A calmodulin like EF hand protein positively regulates oxalate decarboxylase expression by interacting with E-box elements of the promoter

Unveiling fungal strategies: Mycoremediation in multi-metal pesticide environment using proteomics

Micropollutants, such as heavy metals and pesticides, inhibit microbial growth, threatening ecosystems. Yet, the mechanism behind mycoremediation of the pesticide lindane and multiple metals (Cd, Total Cr, Cu, Ni, Pb, Zn) remains poorly understood. In our study, we investigated cellular responses in Aspergillus fumigatus PD-18 using LC-MS/MS, identifying 2190 proteins, 1147 of which were consistently present under both stress conditions. Specifically, Cu-Zn superoxide dismutase and heat shock proteins were up-regulated to counter oxidative stress and protein misfolding. Proteins involved in intracellular trafficking, secretion, and vesicular transport; RNA processing and modification showed enhanced abundance and regulating stress response pathways. Additionally, haloalkane dehalogenase and homogentisate 1,2-dioxygenase played pivotal roles in lindane mineralization. Bioinformatics analysis highlighted enriched pathways such as Glyoxylate and dicarboxylate metabolism and Purine metabolism, that are crucial for combating adverse environments. We identified the hub protein 26 S proteasome regulatory subunit complex as potential biomarker and remedial targets for mycoremediation of wastewater, suggesting practical applications for environmental remediation.

Internal Disorders of Mango Fruit and Their Management-Physiology, Biochemistry, and Role of Mineral Nutrients

Mango (Mangifera indica L.) is a popular fruit grown in tropical and subtropical regions. Mango has a distinctive aroma, flavour, and nutritional properties. Annual global mango production is >50 million tonnes. Major producers of mango include India, Bangladesh, China, Mexico, Pakistan, Indonesia, Brazil, Thailand, and the Philippines, and it is shipped worldwide. Harvested mango fruit are highly perishable, with a short shelf life. Physiological disorders are among the major factors limiting their postharvest quality and shelf life, including when fruit need phytosanitary treatments, such as hot water treatment, vapour heat treatment, and irradiation. This review focuses on problematic physiological disorders of mango flesh, including physiology and biochemistry. It considers factors contributing to the development and/or exacerbation of internal disorders. Improved production practices, including pruning, nutrient application, and irrigation, along with monitoring and managing environmental conditions (viz., temperature, humidity, and vapour pressure deficit), can potentially maintain fruit robustness to better tolerate otherwise stressful postharvest operations. As demand for mangoes on international markets is compromised by internal quality, robust fruit is crucial to maintaining existing and gaining new domestic and export consumer markets. Considering mango quality, a dynamic system, a more holistic approach encompassing pre-, at-, and post-harvest conditions as a continuum is needed to determine fruit predisposition and subsequent management of internal disorders.

Integrated transcriptomic, metabolomic, and functional analyses unravel the mechanism of bagging delaying fruit cracking of pomegranate (Punica granatum L.)

The economic impact of fruit cracking in pomegranate products is substantial. In this study, we present the inaugural comprehensive analysis of transcriptome and metabolome in the outermost pericarp of pomegranate fruit in bagging conditions. Our investigation revealed a notable upregulation of differentially expressed genes (DEGs) associated with the calcium signaling pathway (76.92%) and xyloglucan endotransglucosylase/hydrolase (XTH) genes (87.50%) in the fruit peel of non-cracking fruit under bagging. Metabolomic analysis revealed that multiple phenolics, flavonoids, and tannins were identified in pomegranate. Among these, calmodulin-like 23 (PgCML23) exhibited a significant correlation with triterpenoids and demonstrated a marked upregulation under bagging treatment. The transgenic tomatoes overexpressing PgCML23 exhibited significantly higher cellulose content and xyloglucan endotransglucosylase (XET) enzyme activity in the pericarp at the red ripening stage compared to the wild type. Conversely, water-soluble pectin content, polygalacturonase (PG), and β-galactosidase (β-GAL) enzyme activities were significantly lower in the transgenic tomatoes. Importantly, the heterologous expression of PgCML23 led to a substantial reduction in the fruit cracking rate in tomatoes. Our findings highlight the reduction of fruit cracking in bagging conditions through the manipulation of PgCML23 expression.

Recent Advances of Oxalate Decarboxylase: Biochemical Characteristics, Catalysis Mechanisms, and Gene Expression and Regulation

Oxalate decarboxylase (OXDC) is a typical Mn2+/Mn3+ dependent metal enzyme and splits oxalate to formate and CO2 without any organic cofactors. Fungi and bacteria are the main organisms expressing the OXDC gene, but with a significantly different mechanism of gene expression and regulation. Many articles reported its potential applications in the clinical treatment of hyperoxaluria, low-oxalate food processing, degradation of oxalate salt deposits, oxalate acid diagnostics, biocontrol, biodemulsifier, and electrochemical oxidation. However, some questions still remain to be clarified about the role of substrate binding and/or protein environment in modulating the redox properties of enzyme-bound Mn(II)/Mn(III), the nature of dioxygen involved in the catalytic mechanism, and how OXDC acquires Mn(II) /Mn(III). This review mainly summarizes its biochemical and structure characteristics, gene expression and regulation, and catalysis mechanism. We also deep-mined oxalate decarboxylase gene data from National Center for Biotechnology Information to give some insights to explore new OXDC with diverse biochemical properties.

