Studies of the zein-like alpha-prolamins based on an analysis of amino acid sequences: implications for their evolution and three-dimensional structure

Conformations of a highly expressed Z19 α-zein studied with AlphaFold2 and MD simulations

α-zeins are amphiphilic maize seed storage proteins with material properties suitable for a multitude of applications e.g., in renewable plastics, foods, therapeutics and additive manufacturing (3D-printing). To exploit their full potential, molecular-level insights are essential. The difficulties in experimental atomic-resolution characterization of α-zeins have resulted in a diversity of published molecular models. However, deep-learning α-zein models are largely unexplored. Therefore, this work studies an AlphaFold2 (AF2) model of a highly expressed α-zein using molecular dynamics (MD) simulations. The sequence of the α-zein cZ19C2 gave a loosely packed AF2 model with 7 α-helical segments connected by turns/loops. Compact tertiary structure was limited to a C-terminal bundle of three α-helices, each showing notable agreement with a published consensus sequence. Aiming to chart possible α-zein conformations in practically relevant solvents, rather than the native solid-state, the AF2 model was subjected to MD simulations in water/ethanol mixtures with varying ethanol concentrations. Despite giving structurally diverse endpoints, the simulations showed several patterns: In water and low ethanol concentrations, the model rapidly formed compact globular structures, largely preserving the C-terminal bundle. At ≥ 50 mol% ethanol, extended conformations prevailed, consistent with previous SAXS studies. Tertiary structure was partially stabilized in water and low ethanol concentrations, but was disrupted in ≥ 50 mol% ethanol. Aggregated results indicated minor increases in helicity with ethanol concentration. β-sheet content was consistently low (∼1%) across all conditions. Beyond structural dynamics, the rapid formation of branched α-zein aggregates in aqueous environments was highlighted. Furthermore, aqueous simulations revealed favorable interactions between the protein and the crosslinking agent glycidyl methacrylate (GMA). The proximity of GMA epoxide carbons and side chain hydroxyl oxygens simultaneously suggested accessible reactive sites in compact α-zein conformations and pre-reaction geometries for methacrylation. The findings may assist in expanding the applications of these technologically significant proteins, e.g., by guiding chemical modifications.

Autophagy receptor OsNBR1 modulates salt stress tolerance in rice

KEY MESSAGE

Autophagy receptor OsNBR1 modulates salt stress tolerance by affecting ROS accumulation in rice. The NBR1 (next to BRCA1 gene 1), as important selective receptors, whose functions have been reported in animals and plants. Although the function of NBR1 responses to abiotic stress has mostly been investigated in Arabidopsis thaliana, the role of NBR1 under salt stress conditions remains unclear in rice (Oryza sativa). In this study, by screening the previously generated activation-tagged line, we identified a mutant, activation tagging 10 (AC10), which exhibited salt stress-sensitive phenotypes. TAIL-PCR (thermal asymmetric interlaced PCR) showed that the AC10 line carried a loss-of-function mutation in the OsNBR1 gene. OsNBR1 was found to be a positive regulator of salt stress tolerance and was localized in aggregates. A loss-of-function mutation in OsNBR1 increased salt stress sensitivity, whereas overexpression of OsNBR1 enhanced salt stress resistance. The osnbr1 mutants showed higher ROS (reactive oxygen species) production, whereas the OsNBR1 overexpression (OsNBR1OE) lines showed lower ROS production, than Kitaake plants under normal and salt stress conditions. Furthermore, RNA-seq analysis revealed that expression of OsRBOH9 (respiratory burst oxidase homologue) was increased in osnbr1 mutants, resulting in increased ROS accumulation in osnbr1 mutants. Together our results established that OsNBR1 responds to salt stress by influencing accumulation of ROS rather than by regulating transport of Na+ and K+ in rice.

