Symbiotic Nitrogen Fixation-A Bioinformatics Perspective

Sur, Saubashya; Bothra, Asim K.; Sen, Arnab

doi:10.3923/biotech.2010.257.273

Cited by 12 publications

(13 citation statements)

References 21 publications

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“…While the role of grain legumes in increasing soil nitrogen cannot be denied, other macro-and micronutrients cannot be ignored. A deficiency of other nutrients such as phosphorous, boron and molybdenum may hinder nitrogen fixation [44,45,88]. In addition, subsistence farmers often do not use inoculants to stimulate the formation of nitrogen-fixing nodules.…”

Section: Agronomymentioning

confidence: 99%

“…While the Roman and Egyptian early settlers observed that in the presence of legume species soil was somewhat nutrient rich and plants were greener, it was only in 1888 when German scientists discovered that it was the legume root nodule that was responsible for this [44]. Since then, this made grain legume crops of particular interest in faming systems, especially under marginal conditions [45][46][47].…”

Section: Ecologymentioning

confidence: 99%

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Expounding the Value of Grain Legumes in the Semi- and Arid Tropics

2017

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Approximately 70% of the population in the semi-and arid tropics reside in rural areas and depend on agriculture for their livelihood. Crop production is primarily focused on a few starchy staple crops. While this can ensure adequate calories, it inadvertently neglects the need for dietary diversity. Consequently, food and nutritional insecurity remains prevalent in the semi-and arid tropics. We reviewed the legume value chain with the aim to identify opportunities and challenges to unlocking their value and promoting them in the tropics. Several grain legumes are rich in proteins and micronutrients. They also possess adaptability to marginal environmental conditions such as drought and low input systems which typify rural landscapes. Adaptability to abiotic stresses such as drought makes them key to agriculture in areas that will receive less rainfall in the future. However, this potential was currently not being realized due to a range of challenges. Aspects related to their seed systems, production, post-harvest handling and marketing remain relatively under-researched. This was especially true for minor legumes. There is a need for transdisciplinary research which will address the entire value chain, as has been done for major starchy crops. This could also unlock significant economic opportunities for marginalized groups such as women. This will unlock their value and allow them to contribute meaningfully to food and nutrition security as well as sustainable and resilient cropping systems.

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Section: Agronomymentioning

confidence: 99%

Section: Ecologymentioning

confidence: 99%

Expounding the Value of Grain Legumes in the Semi- and Arid Tropics

2017

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“…The study regarding functional genomics and proteomics of diaztrophs has great importance in twenty-first century (Sur et al, 2010 ). The works related to the genetics of nif was first initiated in Klebseilla , where organization of nif genes were reported (Arnold et al, 1988 ).…”

Section: Discussionmentioning

confidence: 99%

nifPred: Proteome-Wide Identification and Categorization of Nitrogen-Fixation Proteins of Diaztrophs Based on Composition-Transition-Distribution Features Using Support Vector Machine

Meher

Sahu

Mohanty³

et al. 2018

Front. Microbiol.

