On transient climate change at the Cretaceous-Paleogene boundary due to atmospheric soot injections.

Climate simulations that consider injection into the atmosphere of 15,000 Tg of soot, the amount estimated to be present at the Cretaceous-Paleogene boundary, produce what might have been one of the largest episodes of transient climate change in Earth history. The observed soot is believed to originate from global wildfires ignited after the impact of a 10-km-diameter asteroid on the Yucatán Peninsula 66 million y ago. Following injection into the atmosphere, the soot is heated by sunlight and lofted to great heights, resulting in a worldwide soot aerosol layer that lasts several years. As a result, little or no sunlight reaches the surface for over a year, such that photosynthesis is impossible and continents and oceans cool by as much as 28 °C and 11 °C, respectively. The absorption of light by the soot heats the upper atmosphere by hundreds of degrees. These high temperatures, together with a massive injection of water, which is a source of odd-hydrogen radicals, destroy the stratospheric ozone layer, such that Earth's surface receives high doses of UV radiation for about a year once the soot clears, five years after the impact. Temperatures remain above freezing in the oceans, coastal areas, and parts of the Tropics, but photosynthesis is severely inhibited for the first 1 y to 2 y, and freezing temperatures persist at middle latitudes for 3 y to 4 y. Refugia from these effects would have been very limited. The transient climate perturbation ends abruptly as the stratosphere cools and becomes supersaturated, causing rapid dehydration that removes all remaining soot via wet deposition.

Continuous Flow Separation of Hydrophobin Fusion Proteins from Plant Cell Culture Extract.

Fusion to fungal hydrophobins has proven to be a useful tool to enhance accumulation and recovery of recombinant proteins in plants. Aqueous two-phase separation (ATPS) is an attractive system to capture hydrophobin fusion proteins from plant extracts. The process can simultaneously purify and concentrate target protein with minimal background. ATPS avoids the use of chromatographic column steps, can be carried out in a short time frame, and is amenable to industrial-scale protein purification. A drawback of performing ATPS in large volumes is the lengthy time required for phase separation; however, this can be avoided by incorporating continuous systems, which are often preferred by the processing industry. This method chapter illustrates the capture of GFP-HFBI hydrophobin fusion protein from BY-2 plant cell suspension extract using a semi-continuous ATPS method.

Protein body formation in leaves of Nicotiana benthamiana: a concentration-dependent mechanism influenced by the presence of fusion tags.

Protein bodies (PBs) are endoplasmic reticulum (ER) derived organelles originally found in seeds whose function is to accumulate seed storage proteins. It has been shown that PB formation is not limited to seeds and green fluorescent protein (GFP) fused to either elastin-like polypeptide (ELP) or hydrophobin (HFBI) fusion tags induce the formation of PBs in leaves of N. benthamiana. In this study, we compared the ELP- and HFBI-induced PBs and showed that ELP-induced PBs are larger than HFBI-induced PBs. The size of ELP- and HFBI-induced PBs increased over time along with the accumulation levels of their fused protein. Our results show that PB formation is a concentration-dependent mechanism in which proteins accumulating at levels higher than 0.2% of total soluble protein are capable of inducing PBs in vivo. Our results show that the presence of fusion tags is not necessary for the formation of PBs, but affects the distribution pattern and size of PBs. This was confirmed by PBs induced by fluorescent proteins as well as fungal xylanases. We noticed that in the process of PB formation, secretory and ER-resident molecules are passively sequestered into the lumen of PBs. We propose to use this property of PBs as a tool to increase the accumulation levels of erythropoietin and human interleukin-10 by co-expression with PB-inducing proteins.

Yeast oligo-mediated genome engineering (YOGE).

High-frequency oligonucleotide-directed recombination engineering (recombineering) has enabled rapid modification of several prokaryotic genomes to date. Here, we present a method for oligonucleotide-mediated recombineering in the model eukaryote and industrial production host Saccharomyces cerevisiae , which we call yeast oligo-mediated genome engineering (YOGE). Through a combination of overexpression and knockouts of relevant genes and optimization of transformation and oligonucleotide designs, we achieve high gene-modification frequencies at levels that only require screening of dozens of cells. We demonstrate the robustness of our approach in three divergent yeast strains, including those involved in industrial production of biobased chemicals. Furthermore, YOGE can be iteratively executed via cycling to generate genomic libraries up to 10 (5) individuals at each round for diversity generation. YOGE cycling alone or in combination with phenotypic selections or endonuclease-based negative genotypic selections can be used to generate modified alleles easily in yeast populations with high frequencies.

