ARABIDILLO gene homologues in basal land plants: species-specific gene duplication and likely functional redundancy

ARABIDILLO proteins regulate multicellular root development in Arabidopsis thaliana. Conserved ARABIDILLO homologues are present throughout land plants, even in early-evolving plants that do not possess complex root architecture, suggesting that ARABIDILLO genes have additional functions. Here, we have cloned and characterised ARABIDILLO gene homologues from two early-evolving land plants, the bryophyte Physcomitrella patens and the lycophyte Selaginella moellendorffii. We show that two of the PHYSCODILLO genes (PHYSCODILLO1A and -1B) exist as a tail-to-tail tandem array of two almost identical 12?kb sequences, while a third related gene (PHYSCODILLO2) is located elsewhere in the Physcomitrella genome. Physcomitrella possesses a very low percentage of tandemly arrayed genes compared with the later-evolving plants whose genomes have been sequenced to date. Thus, PHYSCODILLO1A and -1B genes represent a relatively unusual gene arrangement. PHYSCODILLO promoters are active largely in the haploid gametophyte, with additional activity at the foot of the sporophyte. The pattern of promoter activity is uniform in filamentous and leafy tissues, suggesting pleiotropic gene functions and likely functional redundancy: the latter possibility is confirmed by the lack of discernible phenotype in a physcodillo2 deletion mutant. Interestingly, the pattern of PHYSCODILLO promoter activity in female reproductive organs is strikingly similar to that of an Arabidopsis homologue, suggesting co-option of some PHYSCODILLO functions or regulation into both the sporophyte and gametophyte. In conclusion, our work identifies and characterises some of the earliest-evolving land plant ARABIDILLO homologues. We confirm that all land plant ARABIDILLO genes arose from a single common ancestor and suggest that PHYSCODILLO proteins have novel and pleiotropic functions, some of which may be conserved in later-evolving plants.     

Lineage-specific gene duplication and loss in human and great ape evolution

Given that gene duplication is a major driving force of evolutionary change and the key mechanism underlying the emergence of new genes and biological processes, this study sought to use a novel genome-wide approach to identify genes that have undergone lineage-specific duplications or contractions among several hominoid lineages. Interspecies cDNA array-based comparative genomic hybridization was used to individually compare copy number variation for 39,711 cDNAs, representing 29,619 human genes, across five hominoid species, including human. We identified 1,005 genes, either as isolated genes or in clusters positionally biased toward rearrangement-prone genomic regions, that produced relative hybridization signals unique to one or more of the hominoid lineages. Measured as a function of the evolutionary age of each lineage, genes showing copy number expansions were most pronounced in human (134) and include a number of genes thought to be involved in the structure and function of the brain. This work represents, to our knowledge, the first genome-wide gene-based survey of gene duplication across hominoid species. The genes identified here likely represent a significant majority of the major gene copy number changes that have occurred over the past 15 million years of human and great ape evolution and are likely to underlie some of the key phenotypic characteristics that distinguish these species.     

The monosaccharide transporter gene family in land plants is ancient and shows differential subfamily expression and expansion across lineages

Background  

In plants, tandem, segmental and whole-genome duplications are prevalent, resulting in large numbers of duplicate loci. Recent studies suggest that duplicate genes diverge predominantly through the partitioning of expression and that breadth of gene expression is related to the rate of gene duplication and protein sequence evolution.     

Function of polyphenol oxidase in higher plants

Recent evidence has supported the folllowing views:
1. Polyphenol oxidase (PPO) is a plastidic enzyme that is unclear-coded, but is inactive until incorporated into the plastid.
2. In healthy green tissues PPO exists in a latent form on the thylakoid membrane and is not involved in synthesis of phenolic compounds. In leucoplasts, proplastids, or amyloplasts PPO is often present in a latent form in rudimentary thylakoids.
3. PPO normally functions as a phenol oxidase in vivo only in sencent or damaged cells.
4. In the functional chloroplast, PPO may be involved in some aspect of oxygen chemistry – pherhaps mediation of pseudocyclic photophosphorylation.     

Conservation and diversification of HAIRY MERISTEM gene family in land plants

The shoot apical meristems (SAMs) of land plants are crucial for plant growth and organ formation. In several angiosperms, the HAIRY MERISTEM (HAM) genes function as key regulators that control meristem development and stem cell homeostasis. To date, the origin and evolutionary history of the HAM family in land plants remains unclear. Potentially shared and divergent functions of HAM family members from angiosperms and non-angiosperms are also not known. In constructing a comprehensive phylogeny of the HAM family, we show that HAM proteins are widely present in land plants and that HAM proteins originated prior to the divergence of bryophytes. The HAM family was duplicated in a common ancestor of angiosperms, leading to two distinct groups: type I and type II. Type-II HAM members are widely present in angiosperms, whereas type-I HAM members were independently lost in different orders of monocots. Furthermore, HAM members from angiosperms and non-angiosperms (including bryophytes, lycophytes, ferns and gymnosperms) are able to replace the role of the type-II HAM genes in Arabidopsis, maintaining established SAMs and promoting the initiation of new stem cell niches. Our results uncover the conserved functions of HAM family members and reveal the conserved regulatory mechanisms underlying HAM expression patterning in meristems, providing insight into the evolution of key stem cell regulators in land plants.     

