Compatibility and incompatibility in S-RNase-based systems

Background: S-RNase-based self-incompatibility (SI) occurs in the Solanaceae, Rosaceae and Plantaginaceae. In all three families, compatibility is controlled by a polymorphic S-locus encoding at least two genes. S-RNases determine the specificity of pollen rejection in the pistil, and S-locus F-box proteins fulfill this function in pollen. S-RNases are thought to function as S-specific cytotoxins as well as recognition proteins. Thus, incompatibility results from the cytotoxic activity of S-RNase, while compatible pollen tubes evade S-RNase cytotoxicity. SCOPE: The S-specificity determinants are known, but many questions remain. In this review, the genetics of SI are introduced and the characteristics of S-RNases and pollen F-box proteins are briefly described. A variety of modifier genes also required for SI are also reviewed. Mutations affecting compatibility in pollen are especially important for defining models of compatibility and incompatibility. In Solanaceae, pollen-side mutations causing breakdown in SI have been attributed to the heteroallelic pollen effect, but a mutation in Solanum chacoense may be an exception. This has been interpreted to mean that pollen incompatibility is the default condition unless the S-locus F-box protein confers resistance to S-RNase. In Prunus, however, S-locus F-box protein gene mutations clearly cause compatibility. CONCLUSIONS: Two alternative mechanisms have been proposed to explain compatibility and incompatibility: compatibility is explained either as a result of either degradation of non-self S-RNase or by its compartmentalization so that it does not have access to the pollen tube cytoplasm. These models are not necessarily mutually exclusive, but each makes different predictions about whether pollen compatibility or incompatibility is the default. As more factors required for SI are identified and characterized, it will be possible to determine the role each process plays in S-RNase-based SI.     

The evolution of reproductive isolation in the ectomycorrhizal Hebeloma crustuliniforme aggregate (Basidiomycetes) in northwestern Europe: a phylogenetic approach

Abstract. To reconstruct the evolution of reproductive isolation in the ectomycorrhizal Hebeloma crustuliniforme aggregate (Basidiomycetes), phylogenetic relationships were determined between strains that belong to a clade consisting of nine intercompatibility groups (ICGs, biological species). Four of these nine ICGs are partially compatible and belong to the H. crustuliniforme aggregate. Different levels of partial compatibility have been found between these four ICGs. Between ICGs 3 and 4, 15% of the combinations were compatible. One strain was compatible with all isolates of both ICGs 3 and 4 and also with one isolate of ICG 2. Both a nuclear phylogeny, based on ribosomal IGS sequence data, and a mitochondrial phylogeny, based on a group-I intron located in the large subunit ribosomal RNA gene (LrRNA), were reconstructed. The level of incompatibility was compared with the phylogenetic history of individuals belonging to this clade.
Different relationships were found between the level of compatibility and the relative age of the most recent common ancestor (MRCA) for different ICGs. On the one hand, the evolution of incompatibility between ICGs 2 and 3/4 is most consistent with the class of "divergence- first" models because a positive correlation was found between the relative age of the MRCA and the level of incompatibility for ICG 2 versus 3/4. On the other hand, the lack of such a correlation for ICGs 3 and 4 shows that (partial) incompatibility between these ICGs has arisen without strong divergence. The ecological (and to a lesser extent geographical) differences found between ICGs 3 and 4 suggest that selection for incompatibility, associated with host tree preference, has been important in the evolution of incompatibility between these two ICGs. The incongruence between the nuclear and mitochondrial trees for ICG 1 could be explained by a hybrid origin of this ICG, with different donors of the mitochondrial and nuclear sequences.     

