Non-plant Proteins Research Articles

The Effect of Plant-Based Protein Ingestion on Athletic Ability in Healthy People-A Bayesian Meta-Analysis with Systematic Review of Randomized Controlled Trials.

Plant-based protein supplements are increasingly popular, yet their efficacy in enhancing athletic performance compared to animal protein, insect protein, or other protein types remains under investigation. This study aimed to assess the effectiveness of plant-based protein on athletic abilities such as muscle strength, endurance performance, and muscle protein synthesis (MPS) rate and compare it to no- or low-protein ingestion and non-plant protein sources. Randomized controlled trials (RCTs) evaluating the beneficial and harmful effects of plant-based protein ingestion on athletic ability in healthy individuals were considered. A systematic search of six databases yielded 2152 studies, which were screened using the Covidence systematic review tool. Thirty-one studies were included for meta-analysis after independent selection, data extraction, and risk of bias assessment by two reviewers. The meta-analysis employed a Bayesian approach using the Markov chain Monte Carlo (MCMC) method through a random-effects model. The results demonstrated that plant-based protein supplements provided greater benefits for athletic performance in healthy individuals compared to the no- or low-protein ingestion group [μ(SMD): 0.281, 95% CI: 0.159 to 0.412; heterogeneity τ: 0.18, 95% CI: 0.017 to 0.362]. However, when compared to other types of protein, plant-based protein ingestion was less effective in enhancing athletic ability [μ(SMD): -0.119, 95% CI: -0.209 to -0.028; heterogeneity τ: 0.076, 95% CI: 0.003 to 0.192]. A subgroup analysis indicated significant improvements in muscle strength and endurance performance in both young and older individuals consuming plant-based protein compared to those with no- or low-protein ingestion. Nonetheless, other protein types showed greater benefits in muscle strength compared to plant-based protein [μ(SMD): -0.133, 95% CI: -0.235 to -0.034; heterogeneity τ: 0.086, 95% CI: 0.004 to 0.214]. In conclusion, while plant-based protein ingestion demonstrates superior efficacy compared to low- or no-protein ingestion, it is not as effective as other protein types such as whey, beef, or milk protein in enhancing athletic performance in healthy individuals. Registration: Registered at the International Prospective Register of Systematic Reviews (PROSPERO) (identification code CRD42024555804).

Development of a Sequence Searchable Database of Celiac Disease-Associated Peptides and Proteins for Risk Assessment of Novel Food Proteins.

Celiac disease (CeD) is an autoimmune enteropathy induced by prolamin and glutelin proteins in wheat, barley, rye, and triticale recognized by genetically restricted major histocompatibility (MHC) receptors. Patients with CeD must avoid consuming these proteins. Regulators in Europe and the United States expect an evaluation of CeD risks from proteins in genetically modified (GM) crops or novel foods for wheat-related proteins. Our database includes evidence-based causative peptides and proteins and two amino acid sequence comparison tools for CeD risk assessment. Sequence entries are based on the review of published studies of specific gluten-reactive T cell activation or intestinal epithelial toxicity. The initial database in 2012 was updated in 2018 and 2022. The current database holds 1,041 causative peptides and 76 representative proteins. The FASTA sequence comparison of 76 representative CeD proteins provides an insurance for possible unreported epitopes. Validation was conducted using protein homologs from Pooideae and non-Pooideae monocots, dicots, and non-plant proteins. Criteria for minimum percent identity and maximum E-scores are guidelines. Exact matches to any of the 1,041 peptides suggest risks, while FASTA alignment to the 76 CeD proteins suggests possible risks. Matched proteins should be tested further by CeD-specific CD4/8+ T cell assays or in vivo challenges before their use in foods.

SubMito-XGBoost: predicting protein submitochondrial localization by fusing multiple feature information and eXtreme gradient boosting.

