Molecular Evolution of a Small Gene Family of Wound Inducible Kunitz Trypsin Inhibitors in Populus

TcTI, a Kunitz-type trypsin inhibitor from cocoa associated with defense against pathogens

Protease inhibitors (PIs) are important biotechnological tools of interest in agriculture. Usually they are the first proteins to be activated in plant-induced resistance against pathogens. Therefore, the aim of this study was to characterize a Theobroma cacao trypsin inhibitor called TcTI. The ORF has 740 bp encoding a protein with 219 amino acids, molecular weight of approximately 23 kDa. rTcTI was expressed in the soluble fraction of Escherichia coli strain Rosetta [DE3]. The purified His-Tag rTcTI showed inhibitory activity against commercial porcine trypsin. The kinetic model demonstrated that rTcTI is a competitive inhibitor, with a Ki value of 4.08 × 10-7 mol L-1. The thermostability analysis of rTcTI showed that 100% inhibitory activity was retained up to 60 °C and that at 70-80 °C, inhibitory activity remained above 50%. Circular dichroism analysis indicated that the protein is rich in loop structures and β-conformations. Furthermore, in vivo assays against Helicoverpa armigera larvae were also performed with rTcTI in 0.1 mg mL-1 spray solutions on leaf surfaces, which reduced larval growth by 70% compared to the control treatment. Trials with cocoa plants infected with Mp showed a greater accumulation of TcTI in resistant varieties of T. cacao, so this regulation may be associated with different isoforms of TcTI. This inhibitor has biochemical characteristics suitable for biotechnological applications as well as in resistance studies of T. cacao and other crops.

Aboveground phytochemical responses to belowground herbivory in poplar trees and the consequence for leaf herbivore preference

Belowground (BG) herbivory can influence aboveground (AG) herbivore performance and food preference via changes in plant chemistry. Most evidence for this phenomenon derives from studies in herbaceous plants but studies in woody plants are scarce. Here we investigated whether and how BG herbivory on black poplar (Populus nigra) trees by Melolontha melolontha larvae influences the feeding preference of Lymantria dispar (gypsy moth) caterpillars. In a food choice assay, caterpillars preferred to feed on leaves from trees that had experienced attack by BG herbivores. Therefore, we investigated the effect of BG herbivory on the phytochemical composition of P. nigra trees alone and in combination with AG feeding by L. dispar caterpillars. BG herbivory did not increase systemic AG tree defences like volatile organic compounds, protease inhibitors and salicinoids. Jasmonates and salicylic acid were also not induced by BG herbivory in leaves but abscisic acid concentrations drastically increased together with proline and few other amino acids. Leaf coating experiments with amino acids suggest that proline might be responsible for the caterpillar feeding preference via presumptive phagostimulatory properties. This study shows that BG herbivory in poplar can modify the feeding preference of AG herbivores via phytochemical changes as a consequence of root-to-shoot signaling.

Recombinant cystatins in plants

Dozens of studies have assessed the practical value of plant cystatins as ectopic inhibitors of Cys proteases in biological systems. The potential of these proteins in crop protection to control herbivorous pests and pathogens has been documented extensively over the past 25 years. Their usefulness to regulate endogenous Cys proteases in planta has also been considered recently, notably to implement novel traits of agronomic relevance in crops or to generate protease activity-depleted environments in plants or plant cells used as bioreactors for recombinant proteins. After a brief update on the basic structural characteristics of plant cystatins, we summarize recent advances on the use of these proteins in plant biotechnology. Attention is also paid to the molecular improvement of their structural properties for the improvement of their protease inhibitory effects or the fine-tuning of their biological target range.

Can Plant Defence Mechanisms Provide New Approaches for the Sustainable Control of the Two-Spotted Spider Mite Tetranychus urticae?

Tetranychus urticae (T. urticae) Koch is a cosmopolitan, polyphagous mite which causes economic losses in both agricultural and ornamental plants. Some traits of T. urticae hamper its management, including a short life cycle, arrhenotokous parthenogenesis, its haplodiploid sex determination system, and its extraordinary ability to adapt to different hosts and environmental conditions. Currently, the use of chemical and biological control are the major control methods used against this mite. In recent years, some studies have focused on plant defence mechanisms against herbivores. Various families of plant compounds (such as flavonoids, glucosinolates, or acyl sugars) have been shown to behave as acaricides. Plants can be induced upon appropriate stimuli to increase their resistance against spider mites. This knowledge, together with the understanding of mechanisms by which T. urticae detoxifies and adapts to pesticides, may complement the control of this pest. Herein, we describe plant volatile compounds (VOCs) with repellent activity, and new findings about defence priming against spider mites, which interfere with the T. urticae performance. The use of VOCs and defence priming can be integrated into current management practices and reduce the damage caused by T. urticae in the field by implementing new, more sustainable crop management tools.

