Detecting the form of selection in the outer membrane protein C of Enterobacter aerogenes strains and Salmonella species

The types of selective pressure operating on the outer membrane protein C (ompC) of Enterobacter aerogenes strains, the causative agent for nosocomial infections, and Salmonella sp., the hazardous pathogen are investigated using the maximum likelihood-based codon substitution models. Although the rate of amino acid replacement to the silent substitution (omega) across the entire codon sites of ompC of E. aerogenes (omega=0.3194) and Salmonella sp. (omega=0.2047) indicate that the gene is subjected to purifying selection (i.e. omega<1), approximately 3.7% of ompC codon sites in E. aerogenes (omega=21.52) are under the influence of positive Darwinian selection (i.e. omega>1). Such contrast in the intensity of selective pressures in both pathogens could be associated with the differential response to the adverse environmental changes. In E. aerogenes, majority of the positively selected sites are located in the hypervariable cell-surface-exposed domains whereas the trans-membrane domains are functionally highly constrained.     

A Link between Arabinose Utilization and Oxalotrophy in Bradyrhizobium japonicum

Rhizobia have a versatile catabolism that allows them to compete successfully with other microorganisms for nutrients in the soil and in the rhizosphere of their respective host plants. In this study, Bradyrhizobium japonicum USDA 110 was found to be able to utilize oxalate as the sole carbon source. A proteome analysis of cells grown in minimal medium containing arabinose suggested that oxalate oxidation extends the arabinose degradation branch via glycolaldehyde. A mutant of the key pathway genes oxc (for oxalyl-coenzyme A decarboxylase) and frc (for formyl-coenzyme A transferase) was constructed and shown to be (i) impaired in growth on arabinose and (ii) unable to grow on oxalate. Oxalate was detected in roots and, at elevated levels, in root nodules of four different B. japonicum host plants. Mixed-inoculation experiments with wild-type and oxc-frc mutant cells revealed that oxalotrophy might be a beneficial trait of B. japonicum at some stage during legume root nodule colonization.     

Molecular Evolutionary and Epidemiological Dynamics of Genotypes 1G and 2B of Rubella Virus

Rubella Virus (RV), which causes measles-like rashes in children, puts millions of infants at risk of congenital defects across the globe. Employing phylogenetic approaches to the whole genome sequence data and E1 glycoprotein sequence data, the present study reports the substitution rates and dates of emergence of all thirteen previously described rubella genotypes, and gains important insights into the epidemiological dynamics of two geographically widely distributed genotypes 1G and 2B. The overall nucleotide substitution rate of this non-vector-borne RV is in the order of 10⁻³ substitutions/site/year, which is considerably higher than the substitution rates previously reported for the vector-borne alphaviruses within the same family. Currently circulating strains of RV share a common ancestor that existed within the last 150 years, with 95% Highest Posterior Density values ranging from 1868 to 1926 AD. Viral strains within the respective genotypes began diverging between the year 1930 s and 1980 s. Both genotype 1G and 2B have shown a decline in effective number of infections since 1990 s, a period during which mass immunization programs against RV were adapted across the globe. Although both genotypes showed some extent of spatial genetic structuring, the analyses also depicted an inter-continental viral dispersal. Such a viral dispersal pattern could be related to the migration of infected individuals across the regions coupled with a low coverage of MMR vaccination.     

Computational and Functional Characterization of Angiogenin Mutations,and Correlation with Amyotrophic Lateral Sclerosis

The Angiogenin (ANG) gene is frequently mutated in patients suffering from the neurodegenerative disease - amyotrophic lateral sclerosis (ALS). Most of the ALS-causing mutations in Angiogenin affect either its ribonucleolytic or nuclear translocation activity. Here we report the functional characterization of two previously uncharacterized missense mutations in Angiogenin - D22G and L35P. We predict the nature of loss-of-function(s) in these mutants through our previously established Molecular Dynamics (MD) simulation extended to 100 ns, and show that the predictions are entirely validated through biochemical studies with wild-type and mutated proteins. Based on our studies, we provide a biological explanation for the loss-of-function of D22G-Angiogenin leading to ALS, and suggest that the L35P-Angiogenin mutation would probably cause ALS symptoms in individuals harboring this mutation. Our study thus highlights the strength of MD simulation-based predictions, and suggests that this method can be used for correlating mutations in Angiogenin or other effector proteins with ALS symptoms.     

Effect of algalization on seed germination of vegetable crops

Soaking seeds of cucumber and pumpkin with an extract of Westiellopsis prolifica, an N₂-fixing cyanobacterium, promoted germination and their subsequent growth and development. An extract of Lyngbya sp., a non-N₂-fixing cyanobacterium, had no significant effect.The authors are with the Algal Physiology Laboratory, Department of Botany, Berhampur University, Berhampur-760007, Orissa, India.     

Antimicrobial activity and molecular characterization of an endophytic fungus, Quambalaria sp. isolated from Ipomoea carnea

An endophytic fungus displaying considerable antimicrobial activity was isolated from stem tissue of an invasive plant species, Ipomoea carnea. The fungus was identified as Quambalaria sp. and confirmed by ITS rDNA sequence analysis. A BLAST search result of the sequence indicated 97 % homology with Quambalaria cyanescens. Crude metabolites of the fungus showed considerable antimicrobial activity against a panel of clinically significant microorganisms. The metabolites showed highest in vitro activity against Shigella dysenteriae followed by Escherichia coli and Candida albicans. Optimum metabolites production required neutral pH and a 15-day incubation period. Bark extracts amended with fungal media demonstrated higher antimicrobial activity. Optimum metabolites activity was recorded in Czapek Dox broth amended with leaf extracts (CDB + LE) of the host plant. The metabolites showed UV λ-max in ethyl acetate at 284.6 nm with an absorbance value of 1.093. Phylogenetic tree generated by the Maximum Parsimony method showed clustering of our isolate with Q. cyanescens with supported bootstrap of 65 %. Species of Quambalaria are pathogens to Eucalyptus and occurrence of this fungus as endophytes support it to be a latent pathogen. Sequence base analysis and RNA secondary structure study also confirmed such a relationship. Secondary structural features like two hinges and a 5’ dangling end were found to be unique to our isolate. These structural features can also be used as potential barcodes for this fungus. The findings indicate that invasive plant species can be a reliable source of novel endophytes with rich antimicrobial metabolites. The study also validates the assumption that endophytes can become parasites and share a close affinity.     

Pathogen-driven Adaptive Evolution of Myxovirus Resistance (Mx) Genes in Fishes

Myxovirus resistance (Mx) proteins, which belong to the dynamin super-family, are known to inhibit RNA viral replication in a wide range of taxonomic groups, including fishes. Given their crucial role in host immune defense, the key amino acid residues in the GTP effector domain (GED) near the C-terminus are expected to evolve adaptively in order to protect the host against invading viral pathogens. The present study reveals the role of recombination and positive selection in the evolution of Mx proteins in fishes. While the GTP-binding domain in the N-terminal domain has experienced purifying selection, several amino acid residues in GED have evolved under positive selection, thus indicating adaptive evolution. Given the antiviral activity of GED, the adaptive evolutionary changes that were observed in this region are therefore predicted to be pathogen-driven.