Stomatal Bioassay to Characterize Bacterial-Stimulated PTI at the Pre-Invasion Phase of Infection

Bacterium-triggered stomatal closure is a functional output of plant immunity, also known as stomatal defense. This is an early response mediated by the recognition of pathogen-associated molecular patterns (PAMPs) by the plant's pathogen recognition receptors (PRRs). Several approaches to analyzing stomatal movement in response to bacteria have been described, but difficulties in fine-tuning the experimental procedures still exist. Here we provide a detailed method for assessing stomatal defense via high-quality microscopic imaging and explain trouble-shooting steps to obtaining robust data. Although this procedure requires minimal manipulation of the leaf sample, it is crucial to control all environmental conditions and extrinsic variables that could interfere with stomatal movement. The method described here is also suitable for in vivo characterization of stomatal response in new pathosystems and can be used in conjunction with other profiling assays to gain a detailed understanding of early PAMP-triggered immunity (PTI).

Stomate-based defense and environmental cues

Environmental conditions play crucial roles in modulating immunity and disease in plants. For instance, many bacterial disease outbreaks occur after periods of high humidity and rain. A critical step in bacterial infection is entry into the plant interior through wounds or natural openings, such as stomata. Bacterium-triggered stomatal closure is an integral part of the plant immune response to reduce pathogen invasion. Recently, we found that high humidity compromises stomatal defense, which is accompanied by regulation of the salicylic acid and jasmonic acid pathways in guard cells. Periods of darkness, when most stomata are closed, are effective in decreasing pathogen penetration into leaves. However, coronatine produced by Pseudomonas syringae pv. tomato (Pst) DC3000 cells can open dark-closed stomata facilitating infection. Thus, a well-known disease-promoting environmental condition (high humidity) acts in part by suppressing stomatal defense, whereas an anti-stomatal defense factor such as coronatine, may provide epidemiological advantages to ensure bacterial infection when environmental conditions (darkness and insufficient humidity) favor stomatal defense.

Stomatal Defense a Decade Later

A decade has passed since the discovery of stomatal defense, and the field has expanded considerably with significant understanding of the basic mechanisms underlying the process.

An HPLC-based Method to Quantify Coronatine Production by Bacteria

Coronatine is a polyketide phytotoxin produced by several pathovars of the plant pathogenic bacterium Pseudomonas syringae. It is one of the most important virulence factors determining the success of bacterial pathogenesis in the plant at both epiphytic and endophytic stages of the disease cycle. This protocol describes an optimized procedure to culture bacterial cells for coronatine production and to quantify the amount of coronatine secreted in the culture medium using an HPLC-based method.

Jasmonate signaling and manipulation by pathogens and insects

Plants synthesize jasmonates (JAs) in response to developmental cues or environmental stresses, in order to coordinate plant growth, development or defense against pathogens and herbivores. Perception of pathogen or herbivore attack promotes synthesis of jasmonoyl-L-isoleucine (JA-Ile), which binds to the COI1-JAZ receptor, triggering the degradation of JAZ repressors and induction of transcriptional reprogramming associated with plant defense. Interestingly, some virulent pathogens have evolved various strategies to manipulate JA signaling to facilitate their exploitation of plant hosts. In this review, we focus on recent advances in understanding the mechanism underlying the enigmatic switch between transcriptional repression and hormone-dependent transcriptional activation of JA signaling. We also discuss various strategies used by pathogens and insects to manipulate JA signaling and how interfering with this could be used as a novel means of disease control.

Surface Inoculation and Quantification of Pseudomonas syringae Population in the Arabidopsis Leaf Apoplast

Bacterial pathogens must enter the plant tissue in order to cause a successful infection. Foliar bacterial pathogens that are not able to directly penetrate the plant epidermis rely on wounds or natural openings to internalize leaves. This protocol describes a procedure to estimate the population size of Pseudomonas syringae in the leaf apoplast after surface inoculation of Arabidopsis rosettes.

