99951
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Abstract
Human cancers often harbor large numbers of somatic mutations. However, only a small proportion of these mutations are expected to contribute to tumor growth and progression. Therefore, determining causal driver mutations and the genes they target is becoming an important challenge in cancer genomics. Here we describe an approach for mapping somatic mutations onto 3D structures of human proteins in complex to identify "driver interfaces." Our strategy relies on identifying protein-interaction interfaces that are unexpectedly biased toward nonsynonymous mutations, which suggests that these interfaces are subject to positive selection during tumorigenesis, implicating the interacting proteins as candidate drivers.
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Affiliation(s)
- Kivilcim Ozturk
- Division of Medical Genetics, Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Bioinformatics Program, University of California San Diego, La Jolla, CA, USA
| | - Hannah Carter
- Division of Medical Genetics, Department of Medicine, University of California San Diego, La Jolla, CA, USA.
- Bioinformatics Program, University of California San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
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99952
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Shoji M, Isobe H, Yamanaka S, Umena Y, Kawakami K, Kamiya N, Yamaguchi K. Theoretical Elucidation of Geometrical Structures of the CaMn4O5 Cluster in Oxygen Evolving Complex of Photosystem II Scope and Applicability of Estimation Formulae of Structural Deformations via the Mixed-Valence and Jahn–Teller Effects. ADVANCES IN QUANTUM CHEMISTRY 2019. [DOI: 10.1016/bs.aiq.2018.05.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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99953
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Nagae M, Yamaguchi Y. Structural Aspects of Carbohydrate Recognition Mechanisms of C-Type Lectins. Curr Top Microbiol Immunol 2019; 429:147-176. [PMID: 31781867 DOI: 10.1007/82_2019_181] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Carbohydrate recognition is an essential function occurring in all living organisms. Lectins are carbohydrate-binding proteins and are classified into several families. In mammals, Ca2+-dependent C-type lectins, such as β-galactoside-binding galectin and sialic acid-binding siglec, play crucial roles in the immune response and homeostasis. C-type lectins are abundant and diverse in animals. Their immunological activities include lymphocyte homing, pathogen recognition, and clearance of apoptotic bodies. C-type lectin domains are composed of 110-130 amino acid residues with highly conserved structural folds. Remarkably, individual lectins can accept a wide variety of sugar ligands and can distinguish subtle structural differences in closely related ligands. In addition, several C-type lectin-like proteins specifically bind to carbohydrate ligands in Ca2+-independent ways. The accumulated 3D structural evidence clarifies the unexpected structural versatility of C-type lectins underlying the variety of ligand binding modes. In this issue, we focus on the structural aspects of carbohydrate recognition mechanisms of C-type lectins and C-type lectin-like proteins.
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Affiliation(s)
- Masamichi Nagae
- Department of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-Ku, Tokyo, 113-0033, Japan.
| | - Yoshiki Yamaguchi
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Miyagi, 981-8558, Japan.
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99954
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Khan MR, Bukhari I, Khan R, Hussain HMJ, Wu M, Thorne RF, Li J, Liu G. TP53LNC-DB, the database of lncRNAs in the p53 signalling network. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2019; 2019:5277247. [PMID: 30624647 PMCID: PMC6323480 DOI: 10.1093/database/bay136] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 11/30/2018] [Indexed: 12/14/2022]
Abstract
The TP53 gene product, p53, is a pleiotropic transcription factor induced by stress, which functions to promote cell cycle arrest, apoptosis and senescence. Genome-wide profiling has revealed an extensive system of long noncoding RNAs (lncRNAs) that is integral to the p53 signalling network. As a research tool, we implemented a public access database called TP53LNC-DB that annotates currently available information relating lncRNAs to p53 signalling in humans.
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Affiliation(s)
- Muhammad Riaz Khan
- Translational Research Institute, Henan Provincial People's Hospital, School of Medicine, Zhengzhou University, Zhengzhou, China
| | - Ihtisham Bukhari
- Translational Research Institute, Henan Provincial People's Hospital, School of Medicine, Zhengzhou University, Zhengzhou, China
| | - Ranjha Khan
- Joint Centre for Human Reproduction and Genetics. Anhui Society for Cell Biology. School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Hafiz Muhammad Jafar Hussain
- Joint Centre for Human Reproduction and Genetics. Anhui Society for Cell Biology. School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, School of Medicine, Zhengzhou University, Zhengzhou, China
| | - Rick Francis Thorne
- Translational Research Institute, Henan Provincial People's Hospital, School of Medicine, Zhengzhou University, Zhengzhou, China
| | - Jinming Li
- Translational Research Institute, Henan Provincial People's Hospital, School of Medicine, Zhengzhou University, Zhengzhou, China
| | - Guangzhi Liu
- Translational Research Institute, Henan Provincial People's Hospital, School of Medicine, Zhengzhou University, Zhengzhou, China
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99955
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Lang S, Nguyen D, Pfeffer S, Förster F, Helms V, Zimmermann R. Functions and Mechanisms of the Human Ribosome-Translocon Complex. Subcell Biochem 2019; 93:83-141. [PMID: 31939150 DOI: 10.1007/978-3-030-28151-9_4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The membrane of the endoplasmic reticulum (ER) in human cells harbors the protein translocon, which facilitates membrane insertion and translocation of almost every newly synthesized polypeptide targeted to organelles of the secretory pathway. The translocon comprises the polypeptide-conducting Sec61 channel and several additional proteins, which are associated with the heterotrimeric Sec61 complex. This ensemble of proteins facilitates ER targeting of precursor polypeptides, Sec61 channel opening and closing, and modification of precursor polypeptides in transit through the Sec61 complex. Recently, cryoelectron tomography of translocons in native ER membranes has given unprecedented insights into the architecture and dynamics of the native, ribosome-associated translocon and the Sec61 channel. These structural data are discussed in light of different Sec61 channel activities including ribosome receptor function, membrane insertion or translocation of newly synthesized polypeptides as well as the possible roles of the Sec61 channel as a passive ER calcium leak channel and regulator of ATP/ADP exchange between cytosol and ER.
