a-protocol-for-phage-display-affinity-selection-using-recombinant

A Protocol for Phage Display and Affinity Selection Using Recombinant Protein Baits

Using  recombinant phage as a scaffold to present various protein portions encoded by  a directionally cloned cDNA library to immobilized bait molecules ...

university of kentucky 

As an adaptive mechanism, hypocotyl dormancy delays emergence of functional leaf until favorable season of growth in Podophyllum hexandrum, an endangered medicinal plant of the western Himalayas. However, upon exposure of the freshly germinated seedlings to favorable temperature (25 degrees C), functional leaves emerged within 20 days. Therefore, we examined regulation mechanisms of growth and development of this alpine plant by temperature under laboratory conditions. The seedlings were exposed to (1) 25 degrees C (temperature prevailing at the time of maximum vegetative growth), (2) 4 degrees C (mean temperature at the onset of winter in its natural habitat), and (3) 10 degrees C (an intermediate temperature). Slackened growth at 4 degrees C was followed by senescence of aerial parts and quiescence of roots and predetermined leaf primordia. Rapid development of leaf primordia at 25 degrees C was associated with increased starch hydrolysis. This was evident from higher alpha-amylase activity and reducing sugars. These parameters decreased on sudden exposure to 4 degrees C. In contrast, the roots (perennating organs) showed a slight increase (1.36-fold) in alpha-amylase activity. Growth and development in seedlings growing at 10 degrees C (temperature less adverse than 4 degrees C) were comparatively faster. The content of reducing sugars and alpha-amylase activity were also higher in all the seedling parts at 10 degrees C as compared to 4 degrees C. This indicated larger requirements for sugar by the seedlings at 10 degrees C. Irrespective of temperature, maximum changes in nitrate and nitrate reductase occurred during the initial 10 days, i.e., when the readily available form of sugars (reducing sugar) was highest. This indicated that a temperature-dependent availability of carbon, but not temperature itself, was an important regulator of uptake and reduction of nitrogen.

Temperature-dependent growth and emergence of functional leaves: an adaptive mechanism in the seedlings of the western Himalayan plant Podophyllum hexandrum.

This study shows an effective but simple method of conserving characterized populations and elite clones through vegetative propagation and genetic diversity through seeds in Podophyllum hexandrum (family Berberidaceae). Seed dormancy has been considered to be a major constraint in these seeds and most of the earlier reports recommended dormancy-breaking pretreatments such as chilling, gibberellic acid (GA(3)), etc. However, seeds of the 14 accessions that we tested exhibited no dormancy and hence did not require any pretreatments. Besides accession, collection of seeds with high moisture content could be one of the reasons for lack of dormancy. Thus, we propose germination of seeds (while they still retained moisture) in sand at 25 degrees C for high and reproducible results within a shorter period of time compared with earlier reports. Hypocotyl dormancy is known to considerably delay plant establishment and hence en masse propagation by preventing the emergence of functional leaves for up to 11-12 months. Manual removal of cotyledonary leaves, being labor and time intensive, is not a feasible method for large-scale seedling establishment. However, in this study, we showed that GA(3) at 200 ppm can alleviate hypocotyl dormancy besides reducing the time taken for true or functional leaf emergence. Treatment of cotyledonary leaves of 1 week-old-seedlings with 200 ppm GA(3 )resulted in true or functional leaf emergence within 7 days, and the resultant plants were also more vigorous than the ones obtained from manual removal of cotyledonary leaves. The study helped advance the establishment of seedlings by one growing season (almost 1 year).

An efficient method of propagation of Podophyllum hexandrum: an endangered medicinal plant of the Western Himalayas under ex situ conditions.

