Lydia Gramzow

A hitchhiker's guide to the MADS world of plants.

Plant life critically depends on the function of MADS-box genes encoding MADS-domain transcription factors, which are present to a limited extent in nearly all major eukaryotic groups, but constitute a large gene family in land plants. There are two types of MADS-box genes, termed type I and type II, and in plants these groups are distinguished by exon-intron and domain structure, rates of evolution, developmental function and degree of functional redundancy. The type I genes are further subdivided into three groups - Mα, Mβ and Mγ - while the type II genes are subdivided into the MIKCC and MIKC* groups. The functional diversification of MIKCC genes is closely linked to the origin of developmental and morphological novelties in the sporophytic (usually diploid) generation of seed plants, most spectacularly the floral organs and fruits of angiosperms. Functional studies suggest different specializations for the different classes of genes; whereas type I genes may preferentially contribute to female gametophyte, embryo and seed development and MIKC*-group genes to male gametophyte development, the MIKCC-group genes became essential for diverse aspects of sporophyte development. Beyond the usual transcriptional regulation, including feedback and feed-forward loops, various specialized mechanisms have evolved to control the expression of MADS-box genes, such as epigenetic control and regulation by small RNAs. In future, more data from genome projects and reverse genetic studies will allow us to understand the birth, functional diversification and death of members of this dynamic and important family of transcription factors in much more detail.

On the origin of MADS-domain transcription factors

MADS-domain transcription factors are involved in signal transduction and developmental control in plants, animals and fungi. Because their diversification is linked to the origin of novelties in multicellular eukaryotes, the early evolution of MADS-domain proteins is of interest, but has remained enigmatic. Employing whole genome sequence information and remote homology detection methods, we demonstrate that the MADS domain originated from a region of topoisomerases IIA subunit A. Furthermore, we provide evidence that gene duplication occurred in the lineage that led to the MRCA of extant eukaryotes, giving rise to SRF-like and MEF2-like MADS-box genes.

Horizontal gene transfer and functional diversification of plant cell wall degrading polygalacturonases: Key events in the evolution of herbivory in beetles

Plant cell walls are the largest reservoir of organic carbon on earth. To breach and utilize this carbohydrate-rich protective barrier, microbes secrete plant cell wall degrading enzymes (PCWDEs) targeting pectin, cellulose and hemicelluloses. There is a growing body of evidence that genomes of some herbivorous insects also encode PCWDEs, raising questions about their evolutionary origins and functions. Among herbivorous beetles, pectin-degrading polygalacturonases (PGs) are found in the diverse superfamilies Chrysomeloidea (leaf beetles, long-horn beetles) and Curculionoidea (weevils). Here our aim was to test whether these arose from a common ancestor of beetles or via horizontal gene transfer (HGT), and whether PGs kept their ancestral function in degrading pectin or evolved novel functions. Transcriptome data derived from 10 beetle species were screened for PG-encoding sequences and used for phylogenetic comparisons with their bacterial, fungal and plant counterparts. These analyses revealed a large family of PG-encoding genes of Chrysomeloidea and Curculionoidea sharing a common ancestor, most similar to PG genes of ascomycete fungi. In addition, 50 PGs from beetle digestive systems were heterologously expressed and functionally characterized, showing a set of lineage-specific consecutively pectin-degrading enzymes, as well as conserved but enzymatically inactive PG proteins. The evidence indicates that a PG gene was horizontally transferred ∼200 million years ago from an ascomycete fungus to a common ancestor of Chrysomeloidea and Curculionoidea. This has been followed by independent duplications in these two lineages, as well as independent replacement in two sublineages of Chrysomeloidea by two other subsequent HGTs. This origin, leading to subsequent functional diversification of the PG gene family within its new hosts, was a key event promoting the evolution of herbivory in these beetles.

MADS goes genomic in conifers: towards determining the ancestral set of MADS-box genes in seed plants

