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Journal of Enzyme Inhibition and... Dec 2023Acid phosphatases (EC 3.1.3.2) are the enzymes that catalyse transphosphorylation reactions and promotes the hydrolysis of numerous orthophosphate esters in acidic... (Review)
Review
Acid phosphatases (EC 3.1.3.2) are the enzymes that catalyse transphosphorylation reactions and promotes the hydrolysis of numerous orthophosphate esters in acidic media, as a crucial element for the metabolism of phosphate in tissues. Inorganic phosphate (Pi) utilisation and scavenging, as well as the turnover of Pi-rich sources found in plant vacuoles, are major processes in which intracellular and secretory acid phosphatases function. Therefore, a thorough understanding of these enzymes' structural characteristics, specificity, and physiochemical properties is required to comprehend the function of acid phosphatases in plant energy metabolism. Furthermore, acid phosphatases are gaining increasing importance in industrial biotechnology due to their involvement in transphosphorylation processes and their ability to reduce phosphate levels in food products. Hence, this review aims to provide a comprehensive overview of the purification methods employed for isolating acid phosphatases from diverse plant sources, as well as their structural and functional properties. Additionally, the review explores the potential applications of these enzymes in various fields.
Topics: Acid Phosphatase; Hydrolysis; Plants; Phosphates
PubMed: 37985663
DOI: 10.1080/14756366.2023.2282379 -
Cell Death Discovery Mar 2024To date, numerous mechanisms have been identified in which one cell engulfs another, resulting in the creation of 'cell-in-cell' (CIC) structures, which subsequently... (Review)
Review
To date, numerous mechanisms have been identified in which one cell engulfs another, resulting in the creation of 'cell-in-cell' (CIC) structures, which subsequently cause cell death. One of the mechanisms of formation of these structures is entosis, which is presumably associated with possible carcinogenesis and tumour progression. The peculiarity of the process is that entotic cells themselves actively invade the host cell, and afterwards have several possible variants of fate. Entotic formations are structures where one cell is engulfed by another cell, creating a cell-in-cell structure. The nucleus of the outer cell has a crescent shape, while the inner cell is surrounded by a large entotic vacuole. These characteristics differentiate entosis from cell cannibalism. It's worth noting that entotic formations are not necessarily harmful and may even be beneficial in some cases. In this article we will consider the mechanism of entosis and variants of entotic cell death, and also put forward hypothesis about possible variants of participation of this process on the formation and progression of cancer. This article also presents our proposed classification of functional forms of entosis.
PubMed: 38429285
DOI: 10.1038/s41420-024-01877-9 -
BMC Bioinformatics Sep 2023Plant vacuoles are essential organelles in the growth and development of plants, and accurate identification of their proteins is crucial for understanding their...
Plant vacuoles are essential organelles in the growth and development of plants, and accurate identification of their proteins is crucial for understanding their biological properties. In this study, we developed a novel model called GraphIdn for the identification of plant vacuole proteins. The model uses SeqVec, a deep representation learning model, to initialize the amino acid sequence. We utilized the AlphaFold2 algorithm to obtain the structural information of corresponding plant vacuole proteins, and then fed the calculated contact maps into a graph convolutional neural network. GraphIdn achieved accuracy values of 88.51% and 89.93% in independent testing and fivefold cross-validation, respectively, outperforming previous state-of-the-art predictors. As far as we know, this is the first model to use predicted protein topology structure graphs to identify plant vacuole proteins. Furthermore, we assessed the effectiveness and generalization capability of our GraphIdn model by applying it to identify and locate peroxisomal proteins, which yielded promising outcomes. The source code and datasets can be accessed at https://github.com/SJNNNN/GraphIdn .
Topics: Plant Proteins; Vacuoles; Neural Networks, Computer; Algorithms; Amino Acid Sequence
PubMed: 37740195
DOI: 10.1186/s12859-023-05475-x -
WMJ : Official Publication of the State... Dec 2023Peripheral smear examination is a simple and cost-effective test that is routinely performed while monitoring patients diagnosed with COVID-19. We sought to summarize... (Review)
Review
INTRODUCTION
Peripheral smear examination is a simple and cost-effective test that is routinely performed while monitoring patients diagnosed with COVID-19. We sought to summarize the peripheral blood morphologic findings in patients with COVID-19 infection.