Positive selection of digestive Cys proteases in herbivorous Coleoptera

Positive selection is thought to contribute to the functional diversification of insect-inducible protease inhibitors in plants in response to selective pressures exerted by the digestive proteases of their herbivorous enemies. Here we assessed whether a reciprocal evolutionary process takes place on the insect side, and whether ingestion of a positively selected plant inhibitor may translate into a measurable rebalancing of midgut proteases in vivo. Midgut Cys proteases of herbivorous Coleoptera, including the major pest Colorado potato beetle (Leptinotarsa decemlineata), were first compared using a codon-based evolutionary model to look for the occurrence of hypervariable, positively selected amino acid sites among the tested sequences. Hypervariable sites were found, distributed within -or close to- amino acid regions interacting with Cys-type inhibitors of the plant cystatin protein family. A close examination of L. decemlineata sequences indicated a link between their assignment to protease functional families and amino acid identity at positively selected sites. A function-diversifying role for positive selection was further suggested empirically by in vitro protease assays and a shotgun proteomic analysis of L. decemlineata Cys proteases showing a differential rebalancing of protease functional family complements in larvae fed single variants of a model cystatin mutated at positively selected amino acid sites. These data confirm overall the occurrence of hypervariable, positively selected amino acid sites in herbivorous Coleoptera digestive Cys proteases. They also support the idea of an adaptive role for positive selection, useful to generate functionally diverse proteases in insect herbivores ingesting functionally diverse, rapidly evolving dietary cystatins.

Geographical structure and adaptive population differentiation in herbivore defence genes in European aspen (Populus tremula L., Salicaceae)

When a phenotypic trait is subjected to spatially variable selection and local adaptation, the underlying genes controlling the trait are also expected to show strong patterns of genetic differentiation because alternative alleles are favoured in different geographical locations. Here, we study 71 single nucleotide polymorphisms (SNPs) from seven genes associated with inducible defence responses in a sample of Populus tremula collected from across Sweden. Four of these genes (PPO2, TI2, TI4 and TI5) show substantial population differentiation, and a principal component analyses conducted on the defence SNPs divides the Swedish population into three distinct clusters. Several defence SNPs show latitudinal clines, although these were not robust to multiple testing. However, five SNPs (located within TI4 and TI5) show strong longitudinal clines that remain significant after multiple test correction. Genetic geographical variation, supporting local adaptation, has earlier been confirmed in genes involved in the photoperiod pathway in P. tremula, but this is, to our knowledge, one of the first times that geographical variation has been found in genes involved in plant defence against antagonists.

Molecular evolution of miraculin-like proteins in soybean Kunitz super-family

Miraculin-like proteins (MLPs) belong to soybean Kunitz super-family and have been characterized from many plant families like Rutaceae, Solanaceae, Rubiaceae, etc. Many of them possess trypsin inhibitory activity and are involved in plant defense. MLPs exhibit significant sequence identity (~30-95%) to native miraculin protein, also belonging to Kunitz super-family compared with a typical Kunitz family member (~30%). The sequence and structure-function comparison of MLPs with that of a classical Kunitz inhibitor have demonstrated that MLPs have evolved to form a distinct group within Kunitz super-family. Sequence analysis of new genes along with available MLP sequences in the literature revealed three major groups for these proteins. A significant feature of Rutaceae MLP type 2 sequences is the presence of phosphorylation motif. Subtle changes are seen in putative reactive loop residues among different MLPs suggesting altered specificities to specific proteases. In phylogenetic analysis, Rutaceae MLP type 1 and type 2 proteins clustered together on separate branches, whereas native miraculin along with other MLPs formed distinct clusters. Site-specific positive Darwinian selection was observed at many sites in both the groups of Rutaceae MLP sequences with most of the residues undergoing positive selection located in loop regions. The results demonstrate the sequence and thereby the structure-function divergence of MLPs as a distinct group within soybean Kunitz super-family due to biotic and abiotic stresses of local environment.