Underwater Bonding with a Biobased Adhesive from Tannic Acid and Zein Protein

Herein are presented several adhesive formulations made from zein protein and tannic acid that can bind to a wide range of surfaces underwater. Higher performance comes from more tannic acid than zein, whereas dry bonding required the opposite case of more zein than tannic acid. Each adhesive works best in the environment that it was designed and optimized for. We show underwater adhesion experiments done on different substrates and in different waters (sea water, saline solution, tap water, deionized water). Surprisingly, the water type does not influence the performance to a great deal but the substrate type does. An additional unexpected result was bond strength increasing over time when exposed to water, contradicting general experiments of working with glues. Initial adhesion underwater was stronger compared to benchtop adhesion, suggesting that water helps to make the glue stick. Temperature effects were determined, indicating maximum bonding at about 30 °C and then another increase at higher temperatures. Once the adhesive was placed underwater, a protective skin formed on the surface, keeping water from entering the rest of the material immediately. The shape of the adhesive could be manipulated easily and, once in place, the skin could be broken to induce faster bond formation. Data indicated that underwater adhesion was predominantly induced by tannic acid, cross-linking within the bulk for adhesion and to the substrate surfaces. The zein protein provided a less polar matrix that helped to keep the tannic acid molecules in place. These studies provide new plant-based adhesives for working underwater and for creating a more sustainable environment.

Accumulation of 22 kDa α-zein-mediated nonzein protein in protein body of maize endosperm

Protein bodies (PBs), the major protein storage organelle in maize (Zea mays) endosperm, comprise zeins and numerous nonzein proteins (NZPs). Unlike zeins, how NZPs accumulate in PBs remains unclear. We characterized a maize miniature kernel mutant, mn*, that produces small kernels and is embryo-lethal. After cloning the Mn* locus, we determined that it encodes the mitochondrial 50S ribosomal protein L10 (mRPL10). MN* localized to mitochondria and PBs as an NZP; therefore, we renamed MN* Non-zein Protein 1 (NZP1). Like other mutations affecting mitochondrial proteins, mn* impaired mitochondrial function and morphology. To investigate its accumulation mechanism to PBs, we performed protein interaction assays between major zein proteins and NZP1, and found that NZP1 interacts with 22 kDa α-zein. Levels of NZP1 and 22 kDa α-zein in various opaque mutants were correlated. Furthermore, NZP1 accumulation in induced PBs depended on its interaction with 22 kDa α-zein. Comparative proteomic analysis of PBs between wild-type and opaque2 revealed additional NZPs. A new NZP with plastidial localization was also found to accumulate in induced PBs via interaction with 22 kDa α-zein. This study thus reveals a mechanism for accumulation of NZPs in PBs and suggests a potential application for the accumulation of foreign proteins in maize PBs.

Interaction mechanism of kafirin with ferulic acid and tetramethyl pyrazine: Multiple spectroscopic and molecular modeling studies

Ferulic acid (FA) and tetramethyl pyrazine (TMP) are intrinsic bioactive compounds in baijiu, and kafirin is the major protein of sorghum, which is the raw material of baijiu. In this study, the interactions of kafirin-FA and kafirin-TMP were investigated by multiple spectroscopic and molecular modeling techniques. Fluorescence spectra showed that intrinsic fluorescence of kafirin drastically quenched because of the formations of kafirin-FA and kafirin-TMP complexes. The CD studies indicated that the combination with FA or TMP decreased the α-helix content of kafirin slightly. The shifts and intensity changes of UV-Vis, FTIR and fluorescence spectra confirmed the formations of complexes. Moreover, the molecular docking and molecular dynamics studies showed that hydrophobic interactions and hydrogen bonds played major roles in the formations of kafirin-FA and kafirin-TMP complexes, and the formations of complexes made kafirin structures more compact. This work is of great importance for further quality improvement in baijiu and alcoholic beverages.

Electrospinning Proteins for Wound Healing Purposes: Opportunities and Challenges

With the growth of the aging population worldwide, chronic wounds represent an increasing burden to healthcare systems. Wound healing is complex and not only affected by the patient's physiological conditions, but also by bacterial infections and inflammation, which delay wound closure and re-epithelialization. In recent years, there has been a growing interest for electrospun polymeric wound dressings with fiber diameters in the nano- and micrometer range. Such wound dressings display a number of properties, which support and accelerate wound healing. For instance, they provide physical and mechanical protection, exhibit a high surface area, allow gas exchange, are cytocompatible and biodegradable, resemble the structure of the native extracellular matrix, and deliver antibacterial agents locally into the wound. This review paper gives an overview on cytocompatible and biodegradable fibrous wound dressings obtained by electrospinning proteins and peptides of animal and plant origin in recent years. Focus is placed on the requirements for the fabrication of such drug delivery systems by electrospinning as well as their wound healing properties and therapeutic potential. Moreover, the incorporation of antimicrobial agents into the fibers or their attachment onto the fiber surface as well as their antimicrobial activity are discussed.