Cytoplasmic Incompatibility and Bacterial Density in Nasonia Vitripennis

Cytoplasmically (maternally) inherited bacteria that cause reproductive incompatibility between strains are widespread among insects. In the parasitoid wasp Nasonia, incompatibility results in improper condensation and fragmentation of the paternal chromosomes in fertilized eggs. Some form of genome imprinting may be involved. Because of haplodiploidy, incompatibility results in conversion of (diploid) female eggs into (haploid) males. Experiments show that bacterial density is correlated with compatibility differences between male and female Nasonia. Males from strains with high bacterial numbers are incompatible with females from strains with lower numbers. Temporal changes in compatibility of females after tetracycline treatment are generally correlated with decreases in bacterial levels in eggs. However, complete loss of bacteria in mature eggs precedes conversion of eggs to the ``asymbiont' compatibility type by 3-4 days. This result is consistent with a critical ``imprinting' period during egg maturation, when cytoplasmic bacteria determine compatibility. Consequent inheritance of reduced bacterial numbers in F(1) progeny has different effects on compatibility type of subsequent male vs. female progeny. In some cases, partial incompatibility occurs which results in reduced offspring numbers, apparently due to incomplete paternal chromosome elimination resulting in aneuploidy.     

An interpretation of snail-trematode infection rates: specificitity based on concordance of compatible phenotypes.

A formula is proposed that bases host-parasite specificity upon genetically determined characters for compatibility in both snail and trematode. Individual snails are thereby considered to be susceptible or resistant to individual miracidia and infections rates are controlled by the relative frequencies of relevant genes in the particular populations concerned. The biological evidence for this hypothesis stems from published geographic, genetic, and histological studies in the Biomphalaria-Schistosoma host-parasite complex. The specific mechanism of incompatibility probably resides in the host cellular reaction to parasites recognized as foreign. The principles governing snail-trematode specificity are considered applicable to all combinations and underlie regional and evolutionary adaptations in these groups. The hypothesis of Dönges that snail populations are homogeneous with regard to susceptibility is discussed.     

COMPARATIVE EVIDENCE FOR THE CORRELATED EVOLUTION OF POLYPLOIDY AND SELF‐COMPATIBILITY IN SOLANACEAE

Breakdown of self‐incompatibility occurs repeatedly in flowering plants with important evolutionary consequences. In plant families in which self‐incompatibility is mediated by S‐RNases, previous evidence suggests that polyploidy may often directly cause self‐compatibility through the formation of diploid pollen grains. We use three approaches to examine relationships between self‐incompatibility and ploidy. First, we test whether evolution of self‐compatibility and polyploidy is correlated in the nightshade family (Solanaceae), and find the expected close association between polyploidy and self‐compatibility. Second, we compare the rate of breakdown of self‐incompatibility in the absence of polyploidy against the rate of breakdown that arises as a byproduct of polyploidization, and we find the former to be greater. Third, we apply a novel extension to these methods to show that the relative magnitudes of the macroevolutionary pathways leading to self‐compatible polyploids are time dependent. Over small time intervals, the direct pathway from self‐incompatible diploids is dominant, whereas the pathway through self‐compatible diploids prevails over longer time scales. This pathway analysis is broadly applicable to models of character evolution in which sequential combinations of rates are compared. Finally, given the strong evidence for both irreversibility of the loss of self‐incompatibility in the family and the significant association between self‐compatibility and polyploidy, we argue that ancient polyploidy is highly unlikely to have occurred within the Solanaceae, contrary to previous claims based on genomic analyses.     

New views of S-RNase-based self-incompatibility

S-RNase-based self-incompatibility (SI) is the most widespread form of genetically controlled mate selection in plants. S-RNase controls pollination specificity in the pistil, while the newly discovered SLF/SFB controls pollination specificity in the pollen. A widely discussed model suggests that compatibility is explained by ubiquitylation and degradation of nonself-S-RNase and that, conversely, incompatibility is caused by failure to degrade self-S-RNase. This model is consistent with the long-standing view that S-RNase inhibition is central to SI. Recent results show, however, that S-RNase is compartmentalized in pollen tubes and, significantly, that compatibility might not require SLF/SFB. S-RNase compartmentalization and dislocation into the pollen tube cytoplasm might be similar to the trafficking of other cytotoxins such as ricin.     

