99951
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Evans CM, Phillips M, Malone KL, Tonelli M, Cornilescu G, Cornilescu C, Holton SJ, Gorjánácz M, Wang L, Carlson S, Gay JC, Nix JC, Demeler B, Markley JL, Glass KC. Coordination of Di-Acetylated Histone Ligands by the ATAD2 Bromodomain. Int J Mol Sci 2021; 22:9128. [PMID: 34502039 PMCID: PMC8430952 DOI: 10.3390/ijms22179128] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 12/15/2022] Open
Abstract
The ATPase Family, AAA domain-containing protein 2 (ATAD2) bromodomain (BRD) has a canonical bromodomain structure consisting of four α-helices. ATAD2 functions as a co-activator of the androgen and estrogen receptors as well as the MYC and E2F transcription factors. ATAD2 also functions during DNA replication, recognizing newly synthesized histones. In addition, ATAD2 is shown to be up-regulated in multiple forms of cancer including breast, lung, gastric, endometrial, renal, and prostate. Furthermore, up-regulation of ATAD2 is strongly correlated with poor prognosis in many types of cancer, making the ATAD2 bromodomain an innovative target for cancer therapeutics. In this study, we describe the recognition of histone acetyllysine modifications by the ATAD2 bromodomain. Residue-specific information on the complex formed between the histone tail and the ATAD2 bromodomain, obtained through nuclear magnetic resonance spectroscopy (NMR) and X-ray crystallography, illustrates key residues lining the binding pocket, which are involved in coordination of di-acetylated histone tails. Analytical ultracentrifugation, NMR relaxation data, and isothermal titration calorimetry further confirm the monomeric state of the functionally active ATAD2 bromodomain in complex with di-acetylated histone ligands. Overall, we describe histone tail recognition by ATAD2 BRD and illustrate that one acetyllysine group is primarily engaged by the conserved asparagine (N1064), the "RVF" shelf residues, and the flexible ZA loop. Coordination of a second acetyllysine group also occurs within the same binding pocket but is essentially governed by unique hydrophobic and electrostatic interactions making the di-acetyllysine histone coordination more specific than previously presumed.
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Affiliation(s)
- Chiara M. Evans
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
| | - Margaret Phillips
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Kiera L. Malone
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.T.); (G.C.); (C.C.); (J.L.M.)
| | - Gabriel Cornilescu
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.T.); (G.C.); (C.C.); (J.L.M.)
| | - Claudia Cornilescu
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.T.); (G.C.); (C.C.); (J.L.M.)
| | - Simon J. Holton
- Bayer AG, Pharmaceuticals, Research & Early Development Oncology, 13353 Berlin, Germany; (S.J.H.); (M.G.)
| | - Mátyás Gorjánácz
- Bayer AG, Pharmaceuticals, Research & Early Development Oncology, 13353 Berlin, Germany; (S.J.H.); (M.G.)
| | - Liping Wang
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (L.W.); (B.D.)
| | - Samuel Carlson
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
| | - Jamie C. Gay
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
| | - Jay C. Nix
- Molecular Biology Consortium, Advanced Light Source, Berkeley, CA 94720, USA;
| | - Borries Demeler
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA; (L.W.); (B.D.)
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - John L. Markley
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI 53706, USA; (M.T.); (G.C.); (C.C.); (J.L.M.)
| | - Karen C. Glass
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA; (C.M.E.); (M.P.); (K.L.M.); (S.C.); (J.C.G.)
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA
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99952
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Sinenko SA, Starkova TY, Kuzmin AA, Tomilin AN. Physiological Signaling Functions of Reactive Oxygen Species in Stem Cells: From Flies to Man. Front Cell Dev Biol 2021; 9:714370. [PMID: 34422833 PMCID: PMC8377544 DOI: 10.3389/fcell.2021.714370] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/01/2021] [Indexed: 12/14/2022] Open
Abstract
Reactive oxygen species (ROS), superoxide anion and hydrogen peroxide, are generated as byproducts of oxidative phosphorylation in the mitochondria or via cell signaling-induced NADPH oxidases in the cytosol. In the recent two decades, a plethora of studies established that elevated ROS levels generated by oxidative eustress are crucial physiological mediators of many cellular and developmental processes. In this review, we discuss the mechanisms of ROS generation and regulation, current understanding of ROS functions in the maintenance of adult and embryonic stem cells, as well as in the process of cell reprogramming to a pluripotent state. Recently discovered cell-non-autonomous ROS functions mediated by growth factors are crucial for controlling cell differentiation and cellular immune response in Drosophila. Importantly, many physiological functions of ROS discovered in Drosophila may allow for deciphering and understanding analogous processes in human, which could potentially lead to the development of novel therapeutic approaches in ROS-associated diseases treatment.
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Affiliation(s)
- Sergey A Sinenko
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | | | - Andrey A Kuzmin
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
| | - Alexey N Tomilin
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
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99953
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Ashaari NS, Ab Rahim MH, Sabri S, Lai KS, Song AAL, Abdul Rahim R, Ong Abdullah J. Kinetic studies and homology modeling of a dual-substrate linalool/nerolidol synthase from Plectranthus amboinicus. Sci Rep 2021; 11:17094. [PMID: 34429465 PMCID: PMC8385045 DOI: 10.1038/s41598-021-96524-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 08/11/2021] [Indexed: 02/07/2023] Open
Abstract
Linalool and nerolidol are terpene alcohols that occur naturally in many aromatic plants and are commonly used in food and cosmetic industries as flavors and fragrances. In plants, linalool and nerolidol are biosynthesized as a result of respective linalool synthase and nerolidol synthase, or a single linalool/nerolidol synthase. In our previous work, we have isolated a linalool/nerolidol synthase (designated as PamTps1) from a local herbal plant, Plectranthus amboinicus, and successfully demonstrated the production of linalool and nerolidol in an Escherichia coli system. In this work, the biochemical properties of PamTps1 were analyzed, and its 3D homology model with the docking positions of its substrates, geranyl pyrophosphate (C10) and farnesyl pyrophosphate (C15) in the active site were constructed. PamTps1 exhibited the highest enzymatic activity at an optimal pH and temperature of 6.5 and 30 °C, respectively, and in the presence of 20 mM magnesium as a cofactor. The Michaelis-Menten constant (Km) and catalytic efficiency (kcat/Km) values of 16.72 ± 1.32 µM and 9.57 × 10-3 µM-1 s-1, respectively, showed that PamTps1 had a higher binding affinity and specificity for GPP instead of FPP as expected for a monoterpene synthase. The PamTps1 exhibits feature of a class I terpene synthase fold that made up of α-helices architecture with N-terminal domain and catalytic C-terminal domain. Nine aromatic residues (W268, Y272, Y299, F371, Y378, Y379, F447, Y517 and Y523) outlined the hydrophobic walls of the active site cavity, whilst residues from the RRx8W motif, RxR motif, H-α1 and J-K loops formed the active site lid that shielded the highly reactive carbocationic intermediates from the solvents. The dual substrates use by PamTps1 was hypothesized to be possible due to the architecture and residues lining the catalytic site that can accommodate larger substrate (FPP) as demonstrated by the protein modelling and docking analysis. This model serves as a first glimpse into the structural insights of the PamTps1 catalytic active site as a multi-substrate linalool/nerolidol synthase.
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Affiliation(s)
- Nur Suhanawati Ashaari
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Mohd Hairul Ab Rahim
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
- Department of Industrial Biotechnology, Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, 26300, Gambang, Kuantan, Pahang, Malaysia
| | - Suriana Sabri
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Kok Song Lai
- Health Sciences Division, Abu Dhabi Women's College, Higher Colleges of Technology, 41012, Abu Dhabi, United Arab Emirates
| | - Adelene Ai-Lian Song
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Raha Abdul Rahim
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Janna Ong Abdullah
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia.
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99954
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Suzuki H, Kise S, Kaizuka Y, Watanabe R, Sugawa T, Furukawa T, Fujii H, Uehara T. Copper-64-Labeled Antibody Fragments for Immuno-PET/Radioimmunotherapy with Low Renal Radioactivity Levels and Amplified Tumor-Kidney Ratios. ACS OMEGA 2021; 6:21556-21562. [PMID: 34471758 PMCID: PMC8388099 DOI: 10.1021/acsomega.1c02516] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/08/2021] [Indexed: 06/01/2023]
Abstract
Copper-64 (64Cu)-labeled antibody fragments such as Fab are useful for molecular imaging (immuno-PET) and radioimmunotherapy. However, these fragments cause high and persistent localization of radioactivity in the kidneys after injection. To solve this problem, this study assessed the applicability of a molecular design to 64Cu, which reduces renal radioactivity levels by liberating a urinary excretory radiometabolite from antibody fragments at the renal brush border membrane (BBM). Since 1,4,7-triazacyclononane-1,4,7-triacetic acid (NOTA) forms a stable complex with Cu, NOTA-conjugated Met-Val-Lys-maleimide (NOTA-MVK-Mal), which is a radio-gallium labeling agent for antibody fragments, was evaluated for applicability to 64Cu. The MVK linkage was recognized by the BBM enzymes to liberate [64Cu]Cu-NOTA-Met although the recognition of the MVK sequence for the [64Cu]Cu-NOTA-MVK derivative was reduced compared with that of its [67Ga]Ga-counterpart, probably due to the difference in the charge of the metal-NOTA complexes. When injected into mice, [64Cu]Cu-NOTA-MVK-Fab resulted in similar renal radioactivity levels to the 67Ga-labeled counterpart. In addition, [64Cu]Cu-NOTA-MVK-Fab resulted in lower renal radioactivity levels than those from 64Cu-labeled Fab using a conventional method, without a reduction in the tumor radioactivity levels. These findings indicate that our approach to reducing renal radioactivity levels by liberating a radiolabeled compound from antibody fragments at the renal BBM for urinary excretion is applicable to 64Cu-labeled antibody fragments and useful for immuno-PET and radioimmunotherapy.
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Affiliation(s)
- Hiroyuki Suzuki
- Laboratory
of Molecular Imaging and Radiotherapy, Graduate School of Pharmaceutical
Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Chiba 260-8675 Japan
| | - Shota Kise
- Laboratory
of Molecular Imaging and Radiotherapy, Graduate School of Pharmaceutical
Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Chiba 260-8675 Japan
| | - Yuta Kaizuka
- Laboratory
of Molecular Imaging and Radiotherapy, Graduate School of Pharmaceutical
Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Chiba 260-8675 Japan
| | - Reo Watanabe
- Laboratory
of Molecular Imaging and Radiotherapy, Graduate School of Pharmaceutical
Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Chiba 260-8675 Japan
| | - Tsubasa Sugawa
- Laboratory
of Molecular Imaging and Radiotherapy, Graduate School of Pharmaceutical
Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Chiba 260-8675 Japan
| | - Takako Furukawa
- Nagoya
University Graduate School of Medicine, 1-1-20 Daiko-Minami, Higashi-ku, Nagoya, Aichi 461-8673, Japan
| | - Hirofumi Fujii
- Division
of Functional Imaging, Exploratory Oncology Research and Clinical
Trial Center, National Cancer Center, 6-5-1 Kashiwanoha, Kashiwa, Chiba 277-8577, Japan
| | - Tomoya Uehara
- Laboratory
of Molecular Imaging and Radiotherapy, Graduate School of Pharmaceutical
Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, Chiba 260-8675 Japan
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99955
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Thiede KI, Born J, Vorster APA. Sleep and conditioning of the siphon withdrawal reflex in Aplysia. J Exp Biol 2021; 224:271187. [PMID: 34346500 DOI: 10.1242/jeb.242431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/30/2021] [Indexed: 11/20/2022]
Abstract
Sleep is essential for memory consolidation after learning as shown in mammals and invertebrates such as bees and flies. Aplysia californica displays sleep, and sleep in this mollusk was also found to support memory for an operant conditioning task. Here, we investigated whether sleep in Aplysia is also required for memory consolidation in a simpler type of learning, i.e. the conditioning of the siphon withdrawal reflex. Two groups of animals (Wake, Sleep, each n=11) were conditioned on the siphon withdrawal reflex, with the training following a classical conditioning procedure where an electrical tail shock served as the unconditioned stimulus (US) and a tactile stimulus to the siphon as the conditioned stimulus (CS). Responses to the CS were tested before (pre-test), and 24 and 48 h after training. While Wake animals remained awake for 6 h after training, Sleep animals had undisturbed sleep. The 24 h test in both groups was combined with extinction training, i.e. the extended presentation of the CS alone over two blocks. At the 24 h test, siphon withdrawal duration in response to the CS was distinctly enhanced in both Sleep and Wake groups with no significant difference between groups, consistent with the view that consolidation of a simple conditioned reflex response does not require post-training sleep. Surprisingly, extinction training did not reverse the enhancement of responses to the CS. On the contrary, at the 48 h test, withdrawal duration in response to the CS was even further enhanced across both groups. This suggests that processes of sensitization, an even simpler non-associative type of learning, contributed to the withdrawal responses. Our study provides evidence for the hypothesis that sleep preferentially benefits consolidation of more complex learning paradigms than conditioning of simple reflexes.