Arabidopsis cargo receptor NBR1 mediates selective autophagy of defective proteins

Aggrephagy, a type of selective autophagy that sequesters protein aggregates for degradation in the vacuole, is an important protein quality control mechanism, particularly during cell stress. In mammalian cells, aggrephagy and several other forms of selective autophagy are mediated by dedicated cargo receptors such as NEIGHBOR OF BRCA1 (NBR1). Although plant NBR1 homologs have been linked to selective autophagy during biotic stress, it remains unclear how they impact selective autophagy under non-stressed and abiotic stress conditions. Through microscopic and biochemical analysis of nbr1 mutants expressing autophagy markers and an aggregation-prone reporter, we tested the connection between NBR1 and aggrephagy in Arabidopsis. Although NBR1 is not essential for general autophagy, or for the selective clearance of peroxisomes, mitochondria, or the ER, we found that NBR1 is required for the heat-induced formation of autophagic vesicles. Moreover, cytoplasmic puncta containing aggregation-prone proteins, which were rarely observed in wild-type plants, were found to accumulate in nbr1 mutants under both control and heat stress conditions. Given that NBR1 co-localizes with these cytoplasmic puncta, we propose that Arabidopsis NBR1 is a plant aggrephagy receptor essential for maintaining proteostasis under both heat stress and non-stress conditions.

Structure, Organization, and Expression of the Alpha Prolamin Multigenic Family Bring New Insights into the Evolutionary Relationships among Grasses

Prolamins are the major seed storage proteins of grasses. In maize and related species, prolamins are classified into α-, β-, γ-, and δ-subclasses by their solubility properties. α-prolamins are encoded by multigene families and have a secondary structure that consists of tandem α-helix repeats. Maize has two α-prolamin subclasses, namely the 19 and 22 kDa subclasses that contain nine and 10 α-helix repeats, respectively. Here, we present an evolutionary study based on the structure, organization, and expression of α-prolamins in maize, sugarcane, sorghum, and coix. True 22 kDa subclasses containing 10 repeats are conserved in all four species, but true 19 kDa subclasses containing nine repeats are found only in maize and sugarcane. We discovered a 19 kDa-like α-coixin that, as in sorghum, is encoded by few genes. These data suggest that a 19 kDa progenitor present in the ancestor common to maize, coix, sorghum, and sugarcane was preserved at low copy number in coix and sorghum, while amplified into multigene family architecture in maize and sugarcane. The expression profiling of α-prolamins, verified by two-dimensional gels, showed highly conserved multispot composition for the 19 kDa α-prolamins in maize and sugarcane. Coix and sorghum did not present true 19 kDa α-prolamin spots. Our data show remarkable similarity between maize and sugarcane 19 kDa α-prolamins regarding both gene structure and expression. Since the multigene architecture of 19 kDa α-canein appeared after sugarcane diverged from sorghum, our data suggest that maize and sugarcane might have acquired the multigene family encoding these storage proteins from a common ancestor.

Nanoscale characterization of zein self-assembly

Zein, a major protein of corn, is rich in α-helical structure. It has an amphiphilic character and is capable of self-assembly. Zein can self-assemble into various mesostructures that may find applications in food, agricultural, and biomedical engineering. Understanding the mechanism of zein self-assembly at the nanoscale is important for further development of zein structures. In this work, high-resolution transmission electron microscopy (TEM) images revealed nanosize zein stripes, rings, and discs containing a 0.35 nm periodicity, which is characteristic of β-sheet. TEM images were interpreted in terms of the transformation of original α-helices into β-sheet conformation after evaporation-induced self-assembly (EISA). The presence of β-sheet was also detected by circular dichroism (CD) spectroscopy. Zein β-sheets self-assembled into stripes, which curled into rings. Rings formed discs and eventually spheres. The formation of zein nanostructures was believed to be the result of β-sheet orientation, alignment, and packing.