Functional Analyses of the Neurospora Crassa Mt a-1 Mating Type Polypeptide

The Neurospora crassa mt a-1 gene, encoding the MT a-1 polypeptide, determines a mating type properties: sexual compatibility and vegetative incompatibility with A mating type. We characterized in vivo and in vitro functions of the MT a-1 polypeptide and specific mutant derivatives. MT a-1 polypeptide produced in Escherichia coli bound to specific DNA sequences whose core was 5'-CTTTG-3'. DNA binding was a function of the MT a-1 HMG box domain (a DNA binding motif found in high mobility group proteins and a diverse set of regulatory proteins). Mutation within the HMG box eliminated DNA binding in vitro and eliminated mating in vivo, but did not interfere with vegetative incompatibility function in vivo. Conversely, deletion of amino acids 216-220 of MT a-1 eliminated vegetative incompatibility, but did not affect mating or DNA binding. Deletion of the carboxyl terminal half of MT a-1 eliminated both mating and vegetative incompatibility in vivo, but not DNA binding in vitro. These results suggest that mating depends upon the ability of MT a-1 polypeptide to bind to, and presumably to regulate the activity of, specific DNA sequences. However, the separation of vegetative incompatibility from both mating and DNA binding indicates that vegetative incompatibility functions by a biochemically distinct mechanism.     

RP1 properties and fertility inhibition among P, N, W, and X incompatibility group plasmids.

Incompatibility group P plasmids demonstrate strong entry exclusion properties. Stringent incompatibility is also observed in the absence of entry exclusion. These observations have been facilitated by the study of a nontransmissible plasmid, RP1-S2, derived from RP1 by transductional shortening. RP1-S2 retains carbenicillin and tetracycline resistances as well as loci that cause either the loss of P plasmids (incp) or a locus specifying susceptibility to curing (sinp) in the presence of a P plasmid. RP1-S2 can be mobilized by an incompatibility group W plasmid, R388, and also freely forms recombinants with R388. P, N, and W incompatibility group plasmids all encode information for the receptor of the cell wall-adsorbing phage PRD1. Based on the premise that the location of this receptor is analogous to entry exclusion factors for F-like plasmids and hence a regulated transfer region determinant, we tested fertility inhibition relationships among these plasmid groups. We detected both reciprocal and nonreciprocal fertility inhibition relationships for bacteria containing various combinations of W, N, and P group plasmids. The nonreciprocal nature of some combinations, we believe, reflects the identity of the point mutation reading to derepression of the plasmid in question. Reciprocal fertility inhibition, on the other hand, may reflect the reconstruction of a fertility inhibition system through complementation. An X incompatibility group plasmid, known to affect the fertility of an N group plasmid, was also shown to inhibit P plasmid fertility. These observations may indicate a possible evolutionary relationship(s) of plasmids unrelated by the criteria of incompatibility, pilus phage specificity, or plasmid host range.     

HET-E and HET-D belong to a new subfamily of WD40 proteins involved in vegetative incompatibility specificity in the fungus Podospora anserina

Vegetative incompatibility, which is very common in filamentous fungi, prevents a viable heterokaryotic cell from being formed by the fusion of filaments from two different wild-type strains. Such incompatibility is always the consequence of at least one genetic difference in specific genes (het genes). In Podospora anserina, alleles of the het-e and het-d loci control heterokaryon viability through genetic interactions with alleles of the unlinked het-c locus. The het-d2(Y) gene was isolated and shown to have strong similarity with the previously described het-e1(A) gene. Like the HET-E protein, the HET-D putative protein displayed a GTP-binding domain and seemed to require a minimal number of 11 WD40 repeats to be active in incompatibility. Apart from incompatibility specificity, no other function could be identified by disrupting the het-d gene. Sequence comparison of different het-e alleles suggested that het-e specificity is determined by the sequence of the WD40 repeat domain. In particular, the amino acids present on the upper face of the predicted beta-propeller structure defined by this domain may confer the incompatible interaction specificity.     