Molecular population genetics of elicitor-induced resistance genes in European aspen (Populus tremula L., Salicaceae)

Owing to their long life span and ecological dominance in many communities, forest trees are subject to attack from a diverse array of herbivores throughout their range, and have therefore developed a large number of both constitutive and inducible defenses. We used molecular population genetics methods to examine the evolution of eight genes in European aspen, Populus tremula, that are all associated with defensive responses against pests and/or pathogens, and have earlier been shown to become strongly up-regulated in poplars as a response to wounding and insect herbivory. Our results show that the majority of these defense genes show patterns of intraspecific polymorphism and site-frequency spectra that are consistent with a neutral model of evolution. However, two of the genes, both belonging to a small gene family of polyphenol oxidases, show multiple deviations from the neutral model. The gene PPO1 has a 600 bp region with a highly elevated K(A)/K(S) ratio and reduced synonymous diversity. PPO1 also shows a skew toward intermediate frequency variants in the SFS, and a pronounced fixation of non-synonymous mutations, all pointing to the fact that PPO1 has been subjected to recurrent selective sweeps. The gene PPO2 shows a marked excess of high frequency, derived variants and shows many of the same trends as PPO1 does, even though the pattern is less pronounced, suggesting that PPO2 might have been the target of a recent selective sweep. Our results supports data from both Populus and other species which have found that the the majority of defense-associated genes show few signs of selection but that a number of genes involved in mediating defense against herbivores show signs of adaptive evolution.

Poplar defense against insects: genome analysis, full-length cDNA cloning, and transcriptome and protein analysis of the poplar Kunitz-type protease inhibitor family

*Kunitz protease inhibitors (KPIs) feature prominently in poplar defense responses against insects. The increasing availability of genomics resources enabled a comprehensive analysis of the poplar (p)KPI family. *Using genome analysis, expressed sequence tag (EST) mining and full-length (FL)cDNA cloning we established an inventory and phylogeny of pKPIs. Microarray and real-time PCR analyses were used to profile pKPI gene expression following real or simulated insect attack. Proteomics of insect midgut content was used to monitor stability of pKPI protein. *We identified 31 pKPIs in the genome and validated gene models by EST mining and cloning of 41 unique FLcDNAs. Genome organization of the pKPI family, with six poplar-specific subfamilies, suggests that tandem duplications have played a major role in its expansion. pKPIs are expressed throughout the plant and many are strongly induced by insect attack, although insect-specific signals seem initially to suppress the tree pKPI response. We found substantial peptide coverage for a potentially intact pKPI protein in insect midgut after eating poplar leaves. *These results highlight the complexity of an important defense gene family in poplar with regard to gene family size, differential constitutive and insect-induced gene expression, and resilience of at least one pKPI protein to digestion by herbivores.

Selective histories of poplar protease inhibitors: elevated polymorphism, purifying selection, and positive selection driving divergence of recent duplicates

To further our understanding of plant defense evolution and the consistency of selection at the nucleotide level we analysed polymorphism data from five protease inhibitor (PI) genes in Populus balsamifera. We compared diversity at the five PI genes to diversity at nondefense loci in both range-wide samples as well as in two subpopulations, one from the northern edge of the species range and one from the southern edge of the range. We also compared our data with previously reported diversity in Populus tremula, a European species with similar ecology to North American P. balsamifera. The PIs show diverse histories, including repeated bouts of positive selection and excess diversity. These genes also exhibit diverse histories in P. tremula but the signatures of selection acting at the specific loci differed between the species. One locus, KTI3, segregates several recent duplicates that show evidence of either positive selection or relaxed selective constraints. The patterns of diversity at the PIs varied within P. balsamifera and between two closely related species. The lack of consistent patterns suggests that evolution of host defense genes, including adaptations to enemy-imposed selection, may often be lineage- and gene-specific.

