 'Lapins'

Recent studies have shown that loss of pollen-S function in S₄' pollen from sweet cherry (Prunus avium) is associated with a mutation in an S haplotype-specific F-box4 (SFB4) gene. However, how this mutation leads to self-compatibility is unclear. Here, we examined this mechanism by analyzing several self-compatible sweet cherry varieties. We determined that mutated SFB4 (SFB4') in S4' pollen (pollen harboring the SFB4' gene) is approximately 6 kD shorter than wild-type SFB4 due to a premature termination caused by a four-nucleotide deletion. SFB4' did not interact with S-RNase. However, a protein in S4' pollen ubiquitinated S-RNase, resulting in its degradation via the 26S proteasome pathway, indicating that factors in S4' pollen other than SFB4 participate in S-RNase recognition and degradation. To identify these factors, we used S₄-RNase as a bait to screen S4' pollen proteins. Our screen identified the protein encoded by S ₄ -SLFL2, a low-polymorphic gene that is closely linked to the S-locus. Further investigations indicate that SLFL2 ubiquitinates S-RNase, leading to its degradation. Subcellular localization analysis showed that SFB4 is primarily localized to the pollen tube tip, whereas SLFL2 is not. When S ₄ -SLFL2 expression was suppressed by antisense oligonucleotide treatment in wild-type pollen tubes, pollen still had the capacity to ubiquitinate S-RNase; however, this ubiquitin-labeled S-RNase was not degraded via the 26S proteasome pathway, suggesting that SFB4 does not participate in the degradation of S-RNase. When SFB4 loses its function, S₄-SLFL2 might mediate the ubiquitination and degradation of S-RNase, which is consistent with the self-compatibility of S4' pollen.

Identification of a Novel SBP1-Containing SCFSFB Complex in Wild Dwarf Almond (Prunus tenella)

S-RNase-based gametophytic self-incompatibility (SI), in which specificities of pistil and pollen are determined by S-RNase and the S locus F-box protein, respectively, has been discovered in the Solanaceae, Plantaginaceae, and Rosaceae families, but some underlying molecular mechanisms remain elusive and controversial. Previous studies discovered SI in wild dwarf almond (Prunus tenella), and pistil S (S-RNase) and pollen S (SFB) determinant genes have been investigated. However, the SCF (SKP1–Cullin1–F-box-Rbx1) complex, which serves as an E3 ubiquitin ligase on non-self S-RNase, has not been investigated. In the current study, PetSSK1 (SLF-interacting-SKP1-like1), SBP1 (S-RNase binding protein 1), CUL1, and SFB genes (S-haplotype-specific F-box) were identified in an accession (ZB1) of P. tenella. Yeast two-hybrid assays revealed interactions between PetSBP1 and PetCUL1 and between PetSBP1 and PetSFBs (SFB16 and SFB17), and subsequent pull-down assays confirmed these interactions, suggesting a novel SBP1-containing SCF^SFB complex in wild dwarf almond. Moreover, despite a putative interaction between PetSSK1 and PetCUL1, we revealed that PetSSK1 does not interact with PetSFB16 or PetSFB17, and thus the canonical SSK1-containing SCF^SFB complex could not be identified. This suggests a novel molecular mechanism of gametophytic SI in Prunus species.

Finding a Compatible Partner: Self-Incompatibility in European Pear (Pyrus communis); Molecular Control, Genetic Determination, and Impact on Fertilization and Fruit Set

Pyrus species display a gametophytic self-incompatibility (GSI) system that actively prevents fertilization by self-pollen. The GSI mechanism in Pyrus is genetically controlled by a single locus, i.e., the S-locus, which includes at least two polymorphic and strongly linked S-determinant genes: a pistil-expressed S-RNase gene and a number of pollen-expressed SFBB genes (S-locus F-Box Brothers). Both the molecular basis of the SI mechanism and its functional expression have been widely studied in many Rosaceae fruit tree species with a particular focus on the characterization of the elusive SFBB genes and S-RNase alleles of economically important cultivars. Here, we discuss recent advances in the understanding of GSI in Pyrus and provide new insights into the mechanisms of GSI breakdown leading to self-fertilization and fruit set. Molecular analysis of S-genes in several self-compatible Pyrus cultivars has revealed mutations in both pistil- or pollen-specific parts that cause breakdown of self-incompatibility. This has significantly contributed to our understanding of the molecular and genetic mechanisms that underpin self-incompatibility. Moreover, the existence and development of self-compatible mutants open new perspectives for pear production and breeding. In this framework, possible consequences of self-fertilization on fruit set, development, and quality in pear are also reviewed.

