Functional Diversity Research Articles

The Spatial-Temporal Alternative Splicing Profile Reveals the Functional Diversity of FXR1 Isoforms in Myogenesis.

Alternative splicing (AS) is a fundamental mechanism contributing to proteome diversity, yet its comprehensive landscape and regulatory dynamics during skeletal muscle development remain largely unexplored. Here, the temporal AS profiles are investigated during myogenesis in five vertebrates, conducting comprehensive profiling across 27 developmental stages in skeletal muscle and encompassing ten tissues in adult pigs. The analysis reveals a pervasive and evolutionarily conserved pattern of alternative exon usage throughout myogenic differentiation, with hundreds of skipped exons (SEs) showing developmental regulation, particularly within skeletal muscle. Notably, this study identifies a muscle-specific SE (exon 15) within the Fxr1 gene, whose AS generates two dynamically expressed isoforms with distinct functions: the isoform without exon 15 (Fxr1E15 -) regulates myoblasts proliferation, while the isoform incorporating exon 15 (Fxr1E15+) promotes myogenic differentiation and fusion. Transcriptome analysis suggests that specifically knocking-down Fxr1E15+ isoform in myoblasts modulates differentiation by influencing gene expression and splicing of specific targets. The increased inclusion of exon 15 during differentiation is mediated by the binding of Rbm24 to the intron. Furthermore, in vivo experiments indicate that the Fxr1E15+ isoform facilitates muscle regeneration. Collectively, these findings provide a comprehensive resource for AS studies in skeletal muscle development, underscoring the diverse functions and regulatory mechanisms governing distinct Fxr1 isoforms in myogenesis.

Specialization restricts the evolutionary paths available to yeast sugar transporters.

Functional innovation at the protein level is a key source of evolutionary novelties. The constraints on functional innovations are likely to be highly specific in different proteins, which are shaped by their unique histories and the extent of global epistasis that arises from their structures and biochemistries. These contextual nuances in the sequence-function relationship have implications both for a basic understanding of the evolutionary process and for engineering proteins with desirable properties. Here, we have investigated the molecular basis of novel function in a model member of an ancient, conserved, and biotechnologically relevant protein family. These Major Facilitator Superfamily sugar porters are a functionally diverse group of proteins that are thought to be highly plastic and evolvable. By dissecting a recent evolutionary innovation in an α-glucoside transporter from the yeast Saccharomyces eubayanus, we show that the ability to transport a novel substrate requires high-order interactions between many protein regions and numerous specific residues proximal to the transport channel. To reconcile the functional diversity of this family with the constrained evolution of this model protein, we generated new, state-of-the-art genome annotations for 332 Saccharomycotina yeast species spanning approximately 400 million years of evolution. By integrating phylogenetic and phenotypic analyses across these species, we show that the model yeast α-glucoside transporters likely evolved from a multifunctional ancestor and became subfunctionalized. The accumulation of additive and epistatic substitutions likely entrenched this subfunction, which made the simultaneous acquisition of multiple interacting substitutions the only reasonably accessible path to novelty.

Past, Present, and Future of Forbs in Old-Growth Tropical and Subtropical Grasslands

Forbs are important contributors to species diversity and ecosystem functions in low-latitude grasslands, where they support diverse herbivore communities and millions of people. Native forb assemblages tolerate disturbances and physiological stressors (fire, herbivory, drought, and frost) that together have shaped their exceptional functional diversity. Yet, compared to trees and grasses, forbs have received much less attention in grassland studies until recently. Here, we review forb-centric literature to illustrate that land conversion and responsible management of fire and herbivory are crucial to maintaining forb diversity. Management practices promoting forb diversity offer (a) high-quality food items and medicinal resources that support rural livelihoods and animal diversity (from wild ungulates and livestock to fossorial rodents and insects), including their adaptive foraging patterns, and (b) carbon and nutrient inputs that regulate belowground processes. Improved understanding of the above- and belowground regeneration strategies of forbs is critical for restoration and conservation to secure their services in future old-growth tropical and subtropical grasslands.

Ancient duplications, multidimensional specializations, and defense role of hexokinases in wheat.

