The Magnaporthe oryzae Effector AvrPiz-t Targets the RING E3 Ubiquitin Ligase APIP6 to Suppress Pathogen-Associated Molecular Pattern–Triggered Immunity in Rice

Although the functions of a few effector proteins produced by bacterial and oomycete plant pathogens have been elucidated in recent years, information for the vast majority of pathogen effectors is still lacking, particularly for those of plant-pathogenic fungi. Here, we show that the avirulence effector AvrPiz-t from the rice blast fungus Magnaporthe oryzae preferentially accumulates in the specialized structure called the biotrophic interfacial complex and is then translocated into rice (Oryza sativa) cells. Ectopic expression of AvrPiz-t in transgenic rice suppresses the flg22- and chitin-induced generation of reactive oxygen species (ROS) and enhances susceptibility to M. oryzae, indicating that AvrPiz-t functions to suppress pathogen-associated molecular pattern (PAMP)-triggered immunity in rice. Interaction assays show that AvrPiz-t suppresses the ubiquitin ligase activity of the rice RING E3 ubiquitin ligase APIP6 and that, in return, APIP6 ubiquitinates AvrPiz-t in vitro. Interestingly, agroinfection assays reveal that AvrPiz-t and AvrPiz-t Interacting Protein 6 (APIP6) are both degraded when coexpressed in Nicotiana benthamiana. Silencing of APIP6 in transgenic rice leads to a significant reduction of flg22-induced ROS generation, suppression of defense-related gene expression, and enhanced susceptibility of rice plants to M. oryzae. Taken together, our results reveal a mechanism in which a fungal effector targets the host ubiquitin proteasome system for the suppression of PAMP-triggered immunity in plants.     

Simple and rapid determination of the activity of recombinant D-amino acid oxidase in cephalosporin C bioconversion with use of a micro pO2 probe

Summary D-Amino acid oxidase (DAAO) genes were amplified from Trigonopsis variabilis and Rhodotorula gracilis by polymerase chain reactions. T. variabilis DAAO gene was cloned into a pUC19 vector. The expression of the T. variabilis DAAO was directly determined in permeabilized E. coli cells using a micro pO₂ probe. The micro pO₂ probe was sensitive enough to be suitable for a simple and rapid estimation of DAAO activity toward cephalosporin C.     

NMR of membrane proteins in micelles and bilayers: the FXYD family proteins

Determining the atomic resolution structures of membrane proteins is of particular interest in contemporary structural biology. Helical membrane proteins constitute one-third of the expressed proteins encoded in a genome, many drugs have membrane-bound proteins as their receptors, and mutations in membrane proteins result in human diseases. Although integral membrane proteins provide daunting technical challenges for all methods of protein structure determination, nuclear magnetic resonance (NMR) spectroscopy can be an extremely versatile and powerful method for determining their structures and characterizing their dynamics, in lipid environments that closely mimic the cell membranes. Once milligram amounts of isotopically labeled protein are expressed and purified, micelle samples can be prepared for solution NMR analysis, and lipid bilayer samples can be prepared for solid-state NMR analysis. The two approaches are complementary and can provide detailed structural and dynamic information. This paper describes the steps for membrane protein structure determination using solution and solid-state NMR. The methods for protein expression and purification, sample preparation and NMR experiments are described and illustrated with examples from the FXYD proteins, a family of regulatory subunits of the Na,K-ATPase.     

Long‐read sequence capture of the haemoglobin gene clusters across codfish species

Combining high‐throughput sequencing with targeted sequence capture has become an attractive tool to study specific genomic regions of interest. Most studies have so far focused on the exome using short‐read technology. These approaches are not designed to capture intergenic regions needed to reconstruct genomic organization, including regulatory regions and gene synteny. Here, we demonstrate the power of combining targeted sequence capture with long‐read sequencing technology for comparative genomic analyses of the haemoglobin (Hb) gene clusters across eight species separated by up to 70 million years. Guided by the reference genome assembly of the Atlantic cod (Gadus morhua) together with genome information from draft assemblies of selected codfishes, we designed probes covering the two Hb gene clusters. Use of custom‐made barcodes combined with PacBio RSII sequencing led to highly continuous assemblies of the LA (~100 kb) and MN (~200 kb) clusters, which include syntenic regions of coding and intergenic sequences. Our results revealed an overall conserved genomic organization of the Hb genes within this lineage, yet with several, lineage‐specific gene duplications. Moreover, for some of the species examined, we identified amino acid substitutions at two sites in the Hbb1 gene as well as length polymorphisms in its regulatory region, which has previously been linked to temperature adaptation in Atlantic cod populations. This study highlights the use of targeted long‐read capture as a versatile approach for comparative genomic studies by generation of a cross‐species genomic resource elucidating the evolutionary history of the Hb gene family across the highly divergent group of codfishes.     

Amenyunnaosides A–C,Three New Neolignans Isolated from Amentotaxus yunnanensis and Their Anti-inflammatory Activities

Phytochemical study on the leaves of Amentotaxus yunnanensis led to the isolation of seventeen phenolic compounds including sixteen neolignans and lignans, and one flavone glycoside. Three among the isolates were previously unreported neolignans and named as amenyunnaosides A–C, respectively. Their structures were elucidated by extensive analyses of HR-ESI-MS, 1D and 2D NMR, and ECD spectra. The isolated neolignans potentially inhibited NO production in LPS-activated RAW264.7 cells with their IC₅₀ values ranging from 11.05 to 44.07 μM, compared to that of the positive control compound, dexamethasone, IC₅₀ value of 16.93 μM. Additionally, amenyunnaoside A dose-dependently reduced production of IL-6 and COX-2 but did not effect to that of TNF-α at concentrations of 0.8, 4, and 20 μM.     