Regulation of Stomatal Defense by Air Relative Humidity

It has long been observed that environmental conditions play crucial roles in modulating immunity and disease in plants and animals. For instance, many bacterial plant disease outbreaks occur after periods of high humidity and rain. A critical step in bacterial infection is entry into the plant interior through wounds and natural openings, such as stomata, which are adjustable microscopic pores in the epidermal tissue. Several studies have shown that stomatal closure is an integral part of the plant immune response to reduce pathogen invasion. In this study, we found that high humidity can effectively compromise Pseudomonas syringae-triggered stomatal closure in both Phaseolus vulgaris and Arabidopsis (Arabidopsis thaliana), which is accompanied by early up-regulation of the jasmonic acid (JA) pathway and simultaneous down-regulation of salicylic acid (SA) pathway in guard cells. Furthermore, SA-dependent response, but not JA-dependent response, is faster in guard cells than in whole leaves, suggesting that the SA signaling in guard cells may be independent from other cell types. Thus, we conclude that high humidity, a well-known disease-promoting environmental condition, acts in part by suppressing stomatal defense and is linked to hormone signaling in guard cells.

Coronatine Facilitates Pseudomonas syringae Infection of Arabidopsis Leaves at Night

In many land plants, the stomatal pore opens during the day and closes during the night. Thus, periods of darkness could be effective in decreasing pathogen penetration into leaves through stomata, the primary sites for infection by many pathogens. Pseudomonas syringae pv. tomato (Pst) DC3000 produces coronatine (COR) and opens stomata, raising an intriguing question as to whether this is a virulence strategy to facilitate bacterial infection at night. In fact, we found that (a) biological concentration of COR is effective in opening dark-closed stomata of Arabidopsis thaliana leaves, (b) the COR defective mutant Pst DC3118 is less effective in infecting Arabidopsis in the dark than under light and this difference in infection is reduced with the wild type bacterium Pst DC3000, and (c) cma, a COR biosynthesis gene, is induced only when the bacterium is in contact with the leaf surface independent of the light conditions. These findings suggest that Pst DC3000 activates virulence factors at the pre-invasive phase of its life cycle to infect plants even when environmental conditions (such as darkness) favor stomatal immunity. This functional attribute of COR may provide epidemiological advantages for COR-producing bacteria on the leaf surface.

The Co-4 locus on chromosome Pv08 contains a unique cluster of 18 COK-4 genes and is regulated by immune response in common bean

The common bean locus Co - 4, traditionally referred to as an anthracnose-resistant gene, contains a cluster of predicted receptor-like kinases (COK-4 and CrRLK1-like), and at least two of these kinases are co-regulated with the plant's basal immunity. Genetic resistance to anthracnose, caused by the fungus Colletotrichum lindemuthianum (Sacc. and Magnus) Briosi and Cavara, is conferred by major loci throughout the Phaseolus vulgaris genome, named Co. The complex Co-4 locus was previously reported to have several copies of the COK-4 gene that is predicted to code for a receptor-like kinase (RLK). In general, plant RLKs are involved in pathogen perception and signal transduction; however, the molecular function of COK-4 remains elusive. Using newly identified molecular markers (PvTA25 and PvSNPCOK-4), the SAS13 marker, COK-4 sequences and phylogeny, and the recently released bean genome sequence, we determined the most probable boundaries of the Co-4 locus: a 325-Kbp region on chromosome Pv08. Out of the 49 predicted transcripts in that region, 24 encode for putative RLKs (including 18 COK-4 copies) with high similarity to members of the Catharanthus roseus RLK1-like (CrRLK1L) protein family from different plant species, including the well-described FERONIA (FER) and ANXUR. We also determined that two RLK-coding genes in the Co-4 locus (COK-4-3 and FER-like) are transcriptionally regulated when bean plants are challenged with the flg22 peptide, a commonly used elicitor of plant immunity, or the bacterium Pseudomonas syringae pv. phaseolicola, the causal agent of halo blight. While COK-4-3 is activated during immune response, FER-like is downregulated suggesting that these genes could play a role in plant responses to biotic stress. These results highlight the importance of dissecting the regulation and molecular function of individual genes within each locus, traditionally referred to as resistance gene based on genetic segregation analysis.