Hexokinases (HXKs), which sense and catalyze cellular sugar, play a critical role in the growth and development of various plants, including wheat, a primary source of human calories frequently attacked by fungal pathogens. However, the evolutionary dynamics and functional diversification of HXKs in wheat, particularly their roles in plant defense, remain unclear. Here, we discovered that the wheat hexokinase gene family originated through multiple ancient gene duplications across different plant lineages and has undergone comprehensive, multidimensional functional specialization in gene expression, subcellular localization, enzyme activity, and regulation of plant defense responses. Gene expression analysis suggests that two-thirds of the TaHXK genes are responsive to fungal infection. Subcellular analysis reveals that while six TaHXKs are localized in mitochondria, three TaHXKs from different phylogenetic branches are sorted into other cellular compartments. Notably, biochemical analysis shows that TaHXKs in mitochondria differ in their glucose-catalyzing activity, with TaHXK5 and TaHXK3 exhibiting the highest and lowest enzyme activity, respectively. Consistently, transient expression analysis suggests that TaHXK5 induces various plant defense responses, while TaHXK3 is defective in activating some plant defense responses. Furthermore, inactivation of the glucokinase activity of TaHXK5 compromised its function in defense activation, suggesting that mitochondrial TaHXKs display functional divergence in both enzyme activity and defense-inducing activity that are intrinsically connected. Overall, our findings reveal that the multidimensional specialization events following the ancient duplication events may have shaped the functional diversity of HXKs in wheat, shedding light on their evolutionary dynamics and potentially contributing to the improvement of wheat defense.

Distribution and diversity of classical deacylases in bacteria

Classical Zn2+-dependent deac(et)ylases play fundamental regulatory roles in life and are well characterized in eukaryotes regarding their structures, substrates and physiological roles. In bacteria, however, classical deacylases are less well understood. We construct a Generalized Profile (GP) and identify thousands of uncharacterized classical deacylases in bacteria, which are grouped into five clusters. Systematic structural and functional characterization of representative enzymes from each cluster reveal high functional diversity, including polyamine deacylases and protein deacylases with various acyl-chain type preferences. These data are supported by multiple crystal structures of enzymes from different clusters. Through this extensive analysis, we define the structural requirements of substrate selectivity, and discovered bacterial de-d-/l-lactylases and long-chain deacylases. Importantly, bacterial deacylases are inhibited by archetypal HDAC inhibitors, as supported by co-crystal structures with the inhibitors SAHA and TSA, and setting the ground for drug repurposing strategies to fight bacterial infections. Thus, we provide a systematic structure-function analysis of classical deacylases in bacteria and reveal the basis of substrate specificity, acyl-chain preference and inhibition.

Interspecific trait differences drive plant community responses on serpentine soils

Abstract Serpentine ecosystems are characterised by multiple environmental stressors: high levels of trace metals such as nickel (Ni), low availability of macronutrients and low water retention. These harsh environmental conditions exert a strong selective force on the vegetation, but their effect on community assembly processes and the functional trait composition remains unknown. In 26 plots on four serpentine sites on Lesbos Island (Greece), we measured six leaf functional traits related to resource acquisition and stress resistance on the 20 most abundant plant species. We quantified the proportion of variance explained by inter‐ and intraspecific trait differences and tested if individual species showed changes in trait values explained by soil Ni content. We investigated the adaptive value and the community level changes for each trait along the natural soil Ni gradient using a mixed model approach and functional diversity analyses. We tested the role of the abundant serpentine endemic and Ni‐hyperaccumulating species Odontarrhena lesbiaca in driving these patterns. Intraspecific variation explained by soil Ni content is smaller than 4%, and most of the variance is explained by interspecific differences in trait values. Most species do not show significant changes in trait values in response to soil Ni. At the community level, low specific leaf areas, small and thick leaves are selected on high Ni soils. Functional diversity analyses suggest a shift towards a stress tolerance syndrome (thick and small leaves with low SLA values) and an increase in functional diversity on Ni‐rich soils. However, these patterns are driven by the increasing abundance of O. lesbiaca. The endemic Ni hyperaccumulator has a stress tolerance strategy with small thick leaves and low SLA, while the community of broadly distributed species show an increase in trait values related to dominance and fast growth. Synthesis. Intraspecific variation in leaf trait responds little to soil metal toxicity. Endemic species harbour unique trait values compared to species with broad distribution which should justify their conservation as a priority.