Bioseparation of recombinant proteins from plant extract with hydrophobin fusion technology.

Two main hurdles hinder the widespread acceptance of plants as a preferred protein expression platform: low accumulation levels and expensive chromatographic purification methods. Fusion of proteins of interest to fungal hydrophobins has provided a tool to address both accumulation and purification issues. In this method, we describe the one-step purification of a GFP-HFBI fusion from crude plant extract using an aqueous two-phase system (ATPS). ATPS can be carried out in a very short time frame, yields relatively pure protein with very few contaminants, and does not require any chromatographic column steps. This purification system takes advantage of the affinity of hydrophobins to the micellar phase of widely available nonionic surfactants, such as Triton X-114, and can be easily scaled up for industrial-scale protein purification.

Protein body-inducing fusions for high-level production and purification of recombinant proteins in plants.

For the past two decades, therapeutic and industrially important proteins have been expressed in plants with varying levels of success. The two major challenges hindering the economical production of plant-made recombinant proteins include inadequate accumulation levels and the lack of efficient purification methods. To address these limitations, several fusion protein strategies have been recently developed to significantly enhance the production yield of plant-made recombinant proteins, while simultaneously assisting in their subsequent purification. Elastin-like polypeptides are thermally responsive biopolymers composed of a repeating pentapeptide 'VPGXG' sequence that are valuable for the purification of recombinant proteins. Hydrophobins are small fungal proteins capable of altering the hydrophobicity of their respective fusion partner, thus enabling efficient purification by surfactant-based aqueous two-phase systems. Zera, a domain of the maize seed storage protein γ-zein, can induce the formation of protein storage bodies, thus facilitating the recovery of fused proteins using density-based separation methods. These three novel protein fusion systems have also been shown to enhance the accumulation of a range of different recombinant proteins, while concurrently inducing the formation of protein bodies. The packing of these fusion proteins into protein bodies may exclude the recombinant protein from normal physiological turnover. Furthermore, these systems allow for quick, simple and inexpensive nonchromatographic purification of the recombinant protein, which can be scaled up to industrial levels of protein production. This review will focus on the similarities and differences of these artificial storage organelles, their biogenesis and their implication for the production of recombinant proteins in plants and their subsequent purification.

Recombinant protein production in a variety of Nicotiana hosts: a comparative analysis.

Although many different crop species have been used to produce a wide range of vaccines, antibodies, biopharmaceuticals and industrial enzymes, tobacco has the most established history for the production of recombinant proteins. To further improve the heterologous protein yield of tobacco platforms, transient and stable expression of four recombinant proteins (i.e. human erythropoietin and interleukin-10, an antibody against Pseudomonas aeruginosa, and a hyperthermostable α-amylase) was evaluated in numerous species and cultivars of Nicotiana. Whereas the transient level of recombinant protein accumulation varied significantly amongst the different Nicotiana plant hosts, the variety of Nicotiana had little practical impact on the recombinant protein concentration in stable transgenic plants. In addition, this study examined the growth rate, amount of leaf biomass, total soluble protein levels and the alkaloid content of the various Nicotiana varieties to establish the best plant platform for commercial production of recombinant proteins. Of the 52 Nicotiana varieties evaluated, Nicotiana tabacum (cv. I 64) produced the highest transient concentrations of recombinant proteins, in addition to producing a large amount of biomass and a relatively low quantity of alkaloids, probably making it the most effective plant host for recombinant protein production.

Green biofactories: recombinant protein production in plants.

Until recently, low accumulation levels have been the major bottleneck for plant-made recombinant protein production. However, several breakthroughs have been described in the past few years allowing for very high accumulation levels, mainly through chloroplast transformation and transient expression, coupled with subcellular targeting and protein fusions. Another important factor influencing our ability to use plants for the production of recombinant proteins is the availability of quick and simple purification strategies. Recent developments using oleosin, zein, ELP and hydrophobin fusion tags have shown promise as efficient and cost-effective methods for non-chromatographic separation. Furthermore, plant glycosylation is a major barrier to the parenteral administration of plant-made biopharmaceuticals because of potential immunogenicity concerns. A major effort has been invested in humanizing plant glycosylation, and several groups have been able to reduce or eliminate immunogenic glycans while introducing mammalian-specific glycans. Finally, biosafety issues and public perception are essential for the acceptance of plants as bioreactors for the production of proteins. Over recent years, it has become clear that food and feed plants carry an inherent risk of contaminating our food supply, and thus much effort has focused on the use of non-food plants. Presently, Nicotiana benthamiana has emerged as the preferred host for transient expression, while tobacco is most frequently used for chloroplast transformation. In this review, we focus on the main issues hindering the economical production of recombinant proteins in plants, describing the current efforts for addressing these limitations, and we include an extensive list of recent patents generated with the intention of solving these limitations.