CRISPR/Cas9-mediated knockout of PiSSK1 reveals essential role of S-locus F-box protein-containing SCF complexes in recognition of non-self S-RNases during cross-compatible pollination in self-incompatible Petunia inflata

Function of Petunia PiSSK1. Self-incompatibility (SI), an inbreeding-preventing mechanism, is regulated in Petunia inflata by the polymorphic S-locus, which houses multiple pollen-specific S-locus F-box (SLF) genes and a single pistil-specific S-RNase gene. S ₂-haplotype and S ₃-haplotype possess the same 17 polymorphic SLF genes (named SLF1 to SLF17), and each SLF protein produced in pollen is assembled into an SCF (Skp1-Cullin1-F-box) E3 ubiquitin ligase complex. A complete suite of SLF proteins is thought to collectively interact with all non-self S-RNases to mediate their ubiquitination and degradation by the 26S proteasome, allowing cross-compatible pollination. For each SCF^SLF complex, the Cullin1 subunit (named PiCUL1-P) and Skp1 subunit (named PiSSK1), like the F-box protein subunits (SLFs), are pollen-specific, raising the possibility that they also evolved specifically to function in SI. Here we used CRISPR/Cas9-meditated genome editing to generate frame-shift indel mutations in PiSSK1 and examined the SI behavior of a T ₀ plant (S ₂ S ₃) with biallelic mutations in the pollen genome and two progeny plants (S ₂ S ₂) each homozygous for one of the indel alleles and not carrying the Cas9-containing T-DNA. Their pollen was completely incompatible with pistils of seven otherwise-compatible S-genotypes, but fully compatible with pistils of an S ₃ S ₃ transgenic plant in which production of S₃-RNase was completely suppressed by an antisense S ₃-RNase gene, and with pistils of immature flower buds, which produce little S-RNase. These results suggest that PiSSK1 specifically functions in SI and support the hypothesis that SLF-containing SCF complexes are essential for compatible pollination.

Cullin1-P is an Essential Component of Non-Self Recognition System in Self-Incompatibility in Petunia

Self-incompatibility (SI) in flowering plants is a genetic reproductive barrier to distinguish self- and non-self pollen to promote outbreeding. In Solanaceae, self-pollen is rejected by the ribonucleases expressed in the styles (S-RNases), via its cytotoxic function. On the other side, the male-determinant is the S-locus F-box proteins (SLFs) expressed in pollen. Multiple SLFs collaboratively detoxify non-self S-RNases, therefore, non-self recognition is the mode of self-/non-self discrimination in Solanaceae. It is considered that SLFs function as a substrate-recognition module of the Skp1-Cullin1-F-box (SCF) complex that inactivates non-self S-RNases via their polyubiquitination, which leads to degradation by 26S proteasome. In fact, PhSSK1 (Petunia hybrida SLF-interacting Skp1-like1) was identified as a specific component of SCF^SLF and was shown to be essential for detoxification of S-RNase in Petunia However, different molecules are proposed as the candidate Cullin1, another component of SCF^SLF, and there is as yet no definite conclusion. Here, we identified five Cullin1s from the expressed sequence tags (ESTs) derived from the male reproductive organ in Petunia Among them, only PhCUL1-P was co-immunoprecipitated with S₇-SLF2. In vitro protein-binding assay suggested that PhSSK1 specifically forms a complex with PhCUL1-P in an SLF-dependent manner. Knockdown of PhCUL1-P suppressed fertility of transgenic pollen in cross-compatible pollination in the functional S-RNase-dependent manner. These results suggested that SCF^SLF selectively uses PhCUL1-P. Phylogeny of Cullin1s indicates that CUL1-P is recruited into the SI machinery during the evolution of Solanaceae, suggesting that the SI components have evolved differently among species in Solanaceae and Rosaceae, despite both families sharing the S-RNase-based SI.

