A new model for the evolution of carnivory in the bladderwort plant (utricularia): adaptive changes in cytochrome C oxidase (COX) provide respiratory power

Global change and plant-ecosystem functioning in freshwaters

Freshwater ecosystems are of worldwide importance for maintaining biodiversity and sustaining the provision of a myriad of ecosystem services to modern societies. Plants, one of the most important components of these ecosystems, are key to water nutrient removal, carbon storage, and food provision. Understanding how the functional connection between freshwater plants and ecosystems is affected by global change will be key to our ability to predict future changes in freshwater systems. Here, we synthesize global plant responses, adaptations, and feedbacks to present-day and future freshwater environments through trait-based approaches, from single individuals to entire communities. We outline the transdisciplinary knowledge benchmarks needed to further understand freshwater plant biodiversity and the fundamental services they provide.

The phylogenomics and evolutionary dynamics of the organellar genomes in carnivorous Utricularia and Genlisea species (Lentibulariaceae)

Utricularia and Genlisea are highly specialized carnivorous plants whose phylogenetic history has been poorly explored using phylogenomic methods. Additional sampling and genomic data are needed to advance our phylogenetic and taxonomic knowledge of this group of plants. Within a comparative framework, we present a characterization of plastome (PT) and mitochondrial (MT) genes of 26 Utricularia and six Genlisea species, with representatives of all subgenera and growth habits. All PT genomes maintain similar gene content, showing minor variation across the genes located between the PT junctions. One exception is a major variation related to different patterns in the presence and absence of ndh genes in the small single copy region, which appears to follow the phylogenetic history of the species rather than their lifestyle. All MT genomes exhibit similar gene content, with most differences related to a lineage-specific pseudogenes. We find evidence for episodic positive diversifying selection in PT and for most of the Utricularia MT genes that may be related to the current hypothesis that bladderworts' nuclear DNA is under constant ROS oxidative DNA damage and unusual DNA repair mechanisms, or even low fidelity polymerase that bypass lesions which could also be affecting the organellar genomes. Finally, both PT and MT phylogenetic trees were well resolved and highly supported, providing a congruent phylogenomic hypothesis for Utricularia and Genlisea clade given the study sampling.

Alternative or cytochrome? Respiratory pathways in traps of aquatic carnivorous bladderwort Utricularia reflexa

Carnivorous plants of the genus Utricularia (bladderwort) form modified leaves into suction bladder traps. The bladders are metabolically active plant tissue with high rates of mitochondrial respiration (R_D). In general, plants possess two mitochondrial electron transport pathways to reduce oxygen to water: cytochrome and an alternative. Due to the high metabolic rate in the bladders, it is tempting to assume that the bladders prefer the cytochrome c oxidative pathway. Surprisingly, we revealed that alternative oxidase (AOX), which yields only a little ATP, is much more abundant in the bladders of Utricularia reflexa in comparison with the shoots. This pattern is similar to the carnivorous plants with passive pitcher traps (e.g. Sarracenia, Nepenthes) and seems to be widespread across many carnivorous taxa. The exact role of AOX in the traps of carnivorous plants remains to be investigated.

The complete mitochondrial genome of carnivorous Genlisea tuberosa (Lentibulariaceae): Structure and evolutionary aspects

Sequenced genomic data for carnivorous plants are scarce, especially regarding the mitogenomes (MTs) and further studies are crucial to obtain a better understanding of the topic. In this study, we sequenced and characterized the mitochondrial genome of the tuberous carnivorous plant Genlisea tuberosa, being the first of its genus to be sequenced. The genome comprises 729,765 bp, encoding 80 identified genes of which 36 are protein-coding, 40 tRNA, four rRNA genes, and three pseudogenes. An intronic region from the cox1 gene was identified that encodes an endonuclease enzyme that is present in the other sequenced species of Lentibulariaceae. Chloroplast genes (pseudogene and complete) inserted in the MT genome were identified, showing possible horizontal transfer between organelles. In addition, 50 pairs of long repeats from 94 to 274 bp are present, possibly playing an important role in the maintenance of the MT genome. Phylogenetic analysis carried out with 34 coding mitochondrial genes corroborated the positioning of the species listed here within the family. The molecular dynamism in the mitogenome (e.g. the loss or pseudogenization of genes, insertion of foreign genes, the long repeats as well as accumulated mutations) may be reflections of the carnivorous lifestyle where a significant part of cellular energy was shifted for the adaptation of leaves into traps molding the mitochondrial DNA. The sequence and annotation of G. tuberosa's MT will be useful for further studies and serve as a model for evolutionary and taxonomic clarifications of the group as well as improving our comprehension of MT evolution.

Alternative oxidase (AOX) in the carnivorous pitcher plants of the genus Nepenthes: what is it good for?

BACKGROUND AND AIMS

The carnivorous pitcher plants of the genus Nepenthes have evolved modified leaves that act as pitcher traps. The traps are specialized for prey attraction, capture, digestion and nutrient uptake but not for photosynthetic assimilation.

METHODS

In this study, we used antibodies against different photosynthetic (D1, Lhcb2, Lhcb4, RbcL) and respiratory-related (AOX, COXII) proteins for semi-quantification of these proteins in the assimilation part of the leaves and the pitcher traps of different Nepenthes species and hybrids. Different functional zones of the trap and the traps from different ontogenetic stages were investigated. The pitcher traps of the distantly related species Sarracenia purpurea ssp. venosa were used as an outgroup. In addition, chlorophyll fluorescence and infrared gas analysis were used for measurements of the net rate of photosynthesis (AN) and respiration in the dark (RD).

KEY RESULTS

The pitcher traps contained the same or lower abundance of photosynthesis-related proteins in accordance with their low AN in comparison to the assimilation part of the leaves. Surprisingly, all traps contained a high amount of alternative oxidase (AOX) and low amount of cytochrome c oxidase subunit II (COX II) than in the assimilation part of the leaves. Thermal imaging did not confirm the role of AOX in pitcher thermogenesis.

CONCLUSIONS

The pitcher traps contain a high amount of AOX enzyme. The possible role of AOX in specialized pitcher tissue is discussed based on knowledge of the role and function of AOX in non-carnivorous plants. The roles of AOX in prey attraction, balance between light and dark reactions of photosynthesis, homeostasis of reactive oxygen species, digestive physiology and nutrient assimilation are discussed.

