Characterization of Brassica S-haplotypes lacking S-locus glycoprotein

Comprehensive computational analysis of the SRK-SP11 molecular interaction underlying self-incompatibility in Brassicaceae using improved structure prediction for cysteine-rich proteins

Plants employ self-incompatibility (SI) to promote cross-fertilization. In Brassicaceae, this process is regulated by the formation of a complex between the pistil determinant S receptor kinase (SRK) and the pollen determinant S-locus protein 11 (SP11, also known as S-locus cysteine-rich protein, SCR). In our previous study, we used the crystal structures of two eSRK-SP11 complexes in Brassica rapa S8 and S9 haplotypes and nine computationally predicted complex models to demonstrate that only the SRK ectodomain (eSRK) and SP11 pairs derived from the same S haplotype exhibit high binding free energy. However, predicting the eSRK-SP11 complex structures for the other 100 + S haplotypes and genera remains difficult because of SP11 polymorphism in sequence and structure. Although protein structure prediction using AlphaFold2 exhibits considerably high accuracy for most protein monomers and complexes, 46% of the predicted SP11 structures that we tested showed < 75 mean per-residue confidence score (pLDDT). Here, we demonstrate that the use of curated multiple sequence alignment (MSA) for cysteine-rich proteins significantly improved model accuracy for SP11 and eSRK-SP11 complexes. Additionally, we calculated the binding free energies of the predicted eSRK-SP11 complexes using molecular dynamics (MD) simulations and observed that some Arabidopsis haplotypes formed a binding mode that was critically different from that of B. rapa S8 and S9. Thus, our computational results provide insights into the haplotype-specific eSRK-SP11 binding modes in Brassicaceae at the residue level. The predicted models are freely available at Zenodo, https://doi.org/10.5281/zenodo.8047768.

S haplotype collection in Brassicaceae crops-an updated list of S haplotypes

Self-incompatibility is the system that inhibits pollen germination and pollen tube growth by self-pollen. This trait is important for the breeding of Brassica and Raphanus species. In these species, self-incompatibility is governed by the S locus, which contains three linked genes (a set called the S haplotype), i.e., S-locus receptor kinase, S-locus cysteine-rich protein/S-locus protein 11, and S-locus glycoprotein. A large number of S haplotypes have been identified in Brassica oleracea, B. rapa, and Raphanus sativus to date, and the nucleotide sequences of their many alleles have also been registered. In this state, it is important to avoid confusion between S haplotypes, i.e., an identical S haplotype with different names and a different S haplotype with an identical S haplotype number. To mitigate this issue, we herein constructed a list of S haplotypes that are easily accessible to the latest nucleotide sequences of S-haplotype genes, together with revisions to and an update of S haplotype information. Furthermore, the histories of the S-haplotype collection in the three species are reviewed, the importance of the collection of S haplotypes as a genetic resource is discussed, and the management of information on S haplotypes is proposed.

Progress on deciphering the molecular aspects of cell-to-cell communication in Brassica self-incompatibility response

The sporophytic system of self-incompatibility is a widespread genetic phenomenon in plant species, promoting out-breeding and maintaining genetic diversity. This phenomenon is of commercial importance in hybrid breeding of Brassicaceae crops and is controlled by single S locus with multiple S haplotypes. The molecular genetic studies of Brassica 'S' locus has revealed the presence of three tightly linked loci viz. S-receptor kinase (SRK), S-locus cysteine-rich protein/S-locus protein 11 (SCR/SP11), and S-locus glycoprotein (SLG). On self-pollination, the allele-specific ligand-receptor interaction activates signal transduction in stigma papilla cells and leads to rejection of pollen tube on stigmatic surface. In addition, arm-repeat-containing protein 1 (ARC1), M-locus protein kinase (MLPK), kinase-associated protein phosphatase (KAPP), exocyst complex subunit (Exo70A1) etc. has been identified in Brassica crops and plays a key role in self-incompatibility signaling pathway. Furthermore, the cytoplasmic calcium (Ca2+) influx in papilla cells also mediates self-incompatibility response in Brassicaceae, but how this cytoplasmic Ca2+ influx triggers signal transduction to inhibit pollen hydration is still obscure. There are many other signaling components which are not well characterized yet. Much progress has been made in elucidating the downstream multiple pathways of Brassica self-incompatibility response. Hence, in this review, we have made an effort to describe the recent advances made on understanding the molecular aspects of genetic mechanism of self-incompatibility in Brassicaceae.