Mitochondria are an essential organelle in most eukaryotes. They not only play an important role in energy metabolism but also take part in many critical cytopathological processes. Abnormal mitochondria can trigger a series of human diseases, such as Parkinson's disease, multifactor disorder and Type-II diabetes. Protein submitochondrial localization enables the understanding of protein function in studying disease pathogenesis and drug design. We proposed a new method, SubMito-XGBoost, for protein submitochondrial localization prediction. Three steps are included: (i) the g-gap dipeptide composition (g-gap DC), pseudo-amino acid composition (PseAAC), auto-correlation function (ACF) and Bi-gram position-specific scoring matrix (Bi-gram PSSM) are employed to extract protein sequence features, (ii) Synthetic Minority Oversampling Technique (SMOTE) is used to balance samples, and the ReliefF algorithm is applied for feature selection and (iii) the obtained feature vectors are fed into XGBoost to predict protein submitochondrial locations. SubMito-XGBoost has obtained satisfactory prediction results by the leave-one-out-cross-validation (LOOCV) compared with existing methods. The prediction accuracies of the SubMito-XGBoost method on the two training datasets M317 and M983 were 97.7% and 98.9%, which are 2.8-12.5% and 3.8-9.9% higher than other methods, respectively. The prediction accuracy of the independent test set M495 was 94.8%, which is significantly better than the existing studies. The proposed method also achieves satisfactory predictive performance on plant and non-plant protein submitochondrial datasets. SubMito-XGBoost also plays an important role in new drug design for the treatment of related diseases. The source codes and data are publicly available at https://github.com/QUST-AIBBDRC/SubMito-XGBoost/. Supplementary data are available at Bioinformatics online.

The mitochondrial monothiol glutaredoxin S15 is essential for iron-sulfur protein maturation in Arabidopsis thaliana

The iron-sulfur cluster (ISC) is an ancient and essential cofactor of many proteins involved in electron transfer and metabolic reactions. In Arabidopsis, three pathways exist for the maturation of iron-sulfur proteins in the cytosol, plastids, and mitochondria. We functionally characterized the role of mitochondrial glutaredoxin S15 (GRXS15) in biogenesis of ISC containing aconitase through a combination of genetic, physiological, and biochemical approaches. Two Arabidopsis T-DNA insertion mutants were identified as null mutants with early embryonic lethal phenotypes that could be rescued by GRXS15. Furthermore, we showed that recombinant GRXS15 is able to coordinate and transfer an ISC and that this coordination depends on reduced glutathione (GSH). We found the Arabidopsis GRXS15 able to complement growth defects based on disturbed ISC protein assembly of a yeast Δgrx5 mutant. Modeling of GRXS15 onto the crystal structures of related nonplant proteins highlighted amino acid residues that after mutation diminished GSH and subsequently ISC coordination, as well as the ability to rescue the yeast mutant. When used for plant complementation, one of these mutant variants, GRXS15K83/A, led to severe developmental delay and a pronounced decrease in aconitase activity by approximately 65%. These results indicate that mitochondrial GRXS15 is an essential protein in Arabidopsis, required for full activity of iron-sulfur proteins.

Soya bean Gα proteins with distinct biochemical properties exhibit differential ability to complement Saccharomyces cerevisiae gpa1 mutant

Signalling pathways mediated by heterotrimeric G-proteins are common to all eukaryotes. Plants have a limited number of each of the G-protein subunits, with the most elaborate G-protein network discovered so far in soya bean (Glycine max, also known as soybean) which has four Gα, four Gβ and ten Gγ proteins. Biochemical characterization of Gα proteins from plants suggests significant variation in their properties compared with the well-characterized non-plant proteins. Furthermore, the four soya bean Gα (GmGα) proteins exhibit distinct biochemical activities among themselves, but the extent to which such biochemical differences contribute to their invivo function is also not known. We used the yeast gpa1 mutant which displays constitutive signalling and growth arrest in the pheromone-response pathway as an invivo model to evaluate the effect of distinct biochemical activities of GmGα proteins. We showed that specific GmGα proteins can be activated during pheromone-dependent receptor-mediated signalling in yeast and they display different strengths towards complementation of yeast gpa1 phenotypes. We also identified amino acids that are responsible for differential complementation abilities of specific Gα proteins. These data establish that specific plant Gα proteins are functional in the receptor-mediated pheromone-response pathway in yeast and that the subtle biochemical differences in their activity are physiologically relevant.