Recent ecophysiological, biochemical and evolutional insights into plant carnivory

BACKGROUND

Carnivorous plants are an ecological group of approx. 810 vascular species which capture and digest animal prey, absorb prey-derived nutrients and utilize them to enhance their growth and development. Extant carnivorous plants have evolved in at least ten independent lineages, and their adaptive traits represent an example of structural and functional convergence. Plant carnivory is a result of complex adaptations to mostly nutrient-poor, wet and sunny habitats when the benefits of carnivory exceed the costs. With a boost in interest and extensive research in recent years, many aspects of these adaptations have been clarified (at least partly), but many remain unknown.

SCOPE

We provide some of the most recent insights into substantial ecophysiological, biochemical and evolutional particulars of plant carnivory from the functional viewpoint. We focus on those processes and traits in carnivorous plants associated with their ecological characterization, mineral nutrition, cost-benefit relationships, functioning of digestive enzymes and regulation of the hunting cycle in traps. We elucidate mechanisms by which uptake of prey-derived nutrients leads to stimulation of photosynthesis and root nutrient uptake.

CONCLUSIONS

Utilization of prey-derived mineral (mainly N and P) and organic nutrients is highly beneficial for plants and increases the photosynthetic rate in leaves as a prerequisite for faster plant growth. Whole-genome and tandem gene duplications brought gene material for diversification into carnivorous functions and enabled recruitment of defence-related genes. Possible mechanisms for the evolution of digestive enzymes are summarized, and a comprehensive picture on the biochemistry and regulation of prey decomposition and prey-derived nutrient uptake is provided.

Is the evolution of carnivory connected with genome size reduction?

PREMISE

As repeatedly shown, the remarkable variation in the genome size of angiosperms can be shaped by extrinsic selective pressures, including nutrient availability. Carnivory has evolved independently in 10 angiosperm clades, but all carnivorous plants share a common affinity to nutrient-poor habitats. As such, carnivory and genome reduction could be responses to the same environmental pressure. Indeed, the smallest genomes among flowering plants are found in the carnivorous family Lentibulariaceae, where a unique mutation in cytochrome c oxidase (COX) is suspected to promote genome miniaturization. Despite these hypotheses, a phylogenetically informed test of genome size and nutrient availability across carnivorous clades has so far been missing.

METHODS

Using linear mixed models, we compared genome sizes of 127 carnivorous plants from 7 diverse angiosperm clades with 1072 of their noncarnivorous relatives. We also tested whether genome size in Lentibulariaceae reflects the presence of the COX mutation.

RESULTS

The genome sizes of carnivorous plants do not differ significantly from those of their noncarnivorous relatives. Based on available data, no significant association between the COX mutation and genome miniaturization could be confirmed, not even when considering polyploidy.

CONCLUSIONS

Carnivory alone does not seem to significantly affect genome size decrease. Plausibly, it might actually counterbalance the effect of nutrient limitation on genome size evolution. The role of the COX mutation in genome miniaturization needs to be evaluated by analysis of a broader data set because current knowledge of its presence across Lentibulariaceae covers less than 10% of the species diversity in this family.

Transcriptome-wide shift from photosynthesis and energy metabolism upon endogenous fluid protein depletion in young Nepenthes ampullaria pitchers

Carnivorous pitcher plants produce specialised pitcher organs containing secretory glands, which secrete acidic fluids with hydrolytic enzymes for prey digestion and nutrient absorption. The content of pitcher fluids has been the focus of many fluid protein profiling studies. These studies suggest an evolutionary convergence of a conserved group of similar enzymes in diverse families of pitcher plants. A recent study showed that endogenous proteins were replenished in the pitcher fluid, which indicates a feedback mechanism in protein secretion. This poses an interesting question on the physiological effect of plant protein loss. However, there is no study to date that describes the pitcher response to endogenous protein depletion. To address this gap of knowledge, we previously performed a comparative RNA-sequencing experiment of newly opened pitchers (D0) against pitchers after 3 days of opening (D3C) and pitchers with filtered endogenous proteins (>10 kDa) upon pitcher opening (D3L). Nepenthes ampullaria was chosen as a model study species due to their abundance and unique feeding behaviour on leaf litters. The analysis of unigenes with top 1% abundance found protein translation and stress response to be overrepresented in D0, compared to cell wall related, transport, and signalling for D3L. Differentially expressed gene (DEG) analysis identified DEGs with functional enrichment in protein regulation, secondary metabolism, intracellular trafficking, secretion, and vesicular transport. The transcriptomic landscape of the pitcher dramatically shifted towards intracellular transport and defence response at the expense of energy metabolism and photosynthesis upon endogenous protein depletion. This is supported by secretome, transportome, and transcription factor analysis with RT-qPCR validation based on independent samples. This study provides the first glimpse into the molecular responses of pitchers to protein loss with implications to future cost/benefit analysis of carnivorous pitcher plant energetics and resource allocation for adaptation in stochastic environments.

Expansin gene loss is a common occurrence during adaptation to an aquatic environment

Expansins comprise a superfamily of plant cell wall loosening proteins that can be divided into four individual families (EXPA, EXPB, EXLA and EXLB). Aside from inferred roles in a variety of plant growth and developmental traits, little is known regarding the function of specific expansin clades, for which there are at least 16 in flowering plants (angiosperms); however, there is evidence to suggest that some expansins have cell-specific functions, in root hair and pollen tube development, for example. Recently, two duckweed genomes have been sequenced (Spirodela polyrhiza strains 7498 and 9509), revealing significantly reduced superfamily sizes. We hypothesized that there would be a correlation between expansin loss and morphological reductions seen among highly adapted aquatic species. In order to provide an answer to this question, we characterized the expansin superfamilies of the greater duckweed Spirodela, the marine eelgrass Zostera marina and the bladderwort Utricularia gibba. We discovered rampant expansin gene and clade loss among the three, including a complete absence of the EXLB family and EXPA-VII. The most convincing correlation between morphological reduction and expansin loss was seen for Utricularia and Spirodela, which both lack root hairs and the root hair expansin clade EXPA-X. Contrary to the pattern observed in other species, four Utricularia expansins failed to branch within any clade, suggesting that they may be the result of neofunctionalization. Last, an expansin clade previously discovered only in eudicots was identified in Spirodela, allowing us to conclude that the last common ancestor of monocots and eudicots contained a minimum of 17 expansins.