Molecular and genetic characterization of a self-compatible apple cultivar, 'CAU-1'

In this study, we characterized a naturally occurring self-compatible apple cultivar, 'CAU-1' (S₁S₉), and studied the underlying mechanism that causes its compatibility. Analyses of both fruit set rate and seed number after self-pollination or cross-pollination with 'Fuji' (S₁S₉), and of pollen tube growth, demonstrated that 'CAU-1' is self-compatible. Genetic analysis by S-RNase PCR-typing of selfed progeny of 'CAU-1' revealed the presence of all progeny classes (S₁S₁, S₁S₉, and S₉S₉). Moreover, no evidence of S-allele duplication was found. These findings support the hypothesis that loss of function of an S-locus unlinked pollen-part mutation (PPM) expressed in pollen, rather than a natural mutation in the pollen-S gene (S₁- and S₉- haplotype), leads to SI breakdown in 'CAU-1'. In addition, there were no significant differences in pollen morphology or fertility between 'Fuji' and 'CAU-1'. However, we found that the effect of S₁- and S₉-RNase on the SI behavior of pollen could not be addressed better in 'CAU-1' than in 'Fuji'. Furthermore, we found that a pollen-expressed hexose transporter, MdHT1, interacted with S-RNases and showed significantly less expression in 'CAU-1' than in 'Fuji' pollen tubes. These findings support the hypothesis that MdHT1 may participate in S-RNase internalization during the SI process, and decrease of MdHT1 expression in 'CAU-1' hindered the release of self S-RNase into the cytoplasm of pollen tubes, thereby protecting pollen from the cytotoxicity of S-RNase, finally probably resulting in self-compatibility. Together, these findings indicate that S-locus external factors are required for gametophytic SI in the Rosaceae subtribe Pyrinae.

A simple, high-throughput modeling approach reveals insights into the mechanism of gametophytic self-incompatibility

Specificity in the GSI response results from the S-haplotype-specific molecular interaction of S-locus F-box (SLF/SFB) and SRNase proteins in the self-incompatibility locus (S-locus). The answer to the question of how these two components of the S-locus (SRNase and SLF/SFB) interact has been gathered from several models. Since there is not enough evidence as to which one is the definitive model, none of them can be ruled out. Despite the identification of interacting protein elements, the mechanism by which SLF/SFB and SRNase interact to differently trigger the self-incompatibility among families and subfamilies remain uncertain. The high-throughput modeling approach demonstrates structural visions into the possible existence of a Collaborative Non-Self Recognition model in apple. These findings postulate several prospects for future investigation providing useful information to guide the implementation of breeding strategies.

Recognition of a wide-range of S-RNases by S locus F-box like 2, a general-inhibitor candidate in the Prunus-specific S-RNase-based self-incompatibility system

Many species in the Rosaceae, the Solanaceae, and the Plantaginaceae exhibit S-RNase-based gametophytic self-incompatibility (GSI). This system comprises S-ribonucleases (S-RNases) as the pistil S determinant and a single or multiple F-box proteins as the pollen S determinants. In Prunus, pollen specificity is determined by a single S haplotype-specific F-box protein (SFB). The results of several studies suggested that SFB exerts cognate S-RNase cytotoxicity, and a hypothetical general inhibitor (GI) is assumed to detoxify S-RNases in non-specific manner unless it is affected by SFB. Although the identity of the GI is unknown, phylogenetic and evolutionary analyses have indicated that S locus F-box like 1-3 (or S locus F-box with low allelic sequence polymorphism 1-3; SLFL1-3), which are encoded by a region of the Prunus genome linked to the S locus, are good GI candidates. Here, we examined the biochemical characteristics of SLFL1-3 to determine whether they have appropriate GI characteristics. Pull-down assays and quantitative expression analyses indicated that Prunus avium SLFL1-3 mainly formed a canonical SCF complex with PavSSK1 and PavCul1A. Binding assays with PavS(1,3,4,6)-RNases showed that PavSLFL1, PavSLFL2, and PavSLFL3 bound to PavS(3)-RNase, all PavS-RNases tested, and none of the PavS-RNases tested, respectively. Together, these results suggested that SLFL2 has the appropriate characteristics to be the GI in sweet cherry pollen, while SLFL1 may redundantly work with SLFL2 to detoxify all S-RNases. We discuss the possible roles of SLFL1-3 as the GI in the Prunus-specific S-RNase-based GSI mechanism.

