Quantitative disease resistance to the bacterial pathogen Xanthomonas campestris involves an Arabidopsis immune receptor pair and a gene of unknown function

Although quantitative disease resistance (QDR) is a durable and broad‐spectrum form of resistance in plants, the identification of the genes underlying QDR is still in its infancy. RKS1 (Resistance related KinaSe1) has been reported recently to confer QDR in Arabidopsis thaliana to most but not all races of the bacterial pathogen Xanthomonas campestris pv. campestris (Xcc). We therefore explored the genetic bases of QDR in A. thaliana to diverse races of X. campestris (Xc). A nested genome‐wide association mapping approach was used to finely map the genomic regions associated with QDR to Xcc12824 (race 2) and XccCFBP6943 (race 6). To identify the gene(s) implicated in QDR, insertional mutants (T‐DNA) were selected for the candidate genes and phenotyped in response to Xc. We identified two major QTLs that confer resistance specifically to Xcc12824 and XccCFBP6943. Although QDR to Xcc12824 is conferred by At5g22540 encoding for a protein of unknown function, QDR to XccCFBP6943 involves the well‐known immune receptor pair RRS1/RPS4. In addition to RKS1, this study reveals that three genes are involved in resistance to Xc with strikingly different ranges of specificity, suggesting that QDR to Xc involves a complex network integrating multiple response pathways triggered by distinct pathogen molecular determinants.     

Inflorescence development in the Vitis–Ampelocissus clade of Vitaceae: the unusual lamellate inflorescence of Pterisanthes

Pterisanthes (Vitaceae) is a genus of c. 20 species of scandent climbers endemic to Southeast Asia with unusual lamellate inflorescences. Molecular phylogenetic analysis supports its relationship in the well‐supported Vitis–Ampelocissus–Nothocissus–Pterisanthes clade (i.e. the Ampelocissus–Vitis clade). Shoot tips and floral buds were collected from wild and greenhouse‐grown P. eriopoda at different developmental stages and were examined using epi‐illumination, light and scanning electron microscopy. Inflorescence and floral ontogeny was studied to discover how the lamellate inflorescence evolved and to make morphological comparisons to infer relationships with closely related members of Vitaceae. The second‐order branches in P. eriopoda are racemose and develop helically around the inflorescence axis in a similar fashion to Vitis and Ampelocissus. Inflorescence branching is restricted to the second order in P. eriopoda, whereas in Vitis and most Ampelocissus species subsequent branching orders culminate in the typical vitaceous determinate dichasium. In P. eriopoda subsequent lateral growth of the second‐order branches combined with the inhibition of peduncle or pedicel formation and loss of dichasial branching results in the unique lamellae in Pterisanthes, on which the floral primordia arise directly in a helical pattern. Floral development in P. eriopoda is the same as in other genera of Vitaceae examined to date with initiation of floral whorls centripetally, the calyx ring developing first and calyx lobes fused to cover the petals and stamen primordia. Given the recent phylogenetic results that placed Pterisanthes firmly within Ampelocissus, the most likely scenario is that the Pterisanthes inflorescence is derived from the thyrse of an Ampelocissus‐like ancestor and that the thyrse is a morphological synapomorphy of the Ampelocissus–Vitis clade. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 179 , 725–741.     

Variation analysis of pathogenic Vibrio spp. and Pseudomonas spp. in Changhai mollusc farming waters using real-time PCR assay during 2011–2014

Bacterial disease has caused high mortality of breeding molluscs from 2009 to 2011 in the Changhai area (Dalian, China). Vibrio spp. and Pseudomonas spp. have been detected as major pathogenic agents for aquatic animals in this area. In the present study, four virulence genes including vsm, toxR, aprX and carA were targeted to develop a real-time PCR assay for the quantitative detection of Vibrio splendidus, V. parahaemolyticus, Pseudomonas fluorescens and P. putida, respectively. The sensitivity and specificity of the assays were verified by experimental samples, and the variation tendencies of pathogenic V. splendidus, V. parahaemolyticus, P. fluorescens and P. putida strains from June to September were also detected in mollusc farming waters during 2011–2014. The concentration of V. splendidus increased from June to July, reduced in August, and then increased again in September. The highest count of V. parahaemolyticus appeared in July, and then dramatically decreased from August to September. Conversely, the counts of P. fluorescens and P. putida remained at lower levels from June to August, and then dramatically peaked in September. All four pathogenic bacteria displayed similar fluctuation tendencies of count variation in each year, and their concentrations were found to have a correlation with the average annual temperature. The variation tendency of pathogenic bacteria with temperature suggested that temperature was one of the most important factors to regulate the bacterial growth in a farming area, which could further provide information for the early warning of disease outbreak by using a convenient real-time PCR assay.     