Functional traits mediate the elevational patterns of functional diversity and community structure of mosses in a tropical mountain area

Functional diversity refers to the value, range, and distribution of functional traits within a community, such as the morphological, physiological and behavioral characteristics of species that determine the role a species plays in an ecosystem. Assessing the drivers of elevational pattern of functional diversity is crucial to predict the effects of global change on functional diversity and community structure. In our research, we collected mosses species data from 65 sampling sites and measured 11 functional traits that are related to their ecological functions. We applied double canonical correspondence analysis (DCCA) to analyze species responses to environmental conditions based on their traits. We applied generalized additive models with a Gaussian function of variance to determine the elevational patterns of functional trait composition, diversity and community structure. We applied and compared boosted regression trees (BRT) without considering functional traits and piecewise structural equation modelling (SEM) mediated with functional traits to relate environmental variables with functional diversity and functional community structure, respectively. We found the first DCCA axis accounted for the largest dissimilarities between the two groups of species and correlated mainly with the water-utilization traits. Although both functional diversity and community structure displayed negatively skewed pattern along the elevational gradient, habitat complexity and climatic variables contributed differently to their respective patterns. The SEM approach consistently outperformed the BRT approach in explaining the variations in both functional diversity and community structure. Our findings highlight the important role of functional traits in mediating the relationship between the environment and functional diversity metrics. Both biotic and abiotic processes play a significant role in shaping the community assemblages, with environmental variables having distinct impacts. Traits related to structure maintenance, water absorption, cell hydration, and nutrient acquisition were found to be key drivers of functional diversity, while water-utilization traits were mainly responsible for regulating functional community structure.

Functional changes of protist communities in soil after glacier retreat.

Soil hosts key components of terrestrial biodiversity providing essential services to the below- and above-ground ecosystems. The worldwide retreat of glaciers is exposing new deglaciated terrains, offering a unique opportunity to understand the development of soil ecosystems under a changing climate. Many studies have investigated how biotic communities change after deglaciation, but protists have often been overlooked despite their key role in multiple ecosystem functions. Here, we aim to understand how protist communities develop along glacier forelands, describing their successional trajectories. Protist communities were characterized in 1251 soil samples from 46 glacier forelands across four continents. We used environmental DNA metabarcoding to identify the Molecular Operational Taxonomic Units (MOTUs) of protists based on a universal eukaryotic marker. The detected MOTUs were combined with information on multiple traits to assess how the functional diversity and composition of protist communities vary through time. Immediately after glacier retreat, protist communities are like those of polar and high-altitude habitats, with consumers being the dominant trophic group, followed by a relevant presence of phototrophs, while parasites were underrepresented. Over the succession, we detected an increase in taxonomic and functional diversity, but some highly specialized groups (e.g. phototrophic algae) declined. The use of a trait-based approach allowed us to identify distinct successional patterns depending on functional groups. Through the functional characterization of a crucial but understudied component of soil biotic communities, our study added one of the final pieces needed to predict how soil ecosystems will develop in the rapidly changing environment of glacier forelands.

Microscopic Strain Mapping: Functional Diversity and Their Demands

Microscopic Strain Mapping: Functional Diversity and Their Demands

Role of the Histone Deacetylase Family in Lipid Metabolism: Structural Specificity and Functional Diversity.

Lipids play crucial roles in signal transduction. Lipid metabolism is associated with several transcriptional regulators, including peroxisome proliferator activated receptor γ, sterol regulatory element-binding protein 1, and acetyl-CoA carboxylase. In recent years, increasing evidence has suggested that members of the histone deacetylase (HDAC) family play key roles in lipid metabolism. However, the mechanisms by which each member of this family regulates lipid metabolism remain unclear. This review discusses the latest research on the roles played by HDACs in fat metabolism. The role of HDACs in obesity, diabetes, and atherosclerosis has also been discussed. In addition, the interaction of HDACs with the gut microbiome and circadian rhythm has been reviewed, and the future development trend in HDACs has been predicted, which may potentiate therapeutic application of targeted HDACs in related metabolic diseases.