Comparative genomic analysis of Genlisea (corkscrew plants-Lentibulariaceae) chloroplast genomes reveals an increasing loss of the ndh genes

In the carnivorous plant family Lentibulariaceae, all three genome compartments (nuclear, chloroplast, and mitochondria) have some of the highest rates of nucleotide substitutions across angiosperms. While the genera Genlisea and Utricularia have the smallest known flowering plant nuclear genomes, the chloroplast genomes (cpDNA) are mostly structurally conserved except for deletion and/or pseudogenization of the NAD(P)H-dehydrogenase complex (ndh) genes known to be involved in stress conditions of low light or CO2 concentrations. In order to determine how the cpDNA are changing, and to better understand the evolutionary history within the Genlisea genus, we sequenced, assembled and analyzed complete cpDNA from six species (G. aurea, G. filiformis, G. pygmaea, G. repens, G. tuberosa and G. violacea) together with the publicly available G. margaretae cpDNA. In general, the cpDNA structure among the analyzed Genlisea species is highly similar. However, we found that the plastidial ndh genes underwent a progressive process of degradation similar to the other terrestrial Lentibulariaceae cpDNA analyzed to date, but in contrast to the aquatic species. Contrary to current thinking that the terrestrial environment is a more stressful environment and thus requiring the ndh genes, we provide evidence that in the Lentibulariaceae the terrestrial forms have progressive loss while the aquatic forms have the eleven plastidial ndh genes intact. Therefore, the Lentibulariaceae system provides an important opportunity to understand the evolutionary forces that govern the transition to an aquatic environment and may provide insight into how plants manage water stress at a genome scale.

Evolution of unusual morphologies in Lentibulariaceae (bladderworts and allies) and Podostemaceae (river-weeds): a pictorial report at the interface of developmental biology and morphological diversification

BACKGROUND

Various groups of flowering plants reveal profound ('saltational') changes of their bauplans (architectural rules) as compared with related taxa. These plants are known as morphological misfits that appear as rather large morphological deviations from the norm. Some of them emerged as morphological key innovations (perhaps 'hopeful monsters') that gave rise to new evolutionary lines of organisms, based on (major) genetic changes.

SCOPE

This pictorial report places emphasis on released bauplans as typical for bladderworts (Utricularia, approx. 230 secies, Lentibulariaceae) and river-weeds (Podostemaceae, three subfamilies, approx. 54 genera, approx. 310 species). Bladderworts (Utricularia) are carnivorous, possessing sucking traps. They live as submerged aquatics (except for their flowers), as humid terrestrials or as epiphytes. Most Podostemaceae are restricted to rocks in tropical river-rapids and waterfalls. They survive as submerged haptophytes in these extreme habitats during the rainy season, emerging with their flowers afterwards. The recent scientific progress in developmental biology and evolutionary history of both Lentibulariaceae and Podostemaceae is summarized.

CONCLUSIONS

Lentibulariaceae and Podostemaceae follow structural rules that are different from but related to those of more typical flowering plants. The roots, stems and leaves - as still distinguishable in related flowering plants - are blurred ('fuzzy'). However, both families have stable floral bauplans. The developmental switches to unusual vegetative morphologies facilitated rather than prevented the evolution of species diversity in both families. The lack of one-to-one correspondence between structural categories and gene expression may have arisen from the re-use of existing genetic resources in novel contexts. Understanding what developmental patterns are followed in Lentibulariaceae and Podostemaceae is a necessary prerequisite to discover the genetic alterations that led to the evolution of these atypical plants. Future molecular genetic work on morphological misfits such as bladderworts and river-weeds will provide insight into developmental and evolutionary aspects of more typical vascular plants.

Fastest predators in the plant kingdom: functional morphology and biomechanics of suction traps found in the largest genus of carnivorous plants

Understanding the physics of plant movements, which describe the interplay between plant architecture, movement speed and actuation principles, is essential for the comprehension of important processes like plant morphogenesis. Recent investigations especially on rapid plant movements at the interface of biology, physics and engineering sciences highlight how such fast motions can be achieved without the presence of muscles, nerves and technical hinge analogies. The suction traps (bladders) of carnivorous bladderworts (Utricularia spp., Lentibulariaceae, Lamiales) are considered as some of the most elaborate moving structures in the plant kingdom. A complex interplay of morphological and physiological adaptations allows the traps to pump water out of their body and to store elastic energy in the deformed bladder walls. Mechanical stimulation by prey entails opening of the otherwise watertight trapdoor, followed by trap wall relaxation, sucking in of water and prey, and consecutive trapdoor closure. Suction can also occur spontaneously in non-stimulated traps. We review the current state of knowledge about the suction trap mechanism with a focus on architectonically homogeneous traps of aquatic bladderwort species from section Utricularia (the so-called 'Utricularia vulgaris trap type'). The functional morphology and biomechanics of the traps are described in detail. We discuss open questions and propose promising aspects for future studies on these sophisticated ultra-fast trapping devices.

A novel insight into the cost-benefit model for the evolution of botanical carnivory

BACKGROUND

The cost-benefit model for the evolution of botanical carnivory provides a conceptual framework for interpreting a wide range of comparative and experimental studies on carnivorous plants. This model assumes that the modified leaves called traps represent a significant cost for the plant, and this cost is outweighed by the benefits from increased nutrient uptake from prey, in terms of enhancing the rate of photosynthesis per unit leaf mass or area (AN) in the microsites inhabited by carnivorous plants.

SCOPE

This review summarizes results from the classical interpretation of the cost-benefit model for evolution of botanical carnivory and highlights the costs and benefits of active trapping mechanisms, including water pumping, electrical signalling and accumulation of jasmonates. Novel alternative sequestration strategies (utilization of leaf litter and faeces) in carnivorous plants are also discussed in the context of the cost-benefit model.