Allelic variation of the β-, γ- and δ-kafirin genes in diverse Sorghum genotypes

The β-, γ- and δ-kafirin genes were sequenced from 35 Sorghum genotypes to investigate the allelic diversity of seed storage proteins. A range of grain sorghums, including inbred parents from internationally diverse breeding programs and landraces, and three wild Sorghum relatives were selected to encompass an extensive array of improved and unimproved germplasm in the Eusorghum. A single locus exists for each of the expressed kafirin-encoding genes, unlike the multigenic α-kafirins. Significant diversity was found for each locus, with the cysteine-rich β-kafirin having four alleles, including the first natural null mutant reported for this prolamin subfamily. This allele contains a frame shift insertion at +206 resulting in a premature stop codon. SDS-PAGE revealed that lines with this allele do not produce β-kafirin. An analysis of flour viscosity reveals that these β-kafirin null lines have a difference in grain quality, with significantly lower viscosity observed over the entire Rapid ViscoAnalyser time course. There was less diversity at the protein level within the cysteine-rich γ-kafirin, with only two alleles in the cultivated sorghums. There were only two alleles for the δ-kafirin locus among the S. bicolor germplasm, with one allele encoding ten extra amino acids, of which five were methionine residues, with an additional methionine resulting from a nucleotide substitution. This longer allele encodes a protein with 19.1% methionine. The Asian species, S. propinquum, had distinct alleles for all three kafirin genes. We found no evidence for selection on the three kafirin genes during sorghum domestication even though the δ-kafirin locus displayed comparatively low genetic variation. This study has identified genetic diversity in all single copy seed storage protein genes, including a null mutant for β-kafirin in Sorghum.

Molecular cloning, mass spectrometric identification, and nutritional evaluation of 10 coixins in adlay ( Coix lachryma-jobi L.)

Adlay (Coix lachryma-jobi L. var. ma-yuen Stapf) is regarded as a nutritive food source as well as herbal medicine. The food nutrition is a consequence of its high protein content and superior amino acid composition. From ca. 200 expressed sequence tag (EST) sequences in maturing adlay grains, clones encoding precursor polypeptides of 10 seed storage proteins in the prolamin family, including 8 alpha-coixin isoforms, 1 delta-coixin, and 1 gamma-coixin, were identified. Full-length cDNA fragments encoding these 10 coixins were obtained by PCR cloning. Mass spectrometric analyses confirmed the presence of these 10 coixins in the extract of adlay grain. Calculated amino acid compositions indicate that all 10 coixins are rich in glutamine (>20% in alpha-coixin isoforms, 13.3% in delta-coixin, and 31.2% in gamma-coixin). The 8 alpha-coixin isoforms are low in methionine, cysteine, and lysine (on average, 0.8, 0.6, and 0.1%, respectively). However, the delta-coixin is a sulfur-rich protein (18.2% methionine and 9.1% cysteine), and the gamma-coixin is a nutritive protein composed of 2.0% methionine, 6.6% cysteine, 2.6% lysine, and 8.9% histidine. The company of delta-coixin and gamma-coixin with alpha-coixin isoforms enhances the nutritional value of alday grain for human consumption.

Effects of enzymatic deamidation by protein-glutaminase on structure and functional properties of alpha-zein

The performance of novel protein-glutaminase (PG) purified from Chryseobacterium proteolyticumon alpha-zein was investigated. Highly insoluble alpha-zein was able to be deamidated to the extent of deamidation degree 62% by using 50 mM potassium phosphate (pH 8) containing 11.7% ethanol, at 40 degrees C for 137 h. Analysis by sodium dodecyl sulfate polyacrylamide-gel electrophoresis showed that deamidated and non-deamidated zeins have different mobilities. Results of circular dichroism spectra revealed the decline in alpha-helix contents of alpha-zein by deamidation. Besides, Fourier transform infrared spectroscopy analysis demonstrated alterations in the secondary structure of alpha-zein by deamidation. The assignment of the amide I region showed a remarkable decrease in antiparallel intermolecular beta-sheets (around 1690 cm(-1)) as an indication of the weakening aggregation ability of the deamidated molecules. Solubility and emulsification properties of alpha-zein, particularly at pH 7, were remarkably improved after the deamidation by PG. Gas chromatography and peroxide value studies pointed out that deamidated alpha-zein in powder form exhibited an inferior antioxidative property as compared with the non-deamidated one.