Analysis of S-locus and expression of S-alleles of self-compatible rapid-cycling Brassica oleracea 'TO1000DH3'

Brassica oleracea is a strictly self-incompatible (SI) plant, but rapid-cycling B. oleracea 'TO1000DH3' is self-compatible (SC). Self-incompatibility in Brassicaceae is controlled by multiple alleles of the S-locus. Three S-locus genes, S-locus glycoprotein (SLG), S-locus receptor kinase (SRK) and S-locus protein 11 or S-locus cysteine-rich (SP11/SCR), have been reported to date, all of which are classified into class I and II. In this study, we investigated the molecular mechanism behind alterations of SI to SC in rapid-cycling B. olerace 'TO1000DH3'. Class I SRK were identified by genomic DNA PCR and PCR-RFLP analysis using SRK specific markers and found to be homozygous. Cloning and sequencing of class I SRK revealed a normal kinase domain without any S-domain/transmembrane domain. Moreover, S-locus sequencing analysis revealed only an SLG sequence, but no SP11/SCR. Expression analysis showed no SRK expression in the stigma, although other genes involved in the SI recognition reaction (SLG, MLPK, ARC1, THL) were found to have normal expression in the stigma. Taken together, the above results suggest that structural aberrations such as deletion of the SI recognition genes may be responsible for the breakdown of SI in rapid-cycling B. oleracea 'TO1000DH3'.

Self-incompatibility in Brassicaceae crops: lessons for interspecific incompatibility

Most wild plants and some crops of the Brassicaceae express self-incompatibility, which is a mechanism that allows stigmas to recognize and discriminate against "self" pollen, thus preventing self-fertilization and inbreeding. Self-incompatibility in this family is controlled by a single S locus containing two multiallelic genes that encode the stigma-expressed S-locus receptor kinase and its pollen coat-localized ligand, the S-locus cysteine-rich protein. Physical interaction between receptor and ligand encoded in the same S locus activates the receptor and triggers a signaling cascade that results in inhibition of "self" pollen. Sequence information for many S-locus haplotypes in Brassica species has spurred studies of dominance relationships between S haplotypes and of S-locus structure, as well as the development of methods for S genotyping. Furthermore, molecular genetic studies have begun to identify genes that encode putative components of the self-incompatibility signaling pathway. In parallel, standard genetic analysis and QTL analysis of the poorly understood interspecific incompatibility phenomenon have been initiated to identify genes responsible for the inhibition of pollen from other species by the stigma. Herewith, we review recent studies of self-incompatibility and interspecific incompatibility, and we propose a model in which a universal pollen-inhibition pathway is shared by these two incompatibility systems.

Commonalities and differences between Brassica and Arabidopsis self-incompatibility

In higher plants, the self-incompatibility mechanism is important for inhibition of self-fertilization and facilitation of out-crossing. In Brassicaceae, the self-incompatibility response is mediated by allele-specific interaction of the stigma-localized S-locus receptor kinase (SRK) with the pollen coat-localized ligand (SCR/SP11). All self-incompatible Brassicaceae plants analyzed have been found to have the SRK and SCR/SP11 genes in the S-locus region. Although Arabidopsis thaliana is self-compatible, transformation with functional SRK-SCR genes from self-incompatible Arabidopsis species confers the self-incompatibility phenotype to A. thaliana. The allele-specific interaction between SRK and SCR activates the downstream signaling cascade of self-incompatibility. Yeast two-hybrid analysis with a kinase domain of SRK as bait and genetic analysis suggested several candidate components of self-incompatibility signaling in Brassica. Recently, A. thaliana genes orthologous to the identified genes for Brassica self-incompatibility signaling were evaluated by using a self-incompatible transgenic A. thaliana plant and these orthologous genes were found not to be involved in self-incompatibility signaling in the transgenic A. thaliana. In this review, we describe common and different aspects of S-locus genomic regions and self-incompatibility signaling between Brassica and Arabidopsis.

Assessment of genetic diversity of accessions in Brassicaceae genetic resources by frequency distribution analysis of S haplotypes

Plant genetic resources are important sources of genetic variation for improving crop varieties as breeding materials. Conservation of such resources of allogamous species requires maintenance of the genetic diversity within each accession to avoid inbreeding depression and loss of rare alleles. For assessment of genetic diversity in the self-incompatibility locus (S locus), which is critically involved in the chance of mating, we developed a dot-blot genotyping method for self-incompatibility (S) haplotypes and applied it to indigenous, miscellaneous landraces of Brassica rapa, provided by the IPK Gene Bank (Gatersleben, Germany) and the Tohoku University Brassica Seed Bank (Sendai, Japan), in which landraces are maintained using different population sizes. This method effectively determined S genotypes of more than 500 individuals from the focal landraces. Although our results suggest that these landraces might possess sufficient numbers of S haplotypes, the strong reduction of frequencies of recessive S haplotypes occurred, probably owing to genetic drift. Based on these results, we herein discuss an appropriate way to conserve genetic diversity of allogamous plant resources in a gene bank.