Common bean reaction to angular leaf spot comprises transcriptional modulation of genes in the ALS10.1 QTL

Genetic resistance of common bean (Phaseolus vulgaris L.) against angular leaf spot (ALS), caused by the fungus Pseudocercospora griseola, is conferred by quantitative trait loci (QTL). In this study, we determined the gene content of the major QTL ALS10.1 located at the end of chromosome Pv10, and identified those that are responsive to ALS infection in resistant (CAL 143) and susceptible (IAC-UNA) genotypes. Based on the current version of the common bean reference genome, the ALS10.1 core region contains 323 genes. Gene Ontology (GO) analysis of these coding sequences revealed the presence of genes involved in signal perception and transduction, programmed cell death (PCD), and defense responses. Two putative R gene clusters were found at ALS10.1 containing evolutionary related coding sequences. Among them, the Phvul.010G025700 was consistently up-regulated in the infected IAC-UNA suggesting its contribution to plant susceptibility to the fungus. We identified six other genes that were regulated during common bean response to P. griseola; three of them might be negative regulators of immunity as they showed opposite expression patterns during resistant and susceptible reactions at the initial phase of fungal infection. Taken together, these findings suggest that common bean reaction to P. griseola involves transcriptional modulation of defense genes in the ALS10.1 locus, contributing to resistance or susceptibility depending on the plant-pathogen interaction.

Common bean reaction to angular leaf spot comprises transcriptional modulation of genes in the ALS10.1 QTL

Genetic resistance of common bean (Phaseolus vulgaris L.) against angular leaf spot (ALS), caused by the fungus Pseudocercospora griseola, is conferred by quantitative trait loci (QTL). In this study, we determined the gene content of the major QTL ALS10.1 located at the end of chromosome Pv10, and identified those that are responsive to ALS infection in resistant (CAL 143) and susceptible (IAC-UNA) genotypes. Based on the current version of the common bean reference genome, the ALS10.1 core region contains 323 genes. Gene Ontology (GO) analysis of these coding sequences revealed the presence of genes involved in signal perception and transduction, programmed cell death (PCD), and defense responses. Two putative R gene clusters were found at ALS10.1 containing evolutionary related coding sequences. Among them, the Phvul.010G025700 was consistently up-regulated in the infected IAC-UNA suggesting its contribution to plant susceptibility to the fungus. We identified six other genes that were regulated during common bean response to P. griseola; three of them might be negative regulators of immunity as they showed opposite expression patterns during resistant and susceptible reactions at the initial phase of fungal infection. Taken together, these findings suggest that common bean reaction to P. griseola involves transcriptional modulation of defense genes in the ALS10.1 locus, contributing to resistance or susceptibility depending on the plant-pathogen interaction.

Plant innate immunity against human bacterial pathogens

Certain human bacterial pathogens such as the enterohemorrhagic Escherichia coli and Salmonella enterica are not proven to be plant pathogens yet. Nonetheless, under certain conditions they can survive on, penetrate into, and colonize internal plant tissues causing serious food borne disease outbreaks. In this review, we highlight current understanding on the molecular mechanisms of plant responses against human bacterial pathogens and discuss salient common and contrasting themes of plant interactions with phytopathogens or human pathogens.

Guard cell purification and RNA isolation suitable for high-throughput transcriptional analysis of cell-type responses to biotic stresses

Stomata, micro-pores on the leaf surface, are formed by a pair of guard cells. In addition to controlling water loss and gas exchange between the plant and the environment, these cells act as immunity gates to prevent pathogen invasion of the plant apoplast. Here, we report a brief procedure to obtain highly pure guard cell preparations using conditions that preserve the guard cell transcriptome as much as possible for a robust high-throughput RNA sequence analysis. The advantages of this procedure included i) substantial shortening of the time required for obtaining high yield of >97% pure guard cell protoplasts (GCP), ii) extraction of enough high quality RNA for direct sequencing, and iii) limited RNA decay during sample manipulation. Gene expression analysis by reverse transcription quantitative polymerase chain reaction revealed that wound-related genes were not induced during release of guard cells from leaves. To validate our approach, we performed a high-throughput deep-sequencing of guard cell transcriptome (RNA-seq). A total of 18,994 nuclear-encoded transcripts were detected, which expanded the transcriptome by 70%. The optimized GCP isolation and RNA extraction protocols are simple, reproducible, and fast, allowing the discovery of genes and regulatory networks inherent to the guard cells under various stresses.

