A Genome-Wide Association Study of the Maize Hypersensitive Defense Response Identifies Genes That Cluster in Related Pathways

Much remains unknown of molecular events controlling the plant hypersensitive defense response (HR), a rapid localized cell death that limits pathogen spread and is mediated by resistance (R-) genes. Genetic control of the HR is hard to quantify due to its microscopic and rapid nature. Natural modifiers of the ectopic HR phenotype induced by an aberrant auto-active R-gene (Rp1-D21), were mapped in a population of 3,381 recombinant inbred lines from the maize nested association mapping population. Joint linkage analysis was conducted to identify 32 additive but no epistatic quantitative trait loci (QTL) using a linkage map based on more than 7000 single nucleotide polymorphisms (SNPs). Genome-wide association (GWA) analysis of 26.5 million SNPs was conducted after adjusting for background QTL. GWA identified associated SNPs that colocalized with 44 candidate genes. Thirty-six of these genes colocalized within 23 of the 32 QTL identified by joint linkage analysis. The candidate genes included genes predicted to be in involved programmed cell death, defense response, ubiquitination, redox homeostasis, autophagy, calcium signalling, lignin biosynthesis and cell wall modification. Twelve of the candidate genes showed significant differential expression between isogenic lines differing for the presence of Rp1-D21. Low but significant correlations between HR-related traits and several previously-measured disease resistance traits suggested that the genetic control of these traits was substantially, though not entirely, independent. This study provides the first system-wide analysis of natural variation that modulates the HR response in plants.     

昆虫脂肪酸合成通路关键基因的研究进展

脂肪酸对昆虫生长、发育、繁殖、信息交流起到重要的作用。主要介绍脂肪酸合成通路中的5个关键基因,乙酰辅酶A羧化酶基因(ACC)、脂肪酸合成酶基因(FAS)、超长链脂肪酸延伸酶基因(ELO)、去饱和酶基因(desat)及脂酰辅酶A还原酶基因(FAR)在昆虫中的研究进展。     

Trehalose Metabolism-Related Genes in Maize

Maize is a cereal crop that is grown widely throughout the world in a range of agro-ecological environments. Trehalose is a nonreducing disaccharide of glucose that has been associated with tolerance to different stress conditions, including salt and drought. Bioinformatic analysis of genes involved in trehalose biosynthesis and degradation in maize has not been reported to date. Through systematic analysis, 1 degradation-related and 36 trehalose biosynthesis-related genes were identified. The conserved domains and phylogenetic relationships among the deduced maize proteins and their homologs, isolated from other plant species such as Arabidopsis and rice, were revealed. Using a comprehensive approach, the intron/exon structures and expression patterns of all identified genes and their responses to salt stress, jasmonic acid, and abscisic acid treatment were analyzed. Microarray data demonstrated that some of the genes show differential, organ-specific expression patterns in the 60 different developmental stages of maize. It was discovered that some of the key enzymes such as hexokinase, trehalose-6-phosphate synthase, and trehalose-6-phosphate phosphatase are encoded by multiple gene members with different expression patterns. The results highlight the complexity of trehalose metabolism and provide useful information for improving maize stress tolerance through genetic engineering.     

Influence of Lanthanides on the Antioxidative Defense System in Maize Seedlings Under Cold Stress

The influence of LaCl₃, CeCl₃, and NdCl₃ on the antioxidative defense system in maize seedlings under cold stress was investigated. It was found that maize seedlings cultivated in cold stress developed distinct cold symptoms, and the plant growth was significantly inhibited as expected, while Ln-treated seedling growth was improved. Cold stress in maize seedlings also increased the permeability of plasma membrane, malondialdehyde as a degradation product of lipid peroxidation, and reactive oxygen species such as superoxide radicals and hydrogen peroxide, and decreased activities of the antioxidant enzymes such as superoxide dismutase, catalase, ascorbate peroxidase, and glutathione content; however, Ln treatments cultivated in cold stress decreased the permeability of plasma membrane, malondialdehyde, and reactive oxygen species, and increased activities of the antioxidative defense system. It implied that Ln could increase oxidative-stress resistance under cold stress. On the other hand, the assay of physiological and biochemical parameters demonstrated that Ce relieving chilling injury of maize seedlings caused by cold stress was most significant, medium in the Nd treatment, and last in the La treatment. These results suggested that the increase of cold resistance of maize seedlings caused by Ln might be closely related to its properties of 4f electron shell and variable valence.     