Preservation of a pseudogene by gene conversion and diversifying selection

Interlocus gene conversion is considered a crucial mechanism for generating novel combinations of polymorphisms in duplicated genes. The importance of gene conversion between duplicated genes has been recognized in the major histocompatibility complex and self-incompatibility genes, which are likely subject to diversifying selection. To theoretically understand the potential role of gene conversion in such situations, forward simulations are performed in various two-locus models. The results show that gene conversion could significantly increase the number of haplotypes when diversifying selection works on both loci. We find that the tract length of gene conversion is an important factor to determine the efficacy of gene conversion: shorter tract lengths can more effectively generate novel haplotypes given the gene conversion rate per site is the same. Similar results are also obtained when one of the duplicated genes is assumed to be a pseudogene. It is suggested that a duplicated gene, even after being silenced, will contribute to increasing the variability in the other locus through gene conversion. Consequently, the fixation probability and longevity of duplicated genes increase under the presence of gene conversion. On the basis of these findings, we propose a new scenario for the preservation of a duplicated gene: when the original donor gene is under diversifying selection, a duplicated copy can be preserved by gene conversion even after it is pseudogenized.

Diverse cell signalling pathways regulate pollen-stigma interactions: the search for consensus

Siphonogamy, the delivery of nonmotile sperm to the egg via a pollen tube, was a key innovation that allowed flowering plants (angiosperms) to carry out sexual reproduction on land without the need for water. This process begins with a pollen grain (male gametophyte) alighting on and adhering to the stigma of a flower. If conditions are right, the pollen grain germinates to produce a pollen tube. The pollen tube invades the stigma and grows through the style towards the ovary, where it enters an ovule, penetrates the embryo sac (female gametophyte) and releases two sperm cells, one of which fertilizes the egg, while the other fuses with the two polar nuclei of the central cell to form the triploid endosperm. The events before fertilization (pollen-pistil interactions) comprise a series of complex cellular interactions involving a continuous exchange of signals between the haploid pollen and the diploid maternal tissue of the pistil (sporophyte). In recent years, significant progress has been made in elucidating the molecular identity of these signals and the cellular interactions that they regulate. Here we review our current understanding of the cellular and molecular interactions that mediate the earliest of these interactions between the pollen and the pistil that occur on or within the stigma - the 'pollen-stigma interaction'.

Molecular characterization of Lal2, an SRK-like gene linked to the S-locus in the wild mustard Leavenworthia alabamica

Single-locus sporophytic self-incompatibility inhibits inbreeding in many members of the mustard family (Brassicaceae). To investigate the genetics of self-incompatibility in the wild mustard Leavenworthia alabamica, diallel crosses were conducted between full siblings. Patterns of incompatibility were consistent with the action of single-locus sporophytic self-incompatibility. DNA sequences related to S-locus receptor kinase (SRK), the gene involved in self-pollen recognition in mustards, were cloned and sequenced. A single sequence with high identity to SRK and several other groups of sequences (Lal1, Lal2, Lal3, Lal8, and Lal14) were isolated from L. alabamica. We propose that either Lal2 sequences are divergent alleles of SRK or Lal2 is in tight linkage with SRK because (1) Lal2 alleles cosegregate with S-alleles inferred from dialleles in all 97 cases tested in five families; (2) Lal2 sequences are highly diverse at both synonymous and nonsynonymous sites and exhibit patterns of selective constraint similar to those observed at SRK in Brassica and Arabidopsis; and (3) transcripts of one Lal2 allele were detected in leaves and the styles of open flowers, but were most abundant in the stigmas of maturing buds. We discuss the utility of the S-linked polymorphism at Lal2 for studying the evolutionary forces acting on self-incompatibility in Leavenworthia.

How far are we from unravelling self-incompatibility in grasses?

The genetic and physiological mechanisms involved in limiting self-fertilization in angiosperms, referred to as self-incompatibility (SI), have significant effects on population structure and have potential diversification and evolutionary consequences. Up to now, details of the underlying genetic control and physiological basis of SI have been elucidated in two different gametophytic SI (GSI) systems, the S-RNase SI and the Papaver SI systems, and the sporophytic SI (SSI) system (Brassica). In the grass family (Poaceae), which contains all the cereal and major forage crops, SI has been known for half a century to be controlled gametophytically by two multiallelic and independent loci, S and Z. But still none of the gene products for S and Z is known and only limited information on related biochemical responses is available. Here we compare current knowledge of grass SI with that of other well-characterized SI systems and speculate about the relationship between SSI and grass SI. Additionally, we discuss comparative mapping as a tool for the further investigation of grass SI.