CONCLUSIONS

Traps of carnivorous plants have lower AN than leaves, and the leaves have higher AN after feeding. Prey digestion, water pumping and electrical signalling represent a significant carbon cost (as an increased rate of respiration, RD) for carnivorous plants. On the other hand, jasmonate accumulation during the digestive period and reprogramming of gene expression from growth and photosynthesis to prey digestion optimizes enzyme production in comparison with constitutive secretion. This inducibility may have evolved as a cost-saving strategy beneficial for carnivorous plants. The similarities between plant defence mechanisms and botanical carnivory are highlighted.

Genome-wide analysis of adaptive molecular evolution in the carnivorous plant Utricularia gibba

The genome of the bladderwort Utricularia gibba provides an unparalleled opportunity to uncover the adaptive landscape of an aquatic carnivorous plant with unique phenotypic features such as absence of roots, development of water-filled suction bladders, and a highly ramified branching pattern. Despite its tiny size, the U. gibba genome accommodates approximately as many genes as other plant genomes. To examine the relationship between the compactness of its genome and gene turnover, we compared the U. gibba genome with that of four other eudicot species, defining a total of 17,324 gene families (orthogroups). These families were further classified as either 1) lineage-specific expanded/contracted or 2) stable in size. The U. gibba-expanded families are generically related to three main phenotypic features: 1) trap physiology, 2) key plant morphogenetic/developmental pathways, and 3) response to environmental stimuli, including adaptations to life in aquatic environments. Further scans for signatures of protein functional specialization permitted identification of seven candidate genes with amino acid changes putatively fixed by positive Darwinian selection in the U. gibba lineage. The Arabidopsis orthologs of these genes (AXR, UMAMIT41, IGS, TAR2, SOL1, DEG9, and DEG10) are involved in diverse plant biological functions potentially relevant for U. gibba phenotypic diversification, including 1) auxin metabolism and signal transduction, 2) flowering induction and floral meristem transition, 3) root development, and 4) peptidases. Taken together, our results suggest numerous candidate genes and gene families as interesting targets for further experimental confirmation of their functional and adaptive roles in the U. gibba's unique lifestyle and highly specialized body plan.

Evolution of genome size and chromosome number in the carnivorous plant genus Genlisea (Lentibulariaceae), with a new estimate of the minimum genome size in angiosperms

BACKGROUND AND AIMS

Some species of Genlisea possess ultrasmall nuclear genomes, the smallest known among angiosperms, and some have been found to have chromosomes of diminutive size, which may explain why chromosome numbers and karyotypes are not known for the majority of species of the genus. However, other members of the genus do not possess ultrasmall genomes, nor do most taxa studied in related genera of the family or order. This study therefore examined the evolution of genome sizes and chromosome numbers in Genlisea in a phylogenetic context. The correlations of genome size with chromosome number and size, with the phylogeny of the group and with growth forms and habitats were also examined.

METHODS

Nuclear genome sizes were measured from cultivated plant material for a comprehensive sampling of taxa, including nearly half of all species of Genlisea and representing all major lineages. Flow cytometric measurements were conducted in parallel in two laboratories in order to compare the consistency of different methods and controls. Chromosome counts were performed for the majority of taxa, comparing different staining techniques for the ultrasmall chromosomes.

KEY RESULTS

Genome sizes of 15 taxa of Genlisea are presented and interpreted in a phylogenetic context. A high degree of congruence was found between genome size distribution and the major phylogenetic lineages. Ultrasmall genomes with 1C values of <100 Mbp were almost exclusively found in a derived lineage of South American species. The ancestral haploid chromosome number was inferred to be n = 8. Chromosome numbers in Genlisea ranged from 2n = 2x = 16 to 2n = 4x = 32. Ascendant dysploid series (2n = 36, 38) are documented for three derived taxa. The different ploidy levels corresponded to the two subgenera, but were not directly correlated to differences in genome size; the three different karyotype ranges mirrored the different sections of the genus. The smallest known plant genomes were not found in G. margaretae, as previously reported, but in G. tuberosa (1C ≈ 61 Mbp) and some strains of G. aurea (1C ≈ 64 Mbp).

CONCLUSIONS

Genlisea is an ideal candidate model organism for the understanding of genome reduction as the genus includes species with both relatively large (∼1700 Mbp) and ultrasmall (∼61 Mbp) genomes. This comparative, phylogeny-based analysis of genome sizes and karyotypes in Genlisea provides essential data for selection of suitable species for comparative whole-genome analyses, as well as for further studies on both the molecular and cytogenetic basis of genome reduction in plants.

Feeding on prey increases photosynthetic efficiency in the carnivorous sundew Drosera capensis

BACKROUND AND AIMS: It has been suggested that the rate of net photosynthesis (AN) of carnivorous plants increases in response to prey capture and nutrient uptake; however, data confirming the benefit from carnivory in terms of increased AN are scarce and unclear. The principal aim of our study was to investigate the photosynthetic benefit from prey capture in the carnivorous sundew Drosera capensis.

METHODS

Prey attraction experiments were performed, with measurements and visualization of enzyme activities, elemental analysis and pigment quantification together with simultaneous measurements of gas exchange and chlorophyll a fluorescence in D. capensis in response to feeding with fruit flies (Drosophila melanogaster).

KEY RESULTS

Red coloration of tentacles did not act as a signal to attract fruit flies onto the traps. Phosphatase, phophodiesterase and protease activities were induced 24 h after prey capture. These activities are consistent with the depletion of phosphorus and nitrogen from digested prey and a significant increase in their content in leaf tissue after 10 weeks. Mechanical stimulation of tentacle glands alone was not sufficient to induce proteolytic activity. Activities of β-D-glucosidases and N-acetyl-β-D-glucosaminidases in the tentacle mucilage were not detected. The uptake of phosphorus from prey was more efficient than that of nitrogen and caused the foliar N:P ratio to decrease; the contents of other elements (K, Ca, Mg) decreased slightly in fed plants. Increased foliar N and P contents resulted in a significant increase in the aboveground plant biomass, the number of leaves and chlorophyll content as well as AN, maximum quantum yield (Fv/Fm) and effective photochemical quantum yield of photosystem II (ΦPSII).

CONCLUSIONS

According to the stoichiometric relationships among different nutrients, the growth of unfed D. capensis plants was P-limited. This P-limitation was markedly alleviated by feeding on fruit flies and resulted in improved plant nutrient status and photosynthetic performance. This study supports the original cost/benefit model proposed by T. Givnish almost 30 years ago and underlines the importance of plant carnivory for increasing phosphorus, and thereby photosynthesis.