Evolutionary Relationships of Three New Species of Enterobacteriaceae Living as Symbionts of Aphids and Other Insects

Ecological studies on three bacterial lineages symbiotic in aphids have shown that they impose a variety of effects on their hosts, including resistance to parasitoids and tolerance to heat stress. Phylogenetic analyses of partial sequences of gyrB and recA are consistent with previous analyses limited to 16S rRNA gene sequences and yield improved confidence of the evolutionary relationships of these symbionts. All three symbionts are in the Enterobacteriaceae. One of the symbionts, here given the provisional designation “Candidatus Serratia symbiotica,” is a Serratia species that has acquired a symbiotic lifestyle. The other two symbionts, here designated “Candidatus Hamiltonella defensa” and “Candidatus Regiella insecticola,” are sister groups to one another and together show a relationship to species of Photorhabdus.     

Molecular Microbial Diversity Survey of Sponge Reproductive Stages and Mechanistic Insights into Vertical Transmission of Microbial Symbionts

Many marine sponges, hereafter termed high-microbial-abundance (HMA) sponges, harbor large and complex microbial consortia, including bacteria and archaea, within their mesohyl matrices. To investigate vertical microbial transmission as a strategy to maintain these complex associations, an extensive phylogenetic analysis was carried out with the 16S rRNA gene sequences of reproductive (n = 136) and adult (n = 88) material from five different Caribbean species, as well as all published 16S rRNA gene sequences from sponge offspring (n = 116). The overall microbial diversity, including members of at least 13 bacterial phyla and one archaeal phylum, in sponge reproductive stages is high. In total, 28 vertical-transmission clusters, defined as clusters of phylotypes that are found both in adult sponges and their offspring, were identified. They are distributed among at least 10 bacterial phyla and one archaeal phylum, demonstrating that the complex adult microbial community is collectively transmitted through reproductive stages. Indications of host-species specificity and cospeciation were not observed. Mechanistic insights were provided using a combined electron microscopy and fluorescence in situ hybridization analysis, and an indirect mechanism of vertical transmission via nurse cells is proposed for the oviparous sponge Ectyoplasia ferox. Based on these phylogenetic and mechanistic results, we suggest the following symbiont transmission model: entire microbial consortia are vertically transmitted in sponges. While vertical transmission is clearly present, additional environmental transfer between adult individuals of the same and even different species might obscure possible signals of cospeciation. We propose that associations of HMA sponges with highly sponge-specific microbial communities are maintained by this combination of vertical and horizontal symbiont transmission.     

Symbionts Commonly Provide Broad Spectrum Resistance to Viruses in Insects: A Comparative Analysis of Wolbachia Strains

In the last decade, bacterial symbionts have been shown to play an important role in protecting hosts against pathogens. Wolbachia, a widespread symbiont in arthropods, can protect Drosophila and mosquito species against viral infections. We have investigated antiviral protection in 19 Wolbachia strains originating from 16 Drosophila species after transfer into the same genotype of Drosophila simulans. We found that approximately half of the strains protected against two RNA viruses. Given that 40% of terrestrial arthropod species are estimated to harbour Wolbachia, as many as a fifth of all arthropods species may benefit from Wolbachia-mediated protection. The level of protection against two distantly related RNA viruses – DCV and FHV – was strongly genetically correlated, which suggests that there is a single mechanism of protection with broad specificity. Furthermore, Wolbachia is making flies resistant to viruses, as increases in survival can be largely explained by reductions in viral titer. Variation in the level of antiviral protection provided by different Wolbachia strains is strongly genetically correlated to the density of the bacteria strains in host tissues. We found no support for two previously proposed mechanisms of Wolbachia-mediated protection — activation of the immune system and upregulation of the methyltransferase Dnmt2. The large variation in Wolbachia''s antiviral properties highlights the need to carefully select Wolbachia strains introduced into mosquito populations to prevent the transmission of arboviruses.     