Cloning and Molecular Characterization of CmOxdc3 Coding for Oxalate Decarboxylase in the Mycoparasite Coniothyrium minitans

Coniothyrium minitans (Cm) is a mycoparasitic fungus of Sclerotinia sclerotiorum (Ss), the causal agent of Sclerotinia stem rot of oilseed rape. Ss can produce oxalic acid (OA) as a phytotoxin, whereas Cm can degrade OA, thereby nullifying the toxic effect of OA. Two oxalate decarboxylase (OxDC)-coding genes, CmOxdc1 and CmOxdc2, were cloned, and only CmOxdc1 was found to be partially responsible for OA degradation, implying that other OA-degrading genes may exist in Cm. This study cloned a novel OxDC gene (CmOxdc3) in Cm and its OA-degrading function was characterized by disruption and complementation of CmOxdc3. Sequence analysis indicated that, unlike CmOxdc1, CmOxdc3 does not have the signal peptide sequence, implying that CmOxDC3 may have no secretory capability. Quantitative RT-PCR showed that CmOxdc3 was up-regulated in the presence of OA, malonic acid and hydrochloric acid. Deletion of CmOxdc3 resulted in reduced capability to parasitize sclerotia of Ss. The polypeptide (CmOxDC3) encoded by CmOxdc3 was localized in cytoplasm and gathered in vacuoles in response to the extracellular OA. Taken together, our results demonstrated that CmOxdc3 is a novel gene responsible for OA degradation, which may work in a synergistic manner with CmOxdc1.

Possible Association of Nucleobindin-1 Protein with Depressive Disorder in Patients with HIV Infection

Background: Mental disorders linked with dysfunction in the temporal cortex, such as anxiety and depression, can increase the morbidity and mortality of people living with HIV (PLWHA). Expressions of both nucleobindin 1 (NUCB1) and cannabinoid receptor 1 (CNR1) in the neurons have been found to alter in patients with depressive disorder, but whether it is involved in the development of depression in the context of HIV infection is unknown. Objectives To investigate the effects of NUCB1 on depressive disorder among PLWHA and preliminarily explore the underlying molecular mechanisms. Methods: Individuals who were newly HIV diagnosed were assessed on the Hospital Anxiety and Depression scale (HADS). Then SHIV-infected rhesus monkeys were used to investigate the possible involvement of the NUCB1 and the CNR1 protein in depression-like behavior. Results: The prevalence rate of depression among PLWHA was 27.33% (41/150). The mechanism results showing elevated NUCB1 levels in cerebrospinal fluid from HIV-infected patients suffering from depression were confirmed compared to those of HIV-infected patients. Moreover, the immunohistochemical analysis indicated the expression of NUCB1 in the temporal cortex neurons of SHIV-infected monkeys was higher than that of the healthy control. Conversely, CNR1 expression was down-regulated at protein levels. Conclusions: Depression symptoms are common among PLWHA and associate with NUCB1 expression increases, and NUCB1 may be a potential target for depression.

Impaired photoprotection in Phaeodactylum tricornutum KEA3 mutants reveals the proton regulatory circuit of diatoms light acclimation

Diatoms are successful phytoplankton clades able to acclimate to changing environmental conditions, including e.g. variable light intensity. Diatoms are outstanding at dissipating light energy exceeding the maximum photosynthetic electron transfer (PET) capacity via the nonphotochemical quenching (NPQ) process. While the molecular effectors of NPQ as well as the involvement of the proton motive force (PMF) in its regulation are known, the regulators of the PET/PMF relationship remain unidentified in diatoms. We generated mutants of the H⁺ /K⁺ antiporter KEA3 in the model diatom Phaeodactylum tricornutum. Loss of KEA3 activity affects the PET/PMF coupling and NPQ responses at the onset of illumination, during transients and in steady-state conditions. Thus, this antiporter is a main regulator of the PET/PMF coupling. Consistent with this conclusion, a parsimonious model including only two free components, KEA3 and the diadinoxanthin de-epoxidase, describes most of the feedback loops between PET and NPQ. This simple regulatory system allows for efficient responses to fast (minutes) or slow (e.g. diel) changes in light environment, thanks to the presence of a regulatory calcium ion (Ca²⁺ )-binding domain in KEA3 modulating its activity. This circuit is likely tuned by the NPQ-effector proteins, LHCXs, providing diatoms with the required flexibility to thrive in different ocean provinces.