Escherichia coli O157:H7 induces stronger plant immunity than Salmonella enterica Typhimurium SL1344

Consumption of fresh produce contaminated with bacterial human pathogens has resulted in various, sometimes deadly, disease outbreaks. In this study, we assessed plant defense responses induced by the fully pathogenic bacteria Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium SL1344 in both Arabidopsis thaliana and lettuce (Lactuca sativa). Unlike SL1344, O157:H7 induced strong plant immunity at both pre-invasion and post-invasion steps of infection. For instance, O157:H7 triggered stomatal closure even under high relative humidity, an environmental condition that generally weakens plant defenses against bacteria in the field and laboratory conditions. SL1344 instead induced a transient stomatal immunity. We also observed that PR1 gene expression was significantly higher in Arabidopsis leaves infected with O157:H7 compared with SL1344. These results suggest that plants may recognize and respond to some human pathogens more effectively than others. Furthermore, stomatal immunity can diminish the penetration of human pathogens through the leaf epidermis, resulting in low bacterial titers in the plant apoplast and suggesting that additional control measures can be employed to prevent food contamination. The understanding of how plant responses can diminish bacterial contamination is paramount in preventing outbreaks and improving the safety of food supplies.

Dissecting Phaseolus vulgaris innate immune system against Colletotrichum lindemuthianum infection

Background

The genus Colletotrichum is one of the most economically important plant pathogens, causing anthracnose on a wide range of crops including common beans (Phaseolus vulgaris L.). Crop yield can be dramatically decreased depending on the plant cultivar used and the environmental conditions. This study aimed to identify potential genetic components of the bean immune system to provide environmentally friendly control measures against this fungus.

Methodology and Principal Findings

As the common bean is not amenable to reverse genetics to explore functionality and its genome is not fully curated, we used putative Arabidopsis orthologs of bean expressed sequence tag (EST) to perform bioinformatic analysis and experimental validation of gene expression to identify common bean genes regulated during the incompatible interaction with C. lindemuthianum. Similar to model pathosystems, Gene Ontology (GO) analysis indicated that hormone biosynthesis and signaling in common beans seem to be modulated by fungus infection. For instance, cytokinin and ethylene responses were up-regulated and jasmonic acid, gibberellin, and abscisic acid responses were down-regulated, indicating that these hormones may play a central role in this pathosystem. Importantly, we have identified putative bean gene orthologs of Arabidopsis genes involved in the plant immune system. Based on experimental validation of gene expression, we propose that hypersensitive reaction as part of effector-triggered immunity may operate, at least in part, by down-regulating genes, such as FLS2-like and MKK5-like, putative orthologs of the Arabidopsis genes involved in pathogen perception and downstream signaling.

Conclusions/Significance

We have identified specific bean genes and uncovered metabolic processes and pathways that may be involved in the immune response against pathogens. Our transcriptome database is a rich resource for mining novel defense-related genes, which enabled us to develop a model of the molecular components of the bean innate immune system regulated upon pathogen attack.

Changes in spatial and temporal gene expression during incompatible interaction between common bean and anthracnose pathogen

Common bean, one of the most important legumes for human consumption, may have drastic reduction in yield due to anthracnose, a disease caused by the fungus Colletotrichum lindemuthianum. Rapid induction of the plant defense mechanisms is essential to establish an incompatible interaction with this pathogenic fungus. In this study, we evaluated spatial (leaves, epicotyls and hypocotyls) and temporal (24, 48, 72 and 96 hours after inoculation [HAI]) relative expression (RE) of 12 defense-related transcripts selected from previously developed ESTs libraries, during incompatible interaction between the resistant common bean genotype SEL 1308 and the avirulent anthracnose pathogen race 73, using real time quantitative RT-PCR (RT-qPCR) analysis. All selected transcripts, including the ones coding for pathogenesis-related (PR) proteins (PR1a, PR1b, PR2, and PR16a and PR16b) were differentially regulated upon pathogen inoculation. The expression levels of these transcripts were dependent on the tissue and time post inoculation. This study contributes to a better understanding of the kinetics of induced defenses against a fungal pathogen of common bean and may be used as a base line to study defenses against a broad range of pathogens including bacteria as well as non-host resistance.

