The NADPH oxidase AoNoxA in <Emphasis Type="Italic">Arthrobotrys oligospora</Emphasis> functions as an initial factor in the infection of <Emphasis Type="Italic">Caenorhabditis elegans</Emphasis>

Reactive oxygen species (ROS) produced by NADPH oxidases can serve as signaling molecules to regulate a variety of physiological processes in multi-cellular organisms. In the nematophagous fungus Arthrobotrys oligospora, we found that ROS were produced during conidial germination, hyphal extension, and trap formation in the presence of nematodes. Generation of an AoNoxA knockout strain demonstrated the crucial role of NADPH oxidase in the production of ROS in A. oligospora, with trap formation impaired in the AoNoxA mutant, even in the presence of the nematode host. In addition, the expression of virulence factor serine protease P186 was up-regulated in the wild-type strain, but not in the mutant strain, in the presence of Caenorhabditis elegans. These results indicate that ROS derived from AoNoxA are essential for full virulence of A. oligospora in nematodes.     

Photosynthetic activity and components of the electron transport chain in the aerobic bacteriochlorophyll <Emphasis Type="Italic">a</Emphasis>-containing bacterium <Emphasis Type="Italic">Roseinatronobacter thiooxidans</Emphasis>

Bioenergetics of the aerobic bacteriochlorophyll a-containing (BCl a) bacterium (ABC bacterium) Roseinatronobacter thiooxidans is a combination of photosynthesis, oxygen respiration, and oxidation of sulfur compounds under alkaliphilic conditions. The photosynthetic activity of Rna. thiooxidans cells was established by the photoinhibition of cell respiration and reversible photobleaching discoloration of the BCl a of reaction centers (RC), connected by the chain of electron transfer with cytochrome c ₅₅₁ oxidation. The species under study, like many purple bacteria and some of the known ABC bacteria, possesses a light-harvesting pigment-protein (LHI) complex with the average number of 30 molecules of antenna BCl a per one photosynthetic RC. Under microaerobic growth conditions, the cells contained bc ₁ complex and two terminal oxidases: cbb ₃-cytochrome oxidase and the alternative cytochrome oxidase of the a ₃ type. Besides, Rna. thiooxidans was shown to have several different soluble low- and high-potential cytochromes c, probably associated with the ability of utilizing sulfur compounds as additional electron donors.     

Gene Expression Prediction and Hierarchical Clustering Analysis of Plant <Emphasis Type="Italic">CCD</Emphasis> genes

Plant carotenoid cleavage dioxygenase (CCD) catalyses the formation of industrially important apocarotenoids. Here, we applied codon-based classification for 72 CCD genes from 35 plant species using hierarchical clustering analysis. The codon adaptation index (CAI) and relative codon bias (RCB) were utilized to estimate the level of gene expression. The codon-based cluster tree result shows neatly clustered subclass of CCD genes except BoCCD1 gene of Bixa orellana. Correlation analysis of CAI values with RCB indicates an overall low-level expression of CCD across different species. Similarly, the closeness in the codon cluster with same CAI values was not reflected in 3-D structural report of selected CCD genes. These finding not only enhances our insights into the classification of CCD gene across the species but also identifies the critical factors responsible for this variation, which could aid in prediction of gene expression and function for newly reported CCD genes.     

<Emphasis Type="Italic">ZmCCD7/ZpCCD7</Emphasis> encodes a carotenoid cleavage dioxygenase mediating shoot branching

Main conclusion

ZmCCD7/ZpCCD7 encodes a carotenoid cleavage dioxygenase that may mediate strigolactone biosynthesis highly responsive to phosphorus deficiency and undergoes negative selection over domestication from Zea ssp. parviglumis to Zea mays.Carotenoid cleavage dioxygenase 7 (CCD7) functions to suppress shoot branching by controlling strigolactone biosynthesis. However, little is known about CCD7 and its functions in maize and its ancestor (Zea ssp. parviglumis) with numerous shoot branches. We found that ZmCCD7 and ZpCCD7 had the same coding sequence, indicating negative selection of the CCD7 gene over domestication from Zea ssp. parviglumis to Zea mays. CCD7 expression was highly responsive to phosphorus deficiency in both species, especially in the meristematic zone and the pericycle of the elongation zone of maize roots. Notably, the crown root had the strongest ZmCCD7 expression in the meristematic zone under phosphorus limitation. Transient expression of GFP tagged ZmCCD7/ZpCCD7 in maize protoplasts indicated their localization in the plastid. Further, ZmCCD7/ZpCCD7 efficiently catalyzed metabolism of six different linear and cyclic carotenoids in E. coli, and generated β-ionone by cleaving β-carotene at the 9,10 (9′,10′) position. Together with suppression of shoot branching in the max3 mutant by transformation of ZmCCD7/ZpCCD7, our work suggested that ZmCCD7/ZpCCD7 encodes a carotenoid cleavage dioxygenase mediating strigolactone biosynthesis in maize and its ancestor.

