Annette Becker

A SHORT HISTORY OF MADS-BOX GENES IN PLANTS

Evolutionary developmental genetics (evodevotics) is a novel scientific endeavor which assumes that changes in developmental control genes are a major aspect of evolutionary changes in morphology. Understanding the phylogeny of developmental control genes may thus help us to understand the evolution of plant and animal form. The principles of evodevotics are exemplified by outlining the role of MADS-box genes in the evolution of plant reproductive structures. In extant eudicotyledonous flowering plants, MADS-box genes act as homeotic selector genes determining floral organ identity and as floral meristem identity genes. By reviewing current knowledge about MADS-box genes in ferns, gymnosperms and different types of angiosperms, we demonstrate that the phylogeny of MADS-box genes was strongly correlated with the origin and evolution of plant reproductive structures such as ovules and flowers. It seems likely, therefore, that changes in MADS-box gene structure, expression and function have been a major cause for innovations in reproductive development during land plant evolution, such as seed, flower and fruit formation.

The major clades of MADS-box genes and their role in the development and evolution of flowering plants

MADS-box genes encode a family of transcription factors which control diverse developmental processes in flowering plants ranging from root to flower and fruit development. Sequencing of (almost) the complete Arabidopsis genome enabled the identification of (almost) all of the Arabidopsis MADS-box genes. MADS-box genes have been divided in two large groups, termed type I and type II genes. The type II genes comprise the MEF2-like genes of animals and fungi and the MIKC-type genes of plants. The majority of MIKC-type genes are of the MIKC(c)-type, which includes all plant MADS-box genes for which expression patterns or mutant phenotypes are known. By phylogeny reconstruction, almost all of the MIKC(c)-type genes can be subdivided into 12 major gene clades, each clade comprising 1-6 paralogs from Arabidopsis and putative orthologs from other seed plants. Here we first briefly describe the deep branching of the MADS-box gene tree to place the MIKC(c)-type genes into an evolutionary context. For every clade of MIKC(c)-type genes we then review what is known about its members from Arabidopsis and well-studied members from other phylogenetically informative plant species. By gene sampling and phylogeny reconstructions we provide minimal estimates for the ages of the different clades. It turns out that 7 of the 12 major gene clades, i.e., AG-, AGL6-, AGL12-, DEF+GLO- (B), GGM13- (B(s)), STMADS11- and TM3-like genes very likely existed already in the most recent common ancestor of angiosperms and gymnosperms about 300MYA. Three of the other clades, i.e., AGL2-, AGL17-, and SQUA-like genes, existed at least already in the most recent common ancestor of monocots and eudicots about 200 MYA. Only for two gene clades, AGL15-like genes (2 genes in Arabidopsis) and FLC-like genes (6 genes) members from plants other than Brassicaceae have not been reported yet. Similarly, only one ancient clade known from other flowering plant species, TM8-like genes, is not represented in Arabidopsis. These findings reveal that the diversity of MADS-box genes in Arabidopsis is rather ancient and representative for other flowering plants. Our studies may thus help to predict the set of MADS-box genes in all other flowering plants, except for relatively young paralogs. For the different gene clades we try to identify ancestral and derived gene functions and review the importance of these clades for seed plant development and evolution. We put special emphasis on gene clades for which insights into their importance has rapidly increased just recently.

Conservation and divergence in the AGAMOUS subfamily of MADS-box genes: evidence of independent sub- and neofunctionalization events