<Emphasis Type="Italic">CaBLIND</Emphasis> regulates axillary meristem initiation and transition to flowering in pepper

Plant architecture is a major motif in plant diversity. The shape of the plant is regulated by genes that have been found to have similar or related functions in different species. However, changes in gene regulation or their recruitment to additional developmental pathways contribute to the wide range of plant patterns. Our aim was to unravel the genetic mechanisms governing the unique architecture of pepper (Capsicum annuum) and to determine whether these genetic factors have conserved functions in other plant species. We describe the pepper CaBLIND (CaBL) gene that is orthologous to the tomato (Solanum lycopersicum) BLIND (BL) and to the Arabidopsis thaliana REGULATOR OF AXILLARY MERISTEMS (RAX). We identified two allelic Cabl mutants that show dramatic reduction in axillary meristem initiation. In addition, Cabl exhibits late flowering and ectopic vegetative growth during the reproductive phase. Double-mutant and expression analyses suggest that CaBL functions independently of FASCICULATE, the pepper ortholog of SELF PRUNING in regulating sympodial growth, but is epistatic to FASCICULATE in controlling axillary meristem formation. Furthermore, CaBL operates independently of CaREVOLUTA and CaLATERAL SUPPRESSOR in regulating axillary branching. Our results provide evidence of CaBL’s conserved function with BL and RAX genes in regulating axillary meristem initiation early in development. In addition, similar to BL but opposite to RAX, CaBL acts to promote the transition from vegetative to reproductive phase. However, in contrast to BL and RAX, CaBL is co-opted to play a role in suppressing vegetative growth during the reproductive phase in pepper.     

Species-specific evolution of telomeric and rDNA repeats in the tobacco composite genome

In order to investigate possible interactions between parental genomes in the composite genome of Nicotiana tabacum we have analyzed the organization of telomeric (TTTAGGG)_n and ribosomal gene (rDNA) repeats in the progenitor genomes Nicotiana sylvestris and Nicotiana tomentosiformis or Nicotiana otophora. Telomeric arrays in the Nicotiana species tested are heterogeneous in length ranging from 20 to 200 kb in N. sylvestris, from 20 to 50 kb in N. tomentosiformis, from 15 to 100kb in N. otophora, and from 40 to 160kb in N. tabacum. The patterns of rDNA repeats (18S, 5.8S, 25S RNA) appeared to be highly homogeneous and speciesspecific; no parental rDNA units corresponding to N. sylvestris, N. tomentosiformis or N. otophora were found in the genome of N. tabacum by Southern hybridization. The results provide evidence for a species-specific evolution of telomeric and ribosomal repeats in the tobacco composite genome.     

Oenothera mitochondrial orf454, a gene involved in cytochrome c biogenesis corresponds to orf169 and orf322 of Marchantia

We have characterized a mitochondrial gene in Oenothera, designated orf454, capable of encoding a component of the cytochrome c biogenesis system. This open reading frame is interrupted by an intron of 941 nucleotides showing high similarity to a group II intron residing in the rpl2 gene. RNA editing, which is observed at 18 cytidine positions within the orf454 reading frame, improves the similarity to protein-coding sequences in bacteria and higher plants and removes the last 16 amino acids. orf454 also shows high sequence similarity to two overlapping reading frames (orf169 and orf322) of Marchantia mitochondria. These ORFs belong to an operon-like cluster of genes in the liverwort that is not conserved in Oenothera mitochondria. However, in bacteria these reading frames are organized like the Marchantia gene cluster. It has been shown by genetical analysis in Rhodobacter capsulatus that these genes are essential for cytochrome c biogenesis. Genes of bacterial operons — ccl1 in Rhodobacter and yejR and nrfE in Escherichia coli — show high sequence similarity to the mitochondrial reading frames orf577 and orf454 of Oenothera. orf454, which we describe here, is homologous to the C-terminal region of these bacterial genes, while the previously described orf577 is homologous to the N-terminal region.     