Green Biofactories: Recombinant Protein Production in Plants.

Until recently, low accumulation levels have been the major bottleneck for plant-made recombinant protein production. However, several breakthroughs have been described in the past few years allowing for very high maccumulation levels, mainly through chloroplast transformation and transient expression, coupled with subcellular targeting and protein fusions. Another important factor influencing our ability to use plants for the production of recombinant proteins is the availability of quick and simple purification strategies. Recent developments using oleosin, zein, ELP and hydrophobin fusion tags have shown promise as efficient and cost-effective methods for nonchromatographic separation. Furthermore, plant glycosylation is a major barrier to the parenteral administration of plantmade biopharmaceuticals because of potential immunogenicity concerns. A major effort has been invested in humanizing plant glycosylation, and several groups have been able to reduce or eliminate immunogenic glycans while introducing mammalian-specific glycans. Finally, biosafety issues and public perception are essential for the acceptance of plants as bioreactors for the production of proteins. Over recent years, it has become clear that food and feed plants carry an inherent risk of contaminating our food supply, and thus much effort has focused on the use of non-food plants. Presently, Nicotiana benthamiana has emerged as the preferred host for transient expression, while tobacco is most frequently used for chloroplast transformation. In this review, we focus on the main issues hindering the economical production of recombinant proteins in plants, describing the current efforts for addressing these limitations, and we include an extensive list of recent patents generated with the intention of solving these limitations.

Temporal and spatial distribution of erythropoietin in transgenic tobacco plants.

Plants have shown promise as bioreactors for the large-scale production of a wide variety of recombinant proteins. To increase the economic feasibility of this technology, numerous molecular approaches have been developed to enhance the production yield of these valuable proteins in plants. Alternatively, we chose to examine the temporal and spatial distribution of erythropoietin (EPO) accumulation during tobacco plant development, in order to establish the optimal harvesting time to further maximize heterologous protein recovery. EPO is used extensively worldwide for the treatment of anaemia and is currently the most commercially valuable biopharmaceutical on the market. Our results indicate that the concentration of recombinant EPO and endogenous total soluble protein (TSP) declined significantly for every leaf of the plant during maturation, although the rate of these declines was strongly dependent on the leaf's position on the plant. As a result, the amount of EPO produced in leaves relative to TSP content remained essentially unchanged over the course of the plant's life. Decreasing levels of recombinant protein in leaves was attributed to proteolytic degradation associated with tissue senescence since transgene silencing was not detected. We found that significantly higher concentrations of EPO within younger leaves more than compensated for their smaller size, when compared to their low-expressing, fully-grown counterparts. This suggests that fast-growing, young leaves should be periodically harvested from the plants as they continue to grow in order to maximize recombinant protein yield. These findings demonstrate that EPO accumulation is highly influenced by the plant's physiology and development.

Hydrophobin fusions for high-level transient protein expression and purification in Nicotiana benthamiana.

Insufficient accumulation levels of recombinant proteins in plants and the lack of efficient purification methods for recovering these valuable proteins have hindered the development of plant biotechnology applications. Hydrophobins are small and surface-active proteins derived from filamentous fungi that can be easily purified by a surfactant-based aqueous two-phase system. In this study, the hydrophobin HFBI sequence from Trichoderma reesei was fused to green fluorescent protein (GFP) and transiently expressed in Nicotiana benthamiana plants by Agrobacterium tumefaciens infiltration. The HFBI fusion significantly enhanced the accumulation of GFP, with the concentration of the fusion protein reaching 51% of total soluble protein, while also delaying necrosis of the infiltrated leaves. Furthermore, the endoplasmic reticulum-targeted GFP-HFBI fusion induced the formation of large novel protein bodies. A simple and scalable surfactant-based aqueous two-phase system was optimized to recover the HFBI fusion proteins from leaf extracts. The single-step phase separation was able to selectively recover up to 91% of the GFP-HFBI up to concentrations of 10 mg mL(-1). HFBI fusions increased the expression levels of plant-made recombinant proteins while also providing a simple means for their subsequent purification. This hydrophobin fusion technology, when combined with the speed and posttranslational modification capabilities of plants, enhances the value of transient plant-based expression systems.

