Isoelectric Point Of Protein Research Articles

Genome-wide identification and characterization of the bZIP family in the Mangrove Plant Kandelia obovata and its role in response to stress

BackgroundThe basic leucine zipper (bZIP) transcription factors play crucial roles in plant growth, development, and responses to environmental changes. The mangrove plant Kandelia obovata, native to subtropical and tropical coastal intertidal zones, has evolved various adaptive mechanisms to cope with unstable muddy substrates, tidal fluctuations, saltwater intrusion, and intense ultraviolet radiation. This study aims to provide a comprehensive characterization of the bZIP gene family in K. obovata and investigate its functional roles in response to environmental stresses.ResultsIn the K. obovata genome, 66 bZIP genes were identified and named KobZIP1 to KobZIP66, categorized based on their chromosomal locations. These KobZIP genes exhibited diversity in physicochemical properties, such as protein length, molecular weight, and isoelectric point, and were all predicted to localize to the nucleus. Phylogenetic and structural analyses classified the KobZIP genes into 12 subfamilies, with subfamily A containing the majority of members. Gene structure analysis revealed variations in the number and position of exons and introns among subfamilies, reflecting their evolutionary history and potential functional diversity. Conserved motif analysis showed that all bZIP family members contained motifs in the basic and hinge regions, with subfamily D displaying the greatest motif diversity. Promoter region analysis identified various cis-acting elements associated with responses to phytohormones (ABA, GA, ET, IAA, MeJA, SA) and environmental stress. The expression patterns of KobZIP genes across different tissues and under various abiotic stress conditions were analyzed using transcriptomic data and experimental validation.ConclusionThis study provides a comprehensive characterization and functional analysis of the bZIP gene family in K. obovata, offering new insights into their roles in plant development and environmental adaptation. The expression profiles of KobZIP genes during root development and post-embryonic stages, along with their responses to ABA, low temperature, and salt stress, underscore their potential significance in the adaptation of mangrove plants to the intertidal environment.

Influence of pH fractionation and salt on Bambara protein–gum arabic interaction and insoluble complex formation

Proteins exhibit remarkable interaction with polysaccharides to form complexes with novel functionality. Nevertheless, the formation of insoluble complexes close to the protein isoelectric point (pI) results in protein–protein interference, low coacervates yield, and limited application in acidified food systems. Hence, pH fractionation with salt was used to extract Bambara groundnut protein to induce a shift in optimum pH (pHopt) of insoluble complexes formed with gum arabic, ultimately improving protein and coacervates yields. Turbidimetric analyses were employed to monitor the interaction between Bambara groundnut protein and gum arabic. Protein isolates from optimised fractionation conditions and insoluble complexes were characterised. The most effective fractionation condition was achieved at pH 2.95, 0.28 M NaCl, producing a substantial pHopt shift to 3.4. This shift was associated with the formation of spherical microparticle complexes and an impressive 70% coacervate yield. Changes in patterns of protein–gum arabic interaction were associated with an increased content of β-sheet, enrichment of legumin subunits, and basic amino acids of the isolate. This approach successfully shifted the formation of insoluble complexes towards a high-acid pH environment, notably away from the pI. Findings from this study create a prospect for future utilisation of pulse grain protein-gum arabic complexes in acidic beverage development.

Large-scale analysis of the PAC domain structure of arogenate dehydratases reveals their evolutionary patterns in angiosperms

Arogenate dehydratase (ADT) is the key limiting enzyme of plant phenylalanine biosynthesis, but some ADTs display a prephenate decarboxylase/dehydratase activity-conferring (PAC) domain. The genome resources of 70 species were employed to identify genes and outline their characteristics, especially the number and type of PAC domain structures. We obtained 522 ADTs, and their size, exon number, amino acid number and putative protein isoelectric point greatly varied from 306 to 2520 bp, 1 to 15, 101 to 839 and 4.37 to 11.18, respectively. We classified the ADTs into Class α (without a PAC domain) (115, 22.0 %), β (with a type I PAC domain) (244, 46.7 %) and γ (with a type II PAC domain) (163, 31.2 %), and their distribution frequencies exhibited large differences among various branches of angiosperms. We found that Class γ members are more conserved than Class β members, although they commonly experienced multiple duplication events and strong purifying selection, which resulted in a small number, and the putative origin order was from Class α to β and then to γ. In addition, the co-occurrence of both Class β and γ members could ensure the survival of angiosperms, while their optimized composition and strategically intertwined regulation may facilitate core eudicot success.

