journal
https://read.qxmd.com/read/38658177/evidence-for-partial-functional-overlap-of-kea-and-msl-transport-proteins-in-the-chloroplast-inner-envelope-of-arabidopsis-thaliana
#21
JOURNAL ARTICLE
Carsten Völkner, Lorenz J Holzner, Katinka Bünger, Beata Szulc, Chance M Lewis, Andreas Klingl, Hans-Henning Kunz
Arabidopsis thaliana possesses two different ion-export mechanisms in the plastid inner envelope membrane. Due to a genome duplication, the transport proteins are encoded by partly redundant loci: K+ -efflux antiporter1 (KEA1) and KEA2 and mechanosensitive channel of small conductance-like2 (MSL2) and MSL3. Thus far, a functional link between these two mechanisms has not been established. Here, we show that kea1msl2 loss-of-function mutants exhibit phenotypes such as slow growth, reduced photosynthesis and changes in chloroplast morphology, several of which are distinct from either single mutants and do not resemble kea1kea2 or msl2msl3 double mutants...
April 24, 2024: FEBS Letters
https://read.qxmd.com/read/38658173/structural-and-functional-insights-into-the-enzymatic-activities-of-lipases-from-burkholderia-stagnalis-and-burkholderia-plantarii
#22
JOURNAL ARTICLE
Saori Kataoka, Sayuri Kawamoto, Sayuri Kitagawa, Wataru Kugimiya, Kazunobu Tsumura, Yukie Akutsu, Tomomi Kubota, Kazuhiko Ishikawa
Lipases with high interesterification activity are important enzymes for industrial use. The lipase from Burkholderia stagnalis (BsL) exhibits higher interesterification activity than that from Burkholderia plantarii (BpL) despite their significant sequence similarity. In this study, we determined the crystal structure of BsL at 1.40 Å resolution. Utilizing structural insights, we have successfully augmented the interesterification activity of BpL by over twofold. This enhancement was achieved by substituting threonine with serine at position 289 through forming an expansive space in the substrate-binding site...
April 24, 2024: FEBS Letters
https://read.qxmd.com/read/38649293/structural-basis-for-the-minimal-bifunctional-alginate-epimerase-alge3-from-azotobacter-chroococcum
#23
JOURNAL ARTICLE
Takaaki Fujiwara, Eriko Mano, Eriko Nango
Among the epimerases specific to alginate, some of them in Azotobacter genera convert β-d-mannuronic acid to α-l-guluronic acid but also have lyase activity to degrade alginate. The remarkable characteristics of these epimerases make it a promising enzyme for tailoring alginates to meet specific demands. Here, we determined the structure of the bifunctional mannuronan C-5 epimerase AlgE3 from Azotobacter chroococcum (AcAlgE3) in complex with several mannuronic acid oligomers as well as in apo form, which allowed us to elucidate the binding manner of each mannuronic acid oligomer, and the structural plasticity, which is dependent on calcium ions...
April 22, 2024: FEBS Letters
https://read.qxmd.com/read/38649155/selection-of-bifunctional-rnas-with-specificity-for-arginine-and-lipid-membranes
#24
JOURNAL ARTICLE
Teresa Janas, Karolina Sapoń, Tadeusz Janas
The molecular mechanisms of selective RNA loading into exosomes and other extracellular vesicles are not yet completely understood. In order to show that a pool of RNA sequences binds both the amino acid arginine and lipid membranes, we constructed a bifunctional RNA 10Arg aptamer specific for arginine and lipid vesicles. The preference of RNA 10Arg for lipid rafts was visualized and confirmed using FRET microscopy in neuroblastoma cells. The selection-amplification (SELEX) method using a doped (with the other three nucleotides) pool of RNA 10Arg sequences yielded several RNA 10Arg(D) sequences, and the affinities of these RNAs both to arginine and liposomes are improved in comparison to pre-doped RNA...
April 22, 2024: FEBS Letters
https://read.qxmd.com/read/38644468/deacylases-structure-function-and-relationship-to-diseases
#25
REVIEW
Shuxian Wang, Xiaoke Xing, Jialin Ma, Sihao Zheng, Qibin Song, Pingfeng Zhang
Reversible S-acylation plays a pivotal role in various biological processes, modulating protein functions such as subcellular localization, protein stability/activity, and protein-protein interactions. These modifications are mediated by acyltransferases and deacylases, among which the most abundant modification is S-palmitoylation. Growing evidence has shown that this rivalrous pair of modifications, occurring in a reversible cycle, is essential for various biological functions. Aberrations in this process have been associated with various diseases, including cancer, neurological disorders, and immune diseases...