Proteolytic processing of polyphenol oxidase from plants and fungi

Polyphenol oxidase (PPO), a metalloenzyme containing a type-3 copper center, is produced by many species of plants, fungi, and bacteria. There is great variability in the subunit molecular mass reported for PPO, even from a single species. In some cases, experimental evidence (usually protein sequencing by Edman degradation) indicates that the variability in molecular mass for PPO from a given species is the result of proteolytic processing at the N and/or C-termini of the protein. In order to identify specific sequence regions where proteolysis occurs in PPO from most species, the experimentally established N and C-termini of these proteolyzed enzymes were compared to the protein sequences of other PPOs for which the N and C-termini have not been established by protein sequencing methods. In all cases the N-terminal proteolysis sites were located prior to a conserved arginine residue, and the C-terminal proteolysis sites were located following a conserved tyrosine motif. Based on the sites of proteolysis, molecular masses were calculated for the enzymes, and the calculated values were used to rationalize the varying molecular masses reported in the literature. To determine the structural implications of N and C-terminal proteolysis, the proteolysis sites were related to the two available PPO structures: Ipomoea batatas catechol oxidase and Streptomyces castaneoglobisporus tyrosinase. A structural “core” region that appears to be essential for structural stability and enzymatic activity was identified.     

The polyphenol oxidase gene family in poplar: phylogeny,differential expression and identification of a novel,vacuolar isoform

Polyphenol oxidases (PPOs) are oxidative enzymes that convert monophenols and o-diphenols to o-quinones using molecular oxygen. The quinone products are highly reactive following tissue damage and can interact with cellular constituents and cause oxidative browning and cross-linking. The induction of PPO in some plants as a result of wounding, herbivore attack, or pathogen infection has implicated them in defense. However, PPO-like enzymes that act as specific hydroxylases, for example in lignan and pigment biosynthesis, have also been discovered. Here, we present the first genome-enabled analysis of a PPO gene family. The Populus trichocarpa genome was found to contain a minimum of nine complete PPO genes, and seven of these were characterized further. The PPO gene family includes both recently duplicated and divergent sequences that are 36–98% identical at the amino acid level. Gene expression profiling in poplar tissues and organs revealed that the PPO genes are all differentially expressed during normal development, but that only a small subset of PPO genes are significantly upregulated by wounding, methyl jasmonate or pathogen infection. Our studies also identified PtrPPO13, a novel PPO gene that is predicted to encode an N-terminal signal peptide. Transient expression of green fluorescent protein fusions demonstrated its localization to the vacuolar lumen. Together, our findings show that the poplar PPO family is diverse and is likely linked to diverse physiological functions.     

Evolution of the class III HD-Zip gene family in land plants

Arabidopsis class III homeodomain-leucine zipper (HD-Zip III) proteins play overlapping, distinct, and antagonistic roles in key aspects of development that have evolved during land plant evolution. To better understand this gene family's role in plant evolution and development as well as to address broader questions of how duplicated genes functionally diversify, we investigated the evolutionary history of this gene family. Phylogenetic analyses including homologs from diverse land plants indicate that a gene duplication event before the angiosperm--gymnosperm split gave rise to two gene lineages that diversified during angiosperm plant radiation. Heterologous expression of an HD-Zip III gene from the nonvascular plant moss within the Arabidopsis HD-zip III revoluta mutant modified but did not complement the phenotype. Comparison of the expression domains of flowering and nonflowering plant homologs indicate an ancestral role in vascular development and organ initiation but not in specifying organ polarity, a prominent role for angiosperm homologs.     

The GapA/B gene duplication marks the origin of Streptophyta (charophytes and land plants)

