Biochemical Role Research Articles

From gene to therapy: a review of deciphering the role of ABCD1 in combating X-Linked adrenoleukodystrophy.

X-linked adrenoleukodystrophy (X-ALD) is a severe genetic disorder caused by ABCD1 mutations, resulting in the buildup of very-long-chain fatty acids, leading to significant neurological decline and adrenal insufficiency. Despite advancements in understanding the mechanisms of X-ALD, its pathophysiology remains incompletely understood, complicating the development of effective treatments. This review provides a comprehensive overview of X-ALD, with a focus on the genetic and biochemical roles of ABCD1 and the impacts of its mutations. Current therapeutic approaches are evaluated, discussing their limitations, and emphasizing the need to fully elucidate the pathogenesis of X-ALD. Additionally, this review highlights the importance of international collaboration to enhance systematic data collection and advance biomarker discovery, ultimately improving patient outcomes with X-ALD.

Seasonal succession, host associations and biochemical roles of aquatic viruses in a eutrophic lake plagued by cyanobacterial blooms

Viruses are implicated as important biogeochemical mediators and ecological drivers in freshwater ecosystems. However, the dynamics of viruses and host associations over the seasons and blooming periods in eutrophic freshwater ecosystems remain elusive. From the water microbiomes of planktonic biomass from Lake Taihu, a large and eutrophic lake that suffered from yearly Microcystis-dominated harmful algal blooms (HABs) in China, we recovered 41,997 unique viral clusters spanning a wide taxonomic range, including 15,139 Caudovirales clusters targeting bacteria and 1,044 NCLDV clusters targeting eukaryotes. The viral community exhibited distinct seasonal succession driven by microbial communities (mainly Cyanobacteria and Planctomycetes) and environmental factors (mainly nutrients and temperature). Host prediction highlighted a more distinct viral impact on bacteria-driven nitrogen pathways than phosphate cycling through infection. HAB-induced microbial and environmental variations affected viral strategies including lifestyles, host range, and virus-encoded auxiliary metabolic genes (vAMGs) distributions. Viruses infecting Proteobacteria and Actinobacteria showed enhanced lysogenic lifestyle and condensed host ranges during HAB peak in summer, while viruses infecting Bacteroidota selected the opposite strategy. Notably, vAMGs were most abundant before HAB outbreak in spring, compensating for host bacterial metabolism including carbohydrates metabolism, photosynthesis, and phosphate regulation. The elucidated relationship between viruses, host microbes, and bloom-associated environment suggested prominent biochemical roles in the eutrophic freshwater ecosystems.

Guidance for establishing and applying tolerable upper intake levels for vitamins and essential minerals.

Vitamins and essential minerals are micronutrients that are required for the normal functioning of the human body. However, they may lead to adverse health effects if consumed in excess. A tolerable upper intake level (UL) is a science-based reference value that supports policy-makers and other relevant actors in managing the risks of excess nutrient intake. EFSA's principles for establishing ULs for vitamins and minerals were originally developed by the Scientific Committee on Food in 2000. This guidance from the EFSA Panel on Nutrition, Novel Foods and Food Allergens provides an updated framework for UL assessments. A draft was published in 2022 and underwent a 2-year piloting period. The present document incorporates revisions based on the experience gained through its practical implementation. It covers aspects related to the planning of the risk assessment (problem formulation and definition of methods) and its implementation (evidence retrieval, appraisal, synthesis, integration, uncertainty analysis). As in the previous framework, the general principles developed for the risk assessment of chemicals in food are applied, i.e. hazard identification, hazard characterisation, intake assessment, risk characterisation. Specific to nutrients are their biochemical and physiological roles and the specific and selective mechanisms that maintain the systemic homeostasis and accumulation of the nutrient in the body. Such considerations must also be taken into account when conducting risk assessments of nutrients.

Thiamine: An indispensable regulator of paediatric neuro-cardiovascular health and diseases.