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Affiliation(s)
- Kathrin I Thiede
- Institute of Medical Psychology and Behavioral Neurobiology and Center for Integrative Neuroscience CIN, University of Tübingen, Tübingen 72076, Germany
| | - Jan Born
- Institute of Medical Psychology and Behavioral Neurobiology and Center for Integrative Neuroscience CIN, University of Tübingen, Tübingen 72076, Germany.,German Center for Diabetes Research (DZD), Institute for Diabetes Research & Metabolic Diseases of the Helmholtz Center Munich at the University of Tübingen (IDM), Tübingen 72076, Germany
| | - Albrecht P A Vorster
- Institute of Medical Psychology and Behavioral Neurobiology and Center for Integrative Neuroscience CIN, University of Tübingen, Tübingen 72076, Germany.,Training Centre of Neuroscience (GTC)/International Max Planck Research School (IMPRS) at the University of Tübingen, Tübingen 72076, Germany
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99956
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Shi D, Zhang Y, Wang J, Ren W, Zhang J, Mbadianya JI, Zhu Y, Chen C, Ma H. S-adenosyl-L-homocysteine hydrolase FgSah1 is required for fungal development and virulence in Fusarium graminearum. Virulence 2021; 12:2171-2185. [PMID: 34424830 PMCID: PMC8386609 DOI: 10.1080/21505594.2021.1965821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2022] Open
Abstract
The S-adenosyl-L-homocysteine hydrolase (Sah1) plays a crucial role in methylation and lipid metabolism in yeast and mammals, yet its function remains elusive in filamentous fungi. In this study, we characterized Sah1 in the phytopathogenic fungus F. graminearum by generating knockout and knockout-complemented strains of FgSAH1. We found that the FgSah1-GFP fusion protein was localized to the cytoplasm, and that deletion of FgSAH1 resulted in defects in vegetative growth, asexual and sexual reproduction, stress responses, virulence, lipid metabolism, and tolerance against fungicides. Moreover, the accumulations of S-adenosyl-L-homocysteine (AdoHcy) and S-adenosyl-L-methionine (AdoMet) (the methyl group donor in most methyl transfer reactions) in ΔFgSah1 were seven- and ninefold higher than those in the wild-type strain, respectively. All of these defective phenotypes in ΔFgSah1 mutants were rescued by target gene complementation. Taken together, these results demonstrate that FgSah1 plays essential roles in methylation metabolism, fungal development, full virulence, multiple stress responses, lipid metabolism, and fungicide sensitivity in F. graminearum. To our knowledge, this is the first report on the systematic functional characterization of Sah1 in F. graminearum.
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Affiliation(s)
- Dongya Shi
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Yu Zhang
- Department of Crop Protection, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Jin Wang
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Weichao Ren
- Department of Plant Pathology, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, China
| | - Jie Zhang
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Jane Ifunanya Mbadianya
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Yuanye Zhu
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Changjun Chen
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Hongyu Ma
- Department of Pesticide Science, College of Plant Protection, Nanjing Agricultural University, Nanjing, China
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99957
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Spontaneous changes in somatic compatibility in Fusarium circinatum. Fungal Biol 2021; 125:725-732. [PMID: 34420699 DOI: 10.1016/j.funbio.2021.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 04/08/2021] [Accepted: 04/26/2021] [Indexed: 11/24/2022]
Abstract
Filamentous fungi grow by the elaboration of hyphae, which may fuse to form a network as a colony develops. Fusion of hyphae can occur between genetically different individuals, provided they share a common allele at loci affecting somatic compatibility. Diversity in somatic compatibility phenotypes reduces the frequency of hyphal fusion in a population, thereby slowing the spread of deleterious genetic elements such as viruses and plasmids, which require direct cytoplasmic contact for transmission. Diverse somatic compatibility phenotypes can be generated by recombining alleles through sexual reproduction, but this mechanism may not fully account for the diversity found in nature. For example, multiple compatibility phenotypes of Fusarium circinatum were shown to be associated with the same clonal lineage, which implies they were derived by a mutation rather than recombination through sexual reproduction. Experimental tests of this hypothesis confirmed that spontaneous changes in somatic compatibility can occur at a frequency between 5 and 8 per million spores. Genomic analysis of F. circinatum strains with altered somatic compatibility revealed no consistent evidence of recombination and supported the hypothesis that a spontaneous mutation generated the observed phenotypic change. Genes known to be involved in somatic compatibility had no mutations, suggesting that mutation occurred in a gene with an as yet unexplored function in somatic compatibility.
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99958
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Monobac System-A Single Baculovirus for the Production of rAAV. Microorganisms 2021; 9:microorganisms9091799. [PMID: 34576695 PMCID: PMC8465638 DOI: 10.3390/microorganisms9091799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/09/2021] [Accepted: 08/13/2021] [Indexed: 11/28/2022] Open
Abstract
Large-scale manufacturing of rAAV is a bottleneck for the development of genetic disease treatments. The baculovirus/Sf9 cell system underpins the first rAAV treatment approved by EMA and remains one of the most advanced platforms for rAAV manufacturing. Despite early successes, rAAV is still a complex biomaterial to produce. Efficient production of the recombinant viral vector requires that AAV replicase and capsid genes be co-located with the recombinant AAV genome. Here, we present the Monobac system, a singular, modified baculovirus genome that contains all of these functions. To assess the relative yields between the dual baculovirus and Monobac systems, we prepared each system with a transgene encoding γSGC and evaluated vectors’ potency in vivo. Our results show that rAAV production using the Monobac system not only yields higher titers of rAAV vector but also a lower amount of DNA contamination from baculovirus.
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99959
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Structural analysis and prediction of potent bioactive molecule for eNOS protein through molecular docking. In Silico Pharmacol 2021; 9:48. [PMID: 34422545 DOI: 10.1007/s40203-021-00106-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/12/2021] [Indexed: 10/20/2022] Open
Abstract
Reactive oxygen species by uncoupled eNOS is linked to endothelial dysfunction. Ellagic acid (EA), a polyphenol possesses numerous biological activities including radical scavenging. whether EA exerts a vasculo-protective effect via antioxidant mechanisms in blood vessels remains unknown. Molecular docking provides an initial model of protein and molecular interactions in various physiological and/or pathological functions. To identify a eNOS modulatory biomolecule through molecular docking as possible vascular protective agent. On the basis of binding affinities and other physicochemical features, a molecular docking-based approach was used to classify and evaluate eNOS binding micronutrients found in natural sources, Lipinski's rule was used taking into account their adsorption, delivery, metabolism, and excretion (ADME). An insilico approach focused on the ligand-protein interaction technique to determine the therapeutic potential of certain phytochemical-based drugs for the vascular remodelling.20 bioactive molecules were screened, docking analysis on human eNOS proteins was performed. The best poses for target protein was established based on binding energy and inhibition constant. EA and caffeine acid are the strongest candidates for eNOS protein functional norms. This provides a novel insight into the interaction properties of known human eNOS protein with EA and used as a therapeutic agent in various pathologies. Predicting interaction of ellagic acid with eNOS protein by molecular docking in endothelial dysfunction.
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99960
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Akram M, Bock J, Dietl A, Barends TR. Specificity of Small c-Type Cytochromes in Anaerobic Ammonium Oxidation. ACS OMEGA 2021; 6:21457-21464. [PMID: 34471748 PMCID: PMC8388095 DOI: 10.1021/acsomega.1c02275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Anaerobic ammonium oxidation (anammox) is a bacterial process in which ammonium and nitrite are combined into dinitrogen gas and water, yielding energy for the cell. This process relies on a series of redox reactions catalyzed by a set of enzymes, with electrons being shuttled to and from these enzymes, likely by small cytochrome c proteins. For this system to work productively, these electron carriers require a degree of specificity toward the various possible redox partners they encounter in the cell. Here, we compare two cytochrome c proteins from the anammox model organism Kuenenia stuttgartiensis. We show that they are highly homologous, are expressed at comparable levels, share the same fold, and display highly similar redox potentials, yet one of them accepts electrons from the metabolic enzyme hydroxylamine oxidase (HAO) efficiently, whereas the other does not. An analysis of the crystal structures supplemented by Monte Carlo simulations of the transient redox interactions suggests that this difference is at least partly due to the electrostatic field surrounding the proteins, illustrating one way in which the electron carriers in anammox could attain the required specificity. Moreover, the simulations suggest a different "outlet" for electrons on HAO than has traditionally been assumed.
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99961
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Deciphering ion transport and ATPase coupling in the intersubunit tunnel of KdpFABC. Nat Commun 2021; 12:5098. [PMID: 34429416 PMCID: PMC8385062 DOI: 10.1038/s41467-021-25242-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023] Open
Abstract
KdpFABC, a high-affinity K+ pump, combines the ion channel KdpA and the P-type ATPase KdpB to secure survival at K+ limitation. Here, we apply a combination of cryo-EM, biochemical assays, and MD simulations to illuminate the mechanisms underlying transport and the coupling to ATP hydrolysis. We show that ions are transported via an intersubunit tunnel through KdpA and KdpB. At the subunit interface, the tunnel is constricted by a phenylalanine, which, by polarized cation-π stacking, controls K+ entry into the canonical substrate binding site (CBS) of KdpB. Within the CBS, ATPase coupling is mediated by the charge distribution between an aspartate and a lysine. Interestingly, individual elements of the ion translocation mechanism of KdpFABC identified here are conserved among a wide variety of P-type ATPases from different families. This leads us to the hypothesis that KdpB might represent an early descendant of a common ancestor of cation pumps.
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99962
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Wang M, Chen D, Zheng H, Zhao L, Xue X, Yu F, Zhang Y, Cheng C, Niu Q, Wang S, Zhang Y, Wu L. Sex-Specific Development in Haplodiploid Honeybee Is Controlled by the Female-Embryo-Specific Activation of Thousands of Intronic LncRNAs. Front Cell Dev Biol 2021; 9:690167. [PMID: 34422813 PMCID: PMC8377728 DOI: 10.3389/fcell.2021.690167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Embryonic development depends on a highly coordinated shift in transcription programs known as the maternal-to-zygotic transition (MZT). It remains unclear how haploid and diploid embryo coordinate their genomic activation and embryonic development during MZT in haplodiploid animals. Here, we applied a single-embryo RNA-seq approach to characterize the embryonic transcriptome dynamics in haploid males vs. diploid females of the haplodiploid insect honeybee (Apis mellifera). We observed typical zygotic genome activation (ZGA) occurred in three major waves specifically in female honeybee embryos; haploid genome activation was much weaker and occurred later. Strikingly, we also observed three waves of transcriptional activation for thousands of long non-coding transcripts (lncRNA), 73% of which are transcribed from intronic regions and 65% were specific to female honeybee embryos. These findings support a model in which introns encode thousands of lncRNAs that are expressed in a diploid-embryo-specific and ZGA-triggered manner that may have potential functions to regulate gene expression during early embryonic development in the haplodiploid insect honeybee.
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Affiliation(s)
- Miao Wang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dong Chen
- ABLife BioBigData Institute, Wuhan, China.,Laboratory for Genome Regulation and Human Health, ABLife Inc., Wuhan, China
| | - Huoqing Zheng
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Liuwei Zhao
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaofeng Xue
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fengyun Yu
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Wuhan, China
| | - Yu Zhang
- ABLife BioBigData Institute, Wuhan, China
| | - Chao Cheng
- ABLife BioBigData Institute, Wuhan, China
| | - Qingsheng Niu
- Department of Scientific Research, Jilin Province Institute of Apicultural Science, Jilin, China
| | - Shuai Wang
- College of Animal Science, Zhejiang University, Hangzhou, China
| | - Yi Zhang
- ABLife BioBigData Institute, Wuhan, China.,Laboratory for Genome Regulation and Human Health, ABLife Inc., Wuhan, China
| | - Liming Wu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, China
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99963
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Huan C, Xu W, Liu Y, Ruan K, Shi Y, Cheng H, Zhang X, Ke Y, Zhou J. Gremlin2 Activates Fibroblasts to Promote Pulmonary Fibrosis Through the Bone Morphogenic Protein Pathway. Front Mol Biosci 2021; 8:683267. [PMID: 34422900 PMCID: PMC8377751 DOI: 10.3389/fmolb.2021.683267] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 06/16/2021] [Indexed: 11/13/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease causing unremitting extracellular matrix deposition. Transforming growth factor-β (TGF-β) superfamily involves bone morphogenetic proteins (BMPs) and TGF-β, and the balance between the activation of TGF-β-dependent SMADs (Smad2/3) and BMP-dependent SMADs (Smad1/5/8) is essential for fibrosis process. GREM2, initially identified as a TGF-β-inducible gene, encodes a small secreted glycoprotein belonging to a group of matricellular proteins, its role in lung fibrosis is not clear. Here, we identified Gremlin2 as a key regulator of fibroblast activation. Gremlin2 was highly expressed in the serum and lung tissues in IPF patients. Bleomycin-induced lung fibrosis model exhibited high expression of Gremlin2 in the bronchoalveolar lavage fluid (BALF) and lung tissue. Isolation of primary cells from bleomycin-induced fibrosis lung showed a good correlation of Gremlin2 and Acta2 (α-SMA) expressions. Overexpression of Gremlin2 in human fetal lung fibroblast 1 (HFL-1) cells increased its invasion and migration. Furthermore, Gremlin2 regulates fibrosis functions through mediating TGF-β/BMP signaling, in which Gremlin2 may activate TGF-β signaling and inhibit BMP signaling. Therefore, we provided in vivo and in vitro evidence to demonstrate that Gremlin2 may be a potential therapeutic target for the treatment of IPF.
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Affiliation(s)
- Caijuan Huan
- Department of Respiratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wangting Xu
- Department of Respiratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yaru Liu
- Department of Pathology and Pathophysiology, Zhejiang University School of Medicine, Hangzhou, China
| | - Kexin Ruan
- Department of Respiratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yueli Shi
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Hongqiang Cheng
- Department of Pathology and Pathophysiology, Zhejiang University School of Medicine, Hangzhou, China
| | - Xue Zhang
- Department of Pathology and Pathophysiology, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuehai Ke
- Department of Pathology and Pathophysiology, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianying Zhou
- Department of Respiratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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99964
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Ramaraju B, Nelson SL, Zheng W, Ghirlando R, Deshmukh L. Quantitative NMR Study of Insulin-Degrading Enzyme Using Amyloid-β and HIV-1 p6 Elucidates Its Chaperone Activity. Biochemistry 2021; 60:2519-2523. [PMID: 34342986 PMCID: PMC8895387 DOI: 10.1021/acs.biochem.1c00342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Insulin-degrading enzyme (IDE) hydrolyzes monomeric polypeptides, including amyloid-β (Aβ) and HIV-1 p6. It also acts as a nonproteolytic chaperone to prevent Aβ polymerization. Here we compare interactions of Aβ and non-amyloidogenic p6 with IDE. Although both exhibited similar proteolysis rates, the binding kinetics to an inactive IDE characterized using relaxation-based NMR were remarkably different. IDE and Aβ formed a sparsely populated complex with a lifetime of milliseconds in which a short hydrophobic cleavage segment of Aβ was anchored to IDE. Strikingly, a second and more stable complex was significantly populated with a subsecond lifetime owing to multiple intermolecular contacts between Aβ and IDE. By selectively sequestering Aβ in this nonproductive complex, IDE likely increases the critical concentration required for fibrillization. In contrast, IDE and p6 formed a transient, submillisecond complex involving a single anchoring p6 motif. Modulation of intermolecular interactions, thus, allows IDE to differentiate between non-amyloidogenic and amyloidogenic substrates.