METHODS
A systematic review was conducted using a standardized keyword search on Medline database (PubMed), med RXIV, Google Scholar, EMBASE, and SCOPUS for studies discussing peripheral blood smear or morphologic blood findings in patients diagnosed with COVID-19.
RESULTS
A total of 28 studies were included in the review. Normocytic normochromic anemia was the most frequently encountered red blood cell finding. Neutrophilia was seen in most of the studies. A variety of morphological changes were observed in neutrophils, including pyknotic nuclei, variable shapes, toxic granules, and cytoplasmic vacuolization. Hyposegmented neutrophils, pseudo-Pegler Huet forms, and hypogranular forms were common findings reported by many studies. Lymphopenia was reported by most studies. Lymphocytes showed numerous morphological changes, including reactive forms, Downey forms, increased large granular lymphocytes, and plasmacytoid cells. The presence of giant platelets was seen frequently.
CONCLUSIONS
The peripheral blood in COVID-19 shows a spectrum of findings, mostly reactive changes in neutrophils, monocytes, lymphocytes, and platelets. Increased neutrophil/lymphocyte ratio and higher neutrophil counts have been associated with poor prognosis, which potentially could help triage patients, but this needs to be confirmed in larger studies.
Topics: Humans; COVID-19
PubMed: 38180924
DOI: No ID Found -
Developmental Cell Mar 2024The lipid droplet (LD) organization proteins Ldo16 and Ldo45 affect multiple aspects of LD biology in yeast. They are linked to the LD biogenesis machinery seipin, and...
The lipid droplet (LD) organization proteins Ldo16 and Ldo45 affect multiple aspects of LD biology in yeast. They are linked to the LD biogenesis machinery seipin, and their loss causes defects in LD positioning, protein targeting, and breakdown. However, their molecular roles remained enigmatic. Here, we report that Ldo16/45 form a tether complex with Vac8 to create vacuole lipid droplet (vCLIP) contact sites, which can form in the absence of seipin. The phosphatidylinositol transfer protein (PITP) Pdr16 is a further vCLIP-resident recruited specifically by Ldo45. While only an LD subpopulation is engaged in vCLIPs at glucose-replete conditions, nutrient deprivation results in vCLIP expansion, and vCLIP defects impair lipophagy upon prolonged starvation. In summary, Ldo16/45 are multifunctional proteins that control the formation of a metabolically regulated contact site. Our studies suggest a link between LD biogenesis and breakdown and contribute to a deeper understanding of how lipid homeostasis is maintained during metabolic challenges.
Topics: Saccharomyces cerevisiae; Lipid Droplets; Vacuoles; Proteins; Phospholipid Transfer Proteins
PubMed: 38367622
DOI: 10.1016/j.devcel.2024.01.016 -
Molecular Biology of the Cell Aug 2023As a prelude to fusion, the R-SNARE on one membrane zippers with Qa-, Qb-, and Qc-SNAREs from its apposed fusion partner, forming a four-helical bundle that draws the...
As a prelude to fusion, the R-SNARE on one membrane zippers with Qa-, Qb-, and Qc-SNAREs from its apposed fusion partner, forming a four-helical bundle that draws the two membranes together. Because Qa- and Qb-SNAREs are anchored to the same membrane and are adjacent in the 4-SNARE bundle, their two anchors might be redundant. Using the recombinant pure protein catalysts of yeast vacuole fusion, we now report that the specific distribution of transmembrane (TM) anchors on the Q-SNAREs is critical for efficient fusion. A TM anchor on the Qa-SNARE supports rapid fusion even when the other two Q-SNAREs are unanchored, while a TM anchor on the Qb-SNARE is dispensable and is insufficient for rapid fusion as the sole Q-SNARE anchor. This does not depend on which specific TM domain is attached to the Qa-SNARE but rather is due to the Qa-SNARE being anchored per se. The need for Qa-SNARE anchoring is even seen when the motypic fusion and vacuole rotein orting protein (HOPS), the physiological catalyst of tethering and SNARE assembly, is replaced by an artificial tether. The need for a Qa TM anchor is thus a fundamental property of vacuolar SNARE zippering-induced fusion and may reflect the need for the Qa juxtamembrane (JxQa) region to be anchored between its SNARE and TM domains. This requirement for Qa-SNARE anchoring and correct JxQa position is bypassed by Sec17/Sec18, exploiting a platform of partially zippered SNAREs. Because Qa is the only synaptic Q-SNARE with a TM anchor, the need for Qa-specific anchoring may reflect a general requirement for SNARE-mediated fusion.