Phylogenetic relationships in Carex, subgenus Vignea (Cyperaceae), based on ITS sequences

To evaluate the sectional classification in Carex, subgenus Vignea, the ITS region of 58 species of 20 sections was analyzed with Neighbor Joining (NJ) and Markov chain Monte Carlo (MCMC) methods. Sections Dioicae, Physodeae and Ovales are found to be monophyletic, with C. bohemica well integrated in the section Ovales. Section Heleonastes turns out to be monophyletic, if C. canescens is treated separately in section Canescentes. Section Elongatae is monophyletic, but C. remota is placed in section Remotae and C. bromoides in section Deweyanae. In both analyses, six representatives of section Arenariae cluster together in a terminal group, whereas C. disticha, C. repens and C. siccata form a basal cluster. C. maritima, as the only member of section Incurvae, shares this basal position. C. chordorrhiza is ascribed to section Chordorrhizeae and not ascribed to the paraphyletic section Divisae. C. vulpina and C. otrubae are assigned to section Vulpinae and separated from the heterogeneous section Stenorhynchae. The other members of sections Divisae, Muehlenbergianae, Multiflorae and Stenorhynchae are scattered throughout the trees. The representatives of section Foetidae are dispersed in both analyses, section Paniculatae appears to be non-monophyletic in the molecular results as well. The subgenus appears subdivided in at least four larger subgroups in all analyses. Whereas these subgroups are strongly supported, the relationships between these subgroups remain only poorly resolved.     

Evolution of the alcohol dehydrogenase (ADH) genes in yeast: characterization of a fourth ADH in Kluyveromyces lactis

Summary Three alcohol dehydrogenase (ADH) genes have recently been characterized in the yeast Kluyveromyces lactis. We report on a fourth ADH in K. lactis (KADH II: KADH2 gene) which is highly similar to other ADHs in K. lactis and Saccharomyces cerevisiae. KADH II appears to be a cytoplasmic enzyme, and after expression of KADH2 in S. cerevisiae enzyme activity comigrated with a K. lactis ADH present in cells grown in glucose or in ethanol. KADH I was also expressed in S. cerevisiae and it comigrated with a major ADH species expressed under glucose growth conditions in K. lactis. The substrate specificities for KADH I and KADH II were shown to be more similar to that of SADH II than to SADH I. SADH I cannot efficiently utilize long chain alcohols, in contrast to other cytoplasmic yeast ADHs, presumably because of the presence of a methionine (residue 271) in its substrate binding cleft. A comparison of the DNA sequences of ADHs among K. lactis, S. cerevisiae and Schizosaccharomyces pombe suggests that the ancestral yeast species contained one cytoplasmic ADH. After divergence from S. pombe, the ADH in the ancestor to K. lactis and S. cerevisiae was duplicated, and one ADH became localized to the mitochondrion, presumably for the oxidative use of ethanol. Following the speciation of S. cerevisiae and K. lactis, the gene encoding the cytoplasmic ADH in S. cerevisiae duplicated, which resulted in the development of the SADH II protein as the primary oxidative enzyme in place of SADH III. In contrast, the K. lactis mitochondrial ADH duplicated to give rise to the highly expressed KADH3 and KADH4 genes, both of which may still play primary roles in oxidative metabolism. These data suggest that K. lactis and S. cerevisiae use different compartments for their metabolism of ethanol. Our results also indicate that the complex regulatory circuits controlling the glucose-repressible SADH2 in S. cerevisiae are a recent acquisition from regulatory networks used for the control of genes other than SADH2.