     

Identification of the di-<Emphasis Type="Italic">n</Emphasis>-butyl phthalate-biodegrading strains and the biodegradation pathway in strain LMB-1

DNA isolated from a greenhouse soil (Nanjing, Jiangsu Province, China) was suitable for PCR amplification of gene segment coding for the 16S rRNA. Diverse PCR products were characterized by cloning and sequencing, and analysis of bacterial colonies showed the presence over 26 phyla. The most bacteria belonged to Proteobacteria, Actinobacteria, Gemmatimonadetes, Acidobacteria and Planctomycetes. Furthermore, after the enrichment procedure of DBP-degrading microorganisms, 4 strains were isolated from the soil sample with di-n-butyl phthalate (DBP) biodegradability, and they were identified to be Rhizobium sp., Streptomyces sp., Pseudomonas sp. and Acinetobacter sp. Analysis of the degradation products by LC-MS led to identification of metabolites of DBP in strain LMB-1 (identified as Rhizobium sp.) which suggests that DBP was degraded through β-oxidation, demethylation, de-esterification and cleavage of aromatic ring.     

<Emphasis Type="Italic">glyA</Emphasis> gene knock-out in <Emphasis Type="Italic">Escherichia coli</Emphasis> enhances L-serine production without glycine addition

In E. coli, glyA encodes for serine hydroxymethyltransferase (SHMT), which converts L-serine to glycine. When engineering L-serine-producing strains, it is therefore favorable to inactivate glyA to prevent L-serine degradation. However, most glyA knockout strains exhibit slow cell growth because of the resulting lack of glycine and C₁ units. To overcome this problem, we overexpressed the gcvTHP genes of the glycine cleavage system (GCV), to increase the C₁ supply before glyA was knocked out. Subsequently, the kbl and tdh genes were overexpressed to provide additional glycine via the L-threonine degradation pathway, thus restoring normal cell growth independent of glycine addition. Finally, the plasmid pPK10 was introduced to overexpress pgk, serA ^Δ197 , serC and serB, and the resulting strain E4G2 (pPK10) accumulated 266.3 mg/L of L-serine in a semi-defined medium without adding glycine, which was 3.18-fold higher than the production achieved by the control strain E3 (pPK10). This strategy can accordingly be applied to disrupt the L-serine degradation pathway in industrial production strains without causing negative side-effects, ultimately making L-serine production more efficient.     

Mutations in <Emphasis Type="Italic">CsPID</Emphasis> encoding a Ser/Thr protein kinase are responsible for round leaf shape in cucumber (<Emphasis Type="Italic">Cucumis sativus</Emphasis> L.)

Key message

Two round-leaf mutants, rl-1 and rl-2, were identified from EMS-induced mutagenesis. High throughput sequencing and map-based cloning suggested CsPID encoding a Ser/Thr protein kinase as the most possible candidate for rl-1. Rl-2 was allelic to Rl-1.

Abstract

Leaf shape is an important plant architecture trait that is affected by plant hormones, especially auxin. In Arabidopsis, PINOID (PID), a regulator for the auxin polar transporter PIN (PIN-FORMED) affects leaf shape formation, but this function of PID in crop plants has not been well studied. From an EMS mutagenesis population, we identified two round-leaf (rl) mutants, C356 and C949. Segregation analysis suggested that both mutations were controlled by single recessive genes, rl-1 and rl-2, respectively. With map-based cloning, we show that CsPID as the candidate gene of rl-1; a non-synonymous SNP in the second exon of CsPID resulted in an amino acid substitution and the round leaf phenotype. As compared in the wild type plant, CsPID had significantly lower expression in the root, leaf and female flowers in C356, which may result in the less developed roots, round leaves and abnormal female flowers, respectively in the rl-1 mutant. Among the three copies of PID genes, CsPID, CsPID2 and CSPID2L (CsPID2-like) in the cucumber genome, CsPID was the only one with significantly differential expression in adult leaves between WT and C356 suggesting CsPID plays a main role in leaf shape formation. The rl-2 mutation in C949 was also cloned, which was due to another SNP in a nearby location of rl-1 in the same CsPID gene. The two round leaf mutants and the work presented herein provide a good foundation for understanding the molecular mechanisms of CsPID in cucumber leaf development.