Assessing stomatal response to live bacterial cells using whole leaf imaging

Stomata are natural openings in the plant epidermis responsible for gas exchange between plant interior and environment. They are formed by a pair of guard cells, which are able to close the stomatal pore in response to a number of external factors including light intensity, carbon dioxide concentration, and relative humidity (RH). The stomatal pore is also the main route for pathogen entry into leaves, a crucial step for disease development. Recent studies have unveiled that closure of the pore is effective in minimizing bacterial disease development in Arabidopsis plants; an integral part of plant innate immunity. Previously, we have used epidermal peels to assess stomatal response to live bacteria (Melotto et al. 2006); however maintaining favorable environmental conditions for both plant epidermal peels and bacterial cells has been challenging. Leaf epidermis can be kept alive and healthy with MES buffer (10 mM KCl, 25 mM MES-KOH, pH 6.15) for electrophysiological experiments of guard cells. However, this buffer is not appropriate for obtaining bacterial suspension. On the other hand, bacterial cells can be kept alive in water which is not proper to maintain epidermal peels for long period of times. When an epidermal peel floats on water, the cells in the peel that are exposed to air dry within 4 hours limiting the timing to conduct the experiment. An ideal method for assessing the effect of a particular stimulus on guard cells should present minimal interference to stomatal physiology and to the natural environment of the plant as much as possible. We, therefore, developed a new method to assess stomatal response to live bacteria in which leaf wounding and manipulation is greatly minimized aiming to provide an easily reproducible and reliable stomatal assay. The protocol is based on staining of intact leaf with propidium iodide (PI), incubation of staining leaf with bacterial suspension, and observation of leaves under laser scanning confocal microscope. Finally, this method allows for the observation of the same live leaf sample over extended periods of time using conditions that closely mimic the natural conditions under which plants are attacked by pathogens.

Molecular battles between plant and pathogenic bacteria in the phyllosphere

The phyllosphere, i.e., the aerial parts of the plant, provides one of the most important niches for microbial colonization. This niche supports the survival and, often, proliferation of microbes such as fungi and bacteria with diverse lifestyles including epiphytes, saprophytes, and pathogens. Although most microbes may complete the life cycle on the leaf surface, pathogens must enter the leaf and multiply aggressively in the leaf interior. Natural surface openings, such as stomata, are important entry sites for bacteria. Stomata are known for their vital role in water transpiration and gas exchange between the plant and the environment that is essential for plant growth. Recent studies have shown that stomata can also play an active role in limiting bacterial invasion of both human and plant pathogenic bacteria as part of the plant innate immune system. As counter-defense, plant pathogens such as Pseudomonas syringae pv tomato (Pst) DC3000 use the virulence factor coronatine to suppress stomate-based defense. A novel and crucial early battleground in host-pathogen interaction in the phyllosphere has been discovered with broad implications in the study of bacterial pathogenesis, host immunity, and molecular ecology of bacterial diseases.

Plant stomata: a checkpoint of host immunity and pathogen virulence

Stomata are microscopic pores formed by pairs of guard cells in the epidermis of terrestrial plants; they are essential for gas exchange with the environment and controlling water loss. Accordingly, plants regulate stomatal aperture in response to environmental conditions, such as relative humidity, CO(2) concentration, and light intensity. Stomatal openings are also a major route of pathogen entry into the plant and plants have evolved mechanisms to regulate stomatal aperture as an immune response against bacterial invasion. In this review, we highlight studies that begin to elucidate signaling events involved in bacterium-triggered stomatal closure and discuss how pathogens may have exploited environmental conditions or, in some cases, have evolved virulence factors to actively counter stomatal closure to facilitate invasion.