Diversification and Independent Evolution of Troponin C Genes in Insects

Troponin C (TpnC), the calcium-binding subunit of the troponin regulatory complex in the muscle thin filament, is encoded by multiple genes in insects. To understand how TpnC genes have evolved, we characterized the gene number and structure in a number of insect species. The TpnC gene complement is five genes in Drosophilidae as previously reported for D. melanogaster. Gene structures are almost identical in D. pseudoobscura, D. suboboscura, and D. virilis. Developmental patterns of expression are also conserved in Drosophila subobscura and D. virilis. Similar, but not completely equivalent, TpnC gene repertoires have been identified in the Anopheles gambiae and Apis mellifera genomes. Insect TpnC sequences can be divided into three groups, allowing a systematic classification of newly identified genes. The pattern of expression of the Apis mellifera genes essentially agrees with the pattern in Drosophilidae, providing further functional support to the classification. A model for the evolution of the TpnC genes is proposed including the most likely pathway of insect TpnC diversification. Our results suggest that the rapid increase in number and sequence specialization of the adult Type III isoforms can be correlated with the evolution of the holometabolous mode of development and the acquisition of asynchronous indirect flight muscle function in insects. This evolutionarily specialization has probably been achieved independently in different insect orders.Reviewing Editor: Dr. Rüdiger Cerff     

Terpene Down-Regulation Triggers Defense Responses in Transgenic Orange Leading to Resistance against Fungal Pathogens