     

Effect of selenium-containing biocomposites based on <Emphasis Type="Italic">Ganoderma</Emphasis> mushroom isolates grown in the presence of oxopropyl-4-hydroxycoumarins,on bacterial phytopathogens

Effect of selenium-containing biocomposites obtained from submerged cultures of macrobasidiomycetes Ganoderma applantum, G. cattienensis, G. colossus G. lucidum, G. neojaponicum, and G. valesiacum, on plant pathogenic bacteria Clavibacter michiganensis ssp. sepedonicus (Cms), Micrococcus luteus, Pectobacterium atrosepticum, Pectobacterium carotovorum subsp. carotovorum, Pseudomonas fluorescens, Pseudomonas viridiflava, and Xanthomonas campestris was studied. Oxopropyl-4-hydroxychromenones were used as components of the fungal nutrient media. The bacteriostatic and bactericidal activity of the Se-containing and Se-free substances of fungal origin against plant pathogenic bacteria was determined using colony-forming units count, the agar well diffusion method, and by turbidity measurements of bacterial suspensions. The composites produced from the extracellular metabolites of G. cattienensis SIE1302 with 4-hydroxy-3-(3-oxo-1,3-diphenyl propyl)-chromen-2-one (S(45)), and of G. lucidum SIE1303 with 4-hydroxy-3-(3-oxo-1-(3-nitrophenyl)-3-phenylpropyl)-chromen-2-one (S(NO₂)) possessed the most pronounced antibacterial action against Cms. The composites produced from the isolates of G. valesiacum 120702 with S(NO₂) showed the maximal antibacterial activity against Xanthomonas campestris B-610. High antimicrobial effect of G. lucidum 1315 with S(NO₂) against Xanthomonas campestris B-610 and of G. colossus SIE1301 against Pseudomonas fluorescens EL-2.1 was revealed. The pioneering information on the biological activity of coumarin series compounds in their application for producing the substances of fungal origin was obtained.     

Functional analysis of an <Emphasis Type="Italic">APETALA1</Emphasis>-like MADS box gene from <Emphasis Type="Italic">Eustoma grandiflorum</Emphasis> in regulating floral transition and formation

An Eustoma grandiflorum APETALA1 (EgAP1) gene showing high homology to the SQUA subfamily of MADS-box genes was isolated and characterized. EgAP1, containing a conserved euAP1 motif at the C-terminus, showed high sequence identity to Antirrhinum majus SQUAMOSA in the SQUA subfamily. EgAP1 mRNA was detected in the leaf and expressed significantly higher in young flower buds than in mature flower buds. In flowers, EgAP1 mRNA was strongly detected in sepal, weakly detected in petal and was absent in stamen and carpel. Transgenic Arabidopsis plants ectopically expressing EgAP1 flowered early and produced terminal flowers. In addition, the conversion of petals into stamen-like structures was also observed in 35S::EgAP1 flowers. 35S::EgAP1 was able to complement the ap1 flower defects by restoring the defect for sepal formation and significantly increasing second whorl petal production in Arabidopsis ap1 mutant plants. These results revealed that EgAP1 is the APETALA1 homolog in E. grandiflorum and that the function of EgAP1 is involved in floral induction and flower formation.     

Autophagic flux is essential for the downregulation of <Emphasis Type="Italic">D</Emphasis>-dopachrome tautomerase by atractylenolide I to ameliorate intestinal adenoma formation

Colorectal cancer is generally believed to progress through an adenoma - carcinoma sequence. Adenomatous polyposis coli (APC) mutations serve as the initiating event in adenoma formation. The Apc^Min/+ mouse harbors a mutation in the APC gene, which is similar or identical to the mutation found in individuals with familial adenomatous polyposis and 70% of all sporadic CRC cases. Autophagy is a constitutive process required for proper cellular homeostasis. However, its role in intestinal adenoma formation is still controversial. Atractylenolide I (AT1) is a sesquiterpenoid that possesses various clinically relevant properties such as anti-tumor and anti-inflammatory activities. The role of AT1 on adenoma formation was tested in Apc^Min/+ mice and its underlying mechanism in regulating autophagy was documented. D-dopachrome tautomerase (D-DT) was identified as a potential target of AT1 by an proteomics-based approach. The effects of p53 modification on autophgic flux was monitored in p53^?/? and p53^+/+ HCT116 cells. Small interfering RNA was used to investigate the function of Atg7 and D-DT on autophagy programme induce by AT1. AT1 effectively reduced the formation of adenoma and downregulated the tumorigenic proteins in Apc^Min/+ mice. Importantly, AT1 stimulated autophagic flux through downregulating acetylation of p53. Activation of Sirt1 by AT1 was essential for the deacetylation of p53 and downregulation of D-DT. The lowered expression of COX-2 and β-catenin by AT1 were partly recovered by Atg7 knockdown. AT1 activates autophagy machinery to downregulate D-DT and reduce intestinal adenoma formation. This discovery provides evidence in vivo and in vitro that inducing autophagy by natural products maybe a potential therapy to ameliorate colorectal adenoma formation.     

