Comparative genome analysis of rice-pathogenic Burkholderia provides insight into capacity to adapt to different environments and hosts

Background

In addition to human and animal diseases, bacteria of the genus Burkholderia can cause plant diseases. The representative species of rice-pathogenic Burkholderia are Burkholderia glumae, B. gladioli, and B. plantarii, which primarily cause grain rot, sheath rot, and seedling blight, respectively, resulting in severe reductions in rice production. Though Burkholderia rice pathogens cause problems in rice-growing countries, comprehensive studies of these rice-pathogenic species aiming to control Burkholderia-mediated diseases are only in the early stages.

Results

We first sequenced the complete genome of B. plantarii ATCC 43733^T. Second, we conducted comparative analysis of the newly sequenced B. plantarii ATCC 43733^T genome with eleven complete or draft genomes of B. glumae and B. gladioli strains. Furthermore, we compared the genome of three rice Burkholderia pathogens with those of other Burkholderia species such as those found in environmental habitats and those known as animal/human pathogens. These B. glumae, B. gladioli, and B. plantarii strains have unique genes involved in toxoflavin or tropolone toxin production and the clustered regularly interspaced short palindromic repeats (CRISPR)-mediated bacterial immune system. Although the genome of B. plantarii ATCC 43733^T has many common features with those of B. glumae and B. gladioli, this B. plantarii strain has several unique features, including quorum sensing and CRISPR/CRISPR-associated protein (Cas) systems.

Conclusions

The complete genome sequence of B. plantarii ATCC 43733^T and publicly available genomes of B. glumae BGR1 and B. gladioli BSR3 enabled comprehensive comparative genome analyses among three rice-pathogenic Burkholderia species responsible for tissue rotting and seedling blight. Our results suggest that B. glumae has evolved rapidly, or has undergone rapid genome rearrangements or deletions, in response to the hosts. It also, clarifies the unique features of rice pathogenic Burkholderia species relative to other animal and human Burkholderia species.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1558-5) contains supplementary material, which is available to authorized users.     

Differential regulation of toxoflavin production and its role in the enhanced virulence of Burkholderia gladioli

Burkholderia gladioli is a causal agent of bacterial panicle blight and sheath/grain browning in rice in many countries. Many strains produce the yellow pigment toxoflavin, which is highly toxic to plants, fungi, animals and microorganisms. Although there have been several studies on the toxoflavin biosynthesis system of B. glumae, it is still unclear how B. gladioli activates toxoflavin biosynthesis. In this study, we explored the genomic organization of the toxoflavin system of B. gladioli and its biological functions using comparative genomic analysis between toxoflavin‐producing strains (B. glumae BGR1 and B. gladioli BSR3) and a strain not producing toxoflavin (B. gladioli KACC11889). The latter exhibits normal physiological characteristics similar to other B. gladioli strains. Burkholderia gladioli KACC11889 possesses all the genes involved in toxoflavin biosynthesis, but lacks the quorum‐sensing (QS) system that functions as an on/off switch for toxoflavin biosynthesis. These data suggest that B. gladioli has evolved to use the QS signalling cascade of toxoflavin production (TofI/TofR of QS → ToxJ or ToxR → tox operons) similar to that in B. glumae. However, some strains may have evolved to eliminate toxoflavin production through deletion of the QS genes. In addition, we demonstrate that the toxoflavin biosynthetic system enhances the virulence of B. gladioli. These findings provide another line of evidence supporting the differential regulation of the toxoflavin system in Burkholderia strains.     

Impact of the invasive painted bug <Emphasis Type="Italic">Bagrada hilaris</Emphasis> on physiological traits of its host <Emphasis Type="Italic">Brassica oleracea</Emphasis> var botrytis

Bagrada hilaris is a herbivorous insect native of Asia and Africa, which has invaded southern Europe and North America where it causes major damage to cole crops. Laboratory experiments were conducted to assess how the infestation of this invasive species damages the host Brassica oleracea var botrytis, and to evaluate the interaction between plant emission of volatile organic compounds (VOC) and B. hilaris adults. Plant responses to insect feeding were evaluated through changes in photosynthesis, stomatal conductance, VOC emission, and visual damage on leaves. The impact of B. hilaris was compared with that of Nezara viridula, a polyphagous species distributed worldwide. Plant VOC role in host plant detection was tested with electroantennography bioassays on B. hilaris antenna. Photosynthesis and stomatal conductance were consistently reduced in plants infested with 40 B. hilaris adults for 24 h. The feeding activity of a single B. hilaris caused larger discolored spots on host leaves in comparison with N. viridula. VOC emitted by B. oleracea changed significantly in response to B. hilaris and N. viridula infestation. In particular, production of limonene was strongly reduced by the infestation of the two pentatomids, while an increase in the emission of acetic acid and 2-ethyl-1-hexanol was observed. EAG dose–response tests using the main plant VOC showed B. hilaris antennal responses to benzaldehyde, octanal, nonanal, and acetic acid, which indicates a role of these compounds in host location.     