Extremely acidic proteomes and metabolic flexibility in bacteria and highly diversified archaea thriving in geothermal chaotropic brines.

Few described archaeal, and fewer bacterial, lineages thrive under salt-saturating conditions, such as solar saltern crystallizers (salinity above 30% w/v). They accumulate molar K+ cytoplasmic concentrations to maintain osmotic balance ('salt-in' strategy) and have proteins adaptively enriched in negatively charged acidic amino acids. Here we analysed metagenomes and metagenome-assembled genomes from geothermally influenced hypersaline ecosystems with increasing chaotropicity in the Danakil Depression. Normalized abundances of universal single-copy genes confirmed that haloarchaea and Nanohaloarchaeota encompass 99% of microbial communities in the near-life-limiting conditions of the Western-Canyon Lakes. Danakil metagenome- and metagenome-assembled-genome-inferred proteomes, compared with those of freshwater, seawater and solar saltern ponds up to saturation (6-14-32% salinity), showed that Western-Canyon Lake archaea encode the most acidic proteomes ever observed (median protein isoelectric points ≤4.4). We identified previously undescribed haloarchaeal families as well as an Aenigmatarchaeota family and a bacterial phylum independently adapted to extreme halophily. Despite phylum-level diversity decreasing with increasing salinity-chaotropicity, and unlike in solar salterns, adapted archaea exceedingly diversified in Danakil ecosystems, challenging the notion of decreasing diversity under extreme conditions. Metabolic flexibility to utilize multiple energy and carbon resources generated by local hydrothermalism along feast-and-famine strategies seemingly shapes microbial diversity in these ecosystems near life limits.

Effect of verjuice (Vitis vinifera L.) on physicochemical and textural properties of beef M. biceps femoris.

The objective of this study was to investigate the effect of verjuice on beef M. biceps femoris (BF). BF blocks were marinated with 30%, 70%, and 100% verjuice solutions containing 2% NaCl, for different marination times (12, 24, 48, and 72 h). Verjuice marination reduced the pH values of BF samples from 6.77 in control sample to 3.66 in 100% of verjuice for 72 h. The decreased values of water holding capacity (from 54.06% to 47.46%) with increasing verjuice concentration (from 30% to 100% for 72 h) confirmed the drop of proteins isoelectric point of the muscle due to salt presence preventing fibers swelling. Less cookout was observed with increasing acid concentration. Marination time had no significant effect on L* and a* coordinates of uncooked samples while acidification made the samples lighter and less red. Enzymatic proteolysis of myosin and troponin-T concomitant with increase in myofibrillar fragmentation index contributed to the decrease of shear force in a way dependent on verjuice concentration and marination time. Sensory panelists gave the highest score to cooked samples marinated with 70% verjuice solution.

Jeotgalibacillus haloalkalitolerans sp. nov., a novel alkalitolerant and halotolerant bacterium, isolated from the confluence of the Fenhe River and the Yellow River.

A Gram-stain positive, aerobic, alkalitolerant and halotolerant bacterium, designated HH7-29T, was isolated from the confluence of the Fenhe River and the Yellow River in Shanxi Province, PR China. Growth occurred at pH 6.0-12.0 (optimum, pH 8.0-8.5) and 15-40℃ (optimum, 32℃) with 0.5-24% NaCl (optimum, 2-9%). The predominant fatty acids (> 10.0%) were iso-C15:0 and anteiso-C15:0. The major menaquinones were MK-7 and MK-8. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol and two unidentified phospholipids. Phylogenetic analyses based on the 16S rRNA gene sequence revealed that strain HH7-29T was a member of the genus Jeotgalibacillus, exhibiting high sequence similarity to the 16S rRNA gene sequences of Jeotgalibacillus alkaliphilus JC303T (98.4%), Jeotgalibacillus salarius ASL-1T (98.1%) and Jeotgalibacillus alimentarius YKJ-13T (98.1%). The genomic DNA G + C content was 43.0%. Gene annotation showed that strain HH7-29T had lower protein isoelectric points (pIs) and possessed genes related to ion transport and organic osmoprotectant uptake, implying its potential tolerance to salt and alkali. The average nucleotide identity, digital DNA-DNA hybridization values, amino acid identity values, and percentage of conserved proteins values between strain HH7-29T and its related species were 71.1-83.8%, 19.5-27.4%, 66.5-88.4% and 59.8-76.6%, respectively. Based on the analyses of phenotypic, chemotaxonomic, phylogenetic and genomic features, strain HH7-29T represents a novel species of the genus Jeotgalibacillus, for which the name Jeotgalibacillus haloalkalitolerans sp. nov. is proposed. The type strain is HH7-29T (= KCTC 43417T = MCCC 1K07541T).