Physicians are recommended to have a low threshold for suspecting thiamine deficiency especially in vulnerable populations. Laboratory diagnosis of thiamine deficiency needs to be implemented as a standard of care, especially in endemic regions. Further, public health policies on food fortification, mandatory supplementation, and surveillance are imperative to eliminate thiamine deficiency-induced health hazards. • South Asian countries report a higher incidence of neonatal and under-five mortalities, many of which are attributed to maternal and perinatal micronutrient deficiencies. • Preventable causes of neonatal/ infantile deaths include birth factors (low birth weight, birth asphyxia), infectious diseases (pneumonia, diarrhoea, tetanus, tuberculosis, measles, diphtheria, malaria, acute infections), deficiency diseases and genetic diseases (vitamin & mineral deficiencies, IEMs, congenital heart disease, unexplained PPHN, SIDS etc). • Acute thiamine deficiency presenting as multisystemic syndromes, has unfortunately been a long standing unresolved public health concern. However, accessible surveillance and diagnostic strategies remain elusive in most clinical settings. • Despite decades of reports and emerging guidelines, diagnosis of thiamine deficiency is often missed and policy mandates at national level are yet to be implemented even in endemic countries. • This review provides a comprehensive summary of the biochemical role of thiamine, its key functions and effects on major organ systems, the diagnostic gap, the enigmatic presentation of acute thiamine deficiency, the plausible role of thiamine in other pathologies and the preventive measures at individual and community level.

CYP5122A1 encodes an essential sterol C4-methyl oxidase in Leishmania donovani and determines the antileishmanial activity of antifungal azoles

Visceral leishmaniasis is a life-threatening parasitic disease, but current antileishmanial drugs have severe drawbacks. Antifungal azoles inhibit the activity of cytochrome P450 (CYP) 51 enzymes which are responsible for removing the C14α-methyl group of lanosterol, a key step in ergosterol biosynthesis in Leishmania. However, they exhibit varying degrees of antileishmanial activities in culture, suggesting the existence of unrecognized molecular targets. Our previous study reveals that, in Leishmania, lanosterol undergoes parallel C4- and C14-demethylation to form 4α,14α-dimethylzymosterol and T-MAS, respectively. In the current study, CYP5122A1 is identified as a sterol C4-methyl oxidase that catalyzes the sequential oxidation of lanosterol to form C4-oxidation metabolites. CYP5122A1 is essential for both L. donovani promastigotes in culture and intracellular amastigotes in infected mice. CYP5122A1 overexpression results in growth delay, increased tolerance to stress, and altered expression of lipophosphoglycan and proteophosphoglycan. CYP5122A1 also helps to determine the antileishmanial effect of antifungal azoles in vitro. Dual inhibitors of CYP51 and CYP5122A1 possess superior antileishmanial activity against L. donovani promastigotes whereas CYP51-selective inhibitors have little effect on promastigote growth. Our findings uncover the critical biochemical and biological role of CYP5122A1 in L. donovani and provide an important foundation for developing new antileishmanial drugs by targeting both CYP enzymes.

Biochemical Role of Folic Acid On Experimentally Induced Pulmonary Toxicity by klebsiella pneumonia in Rats

Biochemical Role of Folic Acid On Experimentally Induced Pulmonary Toxicity by klebsiella pneumonia in Rats

Purine limitation prevents the exogenous pyridoxal 5'-phosphate accumulation of Salmonella enterica yggS mutants.

Pyridoxal 5'-phosphate is the active form of vitamin B6 and is an essential cofactor in all domains of life. PLP can be synthesized de novo or salvaged from the environment from one of the six B6 vitamers. B6 vitamer levels appear to be tightly regulated, and alterations in their levels can have deleterious effects, most notably being the development of B6-dependent epilepsy in humans. YggS homologs are broadly conserved across multiple organisms and considered to be involved in maintaining B6 homeostasis, though no specific mechanism has been defined. The current study showed that the exogenous accumulation of PLP caused by a lack of YggS can be prevented by purine limitation. The demonstration that purine limitation impacts exogenous PLP accumulation separates one consequence of a yggS mutation for further study and contributes to continuing efforts to define the biochemical and physiological roles of the COG0325 family of proteins.

Multiplexed profiling of intracellular protein abundance, activity, interactions and druggability with LABEL-seq.

Here we describe labeling with barcodes and enrichment for biochemical analysis by sequencing (LABEL-seq), an assay for massively parallel profiling of pooled protein variants in human cells. By leveraging the intracellular self-assembly of an RNA-binding domain (RBD) with a stable, variant-encoding RNA barcode, LABEL-seq facilitates the direct measurement of protein properties and functions using simple affinity enrichments of RBD protein fusions, followed by high-throughput sequencing of co-enriched barcodes. Measurement of ~20,000 variant effects for ~1,600 BRaf variants revealed that variation at positions frequently mutated in cancer minimally impacted intracellular abundance but could dramatically alter activity, protein-protein interactions and druggability. Integrative analysis identified networks of positions with similar biochemical roles and enabled modeling of variant effects on cell proliferation and small molecule-promoted degradation. Thus, LABEL-seq enables direct measurement of multiple biochemical properties in a native cellular context, providing insights into protein function, disease mechanisms and druggability.