Vetch aphid, <Emphasis Type="Italic">Megoura crassicauda</Emphasis> (Hemiptera: Aphididae), parasitism does not reduce the bean production of narrow-leaved vetch, <Emphasis Type="Italic">Vicia sativa</Emphasis> subsp. <Emphasis Type="Italic">nigra</Emphasis> (Fabaceae)

Megoura crassicauda Mordvilko (Hemiptera: Aphididae) is a dominant aphid species found on Vicia sativa subsp. nigra (L.) Ehrh. (Fabaceae) in the spring. Worker ants of Formica japonica, the dominant ant species attracted to the extrafloral nectaries of V. s. nigra, often attack ladybirds (Coccinella septempunctata), which are aphid enemies. However, the workers of F. japonica do not attack or exclude M. crassicauda, the non-myrmecophilous aphid. It appears that the “bodyguard” retained by the plant guards the plant’s herbivore by attacking the herbivores’ enemies, rather than guarding the plant itself. The relationship between V. s. nigra and M. crassicauda was observed in the field to examine and evaluate the cost of parasitism. Parasitism by M. crassicauda delayed flower bud formation markedly in V. s. nigra but did not kill the plants. V. s. nigra plants that were parasitized showed a net bean production similar to that of the non-parasitized controls. The parasitism rate of M. crassicauda increased when extrafloral nectaries were used by F. japonica. These results may indicate that M. crassicauda provides V. s. nigra with benefits by preventing other serious disadvantages.     

Tandem duplications of receptor-like kinase genes reshaped the homologous chromosome 1 regions in <Emphasis Type="Italic">Oryza sativa</Emphasis> ssp. <Emphasis Type="Italic">indica</Emphasis> and <Emphasis Type="Italic">japonica</Emphasis> and their possible ancestral genomes

Plant receptor-like kinase (Rlk) genes form a large family, each encoding a protein with a signal motif, a single transmembrane region, and a cytoplasmic kinase domain. Various gene duplications have contributed to the establishment and expansion of the family. Here, we characterized the formation and evolution of the Rlk gene family in cultivated rice and their possible progenitors. Using wheat Rlk gene sequences, we identified orthologs from the genomes of domesticated rice subspecies Oryza sativa ssp. japonica and ssp. indica and their putative progenitors O. glaberrima and O. rufipogon. The four chromosome 1 orthologous regions ranged from 103 to 281 kb comprising 181 syntenic blocks with 75 to 100% sequence identity. These regions contained 11–19 Triticum aestivum kinases (Taks) and 10–15 Lr10 receptor-like kinases (Lrks) organized in clusters and 3–12 transposable elements (TEs). Dot plot analyses showed that the 4 regions had 21–37 conserved catalytic domains, mainly in protein kinases (PKs) and tyrosine kinases (TyrKs) in coupling state. Over 50% of the sequences of glaberrima/rufipogon and japonica/indica pairs were colinear, while japonica/indica displayed a marked sequence expansion with duplicated genes and TEs. A total of 2312 single nucleotide polymorphisms (SNPs) and insertion-deletions (INDELs) were identified between japonica and indica. Duplication of the Rlk genes in O. glaberrima and O. rufipogon occurred after the grass species radiation and before the divergence of O. rufipogon from O. glaberrima; the orthologous Rlk genes from O. japonica and O. indica duplicated after O. sativa separated from O. rufipogon; paralogs, obtained through extensive duplication, happened after the separation of rice from maize. Tandem duplication was the major factor contributing to the gene copy number variation and genome size expansion.     