Induction of protein body formation in plant leaves by elastin-like polypeptide fusions.

BACKGROUND: Elastin-like polypeptides are synthetic biopolymers composed of a repeating pentapeptide 'VPGXG' sequence that are valuable for the simple non-chromatographic purification of recombinant proteins. In addition, elastin-like polypeptide fusions have been shown to enhance the accumulation of a range of different recombinant proteins in plants, thus addressing the major limitation of plant-based expression systems, which is a low production yield. This study's main objectives were to determine the general utility of elastin-like polypeptide protein fusions in various intracellular compartments and to elucidate elastin-like polypeptide's mechanism of action for increasing recombinant protein accumulation in the endoplasmic reticulum of plants. RESULTS: The effect of elastin-like polypeptide fusions on the accumulation of green fluorescent protein targeted to the cytoplasm, chloroplasts, apoplast, and endoplasmic reticulum was evaluated. The endoplasmic reticulum was the only intracellular compartment in which an elastin-like polypeptide tag was shown to significantly enhance recombinant protein accumulation. Interestingly, endoplasmic reticulum-targeted elastin-like polypeptide fusions induced the formation of a novel type of protein body, which may be responsible for elastin-like polypeptide's positive effect on recombinant protein accumulation by excluding the heterologous protein from normal physiological turnover. Although expressed in the leaves of plants, these novel protein bodies appeared similar in size and morphology to the prolamin-based protein bodies naturally found in plant seeds. The elastin-like polypeptide-induced protein bodies were highly mobile organelles, exhibiting various dynamic patterns of movement throughout the cells, which were dependent on intact actin microfilaments and a functional actomyosin motility system. CONCLUSION: An endoplasmic reticulum-targeted elastin-like polypeptide fusion approach provides an effective strategy for depositing large amounts of concentrated heterologous protein within the limited space of the cell via storage in stable protein bodies. Furthermore, encapsulation of recombinant proteins into physiologically inert organelles can function to insulate the protein from normal cellular mechanisms, thus limiting unnecessary stress to the host cell. Since elastin-like polypeptide is a mammalian-derived protein, this study demonstrates that plant seed-specific factors are not required for the formation of protein bodies in vegetative plant tissues, suggesting that the endoplasmic reticulum possesses an intrinsic ability to form protein body-like accretions in eukaryotic cells when overexpressing particular proteins.

SOX15 and SOX7 differentially regulate the myogenic program in P19 cells.

In this study, we have identified novel roles for Sox15 and Sox7 as regulators of muscle precursor cell fate in P19 cells. To examine the role of Sox15 and Sox7 during skeletal myogenesis, we isolated populations of P19 cells with either gene stably integrated into the genome, termed P19[Sox15] and P19[Sox7]. Both SOX proteins were sufficient to upregulate the expression of the muscle precursor markers Pax3/7, Meox1, and Foxc1 in aggregated cells. In contrast to the P19[Sox7] cell lines, which subsequently differentiated into skeletal muscle, myogenesis failed to progress past the precursor stage in P19[Sox15] cell lines, shown by the lack of MyoD and myosin heavy chain (MHC) expression. P19[Sox15] clones showed elevated and sustained levels of the inhibitory factors Msx1 and Id1, which may account for the lack of myogenic progression in these cells. Stable expression of a Sox15 dominant-negative protein resulted in the loss of Pax3/7 and Meox1 transcripts, as well as myogenic regulatory factor (MRF) and MHC expression. These results suggest that Sox15, or genes that are bound by Sox15, are necessary and sufficient for the acquisition of the muscle precursor cell fate. On the other hand, knockdown of endogenous Sox15 caused a decrease in Pax3 and Meox1, but not MRF expression, suggesting that other factors can compensate in the absence of Sox15. Taken together, these results show that both Sox7 and Sox15 are able to induce the early stages of myogenesis, but only Sox7 is sufficient to initiate the formation of fully differentiated skeletal myocytes.

In vivo formation of protein based aqueous microcompartments.