This study reports an appreciable yield of podophyllotoxin (PDT) in P. hexandrum plants grown ex situ under polyhouse conditions of a temperate locale. The PDT content of below-ground parts was affected by both plant age and growth period. However, only the effect of plant age on PDT content was significant. Thus, the highest amounts of PDT were recorded in the below-ground parts of 2-year-old plants harvested during the late-growth period (LGP). High total soluble sugars in the below-ground parts during the early growth period (EGP) and the highest nitrate and nitrate reductase in the leaves of 2-year-old plants during the peak-growth period (PGP) indicated higher mobilization and assimilation of starch and nitrate. Probably the surplus carbon and nitrogen gained during the PGP were diverted from aerial parts to below-ground parts during the LGP and in turn contributed to the synthesis of higher amounts of PDT. This study shows that commercial cultivation of P. hexandrum is possible under ex situ temperate conditions.

Factors affecting podophyllotoxin yield in the ex situ grown Podophyllum hexandrum, an endangered alpine native of the western Himalayas.

Arabidopsis thaliana seeds without functional SEED MATURATION PROTEIN1 (SMP1), a boiling soluble protein predicted to be of intrinsic disorder, presumed to be a LATE EMBRYOGENESIS ABUNDANT (LEA) family protein based on sequence homology, do not enter secondary dormancy after 3 days at 40 °C. We hypothesized that SMP1 may protect a heat labile protein involved in the promotion of secondary dormancy. Recombinant SMP1 and GmPM28, its soybean (Glycine max), LEA4 homologue, protected the labile GLUCOSE-6-PHOSPHATE DEHYROGENASE enzyme from heat stress, as did a known protectant, Bovine Serum Albumin, whether the LEA protein was in solution or attached to the bottom of microtiter plates. Maintenance of a biological function for both recombinant LEA proteins when immobilized encouraged a biopanning approach to screen for potential protein interactors. Phage display with two Arabidopsis seed, T7 phage, cDNA libraries, normalized for transcripts present in the mature, dehydrated, 12-, 24-, or 36-h imbibed seeds, were used in biopans against recombinant SMP1 and GmPM28. Phage titer increased considerably over four rounds of biopanning for both LEA proteins, but not for BSA, at both 25 and at 41 °C, regardless of the library used. The prevalence of multiple, independent clones encoding portions of specific proteins repeatedly retrieved from different libraries, temperatures and baits, provides evidence suggesting these LEA proteins are discriminating which proteins they protect, a novel finding. The identification of putative LEA-interacting proteins provides targets for reverse genetic approaches to further dissect the induction of secondary dormancy in seeds in response to heat stress.

Identification of Late Embryogenesis Abundant (LEA) Protein Putative Interactors Using Phage Display.

This review highlights discoveries made using phage display that impact the use of agricultural products. The contribution phage display made to our fundamental understanding of how various protective molecules serve to safeguard plants and seeds from herbivores and microbes is discussed. The utility of phage display for directed evolution of enzymes with enhanced capacities to degrade the complex polymers of the cell wall into molecules useful for biofuel production is surveyed. Food allergies are often directed against components of seeds; this review emphasizes how phage display has been employed to determine the seed component(s) contributing most to the allergenic reaction and how it has played a central role in novel approaches to mitigate patient response. Finally, an overview of the use of phage display in identifying the mature seed proteome protection and repair mechanisms is provided. The identification of specific classes of proteins preferentially bound by such protection and repair proteins leads to hypotheses concerning the importance of safeguarding the translational apparatus from damage during seed quiescence and environmental perturbations during germination. These examples, it is hoped, will spur the use of phage display in future plant science examining protein-ligand interactions.

Uses of phage display in agriculture: a review of food-related protein-protein interactions discovered by biopanning over diverse baits.