Biochemistry, pharmacology and in vivo function of arginases.

Arginase catalyzes the hydrolysis of L-arginine into L-ornithine and urea. The two existing isoforms Arg1 and Arg2 show different cellular localizations and metabolic functions. Arginase activity is crucial for nitrogen detoxification in the urea cycle, synthesis of polyamines, and control of l-arginine bioavailability and nitric oxide production. Despite significant progress in the understanding of the biochemistry and function of arginases, several open questions remain. Recent studies have revealed that the regulation and function of Arg1 and Arg2 are cell-type-specific, species-specific, and profoundly different in mice and humans. The main differences were found in the distribution and function of Arg1 and Arg2 in immune and erythroid cells. Contrary to what was previously thought, Arg1 activity appears to be only partially related to vascular NO signaling under homeostatic conditions in the vascular wall, but its expression is increased under disease conditions and may be targeted by treatment with arginase inhibitors. Arg2 appears to be mainly a catabolic enzyme involved in the synthesis of L-ornithine, polyamine, and proline but may play a putative role in blood pressure control, at least in mice. The immunosuppressive role of arginase-mediated arginine depletion is a promising target for cancer treatment. This review critically revises and discusses the biochemistry, pharmacology, and in vivo function of arginase, focusing on the insights gained from the analysis of cell-specific Arg1 and Arg2 knockout mice and human studies using arginase inhibitors or pegylated recombinant arginase. Significance Statement The review emphasizes the need for further research to deepen our understanding of the regulation of Arg1 and Arg 2 in different cell types under consideration of their localization, species-specificity, and multiple biochemical and physiological roles. This could lead to better pharmacological strategies to target arginase activity in liver, cardiovascular, hematological, immune/infection diseases and cancer.

Exploring atmospheric nucleation processes: Hydration and fluoroalcoholic complexation of pyruvic acid.

This study examines the intermolecular interactions between small molecules and solvents, with a particular focus on pyruvic acid (PA). PA plays a significant role in biochemistry, astrochemistry, and atmospheric chemistry, particularly in aerosol particle formation. Previous studies on PA have been expanded upon by exploring its hydration and complexation with 2,2,2-trifluoroethanol (TFE). The clusters were generated using a supersonic expansion and characterized by broadband Fourier transform microwave spectroscopy. The structures of the clusters were identified by comparing the experimental results with high-level quantum-chemical computations. Among the possible isomers for the hydrated complex, the Tc-(H2O)2 kinetic complex, where PA exhibits an internal hydrogen bond, was favored over the Tt-(H2O)2 form, predicted to be the most stable conformer. Transitions from both the A and E internal rotation substates were observed exclusively in the dihydrate. The complex with TFE did not exhibit splitting due to the internal rotation of the methyl top. This is attributed to the presence of electronegative fluorine groups in TFE, stabilizing the complex through additional CH⋯F interactions, thereby hindering the internal rotation motion of the methyl top.

Human formin FHOD3-mediated actin elongation is required for sarcomere integrity in cardiomyocytes.

Contractility and cell motility depend on accurately controlled assembly of the actin cytoskeleton. Formins are a large group of actin assembly proteins that nucleate new actin filaments and act as elongation factors. Some formins may cap filaments, instead of elongating them, and others are known to sever or bundle filaments. The Formin HOmology Domain-containing protein (FHOD)-family of formins is critical to the formation of the fundamental contractile unit in muscle, the sarcomere. Specifically, mammalian FHOD3L plays an essential role in cardiomyocytes. Despite our knowledge of FHOD3L's importance in cardiomyocytes, its biochemical and cellular activities remain poorly understood. It has been proposed that FHOD-family formins act by capping and bundling, as opposed to assembling new filaments. Here, we demonstrate that FHOD3L nucleates actin and rapidly but briefly elongates filaments after temporarily pausing elongation, in vitro . We designed function-separating mutants that enabled us to distinguish which biochemical roles are req`uired in the cell. We found that human FHOD3L's elongation activity, but not its nucleation, capping, or bundling activity, is necessary for proper sarcomere formation and contractile function in neonatal rat ventricular myocytes. The results of this work provide new insight into the mechanisms by which formins build specific structures and will contribute to knowledge regarding how cardiomyopathies arise from defects in sarcomere formation and maintenance.

The Biochemical Role of Vitamin D in Human Health: A Comprehensive Review

The Biochemical Role of Vitamin D in Human Health: A Comprehensive Review

The interactome of cystic fibrosis transmembrane conductance regulator and its role in male fertility: A critical review.