The MADS‐box gene AGAMOUS (AG) plays a key role in determining floral meristem and organ identities. We identified three AG homologs, EScaAG1, EScaAG2, and EScaAGL11 from the basal eudicot Eschscholzia californica (California poppy). Phylogenetic analyses indicate that EScaAG1 and EScaAG2 are recent paralogs within the AG clade, independent of the duplication in ancestral core eudicots that gave rise to the euAG and PLENA (PLE) orthologs. EScaAGL11 is basal to core eudicot AGL11 orthologs in a clade representing an older duplication event after the divergence of the angiosperm and gymnosperm lineages. Detailed in situ hybridization experiments show that expression of EScaAG1 and EScaAG2 is similar to AG; however, both genes appear to be expressed earlier in floral development than described in the core eudicots. A thorough examination of available expression and functional data in a phylogenetic context for members of the AG and AGL11 clades reveals that gene expression has been quite variable throughout the evolutionary history of the AG subfamily and that ovule‐specific expression might have evolved more than twice. Although sub‐ and neofunctionalization are inferred to have occurred following gene duplication, functional divergence among orthologs is evident, as is convergence, among paralogs sampled from different species. We propose that retention of multiple AG homologs in several paralogous lineages can be explained by the conservation of ancestral protein activity combined with evolutionarily labile regulation of expression in the AG and AGL11 clades such that the collective functions of the AG subfamily in stamen and carpel development are maintained following gene duplication.

VIGS – genomics goes functional

Genome and EST sequencing projects generate a wealth of sequence information for agronomically and phylogenetically important plant species of which the majority is difficult to subject to functional genomics. Virus-induced gene silencing (VIGS) provides a powerful tool to enable gene functional analysis for species not amenable to stable genetic transformation. Recent approaches allow the use of VIGS as a high throughput method that will exploit the potential of genome and transcriptome projects further.

A novel MADS-box gene subfamily with a sister-group relationship to class B floral homeotic genes

Abstract. Class B floral homeotic genes specify the identity of petals and stamens during the development of angiosperm flowers. Recently, putative orthologs of these genes have been identified in different gymnosperms. Together, these genes constitute a clade, termed B genes. Here we report that diverse seed plants also contain members of a hitherto unknown sister clade of the B genes, termed Bsister (Bs) genes. We have isolated members of the Bs clade from the gymnosperm Gnetum gnemon, the monocotyledonous angiosperm Zea mays and the eudicots Arabidopsis thaliana and Antirrhinum majus. In addition, MADS-box genes from the basal angiosperm Asarum europaeum and the eudicot Petunia hybrida were identified as Bs genes. Comprehensive expression studies revealed that Bs genes are mainly transcribed in female reproductive organs (ovules and carpel walls). This is in clear contrast to the B genes, which are predominantly expressed in male reproductive organs (and in angiosperm petals). Our data suggest that the Bs genes played an important role during the evolution of the reproductive structures in seed plants. The establishment of distinct B and Bs gene lineages after duplication of an ancestral gene may have accompanied the evolution of male microsporophylls and female megasporophylls 400–300 million years ago. During flower evolution, expression of Bs genes diversified, but the focus of expression remained in female reproductive organs. Our findings imply that a clade of highly conserved close relatives of class B floral homeotic genes has been completely overlooked until recently and awaits further evaluation of its developmental and evolutionary importance. Electronic supplementary material to this paper can be obtained by using the Springer Link server located at http://dx.doi.org/10.1007/s00438-001-0615-8.