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Affiliation(s)
- Sven Lang
- Competence Center for Molecular Medicine, Saarland University Medical School, Building 44, 66421, Homburg, Germany.
| | - Duy Nguyen
- Center for Bioinformatics, Saarland University, 66041, Saarbrücken, Germany
| | - Stefan Pfeffer
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152, Martinsried, Germany
- ZMBH, 69120, Heidelberg, Germany
| | - Friedrich Förster
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152, Martinsried, Germany
- Center for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, 66041, Saarbrücken, Germany
| | - Richard Zimmermann
- Competence Center for Molecular Medicine, Saarland University Medical School, Building 44, 66421, Homburg, Germany
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99956
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Dufau ML, Kavarthapu R. Gonadotropin Regulation Testicular RNA Helicase, Two Decades of Studies on Its Structure Function and Regulation From Its Discovery Opens a Window for Development of a Non-hormonal Oral Male Contraceptive. Front Endocrinol (Lausanne) 2019; 10:576. [PMID: 31555207 PMCID: PMC6727037 DOI: 10.3389/fendo.2019.00576] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 08/07/2019] [Indexed: 12/22/2022] Open
Abstract
Gonadotropin Regulated Testicular Helicase (GRTH/DDX25) is member of the DEAD-box family of RNA helicases present in Leydig and germ cells. GRTH is the only family member regulated by hormones, luteinizing hormone, through androgen action. Male mice with knock-out of the GRTH gene are sterile, lack sperm with arrest at round spermatids. GRTH participates on the nuclear export and transport of specific mRNAs, the structural integrity of Chromatoid Bodies of round spermatids, where mRNAs are processed and stored, and in their transit to polyribosomes, where it may regulate translation of relevant genes. GRTH has a central role in the control of germ cell apoptosis and acts as negative regulator of miRNAs which regulate expression of genes involved in the progress of spermatogenesis. In Leydig cells, GRTH gene transcription is regulated by LH via autocrine actions of androgen/androgen receptor and has regulatory effects in steroidogenesis. In germ cells, androgen actions are indirect via receptors in Sertoli cells. Transgenic mice carrying GRTH 5' flanking region-GFP permitted to discern regions in the gene which directs its expression upstream, in germ cells, and downstream in Leydig cells, and the androgen-regulated transcription at interstitial (autocrine), and germ cell (paracrine) compartments. Further evidence for paracrine actions of androgen/androgen receptor is their transcriptional induction of Germ Cell Nuclear Factor as requisite up-regulator of GRTH gene transcription in round spermatids, linking androgen action to two relevant germ cell genes essential for the progress of spermatogenesis. A missense mutation of R to H at amino acid 242 of GRTH found in 5.8% of a patient population with azoospermia causes loss of the cytoplasmic phospho-GRTH species with preservation of the non-phospho form in transfected cells. Mice with knock-in of the human mutation, lack sperm due to arrest at round spermatids. This model permits to discern the function of phospho-GRTH. The GRTH phospho-site resides at a Threonine structurally adjacent to the mutant site found in patients. Molecular modeling of this site elucidated the amino acids that form the GRTH/PKA interphase and provide the basis for drug design for use as male contraceptive.
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99957
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Boudreaux SP, Duren RP, Call SG, Nguyen L, Freire PR, Narayanan P, Redell MS, Conneely OM. Drug targeting of NR4A nuclear receptors for treatment of acute myeloid leukemia. Leukemia 2019; 33:52-63. [PMID: 29884904 PMCID: PMC6286710 DOI: 10.1038/s41375-018-0174-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 04/23/2018] [Accepted: 05/11/2018] [Indexed: 12/15/2022]
Abstract
NR4As are AML tumor suppressors that are frequently silenced in human acute myeloid leukemia (AML). Despite their potential as novel targets for therapeutic intervention, mechanisms of NR4A silencing and strategies for their reactivation remain poorly defined. Here we show that NR4A silencing in AML occurs through blockade of transcriptional elongation rather than epigenetic promoter silencing. By intersection of NR4A-regulated gene signatures captured upon acute, exogenous expression of NR4As in human AML cells with in silico chemical genomics screening, we identify several FDA-approved drugs including dihydroergotamine (DHE) that reactivate NR4A expression and regulate NR4A-dependent gene signatures. We show that DHE induces NR4A expression via recruitment of the super elongation complex to enable elongation of NR4A promoter paused RNA polymerase II. Finally, DHE exhibits AML selective NR4A-dependent anti-leukemic activity in cytogenetically distinct human AML cells in vitro and delays AML progression in mice revealing its potential as a novel therapeutic agent in AML.
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MESH Headings
- Animals
- Apoptosis
- Cell Proliferation
- Dihydroergotamine/pharmacology
- Drug Delivery Systems/methods
- Epigenesis, Genetic
- Female
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Nuclear Receptor Subfamily 4, Group A, Member 1/genetics
- Nuclear Receptor Subfamily 4, Group A, Member 1/metabolism
- Transcriptome
- Tumor Cells, Cultured
- Vasoconstrictor Agents/pharmacology
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Seth P Boudreaux
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, 77030, USA
- New Iberia Research Center, University of Louisiana at Lafayette, New Iberia, LA, 70560, USA
| | - Ryan P Duren
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
- Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Steven G Call
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Loc Nguyen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Pablo R Freire
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Padmini Narayanan
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Michele S Redell
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Orla M Conneely
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
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99958
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Ishiguro K. The cohesin complex in mammalian meiosis. Genes Cells 2019; 24:6-30. [PMID: 30479058 PMCID: PMC7379579 DOI: 10.1111/gtc.12652] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/29/2018] [Accepted: 10/29/2018] [Indexed: 12/13/2022]
Abstract
Cohesin is an evolutionary conserved multi-protein complex that plays a pivotal role in chromosome dynamics. It plays a role both in sister chromatid cohesion and in establishing higher order chromosome architecture, in somatic and germ cells. Notably, the cohesin complex in meiosis differs from that in mitosis. In mammalian meiosis, distinct types of cohesin complexes are produced by altering the combination of meiosis-specific subunits. The meiosis-specific subunits endow the cohesin complex with specific functions for numerous meiosis-associated chromosomal events, such as chromosome axis formation, homologue association, meiotic recombination and centromeric cohesion for sister kinetochore geometry. This review mainly focuses on the cohesin complex in mammalian meiosis, pointing out the differences in its roles from those in mitosis. Further, common and divergent aspects of the meiosis-specific cohesin complex between mammals and other organisms are discussed.