Systematic Identification and Expression Profiling of Calmodulin-binding Transcription Activator Genes Reveal Insights into their Functional Diversity against Pathogens in Sugarcane

Systematic Identification and Expression Profiling of Calmodulin-binding Transcription Activator Genes Reveal Insights into their Functional Diversity against Pathogens in Sugarcane

Diversity and structural-functional insights of alpha-solenoid proteins.

Alpha-solenoids are a significant and diverse subset of structured tandem repeat proteins (STRPs) that are important in various domains of life. This review examines their structural and functional diversity and highlights their role in critical cellular processes such as signaling, apoptosis, and transcriptional regulation. Alpha-solenoids can be classified into three geometric folds: low curvature, high curvature, and corkscrew, as well as eight subfolds: ankyrin repeats; Huntingtin, elongation factor 3, protein phosphatase 2A, and target of rapamycin; armadillo repeats; tetratricopeptide repeats; pentatricopeptide repeats; Pumilio repeats; transcription activator-like; and Sel-1 and Sel-1-like repeats. These subfolds represent distinct protein families with unique structural properties and functions, highlighting the versatility of alpha-solenoids. The review also discusses their association with disease, highlighting their potential as therapeutic targets and their role in protein design. Advances in state-of-the-art structure prediction methods provide new opportunities and challenges in the functional characterization and classification of this kind of fold, emphasizing the need for continued development of methods for their identification and proper data curation and deposition in the main databases.

The Effect of Grazing on Central Anatolian Steppe Vegetation: A Modeling Approach Using Functional Traits.

Grazing is a major ecological driver that influences vegetation dynamics globally. We investigated the long-term effects of different grazing regimes on the vegetation structure of the Central Anatolian steppes, a region characterized by its unique convergence of biogeographical influences and historical land use. We employed the spatially explicit FATELAND model to simulate vegetation dynamics over a 50-year period under three distinct grazing scenarios: no grazing, moderate grazing, and overgrazing. Our simulations incorporated a range of plant functional traits to predict changes across five different vegetation types in Central Anatolia, including woodland steppes and treeless steppes. The simulations revealed that moderate grazing supports the diversity and abundance of various plant functional groups, excluding resprouter trees, which flourish under no grazing conditions. In contrast, overgrazing leads to significant reductions in the abundance of perennial forbs and both spiny and non-spiny subshrubs, often resulting in a shift toward grassland dominated by resprouter gramineae or an annual herb-dominated grassland, depending on the initial abundance of gramineae. Our findings highlight the critical role of grazing management in maintaining biodiversity and ecological stability in steppe ecosystems. While moderate grazing can enhance plant functional group diversity, overgrazing significantly threatens the ecological integrity of the Central Anatolian steppes. In conclusion, our modeling approach reveals that the grazing regime is a major driver in shaping the vegetation structure of Central Anatolian steppes. Grazing management strategies that are adjusted to the ecological characteristics and historical context of specific regions are required to prevent degradation and promote sustainable grassland vegetation.

Expression interplay of genes coding for calcium-binding proteins and transcription factors during the osmotic phase provides insights on salt stress response mechanisms in bread wheat

Bread wheat is an important crop for the human diet, but the increasing soil salinization is reducing the yield. The Ca2+ signaling events at the early stages of the osmotic phase of salt stress are crucial for the acclimation response of the plants through the performance of calcium-sensing proteins, which activate or repress transcription factors (TFs) that affect the expression of downstream genes. Physiological, genetic mapping, and transcriptomics studies performed with the contrasting genotypes Syn86 (synthetic, salt-susceptible) and Zentos (elite cultivar, salt-tolerant) were integrated to gain a comprehensive understanding of the salt stress response. The MACE (Massive Analysis of cDNA 3ʹ-Ends) based transcriptome analysis until 4 h after stress exposure revealed among the salt-responsive genes, the over-representation of genes coding for calcium-binding proteins. The functional and structural diversity within this category was studied and linked with the expression levels during the osmotic phase in the contrasting genotypes. The non-EF-hand category from calcium-binding proteins was found to be enriched for the susceptibility response. On the other side, the tolerant genotype was characterized by a faster and higher up-regulation of genes coding for proteins with EF-hand domain, such as RBOHD orthologs, and TF members. This study suggests that the interplay of calcium-binding proteins, WRKY, and AP2/ERF TF families in signaling pathways at the start of the osmotic phase can affect the expression of downstream genes. The identification of SNPs in promoter sequences and 3ʹ -UTR regions provides insights into the molecular mechanisms controlling the differential expression of these genes through differential transcription factor binding affinity or altered mRNA stability.