Heteroblasty—A Review

Virtually all plants show a certain degree of variation among individual metamers during ontogeny. In some cases, however, there are abrupt and substantial changes in form and function (e.g. in leaf form, leaf size, phyllotaxy, internode length, anthocyanin pigmentation, rooting ability, or wood structure). These plants were called “heteroblastic” by Karl Goebel more than a century ago, but the functional significance of this type of ontogenetic change, the evolutionary trajectories in different plant groups, even their frequency in the plant kingdom are still unresolved issues. We argue that slow progress is partly due to an on-going terminological confusion and the lack of distinction between other developmental processes such as ontogenetic drift. This review develops a conceptual framework for future scientific work, proposes a quantitative index of heteroblasty, and discusses the evidence for developmental regulation, functional significance, and evolutionary implications of heteroblasty to provide a stimulating basis for further research with this fascinating group of plants.ZusammenfassungFast alle Pflanzen zeigen während der Individualentwicklung ein gewisses Maß an Variabilität einzelner Metamere. Bei manchen Arten kommt es jedoch zu einer ausgeprägten und sprunghaften Änderung in Form und Funktion (z.B. in Blattform oder -stellung, Internodienlänge, Pigmentierung, Holzstruktur, oder hinsichtlich der Fähigkeit zur Bildung von Adventivwurzeln). Obwohl diese Arten von Karl Goebel schon vor mehr als einem Jahrhundert als “heteroblastisch” beschrieben wurden, sind die funktionelle Bedeutung des Phänomens, dessen Evolution innerhalb einzelner Pflanzengruppen, wie auch die Häufigkeit im Pflanzenreich immer noch weitgehend ungeklärt. Dieser schleppende Fortschritt mag mit einem weit verbreiteten terminologischen Durcheinander und dem Fehlen einer klaren Abgrenzung von anderen Entwicklungsprozessen wie der “ontogenetischen Drift” zusammenhängen. Unser Übersichtsartikel entwickelt einen klaren konzeptionellen Rahmen, um eine Basis zu schaffen für zukünftige Forschungsarbeiten dieses faszinierenden Entwicklungsphänomens. Dazu schlagen wir einen quantitativen Index der Heteroblastie vor, skizzieren den gegenwärtigen Wissensstand der Regulierung von Entwicklungsprozessen bei Pflanzen, die bisherigen Untersuchungen zur funktionelle Bedeutung heteroblastischer Veränderungen, beleuchten aber auch die evolutionären Implikationen der Heteroblastie.

N-acyl-homoserine lactone primes plants for cell wall reinforcement and induces resistance to bacterial pathogens via the salicylic acid/oxylipin pathway

The bacterial quorum-sensing molecule N-3-oxo-tetradecanoyl-l-homoserine lactone primes the plant for enhanced resistance to bacterial pathogens. The proposed mechanism is based on modifications of the cell wall composition and the responsiveness of stomatal guard cells to pathogen attack. The ability of plants to monitor their surroundings, for instance the perception of bacteria, is of crucial importance. The perception of microorganism-derived molecules and their effector proteins is the best understood of these monitoring processes. In addition, plants perceive bacterial quorum sensing (QS) molecules used for cell-to-cell communication between bacteria. Here, we propose a mechanism for how N-acyl-homoserine lactones (AHLs), a group of QS molecules, influence host defense and fortify resistance in Arabidopsis thaliana against bacterial pathogens. N-3-oxo-tetradecanoyl-l-homoserine lactone (oxo-C14-HSL) primed plants for enhanced callose deposition, accumulation of phenolic compounds, and lignification of cell walls. Moreover, increased levels of oxylipins and salicylic acid favored closure of stomata in response to Pseudomonas syringae infection. The AHL-induced resistance seems to differ from the systemic acquired and the induced systemic resistances, providing new insight into inter-kingdom communication. Consistent with the observation that short-chain AHLs, unlike oxo-C14-HSL, promote plant growth, treatments with C6-HSL, oxo-C10-HSL, or oxo-C14-HSL resulted in different transcriptional profiles in Arabidopsis. Understanding the priming induced by bacterial QS molecules augments our knowledge of plant reactions to bacteria and suggests strategies for using beneficial bacteria in plant protection.

The CRABS CLAW ortholog from California poppy (Eschscholzia californica, Papaveraceae), EcCRC, is involved in floral meristem termination, gynoecium differentiation and ovule initiation

The Arabidopsis transcription factor CRABS CLAW (CRC) is a major determinant of carpel growth and fusion, and, in concert with other redundantly acting genes, of floral meristem termination. Its rice ortholog, however, has additional functions in specifying carpel organ identity. We were interested in understanding the history of gene function modulation of CRC-like genes during angiosperm evolution. Here, we report the identification and functional characterization of EcCRC, the Californica poppy (Eschscholzia californica) CRC ortholog. The downregulation of EcCRC by virus-induced gene silencing (VIGS) produces additional organ whorls that develop exclusively into gynoecia, resulting in a reiteration of the fourth whorl. Additionally, defects in carpel polarity and ovule initiation are apparent, and the observed phenotype is restricted to the gynoecium. Our results further show that the history of CRC-like genes during angiosperm evolution is characterized by gains of function, independent of duplication processes in this gene subfamily. Moreover, our data indicate that the ancestral angiosperm CRC-like gene was involved in floral meristem termination and the promotion of abaxial cell fate in the gynoecium, and that in the lineage leading to Arabidopsis, additional genes have been recruited to adopt some of these functions, resulting in a high degree of redundancy.