Topics: Vacuoles; Saccharomyces cerevisiae Proteins; Saccharomyces cerevisiae; SNARE Proteins; Qa-SNARE Proteins; Q-SNARE Proteins; Recombinant Proteins
PubMed: 37314849
DOI: 10.1091/mbc.E23-02-0052 -
Cell Reports Aug 2023Iron homeostasis, which is pivotal to virulence, is regulated by the phosphatidylinositol 3-kinase CgVps34 in the human fungal pathogen Candida glabrata. Here, we...
Iron homeostasis, which is pivotal to virulence, is regulated by the phosphatidylinositol 3-kinase CgVps34 in the human fungal pathogen Candida glabrata. Here, we identify CgPil1 as a phosphatidylinositol 3-phosphate (PI3P)-binding protein and unveil its role in retaining the high-affinity iron transporter CgFtr1 at the plasma membrane (PM), with PI3P negatively regulating CgFtr1-CgPil1 interaction. PI3P production and its PM localization are elevated in the high-iron environment. Surplus iron also leads to intracellular distribution and vacuolar delivery of CgPil1 and CgFtr1, respectively, from the PM. Loss of CgPil1 or CgFtr1 ubiquitination at lysines 391 and 401 results in CgFtr1 trafficking to the endoplasmic reticulum and a decrease in vacuole-localized CgFtr1. The E3-ubiquitin ligase CgRsp5 interacts with CgFtr1 and forms distinct CgRsp5-CgFtr1 puncta at the PM, with high iron resulting in their internalization. Finally, PI3P controls retrograde transport of many PM proteins. Altogether, we establish PI3P as a key regulator of membrane transport in C. glabrata.
Topics: Humans; Carrier Proteins; Ion Transport; Biological Transport; Phosphatidylinositol Phosphates; Iron; Protein Transport
PubMed: 37490387
DOI: 10.1016/j.celrep.2023.112855 -
Frontiers in Plant Science 2023Phosphorus (P) deficiency hinders cotton ( L.) growth and development, seriously affecting lint yield and fiber quality. However, it is still unclear how P fertilizer...
INTRODUCTION
Phosphorus (P) deficiency hinders cotton ( L.) growth and development, seriously affecting lint yield and fiber quality. However, it is still unclear how P fertilizer affects fiber length.
METHODS
Therefore, a two-year (2019-2020) pool-culture experiment was conducted using the split-plot design, with two cotton cultivars (CCRI-79; low-P tolerant and SCRC-28; low-P sensitive) as the main plot. Three soil available phosphorus (AP) contents (P: 3 ± 0.5, P: 6 ± 0.5, and P (control) with 15 ± 0.5 mg kg) were applied to the plots, as the subplot, to investigate the impact of soil AP content on cotton fiber elongation and length.
