In silico analysis of a Rhizobium sp. RC1 putative haloalkanoic permease sequence motif and classification

Aims@#The transport of haloalkanoic acids (haloacids) is important in the metabolism of haloacid pollutants by bacteria. In this study, a computational analysis of Rhizobium sp. RC1 haloacid permease (DehrP) amino acid sequence was conducted to identify its subfamily, sequence motifs and evolutionary position among closely related transporters. @*Conclusion, significance and impact of study@#Blast search in the Pfam and Transmembrane Classification Databases was used to establish the classification and the subfamily of DehrP. Clustal omega sequence alignment approach and MEME Suite motif-based analysis tools were used to locate the transporter motifs of DehrP. Dotplots of DehrP sequence was computed using the EMBOSS Dotmatcher. MEGA7 software was used to analyze the phylogenetic position of DehrP among closely related symporters in the Transmembrane Classification Database. Comparative analysis by Pfam shows that DehrP is a member of the Major Facilitator Superfamily (#2.A.1). PSI-Blast against the Transmembrane Classification Database shows that DehrP is significantly aligned with a subfamily of transporters called the Metabolite: H+ Symporters (#2.A.1.6). DehrP has six similar sequence motifs with the Metabolite: H+ Symporter proteins including the functional motif of GXXXDRXGRR. DehrP is evolutionarily related to Burkholderia caribensis MBA4 Haloacid: H+ Symporters (Dehp2 and Deh4p). @*Methodology and results@#Based on sequence similarity, DehrP is a Major Facilitator Superfamily protein that belongs to the Metabolite: H+ Symporter protein subfamily which might coordinate the transport of a haloacid coupled with a proton (H+). Mutagenesis of DehrP sequence motifs might be useful in the engineering of Rhizobium sp. RC1 for efficient uptake and degradation of haloacids.

In silico molecular analysis of novel L-specific dehalogenase from Rhizobium sp. RC1

Aims: This study presents the first structural model and proposed the identity of four important key amino acid residues, Asp13, Arg51, Ser131 and Asp207 for the stereospecific haloalkanoic acid dehalogenase from Rhizobium sp. RC1. Methodology and results: The enzyme was built using a homology modeling technique; the structure of crystallized LDEX YL from Pseudomonas sp. strain YL as a template. Model validation was performed using PROCHECK to generate the Ramachandran plot. The results showed 80.4% of its residues were located in the most favoured regions suggested that the model is acceptable. Molecular dynamics simulation of the model protein was performed in water for 10 nanoseconds in which Na+ was added to neutralize the negative charge and achieved energy minimization. The energy value and RMSD fluctuation of Cα backbone of the model were computed and confirmed the stability of the model protein. Conclusion, significance and impact of study: In silico or computationally based function prediction is important to complement with future empirical approaches. L-haloacid dehalogenase (DehL), previously isolated from Rhizobium sp. RC1 was known to degrade halogenated environmental pollutants. However, its structure and functions are still unknown. This structural information of DehL provides insights for future work in the rational design of stereospecific haloalkanoic acid dehalogenases.

Resposta de cultivares de feijoeiro-comum à inoculação das sementes com duas estirpes de rizóbio / Common bean cultivars response to seed inoculation with two rhizobium strains

Fixação simbiótica de nitrogênio pode ser uma alternativa para reduzir, ou mesmo substituir, a adubação nitrogenada do feijoeiro-comum, cultura na qual ainda há descrédito quanto aos benefícios da inoculação e que se caracteriza por aplicações de altas doses de N mineral. Com o objetivo de verificar a resposta de cultivares de feijoeiro-comum à inoculação das sementes com duas estirpes de rizóbio, foram conduzidos dois experimentos de campo na safra de inverno 2010 (Patos de Minas e Uberaba, MG). Utilizou-se o delineamento em blocos casualizados, com três repetições e esquema fatorial 8 x 3, envolvendo oito cultivares (União, Madrepérola, Supremo, Ouro Negro, Ouro Vermelho e Majestoso) e três tipos de inoculação (sementes não inoculadas e estirpes CIAT 899T e UFLA 04-173). Na floração, avaliaram-se o número e massa seca de nódulos, massa seca de parte aérea e teor e acúmulo de nitrogênio (N) na parte aérea e, na colheita, o rendimento de grãos com seus componentes primários, teor e acúmulo de N nos grãos. Constatou-se que as populações nativas promovem nodulação equivalente à das estirpes inoculadas. As estirpes CIAT 899T e UFLA 04-173 favorecem o crescimento vegetativo do feijoeiro. A estirpe CIAT 899T proporciona maior número de vagens e maior massa de grãos que a estirpe UFLA 04-173, e em Uberaba também proporciona maior rendimento de grãos. Quando a inoculação é realizada com a estirpe UFLA 04-173, as cultivares diferem quanto ao teor foliar de N. As cultivares Madrepérola, Ouro Negro e Ouro Vermelho apresentam mais nódulos e maior massa seca de parte aérea, além de maior produtividade em Patos de Minas. Ouro Negro situa-se entre as mais produtivas em Uberaba. Em Uberaba há maior acúmulo de matéria seca de nódulos e de parte aérea, mas o ambiente Patos de Minas resulta em maiores valores do rendimento de grãos e componentes.

The symbiotic nitrogen fixation can be an alternative to reduce, or even replace, the nitrogen (N) fertilization of the common bean crop, characterized by application of high doses of this nutrient. This work aimed to verify the response of common bean cultivars to the seed inoculation with two Rhizobium strains, conducting two field experiments in the winter-spring crop of 2010, at Patos de Minas and Uberaba, Minas Gerais State, Brazil. The experiment had a randomized block design, with three replications and a 8 x 3 factorial squemme, involving eight cultivars and three levels of inoculation. At flowering, it was evaluated the number of nodules, nodules dry mass, shoots dry weight, N content and accumulation in shoots and, at harvest, the grain yield and its primary components (100 grains weight, number of pods per plant, number of grains per pod) and the N content and accumulation in the grains. The Madrepérola, Ouro Negro and Ouro Vermelho cultivars present the highest number of nodules and higher dry mass; in Patos de Minas, the same cultivars show higher productivity, but in Uberaba, only Ouro Negro cultivar is among the most productive. In Uberaba there is the greater nodules dry weight and higher shoots dry matter, but the most favorable conditions in Patos de Minas results in higher values for grain yield and its components. In Uberaba, the CIAT 899T strain overcomes the UFLA 04-173 strain in relation to grain yield. In both environments, the CIAT 899T strain also shows superiority in number of pods per plant and weight of one hundred grains.

Studies on the Fermentation Conditions and Anti-tumor Effect of Exopolysaccharide from Rhizobium sp.N613 / 微生物学通报

The potential of Rhizobium sp. N613 to produce the exopolysaccharide (REPS) was studied in this paper. Using an orthogonal design in a flask-shaker culture system, the fermentation medium and conditions of synthesizing REPS were optimized. Based on these results, the fermentation kinetic parameters were obtained in the batch fermentation with a 10L fermentor. The REPS yield of 11.31g/L was achieved by metabolic regulation during 40 h fed-batch fermentation. Transplanted tumor models of sarcoma 180 in mice were used to evaluate the anti-tumor effect. The result of anti-tumor activities showed that inhibition rate was 53.40%, when dose of REPS was 5mg/kg. These results indicate that REPS has the following properties: the short duration of fermentation, the high yield, the low cost, the effective immunocompetence and thickening. Thus, REPS has the value of development and application.