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Affiliation(s)
- Bhargavi Ramaraju
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Spencer L Nelson
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
| | - Wenwei Zheng
- College of Integrative Sciences and Arts, Arizona State University, Mesa, Arizona 85212, United States
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Lalit Deshmukh
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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99965
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Romero Marcia AD, Yao T, Chen MH, Oles RE, Lindemann SR. Fine Carbohydrate Structure of Dietary Resistant Glucans Governs the Structure and Function of Human Gut Microbiota. Nutrients 2021; 13:nu13092924. [PMID: 34578800 PMCID: PMC8467459 DOI: 10.3390/nu13092924] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 01/01/2023] Open
Abstract
Increased dietary fiber consumption has been shown to increase human gut microbial diversity, but the mechanisms driving this effect remain unclear. One possible explanation is that microbes are able to divide metabolic labor in consumption of complex carbohydrates, which are composed of diverse glycosidic linkages that require specific cognate enzymes for degradation. However, as naturally derived fibers vary in both sugar composition and linkage structure, it is challenging to separate out the impact of each of these variables. We hypothesized that fine differences in carbohydrate linkage structure would govern microbial community structure and function independently of variation in glycosyl residue composition. To test this hypothesis, we fermented commercially available soluble resistant glucans, which are uniformly composed of glucose linked in different structural arrangements, in vitro with fecal inocula from each of three individuals. We measured metabolic outputs (pH, gas, and short-chain fatty acid production) and community structure via 16S rRNA amplicon sequencing. We determined that community metabolic outputs from identical glucans were highly individual, emerging from divergent initial microbiome structures. However, specific operational taxonomic units (OTUs) responded similarly in growth responses across individuals’ microbiota, though in context-dependent ways; these data suggested that certain taxa were more efficient in competing for some structures than others. Together, these data support the hypothesis that variation in linkage structure, independent of sugar composition, governs compositional and functional responses of microbiota.
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Affiliation(s)
- Arianna D. Romero Marcia
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN 47907, USA; (A.D.R.M.); (T.Y.); (M.-H.C.); (R.E.O.)
| | - Tianming Yao
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN 47907, USA; (A.D.R.M.); (T.Y.); (M.-H.C.); (R.E.O.)
| | - Ming-Hsu Chen
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN 47907, USA; (A.D.R.M.); (T.Y.); (M.-H.C.); (R.E.O.)
| | - Renee E. Oles
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN 47907, USA; (A.D.R.M.); (T.Y.); (M.-H.C.); (R.E.O.)
| | - Stephen R. Lindemann
- Whistler Center for Carbohydrate Research, Department of Food Science, Purdue University, West Lafayette, IN 47907, USA; (A.D.R.M.); (T.Y.); (M.-H.C.); (R.E.O.)
- Department of Nutrition Science, Purdue University, West Lafayette, IN 47907, USA
- Correspondence: ; Tel.: +1-765-494-9207
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99966
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Immunoinformatics aided design of peptide-based vaccines against ebolaviruses. VITAMINS AND HORMONES 2021; 117:157-187. [PMID: 34420579 DOI: 10.1016/bs.vh.2021.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Ebolaviruses are at the forefront of emerging viruses and present a very perceptible threat to global peace and harmony. In the last decade, Ebola virus disease has claimed more than 90% of total lives since its inception in 1976. Owing to multiple host immune evasion methods employed by the virus and the limitations of traditional vaccine development approaches, finding a globally effective and reliable counter measure against Ebola virus remains a challenge. Highly conserved peptide fragments belonging to critical viral proteins and containing multiple epitopes which have the capacity to interact with a wide array of HLA molecules present a viable solution. Immunoinformatics or computational immunology enables rapid screening and shortlisting of plausible epitopes with a high immunogenic potential, thus, supporting expeditious elucidation of efficacious vaccine candidates. In light of above facts, we describe a computational methodology in this chapter for identification of potent peptide vaccine candidates against human infecting viruses. By applying this stringent methodology, we were able to identify multiple, immunogenic ebolavirus peptide fragments which, after verification in animal models, might be considered as part of future synthetic Ebola vaccine.
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99967
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Harbison A, Fadda E. An atomistic perspective on antibody-dependent cellular cytotoxicity quenching by core-fucosylation of IgG1 Fc N-glycans from enhanced sampling molecular dynamics. Glycobiology 2021; 30:407-414. [PMID: 31829411 DOI: 10.1093/glycob/cwz101] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/25/2019] [Accepted: 12/04/2019] [Indexed: 12/16/2022] Open
Abstract
The immunoglobulin type G (IgG) Fc N-glycans are known to modulate the interaction with membrane-bound Fc γ receptors (FcγRs), fine-tuning the antibody's effector function in a sequence-dependent manner. Particularly interesting in this respect are the roles of galactosylation, which levels are linked to autoimmune conditions and aging, of core fucosylation, which is known to reduce significantly the antibody-dependent cellular cytotoxicity (ADCC), and of sialylation, which also reduces antibody-dependent cellular cytotoxicity (ADCC) but only in the context of core-fucosylation. In this article, we provide an atomistic level perspective through enhanced sampling computer simulations, based on replica exchange molecular dynamics (REMD), to understand the molecular determinants linking the Fc N-glycans sequence to the observed IgG1 function. Our results indicate that the two symmetrically opposed N-glycans interact extensively through their core trimannose residues. At room temperature, the terminal galactose on the α (1-6) arm is restrained to the protein through a network of interactions that keep the arm outstretched; meanwhile, the α (1-3) arm extends toward the solvent where a terminal sialic acid remains fully accessible. We also find that the presence of core fucose interferes with the extended sialylated α (1-3) arm, altering its conformational propensity and as a consequence of steric hindrance, significantly enhancing the Fc dynamics. Furthermore, structural analysis shows that the core-fucose position within the Fc core obstructs the access of N162 glycosylated FcγRs very much like a "door-stop," potentially decreasing the IgG/FcγR binding free energy. These results provide an atomistic level-of-detail framework for the design of high potency IgG1 Fc N-glycoforms.
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Affiliation(s)
- Aoife Harbison
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Ireland
| | - Elisa Fadda
- Department of Chemistry and Hamilton Institute, Maynooth University, Maynooth, Ireland
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99968
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Chen T, Tian L, Chen J, Zhao X, Zhou J, Guo T, Sheng Q, Zhu L, Liu J, Lv Z. A Comprehensive Genomic Analysis Constructs miRNA-mRNA Interaction Network in Hepatoblastoma. Front Cell Dev Biol 2021; 9:655703. [PMID: 34422793 PMCID: PMC8377242 DOI: 10.3389/fcell.2021.655703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 07/13/2021] [Indexed: 12/04/2022] Open
Abstract
Hepatoblastoma (HB) is a rare disease but nevertheless the most common hepatic tumor in the pediatric population. For patients with advanced HB, the prognosis is dismal and there are limited therapeutic options. Multiple microRNAs (miRNAs) were reported to be involved in HB development, but the miRNA–mRNA interaction network in HB remains elusive. Through a comparison between HB and normal liver samples in the GSE131329 dataset, we detected 580 upregulated differentially expressed mRNAs (DE-mRNAs) and 790 downregulated DE-mRNAs. As for the GSE153089 dataset, the first cluster of differentially expressed miRNAs (DE-miRNAs) were detected between fetal-type tumor and normal liver groups, while the second cluster of DE-miRNAs were detected between embryonal-type tumor and normal liver groups. Through the intersection of these two clusters of DE-miRNAs, 33 upregulated hub miRNAs, and 12 downregulated hub miRNAs were obtained. Based on the respective hub miRNAs, the upstream transcription factors (TFs) were detected via TransmiR v2.0, while the downstream target genes were predicted via miRNet database. The intersection of target genes of respective hub miRNAs and corresponding DE-mRNAs contributed to 250 downregulated candidate genes and 202 upregulated candidate genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses demonstrated the upregulated candidate genes mainly enriched in the terms and pathways relating to the cell cycle. We constructed protein–protein interaction (PPI) network, and obtained 211 node pairs for the downregulated candidate genes and 157 node pairs for the upregulated candidate genes. Cytoscape software was applied for visualizing the PPI network and respective top 10 hub genes were identified using CytoHubba. The expression values of hub genes in the PPI network were subsequently validated through Oncopression database followed by quantitative real-time polymerase chain reaction (qRT-PCR) in HB and matched normal liver tissues, resulting in six significant downregulated genes and seven significant upregulated genes. The miRNA–mRNA interaction network was finally constructed. In conclusion, we uncover various miRNAs, TFs, and hub genes as potential regulators in HB pathogenesis. Additionally, the miRNA–mRNA interaction network, PPI modules, and pathways may provide potential biomarkers for future HB theranostics.
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Affiliation(s)
- Tong Chen
- Department of General Surgery, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Linlin Tian
- Department of Microbiology, Faculty of Basic Medical Sciences, Guilin Medical University, Guilin, China
| | - Jianglong Chen
- Department of General Surgery, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Xiuhao Zhao
- Department of General Surgery, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jing Zhou
- Department of General Surgery, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Ting Guo
- Department of General Surgery, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Qingfeng Sheng
- Department of General Surgery, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Linlin Zhu
- Department of General Surgery, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Jiangbin Liu
- Department of General Surgery, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zhibao Lv
- Department of General Surgery, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
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99969
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Recent Advances in In Silico Target Fishing. Molecules 2021; 26:molecules26175124. [PMID: 34500568 PMCID: PMC8433825 DOI: 10.3390/molecules26175124] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/14/2021] [Accepted: 08/18/2021] [Indexed: 12/24/2022] Open
Abstract
In silico target fishing, whose aim is to identify possible protein targets for a query molecule, is an emerging approach used in drug discovery due its wide variety of applications. This strategy allows the clarification of mechanism of action and biological activities of compounds whose target is still unknown. Moreover, target fishing can be employed for the identification of off targets of drug candidates, thus recognizing and preventing their possible adverse effects. For these reasons, target fishing has increasingly become a key approach for polypharmacology, drug repurposing, and the identification of new drug targets. While experimental target fishing can be lengthy and difficult to implement, due to the plethora of interactions that may occur for a single small-molecule with different protein targets, an in silico approach can be quicker, less expensive, more efficient for specific protein structures, and thus easier to employ. Moreover, the possibility to use it in combination with docking and virtual screening studies, as well as the increasing number of web-based tools that have been recently developed, make target fishing a more appealing method for drug discovery. It is especially worth underlining the increasing implementation of machine learning in this field, both as a main target fishing approach and as a further development of already applied strategies. This review reports on the main in silico target fishing strategies, belonging to both ligand-based and receptor-based approaches, developed and applied in the last years, with a particular attention to the different web tools freely accessible by the scientific community for performing target fishing studies.
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99970
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Hu H, Jiang C, Zhang B, Guo N, Li Z, Guo X, Wang Y, Liu B, He Q. Investigation of morphological changes of HPS membrane caused by cecropin B through scanning electron microscopy and atomic force microscopy. J Vet Sci 2021; 22:e59. [PMID: 34423597 PMCID: PMC8460462 DOI: 10.4142/jvs.2021.22.e59] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 11/20/2022] Open
Abstract
Background Antimicrobial peptides (AMPs) have been identified as promising compounds for consideration as novel antimicrobial agents. Objectives This study analyzed the efficacy of cecropin B against Haemophilus parasuis isolates through scanning electron microscopy (SEM) and atomic force microscopy (AFM) experiments. Results Cecropin B exhibited broad inhibition activity against 15 standard Haemophilus parasuis (HPS) strains and 5 of the clinical isolates had minimum inhibition concentrations (MICs) ranging from 2 to 16 μg/mL. Microelectrophoresis and hexadecane adsorption assays indicated that the more hydrophobic and the higher the isoelectric point (IEP) of the strain, the more sensitive it was to cecropin B. Through SEM, multiple blisters of various shapes and dents on the cell surface were observed. Protrusions and leakage were detected by AFM. Conclusions Based on the results, cecropin B could inhibit HPS via a pore-forming mechanism by interacting with the cytoplasmic membrane of bacteria. Moreover, as cecropin B concentration increased, the bacteria membrane was more seriously damaged. Thus, cecropin B could be developed as an effective anti-HPS agent for use in clinical applications.
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Affiliation(s)
- Han Hu
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, Hubei 430068, China.,State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Changsheng Jiang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Binzhou Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Nan Guo
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zhonghua Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xiaozhen Guo
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yang Wang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, Hubei 430068, China
| | - Binlei Liu
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, Hubei 430068, China
| | - Qigai He
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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99971
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Liang C, Guo P. Identification of Arginine Finger as the Starter of the Biomimetic Motor in Driving Double-Stranded DNA. ACS NANO 2021; 15:13260-13266. [PMID: 34323470 PMCID: PMC8388119 DOI: 10.1021/acsnano.1c02973] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Nanomotors in nanotechnology may be as important as cars in daily life. Biomotors are nanoscale machines ubiquitous in living systems to carry out ATP-driven activities such as walking, breathing, blinking, mitosis, replication, transcription, and trafficking. The sequential action in an asymmetrical hexamer by a revolving mechanism has been confirmed in dsDNA packaging motors of phi29, herpesviruses, bacterial dsDNA translocase FtsK, and Streptomyces TraB for conjugative dsDNA transfer. These elaborate, delicate, and exquisite ring structures have inspired scientists to design biomimetics in nanotechnology. Many multisubunit ATPase rings generate force via sequential action of multiple modules, such as the Walker A, Walker B, P-loop, arginine finger, sensors, and lid. The chemical to mechanical energy conversion usually takes place in sequential order. It is commonly believed that ATP binding triggers such conversion, but how the multimodule motor starts the sequential process has not been explicitly investigated. Identification of the starter is of great significance for biomimetic motor fabrication. Here, we report that the arginine finger is the starter of the motor. Only one amino acid residue change in the arginine finger led to the impediment and elimination of all following steps. Without the arginine finger, the motor failed to assemble, bind ATP, recruit DNA, or hydrolyze ATP and was eventually unable to package DNA. However, the loss of ATPase activity due to an inactive arginine finger can be rescued by an arginine finger from the adjacent subunit of Walker A mutant through trans-complementation. Taken together, we demonstrate that the formation of dimers triggered by the arginine finger initiates the motor action rather than the general belief of initiation by ATP binding.