Cloning and sequencing of a novel glutaryl acylase β-subunit gene ofPseudomonas cepacia BY21 from bioinformatics

Pseudomonas cepacia BY21 was found to produce glutaryl acylase that is capable of deacylating glutaryl-7-aminocephalosporanic acid (glutaryl-7-ACA) to 7-aminocephalosporanic acid (7-ACA), which is a starting material for semi-synthetic cephalosporin antibiotics. Amino acids of the reported glutaryl acylases from variousPseudomonas sp. strains show a high similarity (>93% identity). Thus, with the known nucleotide sequences ofPseudomonas glutaryl acylases in GenBank, PCR primers were designed to clone a glutaryl acylase gene fromP. cepacia BY21. The unknown β-subunit gene of glutaryl acylase from chromosomal DNA ofP. cepacia BY21 was cloned successfully by PCR. The β-subunit amino acids ofP. cepacia BY21 acylase (GenBank accession number AY948547) were similar to those ofPseudomonas diminuta KAC-1 acylase except that Asn408 ofP. diminuta KAC-1 acylase was changed to Leu408.     

Genome organization and evolution of the AVR-Pita avirulence gene family in the Magnaporthe grisea species complex

The avirulence (AVR) gene AVR-Pita in Magnaporthe oryzae prevents the fungus from infecting rice cultivars containing the resistance gene Pi-ta. A survey of isolates of the M. grisea species complex from diverse hosts showed that AVR-Pita is a member of a gene family, which led us to rename it to AVR-Pita1. Avirulence function, distribution, and genomic context of two other members, named AVR-Pita2 and AVR-Pita3, were characterized. AVR-Pita2, but not AVR-Pita3, was functional as an AVR gene corresponding to Pi-ta. The AVR-Pita1 and AVR-Pita2 genes were present in isolates of both M. oryzae and M. grisea, whereas the AVR-Pita3 gene was present only in isolates of M. oryzae. Orthologues of members of the AVR-Pita family could not be found in any fungal species sequenced to date, suggesting that the gene family may be unique to the M. grisea species complex. The genomic context of its members was analyzed in eight strains. The AVR-Pita1 and AVR-Pita2 genes in some isolates appeared to be located near telomeres and flanked by diverse repetitive DNA elements, suggesting that frequent deletion or amplification of these genes within the M. grisea species complex might have resulted from recombination mediated by repetitive DNA elements.     

Glucose sensor based on nano-baskets of tin oxide templated in porous alumina by plasma enhanced CVD

A feasibility study of glucose oxidase (GOx) immobilized tin oxide thin films, consisting of nano-baskets, for glucose sensing is presented. The nano-baskets of SnO(2) were grown on in-house fabricated anodized aluminum oxide pores of approximately 80-nm diameter using plasma enhanced chemical vapor deposition (PECVD) at an RF power of 60W. Hydrated stannic chloride was used as a precursor and O(2) (20 sccm) as a reactant gas. The deposition was carried out from 350 to 450 degrees C at a pressure of 0.2 Torr for 15 min each. Deposition at 450 degrees C resulted in crystalline film with basket-like (nano-sized) structure. GOx was immobilized by physical adsorption (soaking films in GOx solution containing 1000 units for 3h). Increase in film conductivity was noticed after GOx immobilization. The immobilized films were found sensitive to glucose (C(2)H(12)O(6), dextrose) concentration from 10 to 360 mg/dl. Sensitivity increases linearly with glucose concentration. Nano-baskets resulted in higher sensitivity in comparison with other structures. From the elemental analyses of the films after GOx immobilization, GOx was found covalently attached with tin oxide, as evident by N 1s peak in the photoelectron spectra. A possible sensing mechanism is presented and discussed.     

Preparation of a gradient biotinylated polyethylene surface to bind streptavidin-FITC

A novel biotinylated gradient surface was designed to bind a streptavidin-FITC. The gradient polyethylene (PE) surface was prepared by a corona treatment with a power increase along the PE length, and successively, biotinylated gradient PE surface was prepared by the reaction of polyethylenimine (PEI) and biotin. Surface properties of the gradient PE surface changed according to PE length and chemical modification. The biotinylated gradient PE surface provided a continuous gradient of streptavidin-FITC through binding of avidin-biotin. The luminosity of fluorescence that corresponds to a streptavidin-bound FITC on the biotinylated gradient PE surface increased gradually on the surface along the PE length.     

High-level recombinant protein production by overexpression of Mlc in Escherichia coli

Escherichia coli excretes acetate during aerobic growth on LB broth containing glucose and growth ceases before depletion of glucose because of the low pH caused by the accumulation of acetate. It has been known that the acetate accumulation is reduced even when E. coli is grown in the presence of high concentration of glucose if Mlc is overexpressed. The intracellular concentration of Mlc is very low in E. coli because of autoregulation and a low efficiency of mlc translation. We constructed various mutants that can express higher levels of Mlc using site-directed mutagenesis and one of the Mlc-overproducing mutant showed reduced glucose consumption rate and low production of acetate. The mutant showed higher foreign gene expression level than that of its parental strain in the presence of glucose. These results suggest that the Mlc overproducing E. coli strain having an improved ability of glucose utilization can be a better host for high-level production of useful recombinant proteins.