---

     

Pabp binds to the osk 3'UTR and specifically contributes to osk mRNA stability and oocyte accumulation

RNA localization is tightly coordinated with RNA stability and translation control. Bicaudal-D (Bic-D), Egalitarian (Egl), microtubules and their motors are part of a Drosophila transport machinery that localizes mRNAs to specific cellular regions during oogenesis and embryogenesis. We identified the Poly(A)-binding protein (Pabp) as a protein that forms an RNA-dependent complex with Bic-D in embryos and ovaries. pabp also interacts genetically with Bic-D and, similar to Bic-D, pabp is essential in the germline for oocyte growth and accumulation of osk mRNA in the oocyte. In the absence of pabp, reduced stability of osk mRNA and possibly also defects in osk mRNA transport prevent normal oocyte localization of osk mRNA. pabp also interacts genetically with osk and lack of one copy of pabp⁺ causes osk to become haploinsufficient. Moreover, pointing to a poly(A)-independent role, Pabp binds to A-rich sequences (ARS) in the osk 3′UTR and these turned out to be required in vivo for osk function during early oogenesis. This effect of pabp on osk mRNA is specific for this RNA and other tested mRNAs localizing to the oocyte are less and more indirectly affected by the lack of pabp.     

Temperature regulation of membrane composition in the Firmicute,Enterococcus faecalis,parallels that of Escherichia coli

Both Enterococcus faecalis and Escherichia coli can undergo abrupt temperature transitions in nature. E. coli changes the composition of its phospholipid acyl chains in response to shifts growth temperature. This is mediated by a naturally temperature sensitive enzyme, FabF (3-ketoacyl-acyl carrier protein synthase II), that elongates the 16 carbon unsaturated acyl chain palmitoleate to the 18 carbon unsaturated acyl chain, cis-vaccenate. FabF is more active at low temperatures resulting in increased incorporation of cis-vaccenoyl acyl chains into the membrane phospholipids. This response to temperature is an intrinsic property of FabF and does not require increased synthesis of the enzyme. We report that the FabF of the very divergent bacterium, E. faecalis, has properties very similar to E. coli FabF and is responsible for changing E. faecalis membrane phospholipid acyl chain composition in response to temperature. Moreover, expression E. faecalis FabF in an E. coli ∆fabF strain restores temperature regulation to the E. coli strain.     

A dnaB analog ban, specified by bacteriophage P1: genetic and physiological evidence for functional analogy and interactions between the two products.

Summary Bacteriophage P1 has been shown previously to determine a product ban than can substitute in DNA replication for the protein specified by cistron dnaB of Escherichia coli. However, ban product furnished by P1 bac prophage (ban constitutive) substitutes only poorly for DNA replication in the absence of dnaB product in a strain bearing an unsuppressed amber mutation, dnaB266, as shown by the cryosensitivity of the dnaB266 (P1 bac) lysogen and its unability to support growth. An additional mutation (termed crr) in the P1 bac prophage has been obtained which confers cryoresistance to the sup ⁺ dnaB266 (P1 bac crr) lysogen and restores its ability to support growth. ban product produced in P1 bac crr lysogen fulfills all dnaB roles in vivo, especially in the various instances in which ban product expressed in P1 bac lysogens does not. The ban product is expressed constitutively in P1 crr prophage. The crr-1 mutation is tightly linked to the bac-1 and ban-1 mutations and is dominant over crr ⁺. The nature of the crr mutation is discussed: two hypotheses are considered, that of a mutation in the ban gene rendering the ban product more active or that of a site mutation in the ban operon increasing the level of ban expression. Expression of ban product (wild type or altered) leads to interactions with the variously altered dnaB product. Both positive and negative interactions are described. Genetic results presented here suggest that ban and dnaB subunits interact to form hybrid dnaB-like molecules; the average composition of which depends on the relative quantities of ban and dnaB subunits in the cell.     

