Characterization of Biomineralizing and Plant Growth-Promoting Attributes of Lithobiontic Bacteria.

The application of mineral-solubilizing, plant growth-promoting bacteria as inoculants offers a promising alternative to chemical fertilizers. In the present study, lithic bacterial isolates were evaluated for mineral solubilization and plant growth-promoting potential. Among the 57 lithic bacterial isolates associated with different rock samples collected from various locations in Meghalaya, India, nine K-solubilizing isolates, six S-solubilizing isolates, five P- and Si-solubilizing isolates, and three Zn-solubilizing isolates with notable indole-3-acetic acid and siderophore production, and ACC deaminase activity were selected for further study. Based on 16S rRNA gene sequence analysis, isolates were affiliated to nine different genera (Arthrobacter, Acinetobacter, Pseudomonas, Halopseudomonas, Bacillus, Neobacillus, Peribacillus, Pantoea, and Priestia). On performing rice seed germination potentials, Pantoea agglomerans BL26, Priestia megaterium BL9, Bacillus subtilis GP2, Halopseudomonas xinjiangensis BL29, and Pseudomonas sp. BM1 were selected for in vitro pot experiments, being the most potent isolates. Following inoculation, all five isolates were found to significantly enhance growth of rice plants (P < 0.05). The maximum shoot length increased due to P. megaterium BL9, the maximum root length increased due to H. xinjiangensis BL29, and the maximum plant fresh weight increased due to P. megaterium BL9. The findings concluded that these five lithic bacterial isolates have potent plant growth-promoting potential with possible prospection through field trials. To the best of available literature, this is a first report on the characterization of lithic bacterial isolates as mineral solubilizers and plant growth promoters.

Beyond the Cereal Box: Breeding Buckwheat as a Strategic Crop for Human Nutrition.

While intensification of farming systems is essential for achieving the Millennium Development Goal of "Zero hunger", issues such as availability of nutritious foods would demand increased attention if any long-term form of food security is to be achieved. Since wheat, rice and maize have reached near to 80 percent of their yield potential and reliance on these crops alone would not be sufficient to close the gap between demand and supply, there is a need to bring other climate-resilient and nutritionally dense crops into agricultural portfolio. Buckwheat (Fagopyrum spp.) has attracted considerable interest amongst global scientific community due to its nutritional and pharmaceutical properties. The gluten free nature of buckwheat, nutritionally balanced amino acid composition of its grain protein, and high levels of anti-oxidants, such as rutin, makes buckwheat an important crop with immense nutraceutical benefits. However, a key challenge in buckwheat cultivation is the variation in yield between years, which impacts the entire value chain. Current information on buckwheat indicates existence of significant phenotypic variation for agronomic and nutritional traits. However, genetic bottlenecks in conventional breeding restrict effective utilization of the existing diversity in mainstreaming buckwheat cultivation. Availability of high density buckwheat genome map for both the cultivated species viz. F. esculentum and F. tataricum would add to our understanding of genetic basis of their agronomic traits. The review examines the potential of buckwheat as a strategic crop for human nutrition and prospects of effective exploitation genomic information of common and Tartary buckwheat for genome assisted breeding.

Wx alleles in rice: relationship with apparent amylose content of starch and a possible role in rice domestication.

The Waxy locus of rice is a highly polymorphic region embedded with microsatellite repeats in the 5'UTR leader intron 1 region, 23-bp duplication (wx motif) in exon 2, SNPs in exons 4, 6 and 10, p-Sine-r2 element in intron 1 and TnR-1 element in inton 13. Of the 80 polymorphic sites detected on the Wx gene, 24 are located in p-Sine-r2 and TnR-1 elements, revealing a higher substitution rate of bases in these two regions. All the cultivars with chalky endosperm had the 5'-AGTTATA-3' haplotype in intron 1 and 'A' to 'G' substitution at ?497 in exon 4. The AAC of starch from grains of all the accessions showed strong correlation (r=0.967) with GBSS-I activity in the grains. Based on the polymorphic sites of the Waxy locus and the GBSS-I activities, six allelic variants were defined which included wx, Wxop, Wxb, Wxin, Wxa2 and Wxa1, respectively, corresponded to glutinous, very low, low, intermediate, highII and highI amylose classes. Phylogenetic tree developed from alignment matrix of nucleotide sequences of the Waxy locus identified wx, Wxb and Wxin alleles with japonica lineage of Oryza sativa and the Wxop, Wxa2 and Wxa1 with indica lineage.

A multifocal approach towards understanding the complexities of carotenoid biosynthesis and accumulation in rice grains.