Disproportional plastome-wide increase of substitution rates and relaxed purifying selection in genes of carnivorous Lentibulariaceae

Carnivorous Lentibulariaceae exhibit the most sophisticated implementation of the carnivorous syndrome in plants. Their unusual lifestyle coincides with distinct genomic peculiarities such as the smallest angiosperm nuclear genomes and extremely high nucleotide substitution rates across all genomic compartments. Here, we report the complete plastid genomes from each of the three genera Pinguicula, Utricularia, and Genlisea, and investigate plastome-wide changes in their molecular evolution as the carnivorous syndrome unfolds. We observe a size reduction by up to 9% mostly due to the independent loss of genes for the plastid NAD(P)H dehydrogenase and altered proportions of plastid repeat DNA, as well as a significant plastome-wide increase of substitution rates and microstructural changes. Protein-coding genes across all gene classes show a disproportional elevation of nonsynonymous substitutions, particularly in Utricularia and Genlisea. Significant relaxation of purifying selection relative to noncarnivores occurs in the plastid-encoded fraction of the photosynthesis ATP synthase complex, the photosystem I, and in several other photosynthesis and metabolic genes. Shifts in selective regimes also affect housekeeping genes including the plastid-encoded polymerase, for which evidence for relaxed purifying selection was found once during the transition to carnivory, and a second time during the diversification of the family. Lentibulariaceae significantly exhibit enhanced rates of nucleotide substitution in most of the 130 noncoding regions. Various factors may underlie the observed patterns of relaxation of purifying selection and substitution rate increases, such as reduced net photosynthesis rates, alternative paths of nutrient uptake (including organic carbon), and impaired DNA repair mechanisms.

Strategy of nitrogen acquisition and utilization by carnivorous Dionaea muscipula

Plant carnivory represents an exceptional means to acquire N. Snap traps of Dionaea muscipula serve two functions, and provide both N and photosynthate. Using (13)C/(15)N-labelled insect powder, we performed feeding experiments with Dionaea plants that differed in physiological state and N status (spring vs. autumn plants). We measured the effects of (15)N uptake on light-saturated photosynthesis (A(max)), dark respiration (R(D)) and growth. Depending on N status, insect capture briefly altered the dynamics of R(D)/A(max), reflecting high energy demand during insect digestion and nutrient uptake, followed by enhanced photosynthesis and growth. Organic N acquired from insect prey was immediately redistributed, in order to support swift renewal of traps and thereby enhance probability of prey capture. Respiratory costs associated with permanent maintenance of the photosynthetic machinery were thereby minimized. Dionaea's strategy of N utilization is commensurate with the random capture of large prey, occasionally transferring a high load of organic nutrients to the plant. Our results suggest that physiological adaptations to unpredictable resource availability are essential for Dionaea's success with regards to a carnivorous life style.

Quite a few reasons for calling carnivores 'the most wonderful plants in the world'

BACKGROUND

A plant is considered carnivorous if it receives any noticeable benefit from catching small animals. The morphological and physiological adaptations to carnivorous existence is most complex in plants, thanks to which carnivorous plants have been cited by Darwin as 'the most wonderful plants in the world'. When considering the range of these adaptations, one realizes that the carnivory is a result of a multitude of different features.

SCOPE

This review discusses a selection of relevant articles, culled from a wide array of research topics on plant carnivory, and focuses in particular on physiological processes associated with active trapping and digestion of prey. Carnivory offers the plants special advantages in habitats where nutrient supply is scarce. Counterbalancing costs are the investments in synthesis and the maintenance of trapping organs and hydrolysing enzymes. With the progress in genetic, molecular and microscopic techniques, we are well on the way to a full appreciation of various aspects of plant carnivory.

CONCLUSIONS

Sufficiently complex to be of scientific interest and finite enough to allow conclusive appraisal, carnivorous plants can be viewed as unique models for the examination of rapid organ movements, plant excitability, enzyme secretion, nutrient absorption, food-web relationships, phylogenetic and intergeneric relationships or structural and mineral investment in carnivory.

Is GC bias in the nuclear genome of the carnivorous plant Utricularia driven by ROS-based mutation and biased gene conversion?

At less than 90 Mbp, the tiny nuclear genome of the carnivorous bladderwort plant Utricularia is an attractive model system for studying molecular evolutionary processes leading to genome miniaturization. Recently, we reported that expression of genes encoding DNA repair and reactive oxygen species (ROS) detoxification enzymes is highest in Utricularia traps, and we argued that ROS mutagenic action correlates with the high nucleotide substitution rates observed in the Utricularia plastid, mitochondrial, and nuclear genomes. Here, we extend our analysis of 100 nuclear genes from Utricularia and related asterid eudicots to examine nucleotide substitution biases and their potential correlation with ROS-induced DNA lesions. We discovered an unusual bias toward GC nucleotides, most prominently in transition substitutions at the third position of codons, which are presumably silent with respect to adaptation. Given the general tendency of biased gene conversion to drive GC bias, and of ROS to induce double strand breaks requiring recombinational repair, we propose that some of the unusual features of the bladderwort and its genome may be more reflective of these nonadaptive processes than of natural selection.

The F-actin cytoskeleton in syncytia from non-clonal progenitor cells

The actin cytoskeleton of plant syncytia (a multinucleate cell arising through fusion) is poorly known: to date, there have only been reports about F-actin organization in plant syncytia induced by parasitic nematodes. To broaden knowledge regarding this issue, we analyzed F-actin organization in special heterokaryotic Utricularia syncytia, which arise from maternal sporophytic tissues and endosperm haustoria. In contrast to plant syncytia induced by parasitic nematodes, the syncytia of Utricularia have an extensive F-actin network. Abundant F-actin cytoskeleton occurs both in the region where cell walls are digested and the protoplast of nutritive tissue cells fuse with the syncytium and also near a giant amoeboid in the shape nuclei in the central part of the syncytium. An explanation for the presence of an extensive F-actin network and especially F-actin bundles in the syncytia is probably that it is involved in the movement of nuclei and other organelles and also the transport of nutrients in these physiological activity organs which are necessary for the development of embryos in these unique carnivorous plants. We observed that in Utricularia nutritive tissue cells, actin forms a randomly arranged network of F-actin, and later in syncytium, two patterns of F-actin were observed, one characteristic for nutritive cells and second-actin bundles-characteristic for haustoria and suspensors, thus syncytia inherit their F-actin patterns from their progenitors.