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Affiliation(s)
- Chenxi Liang
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy and
College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- James
Comprehensive Cancer Center, The Ohio State
University, Columbus, Ohio 43210, United States
- Dorothy
M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, United States
- Biomedical
Science Graduate Program, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
| | - Peixuan Guo
- Center
for RNA Nanobiotechnology and Nanomedicine, College of Pharmacy and
College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- James
Comprehensive Cancer Center, The Ohio State
University, Columbus, Ohio 43210, United States
- Dorothy
M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, United States
- Biomedical
Science Graduate Program, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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99972
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Green SR, Storey KB. Functional and post-translational characterization of pyruvate dehydrogenase demonstrates repression of activity in the liver but not skeletal muscle of the Richardson's ground squirrel (Urocitellus richardsonii) during hibernation. J Therm Biol 2021; 99:102996. [PMID: 34420628 DOI: 10.1016/j.jtherbio.2021.102996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/27/2021] [Accepted: 05/11/2021] [Indexed: 10/21/2022]
Abstract
Hibernation consists of a series of physiological and biochemical alterations in an animal that allows for reduced body temperatures down to near ambient levels and substantial fuel conservation allowing it to survive on stored fat supplies accumulated during the summer. The Richardson's ground squirrel is one such hibernator that undergoes such changes for as long as 9 months of the year. This study examines the role of regulation of the pyruvate dehydrogenase complex (PDC) during hibernation in the skeletal muscle and liver of the Richardson's ground squirrel. The current study demonstrates a great reduction in the activity of PDC in the hibernating liver, but not in the skeletal muscle. This was matched by a significant increase in the phosphorylation on a regulatory serine residue (S300) of the pyruvate dehydrogenase (PDH) E1α subunit. Examining the expression patterns of the relevant kinases for PDH and the associated phosphatase demonstrated some unexpected results. Specifically, an increase in PDKs 1 and 2 and a decrease in PDK4 was noted in the skeletal muscle tissue in response to hibernation and no alterations in the expression patterns of any of these enzymes were noted in the liver. This suggests that alternative modes of regulation of the kinases may be at play in hibernation to bring about the observed effects. Taken together this study demonstrates that PDH regulatory responses differ markedly between tissues and emphasize the importance of inhibition of the complex in the liver during hibernation.
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Affiliation(s)
- Stuart R Green
- Institute of Biochemistry & Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada
| | - Kenneth B Storey
- Institute of Biochemistry & Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario, K1S 5B6, Canada.
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99973
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De Rose SA, Kuprat T, Isupov MN, Reinhardt A, Schönheit P, Littlechild JA. Biochemical and Structural Characterisation of a Novel D-Lyxose Isomerase From the Hyperthermophilic Archaeon Thermofilum sp. Front Bioeng Biotechnol 2021; 9:711487. [PMID: 34422783 PMCID: PMC8378251 DOI: 10.3389/fbioe.2021.711487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/13/2021] [Indexed: 11/30/2022] Open
Abstract
A novel D-lyxose isomerase has been identified within the genome of a hyperthermophilic archaeon belonging to the Thermofilum species. The enzyme has been cloned and over-expressed in Escherichia coli and biochemically characterised. This enzyme differs from other enzymes of this class in that it is highly specific for the substrate D-lyxose, showing less than 2% activity towards mannose and other substrates reported for lyxose isomerases. This is the most thermoactive and thermostable lyxose isomerase reported to date, showing activity above 95°C and retaining 60% of its activity after 60 min incubation at 80°C. This lyxose isomerase is stable in the presence of 50% (v/v) of solvents ethanol, methanol, acetonitrile and DMSO. The crystal structure of the enzyme has been resolved to 1.4–1.7 A. resolution in the ligand-free form and in complexes with both of the slowly reacting sugar substrates mannose and fructose. This thermophilic lyxose isomerase is stabilised by a disulfide bond between the two monomers of the dimeric enzyme and increased hydrophobicity at the dimer interface. These overall properties of high substrate specificity, thermostability and solvent tolerance make this lyxose isomerase enzyme a good candidate for potential industrial applications.
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Affiliation(s)
- Simone Antonio De Rose
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Tom Kuprat
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Michail N Isupov
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Andreas Reinhardt
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Peter Schönheit
- Institut für Allgemeine Mikrobiologie, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Jennifer A Littlechild
- The Henry Wellcome Building for Biocatalysis, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
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99974
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Fischer V, Plassard D, Ye T, Reina-San-Martin B, Stierle M, Tora L, Devys D. The related coactivator complexes SAGA and ATAC control embryonic stem cell self-renewal through acetyltransferase-independent mechanisms. Cell Rep 2021; 36:109598. [PMID: 34433046 PMCID: PMC8430043 DOI: 10.1016/j.celrep.2021.109598] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/17/2021] [Accepted: 08/03/2021] [Indexed: 01/10/2023] Open
Abstract
SAGA (Spt-Ada-Gcn5 acetyltransferase) and ATAC (Ada-two-A-containing) are two related coactivator complexes, sharing the same histone acetyltransferase (HAT) subunit. The HAT activities of SAGA and ATAC are required for metazoan development, but the role of these complexes in RNA polymerase II transcription is less understood. To determine whether SAGA and ATAC have redundant or specific functions, we compare the effects of HAT inactivation in each complex with that of inactivation of either SAGA or ATAC core subunits in mouse embryonic stem cells (ESCs). We show that core subunits of SAGA or ATAC are required for complex assembly and mouse ESC growth and self-renewal. Surprisingly, depletion of HAT module subunits causes a global decrease in histone H3K9 acetylation, but does not result in significant phenotypic or transcriptional defects. Thus, our results indicate that SAGA and ATAC are differentially required for self-renewal of mouse ESCs by regulating transcription through different pathways in a HAT-independent manner.
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Affiliation(s)
- Veronique Fischer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Damien Plassard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France; Plateforme GenomEast, infrastructure France Génomique, Illkirch, France
| | - Tao Ye
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France; Plateforme GenomEast, infrastructure France Génomique, Illkirch, France
| | - Bernardo Reina-San-Martin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Matthieu Stierle
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Laszlo Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France
| | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch Cedex, France; Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch Cedex, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch Cedex, France; Université de Strasbourg, 67000 Strasbourg, France.
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99975
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Nicholls IA, Golker K, Olsson GD, Suriyanarayanan S, Wiklander JG. The Use of Computational Methods for the Development of Molecularly Imprinted Polymers. Polymers (Basel) 2021; 13:2841. [PMID: 34502881 PMCID: PMC8434026 DOI: 10.3390/polym13172841] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 12/29/2022] Open
Abstract
Recent years have witnessed a dramatic increase in the use of theoretical and computational approaches in the study and development of molecular imprinting systems. These tools are being used to either improve understanding of the mechanisms underlying the function of molecular imprinting systems or for the design of new systems. Here, we present an overview of the literature describing the application of theoretical and computational techniques to the different stages of the molecular imprinting process (pre-polymerization mixture, polymerization process and ligand-molecularly imprinted polymer rebinding), along with an analysis of trends within and the current status of this aspect of the molecular imprinting field.
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Affiliation(s)
- Ian A. Nicholls
- Bioorganic & Biophysical Chemistry Laboratory, Linnaeus University Centre for Biomaterials Chemistry, Department of Chemistry & Biomedical Sciences, Linnaeus University, SE-391 82 Kalmar, Sweden; (K.G.); (G.D.O.); (S.S.); (J.G.W.)
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99976
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Gião T, Saavedra J, Vieira JR, Pinto MT, Arsequell G, Cardoso I. Neuroprotection in early stages of Alzheimer's disease is promoted by transthyretin angiogenic properties. ALZHEIMERS RESEARCH & THERAPY 2021; 13:143. [PMID: 34429155 PMCID: PMC8385857 DOI: 10.1186/s13195-021-00883-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/05/2021] [Indexed: 12/12/2022]
Abstract
Background While still controversial, it has been demonstrated that vascular defects can precede the onset of other AD hallmarks features, making it an important therapeutic target. Given that the protein transthyretin (TTR) has been established as neuroprotective in AD, here we investigated the influence of TTR in the vasculature. Methods We evaluated the thickness of the basement membrane and the length of brain microvessels, by immunohistochemistry, in AβPPswe/PS1A246E (AD) transgenic mice and non-transgenic mice (NT) bearing one (TTR+/−) or two (TTR+/+) copies of the TTR gene. The angiogenic potential of TTR was evaluated in vitro using the tube formation assay, and in vivo using the chick chorioallantoic membrane (CAM) assay. Results AD transgenic mice with TTR genetic reduction, AD/TTR+/−, exhibited a thicker BM in brain microvessels and decreased vessel length than animals with normal TTR levels, AD/TTR+/+. Further in vivo investigation, using the CAM assay, revealed that TTR is a pro-angiogenic molecule, and the neovessels formed are functional. Also, TTR increased the expression of key angiogenic molecules such as proteins interleukins 6 and 8, angiopoietin 2, and vascular endothelial growth factor, by endothelial cells, in vitro, under tube formation conditions. We showed that while TTR reduction also leads to a thicker BM in NT mice, this effect is more pronounced in AD mice than in NT animals, strengthening the idea that TTR is a neuroprotective protein. We also studied the effect of TTR tetrameric stabilization on BM thickness, showing that AD mice treated with the TTR tetrameric stabilizer iododiflunisal (IDIF) displayed a significant reduction of BM thickness and increased vessel length, when compared to non-treated littermates. Conclusion Our in vivo results demonstrate the involvement of TTR in angiogenesis, particularly as a modulator of vascular alterations occurring in AD. Since TTR is decreased early in AD, its tetrameric stabilization can represent a therapeutic avenue for the early treatment of AD through the maintenance of the vascular structure. Supplementary Information The online version contains supplementary material available at 10.1186/s13195-021-00883-8.
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Affiliation(s)
- Tiago Gião
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar (ICBAS), 4050-013, Porto, Portugal
| | - Joana Saavedra
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal
| | - José Ricardo Vieira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,Faculdade de Medicina, Universidade do Porto, Alameda Prof. Hernâni Monteiro, 4200-319, Porto, Portugal
| | - Marta Teixeira Pinto
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Rua Júlio Amaral de Carvalho,45-, 4200-135, Porto, Portugal
| | - Gemma Arsequell
- Institut de Química Avançada de Catalunya (I.Q.A.C.-C.S.I.C.), 08034, Barcelona, Spain
| | - Isabel Cardoso
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal. .,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135, Porto, Portugal. .,Instituto de Ciências Biomédicas Abel Salazar (ICBAS), 4050-013, Porto, Portugal.
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99977
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Andrikopoulos N, Song Z, Wan X, Douek AM, Javed I, Fu C, Xing Y, Xin F, Li Y, Kakinen A, Koppel K, Qiao R, Whittaker AK, Kaslin J, Davis TP, Song Y, Ding F, Ke PC. Inhibition of Amyloid Aggregation and Toxicity with Janus Iron Oxide Nanoparticles. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2021; 33:6484-6500. [PMID: 34887621 PMCID: PMC8651233 DOI: 10.1021/acs.chemmater.1c01947] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Amyloid aggregation is a ubiquitous form of protein misfolding underlying the pathologies of Alzheimer's disease (AD), Parkinson's disease (PD) and type 2 diabetes (T2D), three primary forms of human amyloid diseases. While much has been learned about the origin, diagnosis and management of these neurological and metabolic disorders, no cure is currently available due in part to the dynamic and heterogeneous nature of the toxic oligomers induced by amyloid aggregation. Here we synthesized beta casein-coated iron oxide nanoparticles (βCas IONPs) via a BPA-P(OEGA-b-DBM) block copolymer linker. Using a thioflavin T kinetic assay, transmission electron microscopy, Fourier transform infrared spectroscopy, discrete molecular dynamics simulations and cell viability assays, we examined the Janus characteristics and the inhibition potential of βCas IONPs against the aggregation of amyloid beta (Aβ), alpha synuclein (αS) and human islet amyloid polypeptide (IAPP) which are implicated in the pathologies of AD, PD and T2D. Incubation of zebrafish embryos with the amyloid proteins largely inhibited hatching and elicited reactive oxygen species, which were effectively rescued by the inhibitor. Furthermore, Aβ-induced damage to mouse brain was mitigated in vivo with the inhibitor. This study revealed the potential of Janus nanoparticles as a new nanomedicine against a diverse range of amyloid diseases.