The accumulation of alpha-zein in transgenic tobacco endosperm is stabilized by co-expression of beta-zein

The cysteine-poor alpha-zein is the major prolamin storage protein fraction in maize endosperm and is localized in the interior of protein bodies with delta-zein, whereas the hydrophobic cysteine-rich beta- and gamma-zein are found on the exterior of the PB. In transgenic tobacco endosperm expressing zein genes, alpha-zein was unstable unless co-expressed with gamma-zein. Here we showed that alpha-zein was also stabilized by beta-zein. Small accretions of alpha- and beta-zeins, similar in appearance to maize protein bodies, were localized to the endoplasmic reticulum within tobacco endosperm cells. The zein proteins were also localized to protein storage vacuoles in a more dispersed pattern, suggesting that they were transported there after they were post-translationally sequestered into the ER.

Conformation of the Z19 prolamin by FTIR, NMR, and SAXS

The alpha zein, the maize storage prolamin, is a mixture of several homologous polypeptides that shows two bands in SDS-PAGE, called Z19 and Z22. The conformation studies carried out by several authors in this mixture are conflicting. To elucidate these inconsistencies, we analyzed the conformation of the Z19 fraction, extracted from BR451 maize variety by Fourier transform infrared spectroscopy, nuclear magnetic resonance, and small-angle X-ray scattering. The infrared results show that Z19 has 46% of alpha helix and 22% of beta sheet. The fast N-H to N-D exchange measured by (1)H NMR spectroscopy showed that Z19 is not a compact structure. The scattering measurements indicated an extended structure with 12 by 130 A. With these data, we have modeled the Z19 structure as a hairpin, composed of helical, sheet, turns, and secondary structures, folded back on itself.

Conformation of ? zeins in solid state by Fourier transform IR

The major maize storage proteins (alpha zeins) are deposited as an insoluble mass in the protein bodies of the endosperm. Because they are insoluble in water, most structural studies are performed in alcohol solutions. To solve the question raised by several authors about denaturation of the alpha zein structure by alcohol, we analyze the secondary structure of alpha zeins prepared with and without solubilization in alcohol (corn gluten meal and protein bodies with high concentrations of alpha zeins and traces of beta zeins). The secondary structures of alpha zeins are analyzed in the solid state by Fourier transform IR spectroscopy (FTIR) in KBr pellets and solid-state 13C-NMR spectroscopy. The proportion of secondary structures obtained by FTIR of alpha zeins prepared with and without solubilization in alcohol yield almost identical proportions of alpha helices and beta sheets. The proportion of alpha helices (43%) agrees with that measured by circular dichroism in an alcohol solution. However, the proportion of beta sheets (28%) is higher than the one measured by the same technique. Gluten and protein body samples with high beta zein content showed higher beta sheet and lower alpha helix proportions than that obtained for alpha zein preparations. The solid-state 13C-NMR spectra show the carbonyl peak for the alpha zeins at delta 176 and for the sample rich in beta zeins at delta 172, which demonstrates the presence of a high content of alpha helices and beta sheets, respectively. These results indicate that alcohol solubilization does not affect the conformation of alpha zeins, validating the secondary structure measurements in solution.

Identification of free fatty acids in maize protein bodies and purified alpha zeins by (13)C and (1)H nuclear magnetic resonance

Zeins, the maize storage proteins, are the most abundant proteins in the corn endosperm, and are synthesized on the rough endoplasmatic reticulum and deposited in discrete organelles called protein bodies. Several authors, using circular dichroism and optical rotatory dispersion, have concluded that these proteins have a high alpha-helical content in alcoholic solution. In this work we have studied these proteins, within the protein bodies themselves and after extraction from the corn grains with 70% ethanol, using NMR (nuclear magnetic resonance) spectroscopy. We conclusively demonstrate the presence of free fatty acids within both the protein bodies and also in the alcohol extracted alpha zeins. We present evidence for a direct interaction between the free fatty acids and the alpha zein proteins within the protein body and suggest possible mechanisms by which such an association has arisen during the evolution of the maize endosperm.