Allelic Specificity at the Het-C Heterokaryon Incompatibility Locus of Neurospora Crassa Is Determined by a Highly Variable Domain

In filamentous fungi, the ability to form a productive heterokaryon with a genetically dissimilar individual is controlled by specific loci termed het loci. Only strains homozygous for all het loci can establish a heterokaryon. In Neurospora crassa, 11 loci, including the mating-type locus, regulate the capacity to form heterokaryons. An allele of the het-c locus (het-c(OR)) of N. crassa has been previously characterized and encodes a nonessential 966 amino acid glycine-rich protein. Herein, we describe the genetic and molecular characterization of two het-c alleles, het-c(PA) and het-c(GR), that have a different specificity from that of het-c(OR), showing that vegetative incompatibility is mediated by multiple alleles at het-c. By constructing chimeric alleles, we show that het-c specificity is determined by a highly variable domain of 34-48 amino acids in length. In this regard, het-c is similar to loci that regulate recognition in other species, such as the (S) self-incompatibility locus in plants, the sexual compatibility locus in basidiomycetes and the major histocompatibility complex (MHC) genes in vertebrates.     

The role of negative selection in protein evolution revealed through the energetics of the native state ensemble

Knowing the determinants of conformational specificity is essential for understanding protein structure, stability, and fold evolution. To address this issue, a novel statistical measure of energetic compatibility between sequence and structure was developed using an experimentally validated model of the energetics of the native state ensemble. This approach successfully matched sequences from a diverse subset of the human proteome to their respective folds. Unexpectedly, significant energetic compatibility between ostensibly unrelated sequences and structures was also observed. Interrogation of these matches revealed a general framework for understanding the origins of conformational specificity within a proteome: specificity is a complex function of both the ability of a sequence to adopt folds other than the native, and ability of a fold to accommodate sequences other than the native. The regional variation in energetic compatibility indicates that the compatibility is dominated by incompatibility of sequence for alternative fold segments, suggesting that evolution of protein sequences has involved substantial negative selection, with certain segments serving as “gatekeepers” that presumably prevent alternative structures. Beyond these global trends, a size dependence exists in the degree to which the energetic compatibility is determined from negative selection, with smaller proteins displaying more negative selection. This partially explains how short sequences can adopt unique folds, despite the higher probability in shorter proteins for small numbers of mutations to increase compatibility with other folds. In providing evolutionary ground rules for the thermodynamic relationship between sequence and fold, this framework imparts valuable insight for rational design of unique folds or fold switches. Proteins 2016; 84:435–447. © 2016 Wiley Periodicals, Inc.     

Sea urchin bindin divergence predicts gamete compatibility

Studies on the evolution of reproductive proteins have shown that they tend to evolve more rapidly than other proteins, frequently under positive selection. Progress on understanding the implications of these patterns is possible for marine invertebrates, where molecular evolution can be linked to gamete compatibility. In this study, we surveyed data from the literature from five genera of sea urchins for which there was information on gamete compatibility, divergence of the sperm-egg recognition protein bindin, and mitochondrial divergence. We draw three conclusions: (1) bindin divergence at nonsynonymous sites predicts gamete compatibility, whereas (2) bindin divergence at synonymous sites and mitochondrial DNA divergence do not, and (3) as few as 10 amino acid changes in bindin can lead to complete gamete incompatibility between species. Using mitochondrial divergence as a proxy for time, we find that complete gamete incompatibility can evolve in approximately one and a half million years, whereas sister species can maintain complete gamete compatibility for as long as five million years.     

Comparative analysis of the replicon regions of eleven ColE2-related plasmids.