Heat stress in macrofungi: effects and response mechanisms

Temperature is one of the key factors that affects the growth and development of macrofungi. Heat stress not only negatively affects the morphology and growth rate of macrofungi, but also destroys cell structures and influences cell metabolism. Due to loosed structure of cell walls and increased membrane fluidity, which caused by heat stress, the outflow of intracellular nutrients makes macrofungi more vulnerable to invasion by pathogens. Macrofungi accumulate reactive oxygen species (ROS), Ca²⁺, and nitric oxide (NO) when heat-stressed, which transmit and amplify the heat stimulation signal through intracellular signal transduction pathways. Through regulation of some transcription factors including heat response factors (HSFs), POZCP26 and MYB, macrofungi respond to heat stress by different mechanisms. In this paper, we present mechanisms used by macrofungi to adapt and survive under heat stress conditions, including antioxidant defense systems that eliminate the excess ROS, increase in trehalose levels that prevent enzymes and proteins deformation, and stabilize cell structures and heat shock proteins (HSPs) that repair damaged proteins and synthesis of auxins, which increase the activity of antioxidant enzymes. All of these help macrofungi resist and adapt to heat stress. KEY POINTS: • The effects of heat stress on macrofungal growth and development were described. • The respond mechanisms to heat stress in macrofungi were summarized. • The further research directions of heat stress in macrofungi were discussed.

Interactions between calcium and ABA signaling pathways in the regulation of fruit ripening

Fruit ripening and senescence are finely controlled by plant hormones such as ethylene and abscisic acid (ABA) but also by calcium ions and by calcium-dependent signaling pathways. Although there are extensive data supporting an interaction between ethylene and calcium in fruit ripening, the regulatory mechanisms resulting from the interaction between ABA and calcium have not yet been fully clarified. In this article, we have reviewed the full roles of calcium and its sensors (CaM, CMLs, CDPKs, CBLs) as well as ABA and the interactions between the two signaling pathways in the regulation of stress responses and in fruit ripening. To illustrate the possible interaction between calcium sensors and ABA signaling components in the control of fruit ripening, we propose an interaction model between the calcium and ABA signaling pathways.

Molecular evolution of proteins mediating mitochondrial fission-fusion dynamics

Eukaryotes employ a subset of dynamins to mediate mitochondrial fusion and fission dynamics. Here we report the molecular evolution and diversification of the dynamin-related mitochondrial proteins that drive the fission (Drp1) and the fusion processes (mitofusin and OPA1). We demonstrate that the three paralogs emerged concurrently in an early mitochondriate eukaryotic ancestor. Furthermore, multiple independent duplication events from an ancestral bifunctional fission protein gave rise to specialized fission proteins. The evolutionary history of these proteins is marked by transformations that include independent gain and loss events occurring at the levels of entire genes, specific functional domains, and intronic regions. The domain level variations primarily comprise loss-gain of lineage specific domains that are present in the terminal regions of the sequences.

Manipulation of oxalate metabolism in plants for improving food quality and productivity

Oxalic acid is a naturally occurring metabolite in plants and a common constituent of all plant-derived human diets. Oxalic acid has diverse unrelated roles in plant metabolism, including pH regulation in association with nitrogen metabolism, metal ion homeostasis and calcium storage. In plants, oxalic acid is also a pathogenesis factor and is secreted by various fungi during host infection. Unlike those of plants, fungi and bacteria, the human genome does not contain any oxalate-degrading genes, and therefore, the consumption of large amounts of plant-derived oxalate is considered detrimental to human health. In this review, we discuss recent biotechnological approaches that have been used to reduce the oxalate content of plant tissues.

Genetically modified (GM) crops: milestones and new advances in crop improvement

New advances in crop genetic engineering can significantly pace up the development of genetically improved varieties with enhanced yield, nutrition and tolerance to biotic and abiotic stresses. Genetically modified (GM) crops can act as powerful complement to the crops produced by laborious and time consuming conventional breeding methods to meet the worldwide demand for quality foods. GM crops can help fight malnutrition due to enhanced yield, nutritional quality and increased resistance to various biotic and abiotic stresses. However, several biosafety issues and public concerns are associated with cultivation of GM crops developed by transgenesis, i.e., introduction of genes from distantly related organism. To meet these concerns, researchers have developed alternative concepts of cisgenesis and intragenesis which involve transformation of plants with genetic material derived from the species itself or from closely related species capable of sexual hybridization, respectively. Recombinase technology aimed at site-specific integration of transgene can help to overcome limitations of traditional genetic engineering methods based on random integration of multiple copy of transgene into plant genome leading to gene silencing and unpredictable expression pattern. Besides, recently developed technology of genome editing using engineered nucleases, permit the modification or mutation of genes of interest without involving foreign DNA, and as a result, plants developed with this technology might be considered as non-transgenic genetically altered plants. This would open the doors for the development and commercialization of transgenic plants with superior phenotypes even in countries where GM crops are poorly accepted. This review is an attempt to summarize various past achievements of GM technology in crop improvement, recent progress and new advances in the field to develop improved varieties aimed for better consumer acceptance.