Freeze-Thaw-Induced Embolism and Ultrasonic Emissions in Angiosperms

All organisms including plants share the tetrapyrrole biosynthesis pathway that is critical for the production of compounds such as heme and chlorophyll. During tetrapyrrole biosynthesis, coproporphyrinogen III oxidase (CPO) catalyzes the conversion of coproporphyrinogen III into protoporphyrinogen IX. Pratibha et al. () report the results of the characterization of a mutation in the Arabidopsis gene At5g63290 that is orthologous to bacterial and mammalian CPO. As this gene shows greater homology with HemN-like CPO, they named it AtHEMN1. Loss of AtHEMN1 function increased coproporphyrinogen III level and reduced protoporphyrinogen IX level, suggesting the impairment of tetrapyrrole biosynthesis. Mutations that disrupted AtHEMN1 adversely affected silique length, ovule number, and seed set. Athemn1 mutant alleles could be transmitted via both male and female gametes, but homozygous mutants were never recovered. Embryo development in Athemn1 was arrested at the globular stage but the mutant phenotype was completely rescued by transgenic expression of AtHEMN1. Promoter and transcript analyses indicated that AtHEMN1 is expressed mainly in floral tissues and developing seeds. AtHEMN1-green fluorescent protein fusion protein was found targeted to mitochondria. Athemn1 mutant alleles also showed defects in gametophyte development, including nonviable pollen and embryo sacs with unfused polar nuclei. Improper differentiation of the central cell led to defects in endosperm development. Inactivation of any of the enzymes of the tetrapyrrole biosynthetic pathway leads to the accumulation of porphyrin compounds and causes cell death in plants through reactive oxygen species (ROS) production. As expected, the blockage of tetrapyrrole biosynthesis in the Athemn1 mutant also led to increased ROS accumulation in anthers and embryo sacs, as evidenced by nitroblue tetrazolium staining. Thus, it appears that that the tetrapyrrole/heme biosynthesis pathway operates in mitochondria and its impairment disturbs ROS homeostasis in flower buds, thereby adversely affecting male and female gametophyte development in Arabidopsis.

Nematode Cysts and DNA Methylation

Plant-parasitic cyst nematodes (Heterodera species) are among the most devastating pathogens of plant roots. These obligate parasites initiate a long period of biotic interactions with their host plants where formation of an operative feeding structure, the syncytium, is vital for nematode survival and development. The nematode provokes differentially terminated cells in the vascular root tissues to redifferentiate into a syncytium cell type, a switch that involves simultaneous changes in the expression of thousands of genes. Though the mechanisms controlling gene expression changes in the syncytium remain ill defined, recent studies indicate that epigenetic mechanisms including noncoding small RNAs and DNA methylation may play fundamental roles. DNA methylation can regulate the expression of protein-coding genes and the activity of transposable elements. Hewezi et al. () have generated mRNA and small RNA transcriptomes of Arabidopsis roots infected with the beet cyst nematode Heterodera schachtii as well as methylome maps of single-base resolution. They report extensive differences in the methylomes of Arabidopsis roots during the nematode infective stages corresponding to syncytium formation and maintenance phases. H. schachtii-induced methylome changes are characterized by substantial increases in hypomethylation patterns that occurred predominantly in gene bodies and transposable elements in a context-specific fashion. Collectively, their data suggest that differential DNA methylation associated with gene expression changes in the syncytium may determine the compatibility of the interaction between Arabidopsis and H. schachtii.

Thapisgargin Formation in Thapsia

The Mediterranean plant Thapsia garganica (Apiaceae), also known as deadly carrot, produces the highly toxic compound thapsigargin. This compound is a potent inhibitor of the sarcoplasmic-endoplasmic reticulum Ca2+-ATPase calcium pump in mammals and is of industrial importance as the active moiety of the anticancer drug mipsagargin, currently in clinical trials. Thapsigargin is found in most parts of the plant T. garganica. Ripe fruits contain the highest amount of thapsigargin, with 0.7% to 1.5% of the dry weight, followed by roots (0.2%–1.2% of dry weight) and leaves (0.1% of dry weight). It is well established that many Apiaceae species store lipophilic compounds such as phenyl propanoids and terpenoids in secretory ducts, and this appears to be the case with T. gargantica as well. Andersen et al. () show that transcripts for two key enzymes in thapsigargin biosynthetase are found only in the epithelial cells lining these secretory ducts. This emphasizes the involvement of these cells in the biosynthesis of thapsigargin. This study paves the way for further studies of thapsigargin biosynthesis.