Effects of recombination on hitchhiking diversity in the Brassica self-incompatibility locus complex

In self-incompatibility, a number of S haplotypes are maintained by frequency-dependent selection, which results in trans-specific S haplotypes. The region of several kilobases (approximately 40-60 kb) from SP6 to SP2, including self-incompatibility-related genes and some adjacent genes in Brassica rapa, has high nucleotide diversity due to the hitchhiking effect, and therefore we call this region the "S-locus complex." Recombination in the S-locus complex is considered to be suppressed. We sequenced regions of >50 kb of the S-locus complex of three S haplotypes in B. rapa and found higher nucleotide diversity in intergenic regions than in coding regions. Two highly similar regions of >10 kb were found between BrS-8 and BrS-46. Phylogenetic analysis using trans-specific S haplotypes (called interspecific pairs) of B. rapa and B. oleracea suggested that recombination reduced the nucleotide diversity in these two regions and that the genes not involved in self-incompatibility in the S-locus complex and the kinase domain, but not the S domain, of SRK have also experienced recombination. Recombination may reduce hitchhiking diversity in the S-locus complex, whereas the region from the S domain to SP11 would disfavor recombination.

Self-compatibility in Brassica napus is caused by independent mutations in S-locus genes

Brassica napus is an amphidiploid species with the A genome from Brassica rapa and the C genome from Brassica oleracea. Although B. rapa, B. oleracea and artificially synthesized amphidiploids with the AC genome are self-incompatible, B. napus is self-compatible. Six S genotypes were identified in B. napus, five of which had class I S haplotypes from one species and a class II S haplotype from the other species, and mutations causing self-compatibility were identified in three of these S genotypes. The most predominant S genotype (BnS-1;BnS-6), which is that of cv. 'Westar', had a class I S haplotype similar to B. rapa S-47 (BrS-47) and a class II S haplotype similar to B. oleracea S-15 (BoS-15). The stigmas of 'Westar' rejected the pollen grains of both BrS-47 and BoS-15, while reciprocal crossings were compatible. Insertion of a DNA fragment of about 3.6 kb was found in the promoter region of the SP11/SCR allele of BnS-1, and transcripts of SP11/SCR were not detected in 'Westar'. The nucleotide sequence of the SP11 genomic DNA of BnS-6 was 100% identical to that of SP11 of BoS-15. Class I SP11 alleles from one species showed dominance over class II SP11 alleles from the other species in artificially synthesized B. napus lines, suggesting that the non-functional dominant SP11 allele suppressed the expression of the recessive SP11 allele in 'Westar'. Two other S genotypes in B. napus also had non-functional class I S haplotypes together with recessive BnS-6. These observations suggest independent origins of self-compatibility in B. napus.

Comparison of the genome structure of the self-incompatibility (S) locus in interspecific pairs of S haplotypes

The determinants of recognition specificity of self-incompatibility in Brassica are SRK in the stigma and SP11/SCR in the pollen, both of which are encoded in the S locus. The nucleotide sequence analyses of many SRK and SP11/SCR alleles have identified several interspecific pairs of S haplotypes having highly similar sequences between B. oleracea and B. rapa. These interspecific pairs of S haplotypes are considered to be derived from common ancestors and to have maintained the same recognition specificity after speciation. In this study, the genome structures of three interspecific pairs of S haplotypes were compared by sequencing SRK, SP11/SCR, and their flanking regions. Regions between SRK and SP11/SCR in B. oleracea were demonstrated to be much longer than those of B. rapa and several retrotransposon-like sequences were identified in the S locus in B. oleracea. Among the seven retrotransposon-like sequences, six sequences were found to belong to the ty3 gypsy group. The gag sequences of the retrotransposon-like sequences were phylogenetically different from each other. In Southern blot analysis using retrotransposon-like sequences as probes, the B. oleracea genome showed more signals than the B. rapa genome did. These findings suggest a role for the S locus and genome evolution in self-incompatible plant species.

Peptide hormones in plants

In recent years, numerous biochemical and genetic studies have demonstrated that peptide signaling plays a greater than anticipated role in various aspects of plant growth and development. A substantial proportion of these peptides are secretory and act as local signals mediating cell-to-cell communication. Specific receptors for several peptides were identified as being membrane-localized receptor kinases, the largest family of receptor-like molecules in plants. These findings illustrate the importance of peptide signaling in the regulation of plant growth, functions that were previously ascribed to the combined action of small lipophilic compounds referred to as "traditional plant hormones." Here, we outline recent advances in the current understanding of biologically active peptides in plants, currently regarded as a new class of plant hormones.