Molecular mechanism of the S-RNase-based gametophytic self-incompatibility in fruit trees of Rosaceae

Self-incompatibility (SI) is a major obstacle for stable fruit production in fruit trees of Rosaceae. SI of Rosaceae is controlled by the S locus on which at least two genes, pistil S and pollen S, are located. The product of the pistil S gene is a polymorphic and extracellular ribonuclease, called S-RNase, while that of the pollen S gene is a protein containing the F-box motif, SFB (S haplotype-specific F-box protein)/SFBB (S locus F-box brothers). Recent studies suggested that SI of Rosaceae includes two different systems, i.e., Prunus of tribe Amygdaleae exhibits a self-recognition system in which its SFB recognizes self-S-RNase, while tribe Pyreae (Pyrus and Malus) shows a non-self-recognition system in which many SFBB proteins are involved in SI, each recognizing subset of non-self-S-RNases. Further biochemical and biological characterization of the S locus genes, as well as other genes required for SI not located at the S locus, will help our understanding of the molecular mechanisms, origin, and evolution of SI of Rosaceae, and may provide the basis for breeding of self-compatible fruit tree cultivars.

CrWSKP1, an SKP1-like Gene, Is Involved in the Self-Incompatibility Reaction of "Wuzishatangju" (Citrus reticulata Blanco)

Plant S-phase kinase-associated protein 1 (SKP1) genes play crucial roles in plant development and differentiation. However, the role of SKP1 in citrus is unclear. Herein, we described a novel SKP1-like gene, designated as CrWSKP1, from "Wuzishatangju" (Citrus reticulata Blanco). The cDNA sequence of CrWSKP1 is 779 base pairs (bp) and contains an open reading frame (ORF) of 477 bp. The genomic sequence of the CrWSKP1 gene is 1296 bp with two exons and one intron. CrWSKP1 has high identity with SKP1-like genes from other plant species within two conserved regions. Approximately 85% of pollen tubes of self-pollinated CrWSKP1 transgenic tobaccos became twisted at four days after self-pollination. Pollen tube numbers of self-pollinated CrWSKP1 transformants entering into ovules were significantly fewer than that of the control. Seed number of self-pollinated CrWSKP1 transformants was significantly reduced. These results suggested that the CrWSKP1 is involved in the self-incompatibility (SI) reaction of "Wuzishatangju".

Insight into S-RNase-based self-incompatibility in Petunia: recent findings and future directions

S-RNase-based self-incompatibility in Petunia is a self/non-self recognition system that allows the pistil to reject self-pollen to prevent inbreeding and to accept non-self pollen for outcrossing. Cloning of S-RNase in 1986 marked the beginning of nearly three decades of intensive research into the mechanism of this complex system. S-RNase was shown to be the sole female determinant in 1994, and the first male determinant, S-locus F-box protein1 (SLF1), was identified in 2004. It was discovered in 2010 that additional SLF proteins are involved in pollen specificity, and recently two S-haplotypes of Petunia inflata were found to possess 17 SLF genes based on pollen transcriptome analysis, further increasing the complexity of the system. Here, we first summarize the current understanding of how the interplay between SLF proteins and S-RNase in the pollen tube allows cross-compatible pollination, but results in self-incompatible pollination. We then discuss some of the aspects that are not yet elucidated, including uptake of S-RNase into the pollen tube, nature, and assembly of SLF-containing complexes, the biochemical basis for differential interactions between SLF proteins and S-RNase, and fate of non-self S-RNases in the pollen tube.