Suberin and Seed Dormancy

Environmental signals during seed production are important determinants of seed properties, including seed dormancy and seed longevity. The mother plant plays an important role in this signaling process, collecting signals throughout her life history and modulating dormancy by providing hormones to maturing seeds and by plastic development of the tissues surrounding the embryo. This process is especially important in seeds with physiological dormancy that is coat imposed, which requires the presence and activity of the seed coat and endosperm structures that form a barrier between the embryo and the external environment. In order to further understand the mechanisms by which the control of coat-induced dormancy takes place in Arabidopsis (Arabidopsis thaliana), Fedi et al. () conducted a forward genetic screen to isolate mutants that fail to enter dormancy in response to variation in temperature during seed set. They show that in one of these mutants, designated awake1, the maternal allele is required for entry into strongly dormant states. awake1 mutants show seed phenotypes shown previously to be associated with the loss of suberin in the seed. The authors identify awake1 as an allele of ABCG20, an ATP-binding cassette transporter-encoding gene required for the transport of fatty acids during suberin deposition, and show that further suberin-deficient mutants have seed dormancy defects. It has been previously been established that the suberin composition of seed coats is affected by temperature during seed maturation, but this response appears to be independent of ABCG20. The authors conclude that seed coat suberin is essential for seed dormancy imposition by low temperature and that the exclusion of oxygen and water from the seed by the suberin and tannin layers is important for dormancy imposition.

Blue Light Photoreception by Chlamydomonas

Cryptochromes are flavin-binding proteins that act as blue light receptors in bacteria, fungi, plants and insects and are components of the circadian oscillator in mammals. Animal and plant cryptochromes are evolutionarily divergent, although the unicellular alga Chlamydomonas reinhardtii has both an animal-like cryptochrome and a plant cryptochrome (pCRY; formerly CPH1). Müller et al. () present a functional characterization of pCRY based on an insertional mutant that expresses only 11% of the wild-type pCRY level. The pcry mutant is defective for central properties of the circadian clock. In the mutant, the period is significantly lengthened, ultimately resulting in arrhythmicity, while blue light-based phase shifts show large deviations from what is observed in wild-type cells. Gamete formation by vegetative Chlamydomonas cells is known to mainly triggered by blue light. Thus, it is of interest that pCRY is also involved in gametogenesis in Chlamydomonas. pCRY is down-regulated in pregametes and gametes and in the pcry mutant there is altered transcript accumulation under blue light of the strictly light-dependent, gamete-specific gene GAS28. pCRY acts as a negative regulator for the induction of mating ability in the light and for the loss of mating ability in the dark (during which it accumulates). Moreover, pCRY is necessary for light-dependent germination, during which the zygote undergoes meiosis that gives rise to four vegetative cells. In summary, pCRY is a key blue light receptor in Chlamydomonas that is involved in both circadian timing and life cycle progression.

A Controller of Leaf Angle in Soybean

Soybean (Glycine max) is one of the most important oilseed crops that provides edible oil for humans and is a major renewable feedstock for biodiesel production around the world. As such, increasing soybean yield potential has become a long-term breeding objective. Soybean leaf petiole angle is an important plant architectural trait that affects canopy coverage, photosynthetic efficiency, and ultimately productivity in many legume crops. Leaf petiole angle is mainly controlled by the structure of the pulvinus at the base of a leaf petiole, leaf, or leaflet. Typically, a pulvinus consists of a core of vascular tissues surrounded by a flexible, bulky cylinder of thin-walled parenchyma cells. The outer cells of the parenchyma, termed the motor cells, are responsible for nyctinastic and thigmonastic movement through water-driven volume changes. Gao et al. () report the identification, isolation, and functional characterization of Glycine max Increased Leaf Petiole Angle 1 (GmILPA1), a gene encoding an APC8-like protein, that is a subunit of the anaphase-promoting complex/cyclosome (APC/C) in soybean. A deletion of a fragment involving the 4th exon of GmILPA1 leads to enlarged leaf petiole angles that are associated with reduced motor cell proliferation in the Gmilpa1 mutant. GmILPA1 is mainly expressed in the basal cells of leaf primordia and appears to function by promoting cell growth and division of the pulvinus. GmILPA1 exhibits variable expression levels among varieties with different degrees of leaf petiole angles, and expression levels are correlated with the degrees of the leaf petiole angles. Together, these observations reveal a genetic mechanism modulating plant petiole angle that could pave the way for modifying soybean plant architecture with optimized petiole angles for enhanced yield potential.