Gene conversion from SLG to SRK resulting in self-compatibility in Brassica rapa

Self-compatible S-54 homozygotic plants were found in progenies of an F(1) hybrid cultivar in Chinese cabbage. Pollination tests revealed that this self-compatibility is controlled by the S locus and caused by the loss of the recognition function of the stigma. SRK, the gene for the recognition molecule in the stigma, was normally transcribed and translated in the self-compatible plants. The 1034-bp region in the receptor domain of SRK in the self-compatible plants was 100% identical to SLG in S-54, while that in self-incompatible S-54 homozygotic plants was 95.1% identical. These results suggest that the self-compatibility of the S-54 homozygotes is due to amino-acid changes caused by gene conversion from SLG to SRK.

Species specificity in pollen-pistil interactions

For pollination to succeed, pollen must carry sperm through a variety of different floral tissues to access the ovules within the pistil. The pistil provides everything the pollen requires for success in this endeavor including distinct guidance cues and essential nutrients that allow the pollen tube to traverse enormous distances along a complex path to the unfertilized ovule. Although the pistil is a great facilitator of pollen function, it can also be viewed as an elaborate barrier that shields ovules from access from inappropriate pollen, such as pollen from other species. Each discrete step taken by pollen tubes en route to the ovules is a potential barrier point to ovule access and waste by inappropriate mates. In this review, we survey the current molecular understanding of how pollination proceeds, and ask to what extent is each step important for mate discrimination. As this field progresses, this synthesis of functional biology and evolutionary studies will provide insight into the molecular basis of the species barriers that maintain the enormous diversity seen in flowering plants.

Duplicated SP11 genes produce alternative transcripts in the S15 haplotype of Brassica oleracea

Self-incompatibility (SI) discriminating self and non-self pollen is regulated by S-locus genes in Brassica. In most S haplotypes, a set of three highly polymorphic genes, SLG, SRK, and SP11, is located at the S-locus region. In the present study, we found duplicated SP11 genes, S15-SP11a, S15-SP11b, and S15-SP11b', in the self-incompatible S15 haplotype of B. oleracea. RNA gel blot and reverse transcription polymerase chain reaction (RT-PCR) analyses showed that two different sizes of SP11 transcripts were specifically detected in anther tissues: a 0.65-kb transcript corresponded to S15-SP11a (an exon-1 region of S15-SP11b was also co-transcribed in some cases), and a 1.4-kb transcript contained the duplicated three genes, S15-SP11a, S15-SP11b, and an exon-1 region of S15-SP11b', all three of which were connected to intergenic spacer regions.

Self-incompatibility in plants

Sexual reproduction in many flowering plants involves self-incompatibility (SI), which is one of the most important systems to prevent inbreeding. In many species, the self-/nonself-recognition of SI is controlled by a single polymorphic locus, the S-locus. Molecular dissection of the S-locus revealed that SI represents not one system, but a collection of divergent mechanisms. Here, we discuss recent advances in the understanding of three distinct SI mechanisms, each controlled by two separate determinant genes at the S-locus. In the Brassicaceae, the determinant genes encode a pollen ligand and its stigmatic receptor kinase; their interaction induces incompatible signaling(s) within the stigma papilla cells. In the Solanaceae-type SI, the determinants are a ribonuclease and an F-box protein, suggesting the involvement of RNA and protein degradation in the system. In the Papaveraceae, the only identified female determinant induces a Ca2+-dependent signaling network that ultimately results in the death of incompatible pollen.

Diversification and alteration of recognition specificity of the pollen ligand SP11/SCR in self-incompatibility of Brassica and Raphanus

The recognition specificity of the pollen ligand of self-incompatibility (SP11/SCR) was investigated using Brassica rapa transgenic plants expressing SP11 transgenes, and SP11 of Raphanus sativus S-21 was found to have the same recognition specificity as that of B. rapa S-9. In a set of three S haplotypes, whose sequence identities of SP11 and SRK are fairly high, R. sativus S-6 showed the same recognition specificity as Brassica oleracea S-18 and a slightly different specificity from B. rapa S-52. B. oleracea S-18, however, showed a different specificity from B. rapa S-52. Using these similar S haplotypes, chimeric SP11 proteins were produced by domain swapping. Bioassay using the chimeric SP11 proteins revealed that the incompatibility response induction activity was altered by the replacement of Region III and Region V. Pollen grains of Brassica transgenic plants expressing chimeric SP11 of the B. oleracea SP11-18 sequence with Region III and Region V from B. rapa SP11-52 (chimeric BoSP11-18[52]) were partially incompatible with the B. rapa S-52 stigmas, and those expressing the R. sativus SP11-6 sequence with Region III and Region V from B. rapa SP11-52 (chimeric RsSP11-6[52]) were completely incompatible with the stigmas having B. rapa S-52. However, the transgenic plant expressing chimeric RsSP11-6(52) also showed incompatibility with B. oleracea S-18 stigmas. These results suggest that Regions III and Region V of SP11 are important for determining the recognition specificity, but not the sole determinant. A possible process of the generation of a new S haplotype is herein discussed.