Isolation and characterization of regulatory mutations affecting the expression of the guaBA operon of Escherichia coli K-12

Summary We isolated strains of Escherichia coli K 12 in which the lac structural genes were fused to the structural genes of the guaBA operon. These strains were used to isolate regulatory mutations that increased the expression of the guaBA operon under normal repressing conditions as compared to the wild type parental fusion strain. Three classes of guaBA specific regulatory mutations were identified. Class I regulatory mutations were trans-acting and unlinked to the guaBA operon as shown by bacteriophage P1 transduction. Class II regulatory mutations were tightly linked to the guaBA operon, cis-dominant to the wild type allele in a cis-trans analysis and were regarded as control region mutations. Class III regulatory mutations were tightly linked to the guaBA operon and trans-recessive to the wild type allele in a cis-trans analysis. We have designated the locus responsible for the class III regulatory mutations as guaR. The guaR locus is tightly linked and was mapped to the counterclockwise side of the guaBA operon. The guaR locus is proposed to specify a trans acting regulatory element involved in the regulation of the guaBA operon.     

Grosmannia and Leptographium spp. associated with conifer-infesting bark beetles in Finland and Russia, including Leptographium taigense sp. nov.

Species of Grosmannia with Leptographium anamorphs include important forest pathogens and agents of blue stain in timber. They are commonly found in association with forest pests, such as bark beetles. During a survey of ophiostomatoid fungi in eastern parts of Finland and neighboring Russia, species belonging to the genus Grosmannia were isolated from 12 different bark beetle species infesting Picea abies and Pinus sylvestris, the most economically important conifers in the region. Identification of these fungi was based on morphology, DNA sequence comparisons for three gene regions and phylogenetic analyses. A total of ten taxa were identified. These belonged to six different species complexes in Grosmannia. The phylogenetic analyses provided an opportunity to redefine the G. galeiformis-, L. procerum-, L. lundbergii-, G. piceiperda-, G. olivacea- and G. penicillata-complexes, and to consider the species emerging from the survey within the context of these complexes. The species included G. galeiformis, G. olivacea, L. chlamydatum, L. lundbergii, L. truncatum and a novel taxon, described here as L. taigense sp. nov. In addition, species closely related to G. cucullata, G. olivaceapini comb. nov., G. piceiperda and L. procerum were isolated but their identity could not be resolved. The overall results indicate that the diversity of Grosmannia species in the boreal forests remains poorly understood and that further studies are needed to clarify the status of several species or species complexes.     

Specificity of Chroomonas (Cryptophyceae) as a source of kleptochloroplast for Nusuttodinium aeruginosum (Dinophyceae)

The unarmoured dinoflagellate Nusuttodinium aeruginosum retains a kleptochloroplast, which is a transient chloroplast stolen from members of the cryptomonad genus, Chroomonas. Both N. aeruginosum and the closely related N. acidotum have been shown to restrict their diet to a limited number of species of this blue‐green genus of cryptophyte. However, it is still unclear how flexible the predators are with regard to the ingestion and utilization of Chroomonas spp. as a source of kleptochloroplast. To address specificity of cryptomonad in N. aeruginosum, we collected the cells of N. aeruginosum from several ponds in Japan, and analysed the phylogeny of the kleptochloroplasts based on their plastidial 16S rDNA sequences. All sequences obtained in this study were restricted to only one (the subclade 4) of four subclades known to comprise the Chroomonas/Hemiselmis clade. Therefore, N. aeruginosum is specific in its dietary requirements, selecting their prey within the subclade level.     

Recognising angiosperm clades in the Early Cretaceous fossil record

Studies of the earliest Cretaceous angiosperms in the 1970s made only broad comparisons with living taxa, but discoveries of fossil flowers and increasingly robust molecular phylogenies of living angiosperms allow more secure recognition of extant clades. The middle to late Albian rise of tricolpate pollen and the first local dominance of angiosperm leaves mark the influx of near-basal lines of eudicots. Associated flowers indicate that palmately lobed ‘platanoids’ and Sapindopsis are both stem relatives of Platanus, while Nelumbites was related to Nelumbo (also Proteales) and Spanomera to Buxaceae. Monocots are attested by Aptian Liliacidites pollen and Acaciaephyllum leaves and Albian araceous inflorescences. Several Albian–Cenomanian fossils belong to Magnoliidae in the revised monophyletic sense, including Archaeanthus in Magnoliales and Virginianthus and Mauldinia in Laurales, while late Barremian pollen tetrads (Walkeripollis) are related to Winteraceae. In the basal ANITA grade, Nymphaeales are represented by Aptian and Albian flowers and whole plants (Monetianthus, Carpestella and Pluricarpellatia). Epidermal similarities of lower Potomac leaves to woody members of the ANITA grade are consistent with Albian flowers assignable to Austrobaileyales (Anacostia). Aptian to Cenomanian mesofossils represent both crown group Chloranthaceae (Asteropollis plant) and stem relatives of Chloranthaceae and/or Ceratophyllum (Canrightia, Zlatkocarpus, Pennipollis plant and possibly Appomattoxia).     