Chasing Scattered Genes: Identifying Specialized Metabolite Pathway Genes through Global Co-expression Analysis

Plants produce scores of specialized metabolites (SMs) to attract or repel the organisms around them and to cope with life in a variable environment. For thousands of years, we have been exploiting these compounds to feed, heal, and adorn us. Many more SMs remain to be discovered: the chemical constituents of only 15% of the estimated 350,000 plant species on Earth have thus far been explored (Wurtzel and Kutchan, 2016). Since SMs are not required for plant growth or reproduction, the underlying genes and pathways leading to their production have diversified greatly over time and are not well conserved among species, making them difficult to identify through standard homology searches. However, genes within an SM pathway can be identified through their shared regulatory network, since the successful production of an SM requires the underlying genes to be expressed at the right time and place. Searches for co-expressed genes from global gene expression data have shed light on SM pathways in various plants, but technical constraints and limited data have hampered such analyses.

In addition to their tight regulation, genes in SM pathways, at least in bacteria and fungi, are often clustered together in the genome, forming biosynthetic gene clusters (BGCs). Powerful tools are used to identify BGCs and to predict their involvement in SM pathways. While most known plant SM pathway genes are dispersed across the genome, several plant BGCs have been identified and many more have been predicted (Schlapfer et al., 2017), and the idea that SM pathway genes in plants tend to be clustered together has been gaining traction. If this is not the case, however, techniques for finding plant SM genes based on chromosomal proximity, an easy-to-detect feature, would fail to uncover most SM pathways, prompting Wisecaver et al. (2017) to investigate this issue using data from eight model plant species.

Based on the assumption that genes in an SM pathway form tightly associated co-expression modules, the authors used pairwise measurements of gene co-expression data from hundreds to thousands of experiments to construct MR (mutual ranks)-based co-expression networks. Genes were then assigned to modules of tightly co-expressed genes using the ClusterONE tool. Focusing on small (<50 gene) modules to reflect the typical size of an SM pathway, the authors looked for modules containing SM pathway genes in the Pfam database, finding the fewest such modules in the green alga, Chlamydomonas reinhardtii and the most in the mustard, Brassica rapa.

Many (15.3–52.6%) modules contained two or more known SM biosynthetic genes and genes enriched in SM-related functional categories, as well as many experimentally validated SM pathways. For example, this analysis identified almost all genes involved in the methionine-derived aliphatic glucosinolate (metGSL) biosynthesis pathway and associated biochemical processes in Arabidopsis thaliana (see figure). This approach also revealed all six functionally characterized SM pathways known to form BGCs in the eight plant genomes examined. However, an examination of predicted but not experimentally validated BGCs suggested that these clustered genes are not coexpressed and do not form co-expression modules and might therefore not correspond to functional SM pathways after all. Thus, proximity might not be a reliable index for identifying SM pathways, since most are likely scattered, not clustered. Instead, SM pathways manage to produce their highly coveted products through coordinated expression of their genes, a trait that can now be exploited to facilitate their discovery.

IN BRIEF by Jennifer Lockhart [email protected]

REFERENCES

Schlapfer, P., Zhang, P., Wang, C., Kim, T., Banf, M., Chae, L., Dreher, K., Chavali, A.K., Nilo-Poyanco, R., Bernard, T., Kahn, D., and Rhee, S.Y. (2017). Genome-wide prediction of metabolic enzymes, pathways and gene clusters in plants. Plant Physiol: 173: 2041-2059.

Wisecaver, J.H., Borowsky, A.T., Tzin, V., Jander, G., Kliebenstein, D.J., and Rokas, A. (2017). A global co-expression network approach for connecting genes to specialized metabolic pathways in plants. Plant Cell 29: doi:10.1015/tpc17.00009.

Wurtzel, E.T. and Kutchan, T.M. (2016). Plant metabolism, the diverse chemistry set of the future. Science 353: 1232–1236.

The Plant Cell Reviews Plant Immunity: Receptor-Like Kinases, ROS-RLK Crosstalk, Quantitative Resistance, and the Growth/Defense Tradeoff

Tender green leaves and tasty tubers, roots, and stems are vulnerable to a wide range of pathogens, pests, and herbivores. Perhaps it should not be surprising that they have evolved an equally wide range of defense mechanisms. This issue of The Plant Cell includes reviews of just a few of the many facets of plant immunity.