Antisense suppression of thioredoxin h mRNA in Brassica napus cv. Westar pistils causes a low level constitutive pollen rejection response

In Brassica , the thioredoxin h proteins, THL1 and THL2, were previously found to be potential inhibitors of the S receptor kinase (SRK) in the Brassica self-incompatibility response. To investigate the biological roles of THL1 and THL2 in pollen-pistil interactions, the stigma-specific SLR1 promoter was used to drive antisense THL1/2 expression in Brassica napus cv. Westar. This cultivar is normally compatible, but antisense suppression of THL1/2 led to a low level constitutive rejection of all Brassica napus pollen tested. Fluorescence microscopy revealed that the pollen rejection was a typical Brassica self-incompatibility rejection response with reduced pollen adhesion, germination and pollen tube growth. In addition, Westar was found to express the SLG(15) and SRK(15) proteins which may be the target of regulation by THL1 and THL2. Thus, these results indicate that the THL1 and THL2 are required for full pollen acceptance in B. napus cv. Westar.

Molecular evolution of the s locus controlling mating in the brassicaceae

Flowering plants possess self-incompatibility (SI) mechanisms that promote outbreeding and thereby increase their genetic diversity. In the self-incompatible Brassicaceae, recognition and rejection of self-pollen is based on a receptor-ligand interaction between male and female SI determinants. A transmembrane receptor kinase (S locus Receptor Kinase, SRK) determines the SI specificity in stigmatic cells, whereas a pollen coat-localized ligand (S locus Cysteine-Rich, SCR) determines the SI specificity in pollen. During recent years, major advances have been made in the understanding of the molecular basis of self-pollen recognition by stigmatic cells. In this review, we will focus on evolutionary aspects of the SI system in Brassicaceae. We will describe how the study of the molecular aspect of SI, not only in the historical Brassica model but also in Arabidopsis species, has contributed to highlight certain aspects of evolution of SI in the Brassicaceae.

Receptor kinase signalling in plants

Recent plant genome analyses have revealed a large family of plant receptor kinases with very divergent extracellular domains. While a large proportion of this family remains uncharacterized, emerging functions for several plant receptor kinases reveal roles in a variety of biological processes including growth, development, hormone perception, and plant–microbe interactions. Significant progress has also been made in the understanding of four plant receptor kinase systems including their respective ligands and signalling pathways. Interestingly, a wide range of signalling proteins have been identified as functioning with these receptor kinases. In this review, an overview of plant receptor kinases, their biological functions, and their signalling pathways is presented.Key words: plants, Arabidopsis, receptor kinase, signal transduction.

Ligand-receptor pairs in plant peptide signaling

Extensive studies on plant signaling molecules over the past decade indicate that plant cell-to-cell communication, as is the case with animal systems, makes use of small peptide signals and specific receptors. To date, four peptide-ligand-receptor pairs have been identified and shown to be involved in a variety of processes. Systemin and phytosulfokine (PSK), the first and second signaling peptides identified in plants, were isolated by biochemical purification based on their biological activities. Furthermore, their receptors have been biochemically purified from plasma membranes on the basis of specific ligand-receptor interactions. By contrast, the two other peptide signals, CLAVATA3 (CLV3) and the pollen S determinant SCR/SP11, were genetically identified during searches for specific ligands for receptors that had already been cloned. Systemin functions in the plant wound response, whereas PSK appears to cooperate with auxin and cytokinin to regulate cellular dedifferentiation and redifferentiation. CLV3 is important for meristem organization, binding to a heterodimeric receptor comprising the CLV1 and CLV2 proteins. SCR/SP11 instead plays a role in self-incompatibility, where it activates a signalling cascade that leads to rejection of pollen with the same S haplotype. These ligands all seem to bind to receptors that possess intrinsic kinase activity, and al least two of them are generated by proteolytic processing of larger precursor proteins.

The different mechanisms of sporophytic self-incompatibility

Flowering plants have evolved a multitude of mechanisms to avoid self-fertilization and promote outbreeding. Self-incompatibility (SI) is by far the most common of these, and is found in ca. 60% of flowering plants. SI is a genetically controlled pollen-pistil recognition system that provides a barrier to fertilization by self and self-related pollen in hermaphrodite (usually co-sexual) flowering plants. Two genetically distinct forms of SI can be recognized: gametophytic SI (GSI) and sporophytic SI (SSI), distinguished by how the incompatibility phenotype of the pollen is determined. GSI appears to be the most common mode of SI and can operate through at least three different mechanisms, two of which have been characterized extensively at a molecular level in the Solanaceae and Papaveraceae. Because molecular studies of SSI have been largely confined to species from the Brassicaceae, predominantly Brassica species, it is not yet known whether SSI, like GSI, can operate through different molecular mechanisms. Molecular studies of SSI are now being carried out on Ipomoea trifida (Convolvulaceae) and Senecio squalidus (Asteraceae) and are providing important preliminary data suggesting that SSI in these two families does not share the same molecular mechanism as that of the Brassicaceae. Here, what is currently known about the molecular regulation of SSI in the Brassicaceae is briefly reviewed, and the emerging data on SSI in I. trifida, and more especially in S. squalidus, are discussed.