Marinobacter qingdaonensis sp. nov., a moderately halotolerant bacterium isolated from intertidal sediment.

A Gram-stain-negative, aerobic, rod-shaped and halotolerant bacterium, designated as strain ASW11-75T, was isolated from intertidal sediments in Qingdao, PR China, and identified using a polyphasic taxonomic approach. Growth of strain ASW11-75T occurred at 10-45 °C (optimum, 37 °C), pH 6.5-9.0 (optimum, pH 8.0) and 0.5-18.0 % NaCl concentrations (optimum, 2.5 %). Phylogenetic analyses based on 16S rRNA gene sequences and 1179 single-copy orthologous clusters indicated that strain ASW11-75T is affiliated with the genus Marinobacter. Strain ASW11-75T showed highest 16S rRNA gene sequence similarity to 'Marinobacter arenosus' CAU 1620T (98.5 %). The digital DNA-DNA hybridization and average nucleotide identity values between strain ASW11-75T and its closely related strains (Marinobacter salarius R9SW1T, Marinobacter similis A3d10T, 'Marinobacter arenosus' CAU 1620T, Marinobacter sediminum R65T, Marinobacter salinus Hb8T, Marinobacter alexandrii LZ-8T and Marinobacter nauticus ATCC 49840T) were 19.8-24.5 % and 76.6-80.7 %, respectively. The predominant cellular fatty acids were C16 : 0, C18 : 1 ω9c and C16 : 0 N alcohol. The polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminophospholipid and two unidentified lipids. The major isoprenoid quinone was ubiquinone-9. The genomic DNA G+C content was 62.2 mol%. Based on genomic and gene function analysis, strain ASW11-75T had lower protein isoelectric points with higher ratios of acidic residues to basic residues and possessed genes related to ion transport and organic osmoprotectant uptake, implying its potential tolerance to salt. The results of polyphasic characterization indicated strain ASW11-75T represents a novel Marinobacter species, for which the name Marinobacter qingdaonensis sp. nov. with the type strain ASW11-75T is proposed. The type strain is ASW11-75T (=KCTC 82497T=MCCC 1K05587T).

Orientational Pathways during Protein Translocation through Polymer-Modified Nanopores.

Protein translocation through nanopores holds significant promise for applications in biotechnology, biomolecular analysis, and medicine. However, the interpretation of signals generated by the translocation of the protein remains challenging. In this way, it is crucial to gain a comprehensive understanding on how macromolecules translocate through a nanopore and to identify what are the critical parameters that govern the process. In this study, we investigate the interplay between protein charge regulation, orientation, and nanopore surface modifications using a theoretical framework that allows us to explicitly take into account the acid-base reactions of the titrable amino acids in the proteins and in the polyelectrolytes grafted to the nanopore surface. Our goal is to thoroughly characterize the translocation process of different proteins (GFP, β-lactoglobulin, lysozyme, and RNase) through nanopores modified with weak polyacids. Our calculations show that the charge regulation mechanism exerts a profound effect on the translocation process. The pH-dependent interactions between proteins and charged polymers within the nanopore lead to diverse free energy landscapes with barriers, wells, and flat regions dictating translocation efficiency. Comparison of different proteins allows us to identify the significance of protein isoelectric point, size, and morphology in the translocation behavior. Taking advantage of these insights, we propose pH-responsive nanopores that can load proteins at one pH and release them at another, offering opportunities for controlled protein delivery, separation, and sensing applications.