Interaction between toxin crystals and vegetative insecticidal proteins of <Emphasis Type="Italic">Bacillus thuringiensis</Emphasis> in lepidopteran larvae

Insecticides based on crystalline toxins of Bacillus thuringiensis are very good biological plant protection products. However, the spectrum of activity of some toxins is narrow or resistance among insects has been developed. We tested the insecticidal activity of crystals of the B. thuringiensis MPU B9 strain alone and supplemented with Vip3Aa proteins against important pests: Spodoptera exigua Hübner (Lepidoptera: Noctuidae), Cydia pomonella L. (Lepidoptera: Tortricidae) and Dendrolimus pini L. (Lepidoptera: Lasiocampidae). The Cry toxins were more active for D. pini but less active against S. exigua and C. pomonella than Vip3Aa. Supplementation of Cry toxins by small amounts of vegetative insecticidal proteins demonstrated synergistic effect and significantly enhanced the toxicity of the insecticide. The results indicate the utility of Cry and Vip3Aa toxins mixtures to control populations of crops and forests insect pests.     

Comparative genomic analysis of two Burkholderia glumae strains from different geographic origins reveals a high degree of plasticity in genome structure associated with genomic islands

Burkholderia glumae is the major causal agent of bacterial panicle blight of rice, a growing disease problem in global rice production. To better understand its genome-scale characteristics, the genome of the highly virulent B. glumae strain 336gr-1 isolated from Louisiana, USA was sequenced using the Illumina Genome Analyser II system. De novo assembled 336gr-1 contigs were aligned and compared with the previously sequenced genome of B. glumae strain BGR1, which was isolated from an infected rice plant in South Korea. Comparative analysis of the whole genomes of B. glumae 336gr-1 and B. glumae BGR1 revealed numerous unique genomic regions present only in one of the two strains. These unique regions contained accessory genes including mobile elements and phage-related genes, and some of the unique regions in B. glumae BGR1 corresponded to predicted genomic islands. In contrast, little variation was observed in known and potential virulence genes between the two genomes. The considerable amount of plasticity largely based on accessory genes and genome islands observed from the comparison of the genomes of these two strains of B. glumae may explain the versatility of this bacterial species in various environmental conditions and geographic locations.     

Ectopic expression of cucumber (<Emphasis Type="Italic">Cucumis sativus</Emphasis> L.) <Emphasis Type="Italic">CsTIR</Emphasis>/<Emphasis Type="Italic">AFB</Emphasis> genes enhance salt tolerance in transgenic <Emphasis Type="Italic">Arabidopsis</Emphasis>

Auxin receptors TIR1/AFBs play an essential role in a series of signaling network cascades. These F-box proteins have also been identified to participate in different stress responses via the auxin signaling pathway in Arabidopsis. Cucumber (Cucumis sativus L.) is one of the most important crops worldwide, which is also a model plant for research. In the study herein, two cucumber homologous auxin receptor F-box genes CsTIR and CsAFB were cloned and studied for the first time. The deduced amino acid sequences showed a 78% identity between CsTIR and AtTIR1 and 76% between CsAFB and AtAFB2. All these proteins share similar characteristics of an F-box domain near the N-terminus, and several Leucine-rich repeat regions in the middle. Arabidopsis plants ectopically overexpressing CsTIR or CsAFB were obtained and verified. Shorter primary roots and more lateral roots were found in these transgenic lines with auxin signaling amplified. Results showed that expression of CsTIR/AFB genes in Arabidopsis could lead to higher seeds germination rates and plant survival rates than wild-type under salt stress. The enhanced salt tolerance in transgenic plants is probably caused by maintaining root growth and controlling water loss in seedlings, and by stabilizing life-sustaining substances as well as accumulating endogenous osmoregulation substances. We proposed that CsTIR/AFB-involved auxin signal regulation might trigger auxin mediated stress adaptation response and enhance the plant salt stress resistance by osmoregulation.     

Genome-wide identification and expression analysis of sulphate transporter (<Emphasis Type="Italic">SULTR</Emphasis>) genes under sulfur deficiency in <Emphasis Type="Italic">Brachypodium distachyon</Emphasis>

Sulphur is an important mineral element for plant growth and development. It involves in a number of metabolic processes with crucial functions. This study has performed a genome-wide analysis of sulfate transporter (SULTR) genes in Brachypodium distachyon. Ten putative SULTR genes were identified in Brachypodium genome. BdSULTR genes included 6–17 exons encoding a protein of 647–693 residues with basic nature. BdSULTR proteins included both sulfate_transp (PF00916) and STAS (PF01740) domains. BdSULTRs were classified into 4 groups based on the phylogenetic distribution. Promoter regions of all BdSULTR genes, except for BdSULTR3;3 and 3;5 included the SURECOREATSULTR11 elements. A considerable structural overlap was identified between superimposed SULTR1;3 and 3;1 proteins, indicating that SULTR1 members may also involve in plant stress response/tolerance like SULTR3 members. Microarray and RNA-Seq analyses also revealed the differential expression of SULTR 1 and 3 genes under different biotic/abiotic stresses. Protein–protein interaction partners of BdSULTRs were mainly related with adenylyl-sulfate kinases, 5′-adenylylsulfate reductases, ATP sulfurylases, and acyl carrier proteins. Moreover, expression profiles of identified BdSULTR genes under S-deficiency were analyzed using RT-qPCR. It was revealed that BdSULTR1;1 and 3;1 are highly expressed in plant roots as ~tenfold and ~fivefold, respectively, while BdSULTR2 (~15-fold) and 3;1 (~twofold) are abundantly expressed in leaf tissues.