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Affiliation(s)
- Kei‐ichiro Ishiguro
- Institute of Molecular Embryology and GeneticsKumamoto UniversityKumamotoJapan
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99959
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Trotman JB, Schoenberg *DR. A recap of RNA recapping. WILEY INTERDISCIPLINARY REVIEWS. RNA 2019; 10:e1504. [PMID: 30252202 PMCID: PMC6294674 DOI: 10.1002/wrna.1504] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/13/2018] [Accepted: 08/01/2018] [Indexed: 12/12/2022]
Abstract
The N7-methylguanosine cap is a hallmark of the 5' end of eukaryotic mRNAs and is required for gene expression. Loss of the cap was believed to lead irreversibly to decay. However, nearly a decade ago, it was discovered that mammalian cells contain enzymes in the cytoplasm that are capable of restoring caps onto uncapped RNAs. In this review, we summarize recent advances in our understanding of cytoplasmic RNA recapping and discuss the biochemistry of this process and its impact on regulating and diversifying the transcriptome. Although most studies focus on mammalian RNA recapping, we also highlight new observations for recapping in disparate eukaryotic organisms, with the trypanosome recapping system appearing to be a fascinating example of convergent evolution. We conclude with emerging insights into the biological significance of RNA recapping and prospects for the future of this evolving area of study. This article is categorized under: RNA Processing > RNA Editing and Modification Translation > Translation Regulation RNA Processing > Capping and 5' End Modifications RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Jackson B. Trotman
- Department of Biological Chemistry and Pharmacology, Center for RNA Biology, The Ohio State University, Columbus, OH 43210,
| | - *Daniel R. Schoenberg
- Department of Biological Chemistry and Pharmacology, Center for RNA Biology, The Ohio State University, Columbus, OH 43210, schoenberg,
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99960
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Nath A. Herpes Viruses, Alzheimer's Disease, and Related Dementias: Unifying or Confusing Hypothesis? Neurotherapeutics 2019; 16:180-181. [PMID: 30644072 PMCID: PMC6361066 DOI: 10.1007/s13311-018-00701-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Avindra Nath
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bldg 10; Room 7C-103, 10 Center Drive, Bethesda, MD, 20892, USA.
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99961
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Abstract
G-quadruplexes (G4s) have become one of the most exciting nucleic acid secondary structures. A noncanonical, four-stranded structure formed in guanine-rich DNA and RNA sequences, G-quadruplexes can readily form under physiologically relevant conditions and are globularly folded structures. DNA is widely recognized as a double-helical structure essential in genetic information storage. However, only ~3% of the human genome is expressed in protein; RNA and DNA may form noncanonical secondary structures that are functionally important. G-quadruplexes are one such example which have gained considerable attention for their formation and regulatory roles in biologically significant regions, such as human telomeres, oncogene-promoter regions, replication initiation sites, and 5'- and 3'-untranslated region (UTR) of mRNA. They are shown to be a regulatory motif in a number of critical cellular processes including gene transcription, translation, replication, and genomic stability. G-quadruplexes are also found in nonhuman genomes, particularly those of human pathogens. Therefore, G-quadruplexes have emerged as a new class of molecular targets for drug development. In addition, there is considerable interest in the use of G-quadruplexes for biomaterials, biosensors, and biocatalysts. The First International Meeting on Quadruplex DNA was held in 2007, and the G-quadruplex field has been growing dramatically over the last decade. The methods used to study G-quadruplexes have been essential to the rapid progress in our understanding of this exciting nucleic acid secondary structure.
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Affiliation(s)
- Danzhou Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, Purdue Center for Cancer Research, Purdue Institute for Drug Discovery, West Lafayette, IN USA
| | - Clement Lin
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN USA
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99962
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Structural Insights into Phylloquinone (Vitamin K1), Menaquinone (MK4, MK7), and Menadione (Vitamin K3) Binding to VKORC1. Nutrients 2019; 11:nu11010067. [PMID: 30609653 PMCID: PMC6357001 DOI: 10.3390/nu11010067] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/21/2018] [Accepted: 12/24/2018] [Indexed: 11/17/2022] Open
Abstract
Vitamin K family molecules-phylloquinone (K1), menaquinone (K2), and menadione (K3)-act as γ-glutamyl carboxylase (GGCX)-exclusive cofactors in their hydroquinone state, activating proteins of main importance for blood coagulation in the liver and for arterial calcification prevention and energy metabolism in extrahepatic tissues. Once GGCX is activated, vitamin K is found in the epoxide state, which is then recycled to quinone and hydroquinone states by vitamin K epoxide reductase (VKORC1). Nevertheless, little information is available concerning vitamin K1, K2, or K3 tissue distribution and preferential interactions towards VKORC1. Here we present a molecular modeling study of vitamin K1, menaquinones 4, 7 (MK4, MK7), and K3 structural interactions with VKORC1. VKORC1 was shown to tightly bind vitamins K1 and MK4 in the epoxide and quinone states, but not in the hydroquinone state; five VKORC1 residues were identified as crucial for vitamin K stabilization, and two other ones were essential for hydrogen bond formation. However, vitamin MK7 revealed shaky binding towards VKORC1, induced by hydrophobic tail interactions with the membrane. Vitamin K3 exhibited the lowest affinity with VKORC1 because of the absence of a hydrophobic tail, preventing structural stabilization by the enzyme. Enzymatic activity towards vitamins K1, MK4, MK7, and K3 was also evaluated by in vitro assays, validating our in silico predictions: VKORC1 presented equivalent activities towards vitamins K1 and MK4, but much lower activity with respect to vitamin MK7, and no activity towards vitamin K3. Our results revealed VKORC1's ability to recycle both phylloquinone and some menaquinones, and also highlighted the importance of vitamin K's hydrophobic tail size and membrane interactions.
