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Protein Science : a Publication of the... Jun 2024AF9 (MLLT3) and its paralog ENL(MLLT1) are members of the YEATS family of proteins with important role in transcriptional and epigenetic regulatory complexes. These...
AF9 (MLLT3) and its paralog ENL(MLLT1) are members of the YEATS family of proteins with important role in transcriptional and epigenetic regulatory complexes. These proteins are two common MLL fusion partners in MLL-rearranged leukemias. The oncofusion proteins MLL-AF9/ENL recruit multiple binding partners, including the histone methyltransferase DOT1L, leading to aberrant transcriptional activation and enhancing the expression of a characteristic set of genes that drive leukemogenesis. The interaction between AF9 and DOT1L is mediated by an intrinsically disordered C-terminal ANC1 homology domain (AHD) in AF9, which undergoes folding upon binding of DOT1L and other partner proteins. We have recently reported peptidomimetics that disrupt the recruitment of DOT1L by AF9 and ENL, providing a proof-of-concept for targeting AHD and assessing its druggability. Intrinsically disordered proteins, such as AF9 AHD, are difficult to study and characterize experimentally on a structural level. In this study, we present a successful protein engineering strategy to facilitate structural investigation of the intrinsically disordered AF9 AHD domain in complex with peptidomimetic inhibitors by using maltose binding protein (MBP) as a crystallization chaperone connected with linkers of varying flexibility and length. The strategic incorporation of disulfide bonds provided diffraction-quality crystals of the two disulfide-bridged MBP-AF9 AHD fusion proteins in complex with the peptidomimetics. These successfully determined first series of 2.1-2.6 Å crystal complex structures provide high-resolution insights into the interactions between AHD and its inhibitors, shedding light on the role of AHD in recruiting various binding partner proteins. We show that the overall complex structures closely resemble the reported NMR structure of AF9 AHD/DOT1L with notable difference in the conformation of the β-hairpin region, stabilized through conserved hydrogen bonds network. These first series of AF9 AHD/peptidomimetics complex structures are providing insights of the protein-inhibitor interactions and will facilitate further development of novel inhibitors targeting the AF9/ENL AHD domain.
Topics: Humans; Crystallography, X-Ray; Histone-Lysine N-Methyltransferase; Intrinsically Disordered Proteins; Models, Molecular; Myeloid-Lymphoid Leukemia Protein; Oncogene Proteins, Fusion; Peptidomimetics; Protein Domains
PubMed: 38747396
DOI: 10.1002/pro.5019 -
Frontiers in Microbiology 2024The effects of fructo-oligosaccharides (FOS) on atopic dermatitis (AD) have not been determined.
INTRODUCTION
The effects of fructo-oligosaccharides (FOS) on atopic dermatitis (AD) have not been determined.
METHODS
In a randomized, double-blind, placebo-controlled trial, children with AD aged 24 months to 17 years received either advanced FOS containing 4.25 g of 1-kestose or a placebo (maltose) for 12 weeks.
RESULTS
The SCORAD and itching scores were reduced in patients treated with both FOS (all < 0.01) and maltose ( < 0.05 and < 0.01). Sleep disturbance was improved only in the FOS group ( < 0.01). The FOS group revealed a decreased proportion of linoleic acid (18:2) esterified omega-hydroxy-ceramides (EOS-CERs) with amide-linked shorter chain fatty acids (C28 and C30, all < 0.05), along with an increased proportion of EOS-CERs with longer chain fatty acids (C32, < 0.01).
DISCUSSION
FOS may be beneficial in alleviating itching and sleep disturbance, as well as improving skin barrier function in children with AD.
PubMed: 38741747
DOI: 10.3389/fmicb.2024.1383779 -
International Journal of Molecular... Apr 2024Intelectins belong to a family of lectins with specific and transitory carbohydrate interaction capabilities. These interactions are related to the activity of...
