Mutation@A Glance: An Integrative Web Application for Analysing Mutations from Human Genetic Diseases

Although mutation analysis serves as a key part in making a definitive diagnosis about a genetic disease, it still remains a time-consuming step to interpret their biological implications through integration of various lines of archived information about genes in question. To expedite this evaluation step of disease-causing genetic variations, here we developed Mutation@A Glance (http://rapid.rcai.riken.jp/mutation/), a highly integrated web-based analysis tool for analysing human disease mutations; it implements a user-friendly graphical interface to visualize about 40 000 known disease-associated mutations and genetic polymorphisms from more than 2600 protein-coding human disease-causing genes. Mutation@A Glance locates already known genetic variation data individually on the nucleotide and the amino acid sequences and makes it possible to cross-reference them with tertiary and/or quaternary protein structures and various functional features associated with specific amino acid residues in the proteins. We showed that the disease-associated missense mutations had a stronger tendency to reside in positions relevant to the structure/function of proteins than neutral genetic variations. From a practical viewpoint, Mutation@A Glance could certainly function as a ‘one-stop’ analysis platform for newly determined DNA sequences, which enables us to readily identify and evaluate new genetic variations by integrating multiple lines of information about the disease-causing candidate genes.     

A method for transient expression in maize endosperm

The ability to screen the functionality of gene constructs in a transient system of appropriate tissues informs the researcher of the potential success of stable transformation. For this purpose, we developed a transient system to test the functionality of endosperm-preferred promoters in maize. Two endosperm-preferred promoters from rice (a globulin and a glutelin promoter) were employed. Ears of Zea mays L. were harvested at 17 d after pollination, surface sterilized and the endosperm excised. Using Agrobacterium tumefaciens co-cultivation and sonication, transient expression of the target genes was detected after 4 and 5 d. We demonstrate expression of CBH I and CHB II (both exo-cellulases) up to 1.7% TSP, under the rice globulin and glutelin promoters.     

Production of exopolysaccharides by Agrobacterium sp. CFR-24 using coconut water - a byproduct of food industry

AIMS: The work is intended to explore the suitability of underutilized coconut water (a byproduct of food industry) for the production of exopolysaccharides (EPS) by Agrobacterium sp. CFR 24. METHODS AND RESULTS: Besides checking the suitability of coconut water for the production of water-soluble (WS) and water-insoluble (WIS) EPS, certain fermentation parameters, such as initial pH, incubation period and kinetics of EPS production were investigated. The coconut water medium was found to support the production of both types of EPS. The optimal initial pH and temperature was found to be 6.0 and 30 degrees C, respectively. In shake flask (150 rev min(-1)) studies, high-cell density inoculum resulted in the production of 11.50 g l(-1) of WIS-EPS and 4.01 g l(-1) WS-EPS after 72 and 96 h of fermentation, respectively. CONCLUSIONS: Coconut water was found suitable for the production of microbial EPS by Agrobacterium sp. CFR 24 strain. Under optimum conditions, it produced a good amount of WIS-EPS, which is comparable with that of the sucrose medium (11 g l(-1)). SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first report on the use of coconut water as a fermentation medium for the production of any microbial EPS. Besides producing value-added products, use of this food industry byproduct, which is often being drained out, can significantly reduce the problem of environmental pollution.     

Expression of Xanthomonas campestris pv. vesicatoria type III effectors in yeast affects cell growth and viability

The gram-negative bacterium Xanthomonas campestris pv. vesicatoria is the causal agent of spot disease in tomato and pepper. X. campestris pv. vesicatoria pathogenicity depends on a type III secretion system delivering effector proteins into the host cells. We hypothesized that some X. campestris pv. vesicatoria effectors target conserved eukaryotic cellular processes and examined phenotypes induced by their expression in yeast. Out of 21 effectors tested, 14 inhibited yeast growth in normal or stress conditions. Viability assay revealed that XopB and XopF2 attenuated cell proliferation, while AvrRxo1, XopX, and XopE1 were cytotoxic. Inspection of morphological features and DNA content of yeast cells indicated that cytotoxicity caused by XopX and AvrRxo1 was associated with cell-cycle arrest at G0/1. Interestingly, XopB, XopE1, XopF2, XopX, and AvrRxo1 that inhibited growth in yeast also caused phenotypes, such as chlorosis and cell death, when expressed in either host or nonhost plants. Finally, the ability of several effectors to cause phenotypes in yeast and plants was dependent on their putative catalytic residues or localization motifs. This study supports the use of yeast as a heterologous system for functional analysis of X. campestris pv. vesicatoria type III effectors, and sets the stage for identification of their eukaryotic molecular targets and modes of action.     