In this paper, we report the formation of protein based liquid droplets resulting in the formation of in vivo microcompartments in E. coli or tobacco cells. These microcompartments were generated by expressing elastin-like polypeptides (ELP), which have the ability to undergo a reversible phase transition, resulting in the formation of an aqueous two-phase system (ATPS) in the cytoplasm of the cell. We prove that these microcompartments are liquid by expressing a fusion protein consisting of ELP and GFP and by performing fluorescence recovery after photobleaching (FRAP) experiments at different stages of cell cultivation. In the initial phases of cell growth, the fusion protein concentration is low and is not sufficient to drive the formation of a second aqueous phase. As the intracellular fusion protein concentration increases with longer cultivation time, droplets start forming, and as protein expression continues, the droplets coalesce at the poles of the E. coli cells. FRAP experiments with cells at different growth stages reveals that the protein in these ELP based droplets is comprised of aqueous and not solid aggregates, as seen in typical inclusion bodies. Staining of the ribosomes and coimaging of the ELP-GFP fusion protein showed that these compartments exclude the protein making machinery of the cell, acting as depots for newly formed protein. It is also shown, in vitro, that ELP based droplets result in the exclusion of proteases, protecting proteins from degradation. Additional studies are still required to test this possibility in vivo. To the best of our knowledge, this is the first report characterizing the formation of an engineered extra aqueous phase in a living organism.

Optimization of elastin-like polypeptide fusions for expression and purification of recombinant proteins in plants.

The demand for recombinant proteins for medical and industrial use is expanding rapidly and plants are now recognized as an efficient, inexpensive means of production. Although the accumulation of recombinant proteins in transgenic plants can be low, we have previously demonstrated that fusions with an elastin-like polypeptide (ELP) tag can significantly enhance the production yield of a range of different recombinant proteins in plant leaves. ELPs are biopolymers with a repeating pentapeptide sequence (VGVPG)(n) that are valuable for bioseparation, acting as thermally responsive tags for the non-chromatographic purification of recombinant proteins. To determine the optimal ELP size for the accumulation of recombinant proteins and their subsequent purification, various ELP tags were fused to green fluorescent protein, interleukin-10, erythropoietin and a single chain antibody fragment and then transiently expressed in tobacco leaves. Our results indicated that ELP tags with 30 pentapeptide repeats provided the best compromise between the positive effects of small ELP tags (n = 5-40) on recombinant protein accumulation and the beneficial effects of larger ELP tags (n = 80-160) on recombinant protein recovery during inverse transition cycling (ITC) purification. In addition, the C-terminal orientation of ELP fusion tags produced higher levels of target proteins, relative to N-terminal ELP fusions. Importantly, the ELP tags had no adverse effect on the receptor binding affinity of erythropoietin, demonstrating the inert nature of these tags. The use of ELP fusion tags provides an approach for enhancing the production of recombinant proteins in plants, while simultaneously assisting in their purification.

Plant recombinant erythropoietin attenuates inflammatory kidney cell injury.

Human erythropoietin (EPO) is a pleiotropic cytokine with remarkable tissue-protective activities in addition to its well-established role in red blood cell production. Unfortunately, conventional mammalian cell cultures are unlikely to meet the anticipated market demands for recombinant EPO because of limited capacity and high production costs. Plant expression systems may address these limitations to enable practical, cost-effective delivery of EPO in tissue injury prevention therapeutics. In this study, we produced human EPO in tobacco and demonstrated that plant-derived EPO had tissue-protective activity. Our results indicated that targeting to the endoplasmic reticulum (ER) provided the highest accumulation levels of EPO, with a yield approaching 0.05% of total soluble protein in tobacco leaves. The codon optimization of the human EPO gene for plant expression had no clear advantage; furthermore, the human EPO signal peptide performed better than a tobacco signal peptide. In addition, we found that glycosylation was essential for the stability of plant recombinant EPO, whereas the presence of an elastin-like polypeptide fusion had a limited positive impact on the level of EPO accumulation. Confocal microscopy showed that apoplast and ER-targeted EPO were correctly localized, and N-glycan analysis demonstrated that complex plant glycans existed on apoplast-targeted EPO, but not on ER-targeted EPO. Importantly, plant-derived EPO had enhanced receptor-binding affinity and was able to protect kidney epithelial cells from cytokine-induced death in vitro. These findings demonstrate that tobacco plants may be an attractive alternative for the production of large amounts of biologically active EPO.