Terpenoid volatiles are isoprene compounds that are emitted by plants to communicate with the environment. In addition to their function in repelling herbivores and attracting carnivorous predators in green tissues, the presumed primary function of terpenoid volatiles released from mature fruits is the attraction of seed-dispersing animals. Mature oranges (Citrus sinensis) primarily accumulate terpenes in peel oil glands, with d-limonene accounting for approximately 97% of the total volatile terpenes. In a previous report, we showed that down-regulation of a d-limonene synthase gene alters monoterpene levels in orange antisense (AS) fruits, leading to resistance against Penicillium digitatum infection. A global gene expression analysis of AS versus empty vector (EV) transgenic fruits revealed that the down-regulation of d-limonene up-regulated genes involved in the innate immune response. Basal levels of jasmonic acid were substantially higher in the EV compared with AS oranges. Upon fungal challenge, salicylic acid levels were triggered in EV samples, while jasmonic acid metabolism and signaling were drastically increased in AS orange peels. In nature, d-limonene levels increase in orange fruit once the seeds are fully viable. The inverse correlation between the increase in d-limonene content and the decrease in the defense response suggests that d-limonene promotes infection by microorganisms that are likely involved in facilitating access to the pulp for seed-dispersing frugivores.Plants are sessile organisms that produce and emit a vast array of volatile organic compounds (VOCs) to communicate between parts of the same plant and with other plants. It is generally accepted that the original role of these compounds in nature is related to defense functions (Degenhardt et al., 2003). Most VOCs are terpenoids, fatty acid degradation compounds, phenylpropanoids, and amino acid-derived products. Among these, terpenoids are likely to be the most abundant and expensive to produce (Gershenzon, 1994). Terpenoids are isoprenoid-derived compounds synthesized through the condensation of C5 isoprene units, a process that is catalyzed by a wide diversity of terpene synthases using geranyl diphosphate (GDP), farnesyl diphosphate (FDP), and geranylgeranyl diphosphate (GGDP) as substrates. These reactions give rise to the C5 hemiterpenes, the C10 monoterpenes, the C15 sesquiterpenes, and the C20 diterpenes (Dudareva et al., 2006).In green tissues, volatile terpenoid synthesis is either induced upon wounding or occurs constitutively; terpenes can be then stored in specific organs or tissues where they would be most effective in defense responses, such as leaf trichomes, resin ducts and lacticifers, pockets near the epidermis, or secretory cavities in Citrus spp. (Langenheim, 1994; Turner et al., 2000; Trapp and Croteau, 2001; Voo et al., 2012). Genetic engineering experiments have demonstrated that specific terpenoid compounds emitted by leaves can intoxicate, repel, or deter herbivores (Aharoni et al., 2003; Wu et al., 2006), or they may attract the natural predators and parasitoids of damaging herbivores to protect plants from further damage (Kappers et al., 2005; Schnee et al., 2006). These terpenoids are naturally found in complex mixtures, and it has been proposed that they can act synergistically, as in conifer resin, for simultaneous protection against pests and pathogens (Phillips and Croteau, 1999). Although fatty acid degradation products (such as jasmonates) and phenylpropanoids (such as salicylates) as well as their volatile and nonvolatile precursors are clearly involved in many induced defense responses against pests and pathogens (Glazebrook, 2005), much less is known regarding the participation of terpenoid volatiles in the defense against microorganisms in plants and about the possible interactions of these terpenoids with phytohormones.In contrast to their function in leaves, when released from flowers and mature fruits, the main function of terpenoid volatiles is in the attraction of pollinators (Pichersky and Gershenzon, 2002; Kessler et al., 2008; Junker and Blüthgen, 2010; Schiestl, 2010) and seed-dispersing animals (Lomáscolo et al., 2010; Rodríguez et al., 2011b), respectively. Fruit maturation and ripening are usually associated with large increases in the synthesis and accumulation of specific flavored volatiles, which are proposed to function as signals for seed dispersal (Auldridge et al., 2006; Goff and Klee, 2006; Rodríguez et al., 2013).Upon wounding, plant responses to biotic stresses are orchestrated locally and systemically by signaling molecules. Among these molecules, the jasmonates regulate defenses against arthropod herbivores and necrotroph fungal pathogens as well as biotrophic pathogens, such as some mildews (Ellis and Turner, 2001; Stintzi et al., 2001; Kessler et al., 2004; Li et al., 2005; Wasternack, 2007; Browse and Howe, 2008). In addition to jasmonates, molecules such as salicylic acid (SA) and ethylene appear to regulate distinct defense pathways and are major synergistic (Mur et al., 2006) or antagonistic (De Vos et al., 2005) regulators of plant innate immunity. Plants produce a specific blend of these alarm signals after pathogen or pest attacks, and the production of these molecules varies greatly in quantity, composition, and timing. These signals activate differential sets of defense-related genes that eventually determine the nature of the defense response against the attacker (Reymond and Farmer, 1998; Rojo et al., 2003; De Vos et al., 2005). All genes that encode enzymes involved in the biosynthesis of jasmonates are jasmonic acid (JA) inducible (Wasternack, 2006), indicating that JA biosynthesis is regulated by positive feedback. The precursor for the biosynthesis of JA is α-linolenic acid. The activity of the 13-lipoxygenase (LOX), allene oxide synthase (AOS), and allene oxide cyclase (AOC) enzymes converts α-linolenic acid to cis-(+)-12-oxophytodienoic acid (OPDA). OPDA REDUCTASE3 catalyzes the reduction of OPDA (and dinor-OPDA) to oxo-pentenyl-cycloheptane-octanoic acid, which, in turn, undergoes three rounds of β-oxidation leading to jasmonyl-CoA formation. Jasmonyl-CoA is then cleaved by a putative thioesterase yielding (+)-7-iso-JA, which equilibrates to the more stable (−)-JA (Wasternack and Kombrink, 2010).The exogenous application of jasmonates on plants and the existence of mutant and/or transgenic plants altered in JA biosynthesis or signaling have led to altered susceptibility or resistance to pathogens. Impaired JA biosynthesis or signaling is generally associated with decreased levels of defensive compounds, including VOCs, and reduced plant biomass and/or fitness under insect attack (Howe et al., 1996; Halitschke and Baldwin, 2004). For example, Arabidopsis (Arabidopsis thaliana) mutants defective in JA perception (e.g. coronatine-insensitive1 [coi1]) or biosynthesis (e.g. aos and defective in anther dehiscence1) are susceptible to pathogen infections (Feys et al., 1994; Xie et al., 1998; Park et al., 2002; Turner et al., 2002). In contrast, mutants (e.g. constitutive expression of vegetative storage protein1 and Arabidopsis Ser/Thr phosphatase of type 2C1) with constitutive or wound-induced activation of the JA pathway exhibit enhanced resistance to fungal pathogens and pests and phenotypes characteristic of JA-treated plants (Ellis and Turner, 2001; Ellis et al., 2002; Schweighofer et al., 2007).Sweet orange (Citrus sinensis) is a perennial tree species that is exposed to recurrent biotic and abiotic challenges during its decades of growth in orchards. Orange fruits undergo a nonclimacteric maturation process in which the biochemistry, physiology, and structure of the organ are altered to complete the release of mature seeds. These changes typically include fruit growth and texture modification; color change through the degradation of chlorophylls and a parallel induction of carotenogenesis in the peel (flavedo) and pulp; flavonoid accumulation in the pulp; increases and decreases in the sugar and acid contents, respectively; and global accumulation and selective emission of volatile terpenoids (Spiegel-Roy and Goldschmidt, 1996). In nature, d-limonene accumulates gradually in the oil glands of the peel during fruit development and reaches its maximum level shortly before the breaker stage, followed by a steady decline during maturation (Attaway et al., 1967; Kekelidze et al., 1989; Rodríguez et al., 2011b). The high amount of d-limonene that accumulates in orange peels has a tremendous metabolic cost, suggesting an important biological role for this terpene and other related compounds in the interactions between fruits and the biotic environment.Previously, we examined the biological role of d-limonene by manipulating oil gland chemistry via the antisense (AS) overexpression of a d-limonene synthase gene from Satsuma mandarin (Citrus unshiu) in orange fruits. Compared with empty vector (EV) controls, fruit peels from AS transformants showed a dramatic reduction in d-limonene accumulation; decreased levels of other monoterpenes, sesquiterpenes, and monoterpene aldehydes; and increased levels of monoterpene alcohols. When challenged with the necrotroph fungus Penicillium digitatum, the causal agent of green mold rot, AS-transformed fruits were highly resistant to fungal infection. Full susceptibility to P. digitatum infection was restored when AS fruits were supplemented with d-limonene but not other monoterpene alcohols, indicating that d-limonene accumulation in the orange peel was required for the successful progress of this plant-pathogen interaction (Rodríguez et al., 2011a, 2011b). Green mold rot is the most important postharvest disease of citrus fruit worldwide, accounting for up to 60% to 80% of total losses during postharvest life of the fruit. P. digitatum is considered to be a specialist pathogen of citrus fruits that efficiently infects the peel through injuries in which ubiquitous fungal spores germinate and rapidly colonize the surrounding areas (Droby et al., 2008). The control of this pathogen relies heavily on the use of synthetic chemicals, but concerns regarding their potential negative effects on human health and also the generation of fungicide-resistant strains have encouraged finding alternatives, such as the generation of citrus trees with fruits that are genetically resistant to the pathogen.In this work, to better understand the mechanism underlying the constitutive resistance to P. digitatum conferred by the reduction of limonene in AS orange fruits, we analyzed the pattern of fruit growth and the morphological and biochemical developmental characteristics and performed a global analysis of gene expression using a 20K citrus microarray. The study is supplemented by examining the possible involvement of key hormone signals and isoprenoid precursors in the fruit peel. We report here that the reduced level of d-limonene in AS fruits is tightly associated with the constitutive activation of defense response signaling cascades. Our results establish, to our knowledge for the first time, a correlation between increased volatile terpene content and the decline of defense responses in a fleshy fruit during maturation, which would facilitate necrotroph fungal infections in citrus fruits.     