Three-dimensional structure of maize alpha-zein proteins studied by small-angle X-ray scattering

alpha-zeins of maize (Zea mays) that are storage proteins contain nine or ten tandem repeats comprising of about 20 amino acids. Small-angle X-ray scattering (SAXS) of alpha-zeins was measured in 70% (v/v) aqueous ethanol containing beta-mercaptoethanol or without reagent in a protein concentration range of 2.0 to 40.0 mg/ml. The overall radius of gyration of whole particles, Rg, and the corresponding radius of gyration of the cross-section, Rc, of reduced alpha-zeins are 4.00 +/- 0.03 nm and 1.39 +/- 0.05 nm, respectively, in the 70% (v/v) aqueous ethanol containing 2% (v/v) beta-mercaptoethanol. Analyses using the Rg and Rc values indicate that reduced alpha-zeins exist as asymmetric particles with the length of about 13 nm in the solution. A structural model is developed under assumption that each of tandem repeats units forms single alpha-helix and they are joined by glutamine-rich 'turns' or loops, as employed by Argos et al., [Argos, O., Pedersen, K., Marks, M.D. and Larkins, B.A. (1982) J. Biol. Chem. 257, 9984-9990] and Garratt et al. [Garratt, R., Oliva, G., Caracelli, I., Leite, A. and Arruda, P. (1993) Proteins Struc. Func. Genet. 15, 88-99], and that the longest dimension of 13 nm comes from linear stacking of the anti-parallel helices of tandem repeat in the direction perpendicular to the helical axis. The resultant model is presented by an elongated prism-like shape with an approximate axial ratio of 6:1.

A defective signal peptide in the maize high-lysine mutant floury 2

The maize floury 2 (fl2) mutation enhances the lysine content of the grain, but the soft texture of the endosperm makes it unsuitable for commercial production. The mutant phenotype is linked with the appearance of a 24-kDa alpha-zein protein and increased synthesis of binding protein, both of which are associated with irregularly shaped protein bodies. We have cloned the gene encoding the 24-kDa protein and show that it is expressed as a 22-kDa alpha-zein with an uncleaved signal peptide. Comparison of the deduced N-terminal amino acid sequence of the 24-kDa alpha-zein protein with other alpha-zeins revealed an alanine to valine substitution at the C-terminal position of the signal peptide, a histidine insertion within the seventh alpha-helical repeat, and an alanine to threonine substitution with the same alpha-helical repeat of the protein. Structural defects associated with this alpha-zein explain many of the phenotypic effects of the fl2 mutation.

Sequence analysis of 22 kDa-like alpha-coixin genes and their comparison with homologous zein and kafirin genes reveals highly conserved protein structure and regulatory elements

Several genomic and cDNA clones encoding the 22 kDa-like alpha-coixin, the alpha-prolamin of Coix seeds, were isolated and sequenced. Three contiguous 22 kDa-like alpha-coixin genes designated alpha-3A, alpha-3B and alpha-3C were found in the 15 kb alpha-3 genomic clone. The alpha-3A and alpha-3C genes presented in-frame stop codons at position +652. The two genes with truncated ORFs are flanking the alpha-3B gene, suggesting that the three alpha-coixin genes may have arisen by tandem duplication and that the stop codon was introduced before the duplication. Comparison of the deduced amino acid sequences of alpha-coixin clones with the published sequences of 22 kDa alpha-zein and 22 kDa-like alpha-kafirin revealed a highly conserved protein structure. The protein consists of an N-terminus, containing the signal peptide, followed by ten highly conserved tandem repeats of 15-20 amino acids flanked by polyglutamines, and a short C-terminus. The difference between the 22 kDa-like alpha-prolamins and the 19 kDa alpha-zein lies in the fact that the 19 kDa protein is exactly one repeat motif shorter than the 22 kDa proteins. Several putative regulatory sequences common to the zein and kafirin genes were identified within both the 5' and 3' flanking regions of alpha-3B. Nucleotide sequences that match the consensus TATA, CATC and the ca. -300 prolamin box are present at conserved positions in alpha-3B relative to zein and kafirin genes. Two putative Opaque-2 boxes are present in alpha-3B that occupies approximately the same positions as those identified for the 22 kDa alpha-zein and alpha-kafirin genes. Southern hybridization, using a fragment of a maize Opaque-2 cDNA clone as a probe, confirmed the presence of Opaque-2 homologous sequences in the Coix and sorghum genomes. The overall results suggest that the structural and regulatory genes involved in the expression of the 22 kDa-like alpha-prolamin genes of Coix, sorghum and maize, originated from a common ancestor, and that variations were introduced in the structural and regulatory sequences after species separation.