Intelectins belong to a family of lectins with specific and transitory carbohydrate interaction capabilities. These interactions are related to the activity of agglutinating pathogens, as intelectins play a significant role in immunity. Despite the prominent immune defense function of intelectins, limited information about its structural characteristics and carbohydrate interaction properties is available. This study investigated an intelectin transcript identified in RNA-seq data obtained from the South American lungfish (), namely LpITLN2-B. The structural analyses predicted LpITLN2-B to be a homo-trimeric globular protein with the fibrinogen-like functional domain (FReD), exhibiting a molecular mass of 57 kDa. The quaternary structure is subdivided into three monomers, A, B, and C, and each domain comprises 11 β-sheets: an anti-parallel β-sheet, a β-hairpin, and a disordered β-sheet structure. Molecular docking demonstrates a significant interaction with disaccharides rather than monosaccharides. The preferential interaction with disaccharides highlights the potential interaction with pathogen molecules, such as LPS and Poly(I:C). The hemagglutination assay inhibited lectins activity, especially maltose and sucrose, highlighting lectin activity in samples. Overall, our results show the potential relevance of LpITLN2-B in immune defense against pathogens.
Topics: Animals; Lectins; Immunity, Innate; Fishes; Fish Proteins; Molecular Docking Simulation; Amino Acid Sequence; GPI-Linked Proteins
PubMed: 38732017
DOI: 10.3390/ijms25094798 -
Plant Disease Apr 2024In April 2023, soft rot symptoms were observed in broccoli (Brassica oleracea L. var. italica) commercial fields in Songming County, Yunnan province, China (103°12'E,...
In April 2023, soft rot symptoms were observed in broccoli (Brassica oleracea L. var. italica) commercial fields in Songming County, Yunnan province, China (103°12'E, 25°31'N). The disease incidence in these fields (6 ha in size) was high, exceeding 50%, and it caused significant yield loss. The affected plants displayed characteristic symptoms, with the roots and stems of broccoli becoming soft, yellowish-brown, rotten, and emitting a foul odor. To identify the causal agent, soft rot symptomatic stems were surface sterilized by dipping them in 75% ethanol for 30 seconds, followed by three successive rinses with sterile distilled water. Tissue specimens were then plated onto nutrient agar (NA) plates and incubated at 28°C for 24 hours. (Wang et al. 2022). Three representative bacterial isolates HYC22041801-HYC22041803 from broccoli were selected for further analysis. The colonies on NA plates appeared as white, small, round, and translucent with smooth edges. Physiological and biochemical tests were performed, along with 96 phenotypic screenings using the BIOLOG GENIII microplate system (Biolog, Hayward, CA, USA). Three isolates were negative for D-arabitol, maltose, and sorbitol, but were positive for cellobiose, α-D-glucose, sucrose, glycerol and gentiobiose tests, which are consistent with the reported type strain P. polaris NIBIO1006T (Chen et al. 2021). Total genomic DNA was extracted from three bacterial isolates using the QIAamp DNA Mini Kit (QIAGEN, USA). The 16S rRNA region and nine housekeeping genes (gapA, icdA, mdh, mtlD, pel, pgi, pmrA, proA and rpoS) were amplified with universal primers 27F/1492R (Monciardini et al., 2006) and designed specific primers (Xie et al., 2018), respectively. All amplicons were sequenced and deposited in GenBank with accession numbers ON723841-ON723843 and ON723846-ON723872. The BLASTn analysis of the 16S rRNA amplicons confirmed that the isolates HYC22041801-HYC22041803 belonged to the genus Pectobacterium. Phylogenetic trees based on 16S rRNA gene sequences and multilocus sequence analysis of other nine housekeeping genes of the three isolates were constructed and the results revealed that three isolates clustered with P. polaris type strain NIBIO1006T, which was previously isolated from potato (Dees et al., 2017). To confirm the pathogenicity, nine broccoli seedlings were stab inoculated with a bacterial suspension (108 CFU·ml-1), while sterile distilled liquid LB medium was used as a negative control. The seedlings were kept at 80% relative humidity and 28°C in a growth chamber. Three trials were conducted per isolate (HYC22041801-HYC22041803). After 3 days, the inoculated petioles showed soft rot symptoms similar to those observed initially in the field, while control plants remained asymptomatic. All three isolates were re-isolated successfully from symptomatic tissues to complete Koch's postulates. P. polaris has been previously reported as the causative agent of blackleg in potato in several countries, including Norway, Poland, Russia, and China (Handique et al. 2022; Wang et al. 2022). Additionally, it was reported to cause soft rot in Chinese cabbage in China (Chen et al. 2021). However, this is the first report of P. polaris causing soft rot disease in broccoli in China. This discovery is of great importance for vegetable growers because this bacterium is well established on Cruciferous vegetables in the local area, and effective measures are needed to manage this disease.