April 21, 2024: FEBS Letters
https://read.qxmd.com/read/38639871/increased-ros-levels-in-mitochondrial-outer-membrane-protein-mul1-deficient-oocytes-result-in-abnormal-preimplantation-embryogenesis
#26
JOURNAL ARTICLE
Ann Nakai, Yuki Fukushima, Ayaka Yamamoto, Yuki Amatsu, Xiaoyan Chen, Mitsuhiro Nishigori, Yukino Yoshioka, Mari Kaneko, Takumi Koshiba, Toshio Watanabe
Reactive oxygen species (ROS) are associated with oocyte maturation inhibition, and N-acetyl-l-cysteine (NAC) partially reduces their harmful effects. Mitochondrial E3 ubiquitin ligase 1 (Mul1) localizes to the mitochondrial outer membrane. We found that female Mul1-deficient mice are infertile, and their oocytes contain high ROS concentrations. After fertilization, Mul1-deficient embryos showed a DNA damage response (DDR) and abnormal preimplantation embryogenesis, which was rescued by NAC addition and ROS depletion...
April 19, 2024: FEBS Letters
https://read.qxmd.com/read/38639734/transcriptional-activation-of-the-mycobacterium-tuberculosis-virulence-associated-small-rna-mts1338-by-the-response-regulators-dosr-and-phop
#27
JOURNAL ARTICLE
Krishan Kumar, Tanmay Dutta
MTS1338, a distinctive small RNA in pathogenic mycobacteria, plays a crucial role in host-pathogen interactions during infection. Mycobacterial cells encounter heterogeneous stresses in macrophages, which highly upregulate MTS1338. A dormancy regulatory factor DosR regulates the intracellular abundance of MTS1338. Herein, we investigated the interplay of DosR and a low pH-inducible gene regulator PhoP binding to the MTS1338 promoter. We identified that DosR strongly binds to two regions upstream of the MTS1338 gene...
April 19, 2024: FEBS Letters
https://read.qxmd.com/read/38631897/endogenous-ifn-%C3%AE-facilitates-pneumocystis-infection-and-downregulates-carbohydrate-receptors-in-cd4-t%C3%A2-cell-depleted-mice
#28
JOURNAL ARTICLE
Yi Wang, Hisashi Nagase, Yoh-Ichi Tagawa, Shinsuke Taki, Masaya Takamoto
IFN-γ plays a critical role in host defense against intracellular pathogens. IFN-γ is produced in the bronchoalveolar lavage fluid of mice infected with Pneumocystis, but the role of IFN-γ in host defense against Pneumocystis remains controversial. It has been previously reported that although exogenous IFN-γ has beneficial effects on eradication of Pneumocystis, endogenous IFN-γ has a negative impact on innate immunity in immunocompromised hosts. Surprisingly, CD4+ T cell-depleted IFN-γ deficient (GKO) mice exhibit resistance to Pneumocystis...
April 17, 2024: FEBS Letters
https://read.qxmd.com/read/38627196/molecular-dynamics-simulations-of-intracellular-lipid-droplets-a-new-tool-in-the-toolbox
#29
REVIEW
Jennifer Sapia, Stefano Vanni
Lipid droplets (LDs) are ubiquitous intracellular organelles with a central role in multiple lipid metabolic pathways. However, identifying correlations between their structural properties and their biological activity has proved challenging, owing to their unique physicochemical properties as compared with other cellular membranes. In recent years, molecular dynamics (MD) simulations, a computational methodology allowing the accurate description of molecular assemblies down to their individual components, have been demonstrated to be a useful and powerful approach for studying LD structural and dynamical properties...
April 16, 2024: FEBS Letters
https://read.qxmd.com/read/38627195/ichip-silac-analysis-identifies-epigenetic-regulators-of-cpg-methylation-of-the-p16-ink4a-gene
#30
JOURNAL ARTICLE
Toshitsugu Fujita, Hodaka Fujii
Allele-specific epigenetic events regulate the expression of specific genes such as tumor suppressor genes. Methods to biochemically identify epigenetic regulators remain limited. Here, we used insertional chromatin immunoprecipitation (iChIP) to address this issue. iChIP combined with quantitative mass spectrometry identified DNA methyltransferase 1 (DNMT1) and epigenetic regulators as proteins that potentially interact with a region of the p16INK4A gene that is CpG-methylated in one allele in HCT116 cells...