RESULTS
Low soil AP (P and P) decreased the contents of the osmotically active solutes in the cotton fibers, including potassium ions (K), malate, soluble sugar, and sucrose, by 2.2-10.2%, 14.4-47.3%, 8.7-24.5%, and 10.1-23.4%, respectively, inhibiting the vacuoles from facilitating fiber elongation through osmoregulation. Moreover, soil AP deficiency also reduced the activities of enzymes participated in fiber elongation (plasma membrane H-ATPase (PM-H-ATPase), vacuole membrane H-ATPase (V-H-ATPase), vacuole membrane H-translocating inorganic pyrophosphatase (V-H-PPase), and phosphoenolpyruvate carboxylase (PEPC)). The PM-H-ATPase, V-H-ATPase, V-H-PPase, and PEPC were reduced by 8.4-33.0%, 7.0-33.8%, 14.1-38.4%, and 16.9-40.2%, respectively, inhibiting the transmembrane transport of the osmotically active solutes and acidified conditions for fiber cell wall, thus limiting the fiber elongation. Similarly, soil AP deficiency reduced the fiber length by 0.6-3.0 mm, mainly due to the 3.8-16.3% reduction of the maximum velocity of fiber elongation (V). Additionally, the upper fruiting branch positions (FB) had higher V and longer fiber lengths under low soil AP.
DISCUSSION
Cotton fibers with higher malate content and V-H-ATPase and V-H-PPase activities yielded longer fibers. And the malate and soluble sugar contents and V-H-ATPase and PEPC activities in the SCRC-28's fiber were more sensitive to soil AP deficiency in contrast to those of CCRI-79, possibly explaining the SCRC-28 fiber length sensitivity to low soil AP.
PubMed: 37662180
DOI: 10.3389/fpls.2023.1254103 -
Virulence Dec 2024Cytoplasmic vacuolization is commonly induced by bacteria and viruses, reflecting the complex interactions between pathogens and the host. However, their characteristics...
Cytoplasmic vacuolization is commonly induced by bacteria and viruses, reflecting the complex interactions between pathogens and the host. However, their characteristics and formation remain unclear. Nervous necrosis virus (NNV) infects more than 100 global fish species, causing enormous economic losses. Vacuolization is a hallmark of NNV infection in host cells, but remains a mystery. In this study, we developed a simple aptamer labelling technique to identify red-spotted grouper NNV (RGNNV) particles in fixed and live cells to explore RGNNV-induced vacuolization. We observed that RGNNV-induced vacuolization was positively associated with the infection time and virus uptake. During infection, most RGNNV particles, as well as viral genes, colocalized with vacuoles, but not giant vacuoles > 3 μm in diameter. Although the capsid protein (CP) is the only structural protein of RGNNV, its overexpression did not induce vacuolization, suggesting that vacuole formation probably requires virus entry and replication. Given that small Rab proteins and the cytoskeleton are key factors in regulating cellular vesicles, we further investigated their roles in RGNNV-induced vacuolization. Using live cell imaging, Rab5, a marker of early endosomes, was continuously located in vacuoles bearing RGNNV during giant vacuole formation. Rab5 is required for vacuole formation and interacts with CP according to siRNA interference and Co-IP analysis. Furthermore, actin formed distinct rings around small vacuoles, while vacuoles were located near microtubules. Actin, but not microtubules, plays an important role in vacuole formation using chemical inhibitors. These results provide valuable insights into the pathogenesis and control of RGNNV infections.
Topics: Animals; Actins; Fish Diseases; RNA Virus Infections; Capsid Proteins; Necrosis
PubMed: 38230744
DOI: 10.1080/21505594.2023.2301244 -
Biological Chemistry Jul 2023Atg18, Atg21 and Hsv2 are homologous β-propeller proteins binding to PI3P and PI(3,5)P. Atg18 is thought to organize lipid transferring protein complexes at contact...
Atg18, Atg21 and Hsv2 are homologous β-propeller proteins binding to PI3P and PI(3,5)P. Atg18 is thought to organize lipid transferring protein complexes at contact sites of the growing autophagosome (phagophore) with both the ER and the vacuole. Atg21 is restricted to the vacuole phagophore contact, where it organizes part of the Atg8-lipidation machinery. The role of Hsv2 is less understood, it partly affects micronucleophagy. Atg18 is further involved in regulation of PI(3,5)P synthesis. Recently, a novel Atg18-retromer complex and its role in vacuole homeostasis and membrane fission was uncovered.
Topics: Autophagy; Autophagy-Related Proteins; Membrane Proteins; Phosphatidylinositol Phosphates; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins
PubMed: 37139661
DOI: 10.1515/hsz-2023-0126