Exploring viral particle, soil, and extraction buffer physicochemical characteristics and their impacts on extractable viral communities

Viruses are expected to be pivotal members of soil ecosystems, and recent advances in viral size fraction metagenomic (viromic) approaches have improved our ability to interrogate soil viral ecology. However, viromics relies on extraction buffers to effectively desorb viral particles from the soil matrix for downstream analysis, and viral extraction efficiency could be affected by the interplay between viral particles, soils, and extraction buffer chemistry. Here, we investigated whether extraction buffer chemistry affected extractable viral community composition measured by viromics from different soil types, for both biological (samples collected 1 m apart) and technical (subsamples from the same soil homogenate) replicates. We investigated pH manipulation of protein-supplemented phosphate-buffered saline buffer (PPBS, pHs 4.5, 5.5, 6.5, and 7.5) on forest, grassland and wetland soils that exhibited different soil edaphic properties, and we tested different buffer chemistries (PPBS, Carbonated Buffer, Glycine, and Saline Magnesium) on just the wetland soil. Spatial distance (i.e., biological replicate) was the primary driver of extractable viral community composition across all buffers and soils tested. Differences in viral community composition according to extraction buffer properties were only observed in the grassland technical replicates at PPBS buffer pH 4.5, and in both the wetland technical and biological replicates treated with different buffer chemistries, but the effects of buffer chemistry were secondary to spatial distance in the biological replicates. The lack of buffering capacity in the grassland soil technical replicates likely increased sorption of viral particles at pH 4.5, but neither protein composition nor isoelectric point explained this phenomenon. Given that most soil viral ecological studies to date include sample collection over distances much farther apart than the 1-m distances considered here, results suggest that extraction buffer chemistry is likely of much lower importance than ecological considerations, such as spatial distance, in the design of future soil viral ecological investigations.

Investigating the influence of solvent type and pH on protein adsorption onto silica surface by evanescent-wave cavity ring-down spectroscopy.

Several studies have explored the adsorption of various proteins onto solid-liquid interfaces, revealing the crucial role of buffer solutions in biological processes. However, a comprehensive evaluation of the buffer's influence on protein absorption onto fused silica is still lacking. This study employs evanescent-wave cavity ring-down spectroscopy (EW-CRDS) to assess the influence of buffer solutions and pH on the adsorption kinetics of three globular proteins: hemoglobin (Hb), myoglobin (Mb), and cytochrome c (Cyt-C) onto fused silica. The EW-CRDS tool, with a ring-down time of and a minimum detectable absorbance of , enabled precise optical measurements at solid-liquid interfaces. The three heme proteins' adsorption behavior was investigated at pH 7 in three different solvents: deionized (DI) water, tris(hydroxymethyl)-aminomethane hydrochloride (Tris-HCl), and phosphate buffered saline (PBS). For each protein, the surface coverage, the adsorption and desorption constants, and the surface equilibrium constant were optically measured by our EW-CRDS tool. Depending on the nature of each solvent, the proteins showed a completely different adsorption trend on the silica surface. The adsorption of Mb on the silica surface was depressed in the presence of both Tris-HCl and PBS buffers compared with unbuffered (DI water) solutions. In contrast, Cyt-C adsorption appears to be relatively unaffected by the choice of buffer, as it involves strong electrostatic interactions with the surface. Notably, Hb exhibits an opposite trend, with enhanced protein adsorption in the presence of Tris-HCl and PBS buffer. The pH investigations demonstrated that the electrostatic interactions between the proteins and the surface had a major influence on protein adsorption on the silica surface, with adsorption being greatest when the pH values were around the protein's isoelectric point. This study demonstrated the ability of the highly sensitive EW-CRDS tool to study the adsorption events of the evanescent-field-confined protein species in real-time at low surface coverages with fast resolution, making it a valuable tool for studying biomolecule kinetics at solid-liquid interfaces.

Physico-chemical properties of pea fibre and pea protein blends and the implications for in vitro batch fermentation using human inoculum

The incorporation of fibre into pea protein matrices influences their microstructure, yet our understanding of their gut fermentability remains unexplored. In this study, dietary fibres and protein from yellow pea were investigated for their physico-chemical properties and impact on in vitro colonic fermentation using human inoculum. Pea fibre and pea protein blends were studied at different pH and after thermal treatment at 95 °C for 30 min with oscillatory rheology, static light scattering and confocal laser scanning microscopy. The effect on in vitro colonic fermentation was evaluated measuring gas production, ammonia, and short chain fatty acid (SCFA) production. Rheology indicated that during thermal treatment a firmer gel is formed close to the protein isoelectric point with a structure characterised by aggregation, but less particle swelling compared to other pH. Addition of fibre led to higher storage modulus (G′), with the fibre dominating the rheological properties. Fermentation of samples containing protein led to higher levels of ammonia and SCFA compared to only fibres. Blends produced higher amounts of valerate, i-valerate and caproate, and lower amounts of ammonia. Reduced fermentation of proteins in the presence of fibres was also reflected in a more intact microstructure of the protein particles in the digesta. Although thermal treatment of blends caused particle swelling and induced gelation, only small differences could be discerned in the in vitro colonic fermentation outcomes. Our results highlight that potentially harmful fermentation products from protein, such as ammonia, were reduced in the presence of pea hull fibre.