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Affiliation(s)
- Nicholas Andrikopoulos
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Zhiyuan Song
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Xulin Wan
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Food Science, Southwest University, 2 Tiansheng Rd, Beibei District, Chongqing, 400715, China
| | - Alon M. Douek
- Australian Regenerative Medicine Institute, Monash University, 15 Innovation Walk, Clayton, VIC 3800, Australia
| | - Ibrahim Javed
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane Qld 4072, Australia
| | - Changkui Fu
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane Qld 4072, Australia
| | - Yanting Xing
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Fangyun Xin
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- School of Science, Dalian Maritime University, Dalian 116026, China
| | - Yuhuan Li
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Fudan University, Shanghai, 200032, China
| | - Aleksandr Kakinen
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane Qld 4072, Australia
| | - Kairi Koppel
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Ruirui Qiao
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane Qld 4072, Australia
| | - Andrew K. Whittaker
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane Qld 4072, Australia
| | - Jan Kaslin
- Australian Regenerative Medicine Institute, Monash University, 15 Innovation Walk, Clayton, VIC 3800, Australia
| | - Thomas P. Davis
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane Qld 4072, Australia
- Corresponding Authors: Thomas P. Davis: ; Yang Song, ; Feng Ding: ; Pu Chun Ke:
| | - Yang Song
- Key Laboratory of Luminescence Analysis and Molecular Sensing, Ministry of Education, College of Pharmaceutical Sciences, Southwest University, 2 Tiansheng Rd, Beibei District, Chongqing 400715, China
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- Corresponding Authors: Thomas P. Davis: ; Yang Song, ; Feng Ding: ; Pu Chun Ke:
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
- Corresponding Authors: Thomas P. Davis: ; Yang Song, ; Feng Ding: ; Pu Chun Ke:
| | - Pu Chun Ke
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane Qld 4072, Australia
- The GBA National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou, 510700, China
- Corresponding Authors: Thomas P. Davis: ; Yang Song, ; Feng Ding: ; Pu Chun Ke:
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99978
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Assisted assembly of bacteriophage T7 core components for genome translocation across the bacterial envelope. Proc Natl Acad Sci U S A 2021; 118:2026719118. [PMID: 34417311 DOI: 10.1073/pnas.2026719118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In most bacteriophages, genome transport across bacterial envelopes is carried out by the tail machinery. In viruses of the Podoviridae family, in which the tail is not long enough to traverse the bacterial wall, it has been postulated that viral core proteins assembled inside the viral head are translocated and reassembled into a tube within the periplasm that extends the tail channel. Bacteriophage T7 infects Escherichia coli, and despite extensive studies, the precise mechanism by which its genome is translocated remains unknown. Using cryo-electron microscopy, we have resolved the structure of two different assemblies of the T7 DNA translocation complex composed of the core proteins gp15 and gp16. Gp15 alone forms a partially folded hexamer, which is further assembled upon interaction with gp16 into a tubular structure, forming a channel that could allow DNA passage. The structure of the gp15-gp16 complex also shows the location within gp16 of a canonical transglycosylase motif involved in the degradation of the bacterial peptidoglycan layer. This complex docks well in the tail extension structure found in the periplasm of T7-infected bacteria and matches the sixfold symmetry of the phage tail. In such cases, gp15 and gp16 that are initially present in the T7 capsid eightfold-symmetric core would change their oligomeric state upon reassembly in the periplasm. Altogether, these results allow us to propose a model for the assembly of the core translocation complex in the periplasm, which furthers understanding of the molecular mechanism involved in the release of T7 viral DNA into the bacterial cytoplasm.
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99979
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Shahjaman M, Rezanur Rahman M, Rabiul Auwul M. A network-based systems biology approach for identification of shared Gene signatures between male and female in COVID-19 datasets. INFORMATICS IN MEDICINE UNLOCKED 2021; 25:100702. [PMID: 34423108 PMCID: PMC8372456 DOI: 10.1016/j.imu.2021.100702] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 12/14/2022] Open
Abstract
The novel coronavirus (SARS-CoV-2) has expanded rapidly worldwide. Now it has covered more than 150 countries worldwide. It is referred to as COVID-19. SARS-CoV-2 mainly affects the respiratory systems of humans that can lead up to serious illness or even death in the presence of different comorbidities. However, most COVID-19 infected people show mild to moderate symptoms, and no medication is suggested. Still, drugs of other diseases have been used to treat COVID-19. Nevertheless, the absence of vaccines and proper drugs against the COVID-19 virus has increased the mortality rate. Albeit sex is a risk factor for COVID-19, none of the studies considered this risk factor for identifying biomarkers from the RNASeq count dataset. Men are more likely to undertake severe symptoms with different comorbidities and show greater mortality compared with women. From this standpoint, we aim to identify shared gene signatures between males and females from the human COVID-19 RNAseq count dataset of peripheral blood cells using a robust voom approach. We identified 1341 overlapping DEGs between male and female datasets. The gene ontology (GO) annotation and pathway enrichment analysis revealed that DEGs are involved in various BP categories such as nucleosome assembly, DNA conformation change, DNA packaging, and different KEGG pathways such as cell cycle, ECM-receptor interaction, progesterone-mediated oocyte maturation, etc. Ten hub-proteins (UBC, KIAA0101, APP, CDK1, SUMO2, SP1, FN1, CDK2, E2F1, and TP53) were unveiled using PPI network analysis. The top three miRNAs (mir-17-5p, mir-20a-5p, mir-93-5p) and TFs (PPARG, E2F1 and KLF5) were uncovered. In conclusion, the top ten significant drugs (roscovitine, curcumin, simvastatin, fulvestrant, troglitazone, alvocidib, L-alanine, tamoxifen, serine, and doxorubicin) were retrieved using drug repurposing analysis of overlapping DEGs, which might be therapeutic agents of COVID-19.
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Affiliation(s)
- Md Shahjaman
- Department of Statistics, Begum Rokeya University, Rangpur, 5400, Bangladesh
| | - Md Rezanur Rahman
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, Bangladesh
| | - Md Rabiul Auwul
- Department of Statistics, Begum Rokeya University, Rangpur, 5400, Bangladesh
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99980
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Qu X, Leung TCN, Ngai SM, Tsai SN, Thakur A, Li WK, Lee Y, Leung L, Ng TH, Yam J, Lan L, Lau EHL, Wong EWY, Chan JYK, Meehan K. Proteomic Analysis of Circulating Extracellular Vesicles Identifies Potential Biomarkers for Lymph Node Metastasis in Oral Tongue Squamous Cell Carcinoma. Cells 2021; 10:2179. [PMID: 34571828 PMCID: PMC8468562 DOI: 10.3390/cells10092179] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/10/2021] [Accepted: 08/20/2021] [Indexed: 12/11/2022] Open
Abstract
Lymph node metastasis is the most reliable indicator of a poor prognosis for patients with oral tongue cancers. Currently, there are no biomarkers to predict whether a cancer will spread in the future if it has not already spread at the time of diagnosis. The aim of this study was to quantitatively profile the proteomes of extracellular vesicles (EVs) isolated from blood samples taken from patients with oral tongue squamous cell carcinoma with and without lymph node involvement and non-cancer controls. EVs were enriched using size exclusion chromatography (SEC) from pooled plasma samples of patients with non-nodal and nodal oral tongue squamous cell carcinoma (OTSCC) and non-cancer controls. Protein cargo was quantitatively profiled using isobaric labelling (iTRAQ) and two-dimensional high-performance liquid chromatography followed by tandem mass spectrometry. We identified 208 EV associated proteins and, after filtering, generated a short list of 136 proteins. Over 85% of the EV-associated proteins were associated with the GO cellular compartment term "extracellular exosome". Comparisons between non-cancer controls and oral tongue squamous cell carcinoma with and without lymph node involvement revealed 43 unique candidate EV-associated proteins with deregulated expression patterns. The shortlisted EV associated proteins described here may be useful discriminatory biomarkers for differentiating OTSCC with and without nodal disease or non-cancer controls.
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Affiliation(s)
- Xinyu Qu
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China; (X.Q.); (L.L.); (L.L.); (E.H.L.L.); (E.W.Y.W.); (J.Y.K.C.)
| | - Thomas C. N. Leung
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China; (T.C.N.L.); (S.-M.N.); (S.-N.T.)
| | - Sai-Ming Ngai
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China; (T.C.N.L.); (S.-M.N.); (S.-N.T.)
| | - Sau-Na Tsai
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China; (T.C.N.L.); (S.-M.N.); (S.-N.T.)
| | - Abhimanyu Thakur
- Department of Neuroscience, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong, China; (A.T.); (Y.L.)
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong, China;
- Ben May Department for Cancer Research, Pritzker School of Molecular Engineering, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA
| | - Wing-Kar Li
- Department of Biomedical Sciences, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong, China;
| | - Youngjin Lee
- Department of Neuroscience, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong, China; (A.T.); (Y.L.)
| | - Leanne Leung
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China; (X.Q.); (L.L.); (L.L.); (E.H.L.L.); (E.W.Y.W.); (J.Y.K.C.)
| | - Tung-Him Ng
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China; (T.-H.N.); (J.Y.)
| | - Judy Yam
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, China; (T.-H.N.); (J.Y.)
| | - Linlin Lan
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China; (X.Q.); (L.L.); (L.L.); (E.H.L.L.); (E.W.Y.W.); (J.Y.K.C.)
| | - Eric H. L. Lau
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China; (X.Q.); (L.L.); (L.L.); (E.H.L.L.); (E.W.Y.W.); (J.Y.K.C.)
| | - Eddy W. Y. Wong
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China; (X.Q.); (L.L.); (L.L.); (E.H.L.L.); (E.W.Y.W.); (J.Y.K.C.)
| | - Jason Y. K. Chan
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China; (X.Q.); (L.L.); (L.L.); (E.H.L.L.); (E.W.Y.W.); (J.Y.K.C.)
| | - Katie Meehan
- Department of Otorhinolaryngology, Head and Neck Surgery, The Chinese University of Hong Kong, Sha Tin, Hong Kong, China; (X.Q.); (L.L.); (L.L.); (E.H.L.L.); (E.W.Y.W.); (J.Y.K.C.)
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99981
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Reidelbach M, Zimmer C, Meunier B, Rich PR, Sharma V. Electron Transfer Coupled to Conformational Dynamics in Cell Respiration. Front Mol Biosci 2021; 8:711436. [PMID: 34422907 PMCID: PMC8378252 DOI: 10.3389/fmolb.2021.711436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/26/2021] [Indexed: 11/25/2022] Open
Abstract
Cellular respiration is a fundamental process required for energy production in many organisms. The terminal electron transfer complex in mitochondrial and many bacterial respiratory chains is cytochrome c oxidase (CcO). This converts the energy released in the cytochrome c/oxygen redox reaction into a transmembrane proton electrochemical gradient that is used subsequently to power ATP synthesis. Despite detailed knowledge of electron and proton transfer paths, a central question remains as to whether the coupling between electron and proton transfer in mammalian mitochondrial forms of CcO is mechanistically equivalent to its bacterial counterparts. Here, we focus on the conserved span between H376 and G384 of transmembrane helix (TMH) X of subunit I. This conformationally-dynamic section has been suggested to link the redox activity with the putative H pathway of proton transfer in mammalian CcO. The two helix X mutants, Val380Met (V380M) and Gly384Asp (G384D), generated in the genetically-tractable yeast CcO, resulted in a respiratory-deficient phenotype caused by the inhibition of intra-protein electron transfer and CcO turnover. Molecular aspects of these variants were studied by long timescale atomistic molecular dynamics simulations performed on wild-type and mutant bovine and yeast CcOs. We identified redox- and mutation-state dependent conformational changes in this span of TMH X of bovine and yeast CcOs which strongly suggests that this dynamic module plays a key role in optimizing intra-protein electron transfers.
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Affiliation(s)
- Marco Reidelbach
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Christoph Zimmer
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Brigitte Meunier
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Gif-sur-Yvette, France
| | - Peter R Rich
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Vivek Sharma
- Department of Physics, University of Helsinki, Helsinki, Finland.,HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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99982
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Folding and misfolding of potassium channel monomers during assembly and tetramerization. Proc Natl Acad Sci U S A 2021; 118:2103674118. [PMID: 34413192 DOI: 10.1073/pnas.2103674118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The dynamics and folding of potassium channel pore domain monomers are connected to the kinetics of tetramer assembly. In all-atom molecular dynamics simulations of Kv1.2 and KcsA channels, monomers adopt multiple nonnative conformations while the three helices remain folded. Consistent with this picture, NMR studies also find the monomers to be dynamic and structurally heterogeneous. However, a KcsA construct with a disulfide bridge engineered between the two transmembrane helices has an NMR spectrum with well-dispersed peaks, suggesting that the monomer can be locked into a native-like conformation that is similar to that observed in the folded tetramer. During tetramerization, fluoresence resonance energy transfer (FRET) data indicate that monomers rapidly oligomerize upon insertion into liposomes, likely forming a protein-dense region. Folding within this region occurs along separate fast and slow routes, with τfold ∼40 and 1,500 s, respectively. In contrast, constructs bearing the disulfide bond mainly fold via the faster pathway, suggesting that maintaining the transmembrane helices in their native orientation reduces misfolding. Interestingly, folding is concentration independent despite the tetrameric nature of the channel, indicating that the rate-limiting step is unimolecular and occurs after monomer association in the protein-dense region. We propose that the rapid formation of protein-dense regions may help with the assembly of multimeric membrane proteins by bringing together the nascent components prior to assembly. Finally, despite its name, the addition of KcsA's C-terminal "tetramerization" domain does not hasten the kinetics of tetramerization.