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99963
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Tseng KC, Chiang-Hsieh YF, Pai H, Chow CN, Lee SC, Zheng HQ, Kuo PL, Li GZ, Hung YC, Lin NS, Chang WC. microRPM: a microRNA prediction model based only on plant small RNA sequencing data. Bioinformatics 2019; 34:1108-1115. [PMID: 29136092 DOI: 10.1093/bioinformatics/btx725] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 11/08/2017] [Indexed: 01/15/2023] Open
Abstract
Motivation MicroRNAs (miRNAs) are endogenous non-coding small RNAs (of about 22 nucleotides), which play an important role in the post-transcriptional regulation of gene expression via either mRNA cleavage or translation inhibition. Several machine learning-based approaches have been developed to identify novel miRNAs from next generation sequencing (NGS) data. Typically, precursor/genomic sequences are required as references for most methods. However, the non-availability of genomic sequences is often a limitation in miRNA discovery in non-model plants. A systematic approach to determine novel miRNAs without reference sequences is thus necessary. Results In this study, an effective method was developed to identify miRNAs from non-model plants based only on NGS datasets. The miRNA prediction model was trained with several duplex structure-related features of mature miRNAs and their passenger strands using a support vector machine algorithm. The accuracy of the independent test reached 96.61% and 93.04% for dicots (Arabidopsis) and monocots (rice), respectively. Furthermore, true small RNA sequencing data from orchids was tested in this study. Twenty-one predicted orchid miRNAs were selected and experimentally validated. Significantly, 18 of them were confirmed in the qRT-PCR experiment. This novel approach was also compiled as a user-friendly program called microRPM (miRNA Prediction Model). Availability and implementation This resource is freely available at http://microRPM.itps.ncku.edu.tw. Contact nslin@sinica.edu.tw or sarah321@mail.ncku.edu.tw. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kuan-Chieh Tseng
- College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 70101, Taiwan
| | - Yi-Fan Chiang-Hsieh
- College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 70101, Taiwan
| | - Hsuan Pai
- Institute of Plant and Microbial Biology, Academia Sinica, NanKang, Taipei 115, Taiwan
| | - Chi-Nga Chow
- College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 70101, Taiwan
| | - Shu-Chuan Lee
- Institute of Plant and Microbial Biology, Academia Sinica, NanKang, Taipei 115, Taiwan
| | - Han-Qin Zheng
- College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 70101, Taiwan
| | - Po-Li Kuo
- College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 70101, Taiwan
| | - Guan-Zhen Li
- College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 70101, Taiwan
| | - Yu-Cheng Hung
- College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 70101, Taiwan
| | - Na-Sheng Lin
- Institute of Plant and Microbial Biology, Academia Sinica, NanKang, Taipei 115, Taiwan
| | - Wen-Chi Chang
- College of Biosciences and Biotechnology, Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 70101, Taiwan
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99964
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Bylicky MA, Mueller GP, Day RM. Radiation resistance of normal human astrocytes: the role of non-homologous end joining DNA repair activity. JOURNAL OF RADIATION RESEARCH 2019; 60:37-50. [PMID: 30423138 PMCID: PMC6373697 DOI: 10.1093/jrr/rry084] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/03/2018] [Indexed: 05/27/2023]
Abstract
Radiotherapy is a common modality for treatment of brain cancers, but it can induce long-term physiological and cognitive deficits. The responses of normal human brain cells to radiation is not well understood. Astrocytes have been shown to have a variety of protective mechanisms against oxidative stress and have been shown to protect neurons. We investigated the response of cultured normal human astrocytes (NHAs) to X-ray irradiation. Following exposure to 10 Gy X-irradiation, NHAs exhibited DNA damage as indicated by the formation of γ-H2AX foci. Western blotting showed that NHAs displayed a robust increase in expression of non-homologous end joining DNA repair enzymes within 15 min post-irradiation and increased expression of homologous recombination DNA repair enzymes ~2 h post-irradiation. The cell cycle checkpoint protein p21/waf1 was upregulated from 6-24 h, and then returned to baseline. Levels of DNA repair enzymes returned to basal ~48 h post-irradiation. NHAs re-entered the cell cycle and proliferation was observed at 6 days. In contrast, normal human mesenchymal stem cells (MSCs) failed to upregulate DNA repair enzymes and instead displayed sustained upregulation of p21/waf1, a cell cycle checkpoint marker for senescence. Ectopic overexpression of Ku70 was sufficient to protect MSCs from sustained upregulation of p21/waf1 induced by 10 Gy X-rays. These findings suggest that increased expression of Ku70 may be a key mechanism for the radioresistance of NHAs, preventing their accelerated senescence from high-dose radiation. These results may have implications for the development of novel targets for radiation countermeasure development.
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Affiliation(s)
- Michelle A Bylicky
- Department of Anatomy, Physiology, and Genetics, The Uniformed Services University of the Health Sciences, Jones Bridge Road, Bethesda, MD, USA
| | - Gregory P Mueller
- Department of Anatomy, Physiology, and Genetics, The Uniformed Services University of the Health Sciences, Jones Bridge Road, Bethesda, MD, USA
| | - Regina M Day
- Department of Pharmacology and Molecular Therapeutics, The Uniformed Services University of the Health Sciences, Jones Bridge Road, Bethesda, MD, USA
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99965
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Saldana M, VanderVorst K, Berg AL, Lee H, Carraway KL. Otubain 1: a non-canonical deubiquitinase with an emerging role in cancer. Endocr Relat Cancer 2019; 26:R1-R14. [PMID: 30400005 PMCID: PMC6226034 DOI: 10.1530/erc-18-0264] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 09/03/2018] [Indexed: 12/12/2022]
Abstract
The ubiquitin system regulates diverse biological processes, many involved in cancer pathogenesis, by altering the ubiquitination state of protein substrates. This is accomplished by ubiquitin ligases and deubiquitinases (DUBs), which respectively add or remove ubiquitin from substrates to alter their stability, activity, localization and interactions. While lack of catalytic activity makes therapeutic targeting of ubiquitin ligases difficult, DUB inhibitors represent an active area of research and the identification of cancer-associated DUBs may lead to the development of novel therapeutics. A growing body of literature demonstrates that the DUB Otubain 1 (OTUB1) regulates many cancer-associated signaling pathways including MAPK, ERa, epithelial-mesenchymal transition (EMT), RHOa, mTORC1, FOXM1 and P53 to promote tumor cell survival, proliferation, invasiveness and therapeutic resistance. In addition, clinical studies have associated elevated OTUB1 expression with high grade, invasiveness and metastasis in several tumor types including lung, breast, ovarian, glioma, colon and gastric. Interestingly, in addition to catalytic DUB activity, OTUB1 displays a catalytic-independent, non-canonical activity where it inhibits the transfer of ubiquitin onto protein substrates by sequestration of E2 ubiquitin-conjugating enzymes. The aim of this review is to describe the canonical and non-canonical activities of OTUB1, summarize roles for OTUB1 in cancer-associated pathways and discuss its potential therapeutic targeting.