The cystic fibrosis transmembrane conductance regulator (CFTR) is a cyclic adenosine monophosphate (cAMP)-regulated chloride and bicarbonate ion channel found in many human cells. Its unique biochemical characteristics and role as a member of the adenosine triphosphate (ATP)-binding cassette transporters superfamily are pivotal for the transport of several substrates across cellular membranes. CFTR is known to interact, physically and functionally, with several other cellular proteins. Hence, its properties are essential for moving various substances across cell membranes and ensuring correct cell functioning. Genetic mutations or environmental factors may disrupt CFTR's function resulting in different possible phenotypes due to gene variations that affect not only CFTR's function, localization, and processing within cells, but also those of its interactors. This has been reported as an underlying cause of various diseases, including cystic fibrosis. The severe clinical implications of cystic fibrosis have driven intense research into the role of CFTR in lung function but its significance to fertility, particularly in men, has been comparatively understudied. However, ongoing and more recent research into CFTR and its interacting proteins in the testis or specific testicular cells is beginning to shed light on this field. Herein, we provide a comprehensive and up-to-date overview of the CFTR, its interactome, and its crucial role in male reproduction, highlighting recent discoveries and advancements in understanding the molecular mechanisms involved. The comprehension of these complex interactions may pave the way for potential therapeutic approaches to improve fertility of men suffering from alterations in the function of CFTR.

The Role of Biochemistry in Understanding Kidney Stone Formation andUrinary Health

Renal illness caused by stones is the term for a solid substance concretion that usually develops inside the kidneys. A rising urological condition influences the well-being of people and affects about 12% of the world's population. An increased chance of ending stage of renal failure and they are closely related. There are several types of kidney stones. The CaC2O4 kidney calculi are the most common type. It appears at Randall plaque's renal papillary surfaces. (1) Several physicochemical mechanisms, such as supersaturating, urinary stone nucleation, growth, aggregation, and retention components found in tubular cells, which aid in the complex process of formation of stones. An inequity between the elements that promote or inhibit the crystallization of urine influences these phases. Moreover, Scientists have noticed that renal injury of cells promotes particle retention reticular body. (2)

Helicase HELQ: Molecular Characters Fit for DSB Repair Function.

The protein sequence and spatial structure of DNA helicase HELQ are highly conserved, spanning from archaea to humans. Aside from its helicase activity, which is based on DNA binding and translocation, it has also been recently reconfirmed that human HELQ possesses DNA-strand-annealing activity, similar to that of the archaeal HELQ homolog StoHjm. These biochemical functions play an important role in regulating various double-strand break (DSB) repair pathways, as well as multiple steps in different DSB repair processes. HELQ primarily facilitates repair in end-resection-dependent DSB repair pathways, such as homologous recombination (HR), single-strand annealing (SSA), microhomology-mediated end joining (MMEJ), as well as the sub-pathways' synthesis-dependent strand annealing (SDSA) and break-induced replication (BIR) within HR. The biochemical functions of HELQ are significant in end resection and its downstream pathways, such as strand invasion, DNA synthesis, and gene conversion. Different biochemical activities are required to support DSB repair at various stages. This review focuses on the functional studies of the biochemical roles of HELQ during different stages of diverse DSB repair pathways.

Human AKR1C3 binds agonists of GPR84 and participates in an expanded polyamine pathway.

Altered human aldo-keto reductase family 1 member C3 (AKR1C3) expression has been associated with poor prognosis in diverse cancers, ferroptosis resistance, and metabolic diseases. Despite its clinical significance, the endogenous biochemical roles of AKR1C3 remain incompletely defined. Using untargeted metabolomics, we identified a major transformation mediated by AKR1C3, in which a spermine oxidation product "sperminal" is reduced to "sperminol." Sperminal causes DNA damage and activates the DNA double-strand break response, whereas sperminol induces autophagy invitro. AKR1C3 also pulls down acyl-pyrones and pyrone-211 inhibits AKR1C3 activity. Through G protein-coupled receptor ligand screening, we determined that pyrone-211 is also a potent agonist of the semi-orphan receptor GPR84. Strikingly, mammalian fatty acid synthase produces acyl-pyrones invitro, and this production is modulated by NADPH. Taken together, our studies support a regulatory role of AKR1C3 in an expanded polyamine pathway and a model linking fatty acid synthesis and NADPH levels to GPR84 signaling.