Two-Dimensional Gel Electrophoresis in Studies of Flower and Leaf Proteome of Common Buckwheat.

Two-dimensional gel electrophoresis (2-DE) is a proteomic tool used for the separation of protein mixtures according to protein isoelectric point and molecular mass. Although gel-free quantitative and qualitative proteomic study techniques are now available, 2-DE remains a useful analytical tool. The presented protocol was performed to analyze the flower and leaf proteome of common buckwheat using 24cm immobilized pH gradient strips (pH4-7) and visualization of proteins on gels via colloidal Coomassie G-250 staining.

Novel and environmentally friendly paste-bath dyeing of protein fibers with mulberry leaf and silkworm excrement

Silkworm excrement is one of the most important byproducts of sericulture industry. This work investigated chlorophyll and its derivatives from mulberry leaves and silkworm excrement through FTIR analysis. Thermal stability of mulberry leaves and silkworm excrement were investigated by TG and DTG. Inspired by natural mud dyeing, this work conducted eco-friendly paste-bath dyeing without extracting colorants with organic solvents. Results show that digestive enzyme and microorganism induced formation of pyropheophytins in metabolism of silkworm body is similar to those conducted through acid and/or heating, and that silkworm excrement exhibits excellent thermal stability. When used as natural dye, pyropheophytins within silkworm excrement are able to form connection with amino acid in protein fibers, at protein iso-electric point of around pH 4.8. Silk and wool fabrics dyed with silkworm excrement show deep green brown shade with satisfactory color fastness to wash and light. This work provides evidence that pyropheophytin as natural dye is more thermal and light stable than pheophytin. Functional properties such as UV protection and oxidant inhibition are also found in fabrics dyed with silkworm excrement.

Proteome-Wide Changes in Blood Biomarkers During Hemodialysis

IntroductionDuring hemodialysis, proteins in the blood can decrease in concentration due to diffusion, convective clearance, dialyzer adsorption, or cellular uptake, while others may increase in concentration due to production, cellular release, secretion, or ultrafiltration of water. We examined the impact of hemodialysis on blood protein concentrations on a proteome-wide scale. MethodsA nested cohort of 44 patients (25 male, 19 female) including 29 with intradialytic hypotension were selected from the prospective Hemodialysis Outcomes and SympToms assessment (HOST) cohort. 1,163 proteins were measured before and after a hemodialysis treatment using Olink. Pre- and post-dialysis concentrations were compared, and the impact of protein characteristics and intradialytic hypotension on protein concentration was evaluated. Results189 proteins (16%) significantly decreased and 54 (5%) significantly increased in concentration. Change in concentration was associated with protein molecular weight (r = 0.37, P = 2.8 x 10-16), isoelectric point (r = -0.26, P = 6.4 x 10-14), and pre-dialysis concentration (r = -0.21, P = 3.0 x 10-9). There was enrichment for cardiovascular biomarkers in those nominally associated with a drop in systolic blood pressure during treatment (P = 2.8 x 10-8). ConclusionsChanges in the blood proteome are detectable during hemodialysis on a high throughput scale. Protein properties and intradialytic hypotension events appear associated with changes in biomarker concentration. Larger proteome-wide biomarker studies may identify measures of dialysis adequacy and reveal pathological processes contributing to adverse effects of dialysis.

Polyzwitterionic micelles with antimicrobial-conjugation for eradication of drug-resistant bacterial biofilms

The presence of bacterial biofilms has presented a significant challenge to human health. This study presents the development of biofilm microenvironment-responsive polymeric micelles as a novel approach to address the challenges posed by bacterial biofilms. These micelles are composed of two key components: a zwitterionic component, inspired by protein isoelectric points, containing balanced quantities of primary amines and carboxylic groups that undergo a positive charge transformation in acidic microenvironments, and a hydrophobic triclosan conjugate capable of releasing triclosan in the presence of bacterial lipases. Through the synergistic combination of pH-responsiveness and lipase-responsiveness, we have significantly improved drug penetration into biofilms and enhanced its efficacy in killing bacteria. With their remarkable drug-loading capacity and the ability to specifically target and eliminate bacteria within biofilms, these zwitterionic polymeric micelles hold great promise as an effective alternative for treating biofilm-associated infections. Their unique properties enable efficient drug delivery and heightened effectiveness against biofilm-related infections.