Transcriptomics and molecular evolutionary rate analysis of the bladderwort (Utricularia), a carnivorous plant with a minimal genome

BACKGROUND

The carnivorous plant Utricularia gibba (bladderwort) is remarkable in having a minute genome, which at ca. 80 megabases is approximately half that of Arabidopsis. Bladderworts show an incredible diversity of forms surrounding a defined theme: tiny, bladder-like suction traps on terrestrial, epiphytic, or aquatic plants with a diversity of unusual vegetative forms. Utricularia plants, which are rootless, are also anomalous in physiological features (respiration and carbon distribution), and highly enhanced molecular evolutionary rates in chloroplast, mitochondrial and nuclear ribosomal sequences. Despite great interest in the genus, no genomic resources exist for Utricularia, and the substitution rate increase has received limited study.

RESULTS

Here we describe the sequencing and analysis of the Utricularia gibba transcriptome. Three different organs were surveyed, the traps, the vegetative shoot bodies, and the inflorescence stems. We also examined the bladderwort transcriptome under diverse stress conditions. We detail aspects of functional classification, tissue similarity, nitrogen and phosphorus metabolism, respiration, DNA repair, and detoxification of reactive oxygen species (ROS). Long contigs of plastid and mitochondrial genomes, as well as sequences for 100 individual nuclear genes, were compared with those of other plants to better establish information on molecular evolutionary rates.

CONCLUSION

The Utricularia transcriptome provides a detailed genomic window into processes occurring in a carnivorous plant. It contains a deep representation of the complex metabolic pathways that characterize a putative minimal plant genome, permitting its use as a source of genomic information to explore the structural, functional, and evolutionary diversity of the genus. Vegetative shoots and traps are the most similar organs by functional classification of their transcriptome, the traps expressing hydrolytic enzymes for prey digestion that were previously thought to be encoded by bacteria. Supporting physiological data, global gene expression analysis shows that traps significantly over-express genes involved in respiration and that phosphate uptake might occur mainly in traps, whereas nitrogen uptake could in part take place in vegetative parts. Expression of DNA repair and ROS detoxification enzymes may be indicative of a response to increased respiration. Finally, evidence from the bladderwort transcriptome, direct measurement of ROS in situ, and cross-species comparisons of organellar genomes and multiple nuclear genes supports the hypothesis that increased nucleotide substitution rates throughout the plant may be due to the mutagenic action of amplified ROS production.

The smallest but fastest: ecophysiological characteristics of traps of aquatic carnivorous Utricularia

Aquatic Utricularia species usually grow in standing, nutrient-poor humic waters. They take up all necessary nutrients either directly from the water by rootless shoots or from animal prey by traps. The traps are hollow bladders, 1-6 mm long with elastic walls and have a mobile trap door. The inner part of the trap is densely lined with quadrifid and bifid glands and these are involved in the secretion of digestive enzymes, resorption of nutrients and pumping out the water. The traps capture small aquatic animals but they also host a community of microorganisms considered as commensals. How do these perfect traps function, kill and digest their prey? How do they provide ATP energy for their demanding physiological functions? What are the nature of the interactions between the traps and the mutualistic microorganisms living inside as commensals? In this mini review, all of these questions are considered from an ecophysiologist's point of view, based on the most recent literature data and unpublished results. A new concept on the role of the commensal community for the plants is presented.

The smallest but fastest: ecophysiological characteristics of traps of aquatic carnivorous Utricularia

Aquatic Utricularia species usually grow in standing, nutrient-poor humic waters. They take up all necessary nutrients either directly from the water by rootless shoots or from animal prey by traps. The traps are hollow bladders, 1-6 mm long with elastic walls and have a mobile trap door. The inner part of the trap is densely lined with quadrifid and bifid glands and these are involved in the secretion of digestive enzymes, resorption of nutrients and pumping out the water. The traps capture small aquatic animals but they also host a community of microorganisms considered as commensals. How do these perfect traps function, kill and digest their prey? How do they provide ATP energy for their demanding physiological functions? What are the nature of the interactions between the traps and the mutualistic microorganisms living inside as commensals? In this mini review, all of these questions are considered from an ecophysiologist's point of view, based on the most recent literature data and unpublished results. A new concept on the role of the commensal community for the plants is presented.

Female germ unit in Genlisea and Utricularia, with remarks about the evolution of the extra-ovular female gametophyte in members of Lentibulariaceae

Lentibulariaceae is the largest family among carnivorous plants which displays not only an unusual morphology and anatomy but also the special evolution of its embryological characteristics. It has previously been reported by authors that Utricularia species lack a filiform apparatus in the synergids. The main purposes of this study were to determine whether a filiform apparatus occurs in the synergids of Utricularia and its sister genus Genlisea, and to compare the female germ unit in these genera. The present studies clearly show that synergids in both genera possess a filiform apparatus; however, it seems that Utricularia quelchii synergids have a simpler structure compared to Genlisea aurea and other typical angiosperms. The synergids are located at the terminal position in the embryo sacs of Pinguicula, Genlisea and were probably also located in that position in common Utricularia ancestor. This ancestral characteristic still occurs in some species from the Bivalvaria subgenus. An embryo sac, which grows out beyond the limit of the integument and has contact with nutritive tissue, appeared independently in different Utricularia lineages and as a consequence of this, the egg apparatus changes position from apical to lateral.

Spatio-temporal changes of photosynthesis in carnivorous plants in response to prey capture, retention and digestion

Carnivorous plants have evolved modified leaves into the traps which assist in nutrient uptake from captured prey. It is known that the traps of carnivorous plants have usually lower photosynthetic rates than assimilation leaves as a result of adaptation to carnivory. However a few recent studies have indicated that photosynthesis and respiration undergo spatio-temporal changes during prey capture and retention, especially in the genera with active trapping mechanisms. This study describes the spatio-temporal changes of effective quantum yield of photochemical energy conversion in photosystem II (Ф PSII) in response to ant-derived formic acid during its capture and digestion.