BACKGROUND AND AIMS MADS-box genes comprise a gene family coding for transcription factors. This gene family expanded greatly during land plant evolution such that the number of MADS-box genes ranges from one or two in green algae to around 100 in angiosperms. Given the crucial functions of MADS-box genes for nearly all aspects of plant development, the expansion of this gene family probably contributed to the increasing complexity of plants. However, the expansion of MADS-box genes during one important step of land plant evolution, namely the origin of seed plants, remains poorly understood due to the previous lack of whole-genome data for gymnosperms. METHODS The newly available genome sequences of Picea abies, Picea glauca and Pinus taeda were used to identify the complete set of MADS-box genes in these conifers. In addition, MADS-box genes were identified in the growing number of transcriptomes available for gymnosperms. With these datasets, phylogenies were constructed to determine the ancestral set of MADS-box genes of seed plants and to infer the ancestral functions of these genes. KEY RESULTS Type I MADS-box genes are under-represented in gymnosperms and only a minimum of two Type I MADS-box genes have been present in the most recent common ancestor (MRCA) of seed plants. In contrast, a large number of Type II MADS-box genes were found in gymnosperms. The MRCA of extant seed plants probably possessed at least 11-14 Type II MADS-box genes. In gymnosperms two duplications of Type II MADS-box genes were found, such that the MRCA of extant gymnosperms had at least 14-16 Type II MADS-box genes. CONCLUSIONS The implied ancestral set of MADS-box genes for seed plants shows simplicity for Type I MADS-box genes and remarkable complexity for Type II MADS-box genes in terms of phylogeny and putative functions. The analysis of transcriptome data reveals that gymnosperm MADS-box genes are expressed in a great variety of tissues, indicating diverse roles of MADS-box genes for the development of gymnosperms. This study is the first that provides a comprehensive overview of MADS-box genes in conifers and thus will provide a framework for future work on MADS-box genes in seed plants.

Phylogenomics of MADS-Box Genes in Plants - Two Opposing Life Styles in One Gene Family.

The development of multicellular eukaryotes, according to their body plan, is often directed by members of multigene families that encode transcription factors. MADS (for MINICHROMOSOME MAINTENANCE1, AGAMOUS, DEFICIENS and SERUM RESPONSE FACTOR)-box genes form one of those families controlling nearly all major aspects of plant development. Knowing the complete complement of MADS-box genes in sequenced plant genomes will allow a better understanding of the evolutionary patterns of these genes and the association of their evolution with the evolution of plant morphologies. Here, we have applied a combination of automatic and manual annotations to identify the complete set of MADS-box genes in 17 plant genomes. Furthermore, three plant genomes were reanalyzed and published datasets were used for four genomes such that more than 2,600 genes from 24 species were classified into the two types of MADS-box genes, Type I and Type II. Our results extend previous studies, highlighting the remarkably different evolutionary patterns of Type I and Type II genes and provide a basis for further studies on the evolution and function of MADS-box genes.

Live and Let Die - The Bsister MADS-Box Gene OsMADS29 Controls the Degeneration of Cells in Maternal Tissues during Seed Development of Rice (Oryza sativa)

Bsister genes have been identified as the closest relatives of class B floral homeotic genes. Previous studies have shown that Bsister genes from eudicots are involved in cell differentiation during ovule and seed development. However, the complete function of Bsister genes in eudicots is masked by redundancy with other genes and little is known about the function of Bsister genes in monocots, and about the evolution of Bsister gene functions. Here we characterize OsMADS29, one of three MADS-box Bsister genes in rice. Our analyses show that OsMADS29 is expressed in female reproductive organs including the ovule, ovule vasculature, and the whole seed except for the outer layer cells of the pericarp. Knock-down of OsMADS29 by double-stranded RNA-mediated interference (RNAi) results in shriveled and/or aborted seeds. Histological analyses of the abnormal seeds at 7 days after pollination (DAP) indicate that the symplastic continuity, including the ovular vascular trace and the nucellar projection, which is the nutrient source for the filial tissue at early development stages, is affected. Moreover, degeneration of all the maternal tissues in the transgenic seeds, including the pericarp, ovular vascular trace, integuments, nucellar epidermis and nucellar projection, is blocked as compared to control plants. Our results suggest that OsMADS29 has important functions in seed development of rice by regulating cell degeneration of maternal tissues. Our findings provide important insights into the ancestral function of Bsister genes.

SR1—a small RNA with two remarkably conserved functions

SR1 is a dual-function sRNA that acts as a base-pairing regulatory RNA on the ahrC mRNA and as a peptide-encoding mRNA on the gapA operon. The SR1-encoded peptide SR1P binds GapA thereby stabilizing gapA mRNA. Under glycolytic conditions, SR1 transcription is repressed by CcpN and CcpA. A computer-based search identified 23 SR1 homologues in Bacillus, Geobacillus, Anoxybacillus and Brevibacillus species. All homologues share a high structural identity with Bacillus subtilis SR1, and the encoded SR1P peptides are highly similar. In the Bacillus cereus group, the sr1p region is present in triplicate or duplicate resulting in longer SR1 species. In all cases, sr1 expression is under control of CcpN, and transcriptional lacZ fusions of nine examined SR1 homologues were sensitive to glucose. Two homologues showed an additional glucose-independent repression by CcpN and an unknown factor. A total of 10 out of 11 tested SR1P homologues complemented a B. subtilis Δsr1 strain in their ability to stabilize gapA mRNA, but only five of them bound GapA tightly. In vitro binding assays with six SR1/ahrC pairs suggest that—despite divergent primary sequences—the base-pairing function is also preserved. In summary, SR1 is an sRNA with two functions that have been conserved over ≈1 billion years.