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Affiliation(s)
- Matthew Saldana
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, UC Davis Comprehensive Cancer Center, Sacramento, California, USA
| | - Kacey VanderVorst
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, UC Davis Comprehensive Cancer Center, Sacramento, California, USA
| | - Anastasia L Berg
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, UC Davis Comprehensive Cancer Center, Sacramento, California, USA
| | - Hyun Lee
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, UC Davis Comprehensive Cancer Center, Sacramento, California, USA
| | - Kermit L Carraway
- Department of Biochemistry and Molecular Medicine, UC Davis School of Medicine, UC Davis Comprehensive Cancer Center, Sacramento, California, USA
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99966
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Li X, He Y, Zhang L, Xu Z, Ben H, Gaffrey MJ, Yang Y, Yang S, Yuan JS, Qian WJ, Yang B. Discovery of potential pathways for biological conversion of poplar wood into lipids by co-fermentation of Rhodococci strains. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:60. [PMID: 30923568 PMCID: PMC6423811 DOI: 10.1186/s13068-019-1395-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 03/06/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND Biological routes for utilizing both carbohydrates and lignin are important to reach the ultimate goal of bioconversion of full carbon in biomass into biofuels and biochemicals. Recent biotechnology advances have shown promises toward facilitating biological transformation of lignin into lipids. Natural and engineered Rhodococcus strains (e.g., R. opacus PD630, R. jostii RHA1, and R. jostii RHA1 VanA-) have been demonstrated to utilize lignin for lipid production, and co-culture of them can promote lipid production from lignin. RESULTS In this study, a co-fermentation module of natural and engineered Rhodococcus strains with significant improved lignin degradation and/or lipid biosynthesis capacities was established, which enabled simultaneous conversion of glucose, lignin, and its derivatives into lipids. Although Rhodococci sp. showed preference to glucose over lignin, nearly half of the lignin was quickly depolymerized to monomers by these strains for cell growth and lipid synthesis after glucose was nearly consumed up. Profiles of metabolites produced by Rhodococcus strains growing on different carbon sources (e.g., glucose, alkali lignin, and dilute acid flowthrough-pretreated poplar wood slurry) confirmed lignin conversion during co-fermentation, and indicated novel metabolic capacities and unexplored metabolic pathways in these organisms. Proteome profiles suggested that lignin depolymerization by Rhodococci sp. involved multiple peroxidases with accessory oxidases. Besides the β-ketoadipate pathway, the phenylacetic acid (PAA) pathway was another potential route for the in vivo ring cleavage activity. In addition, deficiency of reducing power and cellular oxidative stress probably led to lower lipid production using lignin as the sole carbon source than that using glucose. CONCLUSIONS This work demonstrated a potential strategy for efficient bioconversion of both lignin and glucose into lipids by co-culture of multiple natural and engineered Rhodococcus strains. In addition, the involvement of PAA pathway in lignin degradation can help to further improve lignin utilization, and the combinatory proteomics and bioinformatics strategies used in this study can also be applied into other systems to reveal the metabolic and regulatory pathways for balanced cellular metabolism and to select genetic targets for efficient conversion of both lignin and carbohydrates into biofuels.
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Affiliation(s)
- Xiaolu Li
- Bioproducts, Sciences and Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, 2710 Crimson Way, Richland, WA 99354 USA
| | - Yucai He
- Bioproducts, Sciences and Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, 2710 Crimson Way, Richland, WA 99354 USA
| | - Libing Zhang
- Bioproducts, Sciences and Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, 2710 Crimson Way, Richland, WA 99354 USA
| | - Zhangyang Xu
- Bioproducts, Sciences and Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, 2710 Crimson Way, Richland, WA 99354 USA
| | - Haoxi Ben
- Bioproducts, Sciences and Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, 2710 Crimson Way, Richland, WA 99354 USA
| | - Matthew J. Gaffrey
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - Yongfu Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-resources, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Joshua S. Yuan
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77840 USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - Bin Yang
- Bioproducts, Sciences and Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, 2710 Crimson Way, Richland, WA 99354 USA
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352 USA
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99967
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Abstract
γ-aminobutyric acid has become one of the most widely known neurotransmitter molecules in the brain over the last 50 years, recognised for its pivotal role in inhibiting neural excitability. It emerged from studies of crustacean muscle and neurons before its significance to the mammalian nervous system was appreciated. Now, after five decades of investigation, we know that most neurons are γ-aminobutyric-acid-sensitive, it is a cornerstone of neural physiology and dysfunction to γ-aminobutyric acid signalling is increasingly documented in a range of neurological diseases. In this review, we briefly chart the neurodevelopment of γ-aminobutyric acid and its two major receptor subtypes: the γ-aminobutyric acidA and γ-aminobutyric acidB receptors, starting from the humble invertebrate origins of being an 'interesting molecule' acting at a single γ-aminobutyric acid receptor type, to one of the brain's most important neurochemical components and vital drug targets for major therapeutic classes of drugs. We document the period of molecular cloning and the explosive influence this had on the field of neuroscience and pharmacology up to the present day and the production of atomic γ-aminobutyric acidA and γ-aminobutyric acidB receptor structures. γ-Aminobutyric acid is no longer a humble molecule but the instigator of rich and powerful signalling processes that are absolutely vital for healthy brain function.