Multilocus patterns of nucleotide polymorphism and the demographic history of Populus tremula

I have studied nucleotide polymorphism and linkage disequilibrium using multilocus data from 77 fragments, with an average length of fragments of 550 bp, in the deciduous tree Populus tremula (Salicaceae). The frequency spectrum across loci showed a modest excess of mutations segregating at low frequency and a marked excess of high-frequency derived mutations at silent sites, relative to neutral expectations. These excesses were also seen at replacement sites, but were not so pronounced for high-frequency derived mutations. There was a marked excess of low-frequency mutations at replacement sites, likely indicating deleterious amino acid-changing mutations that segregate at low frequencies in P. tremula. I used approximate Bayesian computation (ABC) to evaluate a number of different demographic scenarios and to estimate parameters for the best-fitting model. The data were found to be consistent with a historical reduction in the effective population size of P. tremula through a bottleneck. The timing inferred for this bottleneck is largely consistent with geological data and with data from several other long-lived plant species. The results show that P. tremula harbors substantial levels of nucleotide polymorphism with the posterior mode of the scaled mutation rate, theta = 0.0177 across loci. The ABC analyses also provided an estimate of the scaled recombination rate that indicates that recombination rates in P. tremula are likely to be 2-10 times higher than the mutation rate. This study reinforces the notion that linkage disequilibrium is low and decays to negligible levels within a few hundred base pairs in P. tremula.

Duplication and adaptive evolution of the COR15 genes within the highly cold-tolerant Draba lineage (Brassicaceae)

Plants have evolved diverse adaptive mechanisms that enable them to tolerate abiotic stresses, to varying degrees, and such stresses may have strongly influenced evolutionary changes at levels ranging from molecular to morphological. Previous studies on these phenomena have focused on the adaptive evolution of stress-related orthologous genes in specific lineages. However, heterogenetic evolution of the paralogous genes following duplication has only been examined in a very limited number of stress-response gene families. The COR15 gene encodes a low molecular weight protein that plays an important role in protecting plants from cold stresses. Although two different copies of this gene have been found in the model species, Arabidopsis thaliana, evolutionary patterns of this small gene family in plants have not been previously explored. In this study, we cloned COR15-like sequences and performed evolutionary analyses of these sequences (including those previously reported) in the highly cold-tolerant Draba lineage and related lineages of Brassicaceae. Our phylogenetic analyses indicate that all COR15-like sequences clustered into four clades that corresponded well to the morphological lineages. Gene conversions were found to have probably occurred before/during the divergence of Brassica and Draba lineage. However, repeated, independent duplications of this gene have occurred in different lineages of Brassicaceae. Further comparisons of all sequences suggest that there have been significant inter-lineage differences in evolutionary rates between the duplicated and original genes. We assessed the likelihood that the differences between two well-supported gene subfamilies that appear to have originated from a single duplication, COR15a and COR15b, within the Draba lineage have been driven by adaptive evolution. Comparisons of their non-synonymous/synonymous substitution ratios and rates of predicted amino acid changes indicate that these two gene groups are evolving under different selective pressures and may be functionally divergent. This functional divergence was confirmed by comparing site-specific shifts in evolution indexes of the two groups of predicted proteins. The evidence of differential selection and possible functional divergence suggests that the duplication may be of adaptive significance, with possible implications for the explosive diversification of the Draba lineage during the cooling Quaternary stages and the following worldwide colonization of arid alpine and artic regions.

Functional analysis of the Kunitz trypsin inhibitor family in poplar reveals biochemical diversity and multiplicity in defense against herbivores

We investigated the functional and biochemical variability of Kunitz trypsin inhibitor (KTI) genes of Populus trichocarpa x Populus deltoides. Phylogenetic analysis, expressed sequence tag databases, and western-blot analysis confirmed that these genes belong to a large and diverse gene family with complex expression patterns. Five wound- and herbivore-induced genes representing the diversity of the KTI gene family were selected for functional analysis and shown to produce active KTI proteins in Escherichia coli. These recombinant KTI proteins were all biochemically distinct and showed clear differences in efficacy against trypsin-, chymotrypsin-, and elastase-type proteases, suggesting functional specialization of different members of this gene family. The in vitro stability of the KTIs in the presence of reducing agents and elevated temperature also varied widely, emphasizing the biochemical differences of these proteins. Significantly, the properties of the recombinant KTI proteins were not predictable from primary amino acid sequence data. Proteases in midgut extracts of Malacosoma disstria, a lepidopteran pest of Populus, were strongly inhibited by at least two of the KTI gene products. This study suggests that the large diversity in the poplar (Populus spp.) KTI family is important for biochemical and functional specialization, which may be important in the maintenance of pest resistance in long-lived plants such as poplar.