Genome-wide identification, molecular structures and functional exploration of the membrane attack complex/perforin domain-containing proteins and validation of GmmiRNA169o-GmMACPF-9 module in soybean cold stress

Soybean (Glycine max L.) is a widely cultivated legume and an enriched source of edible oil and protein. Membrane Attack Complex/Perforin Domain-Containing Proteins (MACPFs) played significant roles in plant growth and biotic and abiotic stresses. Here, we performed a genome-wide scanning for the putative GmMACPFs and a total of 20 GmMACPFs were identified in soybean. The conserved domain and phylogenetic analysis of MACPF showed the evolutionary diversification of MACPF genes family among legumes. The GmMACPFs protein characteristics were predicted, including theoretical molecular weight (38.06 to 68.38 kDa), protein isoelectric point (6.61 to 9.41), subcellular localization (nucleus, cytoplasm or mitochondria) and various TFs binding sites. GmMACPFs are located on 12 chromosomes out of a total 20 chromosomes in soybean. The 2 kb promoter analysis revealed that GmMACPFs contains a large number of phytohormones and stress responsive cis-acting elements (CAE) and transcription factor binding sites. We explored the 3D protein structure of GmMACPFs, their posttranscriptional regulators especially abiotic stress responsive miRNAs, and the evolutionary relationship among different legumes and Arabidopsis. GmMACPFs expression pattern was retrieved from RNA-seq libraries for tissue specific and under various abiotic stresses in soybean. According to the results, GmMACPF genes exhibited spatiotemporal, tissue, development stage and abiotic stress specific expression patterns in soybean. Our RT-qPCR analysis indicates the antagonistic expression pattern between GmmiRNA-GmMACPF modules under cold, salt, drought and heat stresses. Transient over expression of GmmiRNA169o-GmMACPF-9 module in soybean hairy root and biochemical analysis showed that GmmiRNA169o-OE plants accumulated less reactive oxygen species (ROS), malondialdehyde (MDA) and accumulated higher superoxide dismutase (SOD) and peroxidase (POD) to enhance cold stress tolerance. These results enriched our knowledge of the functions of GmmiRNA169o and GmMACPF-9 and provided candidate miRNAs-GmMACPFs modules especially GmmiRNA169o for environmental stress resilient soybean breeding through genetic engineering.

Improving physical stability of pea protein-based emulsions near the isoelectric point via polysaccharide complexation

Development of plant protein-based mildly acidic beverages remains challenging as the pH range falls near the protein isoelectric point, destabilizing emulsions. To overcome this problem, it was hypothesized that complexation between plant proteins and polysaccharides could provide emulsion stability in this critical pH range. Four different polysaccharides (sugar beet pectin, gum Arabic (GA), guar gum, gellan gum) were mixed separately with pea protein isolate (PPI) in 1:1 ratio, and the critical pH values for the formation of soluble complexes were determined. Heating the mixture widened the optimal pH range for soluble complexation for pectin-PPI and GA-PPI below the isoelectric point, which was then used to prepare 5 wt% O/W emulsions with an aqueous phase containing 0.5 wt% biopolymers at pH 8.0 and pH 4.5. Emulsion stability was characterized using droplet size, charge, visual observation, microstructure, and accelerated gravitational separation. PPI-only emulsions were stable at pH 8.0 but extensively destabilized at pH 4.5. The GA-PPI emulsions showed high stability at pH 8.0; however, at pH 4.5, the soluble complexes failed to provide a stable emulsion due to extensive droplet aggregation and phase separation. The emulsion prepared with a co-soluble pectin-PPI mixture at pH 8.0 also showed droplet aggregation and phase separation. The most improved emulsion stability (smallest droplet size, no aggregation) was observed for the pectin-PPI soluble complex at pH 4.5. Findings from this study showed that soluble complexes could be obtained at the desired pH range depending on the polysaccharide sources, which can stabilize O/W emulsions even near the protein's isoelectric point.