Phylogeny and a structural model of plant MHX transporters.

BackgroundThe Arabidopsis thaliana MHX gene (AtMHX) encodes a Mg2+/H+ exchanger. Among non-plant proteins, AtMHX showed the highest similarity to mammalian Na+/Ca2+ exchanger (NCX) transporters, which are part of the Ca2+/cation (CaCA) exchanger superfamily.ResultsSequences showing similarity to AtMHX were searched in the databases or sequenced from cDNA clones. Phylogenetic analysis showed that the MHX family is limited to plants, and constitutes a sixth family within the CaCA superfamily. Some plants include, besides a full MHX gene, partial MHX-related sequences. More than one full MHX gene was currently identified only in Oryza sativa and Mimulus guttatus, but an EST for more than one MHX was identified only in M. guttatus. MHX genes are not present in the currently available chlorophyte genomes. The prevalence of upstream ORFs in MHX genes is much higher than in most plant genes, and can limit their expression. A structural model of the MHXs, based on the resolved structure of NCX1, implies that the MHXs include nine transmembrane segments. The MHXs and NCXs share 32 conserved residues, including a GXG motif implicated in the formation of a tight-turn in a reentrant-loop. Three residues differ between all MHX and NCX proteins. Altered mobility under reducing and non-reducing conditions suggests the presence of an intramolecular disulfide-bond in AtMHX.ConclusionsThe absence of MHX genes in non-plant genomes and in the currently available chlorophyte genomes, and the presence of an NCX in Chlamydomonas, are consistent with the suggestion that the MHXs evolved from the NCXs after the split of the chlorophyte and streptophyte lineages of the plant kingdom. The MHXs underwent functional diploidization in most plant species. De novo duplication of MHX occurred in O. sativa before the split between the Indica and Japonica subspecies, and was apparently followed by translocation of one MHX paralog from chromosome 2 to chromosome 11 in Japonica. The structural analysis presented and the identification of elements that differ between the MHXs and the NCXs, or between the MHXs of specific plant groups, can contribute to clarification of the structural basis of the function and ion selectivity of MHX transporters.

Predicting Protein Subcellular Location Using Chous Pseudo Amino Acid Composition and Improved Hybrid Approach

The location of a protein in a cell is closely correlated with its biological function. Based on the concept that the protein subcellular location is mainly determined by its amino acid and pseudo amino acid composition (PseAA), a new algorithm of increment of diversity combined with support vector machine is proposed to predict the protein subcellular location. The subcellular locations of plant and non-plant proteins are investigated by our method. The overall prediction accuracies in jackknife test are 88.3% for the eukaryotic plant proteins and 92.4% for the eukaryotic non-plant proteins, respectively. In order to estimate the effect of the sequence identity on predictive result, the proteins with sequence identity <or=40% are selected. The overall success rates of prediction are 86.2% and 92.3% for plant and non-plant proteins in jackknife test, respectively.

Bidirectional Long Short-Term Memory Networks for Predicting the Subcellular Localization of Eukaryotic Proteins

An algorithm called Bidirectional Long Short-Term Memory Networks (BLSTM) for processing sequential data is introduced. This supervised learning method trains a special recurrent neural network to use very long ranged symmetric sequence context using a combination of nonlinear processing elements and linear feedback loops for storing long-range context. The algorithm is applied to the sequence-based prediction of protein localization and predicts 93.3 percent novel non-plant proteins and 88.4 percent novel plant proteins correctly, which is an improvement over feedforward and standard recurrent networks solving the same problem. The BLSTM system is available as a web-service (http://www.stepc.gr/~synaptic/blstm.html).