Dark respiration of leaves and traps of terrestrial carnivorous plants: are there greater energetic costs in traps?

In this study, O2-based dark respiration rate (RD) in leaf and trap cuttings was compared in 9 terrestrial carnivorous plant species of 5 genera to decide whether traps represent a greater energetic (maintanence) cost than leaves or photosynthetic parts of traps. RD values of cut strips of traps or leaves of terrestrial carnivorous plants submerged in water ranged between 2.2 and 8.4 nmol g−1 s−1 (per unit dry weight) in pitcher traps of the genera Sarracenia, Nepenthes, and Cephalotus, while between 7.2 and 25 nmol g−1 DW s−1 in fly-paper or snapping traps or leaves of Dionaea and Drosera. No clear relationship between RD values of traps (or pitcher walls) and leaves (or pitcher wings or petioles) was found. However, RD values of separated Drosera prolifera tentacles exceeded those of leaf lamina 7.3 times.

The carnivorous bladderwort (Utricularia, Lentibulariaceae): a system inflates

Carnivorous plants inhabit nutrient-poor environments, where prominent targets of prey capture are organic nitrogen and phosphorus. Some carnivorous plants also acquire carbon from their victims. A new report focusing on Utricularia, the bladderwort, demonstrates that carbon assimilated from photosynthesis is paradoxically secreted into the trapping environment, where it may help to support a mutualistic bacterial community. This bacterial community may also secrete allelochemicals that attract microcrustaceans which bear a strong overt resemblance to bladderwort traps. Furthermore, Utricularia and its sister genus Genlisea share anomalous molecular evolutionary features, such as highly increased rates of nucleotide substitution and dynamic evolution of genome size, from approximately 60-1500 megabases depending on the species or even population. A mechanistic hypothesis, based on the mutagenic action of reactive oxygen species (ROS) is proposed to underlie these phenomena, involving error-prone repair at the level of DNA bases and double-strand breaks. It is argued that these plants are prime candidates for further research on the complexities of plant physiology associated with carnivory, metagenomic surveys of trap microbial communities, novel plant nitrogen/nutrient utilization pathways, the ecology of prey attraction, whole-plant and trap comparative development, and, finally, evolution of the minimal angiosperm genome.

Trap closure and prey retention in Venus flytrap (Dionaea muscipula) temporarily reduces photosynthesis and stimulates respiration

BACKGROUND AND AIMS

The carnivorous plant Venus flytrap (Dionaea muscipula) produces a rosette of leaves: each leaf is divided into a lower part called the lamina and an upper part, the trap, with sensory trigger hairs on the adaxial surface. The trap catches prey by very rapid closure, within a fraction of a second of the trigger hairs being touched twice. Generation of action potentials plays an important role in closure. Because electrical signals are involved in reduction of the photosynthetic rate in different plant species, we hypothesized that trap closure and subsequent movement of prey in the trap will result in transient downregulation of photosynthesis, thus representing the energetic costs of carnivory associated with an active trapping mechanism, which has not been previously described.

METHODS

Traps were enclosed in a gas exchange cuvette and the trigger hairs irritated with thin wire, thus simulating insect capture and retention. Respiration rate was measured in darkness (RD). In the light, net photosynthetic rate (AN), stomatal conductance (gs) and intercellular CO2 concentration (ci) were measured, combined with chlorophyll fluorescence imaging. Responses were monitored in the lamina and trap separately.

KEY RESULTS

Irritation of trigger hairs resulted in decreased AN and increased RD, not only immediately after trap closure but also during the subsequent period when prey retention was simulated in the closed trap. Stomatal conductance remained stable, indicating no stomatal limitation of AN, so ci increased. At the same time, the effective quantum yield of photosystem II (PSII) decreased transiently. The response was confined mainly to the digestive zone of the trap and was not observed in the lamina. Stopping mechanical irritation resulted in recovery of AN, RD and PSII.

CONCLUSIONS

We put forward the first experimental evidence for energetic demands and carbon costs during insect trapping and retention in carnivorous plants, providing a new insight into the cost/benefit model of carnivory.

Functional anatomy of the ovule in Genlisea with remarks on ovule evolution in Lentibulariaceae

The Lentibulariaceae are highly evolved and specialized carnivorous angiosperms displaying not only unusual morphology and embryology but also specific changes in the genome and chromosomes as large as bacterial chromosomes. Comparative study of the morphology and detailed anatomy of the ovule in the genera Genlisea, Utricularia, and Pinguicula should shed new light on the phylogeny of this family. The clade Genlisea + Utricularia is sister to the genus Pinguicula, which is considered the most primitive taxon within Lentibulariaceae. Thus we should expect the ovules of Genlisea to be more similar to those of the more closely related genus Utricularia than to Pinguicula. Surprisingly, the ovules of Genlisea retain characters (free funiculus, ES remaining in the ovule) in common with Pinguicula, presumably inherited from a common ancestor. Genlisea ovules have only one main character in common with subgenus Polypompholyx (Utricularia): a well-developed funiculus. There are differences between the ovules of the subgenera Genlisea and Tayloria. In subgenus Genlisea the micropyle tends to be closer to the funiculus and the ovule forms an unusual jacket-like nutritive tissue of integumental origin. The most specialized ovules in Lentibulariaceae evolved in the genus Utricularia. The special chalazal nutritive tissue in Genlisea and Utricularia is simply a hypostase.

Synthesis, Redox Properties, and Conformational Analysis of Vicinal Disulfide Ring Mimics

A vicinal disulfide ring (VDR) results from disulfide bond formation between two adjacent cysteine residues. This 8-membered ring is a rare motif in protein structures and is functionally important to those few proteins that posses it. This article focuses on the construction of strained and unstrained VDR mimics, discernment of the preferred conformation of these mimics, and the determination of their respective disulfide redox potentials.