Independent evidence from morphological, ultrastructural, biochemical, and molecular data have shown that land plants originated from charophycean green algae. However, the branching order within charophytes is still unresolved, and contradictory phylogenies about, for example,the position of the unicellular green alga Mesostigma viride are difficult to reconcile. A comparison of nuclear-encoded Calvin cycle glyceraldehyde-3-phosphate dehydrogenases (GAPDH) indicates that a crucial duplication of the GapA gene occurred early in land plant evolution. The duplicate called GapB acquired a characteristic carboxy-terminal extension (CTE) from the general regulator of the Calvin cycle CP12. This CTE is responsible for thioredoxin-dependent light/dark regulation. In this work, we established GapA, GapB, and CP12 sequences from bryophytes, all orders of charophyte as well as chlorophyte green algae, and the glaucophyte Cyanophora paradoxa. Comprehensive phylogenetic analyses of all available plastid GAPDH sequences suggest that glaucophytes and green plants are sister lineages and support a positioning of Mesostigma basal to all charophycean algae. The exclusive presence of GapB in terrestrial plants, charophytes, and Mesostigma dates the GapA/B gene duplication to the common ancestor of Streptophyta. The conspicuously high degree of GapB sequence conservation suggests an important metabolic role of the newly gained regulatory function. Because the GapB-mediated protein aggregation most likely ensures the complete blockage of the Calvin cycle at night, we propose that this mechanism is also crucial for efficient starch mobilization. This innovation may be one prerequisite for the development of storage tissues in land plants.     

The RecQ gene family in plants

RecQ helicases are conserved throughout all kingdoms of life regarding their overall structure and function. They are 3'-5' DNA helicases resolving different recombinogenic DNA structures. The RecQ helicases are key factors in a number of DNA repair and recombination pathways involved in the maintenance of genome integrity. In eukaryotes the number of RecQ genes and the structure of RecQ proteins vary strongly between organisms. Therefore, they have been named RecQ-like genes. Knockouts of several RecQ-like genes cause severe diseases in animals or harmful cellular phenotypes in yeast. Until now the largest number of RecQ-like genes per organism has been found in plants. Arabidopsis and rice possess seven different RecQ-like genes each. In the almost completely sequenced genome of the moss Physcomitrella patens at least five RecQ-like genes are present. One of the major present and future research aims is to define putative plant-specific functions and to assign their roles in DNA repair and recombination pathways in relation to RecQ genes from other eukaryotes. Regarding their intron positions, the structures of six RecQ-like genes of dicots and monocots are virtually identical indicating a conservation over a time scale of 150 million years. In contrast to other eukaryotes one gene (RecQsim) exists exclusively in plants. It possesses an interrupted helicase domain but nevertheless seems to have maintained the RecQ function. Owing to a recent gene duplication besides the AtRecQl4A gene an additional RecQ-like gene (AtRecQl4B) exists in the Brassicaceae only. Genetic studies indicate that a AtRecQl4A knockout results in sensitivity to mutagens as well as an hyper-recombination phenotype. Since AtRecQl4B was still present, both genes must have non-redundant roles. Analysis of plant RecQ-like genes will not only increase the knowledge on DNA repair and recombination, but also on the evolution and radiation of protein families.     

The Arabidopsis acyl-CoA oxidase gene family

A family of acyl-CoA oxidase isozymes catalyse the first step in the peroxisomal fatty acid beta-oxidation spiral. Our group and others have recently characterized four genes from this family in the model oilseed Arabidopsis. These genes encode isozymes with different acyl-CoA substrate specificities, which together encompass the full range of fatty acid chain lengths that exist in vivo. Here we review the biochemical properties and physiological roles of the acyl-CoA oxidase isozymes.     

Comparative and phylogenomic analyses of cinnamoyl-CoA reductase and cinnamoyl-CoA-reductase-like gene family in land plants

The biosynthesis of monolignols, the main components of lignin, involves many intermediates and enzymes. The cinnamoyl-CoA reductase (CCR) enzyme catalyzes the conversion of cinnamoyl-CoAs to cinnamaldehydes, i.e. the first specific step in lignin synthesis. The CCR and CCR-like gene family was studied partially in several plant species. This is a comprehensive study of the CCR and CCR-like gene family including genome organization, gene structure, phylogeny across land plant species, and, expression profiling in Populus. Analysis of amino acid motifs enabled the identification of sequence variations in the CCR catalytic site and annotates CCR and CCR-like genes. CCR and CCR-like genes were distributed in three major phylogenetic classes of which one includes the bona fide CCR genes. The other two classes include CCR and CCR-like, of which several genes present a high similarity to cinnamyl alcohol dehydrogenase, or dihydroflavonol reductase (DFR) genes. All CCR, CCR-like, and DFR classes were deeply rooted in the phylogeny of land plants suggesting that their evolution preceded the evolution of lycophytes. Over two thirds of CCR and CCR-like Populus genes were physically distributed on duplicated regions. This suggests that these duplication/retention processes contributed significantly to the size of the CCR and CCR-like gene family. The Populus CCR and CCR-like genes showed six expression patterns in the tissues studied with a preferential expression of PoptrCCR12 in xylem. The other genes present divergent expression profiles with some preferentially expressed in leaves, bark, or both. Several CCR and CCR-like genes were induced or repressed under various abiotic stresses suggesting that their duplication was followed by the evolution of divergent expression profiles and divergence of functions.