The Molecular Evolution of Cytochrome P450 Genes within and between Drosophila Species

We map 114 gene gains and 74 gene losses in the P450 gene family across the phylogeny of 12 Drosophila species by examining the congruence of gene trees and species trees. Although the number of P450 genes varies from 74 to 94 in the species examined, we infer that there were at least 77 P450 genes in the ancestral Drosophila genome. One of the most striking observations in the data set is the elevated loss of P450 genes in the Drosophila sechellia lineage. The gain and loss events are not evenly distributed among the P450 genes—with 30 genes showing no gene gains or losses whereas others show as many as 20 copy number changes among the species examined. The P450 gene clades showing the fewest number of gene gain and loss events tend to be those evolving with the most purifying selection acting on the protein sequences, although there are exceptions, such as the rapid rate of amino acid replacement observed in the single copy phantom (Cyp306a1) gene. Within D. melanogaster, we observe gene copy number polymorphism in ten P450 genes including multiple cases of interparalog chimeras. Nonallelic homologous recombination (NAHR) has been associated with deleterious mutations in humans, but here we provide a second possible example of an NAHR event in insect P450s being adaptive. Specifically, we find that a polymorphic Cyp12a4/Cyp12a5 chimera correlates with resistance to an insecticide. Although we observe such interparalog exchange in our within-species data sets, we have little evidence of it between species, raising the possibility that such events may occur more frequently than appreciated but are masked by subsequent sequence change.

SplamiR—prediction of spliced miRNAs in plants

MOTIVATION MicroRNAs (miRNAs) are important regulators of biological processes in plants and animals. Recently, miRNA genes have been discovered, whose primary transcripts are spliced and which cannot be predicted directly from genomic sequence. Hence, more sophisticated programs for the detection of spliced miRNAs are required. RESULTS Here, we present the first method for the prediction of spliced miRNAs in plants. For a given genomic sequence, SplamiR creates a database of complementary sequence pairs, which might encode for RNAs folding into stem-loop structures. Next, in silico splice variants of database sequences with complementarity to an mRNA of interest are classified as to whether they could represent miRNAs targeting this mRNA. Our method identifies all known cases of spliced miRNAs in rice, and a previously undiscovered miRNA in maize which is supported by an expressed sequence tag (EST). SplamiR permits identification of spliced miRNAs for a given target mRNA in many plant genomes. AVAILABILITY The program is freely available at http://www.uni-jena.de/SplamiR.html.

Structure and Evolution of Plant MADS Domain Transcription Factors

MADS domain transcription factors are involved in controlling many developmental processes in flowering plants, ranging from pollen and embryo sac development to root, flower, and fruit development. Beyond that they are probably of developmental importance in all other green plants. The developmental versatility of MADS domain proteins may depend in part on specific features of their MADS domain (i.e., highly conserved DNA-binding, dimerization, and nuclear localization domain). It makes DNA– and protein–protein interactions in quite a unique way, including recognition of a narrowed minor groove of DNA by the insertion of an arginine side chain. Presence of a MADS domain is the only common denominator uniting all MADS domain transcription factors, but a developmentally and evolutionarily important lineage of plant proteins, the MIKC-type proteins, acquired a second remarkable domain, the keratin-like (K) domain. This domain presents separate dimerization and tetramerization interfaces and thus enables combinatorial multimerization of MIKC-type MADS domain proteins. The number of MADS domain transcription factors increased by two orders of magnitude during the evolution of land plans, and acquired diverse, often complex and organ specific, expression domains. Heterotetramers of some MIKC-type proteins bind to two DNA sequence elements by looping the DNA in between. Such “floral quartets” act as important developmental switches determining floral organ identity and possibly many other developmental decisions in land plants as well. Thus, it seems that the developmental and evolutionary importance of plant MADS domain transcription factors is a consequence of their versatile mode of DNA binding and combinatorial multimerization. We are now a good way toward understanding these special features of MADS domain transcription factors in terms of the molecular details of their DNA-binding and protein–protein interaction domains.