Genomic organization of the S core region and the S flanking regions of a class-II S haplotype in Brassica rapa

The nucleotide sequence of an 86.4-kb region that includes the SP11, SRK, and SLG genes of Brassica rapa S-60 (a class-II S haplotype) was determined. In the sequenced region, 13 putative genes were found besides SP11-60, SRK-60, and SLG-60. Five of these sequences were isolated as cDNAs, five were homologues of known genes, cDNAs, or ORFs, and three are hypothetical ORFs. Based on their nucleotide sequences, however, some of them are thought to be non-functional. Two regions of colinearity between the class-II S-60 and Brassica class-I S haplotypes were identified, i.e., S flanking region 1 which shows partial colinearity of non-genic sequences and S flanking region 2 which shows a high level of colinearity. The observed colinearity made it possible to compare the order of SP-11, SRK, and SLG genes in the S locus between the five sequenced S haplotypes. It emerged that the order of SRK and SLG in class-II S-60 is the reverse of that in the four class-I S haplotypes reported so far, and the order of SP11, SRK and SLG is the opposite of that in the class-I haplotype S-910. The possible gene designated as SAN1 (S locus Anther-expressed Non-coding RNA like-1), which is located in the region between SP11-60 and SRK-60, has features reminiscent of genes for non-coding RNAs (ncRNAs), but no homologous sequences were found in the databases. This sequence is transcribed in anthers but not in stigmas or leaves. These features of the genomic structure of S-60 are discussed with special reference to the characteristics of class-II S haplotypes.

The S haplotypes lacking SLG in the genome of Brassica rapa

Self-incompatibility (SI) discriminating self- and non-self pollen is regulated by S-locus genes in Brassica. In most of the S haplotypes, a highly polymorphic S-locus glycoprotein ( SLG) gene is tightly linked to genes for the SI determinants, S-receptor kinase ( SRK) and SP11, although the precise function of SLG in SI has not been clarified. In the present study, we performed DNA gel blot analysis for S(32), S(33), and S(36) haplotypes of Brassica rapa showing normal SI phenotypes and concluded that there might be no SLG in their genome. RNA gel blot analysis of the SLG-less S haplotypes indicated the possible existence of eSRK transcripts in the stigma. These three S haplotypes are useful resources to discern the molecular mechanism of the SI reaction without SLG.

Receptor kinase signaling in plant development

The Arabidopsis genome sequence has revealed that plants contain a much larger complement of receptor kinase genes than other organisms. Early analysis of these genes revealed involvement in a diverse array of developmental and defense functions that included gametophyte development, pollen-pistil interactions, shoot apical meristem equilibrium, hormone perception, and cell morphogenesis. Amino acid sequence motifs and binding studies indicate that the ectodomains are capable of binding, either directly or indirectly, various classes of molecules including proteins, carbohydrates, and steroids. Genetic and biochemical approaches have begun to identify other components of several signal transduction pathways. Some receptor-like kinases (RLKs) appear to function with coreceptors lacking kinase domains, and genome analysis suggests this might be true for many RLKs. The KAPP protein phosphatase functions as a negative regulator of at least two RLK systems, and in vitro studies suggest it could be a common component of more. Whether plant signaling systems display a modularity similar to animal systems remains to be determined. Future efforts will reveal unknown functions of other RLKs and elucidate the relationships among their signaling networks.

Just how complex is the Brassica S-receptor complex?

Of the plant self-incompatibility (SI) systems investigated to date, that possessed by members of the Brassicaceae is currently the best understood. Whilst the recent demonstrations of interactions between the male determinant (S-locus cysteine rich protein, SCR) and the female determinant (S-locus receptor kinase, SRK) indicate the minimal requirement for SI in Brassica, no consensus exists as to the nature of these molecules in vivo and the potential involvement of accessory molecules in establishing the active S-receptor complex. Variation between S haplotypes appears to be present in the molecular composition of the receptor complex, the regulation of downstream signalling and the requirement for accessory molecules. This review discusses what constitutes an active receptor complex and highlights potential differences between haplotypes. The role of accessory molecules, in particular SLG (S-locus glycoprotein) and low molecular weight pollen coat proteins (PCPs), in pollination are discussed, as is the link between SI and unilateral incompatibility (UI).