WVD2 is a novel microtubule‐associated protein in Arabidopsis thaliana

Arabidopsis WAVE-DAMPENED 2 (WVD2) was identified by forward genetics as an activation-tagged allele that causes plant and organ stockiness and inversion of helical root growth handedness on agar surfaces. Plants with high constitutive expression of WVD2 or other members of the WVD2-LIKE (WDL) gene family have stems and roots that are short and thick, have reduced anisotropic cell elongation, are suppressed in a root-waving phenotype, and have inverted handedness of twisting in hypocotyls and roots compared with wild-type. The wvd2-1 mutant shows aberrantly organized cortical microtubules in peripheral root cap cells as well as reduced branching of trichomes, unicellular leaf structures whose development is regulated by microtubule stability. Orthologs of the WVD2/WDL family are found widely throughout the plant kingdom, but are not similar to non-plant proteins with the exception of a C-terminal domain distantly related to the vertebrate microtubule-associated protein TPX2. in vivo, WVD2 and its closest paralog WDL1 are localized to interphase cortical microtubules in leaves, hypocotyls and roots. Recombinant glutathione-S-transferase:WVD2 or maltose binding protein:WVD2 protein bind to and bundle microtubules in vitro. We speculate that a C-terminal domain of TPX2 has been utilised by the WVD2 family for functions critical to the organization of plant microtubules.

PTARGET: a web server for predicting protein subcellular localization

The pTARGET web server enables prediction of nine distinct protein subcellular localizations in eukaryotic non-plant species. Predictions are made using a new algorithm [C. Guda and S. Subramaniam (2005) pTARGET [corrected] a new method for predicting protein subcellular localization in eukaryotes. Bioinformatics, 21, 3963–3969], which is primarily based on the occurrence patterns of location-specific protein functional domains in different subcellular locations. We have implemented a relational database, PreCalcDB, to store pre-computed prediction results for all eukaryotic non-plant protein sequences in the public domain that includes about 770 000 entries. Queries can be made by entering protein sequences or by uploading a file containing up to 5000 protein sequences in FASTA format. Prediction results for queries with matching entries in the PreCalcDB will be retrieved instantly; while for the missing ones new predictions will be computed and sent by email. Pre-computed predictions can also be downloaded for complete proteomes of Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila, Mus musculus and Homo sapiens. The server, its documentation and the data are accessible from .

An alternative test protein for the determination of protein precipitation capacity of tannins

Tannins are secondary plant compounds frequently encountered in tropical feeds. They are known to complex with proteins, thus reducing the availability of protein to ruminants. Tannin determination is thus a crucial factor when estimating the feed quality of tropical plants. Bovine serum albumin (BSA), which is commonly used in tannin binding assays has the drawbacks of being a non-plant protein and requires a rather low pH (4.9, iso-electric point of BSA) for complex formation with tannins. Papain is a commercially available pure protein from Carica papaya that may be a suitable alternative. This study evaluates papain as a test protein in a tannin binding assay in comparison to BSA by determining the specific protein precipitation capacity (sPPC) of the tannin rich plants, Salix alba (salix) and Rhus typhina (sumach). Salix and sumach leaves contain exclusively condensed tannins and hydrolysable tannins respectively.

From endonucleases to transcription factors: evolution of the AP2 DNA binding domain in plants.

All members of the AP2/ERF family of plant transcription regulators contain at least one copy of a DNA binding domain called the AP2 domain. The AP2 domain has been considered plant specific. Here, we show that homologs are present in the cyanobacterium Trichodesmium erythraeum, the ciliate Tetrahymena thermophila, and the viruses Enterobacteria phage Rb49 and Bacteriophage Felix 01. We demonstrate that the T. erythraeum AP2 domain selectively binds stretches of poly(dG)/poly(dC) showing functional conservation with plant AP2/ERF proteins. The newly discovered nonplant proteins bearing an AP2 domain are predicted to be HNH endonucleases. Sequence conservation extends outside the AP2 domain to include part of the endonuclease domain for the T. erythraeum protein and some plant AP2/ERF proteins. Our phylogenetic analysis of the broader family of AP2 domains supports the possibility of lateral gene transfer. We hypothesize that a horizontal transfer of an HNH-AP2 endonuclease from bacteria or viruses into plants may have led to the origin of the AP2/ERF family of transcription factors via transposition and homing processes.