The incA gene product of ColE2-P9 and ColE3-CA38 plasmids is an antisense RNA that regulates the production of the plasmid-coded Rep protein essential for replication. The Rep protein specifically binds to the origin and synthesizes a unique primer RNA at the origin. The IncB incompatibility is due to competition for the Rep protein among the origins of the same binding specificity. We localized the regions sufficient for autonomous replication of 15 ColE plasmids related to ColE2-P9 and ColE3-CA38 (ColE2-related plasmids), analyzed their incompatibility properties, and determined the nucleotide sequences of the replicon regions of 9 representative plasmids. The results suggest that all of these plasmids share common mechanisms for initiation of DNA replication and its control. Five IncA specificity types, 4 IncB specificity types, and 9 of the 20 possible combinations of the IncA and IncB types were found. The specificity of interaction of the Rep proteins and the origins might be determined by insertion or deletion of single nucleotides and substitution of several nucleotides at specific sites in the origins and by apparently corresponding insertion or deletion and substitution of amino acid sequences at specific regions in the C-terminal portions of the Rep proteins. For plasmids of four IncA specificity types, the nine-nucleotide sequences at the loop regions of the stem-loop structures of antisense RNAs are identical, suggesting an evolutionary significance of the sequence. The mosaic structures of the replicon regions with homologous and nonhomologous segments suggest that some of them were generated by exchanging functional parts through homologous recombination.     

THE ROLE OF INBREEDING DEPRESSION AND MATING SYSTEM IN THE EVOLUTION OF HETEROSTYLY

We investigated the role of morph‐based differences in the expression of inbreeding depression in loss of the mid‐styled morph from populations of tristylous Oxalis alpina. The extent of self‐compatibility (SC) of reproductive morphs, the degree of self‐fertilization, and the magnitude of inbreeding depression were investigated in three populations of O. alpina differing in their tristylous incompatibility relationships. All three populations exhibited significant inbreeding depression. In two populations with highly modified tristylous incompatibility, manifested as increased reciprocal compatibility between short‐ and long‐styled morphs, substantial SC and self‐fertilization of mid‐styled morphs were detected, and expected to result in expression of inbreeding depression in the progeny of mid‐styled morphs in the natural populations. In contrast, significant self‐fertility of the mid‐styled morph was absent from the population with typical tristylous incompatibility, and no self‐fertilization could be detected. Although self‐fertilization and expression of inbreeding depression should result in selection against the mid‐styled morph in the later stages of the transition from tristyly to distyly, in O. alpina selection against the mid‐styled morph in the early phases of the evolution of distyly is likely due to genic selection against mid‐alleles associated with modified tristylous incompatibility, rather than expression of inbreeding depression.     

The location and analysis of two heterokaryon incompatibility (het) loci in strains of Aspergillus nidulans

The heterokaryon incompatibility system in Aspergillus nidulans has been investigated by parasexual methods. The use of complementary auxotrophs with a repeated serial transfer method or with a protoplast fusion technique has enabled heterokaryons and diploid strains to be recovered from heterokaryon incompatible combinations of strains. The effects of allelic interaction at heterokaryon incompatibility (het) loci on the morphologies of the heterokaryon and diploid colonies isolated are described. Parasexual analyses conducted among strains belonging to the heterokaryon compatibility groups, h-cGl and h-cB, and the two recombinant compatibility classes, have located the hetA and hetB genes to linkage groups V and VI respectively.     

Mentor pollen: Possible role of wall-held pollen growth promoting substances in overcoming intra- and interspecific incompatibility

Recent studies have shown that certain normally incompatible, interspecific combinations in the genus Populus, and intraspecific combination in Cosmos bipinnatus can be made compatible by mixing irradiation- or chemically-killed compatible pollen (mentor) with normal incompatible pollen at the time of pollination. Knox and associates have proposed that in the sporophytic system of incompatibility the compatible mentor pollen provides the so-called specific recognition substances to the incompatible pollen thereby making the latter compatible. In the present experiments mentor pollen was used in attempts to overcome both intra- and interspecific incompatibility in the genus Nicotiana which has a gametophytic intraspecific incompatibility system. Although not denying that recognition substances specific to pollenpistil incompatibility reactions are present in pollen walls, the results suggest that a role of mentor pollen in overcoming incompatibility may be to provide extra free pollen growth promoting substances (PGS). These substances are apparently able to promote just sufficient further growth to allow some fertilizations by certain pollen tubes with inherently weak expression of incompatibility.The present proposed PGS-Hypothesis also elucidates the physiological basis of the widely-held relationship found between genetic systems of self-incompatibility and sites of pollen inhibition.     