Functional analysis of the N terminus of the Erwinia amylovora secreted effector DspA/E reveals features required for secretion, translocation, and binding to the chaperone DspB/F

DspA/E is a type III secreted effector protein required for pathogenicity in the apple and pear pathogen Erwinia amylovora, and DspB/F is a small chaperone protein involved in DspA/E secretion. While the secretion and translocation signals of many type III secretion effector proteins in human enteric pathogens have been characterized extensively, relatively little is known about the translocation requirements of many effectors in plant pathogens, including large DspE-like proteins. In this study, we report a functional analysis of the N terminus of DspE. The minimal requirements for secretion, translocation, and chaperone binding were characterized. Translocation assays using an adenylate cyclase (CyaA) reporter indicated that the first 51 amino acids of DspE were sufficient for translocation and that 150 amino acids were required for optimal translocation levels. The minimal translocation signal corresponded with the requirements for secretion into culture media. Mutations of conserved regions in amino acids 2 through 10 and 31 through 40 were found to influence translocation levels of an N-terminal DspE-CyaA fusion. Yeast two-hybrid and in-vitro pull-down assays revealed a chaperone-binding site within amino acids 51 through 100 of DspE and binding to DspF in this region was disrupted by specific mutations. However, neither disruption of the chaperone-binding domain nor deletion of the dspF gene had a significant impact on translocation levels of N-terminal DspE-CyaA fusions. Our results indicate that the minimal translocation signal of DspE is not coincident with the signal for DspF binding and that translocation of the N terminus of DspE is not dependent on the N-terminal DspF-binding domain.

A critical role of two positively charged amino acids in the Jas motif of Arabidopsis JAZ proteins in mediating coronatine- and jasmonoyl isoleucine-dependent interactions with the COI1 F-box protein

SUMMARY

Coronatine is an important virulence factor produced by several pathovars of the bacterial pathogen Pseudomonas syringae. The structure of coronatine is similar to that of a class of plant hormones called jasmonates (JAs). An important step in JA signaling is the SCF(COI1) E3 ubiquitin ligase-dependent degradation of JAZ repressor proteins. We have recently shown that jasmonoyl isoleucine (JA-Ile) promotes physical interaction between Arabidopsis JAZ1 and COI1 (the F-box component of SCF(COI1)) proteins, and that the JA-Ile-dependent COI1-JAZ1 interaction could be reconstituted in yeast cells (i.e. in the absence of other plant proteins). Here we show that coronatine, but not its two biosynthetic precursors, also promotes interaction between Arabidopsis COI1 and multiple JAZ proteins. The C-terminal Jas motif, but not the N-terminal (NT) domain or central ZIM domain of JAZ proteins, is critical for JA-Ile/coronatine-dependent interaction with COI1. Two positively charged amino acid residues in the Jas domain were identified as essential for coronatine-dependent COI1-JAZ interactions. Mutations of these two residues did not affect the ability of JAZ1 and JAZ9 to interact with the transcription factor AtMYC2. Importantly, transgenic Arabidopsis plants expressing JAZ1 carrying these two mutations exhibited JA-insensitive phenotypes, including male sterility and enhanced resistance to P. syringae infection. These results not only suggest that coronatine and JA-Ile target the physical interaction between COI1 and the Jas domain of JAZ repressors, but also illustrate the critical role of positively charged amino acids in the Jas domain in mediating the JA-Ile/coronatine-dependent JAZ interaction with COI1.

Role of stomata in plant innate immunity and foliar bacterial diseases

Pathogen entry into host tissue is a critical first step in causing infection. For foliar bacterial plant pathogens, natural surface openings, such as stomata, are important entry sites. Historically, these surface openings have been considered as passive portals of entry for plant pathogenic bacteria. However, recent studies have shown that stomata can play an active role in limiting bacterial invasion as part of the plant innate immune system. As a counter-defense, the plant pathogen Pseudomonas syringae pv. tomato DC3000 uses the virulence factor coronatine to actively open stomata. In nature, many foliar bacterial disease outbreaks require high humidity, rain, or storms, which could favor stomatal opening and/or bypass stomatal defense by creating wounds as alternative entry sites. Further studies on microbial and environmental regulation of stomatal closure and opening could fill gaps in our understanding of bacterial pathogenesis, disease epidemiology, and microbiology of the phyllosphere.