Gymnosperm Orthologues of Class B Floral Homeotic Genes and Their Impact on Understanding Flower Origin

Class B floral homeotic genes play a key role in specifying the identity of male reproductive organs (stamens) and petals during the development of flowers. Recently, close relatives (orthologues) of these genes have been found in diverse gymnosperms, the sister group of the flowering plants (angiosperms). The fact that such genes have not been found so far, despite considerable efforts, in mosses, ferns or algae, has been taken as evidence to suggest that B genes originated 300–400 million years ago in a lineage that led to extant seed plants. Gymnosperms do not develop petals, and their male reproductive organs deviate considerably from angiosperm stamens. So what is the function of gymnosperm B genes? Recent experiments revealed that B genes from diverse extant gymnosperms are exclusively expressed in male reproductive organs (microsporophylls). At least for some of these genes it has been shown that they can partially substitute for the Arabidopsis B genes AP3 and PI in ectopic expression experiments, or even partially substitute these genes in different class B floral organ identity gene mutants. This functional complementation, however, is restricted to male organ development. These findings strongly suggest that gymnosperm and angiosperm B genes have highly related interaction partners and equivalent functions in the male organs of their different host species. It seems likely that in extant gymnosperms B genes have a function in specifying male reproductive organs. This function was probably established already in the most recent common ancestor of extant gymnosperms and angiosperms (seed plants) 300 million years ago and thus represents the ancestral function of seed plant B genes, from which other functions (e.g., in specifying petal identity) might have been derived. This suggests that the B gene function is part of an ancestral sex determination system in which B gene expression specifies male reproductive organ development, while the absence of B gene expression leads to the formation of female reproductive organs. Such a simple switch mechanism suggests that B genes might have played a central role during the origin of flowers. In the out-of-male and out-of-female hypotheses changes in B gene expression led to the origin of hermaphroditic flower precursors out of male or female gymnosperm reproductive cones, respectively. We compare these hypotheses with other recent molecular hypotheses on the origin of flowers, in which C/D and FLORICAULA/LEAFY-like genes is given a more prominent role, and we suggest how these hypotheses might be tested in the future.

The Tarenaya hassleriana Genome Provides Insight into Reproductive Trait and Genome Evolution of Crucifers

A comparative analysis of the genome of the spider flower (Tarenaya hassleriana) from the Brassicaceae sister family, the Cleomaceae, with Arabidopsis and Brassica crops shows that genome evolution following ancient polyploidy and gene duplication events affect reproductively important traits, including floral development and self-incompatibility systems. The Brassicaceae, including Arabidopsis thaliana and Brassica crops, is unmatched among plants in its wealth of genomic and functional molecular data and has long served as a model for understanding gene, genome, and trait evolution. However, genome information from a phylogenetic outgroup that is essential for inferring directionality of evolutionary change has been lacking. We therefore sequenced the genome of the spider flower (Tarenaya hassleriana) from the Brassicaceae sister family, the Cleomaceae. By comparative analysis of the two lineages, we show that genome evolution following ancient polyploidy and gene duplication events affect reproductively important traits. We found an ancient genome triplication in Tarenaya (Th-α) that is independent of the Brassicaceae-specific duplication (At-α) and nested Brassica (Br-α) triplication. To showcase the potential of sister lineage genome analysis, we investigated the state of floral developmental genes and show Brassica retains twice as many floral MADS (for MINICHROMOSOME MAINTENANCE1, AGAMOUS, DEFICIENS and SERUM RESPONSE FACTOR) genes as Tarenaya that likely contribute to morphological diversity in Brassica. We also performed synteny analysis of gene families that confer self-incompatibility in Brassicaceae and found that the critical SERINE RECEPTOR KINASE receptor gene is derived from a lineage-specific tandem duplication. The T. hassleriana genome will facilitate future research toward elucidating the evolutionary history of Brassicaceae genomes.