Raghvendra Pratap Singh

Structure prediction and analysis of MxaF from obligate, facultative and restricted facultative methylobacterium

Methylobacteria are ubiquitous in the biosphere which are capable of growing on C1 compounds such as formate, formaldehyde, methanol and methylamine as well as on a wide range of multi-carbon growth substrates such as C2, C3 and C4 compounds due to the methylotrophic enzymes methanol dehydrogenase (MDH). MDH is performing these functions with the help of a key protein mxaF. Unfortunately, detailed structural analysis and homology modeling of mxaF is remains undefined. Hence, the objective of this research is the characterization and three dimensional modeling of mxaF protein from three different methylotrophs by using I-TASSER server. The predicted model were further optimize and validate by Profile 3D, Errat, Verifiy3-D and PROCHECK server. Predicted and best evaluated models have been successfully deposited to PMDB database with PMDB ID PM0077505, PM0077506 and PM0077507. Active site identification revealed 11, 13 and 14 putative functional site residues in respected models. It may play a major role during protein-protein, and protein-cofactor interactions. This study can provide us an ab-initio and detail information to understand the structure, mechanism of action and regulation of mxaF protein.

Structure prediction and evolution of a halo-acid dehalogenase of Burkholderia mallei.

Environmental pollutants containing halogenated organic compounds e.g. haloacid, can cause a plethora of health problems. The structural and functional analyses of the gene responsible of their degradation are an important aspect for environmental studies and are important to human well-being. It has been shown that some haloacids are toxic and mutagenic. Microorganisms capable of degrading these haloacids can be found in the natural environment. One of these, a soil-borne Burkholderia mallei posses the ability to grow on monobromoacetate (MBA). This bacterium produces a haloacid dehalogenase that allows the cell to grow on MBA, a highly toxic and mutagenic environmental pollutant. For the structural and functional analysis, a 346 amino acid encoding protein sequence of haloacid dehalogenase is retrieve from NCBI data base. Primary and secondary structure analysis suggested that the high percentage of helices in the structure makes the protein more flexible for folding, which might increase protein interactions. The consensus protein sub-cellular localization predictions suggest that dehalogenase protein is a periplasmic protein 3D2GO server, suggesting that it is mainly employed in metabolic process followed by hydrolase activity and catalytic activity. The tertiary structure of protein was predicted by homology modeling. The result suggests that the protein is an unstable protein which is also an important characteristic of active enzyme enabling them to bind various cofactors and substrate for proper functioning. Validation of 3D structure was done using Ramachandran plot ProsA-web and RMSD score. This predicted information will help in better understanding of mechanism underlying haloacid dehalogenase encoding protein and its evolutionary relationship.

Symbiotic characteristics of Bradyrhizobium diazoefficiens USDA 110 mutants associated with shrubby sophora (Sophora flavescens) and soybean (Glycine max)

Site-specific insertion plasmid pVO155 was used to knockout the genes involved in the alternation of host range of strain Bradyrhizobium diazoefficiens USDA 110 from its original determinate-nodule-forming host soybean (Glycine max), to promiscuous and indeterminate-nodule-forming shrubby legume sophora (Sophora flavescens). Symbiotic phenotypes of these mutants inoculated to these two legumes, were compared to those infected by wild-type strain USDA 110. Six genes of the total fourteen Tn5 transposon mutated genes were broken using the pVO155 plasmid. Both Tn5 and pVO155-inserted mutants could nodulate S. flavescens with different morphologies of low-efficient indeterminate nodules. One to several rod or irregular bacteroids, containing different contents of poly-β-hydroxybutyrate or polyphosphate were found within the symbiosomes in nodulated cells of S. flavescens infected by the pVO155-inserted mutants. Moreover, none of bacteroids were observed in the pseudonodules of S. flavescens, infected by wild-type strain USDA 110. These mutants had the nodulation ability with soybean but the symbiotic efficiency reduced to diverse extents. These findings enlighten the complicated interactions between rhizobia and legumes, i. e., mutation of genes involved in metabolic pathways, transporters, chemotaxis and mobility could alter the rhizobial entry and development of the bacteroid inside the nodules of a new host legume.

Grape berry surface bacterial microbiome: impact from the varieties and clones in the same vineyard from central China

Bacterial microbiome on grape berry surface may play an important role in grape quality and health. This study aims to investigate the impact of grape varieties and clones on grape berry surface bacterial microbiome from the same vineyard.

Mycorrhiza: Creating Good Spaces for Interactions

Soil is a complicate environment, where complex systems of multiple interactions between the organisms take place. Plant health is majorly determined by these vital interactions in the soil. The ubiquitous arbuscular mycorrhizal (AM) fungi and a number of microbes interact synergistically to enhance the fitness of each other as well as plants they are associated with. Both the interacting partners are cross facilitators, where AM fungi provide suitable specialized ecological niches as well as nutrients for bacteria, and in turn bacteria improves the mycorrhization, provides pool of available P and N, and helps in management of biotic and abiotic stresses. Given the importance of AM and the interacting microbes in low-input sustainable agriculture, it is important to understand their interactions.

Biofuels - The Way Ahead

Depletion of petroleum derived fuel and environmental concern have emphasized the need to produce sustainable renewable fuels and chemicals. Biofuel from renewable sources can be an alternative to impart a remarkable role for maintaining sustainability and security in energy sector. A complete substitution of petroleum derived fuels by biofuel is impossible yet, marginal replacement of fossil fuels by biofuels can delay the depletion of petroleum resources and abate the radical climate change caused by automotive pollutants. Biofuels are broadly classified into three categories: first generation biofuels-from biomass that is usually edible; second generation biofuels-from lignocellulosic feedstocks or municipal wastes; third generation biofuelsfrom microorganisms, majorly from algae. In terms of food security, the use of those energy crops which are used as food products for biofuel production is of concern. Biofuel production using microalgae is attractive prospect in this scenario. The review presents an overview of the usage and sustainability challenges of biofuels.