Energetics and the evolution of carnivorous plants--Darwin's 'most wonderful plants in the world'

Carnivory has evolved independently at least six times in five angiosperm orders. In spite of these independent origins, there is a remarkable morphological convergence of carnivorous plant traps and physiological convergence of mechanisms for digesting and assimilating prey. These convergent traits have made carnivorous plants model systems for addressing questions in plant molecular genetics, physiology, and evolutionary ecology. New data show that carnivorous plant genera with morphologically complex traps have higher relative rates of gene substitutions than do those with simple sticky traps. This observation suggests two alternative mechanisms for the evolution and diversification of carnivorous plant lineages. The 'energetics hypothesis' posits rapid morphological evolution resulting from a few changes in regulatory genes responsible for meeting the high energetic demands of active traps. The 'predictable prey capture hypothesis' further posits that complex traps yield more predictable and frequent prey captures. To evaluate these hypotheses, available data on the tempo and mode of carnivorous plant evolution were reviewed; patterns of prey capture by carnivorous plants were analysed; and the energetic costs and benefits of botanical carnivory were re-evaluated. Collectively, the data are more supportive of the energetics hypothesis than the predictable prey capture hypothesis. The energetics hypothesis is consistent with a phenomenological cost-benefit model for the evolution of botanical carnivory, and also accounts for data suggesting that carnivorous plants have leaf construction costs and scaling relationships among leaf traits that are substantially different from those of non-carnivorous plants.

Synthesis of peptide substrates for mammalian thioredoxin reductase

Mammalian thioredoxin reductase (TR) catalyzes the reduction of the redox-active disulfide bond of thioredoxin (Trx) and is similar in structure and mechanism to glutathione reductase except for a C-terminal 16-amino acid extension containing a rare vicinal selenylsulfide bond. This vicinal selenylsulfide bond is essentially a substrate for the enzyme's N-terminal redox center. Here we report the synthesis of peptide substrates for the truncated enzyme missing the C-terminal redox center. We developed a procedure for the synthesis of peptides containing cyclic vicinal disulfide/selenylsulfide bonds as well as their corresponding acyclic heterodimers. Vicinal disulfide bonds form eight-membered ring structures and are difficult to synthesize owing to their propensity to dimerize during oxidation. Our procedure makes use of two key improvements for on-resin disulfide bond formation presented previously by Galande and coworkers (Galande AK, Weissleder R, Tung C-H. An effective method of on-resin disulfide bond formation in peptides. J. Comb. Chem. 2005; 7: 174-177). First, the addition of an amine base to the deprotection solution allows the complete removal of the StBu group, allowing it to be replaced with a 5-Npys group. The second enhancement is the direct use of a Cys(Mob) or Sec(Mob) derivative as the nucleophilic partner instead of utilizing a naked sulfhydryl or selenol. These improvements result in the formation of a vicinal disulfide (or selenylsulfide) bond in high purity and yield. A direct comparison with the Galande procedure is presented. We also present a novel strategy for the formation of an acyclic, interchain selenylsulfide-linked peptide (linking H-PTVTGC-OH and H-UG-OH). Cysteine analogs of the cyclic and acyclic peptides were also synthesized. The results show that the ring structure contributes a factor of 52 to the rate, but the presence of selenium in the peptide is more important to catalysis than the presence of the ring.

Oxygen concentrations inside the traps of the carnivorous plants Utricularia and Genlisea (Lentibulariaceae)

BACKGROUND AND AIMS

Species of Utricularia and Genlisea (Lentibulariaceae) are carnivorous, capturing small prey in traps which are physiologically very active, with abundant quadrifid and bifid glands. Traps of Utricularia have walls composed of two cell layers, and are filled with water. Diverse communities of commensal microorganisms often live inside the traps. Genlisea forms long, hollow subterranean traps of foliar origin, growing in anoxic wet substrate. Knowledge of the O(2) concentrations inside Utricularia and Genlisea traps is vital for understanding their physiological functioning and conditions for the life of commensals. To test the hypothesis that prey are killed by anoxia inside the traps, and to measure respiration of traps, [O(2)] was measured in the fluid in mature traps of these species.

METHODS

Oxygen concentration and electrical redox potential were measured using a small Clark-type oxygen sensor and a miniature platinum electrode, respectively, in the fluid of excised and intact traps of six aquatic Utricularia species and in Genlisea hispidula traps.

KEY RESULTS

Steady-state [O(2)] in the traps of both genera always approached zero (median 0.0-4.7 microm). The [O(2)] decreased after electrodes were inserted into Utricularia traps at a rate which ranged from 0.09 to 1.23 mm h(-1) and was lower in traps of irradiated and intact shoots with higher [O(2)] in shoot tissues. Redox potential ranged from -24 to -105 mV in the traps, confirming the very small or zero [O(2)].

CONCLUSIONS

Very small or zero [O(2)], effectively anoxia, is demonstrated in Utricularia and Genlisea traps. This is probably below the critical [O(2)] for prey survival, and causes captured prey to die of suffocation. Internal trap glands and trap commensals are considered to be adapted to facultative anoxia interrupted by limited periods of higher [O(2)] after firings.

Respiration and photosynthesis of bladders and leaves of aquatic utricularia species

In aquatic species of carnivorous utricularia, about 10 - 50 % of the total biomass consists of bladders. Utricularia bladders are physiologically very active organs though their chlorophyll content may greatly be reduced. To specify energetic costs of carnivory, respiration (RD) and net photosynthetic rate (PN) were compared in bladders and leaves or shoot segments of six aquatic utricularia species with differentiated (U. ochroleuca, U. intermedia, U. floridana) or non-differentiated shoots (U. vulgaris, U. australis, U. bremii) under optimum conditions (20 degrees C, [CO (2)] 0.20 mM, 400 micromol m (-2) s (-1) PAR). RD of bladders of six utricularia species (5.1 - 8.6 mmol kg (-1)(FW) h (-1)) was 75 - 200 % greater, than that in leaves in carnivorous or photosynthetic shoots (1.7 - 6.1 mmol kg (-1)(FW) h (-1)). Within individual species, this difference was statistically significant at P < 0.002 - 0.01. However, PN in photosynthetic leaves/shoots (40 - 117 mmol kg (-1)(FW) h (-1)) exceeded that in bladders (5.2 - 14.7 mmol kg (-1)(FW) h (-1)) 7 - 10 times. RD of empty bladders of U. ochroleuca was exactly the same as that in bladders containing prey. Though utricularia bladders are essential for uptake of growth limiting mineral nutrients N and P from prey as the main benefit of carnivory, the current results support previous work showing that bladder function requires greater metabolic (maintenance) cost and very low photosynthetic efficiency (great RD : PN ratio).