Plant immunity to insect herbivores

Herbivorous insects use diverse feeding strategies to obtain nutrients from their host plants. Rather than acting as passive victims in these interactions, plants respond to herbivory with the production of toxins and defensive proteins that target physiological processes in the insect. Herbivore-challenged plants also emit volatiles that attract insect predators and bolster resistance to future threats. This highly dynamic form of immunity is initiated by the recognition of insect oral secretions and signals from injured plant cells. These initial cues are transmitted within the plant by signal transduction pathways that include calcium ion fluxes, phosphorylation cascades, and, in particular, the jasmonate pathway, which plays a central and conserved role in promoting resistance to a broad spectrum of insects. A detailed understanding of plant immunity to arthropod herbivores will provide new insights into basic mechanisms of chemical communication and plant-animal coevolution and may also facilitate new approaches to crop protection and improvement.

Poplar defense against insect herbivoresThis review is one of a selection of papers published in the Special Issue on Poplar Research in Canada

The availability of a poplar ( Populus trichocarpa Torr & A. Gray, black cottonwood) genome sequence is enabling new research approaches in angiosperm tree biology. Much of the recent genomics research in poplars has been on wood formation, growth and development, resistance to abiotic stress and pathogens, motivated, at least in part, by the fact that poplars provide an important system for large-scale, short-rotation plantation forestry in the Northern Hemisphere. To sustain productivity and ecosystem health of natural and planted poplar forests it is of critical importance to also develop a better understanding of the molecular mechanisms of defense and resistance of poplars against insect pests. Previous research has established a solid foundation of the chemical ecology of poplar defense against insects. This review summarizes some of the relevant literature on defense against insect herbivores in poplars with an emphasis on molecular, biochemical, and emerging genomic research in this important field within forest biotechnology and chemical ecology. Following a general introduction, we provide a brief overview of some of the most relevant insect pests of poplars; we then describe some of the general defense strategies of poplars along with selected examples of their activities. We conclude with a summary of emerging results and perspectives from recent advances in genomics research on poplar defense against insects.

Small cysteine-rich peptides resembling antimicrobial peptides have been under-predicted in plants

Multicellular organisms produce small cysteine-rich antimicrobial peptides as an innate defense against pathogens. While defensins, a well-known class of such peptides, are common among eukaryotes, there are other classes restricted to the plant kingdom. These include thionins, lipid transfer proteins and snakins. In earlier work, we identified several divergent classes of small putatively secreted cysteine-rich peptides (CRPs) in legumes [Graham et al. (2004)Plant Physiol. 135, 1179-97]. Here, we built sequence motif models for each of these classes of peptides, and iteratively searched for related sequences within the comprehensive UniProt protein dataset, the Institute for Genomic Research's 33 plant gene indices, and the entire genomes of the model dicot, Arabidopsis thaliana, and the model monocot and crop species, Oryza sativa (rice). Using this search strategy, we identified approximately 13,000 plant genes encoding peptides with common features: (i) an N-terminal signal peptide, (ii) a small divergent charged or polar mature peptide with conserved cysteines, (iii) a similar intron/exon structure, (iv) spatial clustering in the genomes studied, and (v) overrepresentation in expressed sequences from reproductive structures of specific taxa. The identified genes include classes of defensins, thionins, lipid transfer proteins, and snakins, plus other protease inhibitors, pollen allergens, and uncharacterized gene families. We estimate that these classes of genes account for approximately 2-3% of the gene repertoire of each model species. Although 24% of the genes identified were not annotated in the latest Arabidopsis genome releases (TIGR5, TAIR6), we confirmed expression via RT-PCR for 59% of the sequences attempted. These findings highlight limitations in current annotation procedures for small divergent peptide classes.

Populus: a model system for plant biology

With the completion of the Populus trichocarpa genome sequence and the development of various genetic, genomic, and biochemical tools, Populus now offers many possibilities to study questions that cannot be as easily addressed in Arabidopsis and rice, the two prime model systems of plant biology and genomics. Tree-specific traits such as wood formation, long-term perennial growth, and seasonality are obvious areas of research, but research in other areas such as control of flowering, biotic interactions, and evolution of adaptive traits is enriched by adding a tree to the suite of model systems. Furthermore, the reproductive biology of Populus (a dioeceous wind-pollinated long-lived tree) offers both new possibilities and challenges in the study and analysis of natural genetic and phenotypic variation. The relatively close phylogenetic relationship of Populus to Arabidopsis in the Eurosid clade of Eudicotyledonous plants aids in comparative functional studies and comparative genomics, and has the potential to greatly facilitate studies on genome and gene family evolution in eudicots.