Predicting subcellular localization of proteins by hybridizing functional domain composition and pseudo-amino acid composition.

Recent advances in large-scale genome sequencing have led to the rapid accumulation of amino acid sequences of proteins whose functions are unknown. Since the functions of these proteins are closely correlated with their subcellular localizations, many efforts have been made to develop a variety of methods for predicting protein subcellular location. In this study, based on the strategy by hybridizing the functional domain composition and the pseudo-amino acid composition (Cai and Chou [2003]: Biochem. Biophys. Res. Commun. 305:407-411), the Intimate Sorting Algorithm (ISort predictor) was developed for predicting the protein subcellular location. As a showcase, the same plant and non-plant protein datasets as investigated by the previous investigators were used for demonstration. The overall success rate by the jackknife test for the plant protein dataset was 85.4%, and that for the non-plant protein dataset 91.9%. These are so far the highest success rates achieved for the two datasets by following a rigorous cross validation test procedure, further confirming that such a hybrid approach may become a very useful high-throughput tool in the area of bioinformatics, proteomics, as well as molecular cell biology.

Analysis of the plastidic phosphate translocator gene family in Arabidopsis and identification of new phosphate translocator-homologous transporters, classified by their putative substrate-binding site.

Analysis of the Arabidopsis genome revealed the complete set of plastidic phosphate translocator (pPT) genes. The Arabidopsis genome contains 16 pPT genes: single copies of genes coding for the triose phosphate/phosphate translocator and the xylulose phosphate/phosphate translocator, and two genes coding for each the phosphoenolpyruvate/phosphate translocator and the glucose-6-phosphate/phosphate translocator. A relatively high number of truncated phosphoenolpyruvate/phosphate translocator genes (six) and glucose-6-phosphate/phosphate translocator genes (four) could be detected with almost conserved intron/exon structures as compared with the functional genes. In addition, a variety of PT-homologous (PTh) genes could be identified in Arabidopsis and other organisms. They all belong to the drug/metabolite transporter superfamily showing significant similarities to nucleotide sugar transporters (NSTs). The pPT, PTh, and NST proteins all possess six to eight transmembrane helices. According to the analysis of conserved motifs in these proteins, the PTh proteins can be divided into (a) the lysine (Lys)/arginine group comprising only non-plant proteins, (b) the Lys-valine/alanine/glycine group of Arabidopsis proteins, (c) the Lys/asparagine group of Arabidopsis proteins, and (d) the Lys/threonine group of plant and non-plant proteins. None of these proteins have been characterized so far. The analysis of the putative substrate-binding sites of the pPT, PTh, and NST proteins led to the suggestion that all these proteins share common substrate-binding sites on either side of the membrane each of which contain a conserved Lys residue.

Potential β-Sheet Surfaces of Corn and Wheat Proteins

Comparison of computed profiles for β-sheet conformations of zein, glutelin, gliadin, glutenin, and other cereal or nonplant proteins discloses unusual distributions of volume, polarity, and chemic...

Plant hormone receptors: Comparison of napthaleneacetic acid binding by maize extracts and by a non-plant protein

The binding of napthaleneacetic acid (NAA) by the animal protein bovine serum albumin has been studied and compared with the properties of NAA binding by maize extracts. In both systems binding is optimal at an acid pH, it is reversible, saturable and the equilibrium is rapidly established. The ability of a number of auxins, anti-auxins and structurally-related compounds to compete with NAA binding in the two systems have been compared. The results indicate that in assessing whether a plant protein capable of binding auxins is involved in a hormonal response, the ability to bind auxins in a specific and competitive manner should be interpreted with caution.