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Affiliation(s)
- Trevor G Smart
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
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99968
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Reiding KR, Bondt A, Hennig R, Gardner RA, O'Flaherty R, Trbojević-Akmačić I, Shubhakar A, Hazes JMW, Reichl U, Fernandes DL, Pučić-Baković M, Rapp E, Spencer DIR, Dolhain RJEM, Rudd PM, Lauc G, Wuhrer M. High-throughput Serum N-Glycomics: Method Comparison and Application to Study Rheumatoid Arthritis and Pregnancy-associated Changes. Mol Cell Proteomics 2019; 18:3-15. [PMID: 30242110 PMCID: PMC6317482 DOI: 10.1074/mcp.ra117.000454] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 05/14/2018] [Indexed: 11/06/2022] Open
Abstract
N-Glycosylation is a fundamentally important protein modification with a major impact on glycoprotein characteristics such as serum half-life and receptor interaction. More than half of the proteins in human serum are glycosylated, and the relative abundances of protein glycoforms often reflect alterations in health and disease. Several analytical methods are currently capable of analyzing the total serum N-glycosylation in a high-throughput manner.Here we evaluate and compare the performance of three high-throughput released N-glycome analysis methods. Included were hydrophilic-interaction ultra-high-performance liquid chromatography with fluorescence detection (HILIC-UHPLC-FLD) with 2-aminobenzamide labeling of the glycans, multiplexed capillary gel electrophoresis with laser-induced fluorescence detection (xCGE-LIF) with 8-aminopyrene-1,3,6-trisulfonic acid labeling, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) with linkage-specific sialic acid esterification. All methods assessed the same panel of serum samples, which were obtained at multiple time points during the pregnancies and postpartum periods of healthy women and patients with rheumatoid arthritis (RA). We compared the analytical methods on their technical performance as well as on their ability to describe serum protein N-glycosylation changes throughout pregnancy, with RA, and with RA disease activity.Overall, the methods proved to be similar in their detection and relative quantification of serum protein N-glycosylation. However, the non-MS methods showed superior repeatability over MALDI-TOF-MS and allowed the best structural separation of low-complexity N-glycans. MALDI-TOF-MS achieved the highest throughput and provided compositional information on higher-complexity N-glycans. Consequentially, MALDI-TOF-MS could establish the linkage-specific sialylation differences within pregnancy and RA, whereas HILIC-UHPLC-FLD and xCGE-LIF demonstrated differences in α1,3- and α1,6-branch galactosylation. While the combination of methods proved to be the most beneficial for the analysis of total serum protein N-glycosylation, informed method choices can be made for the glycosylation analysis of single proteins or samples of varying complexity.
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Affiliation(s)
| | - Albert Bondt
- From the ‡Center for Proteomics and Metabolomics,; §Department of Rheumatology, Leiden University Medical Center (LUMC), Leiden, The Netherlands
| | - René Hennig
- ¶Max Planck Institute (MPI) for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany;; ‖glyXera GmbH., 39120 Magdeburg, Germany
| | - Richard A Gardner
- **Ludger, Ltd., Culham Science Centre, Abingdon, Oxfordshire, United Kingdom
| | - Roisin O'Flaherty
- ‡‡GlycoScience Group, National Institute for Bioprocessing Research and Training (NIBRT), Fosters Avenue, Blackrock, Co. Dublin, Ireland
| | | | - Archana Shubhakar
- **Ludger, Ltd., Culham Science Centre, Abingdon, Oxfordshire, United Kingdom
| | - Johanna M W Hazes
- ¶¶Department of Rheumatology, Erasmus University Medical Center, Rotterdam, The Netherland
| | - Udo Reichl
- ¶Max Planck Institute (MPI) for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany;; ‖‖Otto von Guericke University Magdeburg, Chair of Bioprocess Engineering, 39106 Magdeburg, Germany
| | - Daryl L Fernandes
- **Ludger, Ltd., Culham Science Centre, Abingdon, Oxfordshire, United Kingdom
| | | | - Erdmann Rapp
- ¶Max Planck Institute (MPI) for Dynamics of Complex Technical Systems, 39106 Magdeburg, Germany;; ‖glyXera GmbH., 39120 Magdeburg, Germany
| | - Daniel I R Spencer
- **Ludger, Ltd., Culham Science Centre, Abingdon, Oxfordshire, United Kingdom
| | - Radboud J E M Dolhain
- ¶¶Department of Rheumatology, Erasmus University Medical Center, Rotterdam, The Netherland
| | - Pauline M Rudd
- ‡‡GlycoScience Group, National Institute for Bioprocessing Research and Training (NIBRT), Fosters Avenue, Blackrock, Co. Dublin, Ireland
| | - Gordan Lauc
- §§Genos Glycoscience Research Laboratory, Zagreb, Croatia;; ***Faculty of Pharmacy and Biochemistry, University of Zagreb, 10000 Zagreb, Croatia
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99969
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Allen KN, Entova S, Ray LC, Imperiali B. Monotopic Membrane Proteins Join the Fold. Trends Biochem Sci 2019; 44:7-20. [PMID: 30337134 PMCID: PMC6309722 DOI: 10.1016/j.tibs.2018.09.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/18/2018] [Accepted: 09/19/2018] [Indexed: 12/22/2022]
Abstract
Monotopic membrane proteins, classified by topology, are proteins that embed into a single face of the membrane. These proteins are generally underrepresented in the Protein Data Bank (PDB), but the past decade of research has revealed new examples that allow the description of generalizable features. This Opinion article summarizes shared characteristics including oligomerization states, modes of membrane association, mechanisms of interaction with hydrophobic or amphiphilic substrates, and homology to soluble folds. We also discuss how associations of monotopic enzymes in pathways can be used to promote substrate specificity and product composition. These examples highlight the challenges in structure determination specific to this class of proteins, but also the promise of new understanding from future study of these proteins that reside at the interface.