Carotenoids are mostly C40 terpenoids that participate in several important functions in plants including photosynthesis, responses to various forms of stress, signal transduction and photoprotection. While the antioxidant potential of carotenoids is of particular importance for human health, equally important is the role of ß-carotene as the precursor for vitamin A in the human diet. Rice, which contributes upto 40% of dietary energy for mankind, contains very low level of ß-carotene, thereby making it an important crop for enhancing ß-carotene accumulation in its grains and consequently targeting vitamin A deficiency. Biosynthesis of carotenoids in the endosperm of white rice is blocked at the first enzymatic step wherein geranylgeranyl diphosphate is converted to phytoene by the action of phytoene synthase (PSY). Strategies aimed at enhancing ß-carotene levels in the endosperm of white rice identified Narcissus pseudonarcissus (npPSY) and bacterial CRT1 as the regulators of the carotenoid biosynthetic pathway in rice. Besides transcriptional regulation of PSY, posttranscriptional regulation of PSY expression by OR gene, molecular synergism between ε-LCY and ß-LCY and epigenetic control of CRITSO through SET DOMAIN containing protein appear to be the other regulatory nodes which regulate carotenoid biosynthesis and accumulation in rice grains. In this review, we elucidate a comprehensive and deeper understanding of the regulatory mechanisms of carotenoid metabolism in crops that will enable us to identify an effective tool to alleviate carotenoid content in rice grains.

Deciphering species relationships and evolution in Chenopodium through sequence variations in nuclear internal transcribed spacer region and amplified fragment-length polymorphism in nuclear DNA.

Evaluation of sequence variations in the internal transcribed spacer (ITS) region of 19 accessions, comprising of 11 accessions of Chenopodium quinoa, eight accessions of Chenopodium album and 165 retrieved sequences of different species of Chenopodium belonging to subfamily Chenopodioideae revealed a higher intraspecific genetic diversity in Himalayan C. album than that in C. quinoa. ITS and amplified fragment-length profiles of the accessions suggest the existence of accessions of Himalayan C. album as heteromorphs of the same species rather than a heterogenous assemblage of taxa. While the evolutionary relationship reconstructed from variations in 184 sequences of ITS region from species belonging to Chenopodiaceae, Amaranthaceae, Polygonaceae and Nelumbonaceae established a paraphyletic evolution of family Chenopodiaceae, it also revealed a monophyletic evolution of Chenopodieae I. The reconstruction also established five independent lineages of the subfamily Chenopodioideae with C. album as a sister clade of C. quinoa within the tribe Chenopodieae I. The results also indicate a much younger age for Himalayan chenopods (C. album) than the reported crown age of Chenopodieae I.

Comparative transcriptomics approach in elucidation of carotenoid biosynthesis regulation in grains of rice (Oryza sativa L.).

Estimation of phytoene, lycopene, ß-carotene, lutein, and zeaxanthin in grains of white, brown and purple cultivars of rice revealed marked differences in the levels of these carotenoid intermediates amongst the cultivars. Grains of white rice did not show any significant accumulation of carotenoid intermediates at any stage of development. On the other hand, grains of the purple cultivar accumulated 49.16 ± 5 µg of ß-carotene, 28.89 ± 3.2 µg of lutein and 34.65 ± 4.6 µg of zeaxanthin per gm of grain fresh weight. In addition to PSY1, higher expression of ßLCY than εLCY appears to be an important factor in determining the flux of pathway towards synthesis of ß-ß branch carotenoids in purple rice. This cultivar showed a higher fold change in carotenoid precursors during transition from milky to doughing stages and an enhanced flux of lycopene towards ß-carotene during grain maturation. Our results indicate that higher level of carotenoids in purple rice is a consequence of higher expression of genes involved in pyruvate metabolism as well as those involved in carotenoid biosynthesis such as PSY1, PDS and ß-LCY. Co-expression networking revealed a strong positive relationship between the expression profiles of genes involved in carotenoid biosynthesis and genes coding for geranylgeranyl transferase type II, glutathione S-transferase, DnaJ and SET domain containing proteins as well as MADS26 and R2R3MYB family of transcription factors.

Functional genomics of apocarotenoids in saffron: insights from chemistry, molecular biology and therapeutic applications.

Saffron is considered to be the costliest spice of the world. It has been regarded as highly valued medicinal plant in Ayurveda to treat various ailments. Over the past few years, considerable interest has developed in saffron because of its anticancer, antimutagenic, antioxidant and immunomodulatory properties. Saffron's colour, bitter taste and aroma are its three main and peculiar characteristics, which are conferred by three chemicals namely: crocin, picrocrocin and safranal, respectively. The present review focuses on recent research/progress made in saffron in the area of functional genomics and highlights the potential of several genes and transcription factors involved in carotenoid/apocarotenoid pathway and responsible for flavour and aroma of saffron.

Molecular modelling, dynamics simulation and characterization of antifungal chitinase from Sechium edule.