Molecular mechanism of self-recognition in Brassica self-incompatibility

In most self-incompatible plant species, recognition of self-pollen is controlled by a single locus, termed the S-locus. In Brassica, genetic dissection of the S-locus has revealed the presence of three highly-polymorphic genes: S-receptor kinase (SRK), S-locus protein 11 (SP11) (also known as S-locus cysteine-rich protein; SCR) and S-locus glycoprotein (SLG). SRK encodes a membrane-spanning serine/threonine kinase that determines the S-haplotype specificity of the stigma. SP11 encodes a small cysteine-rich protein that determines the S-haplotype specificity of pollen. SLG encodes a secreted form of stigma protein similar to the extracellular domain of SRK. Recent biochemical studies have revealed that SP11 functions as the sole ligand for its cognate SRK receptor complex. Their interaction induces the autophosphorylation of SRK, which is expected to trigger the signalling cascade that results in the rejection of self-pollen. This so-called ligand-receptor complex interaction and receptor activation occur in an S-haplotype-specific manner, and this specificity is almost certainly the basis for self-pollen recognition.

Coevolution of the S-locus genes SRK, SLG and SP11/SCR in Brassica oleracea and B. rapa

Brassica self-incompatibility (SI) is controlled by SLG and SRK expressed in the stigma and by SP11/SCR expressed in the anther. We determined the sequences of the S domains of 36 SRK alleles, 13 SLG alleles, and 14 SP11 alleles from Brassica oleracea and B. rapa. We found three S haplotypes lacking SLG genes in B. rapa, confirming that SLG is not essential for the SI recognition system. Together with reported sequences, the nucleotide diversities per synonymous and nonsynonymous site (pi(S) and pi(N)) at the SRK, SLG, and SP11 loci within B. oleracea were computed. The ratios of pi(N):pi(S) for SP11 and the hypervariable region of SRK were significantly >1, suggesting operation of diversifying selection to maintain the diversity of these regions. In the phylogenetic trees of 12 SP11 sequences and their linked SRK alleles, the tree topology was not significantly different between SP11 and SRK, suggesting a tight linkage of male and female SI determinants during the evolutionary course of these haplotypes. Genetic exchanges between SLG and SRK seem to be frequent; three such recent exchanges were detected. The evolution of S haplotypes and the effect of gene conversion on self-incompatibility are discussed.

Direct ligand-receptor complex interaction controls Brassica self-incompatibility

Many higher plants have evolved self-incompatibility mechanisms to prevent self-fertilization. In Brassica self-incompatibility, recognition between pollen and the stigma is controlled by the S locus, which contains three highly polymorphic genes: S-receptor kinase (SRK), S-locus protein 11 (SP11) (also called S-locus cysteine-rich protein; SCR) and S-locus glycoprotein (SLG). SRK encodes a membrane-spanning serine/threonine kinase that determines the S-haplotype specificity of the stigma, and SP11 encodes a small cysteine-rich protein that determines the S-haplotype specificity of pollen. SP11 is localized in the pollen coat. It is thought that, during self-pollination, SP11 is secreted from the pollen coat and interacts with its cognate SRK in the papilla cell of the stigma to elicit the self-incompatibility response. SLG is a secreted stigma protein that is highly homologous to the SRK extracellular domain. Although it is not required for S-haplotype specificity of the stigma, SLG enhances the self-incompatibility response; however, how this is accomplished remains controversial. Here we show that a single form of SP11 of the S8 haplotype (S8-SP11) stabilized with four intramolecular disulphide bonds specifically binds the stigma membrane of the S8 haplotype to induce autophosphorylation of SRK8, and that SRK8 and SLG8 together form a high-affinity receptor complex for S8-SP11 on the stigma membrane.

Effects of double mutation at two distant IgE-binding sites in the three-dimensional structure of the major house dust mite allergen Der f 2 on IgE-binding and histamine-releasing activity

Recently, we reported that introduction of mutations that induced conformational changes of the major mite allergen Der f 2 was an efficient strategy to reduce the allergenicity for safer allergen-specific immunotherapy. In this study, we evaluated another strategy, disruption of two independent IgE epitopes without inducing conformational change. We analyzed allergenicities of the wild-type Der f 2, two single mutants with a mutation at either of the two IgE-binding sites (K15A and K77A), and a double mutant with mutations at both of the sites (K15/77A). Purified recombinant forms of Der f 2 expressed in Escherichia coli had correct disulfide bonds, equivalent apparent molecular masses of approximately 15 kDa, and similar secondary structures. The mutants of Der f 2 had less IgE reactivities than the wild-type Der f 2 and reduced inhibitory activities for IgE-binding to the wild-type Der f 2. However, the mutations did not significantly reduce histamine-releasing activity.