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99983
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Asante J, Hetsa BA, Amoako DG, Abia ALK, Bester LA, Essack SY. Genomic Analysis of Antibiotic-Resistant Staphylococcus epidermidis Isolates From Clinical Sources in the Kwazulu-Natal Province, South Africa. Front Microbiol 2021; 12:656306. [PMID: 34421833 PMCID: PMC8374169 DOI: 10.3389/fmicb.2021.656306] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 07/07/2021] [Indexed: 12/28/2022] Open
Abstract
Staphylococcus epidermidis has become an important nosocomial pathogen. Multidrug resistance makes S. epidermidis infections difficult to treat. The study aims to describe the genomic characteristics of methicillin-resistant S. epidermidis (MRSE) isolated from clinical sources, to comprehend the genetic basis of antibiotic resistance, virulence, and potential pathogenicity. Sixteen MRSE underwent whole-genome sequencing, and bioinformatics analyses were carried out to ascertain their resistome, virulome, mobilome, clonality, and phylogenomic relationships. In all, 75% of isolates displayed multidrug resistance and were associated with the carriage of multiple resistance genes including mecA, blaZ, tet(K), erm(A), erm(B), erm(C), dfrG, aac(6')-aph(2''), and cat(pC221) conferring resistance to β-lactams, tetracyclines, macrolide-lincosamide-streptogramin B, aminoglycosides, and phenicols, which were located on both plasmids and chromosomes. Their virulence profiles were evidenced by the presence of genes involved in adherence/biofilm formation (icaA, icaB, icaC, atl, ebh, and ebp), immune evasion (adsA, capC, and manA), and antiphagocytosis (rmlC, cdsA, and A). The community-acquired SCCmec type IV was the most common SCCmec type. The CoNS belonged to seven multilocus sequence types (MLSTs) and carried a diversity of mobile genetic elements such as phages, insertion sequences, and plasmids. The bacterial anti-phage defense systems clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR-Cas) immunity phage system and restriction-modification system (R-M system) and the arginine catabolic mobile element (ACME) involved in immune evasion and transport of virulence genes were also found. The insertion sequence, IS256, linked with virulence, was found in 56.3% of isolates. Generally, the isolates clustered according to STs, with some similarity but also considerable variability within isolates. Whole-genome sequencing and bioinformatics analysis provide insights into the likely pathogenicity and antibiotic resistance of S. epidermidis, necessitating surveillance of this emerging pathogen.
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Affiliation(s)
- Jonathan Asante
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Bakoena A Hetsa
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Daniel G Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Akebe L K Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Linda A Bester
- Biomedical Research Unit, University of KwaZulu-Natal, Durban, South Africa
| | - Sabiha Y Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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99984
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Abstract
Gold nanorods assembled in a side-by-side chiral configuration have potential applications in sensing due to their strong chiroptical surface plasmon resonances. Recent experiments have shown that dimers of gold nanorods bridged by double-stranded DNA exhibit variable chiral configurations depending on the chemical and ionic properties of the solvent medium. Here, we uncover the underlying physics governing this intriguing chiral behavior of such DNA-bridged nanorods by theoretically evaluating their configurational free energy landscape. Our results reveal how chiral configurations emerge from an interplay between the twist-stretch coupling of the intervening DNA and the intermolecular interactions between the nanorods, with dimers exhibiting left-handed chirality when the interparticle interactions are dominated by attractive depletion or van der Waals forces and right-handed chirality when dominated by repulsive electrostatic or steric forces. We demonstrate how changes in the depletant or ion concentration of the solvent medium lead to different classes of configurational responses by the dimers, including chirality-switching behavior, in good agreement with experimental observations. Based on extensive analyses of how material properties like nanorod aspect ratio, DNA length, and graft height modulate the free energy landscape, we propose strategies for tuning the environmentally responsive reconfigurability of the nanorod dimers. Overall, this work should help control the chirality and related optical activity of nanoparticle dimers and higher-order assemblies for various applications.
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Affiliation(s)
- Brian Hyun-Jong Lee
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
| | - Nicholas A Kotov
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, United States
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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99985
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Suter EC, Schmid EM, Harris AR, Voets E, Francica B, Fletcher DA. Antibody:CD47 ratio regulates macrophage phagocytosis through competitive receptor phosphorylation. Cell Rep 2021; 36:109587. [PMID: 34433055 PMCID: PMC8477956 DOI: 10.1016/j.celrep.2021.109587] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 04/19/2021] [Accepted: 08/02/2021] [Indexed: 01/04/2023] Open
Abstract
Cancer immunotherapies often modulate macrophage effector function by introducing either targeting antibodies that activate Fcγ receptors (FcγRs) or blocking antibodies that disrupt inhibitory SIRPα-CD47 engagement. However, how these competing signals are integrated is poorly understood, raising questions about how to effectively titrate immune responses. Here, we find that macrophage phagocytic decisions are regulated by the ratio of activating ligand to inhibitory ligand over a broad range of absolute molecular densities. Using both endogenous and chimeric receptors, we show that activating:inhibitory ligand ratios of at least 10:1 are required to promote phagocytosis of model antibody-opsonized CD47-inhibited targets and that lowering that ratio reduces FcγR phosphorylation because of inhibitory phosphatases recruited to CD47-bound SIRPα. We demonstrate that ratiometric signaling is critical for phagocytosis of tumor cells and can be modified by blocking SIRPα, indicating that balancing targeting and blocking antibodies may be important for controlling macrophage phagocytosis in cancer immunotherapy.
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Affiliation(s)
- Emily C Suter
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA; UC Berkeley/UC San Francisco Graduate Group in Bioengineering, Berkeley, CA, USA
| | - Eva M Schmid
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Andrew R Harris
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA; Department of Mechanical and Aerospace Engineering, Carleton University, Ottawa, ON, Canada
| | - Erik Voets
- Aduro Biotech Europe, Oss, the Netherlands
| | | | - Daniel A Fletcher
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA; UC Berkeley/UC San Francisco Graduate Group in Bioengineering, Berkeley, CA, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
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99986
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Harshbarger W, Abeyrathne PD, Tian S, Huang Y, Chandramouli S, Bottomley MJ, Malito E. Improved epitope resolution of the prefusion trimer-specific antibody AM14 bound to the RSV F glycoprotein. MAbs 2021; 13:1955812. [PMID: 34420474 PMCID: PMC8386734 DOI: 10.1080/19420862.2021.1955812] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Respiratory syncytial virus (RSV) is the most common cause of acute lower respiratory tract infections resulting in medical intervention and hospitalizations during infancy and early childhood, and vaccination against RSV remains a public health priority. The RSV F glycoprotein is a major target of neutralizing antibodies, and the prefusion stabilized form of F (DS-Cav1) is under investigation as a vaccine antigen. AM14 is a human monoclonal antibody with the exclusive capacity of binding an epitope on prefusion F (PreF), which spans two F protomers. The quality of recognizing a trimer-specific epitope makes AM14 valuable for probing PreF-based immunogen conformation and functionality during vaccine production. Currently, only a low-resolution (5.5 Å) X-ray structure is available of the PreF-AM14 complex, revealing few reliable details of the interface. Here, we perform complementary structural studies using X-ray crystallography and cryo-electron microscopy (cryo-EM) to provide improved resolution structures at 3.6 Å and 3.4 Å resolutions, respectively. Both X-ray and cryo-EM structures provide clear side-chain densities, which allow for accurate mapping of the AM14 epitope on DS-Cav1. The structures help rationalize the molecular basis for AM14 loss of binding to RSV F monoclonal antibody-resistant mutants and reveal flexibility for the side chain of a key antigenic residue on PreF. This work provides the basis for a comprehensive understanding of RSV F trimer specificity with implications in vaccine design and quality assessment of PreF-based immunogens.
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Affiliation(s)
| | | | - Sai Tian
- GSK, Vaccine Design and Cellular Immunology, Rockville, MD, USA
| | - Ying Huang
- GSK, Vaccine Design and Cellular Immunology, Rockville, MD, USA
| | | | | | - Enrico Malito
- GSK, Vaccine Design and Cellular Immunology, Rockville, MD, USA
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99987
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Sun T, Huang Z, Liang WC, Yin J, Lin WY, Wu J, Vernes JM, Lutman J, Caplazi P, Jeet S, Wong T, Wong M, DePianto DJ, Morshead KB, Sun KH, Modrusan Z, Vander Heiden JA, Abbas AR, Zhang H, Xu M, N'Diaye EN, Roose-Girma M, Wolters PJ, Yadav R, Sukumaran S, Ghilardi N, Corpuz R, Emson C, Meng YG, Ramalingam TR, Lupardus P, Brightbill HD, Seshasayee D, Wu Y, Arron JR. TGFβ2 and TGFβ3 isoforms drive fibrotic disease pathogenesis. Sci Transl Med 2021; 13:13/605/eabe0407. [PMID: 34349032 DOI: 10.1126/scitranslmed.abe0407] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 12/19/2020] [Accepted: 06/06/2021] [Indexed: 12/14/2022]
Abstract
Transforming growth factor-β (TGFβ) is a key driver of fibrogenesis. Three TGFβ isoforms (TGFβ1, TGFβ2, and TGFβ3) in mammals have distinct functions in embryonic development; however, the postnatal pathological roles and activation mechanisms of TGFβ2 and TGFβ3 have not been well characterized. Here, we show that the latent forms of TGFβ2 and TGFβ3 can be activated by integrin-independent mechanisms and have lower activation thresholds compared to TGFβ1. Unlike TGFB1, TGFB2 and TGFB3 expression is increased in human lung and liver fibrotic tissues compared to healthy control tissues. Thus, TGFβ2 and TGFβ3 may play a pathological role in fibrosis. Inducible conditional knockout mice and anti-TGFβ isoform-selective antibodies demonstrated that TGFβ2 and TGFβ3 are independently involved in mouse fibrosis models in vivo, and selective TGFβ2 and TGFβ3 inhibition does not lead to the increased inflammation observed with pan-TGFβ isoform inhibition. A cocrystal structure of a TGFβ2-anti-TGFβ2/3 antibody complex reveals an allosteric isoform-selective inhibitory mechanism. Therefore, inhibiting TGFβ2 and/or TGFβ3 while sparing TGFβ1 may alleviate fibrosis without toxicity concerns associated with pan-TGFβ blockade.
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Affiliation(s)
- Tianhe Sun
- Department of Immunology Discovery, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
| | - Zhiyu Huang
- Department of Translational Immunology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Wei-Ching Liang
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jianping Yin
- Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Wei Yu Lin
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jia Wu
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jean-Michel Vernes
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jeff Lutman
- Department of Preclinical and Translational Pharmacokinetics, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Patrick Caplazi
- Department of Pathology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Surinder Jeet
- Department of Translational Immunology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Tiffany Wong
- Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Manda Wong
- Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Daryle J DePianto
- Department of Immunology Discovery, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Katrina B Morshead
- Department of Immunology Discovery, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Kai-Hui Sun
- Department of Protein Sciences, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Zora Modrusan
- Department of Protein Sciences, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Jason A Vander Heiden
- Department of OMNI Bioinformatics, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Alexander R Abbas
- Department of OMNI Bioinformatics, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Hua Zhang
- Department of Translational Immunology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Min Xu
- Department of Translational Immunology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Elsa-Noah N'Diaye
- Department of Immunology Discovery, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Meron Roose-Girma
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Paul J Wolters
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Rajbharan Yadav
- Department of Preclinical and Translational Pharmacokinetics, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Siddharth Sukumaran
- Department of Preclinical and Translational Pharmacokinetics, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Nico Ghilardi
- Department of Immunology Discovery, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Racquel Corpuz
- Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Claire Emson
- Department of Translational Immunology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Y Gloria Meng
- Department of Biochemical and Cellular Pharmacology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Thirumalai R Ramalingam
- Department of Biomarker Discovery OMNI, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Patrick Lupardus
- Department of Structural Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Hans D Brightbill
- Department of Translational Immunology, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Dhaya Seshasayee
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Yan Wu
- Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA
| | - Joseph R Arron
- Department of Immunology Discovery, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.
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99988
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Sun G, Wang T, Shi M, Zhou H, Wang J, Huang Z, Zhang H, Shi J. Low expression of IL6R predicts poor prognosis for lung adenocarcinoma. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1057. [PMID: 34422969 PMCID: PMC8339841 DOI: 10.21037/atm-21-36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 04/25/2021] [Indexed: 11/06/2022]
Abstract
Background Interleukin 6 (IL6) is both a pleiotropic cytokine and an immune-related gene. Interleukin 6 receptor (IL6R) is the receptor for IL6. It may be closely connected to the development of lung cancer. This research aims to explore the prognostic value of IL6R and prevent overtreatment of patients with lung adenocarcinoma (LUAD). Methods In this study, the expression of IL6R in tumor tissues and surrounding tissues was first analyzed by immunohistochemistry in the Affiliated Hospital of Nantong University (NTU) cohort. Secondly, we downloaded information from The Cancer Genome Atlas (TCGA) for the TCGA cohort and used this information to explore the messenger RNA (mRNA) level of IL6R. We then used Kaplan-Meier survival analyses, univariate and multivariate Cox analyses, nomogram models, and decision curve analyses to assess the prognostic value of IL6R. In addition, we also analyzed immune cell infiltration and the signaling pathways related to IL6R through Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA). Results Through the data analysis of the NTU cohort and the TCGA cohort, it was found that the expression of IL6R in normal tissues around the tumor was higher than that in tumor tissue, and was positively correlated with the overall survival (OS) of LUAD patients. Additionally, low expression of IL6R was found to be an independent predictor of poor prognosis among the patients in these two research cohorts. Next, using GO, KEGG, and GSEA analyses, we found that partially infiltrated tumor immune cells might be related to earlier staging and better prognosis of patients with LUAD. Finally, the study of the 3-5-year survival rate of LUAD patients through the nomogram showed that the expression of IL6R could improve the accuracy of prediction to prevent the overtreatment of some LUAD patients. Conclusions In summary, our study indicated that the low expression of IL6R was associated with poor prognosis among LUAD patients and that low expression of IL6R is a potential independent risk factor that could provide a basis for strengthening postoperative classification management of such patients.