Biochemical role of FOXM1-dependent histone linker H1B in human epidermal stem cells

Epidermal stem cells orchestrate epidermal renewal and timely wound repair through a tight regulation of self-renewal, proliferation, and differentiation. In culture, human epidermal stem cells generate a clonal type referred to as holoclone, which give rise to transient amplifying progenitors (meroclone and paraclone-forming cells) eventually generating terminally differentiated cells. Leveraging single-cell transcriptomic data, we explored the FOXM1-dependent biochemical signals controlling self-renewal and differentiation in epidermal stem cells aimed at improving regenerative medicine applications. We report that the expression of H1 linker histone subtypes decrease during serial cultivation. At clonal level we observed that H1B is the most expressed isoform, particularly in epidermal stem cells, as compared to transient amplifying progenitors. Indeed, its expression decreases in primary epithelial culture where stem cells are exhausted due to FOXM1 downregulation. Conversely, H1B expression increases when the stem cells compartment is sustained by enforced FOXM1 expression, both in primary epithelial cultures derived from healthy donors and JEB patient. Moreover, we demonstrated that FOXM1 binds the promotorial region of H1B, hence regulates its expression. We also show that H1B is bound to the promotorial region of differentiation-related genes and negatively regulates their expression in epidermal stem cells. We propose a novel mechanism wherein the H1B acts downstream of FOXM1, contributing to the fine interplay between self-renewal and differentiation in human epidermal stem cells. These findings further define the networks that sustain self-renewal along the previously identified YAP-FOXM1 axis.

Reintegration of Dairy in Daily American Diets: A Biochemical and Nutritional Perspective

This paper explores the reintegration of dairy products into the daily diets of Americans, with a focus on the biochemical role of lactase, the enzyme responsible for lactose digestion. It examines the benefits of dairy consumption, practical strategies for reintroducing dairy into the diet, and the use of lactase supplements to manage lactose intolerance. This approach aims to enhance nutritional intake and overall health in the lactose- intolerant population.

Predicting the amino group pKa of amino acids using machine learning-QSPR methods

Amino acids are one of the main building blocks of proteins, and because of this connection and their main role in biochemistry, they are of great interest in pharmaceutical industries today. In nature, there are approximately 300 amino acids, out of which 20 are present in the human body and are responsible for protein synthesis. As a result, amino acids are widely used in various fields such as biological sciences, chemistry, medicine, and various industries. This research focuses on estimating the acid dissociation constant (pKa) of the amino group related to 52 amino acids using the quantitative structure–property relationship (QSPR) method, employing four different regression models: Genetic Algorithm-Multivariable Linear Regression (GA-MLR), Particle Swarm Optimization-Support Vector Machine (PSO-SVM), Feed Forward Neural Network (FFNN), and Decision Tree (DT). Using the GA-MLR, the optimal number of descriptors for estimating pKa was determined to be 9. By comparing different machine learning models, it can be observed that the coefficient of determination (R2) follows the trend R2 PSO-SVM = 0.9681 > R2 FFNN = 0.9539 > R2 DT = 0.9329 > R2 GA-MLR = 0.9231. Therefore, the PSO-SVM model provided the best prediction, while the FFNN, DT, and GA-MLR models ranked next in terms of precision in predicting the pKa of amino acids. By dividing the data into test/train sets in a ratio of approximately 20/80, the model's validity was confirmed due to the nearness of the R2 values between the training and testing sets. Ultimately, the best model is capable of predicting the pKa value of the amino group in amino acids with a mean absolute percent error of 1.18 %.

Feasible and economic DIY procedures of a hand-held fluorescence detector set-FluorDetector to assist laboratory course development.

Fluorescence-related experimental techniques play an important role in biochemistry, molecular biology, and cell biology. However, fluorescence-related experiments are rarely included in the laboratory courses of most Chinese universities. This is mainly due to the conflict between large class size (50-60 students in one room) and funding/space limitations to purchase and accommodate enough fluorescence detection equipment. Here, we proposed feasible and economical Do It Yourself (DIY) procedures of a hand-held fluorescence detector set-FluorDetector to support the development of laboratory courses. Tested on several samples, clear fluorescence signals could be directly observed by FluorDetector and photographed with a smartphone. In addition, FluorDetector was able to turn a conventional stereomicroscope into a fluorescence stereomicroscope, detecting fluorescence signals with clean background. FluorDetector is easy to make with a 3D printer, with an extremely low cost ($200 each) when compared with a commercial fluorescence microscope or fluorescence stereomicroscope, and almost as sensitive as a microplate reader in measuring fluorescence. Therefore, FluorDetector is a possible strategy to solve the problem and help to integrate fluorescence-related experimental modules in laboratory courses.