γδ T Cells Mediate Protection against Neutrophil-associated Lung Inflammation in Pulmonary Melioidosis.

Pulmonary melioidosis is a severe tropical infection caused by Burkholderia pseudomallei and is associated with high mortality, despite early antibiotic treatment. γδ T cells have been increasingly implicated as drivers of the host neutrophil response during bacterial pneumonia, but their role in pulmonary melioidosis is unknown. Here, we report that in patients with melioidosis, a lower peripheral blood γδ T-cell concentration is associated with higher mortality, even when adjusting for severity of illness. γδ T cells were also enriched in the lung and protected against mortality in a mouse model of pulmonary melioidosis. γδ T-cell deficiency in infected mice induced an early recruitment of neutrophils to the lung, independent of bacterial burden. Subsequently, γδ T-cell deficiency resulted in increased neutrophil-associated inflammation in the lung as well as impaired bacterial clearance. In addition, γδ T cells influenced neutrophil function and subset diversity in the lung after infection. Our results indicate that γδ T cells serve a novel protective role in the lung during severe bacterial pneumonia by regulating excessive neutrophil-associated inflammation.

Spatial context of immune checkpoints as predictors of overall survival in patients with resectable colorectal cancer independent of standard TNM stages.

While immune checkpoint blockade (ICB) therapy has shown promising results in a small subset of colorectal cancer patients with high microsatellite instability (MSI-H), the majority of patients with colorectal cancer do not respond to ICB therapy. The main obstacle to the success of immunotherapy in cancer treatment is the exhaustion of tumor-infiltrating lymphocytes (TILs). Elucidating the spatial organization of immune checkpoints within the tumor microenvironment could pave the way for the development of novel prognostic tools and therapeutic strategies to enhance antitumor immune responses. To clarify the spatial and functional diversity of tumor-infiltrating lymphocytes (TILs) in the colorectal tumor microenvironment (TME), we performed multiplexed IHC to examine the exhaustion of TILs in the TME (the expression of PD-1 and TIM-3 (T-cell immunoglobulin and mucin-domain-containing protein 3), which are major biomarkers of T-cell exhaustion) and Lasso-Cox analyses of the correlation between CRC prognosis and TME features. For proof of concept, the antitumor efficacy of TIM-3 and PD-1 dual blockade in CRC was further evaluated in a CT26 subcutaneous tumor model of human CRC. We found that the spatial context of PD-1 and TIM-3 successfully predicted the overall survival of CRC patients independent of TNM stage. Dual targeting of PD-1 and TIM-3 in mouse tumor models inhibited tumor progression and reduced T-cell exhaustion, indicating a potential strategy for improving the clinical treatment of CRC.

Construction and Optimization of a Yeast Cell Factory for Producing Active Unnatural Ginsenoside 3β-O-Glc2-DM.

Ginsenosides are major active components of Panax ginseng, which are generally glycosylated at C3-OH and/or C20-OH of protopanaxadiol (PPD) and C6-OH and/or C20-OH of protopanaxatriol. However, the glucosides of dammarenediol-II (DM), which is the direct precursor of PPD, have scarcely been separated from P. ginseng. Because different positions and numbers of the hydroxyl and glycosyl groups lead to a diversity of structure and function of the ginsenosides, it can be inferred that DM glucosides may have different pharmacological activities compared with natural ginsenosides. Herein, we first constructed the cell factory for de novo biosynthesis of 3-O-(β-D-glucopyranosyl-(1→2)-β-D-glucopyranosyl)-dammar-24-ene-3β,20S-diol (3β-O-Glc2-DM) by introducing the codon-optimized genes encoding dammarenediol-II synthase, two UDP-glycosyltransferases (UGTs) including UGT74AC1-M7 from Siraitia grosvenorii and UGTPg29 from P. ginseng in Saccharomyces cerevisiae via the CRISPR/Cas9 system. The titer of 3β-O-Glc2-DM was then increased from 18.9 to 148.0 mg/L by several metabolic engineering strategies including overexpressing the rate-limiting enzymes of triterpenoid biosynthesis, balancing carbon flux of biosynthetic pathways of triterpenoid and ergosterol, and engineering endoplasmic reticulum. Furthermore, the 3β-O-Glc2-DM titer of 766.3 mg/L was achieved through fed-batch fermentation in a 3-L bioreactor. Finally, in vitro assays demonstrated that 3β-O-Glc2-DM exhibited a protective effect on H/R-induced cardiomyocyte damage. This work provides a feasible approach for production of 3β-O-Glc2-DM as a potential cardioprotective drug candidate.