Development, characterization, and comparative analysis of polymorphism at common bean SSR loci isolated from genic and genomic sources

Microsatellites or SSRs (single sequence repeats) have been used to construct and integrate genetic maps in crop species, including Phaseolus vulgaris. In the present study, 3 cDNA libraries generated by the Bean EST project (http://lgm.esalq.usp.br/BEST/), comprising a unigene collection of 3126 sequences and a genomic microsatellite-enriched library, were analyzed for the presence of SSRs. A total of 219 expressed sequence tags (ESTs) were found to carry 240 SSRs (named EST-SSR), whereas 714 genomic sequences contained 471 SSRs (named genomic-SSR). A subset of 80 SSRs, 40 EST-SSRs, and 40 genomic-SSRs were evaluated for molecular polymorphism in 23 genotypes of cultivated beans from the Mesoamerican and Andean genetic pools, including Brazilian cultivars and 2 related species. Of the common bean genotypes, 31 EST-SSR loci were polymorphic, yielding 2-12 alleles as compared with 26 polymorphic genomic-SSRs, accounting for 2-7 alleles. Cluster analysis from data using both genic and genomic-SSR revealed a clear separation between Andean and Mesoamerican beans. The usefulness of these loci for distinguishing bean genotypes and genetic mapping is discussed.

JAZ repressor proteins are targets of the SCF(COI1) complex during jasmonate signalling

Jasmonate and related signalling compounds have a crucial role in both host immunity and development in plants, but the molecular details of the signalling mechanism are poorly understood. Here we identify members of the jasmonate ZIM-domain (JAZ) protein family as key regulators of jasmonate signalling. JAZ1 protein acts to repress transcription of jasmonate-responsive genes. Jasmonate treatment causes JAZ1 degradation and this degradation is dependent on activities of the SCF(COI1) ubiquitin ligase and the 26S proteasome. Furthermore, the jasmonoyl-isoleucine (JA-Ile) conjugate, but not other jasmonate-derivatives such as jasmonate, 12-oxo-phytodienoic acid, or methyl-jasmonate, promotes physical interaction between COI1 and JAZ1 proteins in the absence of other plant proteins. Our results suggest a model in which jasmonate ligands promote the binding of the SCF(COI1) ubiquitin ligase to and subsequent degradation of the JAZ1 repressor protein, and implicate the SCF(COI1)-JAZ1 protein complex as a site of perception of the plant hormone JA-Ile.

Comparative bioinformatic analysis of genes expressed in common bean (Phaseolus vulgaris L.) seedlings

To rapidly and cost-effectively generate gene expression data, we developed an annotated unigene database of common bean (Phaseolus vulgaris L.). In this study, 3 cDNA libraries were constructed from the bean breeding line SEL1308, 1 from young leaf and 2 from seedlings inoculated or not inoculated with the fungal pathogen Colletotrichum lindemuthianum (Sacc. & Magnus) Briosi & Cavara, which causes anthracnose in common bean. To this date, 5255 single-pass sequences have been included in the database after selection based on sequence quality. These ESTs were trimmed and clustered using the computer programs Phred and CAP3 to form a unigene collection of 3126 unique sequences. Within clusters, 318 single nucleotide polymorphisms (SNPs) and 68 insertions-deletions (indels) were found, indicating the presence of paralogous gene families in our database. Each unigene sequence was analyzed for possible function using their similarity to known genes represented in the GenBank database and classified into 14 categories. Only 314 unigenes showed significant similarities to Phaseolus genomic sequences and P. vulgaris ESTs, which indicates that 90% (2818 unigenes) of our database represent newly discovered common bean genes. In addition, 12% (387 unigenes) were shown to be specific to common bean. This study represents a first step towards the discovery of novel genes in beans and a valuable source of molecular markers for expressed gene tagging and mapping.