April 16, 2024: FEBS Letters
https://read.qxmd.com/read/38627103/why-an-integrated-view-of-gene-expression-studies-on-hematopoiesis-in-mouse-aging-is-better-than-the-sum-of-their-parts
#31
REVIEW
Leonid V Bystrykh
Globally, the human population is aging, with an increased proportion of people in "old age" (over 60 years). This trend leads to a growing demand in aging research, stimulating studies in animal models such as mice, fish, and invertebrates. Recently, we published a research summary on the aging of hematopoietic stem cells (HSCs) in C57BL/6 mice based on 12 gene expression datasets. Here, I discuss in greater detail the added value of taking an integrated view, rather than considering each publication separately, to determine genes involved in aging...
April 16, 2024: FEBS Letters
https://read.qxmd.com/read/38622055/ngk1-kinase-mediated-n-acetylglucosamine-metabolism-promotes-udp-glcnac-biosynthesis-in-saccharomyces-cerevisiae
#32
JOURNAL ARTICLE
Ayano Nishikawa, Shuichi Karita, Midori Umekawa
N-acetylglucosamine (GlcNAc) is an important structural component of the cell wall chitin, N-glycans, glycolipids, and GPI-anchors in eukaryotes. GlcNAc kinase phosphorylates GlcNAc into GlcNAc-6-phosphate, a precursor of uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) that serves as a substrate for glycan synthesis. Although GlcNAc kinase is found widely in organisms ranging from microorganisms to mammals, it has never been found in the model yeast Saccharomyces cerevisiae. Here, we demonstrate the presence of GlcNAc metabolism for UDP-GlcNAc biosynthesis in S...
April 15, 2024: FEBS Letters
https://read.qxmd.com/read/38605280/pat-mrna-decapping-factors-are-required-for-proper-development-in-arabidopsis
#33
JOURNAL ARTICLE
Zhangli Zuo, Milena Edna Roux, Yasin F Dagdas, Eleazar Rodriguez, Morten Petersen
Evolutionarily conserved protein associated with topoisomerase II (PAT1) proteins activate mRNA decay through binding mRNA and recruiting decapping factors to optimize posttranscriptional reprogramming. Here, we generated multiple mutants of pat1, pat1 homolog 1 (path1), and pat1 homolog 2 (path2) and discovered that pat triple mutants exhibit extremely stunted growth and all mutants with pat1 exhibit leaf serration while mutants with pat1 and path1 display short petioles. All three PATs can be found localized to processing bodies and all PATs can target ASYMMETRIC LEAVES 2-LIKE 9 transcripts for decay to finely regulate apical hook and lateral root development...
April 11, 2024: FEBS Letters
https://read.qxmd.com/read/38605276/the-components-of-the-ahr-molecular-chaperone-complex-differ-depending-on-whether-the-ligands-are-toxic-or-non-toxic
#34
JOURNAL ARTICLE
Yukihiko Narita, Arisa Tamura, Shiori Hatakeyama, Seiya Uemura, Atsuko Miura, Asami Haga, Noriko Tsuji, Nozomi Fujie, Yukina Izumi, Taku Sugawara, Michiro Otaka, Ken Okamoto, Peng Lu, Suguru Okuda, Michio Suzuki, Koji Nagata, Hiroaki Shimizu, Hideaki Itoh
The aryl hydrocarbon receptor (AhR) forms a complex with the HSP90-XAP2-p23 molecular chaperone when the cells are exposed to toxic compounds. Recently, 1,4-dihydroxy-2-naphthoic acid (DHNA) was reported to be an AhR ligand. Here, we investigated the components of the molecular chaperone complex when DHNA binds to AhR. Proteins eluted from the 3-Methylcolanthrene-affinity column were AhR-HSP90-XAP2-p23 complex. The AhR-molecular chaperone complex did not contain p23 in the eluents from the DHNA-affinity column...
April 11, 2024: FEBS Letters
https://read.qxmd.com/read/38604996/the-lipid-droplet-lipidome
#35
REVIEW
Michele Wölk, Maria Fedorova
Lipid droplets (LDs) are intracellular organelles with a hydrophobic core formed by neutral lipids surrounded by a phospholipid monolayer harboring a variety of regulatory and enzymatically active proteins. Over the last few decades, our understanding of LD biology has evolved significantly. Nowadays, LDs are appreciated not just as passive energy storage units, but rather as active players in the regulation of lipid metabolism and quality control machineries. To fulfill their functions in controlling cellular metabolic states, LDs need to be highly dynamic and responsive organelles...