Plant receptor-like kinases (RLKs) comprise a superfamily of transmembrane proteins, many of which function in pathogen detection as Pattern Recognition Receptors (PRRs). Tang et al. (2017) review recent work on plant RLKs, with a focus on plant-pathogen interactions. The authors present an extended list of known PRRs involved in plant immunity, review their mechanism of action (ligand binding and the formation and regulation of PRR receptor complexes), and highlight new approaches for discovering microbial patterns and their cognate plant PRRs. RLKs play important roles in growth/development as well as immunity, and the authors review what is known about crosstalk and coordination of these pathways. For example, some pathogen effectors actively manipulate RLKs to increase plant susceptibility by mimicking host plant peptide hormones.

Reactive oxygen species (ROS) are produced in response to pathogen invasion and other environmental signals in a manner that is intimately tied to RLK signaling. Kimura et al. (2017) review the role of ROS in RLK signaling and how the regulation of ROS-RLK crosstalk may be a critical component of communication between the cell interior and the environment. The authors discuss the importance of the apoplast as an arena for ROS production and the initiation of ROS-RLK crosstalk, the role of oxidative post-translational modifications in ROS perception, and propose a role for RLK-dependent modulation of both apoplastic and intracellular conditions in facilitating ROS perception and signaling. The importance of RLK-ROS crosstalk is illustrated in the context of stomatal immunity, where the control of stomatal closure restricts a pathogens entry into the plant. Stomatal closure is controlled by a complex interplay of signaling pathways dependent on abscisic acid and other plant hormones, which also intersect with immunity signaling pathways that involve numerous RLK- and ROS-dependent events. Although guard cell ROS production is poorly understood, RLKs appear to play a key role.

Traditional approaches to understanding plant immunity often focus on individual resistance genes that have large effects on plant disease resistance in specific contexts. Corwin and Kliebenstein (2017) argue that quantitative resistance governs most plant-pathogen interactions by the combined effects of many genes with small to moderate effects. The complexity of quantitative resistance and limited power of mapping populations used to study the trait have constrained efforts to understand the underlying mechanisms. The development of new mapping populations with improved power and resolution in a number of model species, such as maize and rice in addition to Arabidopsis, combined with systems biology approaches, such as whole-transcriptome gene expression QTL analysis, are helping to identify causal loci and understand the molecular basis of quantitative resistance. Broad-spectrum resistance is an important concept in plant immunity, but the authors argue that it is poorly understood, and the classical definition of the ability of a host plant to resist multiple genotypes within a single pathogen species may be evolutionarily distinct from the ability to resist specific isolates from numerous different pathogen species. Thus, an important element of studies aimed at understanding broad spectrum resistance may be to consider the role of host and pathogen variation in quantitative resistance across pathogen species.

Plant defense should theoretically impart a cost of reduced growth and reproduction as resources must be diverted to ward off an attack. Karasov et al. (2017) review various means by which plants are able to minimize these costs and optimize growth and defense. Tight regulation of antagonistic crosstalk among growth and defense signaling pathways has been well-characterized, but the selective advantages and evolution of such crosstalk is poorly understood. The authors discuss three types of defense regulation that occur over different time-frames in the plant life cycle: directly induced responses, priming, and transgenerational defense induction. Directly induced responses act to suppress the effects of an ongoing infection and avoid the cost of constitutive expression of defense; priming allows for faster induction of defense to future attacks after the establishment of resistance to an initial attack, and transgenerational memory sets up primed or constitutive means of fighting infection in a future generation. A case study of R genes highlights how evolution may have shaped genetic architecture to allow fine-scale regulation of defense genes to optimize the defense/growth tradeoff. Finally, the authors discuss new evidence that plants exert genetic control over their microbiome to optimize defense.

These four reviews covering different but highly related aspects of plant immunity provide excellent background, explore exciting new directions, and offer insightful perspectives to stimulate future research in this important field of plant biology.

IN BRIEF by Nancy Eckardt [email protected]

REFERENCES

Corwin, J.A., and Kliebenstein, D.J. (2017). Quantitative Resistance: More than Just Perception of a Pathogen. Plant Cell doi: 10.1105/tpc.16.00915.

Karasov, T.L., Chae, E., Herman, J.J., and Bergelson, J. (2017). Mechanisms to mitigate the growth/defense tradeoff. Plant Cell doi: 10.1105/tpc.16.00931.

Kimura, S., Waszczak, C. Hunter, K., and Wrzaczek, M. (2017). Bound by Fate: The Role of Reactive Oxygen Species in Receptor-Like Kinase Signaling. Plant Cell doi: 10.1105/tpc.16.00947.