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Affiliation(s)
- Gaofeng Sun
- Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases, Affiliated Hospital of Nantong University, Nantong, China.,Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Tianyi Wang
- Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases, Affiliated Hospital of Nantong University, Nantong, China.,Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Muqi Shi
- Medical College of Nantong University, Nantong China
| | - Hao Zhou
- Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases, Affiliated Hospital of Nantong University, Nantong, China.,Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Jinjie Wang
- Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases, Affiliated Hospital of Nantong University, Nantong, China.,Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Zhanghao Huang
- Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases, Affiliated Hospital of Nantong University, Nantong, China.,Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong, China
| | - Haijian Zhang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Jiahai Shi
- Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases, Affiliated Hospital of Nantong University, Nantong, China.,Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong, China
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99989
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Palma M. Perspectives on passive antibody therapy and peptide-based vaccines against emerging pathogens like SARS-CoV-2. Germs 2021; 11:287-305. [PMID: 34422699 DOI: 10.18683/germs.2021.1264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 04/25/2021] [Accepted: 06/01/2021] [Indexed: 12/12/2022]
Abstract
The current epidemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is raising awareness of the need to act faster when dealing with new pathogens. Exposure to an emerging pathogen generates an antibody response that can be used for preventing and treating the infection. These antibodies might have a high specificity to a target, few side effects, and are useful in the absence of an effective vaccine for treating immunocompromised individuals. The approved antibodies against the receptor-binding domain (RBD) of the viral spike protein of SARS-CoV-2 (e.g., regdanvimab, bamlanivimab, etesevimab, and casirivimab/imdevimab) have been selected from the antibody repertoire of B cells from convalescent patients using flow cytometry, next-generation sequencing, and phage display. This encourages use of these techniques especially phage display, because it does not require expensive types of equipment and can be performed on the lab bench, thereby making it suitable for labs with limited resources. Also, the antibodies in blood samples from convalescent patients can be used to screen pre-made peptide libraries to identify epitopes for vaccine development. Different types of vaccines against SARS-CoV-2 have been developed, including inactivated virus vaccines, mRNA-based vaccines, non-replicating vector vaccines, and protein subunits. mRNA vaccines have numerous advantages over existing vaccines, such as efficacy, ease of manufacture, safety, and cost-effectiveness. Additionally, epitope vaccination may constitute an attractive strategy to induce high levels of antibodies against a pathogen and phages might be used as immunogenic carriers of such peptides. This is a point worth considering further, as phage-based vaccines have been shown to be safe in clinical trials and phages are easy to produce and tolerate high temperatures. In conclusion, identification of the antibody repertoire of recovering patients, and the epitopes they recognize, should be an attractive alternative option for developing therapeutic and prophylactic antibodies and vaccines against emerging pathogens.
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Affiliation(s)
- Marco Palma
- PhD, Independent researcher, Calle San Jose, Torrevieja, 03181, Spain
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99990
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Ruple BA, Godwin JS, Mesquita PHC, Osburn SC, Vann CG, Lamb DA, Sexton CL, Candow DG, Forbes SC, Frugé AD, Kavazis AN, Young KC, Seaborne RA, Sharples AP, Roberts MD. Resistance training rejuvenates the mitochondrial methylome in aged human skeletal muscle. FASEB J 2021; 35:e21864. [PMID: 34423880 DOI: 10.1096/fj.202100873rr] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 11/11/2022]
Abstract
Resistance training (RT) dynamically alters the skeletal muscle nuclear DNA methylome. However, no study has examined if RT affects the mitochondrial DNA (mtDNA) methylome. Herein, ten older, Caucasian untrained males (65 ± 7 y.o.) performed six weeks of full-body RT (twice weekly). Body composition and knee extensor torque were assessed prior to and 72 h following the last RT session. Vastus lateralis (VL) biopsies were also obtained. VL DNA was subjected to reduced representation bisulfite sequencing providing excellent coverage across the ~16-kilobase mtDNA methylome (254 CpG sites). Biochemical assays were also performed, and older male data were compared to younger trained males (22 ± 2 y.o., n = 7, n = 6 Caucasian & n = 1 African American). RT increased whole-body lean tissue mass (p = .017), VL thickness (p = .012), and knee extensor torque (p = .029) in older males. RT also affected the mtDNA methylome, as 63% (159/254) of the CpG sites demonstrated reduced methylation (p < .05). Several mtDNA sites presented a more "youthful" signature in older males after RT in comparison to younger males. The 1.12 kilobase mtDNA D-loop/control region, which regulates replication and transcription, possessed enriched hypomethylation in older males following RT. Enhanced expression of mitochondrial H- and L-strand genes and complex III/IV protein levels were also observed (p < .05). While limited to a shorter-term intervention, this is the first evidence showing that RT alters the mtDNA methylome in skeletal muscle. Observed methylome alterations may enhance mitochondrial transcription, and RT evokes mitochondrial methylome profiles to mimic younger men. The significance of these findings relative to broader RT-induced epigenetic changes needs to be elucidated.
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Affiliation(s)
- Bradley A Ruple
- School of Kinesiology, Auburn University, Auburn, Alabama, USA
| | - Joshua S Godwin
- School of Kinesiology, Auburn University, Auburn, Alabama, USA
| | | | - Shelby C Osburn
- School of Kinesiology, Auburn University, Auburn, Alabama, USA
| | | | - Donald A Lamb
- Department of Nutrition, Dietetics and Hospitality Management, Auburn University, Auburn, Alabama, USA
| | - Casey L Sexton
- School of Kinesiology, Auburn University, Auburn, Alabama, USA
| | - Darren G Candow
- Faculty of Kinesiology and Health Studies, University of Regina, Regina, Saskatchewan, Canada
| | - Scott C Forbes
- Faculty of Education, Department of Physical Education Studies, Brandon University, Brandon, Manitoba, Canada
| | - Andrew D Frugé
- Department of Nutrition, Dietetics and Hospitality Management, Auburn University, Auburn, Alabama, USA
| | | | - Kaelin C Young
- School of Kinesiology, Auburn University, Auburn, Alabama, USA.,Edward Via College of Osteopathic Medicine, Auburn, Alabama, USA
| | - Robert A Seaborne
- Centre for Genomics and Child Health, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Adam P Sharples
- Institute for Physical Performance, Norwegian School of Sport Sciences, Olso, Norway
| | - Michael D Roberts
- School of Kinesiology, Auburn University, Auburn, Alabama, USA.,Edward Via College of Osteopathic Medicine, Auburn, Alabama, USA
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99991
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Albarqi MMY, Ryder SP. The endogenous mex-3 3´UTR is required for germline repression and contributes to optimal fecundity in C. elegans. PLoS Genet 2021; 17:e1009775. [PMID: 34424904 PMCID: PMC8412283 DOI: 10.1371/journal.pgen.1009775] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 09/02/2021] [Accepted: 08/11/2021] [Indexed: 11/18/2022] Open
Abstract
RNA regulation is essential to successful reproduction. Messenger RNAs delivered from parent to progeny govern early embryonic development. RNA-binding proteins (RBPs) are the key effectors of this process, regulating the translation and stability of parental transcripts to control cell fate specification events prior to zygotic gene activation. The KH-domain RBP MEX-3 is conserved from nematode to human. It was first discovered in Caenorhabditis elegans, where it is essential for anterior cell fate and embryo viability. Here, we show that loss of the endogenous mex-3 3´UTR disrupts its germline expression pattern. An allelic series of 3´UTR deletion variants identify repressing regions of the UTR and demonstrate that repression is not precisely coupled to reproductive success. We also show that several RBPs regulate mex-3 mRNA through its 3´UTR to define its unique germline spatiotemporal expression pattern. Additionally, we find that both poly(A) tail length control and the translation initiation factor IFE-3 contribute to its expression pattern. Together, our results establish the importance of the mex-3 3´UTR to reproductive health and its expression in the germline. Our results suggest that additional mechanisms control MEX-3 function when 3´UTR regulation is compromised. In sexually reproducing organisms, germ cells undergo meiosis and differentiate to form oocytes or sperm. Coordination of this process requires a gene regulatory program that acts while the genome is undergoing chromatin condensation. As such, RNA regulatory pathways are an important contributor. The germline of the nematode Caenorhabditis elegans is a suitable model system to study germ cell differentiation. Several RNA-binding proteins (RBPs) coordinate each transition in the germline such as the transition from mitosis to meiosis. MEX-3 is a conserved RNA-binding protein found in most animals including humans. In C. elegans, MEX-3 displays a highly restricted pattern of expression. Here, we define the importance of the 3´UTR in regulating MEX-3 expression pattern in vivo and characterize the RNA-binding proteins involved in this regulation. Our results show that deleting various mex-3 3´UTR regions alter the pattern of expression in the germline in various ways. These mutations also reduced—but did not eliminate—reproductive capacity. Finally, we demonstrate that multiple post-transcriptional mechanisms control MEX-3 levels in different domains of the germline. Our data suggest that coordination of MEX-3 activity requires multiple layers of regulation to ensure reproductive robustness.
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Affiliation(s)
- Mennatallah M. Y. Albarqi
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Sean P. Ryder
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail:
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99992
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Aramide Modupe Dosunmu-Ogunbi A, Galley JC, Yuan S, Schmidt HM, Wood KC, Straub AC. Redox Switches Controlling Nitric Oxide Signaling in the Resistance Vasculature and Implications for Blood Pressure Regulation: Mid-Career Award for Research Excellence 2020. Hypertension 2021; 78:912-926. [PMID: 34420371 DOI: 10.1161/hypertensionaha.121.16493] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The arterial resistance vasculature modulates blood pressure and flow to match oxygen delivery to tissue metabolic demand. As such, resistance arteries and arterioles have evolved a series of highly orchestrated cell-cell communication mechanisms between endothelial cells and vascular smooth muscle cells to regulate vascular tone. In response to neurohormonal agonists, release of several intracellular molecules, including nitric oxide, evokes changes in vascular tone. We and others have uncovered novel redox switches in the walls of resistance arteries that govern nitric oxide compartmentalization and diffusion. In this review, we discuss our current understanding of redox switches controlling nitric oxide signaling in endothelial and vascular smooth muscle cells, focusing on new mechanistic insights, physiological and pathophysiological implications, and advances in therapeutic strategies for hypertension and other diseases.
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Affiliation(s)
- Atinuke Aramide Modupe Dosunmu-Ogunbi
- Heart, Lung, Blood and Vascular Medicine Institute (A.A.M.D.-O., J.C.G., S.Y., H.M.S., K.C.W., A.C.S.), University of Pittsburgh, PA.,Department of Pharmacology and Chemical Biology (A.A.M.D.-O., J.C.G., H.M.S., A.C.S), University of Pittsburgh, PA
| | - Joseph C Galley
- Heart, Lung, Blood and Vascular Medicine Institute (A.A.M.D.-O., J.C.G., S.Y., H.M.S., K.C.W., A.C.S.), University of Pittsburgh, PA.,Department of Pharmacology and Chemical Biology (A.A.M.D.-O., J.C.G., H.M.S., A.C.S), University of Pittsburgh, PA
| | - Shuai Yuan
- Heart, Lung, Blood and Vascular Medicine Institute (A.A.M.D.-O., J.C.G., S.Y., H.M.S., K.C.W., A.C.S.), University of Pittsburgh, PA
| | - Heidi M Schmidt
- Heart, Lung, Blood and Vascular Medicine Institute (A.A.M.D.-O., J.C.G., S.Y., H.M.S., K.C.W., A.C.S.), University of Pittsburgh, PA.,Department of Pharmacology and Chemical Biology (A.A.M.D.-O., J.C.G., H.M.S., A.C.S), University of Pittsburgh, PA
| | - Katherine C Wood
- Heart, Lung, Blood and Vascular Medicine Institute (A.A.M.D.-O., J.C.G., S.Y., H.M.S., K.C.W., A.C.S.), University of Pittsburgh, PA
| | - Adam C Straub
- Heart, Lung, Blood and Vascular Medicine Institute (A.A.M.D.-O., J.C.G., S.Y., H.M.S., K.C.W., A.C.S.), University of Pittsburgh, PA.,Department of Pharmacology and Chemical Biology (A.A.M.D.-O., J.C.G., H.M.S., A.C.S), University of Pittsburgh, PA.,Center for Microvascular Research (A.C.S.), University of Pittsburgh, PA
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99993
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Mongad DS, Chavan NS, Narwade NP, Dixit K, Shouche YS, Dhotre DP. MicFunPred: A conserved approach to predict functional profiles from 16S rRNA gene sequence data. Genomics 2021; 113:3635-3643. [PMID: 34450292 DOI: 10.1016/j.ygeno.2021.08.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 07/01/2021] [Accepted: 08/21/2021] [Indexed: 10/20/2022]
Abstract
The 16S rRNA gene amplicon sequencing is a popular technique that provides accurate characterization of microbial taxonomic abundances but does not provide any functional information. Several tools are available to predict functional profiles based on 16S rRNA gene sequence data that use different genome databases and approaches. As variable regions of partially-sequenced 16S rRNA gene cannot resolve taxonomy accurately beyond the genus level, these tools may give inflated results. Here, we developed 'MicFunPred', which uses a novel approach to derive imputed metagenomes based on a set of core genes only, thereby minimizing false-positive predictions. On simulated datasets, MicFunPred showed the lowest False Positive Rate (FPR) with mean Spearman's correlation of 0.89 (SD = 0.03), while on seven real datasets the mean correlation was 0.75 (SD = 0.08). MicFunPred was found to be faster with low computational requirements and performed better or comparable when compared with other tools.
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Affiliation(s)
- Dattatray S Mongad
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune, Maharashtra 411007, India
| | - Nikeeta S Chavan
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune, Maharashtra 411007, India; Persistent Systems Limited, Pune, India
| | - Nitin P Narwade
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune, Maharashtra 411007, India; Universidad Miguel Hernández de Elche, Alicante, Spain
| | - Kunal Dixit
- Symbiosis School of Biological Sciences (SSBS), Symbiosis International (Deemed University), Pune, Maharashtra 412115, India
| | - Yogesh S Shouche
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune, Maharashtra 411007, India.
| | - Dhiraj P Dhotre
- National Centre for Cell Science, Savitribai Phule Pune University Campus, Ganeshkhind, Pune, Maharashtra 411007, India.