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Affiliation(s)
- Karen N Allen
- Department of Chemistry, Boston University, Boston, MA 02215, USA; Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, MA 02118, USA.
| | - Sonya Entova
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Leah C Ray
- Program in Biomolecular Pharmacology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Barbara Imperiali
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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99970
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Chen CH, Ferreira JCB, Mochly-Rosen D. ALDH2 and Cardiovascular Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1193:53-67. [PMID: 31368097 DOI: 10.1007/978-981-13-6260-6_3] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Aldehyde dehydrogenase 2 (ALDH2) is a non-cytochrome P450 mitochondrial aldehyde oxidizing enzyme. It is best known for its role in the metabolism of acetaldehyde, a common metabolite from alcohol drinking. More evidences have been accumulated in recent years to indicate a greater role of ALDH2 in the metabolism of other endogenous and exogenous aldehydes, especially lipid peroxidation-derived reactive aldehyde under oxidative stress. Many cardiovascular diseases are associated with oxidative stress and mitochondria dysfunction. Considering that an estimated 560 million East Asians carry a common ALDH2 deficient variant which causes the well-known alcohol flushing syndrome due to acetaldehyde accumulation, the importance of understanding the role of ALDH2 in these diseases should be highlighted. There are several unfavorable cardiovascular conditions that are associated with ALDH2 deficiency. This chapter reviews the function of ALDH2 in various pathological conditions of the heart in relation to aldehyde toxicity. It also highlights the importance and clinical implications of interaction between ALDH2 deficiency and alcohol drinking on cardiovascular disease among the East Asians.
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Affiliation(s)
- Che-Hong Chen
- Department of Chemical and Systems Biology, Stanford University, School of Medicine, Stanford, CA, USA
| | - Julio C B Ferreira
- Department of Anatomy, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Daria Mochly-Rosen
- Department of Chemical and Systems Biology, Stanford University, School of Medicine, Stanford, CA, USA.
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99971
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Abstract
The tick-borne pathogen Powassan virus is a rare cause of encephalitis in North America and the Russian Far East. The number of documented cases described since the discovery of Powassan virus in 1958 may be <150, although detection of cases has increased over the past decade. In the United States, the incidence of Powassan virus infections expanded from the estimated 1 case per year prior to 2005 to 10 cases per year during the subsequent decade. The increased detection rate may be associated with several factors, including enhanced surveillance, the availability of improved laboratory diagnostic methods, the expansion of the vector population, and, perhaps, altered human activities that lead to more exposure. Nonetheless, it remains unclear whether Powassan virus is indeed an emerging threat or if enzootic cycles in nature remain more-or-less stable with periodic fluctuations of host and vector population sizes. Despite the low disease incidence, the approximately 10% to 15% case fatality rate of neuroinvasive Powassan virus infection and the temporary or prolonged sequelae in >50% of survivors make Powassan virus a medical concern requiring the attention of public health authorities and clinicians. The medical importance of Powassan virus justifies more research on developing specific and effective treatments and prevention and control measures.
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Affiliation(s)
- Gábor Kemenesi
- Virological Research Group, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
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99972
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99973
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Neesse A, Bauer CA, Öhlund D, Lauth M, Buchholz M, Michl P, Tuveson DA, Gress TM. Stromal biology and therapy in pancreatic cancer: ready for clinical translation? Gut 2019; 68:159-171. [PMID: 30177543 DOI: 10.1136/gutjnl-2018-316451] [Citation(s) in RCA: 223] [Impact Index Per Article: 44.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 08/05/2018] [Accepted: 08/06/2018] [Indexed: 12/12/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDA) is notoriously aggressive and hard to treat. The tumour microenvironment (TME) in PDA is highly dynamic and has been found to promote tumour progression, metastasis niche formation and therapeutic resistance. Intensive research of recent years has revealed an incredible heterogeneity and complexity of the different components of the TME, including cancer-associated fibroblasts, immune cells, extracellular matrix components, tumour vessels and nerves. It has been hypothesised that paracrine interactions between neoplastic epithelial cells and TME compartments may result in either tumour-promoting or tumour-restraining consequences. A better preclinical understanding of such complex and dynamic network systems is required to develop more powerful treatment strategies for patients. Scientific activity and the number of compelling findings has virtually exploded during recent years. Here, we provide an update of the most recent findings in this area and discuss their translational and clinical implications for basic scientists and clinicians alike.
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Affiliation(s)
- Albrecht Neesse
- Department of Gastroenterology and Gastrointestinal Oncology, University Medicine Goettingen, Goettingen, Germany
| | - Christian Alexander Bauer
- Department of Gastroenterology, Endocrinology, Metabolism and Infectiology, University Hospital Marburg, UKGM, Philipps University Marburg, Marburg, Germany
| | - Daniel Öhlund
- Department of Radiation Sciences, Umeå University, Umeå, Sweden.,Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Matthias Lauth
- Department of Medicine, Philipps University, Center for Tumour and Immune Biology, Marburg, Germany
| | - Malte Buchholz
- Department of Gastroenterology, Endocrinology, Metabolism and Infectiology, University Hospital Marburg, UKGM, Philipps University Marburg, Marburg, Germany
| | - Patrick Michl
- Department of Internal Medicine I, Martin, Luther University Halle-Wittenberg, Halle, Germany
| | - David A Tuveson
- Lustgarten Foundation Designated Pancreatic Cancer Research Lab at Cold Spring Harbor Laboratory, New York, USA
| | - Thomas M Gress
- Department of Gastroenterology, Endocrinology, Metabolism and Infectiology, University Hospital Marburg, UKGM, Philipps University Marburg, Marburg, Germany
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99974
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Sweeney MD, Zhao Z, Montagne A, Nelson AR, Zlokovic BV. Blood-Brain Barrier: From Physiology to Disease and Back. Physiol Rev 2019; 99:21-78. [PMID: 30280653 PMCID: PMC6335099 DOI: 10.1152/physrev.00050.2017] [Citation(s) in RCA: 1207] [Impact Index Per Article: 241.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 04/17/2018] [Accepted: 04/17/2018] [Indexed: 12/12/2022] Open
Abstract
The blood-brain barrier (BBB) prevents neurotoxic plasma components, blood cells, and pathogens from entering the brain. At the same time, the BBB regulates transport of molecules into and out of the central nervous system (CNS), which maintains tightly controlled chemical composition of the neuronal milieu that is required for proper neuronal functioning. In this review, we first examine molecular and cellular mechanisms underlying the establishment of the BBB. Then, we focus on BBB transport physiology, endothelial and pericyte transporters, and perivascular and paravascular transport. Next, we discuss rare human monogenic neurological disorders with the primary genetic defect in BBB-associated cells demonstrating the link between BBB breakdown and neurodegeneration. Then, we review the effects of genes underlying inheritance and/or increased susceptibility for Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease, and amyotrophic lateral sclerosis (ALS) on BBB in relation to other pathologies and neurological deficits. We next examine how BBB dysfunction relates to neurological deficits and other pathologies in the majority of sporadic AD, PD, and ALS cases, multiple sclerosis, other neurodegenerative disorders, and acute CNS disorders such as stroke, traumatic brain injury, spinal cord injury, and epilepsy. Lastly, we discuss BBB-based therapeutic opportunities. We conclude with lessons learned and future directions, with emphasis on technological advances to investigate the BBB functions in the living human brain, and at the molecular and cellular level, and address key unanswered questions.