Molecular and functional analysis of the ruv region of Escherichia coli K-12 reveals three genes involved in DNA repair and recombination

Summary Recombinant plasmids carrying ruvA, ruvB, or both were constructed and used to investigate the genetic defects in a collection of UV-sensitive ruv mutants. The results revealed that efficient survival of UV-irradiated cells depends on both ruvA and ruvB, and on a third gene, ruvC, located upstream of the ruvAB operon. Southern blotting analysis was used to locate insertions in ruv and to examine putative deletion mutants. Two Tn10 insertions were located to the region encoding ruvA. Since these insertions caused a deficiency in the activities of both ruvA and ruvB, we concluded that they must exert a polar effect on ruvB. Two putative ruv deletion mutants were shown to be the result of deletion-inversion events mediated during imprecise excision of Tn10. The relevant inversion breakpoints in these mutants were located to ruvA and ruvC.     

Trichoderma reesei sequences that bind to the nuclear matrix enhance transformation frequency

Three DNA fragments, trs1, 2 and 3, were isolated from the Trichoderma reesei genome on the basis of their ability to promote autonomous replication of plasmids in Saccharomyces cerevisiae. Each trs element bound specifically to the isolated T. reesei nuclear matrix in vitro, and two of them bound in vivo, indicating that they are matrix attachment regions (MARs). A similar sequence previously isolated from Aspergillus nidulans (ans1) was also shown to bind specifically to the T. reesei nuclear matrix in vitro. The T. reesei MARs are AT-rich sequences containing 70%, 86% and 73% A+T over 2.9, 0.8 and 3.7 kb, respectively for trs1, 2 and 3. They exhibited no significant sequence homology, but were shown to contain a number of sequence motifs that occur frequently in many MARs identified in other eukaryotes. However, these motifs occurred as frequently in the trs elements as in randomly generated sequences with the same A+T content. trs1 and 3 were shown to be present as single copies in the T. reesei genome. The presence of the trs elements in transforming plasmids enhanced the frequency of integrative transformation of T. reesei up to five fold over plasmids without a trs. No evidence was obtained to suggest that the trs elements promoted efficient replication of plasmids in T. reseei. A mechanism for the enhancement of transformation frequency by the trs elements is proposed. Received: 1 March 1997 / Accepted: 13 May 1997     

RTA2, a novel gene involved in azole resistance in Candida albicans

Widespread and repeated use of azoles, particularly fluconazole, has led to the rapid development of azole resistance in Candida albicans. Overexpression of CDR1, CDR2, and CaMDR1 has been reported contributing to azole resistance in C. albicans. In this study, hyper-resistant C. albicans mutant, with the above three genes deleted, was obtained by exposure to fluconazole and fluphenezine for 28 passages. Thirty-five differentially expressed genes were identified in the hyper-resistant mutant by microarray analysis; among the 13 up-regulated genes, we successfully constructed the rta2 and ipf14030 null mutants in C. albicans strain with deletions of CDR1, CDR2 and CaMDR1. Using spot dilution assay, we demonstrated that the disruption of RTA2 increased the susceptibility of C. albicans to azoles while the disruption of IPF14030 did not influence the sensitivity of C. albicans to azoles. Meanwhile, we found that ectopic overexpression of RTA2 in C. albicans strain with deletions of CDR1, CDR2 and CaMDR1 conferred resistance to azoles. RTA2 expression was found elevated in clinical azole-resistant isolates of C. albicans. In conclusion, our findings suggest that RTA2 is involved in the development of azole resistance in C. albicans.