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As inorganic nitrogen compounds are essential for basic building blocks of life (e.g., nucleotides and amino acids), the role of biological nitrogen-fixation (BNF) is indispensible. All nitrogen fixing microbes rely on the same nitrogenase enzyme for nitrogen reduction, which is in fact an enzyme complex consists of as many as 20 genes. However, the occurrence of six genes viz., nifB, nifD, nifE, nifH, nifK, and nifN has been proposed to be essential for a functional nitrogenase enzyme. Therefore, identification of these genes is important to understand the mechanism of BNF as well as to explore the possibilities for improving BNF from agricultural sustainability point of view. Further, though the computational tools are available for the annotation and phylogenetic analysis of nifH gene sequences alone, to the best of our knowledge no tool is available for the computational prediction of the above mentioned six categories of nitrogen-fixation (nif) genes or proteins. Thus, we proposed an approach, which is first of its kind for the computational identification of nif proteins encoded by the six categories of nif genes. Sequence-derived features were employed to map the input sequences into vectors of numeric observations that were subsequently fed to the support vector machine as input. Two types of classifier were constructed: (i) a binary classifier for classification of nif and non-nitrogen-fixation (non-nif) proteins, and (ii) a multi-class classifier for classification of six categories of nif proteins. Higher accuracies were observed for the combination of composition-transition-distribution (CTD) feature set and radial kernel, as compared to the other feature-kernel combinations. The overall accuracies were observed >90% in both binary and multi-class classifications. The developed approach further achieved >92% accuracy, while evaluated with blind (independent) test datasets. The developed approach also produced higher accuracy in identifying nif proteins, while evaluated using proteome-wide datasets of several species. Furthermore, we established a prediction server nifPred (http://webapp.cabgrid.res.in/nifPred) to assist the scientific community for proteome-wide identification of six categories of nif proteins. Besides, the source code of nifPred is also available at https://github.com/PrabinaMeher/nifPred. The developed web server is expected to supplement the transcriptional profiling and comparative genomics studies for the identification and functional annotation of genes related to BNF.

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“…Thus, most of the studies in this field of research were conducted to optimize the N2 fixation activities (Rebah et al, 2007). The most important factor for effective BNF process is the occurrence of nitrogenase enzyme that catalyse the fixation process (Sur et al, 2010). The reaction involved is as follows (Giller, 2001):…”

Section: Introductionmentioning

confidence: 99%

Estimation of Nitrogenase Enzyme Activities and Plant Growth of Legume and Non-legume Inoculated with Diazotrophic Bacteria

Salwani¹,

Amir²,

Najimudin³

2012

MJM

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Biological Nitrogen Fixation (BNF) process benefits the agriculture sector especially for reducing cost of nitrogen fertilizer. In the process, the diazotrophs convert N2 into ammonia (NH3) which is useable by plants. The BNF process is catalysed by nitrogenase enzyme that involved protons and electrons together with evolution of H2 therefore, the assessment of N2 fixation is also available via H2 production and electron allocation analysis. Thus, the aims of this experiment were to estimate the nitrogenase enzyme activities and observe the influence of diazothrophs on growth of legume (soybean) and non legume (rice) plants. Host plants were inoculated with respective inocula; Bradyrhizobium japonicum (strain 532C) for soybean while Azospirillum brasilense (Sp7) and locally isolated diazotroph (isolate 5) for rice. At harvest, the plants were observed for plant growth parameters, H2 evolution, N2 fixation and electron allocation coefficient (EAC) values. The experiment recorded N2 fixation activities of inoculated soybean plants at 141.2 µmol N2 h-1 g-1 dry weight nodule, and the evolution of H2 at 144.4 µmol H2 h-1 g-1 dry weight nodule. The electron allocation coefficient (EAC) of soybean was recorded at 0.982. For inoculated rice plants, none of the observations was successfully recorded. However, results for chlorophyll contents and plant dry weight of both plants inoculated with respective inocula were similar to the control treatments supplied with full nitrogen fertilization (+N). The experiment clearly showed that inoculation of diazotrophic bacteria could enhance growth of the host plants similar to plants treated with nitrogenous fertilizer due to efficient N2 fixation process

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Symbiotic Nitrogen Fixation-A Bioinformatics Perspective

Cited by 12 publications

References 21 publications

Expounding the Value of Grain Legumes in the Semi- and Arid Tropics

Expounding the Value of Grain Legumes in the Semi- and Arid Tropics

nifPred: Proteome-Wide Identification and Categorization of Nitrogen-Fixation Proteins of Diaztrophs Based on Composition-Transition-Distribution Features Using Support Vector Machine

Estimation of Nitrogenase Enzyme Activities and Plant Growth of Legume and Non-legume Inoculated with Diazotrophic Bacteria

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