Tang, D., Wang, G., and Zhou, J.-M. (2017). Receptor kinases in plant-pathogen interactions: more than pattern-recognition. Plant Cell doi: 10.1105/tpc.16.00891.

Saddle Up, Soybean Seed Pigments: Argonaute5 in Spatially Regulated Silencing of Chalcone Synthase Genes

Most soybean seeds you see, whether in bins at the store, or in train cars as a commodity crop, have a yellow seed coat that may have only a tiny fleck of dark pigment at the hilum, where the seed attaches to the pod. The predominant yellow color results from silencing of chalcone synthase (CHS) genes by RNA interference (RNAi) due to the presence of I or ii alleles. The ii allele has an inverted duplication of CHS1, CHS3, and CHS4, causing the production of small interfering RNAs (siRNAs) that target CHS mRNAs and prevent pigment synthesis. Seeds carrying the rare ik allele have a larger region of pigment, producing a saddle pattern of dark purple pigment with black appearance on the yellow bean, more like a black-eyed pea. In a classic example of epistasis, the recessive k1 allele of the K1 locus overcomes the restriction of pigment to the hilum in ii plants: ii K1 soybeans have yellow seeds with a black hilum, but ii k1 soybeans have seeds with a black saddle (similar to ik K1 seeds), and I k1 soybeans have seeds that are entirely black.

To identify the K1 locus, Cho et al. (2017) used RNA sequencing to compare ik K1 and ii k1 seeds, which have similar pigmentation patterns (figure). This showed that k1 has a 129-bp deletion in a gene encoding Argonaute5 (AGO5). AGO proteins bind small RNAs and participate in RNAi by different mechanisms, such as cleavage of mRNAs, inhibition of translation, sequestration of other small RNAs, and repression of transcription via DNA methylation (reviewed in Fang and Qi, 2016). Work in Arabidopsis thaliana and rice (Oryza sativa) implicated AGO5 homologs in the development of germ cells and defense against viruses (reviewed in Fang and Qi, 2016).

The AGO5 transcript from the k1 allele produces a spliced transcript that lacks all of exon 7; this transcript encodes a truncated protein missing one domain (and with partial deletion of another) that is essential for interaction with small RNAs. This change and the recessive nature of the k1 allele indicate that the AGO5 produced by this allele is non-functional. Re-sequencing of AGO5 in four independent lines with saddle patterns identified additional mutations in AGO5, supporting the hypothesis that loss of AGO5 function causes the epistatic effect with alleles of I.

To examine the mechanism by which the lack of AGO5 affects seed pigmentation, the authors dissected different regions (pigmented and un-pigmented) of the seed coat to compare siRNA abundance. The siRNAs targeting CHS are most abundant before the pigment develops; therefore, they dissected regions of the green seed coat based on position. High-throughput sequencing of small RNAs showed that the Williams cultivar, which has the ii K1 genotype, showed about 20-fold more siRNAs that target CHS loci in the region that will become yellow than in the hilum region that will become pigmented. Similarly, Clark 8a (ik K1 saddle pattern) and Clark 18a (ii k1 saddle pattern) seeds showed higher levels of siRNAs targeting CHS loci in the un-pigmented region. RNA-sequencing data (the same data used to identify K1 above) showed that the regions with high levels of CHS siRNAs had correspondingly low levels of CHS mRNAs. These non-pigmented regions also had the highest levels of AGO5 mRNA, and AGO5 mRNA levels were much lower in k1 seed coats, compared with K1. Intriguingly, of the twenty annotated AGO loci in the soybean genome, many were highly expressed in the seed coat and several, including AGO10, showed higher expression levels in the non-pigmented regions.

This interesting study showed that AGO5 affects the distribution of siRNAs targeting the CHS genes in the soybean seed coat. As the authors point out, many soybean AGOs likely function in the RNAi suppression of CHS genes in the seed coats. Moreover, elucidation of developmental factors that specify the spatial boundary and how the RNAi factors spatially regulate the levels of siRNAs, whether via effects on transcription, RNA cleavage, small RNA biogenesis, or another mechanism, remains an intriguing topic for future studies.

IN BRIEF by Jennifer Mach [email protected]

REFERENCES

Cho, Y.B., Jones, S.I., and Vodkin, L.O. (2017) Mutations in Argonaute5 Illuminate Epistatic Interactions of the K1 and I Loci Leading to Saddle Seed Color Patterns in Glycine max. Plant Cell 10.1105/tpc.17.00162.

Fang, X. and Qi, Y. (2016).  RNAi in Plants:  An Argonaute-Centered View.  The Plant Cell 28272-285.