A group of intrinsically disordered, hydrophilic proteins-Late Embryogenesis Abundant (LEA) proteins-has been linked to survival in plants and animals in periods of stress, putatively through safeguarding enzymatic function and prevention of aggregation in times of dehydration/heat. Yet despite decades of effort, the molecular-level mechanisms defining this protective function remain unknown. A recent effort to understand LEA functionality began with the unique application of phage display, wherein phage display and biopanning over recombinant Seed Maturation Protein homologs from Arabidopsis thaliana and Glycine max were used to retrieve client proteins at two different temperatures, with one intended to represent heat stress. From this previous study, we identified 21 client proteins for which clones were recovered, sometimes repeatedly. Here, we use sequence analysis and homology modeling of the client proteins to ascertain common sequence and structural properties that may contribute to binding affinity with the protective LEA protein. Our methods uncover what appears to be a predilection for protein-nucleic acid interactions among LEA client proteins, which is suggestive of subcellular residence. The results from this initial computational study will guide future efforts to uncover the protein protective mechanisms during heat stress, potentially leading to phage-display-directed evolution of synthetic LEA molecules.

Uses of phage display in agriculture: sequence analysis and comparative modeling of late embryogenesis abundant client proteins suggest protein-nucleic acid binding functionality.

Improving saccharification efficiency in bioenergy crop species remains an important challenge. Here, we report the characterization of a Sorghum (Sorghum bicolor L.) mutant, named REDforGREEN (RG), as a bioenergy feedstock.

Sorghum mutant RG displays antithetic leaf shoot lignin accumulation resulting in improved stem saccharification properties.

Natural food colorants with functional properties are of increasing interest. Prior papers indicate the chemical suitability of sorghum leaf 3-deoxyanthocyanidins as natural food colorants. Via mutagenesis-assisted breeding, a sorghum variety that greatly overaccumulates 3-deoxyanthocyanidins of leaf tissue, named REDforGREEN (RG), has been isolated and characterized. Interestingly, RG not only caused increased 3-deoxyanthocyanidins but also caused increased tannins, chlorogenic acid, and total phenolics in the leaf tissue. Chemical composition of pigments was established through high-performance liquid chromatography (HPLC) that identified luteolinidin (LUT) and apigeninidin (APG) as the main 3-deoxyanthocianidin species. Specifically, 3-deoxyanthocianidin levels were 1768 μg g(-1) LUT and 421 μg g(-1) APG in RG leaves compared with trace amounts in wild type, representing 1000-fold greater levels in the mutant leaves. Thus, RG represents a useful sorghum mutagenesis variant to develop as a functionalized food colorant.

Article	Year
Temperature-dependent growth and emergence of functional leaves: an adaptive mechanism in the seedlings of the western Himalayan plant Podophyllum hexandrum. Journal of plant research\| PubMed ID: 18338104	2008
An efficient method of propagation of Podophyllum hexandrum: an endangered medicinal plant of the Western Himalayas under ex situ conditions. Journal of natural medicines\| PubMed ID: 18404326	2008
Factors affecting podophyllotoxin yield in the ex situ grown Podophyllum hexandrum, an endangered alpine native of the western Himalayas. Journal of natural medicines\| PubMed ID: 21625946	2012
Identification of Late Embryogenesis Abundant (LEA) Protein Putative Interactors Using Phage Display. International journal of molecular sciences\| PubMed ID: 22837651	2012
Uses of phage display in agriculture: a review of food-related protein-protein interactions discovered by biopanning over diverse baits. Computational and mathematical methods in medicine\| PubMed ID: 23710253	2013
Uses of phage display in agriculture: sequence analysis and comparative modeling of late embryogenesis abundant client proteins suggest protein-nucleic acid binding functionality. Computational and mathematical methods in medicine\| PubMed ID: 23956788	2013
Sorghum mutant RG displays antithetic leaf shoot lignin accumulation resulting in improved stem saccharification properties. Biotechnology for biofuels\| PubMed ID: 24103129	2013
Mutagenesis Breeding for Increased 3-Deoxyanthocyanidin Accumulation in Leaves of Sorghum bicolor (L.) Moench: A Source of Natural Food Pigment. Journal of agricultural and food chemistry\| PubMed ID: 24460064	2014

Rekha Kushwaha

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