Imprints of Soil Microbial Activity Accredited to Residue-Management and Tillage Practices for Boosting Rice and Wheat Production

The sustainable productivity of rice–wheat cropping systems relies on soil health, and soil health can be positively influenced by treating previous crop residues using conservation tillage practices. The present study examined the impact of three rice residue-management practices under zero-tilled wheat (ZTW) and conventionally tilled wheat (CTW), along with two rice-sowing practices, during rice cultivation on soil functional microbial diversity, physiological profiling, and grain yields of rice and wheat. Anchored residues (ARs) under ZTW exhibited significantly (p ≤ 0.05) high average well color development—31.43% more than CTW with no residue (NR). CTW with residue burning (BUR) showed a 5.42% increase in the Shannon diversity index compared to CTW-NR. Substrate richness was 10.02% higher in CTW-BUR compared to CTW-NR. CTW-BUR demonstrated the highest 17.98% increase in the Shannon evenness index compared to CTW-NR. The direct-seeded rice (DSR) system generally surpassed puddled transplanted rice (PTR) in most indices, except for the Shannon evenness index values. ZTW-AR exhibited the highest utilization of amino acids, carboxylic acids, and phenolic compounds, while CTW-BUR exhibited the highest utilization of carbohydrates and polymers utilization, and ZTW with no-residue (NR) exhibited the highest utilization of amines. Rice and wheat grain yields were highest with full residue in ZTW and lowest in CTW-NR. PTR supported higher rice yields, while DSR was superior for wheat. These findings highlight the favorable role of residue retention with no tillage during wheat cultivation in the maintenance of soil quality and rice–wheat productivity.

Evaluating the impact of residual low chlorine concentration on phytoplankton communities by flow cytometry.

Chlorination is widely used to prevent biological fouling in power station cooling water systems. It may impact non-target organisms both within the cooling system and after discharge (primary and secondary entrainment). However, there is a lack of data on the impacts of the low chlorine concentrations that occur in the discharged plume on marine phytoplankton community structure and function. We examine the impacts on natural phytoplankton communities of single and multiple exposures to chlorination at concentrations between 0.02 and 0.1 mg/L total residual oxidants (TRO). Low-level chlorination causes limited changes in diversity and has no impact on total biomass. However, changes in size structure and functional diversity quantified using flow cytometry do show a reduction in smaller cells, particularly eukaryote picophytoplankton. These impacts are not detectable using chlorophyll a concentration alone, so flow cytometry provides important additional information over more standard ecotoxicological methods. The effects are likely to be localised in the vicinity of the discharges (mixing zone) where the environmental quality standard (EQS) of 10 μg/L for chlorine is exceeded, but impacts on coastal food webs and biogeochemical cycles should be further evaluated.

Research progress of two-pore potassium channel in myocardial ischemia-reperfusion injury

Myocardial ischemia-reperfusion injury (MIRI) is a secondary injury caused by restoring blood flow after acute myocardial infarction, which may lead to serious arrhythmia and heart damage. In recent years, the role of potassium channels in MIRI has attracted much attention, especially the members of the two-pore domain potassium (K2P) channel family. K2P channel has unique structure and function, and the formation of its heterodimer increases its functional diversity. This paper reviews the structural characteristics, types, expression and physiological functions of K2P channel in the heart. In particular, we pay attention to whether members of the subfamily such as TWIK, TREK, TASK, TALK, THIK and TRESK participate in MIRI and their related mechanisms. Future research will help to reveal the molecular mechanism of K2P channel in MIRI and provide new strategies for the treatment of cardiovascular diseases.