PubMed: 38687572
DOI: 10.1094/PDIS-08-23-1475-PDN -
Nature Communications Apr 2024Controlled assembly of a protein shell around a viral genome is a key step in the life cycle of many viruses. Here we report a strategy for regulating the co-assembly of...
Controlled assembly of a protein shell around a viral genome is a key step in the life cycle of many viruses. Here we report a strategy for regulating the co-assembly of nonviral proteins and nucleic acids into highly ordered nucleocapsids in vitro. By fusing maltose binding protein to the subunits of NC-4, an engineered protein cage that encapsulates its own encoding mRNA, we successfully blocked spontaneous capsid assembly, allowing isolation of the individual monomers in soluble form. To initiate RNA-templated nucleocapsid formation, the steric block can be simply removed by selective proteolysis. Analyses by transmission and cryo-electron microscopy confirmed that the resulting assemblies are structurally identical to their RNA-containing counterparts produced in vivo. Enzymatically triggered cage formation broadens the range of RNA molecules that can be encapsulated by NC-4, provides unique opportunities to study the co-assembly of capsid and cargo, and could be useful for studying other nonviral and viral assemblies.
Topics: Nucleocapsid; Cryoelectron Microscopy; Maltose-Binding Proteins; Virus Assembly; Capsid; RNA, Viral; Capsid Proteins; RNA, Messenger
PubMed: 38678040
DOI: 10.1038/s41467-024-47808-1 -
Microorganisms Apr 2024was primarily identified based on the characteristics of its conidia and several sequences. The fungus causes severe leaf spot disease on hairy vetch ( var. ) in Yunnan...
was primarily identified based on the characteristics of its conidia and several sequences. The fungus causes severe leaf spot disease on hairy vetch ( var. ) in Yunnan Province in China. The growth, sporulation, fungicide efficacy, and host range of the pathogen were evaluated to aid in disease management. Different types of culture media and carbon and nitrogen sources were used to evaluate the growth of Oatmeal, maltose, and potassium nitrate agar had a higher amount of sporulation. Difenoconazole (10%) was the most effective fungicide against the leaf disease caused by . In addition, foliar inoculation sprays were used to assess the host range of in six different plant species, including alfalfa ( L.), sainfoin ( Scop.), erect milkvetch ( Pall.), common vetch ( L.), red clover ( L.), and white clover ( L.). successfully infected these plants, indicating that it has a wider host range than hairy vetches.
PubMed: 38674710
DOI: 10.3390/microorganisms12040766 -
International Journal of Molecular... Apr 2024Membrane proteins constitute about 20% of the human proteome and play crucial roles in cellular functions. However, a complete understanding of their structure and...
Membrane proteins constitute about 20% of the human proteome and play crucial roles in cellular functions. However, a complete understanding of their structure and function is limited by their hydrophobic nature, which poses significant challenges in purification and stabilization. Detergents, essential in the isolation process, risk destabilizing or altering the proteins' native conformations, thus affecting stability and functionality. This study leverages single-particle cryo-electron microscopy to elucidate the structural nuances of membrane proteins, focusing on the SLAC1 bacterial homolog from (TehA) purified with diverse detergents, including n-dodecyl β-D-maltopyranoside (DDM), glycodiosgenin (GDN), β-D-octyl-glucoside (OG), and lauryl maltose neopentyl glycol (LMNG). This research not only contributes to the understanding of membrane protein structures but also addresses detergent effects on protein purification. By showcasing that the overall structural integrity of the channel is preserved, our study underscores the intricate interplay between proteins and detergents, offering insightful implications for drug design and membrane biology.