April 11, 2024: FEBS Letters
https://read.qxmd.com/read/38604989/%C3%AE%C2%BAb-ras-proteins-are-fast-exchanging-gtpases-and-function%C3%A2-via-nucleotide-independent-binding-of-ral-gtpase-activating-protein-complexes
#36
JOURNAL ARTICLE
René Rasche, Lisa Helene Apken, Esther Michalke, Daniel Kümmel, Andrea Oeckinghaus
κB-Ras (NF-κB inhibitor-interacting Ras-like protein) GTPases are small Ras-like GTPases but harbor interesting differences in important sequence motifs. They act in a tumor-suppressive manner as negative regulators of Ral (Ras-like) GTPase and NF-κB signaling, but little is known about their mode of function. Here, we demonstrate that, in contrast to predictions based on primary structure, κB-Ras GTPases possess hydrolytic activity. Combined with low nucleotide affinity, this renders them fast-cycling GTPases that are predominantly GTP-bound in cells...
April 11, 2024: FEBS Letters
https://read.qxmd.com/read/38604984/characterization-of-the-endogenous-retrovirus-derived-placenta-specific-soluble-protein-envv-fca-from-domestic-cats
#37
JOURNAL ARTICLE
Didik Pramono, Kenji Sugimoto, Tohru Kimura, Ariko Miyake, Kazuo Nishigaki
Endogenous retroviruses (ERVs) are remnants of ancestral viruses in the host genome. The present study identified the expression of a defective retroviral env gene belonging to the ERV group V member Env (EnvV) in Felis catus (EnvV-Fca). EnV-Fca was specifically detected in the placental trophoblast syncytiotrophobic layer and expressed as a secreted protein in cultured cells. Genetic analyses indicated that EnvV2 genes are widely present in vertebrates and are under purifying selection among carnivores, suggesting a potential benefit for the host...
April 11, 2024: FEBS Letters
https://read.qxmd.com/read/38604982/rejuvenating-aged-stem-cells-therapeutic-strategies-to-extend-health-and-lifespan
#38
REVIEW
Francesca Matteini, Sara Montserrat-Vazquez, M Carolina Florian
Aging is associated with a global decline in stem cell function. To date, several strategies have been proposed to rejuvenate aged stem cells: most of these result in functional improvement of the tissue where the stem cells reside, but the impact on the lifespan of the whole organism has been less clearly established. Here, we review some of the most recent work dealing with interventions that improve the regenerative capacity of aged somatic stem cells in mammals and that might have important translational possibilities...
April 11, 2024: FEBS Letters
https://read.qxmd.com/read/38594215/otud6a-orchestrates-complex-modulation-of-tead4-mediated-transcriptional-programs
#39
JOURNAL ARTICLE
Hyo Jin Kim, Yunsik Choi, Yuri Lee, Mi Hwangbo, Jongchan Kim
TEAD transcription factors play a central role in the Hippo signaling pathway. In this study, we focused on transcriptional enhancer factor TEF-3 (TEAD4), exploring its regulation by the deubiquitinase OTU domain-containing protein 6A (OTUD6A). We identified OTUD6A as a TEAD4-interacting deubiquitinase, positively influencing TEAD-driven transcription without altering TEAD4 stability. Structural analyses revealed specific interaction domains: the N-terminal domain of OTUD6A and the YAP-binding domain of TEAD4...
April 9, 2024: FEBS Letters
https://read.qxmd.com/read/38594214/the-dmt1-isoform-lacking-the-iron-response-element-regulates-normal-and-malignant-hematopoiesis-via-notch-pathway-activation
#40
JOURNAL ARTICLE
Judith Hounjet, Linde Van Aerschot, Kim De Keersmaecker, Marc Vooijs, Kim R Kampen
Natural resistance-associated macrophage protein 2 (NRAMP 2; also known as DMT1 and encoded by SLC11A2) is mainly known for its iron transport activity. Recently, the DMT1 isoform lacking the iron-response element (nonIRE) was associated with aberrant NOTCH pathway activity. In this report, we investigated the function of DMT1 nonIRE in normal and malignant hematopoiesis. Knockdown of Dmt1 nonIRE in mice showed that it has non-canonical functions in hematopoietic stem cell differentiation: its knockdown suppressed development along the myeloid and lymphoid lineages, while promoting the production of platelets...
April 9, 2024: FEBS Letters
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