Protein length distribution is remarkably uniform across the tree of life

BackgroundIn every living species, the function of a protein depends on its organization of structural domains, and the length of a protein is a direct reflection of this. Because every species evolved under different evolutionary pressures, the protein length distribution, much like other genomic features, is expected to vary across species but has so far been scarcely studied.ResultsHere we evaluate this diversity by comparing protein length distribution across 2326 species (1688 bacteria, 153 archaea, and 485 eukaryotes). We find that proteins tend to be on average slightly longer in eukaryotes than in bacteria or archaea, but that the variation of length distribution across species is low, especially compared to the variation of other genomic features (genome size, number of proteins, gene length, GC content, isoelectric points of proteins). Moreover, most cases of atypical protein length distribution appear to be due to artifactual gene annotation, suggesting the actual variation of protein length distribution across species is even smaller.ConclusionsThese results open the way for developing a genome annotation quality metric based on protein length distribution to complement conventional quality measures. Overall, our findings show that protein length distribution between living species is more uniform than previously thought. Furthermore, we also provide evidence for a universal selection on protein length, yet its mechanism and fitness effect remain intriguing open questions.

Adaptive genetic traits in pelagic freshwater microbes.

Pelagic microbes have adopted distinct strategies to inhabit the pelagial of lakes and oceans and can be broadly categorized in two groups: free-living, specialized oligotrophs and patch-associated generalists or copiotrophs. In this review, we aim to identify genomic traits that enable pelagic freshwater microbes to thrive in their habitat. To do so, we discuss the main genetic differences of pelagic marine and freshwater microbes that are both dominated by specialized oligotrophs and the difference to freshwater sediment microbes, where copiotrophs are more prevalent. We phylogenomically analysed a collection of >7700 metagenome-assembled genomes, classified habitat preferences on different taxonomic levels, and compared the metabolic traits of pelagic freshwater, marine, and freshwater sediment microbes. Metabolic differences are mainly associated with transport functions, environmental information processing, components of the electron transport chain, osmoregulation and the isoelectric point of proteins. Several lineages with known habitat transitions (Nitrososphaeria, SAR11, Methylophilaceae, Synechococcales, Flavobacteriaceae, Planctomycetota) and the underlying mechanisms in this process are discussed in this review. Additionally, the distribution, ecology and genomic make-up of the most abundant freshwater prokaryotes are described in details in separate chapters for Actinobacteriota, Bacteroidota, Burkholderiales, Verrucomicrobiota, Chloroflexota, and 'Ca. Patescibacteria'.

Air nanobubbles induced reversible self-assembly of 7S globulins isolated from pea (Pisum Sativum L.)

The interplay of food proteins and macro or microscopic bubbles at the air-water interface that shaped the ultimate structures of proteins is well-known, yet knowledge was blank on the interactions between food proteins and nanoscopic bubbles (i.e., nanobubbles). In this study, bulk air nanobubbles were successfully fabricated in the aqueous solutions following a facile “cyclic compression-expansion” method. Subsequently, the effects of generated air nanobubbles and various factors including pH, protein concentration, nanobubble concentration, and ionic strength on the self-assembly behavior of 7S globulins isolated from pea proteins were investigated. It was revealed that air nanobubbles acted as soft templates to trigger 7S globulins self-assembly into core-shell nanospheres adjacent to the protein isoelectric point (∼pH 5). An enhancement of ionic strength from 0 to 0.4 mol L −1 led to increased particle size, whereas attenuating interactions between 7S globulins and air nanobubbles. The particle size of nanoparticles was also demonstrated to be protein and nanobubble concentration-dependent. Protein secondary structures were modified by air nanobubbles with apparently increased contents in random coils and decreased contents in α-helix. Changes in protein tertiary structures demonstrated that 7S globulins are exposed to a more hydrophobic microenvironment with reduced surface hydrophobicity, after complexing with air nanobubbles through electrostatic and hydrophobic interactions. The nanoparticles at pH 6 slightly shrunk during the 30-day refrigeration at 4 °C compared to those at pH 4, and the original nanostructures could revive after replenishing with fresh air nanobubble suspensions, indicating their high stability for future potential applications in food structure design innovation. • Air nanobubbles were generated using a “cyclic compression and expansion” method. • Interplay of 7S globulins and nanobubbles was impacted by extrinsic factors. • Nanobubbles induced reversible protein self-assembly to core-shell nanoparticles. • Air nanobubbles modified secondary and tertiary structures of 7S globulins. • Protein self-assembly behavior were driven by ionic and hydrophobic interactions.