Histological and cytological studies of plant infection by <Emphasis Type="Italic">Erysiphe euonymi</Emphasis>-<Emphasis Type="Italic">japonici</Emphasis>

Powdery mildew caused by Erysiphe euonymi-japonici (Eej) is an increasingly serious fungal disease on Euonymus japonicus that is an important ornamental plant. However, little is currently known about infection and pathogenesis of Eej on E. japonicus. Here, we report plant infection by Eej at the histological and cytological levels. Eej caused severe disease symptoms with white and snow-like colonies on leaf surfaces of E. japonicus. Microscopic observations were conducted continuously to define infection process of Eej on E. japonicus. Eej conidia germinated to produce appressorial germ tubes on leaf surfaces and formed irregular haustoria in plant epidermal cells at 6 h post-inoculation (hpi) and 12 hpi, respectively. After uptaking nutrients from host cells by haustoria, Eej formed numerous hyphae and extensive colonization on leaf surfaces at 96 hpi and finally produced abundant conidiophores and new conidia on leaf surfaces at 168 hpi. In addition, there was consistently a single nucleus in different Eej infection structures and haustorial development could be divided into three major stages, including formation of penetration peg, formation of haustorial neck and initial haustorium, and maturation of haustorium. These results provide useful information for further determination of Eej pathogenesis and finally controlling the disease.     

A novel uncultured bacterium of the family <Emphasis Type="Italic">Gallionellaceae</Emphasis>: Description and genome reconstruction based on metagenomic analysis of microbial community in acid mine drainage

Drainage waters at the metal mining areas often have low pH and high content of dissolved metals due to oxidation of sulfide minerals. Extreme conditions limit microbial diversity in such habitats. A microbial community of cold acid mine drainage (6.5°C, pH 2.65) at the Sherlovaya Gora polymetallic open-cast mine (Transbaikal region, Eastern Siberia, Russia) was studied using metagenomic techniques. Most of microorganisms belonged to a single uncultured lineage representing a new species of the Betaproteobacteria genus Gallionella. Bacteria of the genera Thiobacillus, Acidobacterium, Acidisphaera, and Acidithiobacillus were the minor components of the community. Almost complete (3.4 Mb) composite genome of the new bacterial lineage designated Candidatus Gallionella acididurans ShG14-8 was reconstructed using metagenomic data. Genome analysis revealed that Fe(II) oxidation probably involved the cytochromes localized on the outer cell membrane. The electron transport chain included NADH dehydrogenase, a cytochrome bc1 complex, an alternative complex III, and bd-, cbb3-, and bo3-types cytochrome oxidases. Oxidation of reduced sulfur compounds probably involved the Sox system, sulfide–quinone oxidoreductase, adenyl sulfate reductase, and sulfate adenyltransferase. The genes involved in autotrophic carbon assimilation via the Calvin cycle were present, while no pathway for nitrogen fixation was revealed. High numbers of RND metal transporters and P type ATPases were probably responsible for resistance to heavy metals. The new microorganism was an aerobic chemolithoautotroph that belonged to the group of psychrotolerant iron- and sulfur-oxidizing acidophiles of the family Gallionellaceae, which are widely distributed in acid mine drainage.     

Abscisic acid biosynthesis under water stress: anomalous behavior of the 9-<Emphasis Type="Italic">cis</Emphasis>-epoxycarotenoid dioxygenase1 (<Emphasis Type="Italic">NCED1</Emphasis>) gene in rice

The gene NCED1 encodes 9-cis-epoxycarotenoid dioxygenase, which catalyzes oxidative cleavage of 9-cis-epoxycarotenoids neoxanthin and violaxanthin to xanthoxin, a key step in the biosynthesis of abscisic acid (ABA) in higher plants. In the present study, the complete NCED1 of 1 917 bp was cloned and characterized from rice (Oryza sativa L. cv. N22) as no earlier reports were available for its characterization from the indica cultivar. The NCED1 had no intron and encoded a protein of 639 amino acids with a predicted molecular mass of 68.62 kD and pI of 6.07. The aliphatic index and grand average of hydropathicity were found to be 77.04 and -0.148, respectively. Multiple alignment analysis revealed that the sequence shared a high identity with the Oryza sativa japonica group (100 %) followed by Triticum aestivum (90 %), Hordeum vulgare (90 %), and Zea mays (89 %). The enzyme had a RPE65 domain of 476 amino acid residues. The RPE65 domain requires Fe(II) as a cofactor coordinated with 4 histidine residues and 3 glutamic acid residues. The phylogenic tree shows that NCED1 of japonica rice and NCED1 of indica rice were in the same group. They might have been evolved from a common ancestor. Analysis with a PSORT III tool shows that NCED is a chloroplastic protein. The real-time quantitative PCR and RNA-sequencing studies show that the expression of NCED1 was progressively reduced with increasing water stress, and a negative correlation between expression of OsNCED1 and severity of stress was established. Further, NCED1 expression negatively correlated with ABA accumulation under water stress whereas in some other species, its expression increased along with ABA accumulation. This might be due to feedback inhibition of the ABA biosynthesis in rice.