Comprehensive proteomic analysis of human bile

Bile serves diverse functions from metabolism to transport. In addition to acids and salts, bile is composed of proteins secreted or shed by the hepatobiliary system. Although there have been previous efforts to catalog biliary proteins, an in-depth analysis of the bile proteome has not yet been reported. We carried out fractionation of non-cancerous bile samples using a multipronged approach (SDS-PAGE, SCX and OFFGEL) followed by MS analysis on an LTQ-Orbitrap Velos mass spectrometer using high resolution at both MS and MS/MS levels. We identified 2552 proteins - the largest number of proteins reported in human bile till date. To our knowledge, there are no previous studies employing high-resolution MS reporting a more detailed catalog of any body fluid proteome in a single study. We propose that extensive fractionation coupled to high-resolution MS can be used as a standard methodology for in-depth characterization of any body fluid. This catalog should serve as a baseline for the future studies aimed at discovering biomarkers from bile in gallbladder, hepatic, and biliary cancers.     

A proteogenomic approach to map the proteome of an unsequenced pathogen - Leishmania donovani

Visceral leishmaniasis or kala azar is the most severe form of leishmaniasis and is caused by the protozoan parasite Leishmania donovani. There is no published report on L. donovani genome sequence available till date, although the genome sequences of three related Leishmania species are already available. Thus, we took a proteogenomic approach to identify proteins from two different life stages of L. donovani. From our analysis of the promastigote (insect) and amastigote (human) stages of L. donovani, we identified a total of 22,322 unique peptides from a homology-based search against proteins from three Leishmania species. These peptides were assigned to 3711 proteins in L. infantum, 3287 proteins in L. major, and 2433 proteins in L. braziliensis. Of the 3711 L. donovani proteins that were identified, the expression of 1387 proteins was detectable in both life stages of the parasite, while 901 and 1423 proteins were identified only in promastigotes and amastigotes life stages, respectively. In addition, we also identified 13 N-terminally and one C-terminally extended proteins based on the proteomic data search against the six-frame translated genome of the three related Leishmania species. Here, we report results from proteomic profiling of L. donovani, an organism with an unsequenced genome.     

AtPLAI is an acyl hydrolase involved in basal jasmonic acid production and Arabidopsis resistance to Botrytis cinerea

Intracellular phospholipase A2 (PLA2) plays an important role in regulating oxylipin biosynthesis in mammals, but the molecular and biochemical nature of intracellular PLA2 is not well understood in plants. Arabidopsis thaliana gene At1g61850 (AtPLAI) encodes a 140-kDa protein that is most similar to mammalian calcium-independent PLA2, and additionally contains leucine-rich repeats and Armadillo repeats. AtPLAI hydrolyzes phospholipids at both the sn-1 and sn-2 positions, but prefers galactolipids to phospholipids as substrates. Profiling of lipid species altered in response to the necrotrophic fungus Botrytis cinerea revealed decreases in the levels of phosphatidylglycerol and digalactosyldiacylglycerol, suggesting that hydrolysis of plastidic polar lipids might provide precursors for pathogen-induced jasmonic acid (JA) production. Disruption of AtPLAI by T-DNA insertion reduced the basal level of JA, but did not impede pathogen-induced production of JA, free linolenic acid, or hydrolysis of plastidic lipids. Still, AtPLAI-deficient plants exhibited more damage than wild type plants after B. cinerea infection, and pretreatment of plants with methyl jasmonate alleviated pathogen damage to the mutant plants. The study shows that AtPLAI is an acyl hydrolase, rather than a specific phospholipase A. AtPLAI is involved in basal JA production and Arabidopsis resistance to the necrotrophic fungus B. cinerea.