Chitinases are varied sized proteins which have the ability to degrade chitin and are present in a huge range of organisms like fungi, yeasts, arthropods, humans etc. and have been getting increased attention due to their biocontrol properties. In silico analysis sheds light on the extensive properties of this plant protein. In this paper, a particular antifungal protein Chitinase sourced from Sechium edule from East Khasi Hills, Meghalaya was characterized using an array of bioinformatics tools. The modelled protein showed conserved domains characteristic to glycosyl hydrolase, family 18 superfamily. Likewise, a part of the conserved domain area fits in with xylanase inhibitor Xip-1 and the class ΙΙΙ plant chitinases, for example, concanavalin B, hevamine, which have a GH18 area. The modelled wild type protein exhibited secondary characteristics comprising of 48.8% helix, 62.2% sheets and 13.8% turns, displaying an aliphatic index of 80.53 and instability index of 48.88 inferring upon the fact that the protein is relatively unstable without its appropriate environment. The paper functions as the first attempt to portray molecular dynamics simulation of Chitinase from Sechium edule reinforced by modelling and thorough characteristic analysis of the protein by employing parameters like Ramachandran Plot, Chou and Fasman Secondary Structure prediction, ProtParam etc. Further approaches like protein engineering and activity analysis suggested.

Deciphering ligand specificity of a Clostridium thermocellum family 35 carbohydrate binding module (CtCBM35) for gluco- and galacto- substituted mannans and its calcium induced stability.

This study investigated the role of CBM35 from Clostridium thermocellum (CtCBM35) in polysaccharide recognition. CtCBM35 was cloned into pET28a (+) vector with an engineered His6 tag and expressed in Escherichia coli BL21 (DE3) cells. A homogenous 15 kDa protein was purified by immobilized metal ion chromatography (IMAC). Ligand binding analysis of CtCBM35 was carried out by affinity electrophoresis using various soluble ligands. CtCBM35 showed a manno-configured ligand specific binding displaying significant association with konjac glucomannan (Ka = 14.3×10(4) M(-1)), carob galactomannan (Ka = 12.4×10(4) M(-1)) and negligible association (Ka = 12 µM(-1)) with insoluble mannan. Binding of CtCBM35 with polysaccharides which was calcium dependent exhibited two fold higher association in presence of 10 mM Ca(2+) ion with konjac glucomannan (Ka = 41×10(4) M(-1)) and carob galactomannan (Ka = 30×10(4) M(-1)). The polysaccharide binding was further investigated by fluorescence spectrophotometric studies. On binding with carob galactomannan and konjac glucomannan the conformation of CtCBM35 changed significantly with regular 21 nm peak shifts towards lower quantum yield. The degree of association (K a) with konjac glucomannan and carob galactomannan, 14.3×10(4) M(-1) and 11.4×10(4) M(-1), respectively, corroborated the findings from affinity electrophoresis. The association of CtCBM35with konjac glucomannan led to higher free energy of binding (ΔG) -25 kJ mole(-1) as compared to carob galactomannan (ΔG) -22 kJ mole(-1). On binding CtCBM35 with konjac glucomannan and carob galactomannan the hydrodynamic radius (RH) as analysed by dynamic light scattering (DLS) study, increased to 8 nm and 6 nm, respectively, from 4.25 nm in absence of ligand. The presence of 10 mM Ca(2+) ions imparted stiffer orientation of CtCBM35 particles with increased RH of 4.52 nm. Due to such stiffer orientation CtCBM35 became more thermostable and its melting temperature was shifted to 70°C from initial 50°C.

Mycorrhizal status and diversity of fungal endophytes in roots of common buckwheat (Fagopyrum esculentum) and tartary buckwheat (F. tataricum).

To determine the mycorrhizal status and to identify the fungi colonising the roots of the plants, common buckwheat (Fagopyrum esculentum) and tartary buckwheat (F. tataricum) were inoculated with an indigenous fungal mixture from a buckwheat field. Root colonisation was characterised by the hyphae and distinct microsclerotia of dark septate endophytes, with occasional arbuscules and vesicles of arbuscular mycorrhizal fungi. Sequences of arbuscular mycorrhizal fungi colonising tartary buckwheat clustered close to the Glomus species group A. Sequences with similarity to the Ceratobasidium/Rhizoctonia complex, a putative dark septate endophyte fungus, were amplified from the roots of both common and tartary buckwheat. To the best of our knowledge, this is the first report of arbuscular mycorrhizal colonisation in tartary buckwheat and the first molecular characterisation of these fungi that can colonise both of these economically important plant species.

Amino acid sequence of the 26 kDa subunit of legumin-type seed storage protein of common buckwheat (Fagopyrum esculentum Moench): molecular characterization and phylogenetic analysis.

The paper describes the amino acid sequence of a 26 kDa basic subunit of 13S globulin of common buckwheat (Fagopyrum esculentum Moench). The protein has 93 and 75% sequence homology with 11S globulin of Coffea arabica and beta subunit of 11S globulin of Cucurbita pepo respectively. The subunit has the "globally conserved" N-terminal sequence consisting of Gly-Ile-Asp-Glu and the cysteine at P7' from the proteolytic processing site. A conserved 7 residue domain of Pro-His-Trp-Asn-Ile-Asn-Ala, characteristic of basic subunits of legumins from non-leguminous angiosperms, is also present in this protein. A distinguishing features of this subunit is the relatively high level of lysine and methionine.