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99994
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Šečić E, Zanini S, Wibberg D, Jelonek L, Busche T, Kalinowski J, Nasfi S, Thielmann J, Imani J, Steinbrenner J, Kogel KH. A novel plant-fungal association reveals fundamental sRNA and gene expression reprogramming at the onset of symbiosis. BMC Biol 2021; 19:171. [PMID: 34429124 PMCID: PMC8385953 DOI: 10.1186/s12915-021-01104-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 07/16/2021] [Indexed: 01/15/2023] Open
Affiliation(s)
- Ena Šečić
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Silvia Zanini
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Daniel Wibberg
- Center for Biotechnology - CeBiTec, Bielefeld University, 33615, Bielefeld, Germany
| | - Lukas Jelonek
- Institute of Bioinformatics and Systems Biology, Justus Liebig University, 35392, Giessen, Germany
| | - Tobias Busche
- Center for Biotechnology - CeBiTec, Bielefeld University, 33615, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology - CeBiTec, Bielefeld University, 33615, Bielefeld, Germany
| | - Sabrine Nasfi
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Jennifer Thielmann
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Jafargholi Imani
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Jens Steinbrenner
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany
| | - Karl-Heinz Kogel
- Institute of Phytopathology, Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392, Giessen, Germany.
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99995
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Rabalski L, Kosinski M, Smura T, Aaltonen K, Kant R, Sironen T, Szewczyk B, Grzybek M. Severe Acute Respiratory Syndrome Coronavirus 2 in Farmed Mink (Neovison vison), Poland. Emerg Infect Dis 2021; 27:2333-2339. [PMID: 34423763 PMCID: PMC8386773 DOI: 10.3201/eid2709.210286] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of coronavirus disease and has been spreading worldwide since December 2019. The virus can infect different animal species under experimental conditions, and mink on fur farms in Europe and other areas are susceptible to SARS-CoV-2 infection. We investigated SARS-CoV-2 infection in 91 mink from a farm in northern Poland. Using reverse transcription PCR, antigen detection, and next-generation sequencing, we confirmed that 15 animals were positive for SARS-CoV-2. We verified this finding by sequencing full viral genomes and confirmed a virus variant that has sporadic mutations through the full genome sequence in the spike protein (G75V and C1247F). We were unable to find other SARS-CoV-2 sequences simultaneously containing these 2 mutations. Country-scale monitoring by veterinary inspection should be implemented to detect SARS-CoV-2 in other mink farms.
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99996
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Makhneva ZK, Bolshakov MA, Moskalenko AA. Carotenoids Do Not Protect Bacteriochlorophylls in Isolated Light-Harvesting LH2 Complexes of Photosynthetic Bacteria from Destructive Interactions with Singlet Oxygen. Molecules 2021; 26:5120. [PMID: 34500552 PMCID: PMC8434301 DOI: 10.3390/molecules26175120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 11/22/2022] Open
Abstract
The effect of singlet oxygen on light-harvesting (LH) complexes has been studied for a number of sulfur (S+) and nonsulfur (S-) photosynthetic bacteria. The visible/near-IR absorption spectra of the standard LH2 complexes (B800-850) of Allochromatium (Alc.) vinosum (S+), Rhodobacter (Rba.) sphaeroides (S-), Rhodoblastus (Rbl.) acidophilus (S-), and Rhodopseudomonas (Rps.) palustris (S-), two types LH2/LH3 (B800-850 and B800-830) of Thiorhodospira (T.) sibirica (S+), and an unusual LH2 complex (B800-827) of Marichromatium (Mch.) purpuratum (S+) or the LH1 complex from Rhodospirillum (Rsp.) rubrum (S-) were measured in aqueous buffer suspensions in the presence of singlet oxygen generated by the illumination of the dye Rose Bengal (RB). The content of carotenoids in the samples was determined using HPLC analysis. The LH2 complex of Alc. vinosum and T. sibirica with a reduced content of carotenoids was obtained from cells grown in the presence of diphenylamine (DPA), and LH complexes were obtained from the carotenoidless mutant of Rba. sphaeroides R26.1 and Rps. rubrum G9. We found that LH2 complexes containing a complete set of carotenoids were quite resistant to the destructive action of singlet oxygen in the case of Rba. sphaeroides and Mch. purpuratum. Complexes of other bacteria were much less stable, which can be judged by a strong irreversible decrease in the bacteriochlorophyll (BChl) absorption bands (at 850 or 830 nm, respectively) for sulfur bacteria and absorption bands (at 850 and 800 nm) for nonsulfur bacteria. Simultaneously, we observe the appearance of the oxidized product 3-acetyl-chlorophyll (AcChl) absorbing near 700 nm. Moreover, a decrease in the amount of carotenoids enhanced the spectral stability to the action of singlet oxygen of the LH2 and LH3 complexes from sulfur bacteria and kept it at the same level as in the control samples for carotenoidless mutants of nonsulfur bacteria. These results are discussed in terms of the current hypothesis on the protective functions of carotenoids in bacterial photosynthesis. We suggest that the ability of carotenoids to quench singlet oxygen (well-established in vitro) is not well realized in photosynthetic bacteria. We compared the oxidation of BChl850 in LH2 complexes of sulfur bacteria under the action of singlet oxygen (in the presence of 50 μM RB) or blue light absorbed by carotenoids. These processes are very similar: {[BChl + (RB or carotenoid) + light] + O2} → AcChl. We speculate that carotenoids are capable of generating singlet oxygen when illuminated. The mechanism of this process is not yet clear.
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Affiliation(s)
| | | | - Andrey A. Moskalenko
- Institute of Basic Biological Problems RAS, 142290 Pushchino, Russia; (Z.K.M.); (M.A.B.)
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99997
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Hatfull GF, Dedrick RM, Schooley RT. Phage Therapy for Antibiotic-Resistant Bacterial Infections. Annu Rev Med 2021; 73:197-211. [PMID: 34428079 DOI: 10.1146/annurev-med-080219-122208] [Citation(s) in RCA: 173] [Impact Index Per Article: 57.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Antibiotic resistance in bacterial pathogens presents a substantial threat to the control of infectious diseases. Development of new classes of antibiotics has slowed in recent years due to pressures of cost and market profitability, and there is a strong need for new antimicrobial therapies. The therapeutic use of bacteriophages has long been considered, with numerous anecdotal reports of success. Interest in phage therapy has been renewed by recent clinical successes in case studies with personalized phage cocktails, and several clinical trials are in progress. We discuss recent progress in the therapeutic use of phages and contemplate the key factors influencing the opportunities and challenges. With strong safety profiles, the main challenges of phage therapeutics involve strain variation among clinical isolates of many pathogens, battling phage resistance, and the potential limitations of host immune responses. However, the opportunities are considerable, with the potential to enhance current antibiotic efficacy, protect newly developed antibiotics, and provide a last resort in response to complete antibiotic failure. Expected final online publication date for the Annual Review of Medicine, Volume 73 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Graham F Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA; ,
| | - Rebekah M Dedrick
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA; ,
| | - Robert T Schooley
- Department of Medicine, University of California, San Diego, La Jolla, California 92093, USA;
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99998
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Naidoo D, Kar P, Roy A, Mutanda T, Bwapwa J, Sen A, Anandraj A. Structural Insight into the Binding of Cyanovirin-N with the Spike Glycoprotein, M pro and PL pro of SARS-CoV-2: Protein-Protein Interactions, Dynamics Simulations and Free Energy Calculations. Molecules 2021; 26:molecules26175114. [PMID: 34500548 PMCID: PMC8434238 DOI: 10.3390/molecules26175114] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/15/2021] [Accepted: 07/26/2021] [Indexed: 02/06/2023] Open
Abstract
The emergence of COVID-19 continues to pose severe threats to global public health. The pandemic has infected over 171 million people and claimed more than 3.5 million lives to date. We investigated the binding potential of antiviral cyanobacterial proteins including cyanovirin-N, scytovirin and phycocyanin with fundamental proteins involved in attachment and replication of SARS-CoV-2. Cyanovirin-N displayed the highest binding energy scores (−16.8 ± 0.02 kcal/mol, −12.3 ± 0.03 kcal/mol and −13.4 ± 0.02 kcal/mol, respectively) with the spike protein, the main protease (Mpro) and the papainlike protease (PLpro) of SARS-CoV-2. Cyanovirin-N was observed to interact with the crucial residues involved in the attachment of the human ACE2 receptor. Analysis of the binding affinities calculated employing the molecular mechanics-Poisson–Boltzmann surface area (MM-PBSA) approach revealed that all forms of energy, except the polar solvation energy, favourably contributed to the interactions of cyanovirin-N with the viral proteins. With particular emphasis on cyanovirin-N, the current work presents evidence for the potential inhibition of SARS-CoV-2 by cyanobacterial proteins, and offers the opportunity for in vitro and in vivo experiments to deploy the cyanobacterial proteins as valuable therapeutics against COVID-19.
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Affiliation(s)
- Devashan Naidoo
- Centre for Algal Biotechnology, Mangosuthu University of Technology, P.O. Box 12363, Durban 4026, South Africa; (T.M.); (J.B.); (A.A.)
- Correspondence: (D.N.); (A.R.)
| | - Pallab Kar
- Bioinformatics Facility, Department of Botany, University of North Bengal, Siliguri 734013, India; (P.K.); (A.S.)
| | - Ayan Roy
- Department of Biotechnology, Lovely Professional University, Phagwara 144411, India
- Correspondence: (D.N.); (A.R.)
| | - Taurai Mutanda
- Centre for Algal Biotechnology, Mangosuthu University of Technology, P.O. Box 12363, Durban 4026, South Africa; (T.M.); (J.B.); (A.A.)
| | - Joseph Bwapwa
- Centre for Algal Biotechnology, Mangosuthu University of Technology, P.O. Box 12363, Durban 4026, South Africa; (T.M.); (J.B.); (A.A.)
| | - Arnab Sen
- Bioinformatics Facility, Department of Botany, University of North Bengal, Siliguri 734013, India; (P.K.); (A.S.)
| | - Akash Anandraj
- Centre for Algal Biotechnology, Mangosuthu University of Technology, P.O. Box 12363, Durban 4026, South Africa; (T.M.); (J.B.); (A.A.)
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99999
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Integration of transcription coregulator complexes with sequence-specific DNA-binding factor interactomes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1864:194749. [PMID: 34425241 PMCID: PMC10359485 DOI: 10.1016/j.bbagrm.2021.194749] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 08/13/2021] [Accepted: 08/19/2021] [Indexed: 12/22/2022]
Abstract
The domain of transcription regulation has been notoriously difficult to annotate in the Gene Ontology, partly because of the intricacies of gene regulation which involve molecular interactions with DNA as well as amongst protein complexes. The molecular function 'transcription coregulator activity' is a part of the biological process 'regulation of transcription, DNA-templated' that occurs in the cellular component 'chromatin'. It can mechanistically link sequence-specific DNA-binding transcription factor (dbTF) regulatory DNA target sites to coactivator and corepressor target sites through the molecular function 'cis-regulatory region sequence-specific DNA binding'. Many questions arise about transcription coregulators (coTF). Here, we asked how many unannotated, putative coregulators can be identified in protein complexes? Therefore, we mined the CORUM and hu.MAP protein complex databases with known and strongly presumed human transcription coregulators. In addition, we trawled the BioGRID and IntAct molecular interaction databases for interactors of the known 1457 human dbTFs annotated by the GREEKC and GO consortia. This yielded 1093 putative transcription factor coregulator complex subunits, of which 954 interact directly with a dbTF. This substantially expands the set of coTFs that could be annotated to 'transcription coregulator activity' and sets the stage for renewed annotation and wet-lab research efforts. To this end, we devised a prioritisation score based on existing GO annotations of already curated transcription coregulators as well as interactome representation. Since all the proteins that we mined are parts of protein complexes, we propose to concomitantly engage in annotation of the putative transcription coregulator-containing complexes in the Complex Portal database.
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100000
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Cancer predisposition and germline CTNNA1 variants. Eur J Med Genet 2021; 64:104316. [PMID: 34425242 DOI: 10.1016/j.ejmg.2021.104316] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 07/16/2021] [Accepted: 08/18/2021] [Indexed: 12/25/2022]
Abstract
Hereditary Diffuse Gastric Cancer (HDGC) is a cancer predisposing syndrome mainly caused by germline inactivating variants in CDH1, encoding E-cadherin. Early-onset diffuse gastric cancer (DGC) and/or invasive lobular breast cancer (LBC) are the main phenotypes in CDH1-associated HDGC. CTNNA1, encoding for α-E-catenin, and E-cadherin-partner in the adherens junction complex, has been recently classified as a HDGC predisposing gene. Nevertheless, little is known about CTNNA1 tumor spectrum in variant carriers and variant-type associated causality. Herein, we systematically reviewed the literature searching for CTNNA1 germline variants carriers, further categorized them according to HDGC clinical criteria (HDGC vs non-HDGC), collected phenotypes, classified variants molecularly and according to CDH1 ACMG/AMP guidelines and performed genotype-phenotype analysis. We found 41 families carrying CTNNA1 germline variants encompassing in total 105 probands and relatives. All probands from 13 HDGC families presented DGC and their average age of onset was 40 ± 17 years; 10/13 (77%) HDGC families carried a pathogenic (P) variant. Most probands from 28 non-HDGC families developed unspecified-BC, as well as most of their relatives; 4/28 (14%) carried a P variant, 16/28 (57%) carried a likely pathogenic (LP) variant, 7/28 (25%) carried variants of unknown significance (VUS) and 1/28 (4%) carried a likely benign variant. Regardless of clinical criteria, 97% (32/33) of probands and relatives from P variant-carrier families had DGC/unspecified-GC. In LP variant-carrier families, 82% (28/34) of probands and relatives had unspecified-BC. Only 2/105 individuals had LBC. A cluster of frameshift and nonsense variants was found in CTNNA1 last exon of non-HDGC families and classified as VUS. In conclusion, current available data confirms an association of CTNNA1 P variants with early-onset DGC, but not with LBC. We demonstrate that in ascertained cohorts, CTNNA1 P variants explain <2% of HDGC families and support the use of ACMG/AMP CDH1 specific variant curation guidelines, while no specific guidelines are developed for CTNNA1 variant classification. Moreover, we demonstrated that truncating variants at the CTNNA1 NMD-incompetent last exon have limited deleteriousness, and that CTNNA1 LP variants have lower actionability than CDH1 LP variants. Current knowledge supports considering only CTNNA1 P variants as clinically actionable in HDGC carrying families.
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