Genome-Wide Analysis of bZIP-Encoding Genes in Maize

In plants, basic leucine zipper (bZIP) proteins regulate numerous biological processes such as seed maturation, flower and vascular development, stress signalling and pathogen defence. We have carried out a genome-wide identification and analysis of 125 bZIP genes that exist in the maize genome, encoding 170 distinct bZIP proteins. This family can be divided into 11 groups according to the phylogenetic relationship among the maize bZIP proteins and those in Arabidopsis and rice. Six kinds of intron patterns (a–f) within the basic and hinge regions are defined. The additional conserved motifs have been identified and present the group specificity. Detailed three-dimensional structure analysis has been done to display the sequence conservation and potential distribution of the bZIP domain. Further, we predict the DNA-binding pattern and the dimerization property on the basis of the characteristic features in the basic and hinge regions and the leucine zipper, respectively, which supports our classification greatly and helps to classify 26 distinct subfamilies. The chromosome distribution and the genetic analysis reveal that 58 ZmbZIP genes are located in the segmental duplicate regions in the maize genome, suggesting that the segment chromosomal duplications contribute greatly to the expansion of the maize bZIP family. Across the 60 different developmental stages of 11 organs, three apparent clusters formed represent three kinds of different expression patterns among the ZmbZIP gene family in maize development. A similar but slightly different expression pattern of bZIPs in two inbred lines displays that 22 detected ZmbZIP genes might be involved in drought stress. Thirteen pairs and 143 pairs of ZmbZIP genes show strongly negative and positive correlations in the four distinct fungal infections, respectively, based on the expression profile and Pearson''s correlation coefficient analysis.     

Interferon Induced IFIT Family Genes in Host Antiviral Defense

Secretion of interferons (IFNs) from virus-infected cells is a hallmark of host antiviral immunity and in fact, IFNs exert their antiviral activities through the induction of antiviral proteins. The IFN-induced protein with tetratricopeptide repeats (IFITs) family is among hundreds of IFN-stimulated genes. This family contains a cluster of duplicated loci. Most mammals have IFIT1, IFIT2, IFIT3 and IFIT5; however, bird, marsupial, frog and fish have only IFIT5. Regardless of species, IFIT5 is always adjacent to SLC16A12. IFIT family genes are predominantly induced by type I and type III interferons and are regulated by the pattern recognition and the JAK-STAT signaling pathway. IFIT family proteins are involved in many processes in response to viral infection. However, some viruses can escape the antiviral functions of the IFIT family by suppressing IFIT family genes expression or methylation of 5'' cap of viral molecules. In addition, the variants of IFIT family genes could significantly influence the outcome of hepatitis C virus (HCV) therapy. We believe that our current review provides a comprehensive picture for the community to understand the structure and function of IFIT family genes in response to pathogens in human, as well as in animals.     

Proteorhodopsin-Like Genes Present in Thermoacidophilic High-Mountain Microbial Communities

Proteorhodopsin (PR) sequences were PCR amplified from three Andean acidic hot spring samples. These sequences were similar to freshwater and marine PRs and they contained residues indicative of proton-pumping activity and of proteins that absorb green light; these findings suggest that PRs might contribute to cellular metabolism in these habitats.