ARE SPECIES REAL? THE SHAPE OF THE SPECIES BOUNDARY WITH EXPONENTIAL FAILURE,REINFORCEMENT, AND THE “MISSING SNOWBALL”

Under simple assumptions, the evolution of epistatic "Dobzhansky–Muller" incompatibilities between a pair of species should yield an accelerating decline of log overall reproductive compatibility—a "snowball" effect that might rapidly provide new species with "reality." Possible alternatives include: (1) simple exponential failure, giving a linear rate of log compatibility loss, and (2) "slowdown," likely during reinforcement in which mate choice evolves to prevent deleterious hybridization, yielding a decelerating log compatibility loss. In analyses of multiple datasets, we find little support for the snowball effect, except possibly in Lepidoptera hybrid viability. The snowball predicts a slow initial rate of incompatibility acquisition, with low initial variance; instead, highly variable compatibility is almost universally observed at low genetic distances. Another deviation from predictions is that reproductive isolation usually remains incomplete until long after speciation. These results do not disprove snowball compatibility decay, but can result if large deleterious effects are due to relatively few genetic changes, or if different types of incompatibility evolve at very different rates. On the other hand, data on Bacillus and Saccharomyces , as well as theories of chromosomal evolution, suggest that some kinds of incompatibility accumulate approximately linearly, without Dobzhansky–Muller effects. In microorganisms, linearity can result from direct negative effects of DNA sequence divergence on compatibility. Finally, a decelerating slowdown model is supported for sympatric Leptasterias starfish, and in Drosophila prezygotic isolation in sympatry but not allopatry, providing novel comparative evidence for reinforcement.     

Rapid loss of self‐incompatibility in experimental populations of the perennial outcrossing plant Linaria cavanillesii

Transitions from self‐incompatibility to self‐compatibility in angiosperms may be frequently driven by selection for reproductive assurance when mates or pollinators are rare, and are often succeeded by loss of inbreeding depression by purging. Here, we use experimental evolution to investigate the spread of self‐compatibility from one such population of the perennial plant Linaria cavanillesii into self‐incompatible (SI) populations that still have high inbreeding depression. We introduced self‐compatible (SC) individuals at different frequencies into replicate experimental populations of L. cavanillesii that varied in access to pollinators. Our experiment revealed a rapid shift to self‐compatibility in all replicates, driven by both greater seed set and greater outcross siring success of SC individuals. We discuss our results in the light of computer simulations that confirm the tendency of self‐compatibility to spread into SI populations under the observed conditions. Our study illustrates the ease with which self‐compatibility can spread among populations, a requisite for species‐wide transitions from self‐incompatibility to self‐compatibility.     

Ultraviolet Light-Induced Heterokaryon Formation and Parasexuality in Cryphonectria parasitica

Rizwana, R., and Powell, W. A. 1995. Ultraviolet light-induced heterokaryon formation and parasexuality in Cryphonectria parasitica. Experimental Mycology 19, 48-60. The effect of ultraviolet-light on heterokaryon formation, vegetative compatibility, and parasexuality in Cryphonectria parasitica was examined. Heterokaryons of complementary auxotrophic strains could not be made by hyphal anastomosis if the strains belonged to different vegetative compatibility groups. Protoplast fusions overcame incompatibility of strains differing in the alleles of a single but not multiple vegetative incompatibility loci. Fusion of protoplasts from ultraviolet light-treated complementary auxotrophs increased heterokaryon formation by 10⁴ to 10⁵ using the strains differing in alleles of a single vegetative incompatibility gene but had no detectable effect on strains differing in multiple vegetative incompatibility genes. Vegetative compatibility tests of single conidial isolates resolved from these heterokaryons suggest that diploids had formed followed by the loss of one of the VIC alleles. Presence of both auxotrophic markers in some of these single conidial isolates confirms the occurrence of a parasexual cycle. These experiments demonstrate that ultraviolet-light can enhance heterokaryon formation and parasexuality in C. parasitica .