Topics: Cryoelectron Microscopy; Haemophilus influenzae; Bacterial Proteins; Detergents; Microscopy, Electron, Transmission; Membrane Proteins
PubMed: 38674110
DOI: 10.3390/ijms25084528 -
Pathogens (Basel, Switzerland) Apr 2024A novel coagulase-negative strain (H164) was isolated from soymilk in Taiwan. Comparative sequence analysis of the 16S rRNA gene revealed that the H164 strain is a...
A novel coagulase-negative strain (H164) was isolated from soymilk in Taiwan. Comparative sequence analysis of the 16S rRNA gene revealed that the H164 strain is a member of the genus . We used multilocus sequence analysis (MLSA) and phylogenomic analyses to demonstrate that the novel strain was closely related to , , , and . The average nucleotide identity and digital DNA-DNA hybridization values between H164 and its closest relatives were <95% and <70%, respectively. The H164 strain could also be distinguished from its closest relatives by the fermentation of -fructose, -maltose, -trehalose, and -mannitol, as well as by the activities of α-glucosidase and alkaline phosphatase. The major cellular fatty acids were C15:0 iso and C15:0 anteiso, and the predominant menaquinones were MK-7 and MK-8, respectively. The major cellular fatty acids and predominant menaquinones were C iso and C anteiso and MK-7 and MK-8, respectively. In conclusion, this strain represents a novel species, named sp. nov., with the type strain H164 (=BCRC 81404 = NBRC 116174).
PubMed: 38668298
DOI: 10.3390/pathogens13040343 -
Journal of Fungi (Basel, Switzerland) Mar 2024Sialidases (neuraminidases) catalyze the removal of terminal sialic acid residues from glycoproteins. Novel enzymes from non-clinical isolates are of increasing interest...
Sialidases (neuraminidases) catalyze the removal of terminal sialic acid residues from glycoproteins. Novel enzymes from non-clinical isolates are of increasing interest regarding their application in the food and pharmaceutical industry. The present study aimed to evaluate the participation of carbon catabolite repression (CCR) in the regulation of cold-active sialidase biosynthesis by the psychrotolerant fungal strain P29, isolated from Antarctica. The presence of glucose inhibited sialidase activity in growing and non-growing fungal mycelia in a dose- and time-dependent manner. The same response was demonstrated with maltose and sucrose. The replacement of glucose with glucose-6-phosphate also exerted CCR. The addition of cAMP resulted in the partial de-repression of sialidase synthesis. The CCR in the psychrotolerant strain P29 did not depend on temperature. Sialidase might be subject to glucose repression by both at 10 and 25 °C. The fluorescent assay using 4MU-Neu5Ac for enzyme activity determination under increasing glucose concentrations evidenced that CCR may have a regulatory role in sialidase production. The real-time RT-PCR experiments revealed that the sialidase gene was subject to glucose repression. To our knowledge, this is the first report that has studied the effect of CCR on cold-active sialidase, produced by an Antarctic strain.
PubMed: 38667912
DOI: 10.3390/jof10040241 -
Insects Apr 2024Alterative nutritional foods consumed by adult parasitoids play an important role in their fitness and ability to control pests because of food scarcity in many crops....
Alterative nutritional foods consumed by adult parasitoids play an important role in their fitness and ability to control pests because of food scarcity in many crops. While adult parasitoids feed on various sugars, they vary in their nutritional value for parasitoids. We assessed the effects of seven sugars (fructose, glucose, sucrose, trehalose, maltose, melezitose, and sorbitol) on the longevity, parasitism ability, parasitism behavior, and flight ability of , an important parasitoid of cotton aphids. We found that access to glucose, sucrose, or fructose, increased adult longevity more than the other sugars offered. All sugars except trehalose increased the parasitism rate to more than 50% compared to the starved control (only provided with water). We then compared parasitoid behaviors of wasps fed glucose, sucrose, or fructose to that of the starved control (with access only to water) and found that those fed spent more time either examining or attacking aphids than parasitoids in the control group, which spent more time walking or resting. Also, consumption of glucose, sucrose, or fructose also significantly improved the flight ability (the total flight distance, flight time, and average flight speed) of .
PubMed: 38667375
DOI: 10.3390/insects15040245