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Affiliation(s)
- Melanie D Sweeney
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California , Los Angeles, California ; and Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California , Los Angeles, California
| | - Zhen Zhao
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California , Los Angeles, California ; and Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California , Los Angeles, California
| | - Axel Montagne
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California , Los Angeles, California ; and Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California , Los Angeles, California
| | - Amy R Nelson
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California , Los Angeles, California ; and Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California , Los Angeles, California
| | - Berislav V Zlokovic
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California , Los Angeles, California ; and Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California , Los Angeles, California
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99975
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Mustafin RN. The Relationship between Transposons and Transcription Factors in the Evolution of Eukaryotes. J EVOL BIOCHEM PHYS+ 2019. [DOI: 10.1134/s0022093019010022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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99976
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Abstract
The capsid protein is a promising target for the development of therapeutic anti-virus agents.
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Affiliation(s)
- Ding-Yi Fu
- State Key Laboratory of Supramolecular Structure and Materials
- Institute of Theoretical Chemistry
- Jilin University
- Changchun
- China
| | - Ya-Rong Xue
- State Key Laboratory of Supramolecular Structure and Materials
- Institute of Theoretical Chemistry
- Jilin University
- Changchun
- China
| | - Xianghui Yu
- National Engineering Laboratory for AIDS Vaccine
- School of Life Sciences
- Jilin University
- Changchun
- China
| | - Yuqing Wu
- State Key Laboratory of Supramolecular Structure and Materials
- Institute of Theoretical Chemistry
- Jilin University
- Changchun
- China
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99977
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李 婷, 李 典. 酵母流式细胞荧光分选流程. Bio Protoc 2019. [DOI: 10.21769/bioprotoc.1010332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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99978
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Fox ZR, Munsky B. The finite state projection based Fisher information matrix approach to estimate information and optimize single-cell experiments. PLoS Comput Biol 2019; 15:e1006365. [PMID: 30645589 PMCID: PMC6355035 DOI: 10.1371/journal.pcbi.1006365] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 01/31/2019] [Accepted: 12/02/2018] [Indexed: 12/31/2022] Open
Abstract
Modern optical imaging experiments not only measure single-cell and single-molecule dynamics with high precision, but they can also perturb the cellular environment in myriad controlled and novel settings. Techniques, such as single-molecule fluorescence in-situ hybridization, microfluidics, and optogenetics, have opened the door to a large number of potential experiments, which begs the question of how to choose the best possible experiment. The Fisher information matrix (FIM) estimates how well potential experiments will constrain model parameters and can be used to design optimal experiments. Here, we introduce the finite state projection (FSP) based FIM, which uses the formalism of the chemical master equation to derive and compute the FIM. The FSP-FIM makes no assumptions about the distribution shapes of single-cell data, and it does not require precise measurements of higher order moments of such distributions. We validate the FSP-FIM against well-known Fisher information results for the simple case of constitutive gene expression. We then use numerical simulations to demonstrate the use of the FSP-FIM to optimize the timing of single-cell experiments with more complex, non-Gaussian fluctuations. We validate optimal simulated experiments determined using the FSP-FIM with Monte-Carlo approaches and contrast these to experiment designs chosen by traditional analyses that assume Gaussian fluctuations or use the central limit theorem. By systematically designing experiments to use all of the measurable fluctuations, our method enables a key step to improve co-design of experiments and quantitative models.
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Affiliation(s)
- Zachary R Fox
- Keck Scholars, School of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA
| | - Brian Munsky
- Keck Scholars, School of Biomedical Engineering, Colorado State University, Fort Collins, CO, USA
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO, USA
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99979
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Mahan VL. Neurointegrity and neurophysiology: astrocyte, glutamate, and carbon monoxide interactions. Med Gas Res 2019; 9:24-45. [PMID: 30950417 PMCID: PMC6463446 DOI: 10.4103/2045-9912.254639] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 02/15/2019] [Indexed: 12/27/2022] Open
Abstract
Astrocyte contributions to brain function and prevention of neuropathologies are as extensive as that of neurons. Astroglial regulation of glutamate, a primary neurotransmitter, is through uptake, release through vesicular and non-vesicular pathways, and catabolism to intermediates. Homeostasis by astrocytes is considered to be of primary importance in determining normal central nervous system health and central nervous system physiology - glutamate is central to dynamic physiologic changes and central nervous system stability. Gasotransmitters may affect diverse glutamate interactions positively or negatively. The effect of carbon monoxide, an intrinsic central nervous system gasotransmitter, in the complex astrocyte homeostasis of glutamate may offer insights to normal brain development, protection, and its use as a neuromodulator and neurotherapeutic. In this article, we will review the effects of carbon monoxide on astrocyte homeostasis of glutamate.
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Affiliation(s)
- Vicki L. Mahan
- Division of Pediatric Cardiothoracic Surgery in the Department of Surgery, St. Christopher's Hospital for Children/Drexel University College of Medicine, Philadelphia, PA, USA
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99980
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Di Palma F, Daino GL, Ramaswamy VK, Corona A, Frau A, Fanunza E, Vargiu AV, Tramontano E, Ruggerone P. Relevance of Ebola virus VP35 homo-dimerization on the type I interferon cascade inhibition. Antivir Chem Chemother 2019; 27:2040206619889220. [PMID: 31744306 PMCID: PMC6883671 DOI: 10.1177/2040206619889220] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 08/13/2019] [Indexed: 01/10/2023] Open
Abstract
Ebola virus high lethality relies on its ability to efficiently bypass the host innate antiviral response, which senses the viral dsRNA through the RIG-I receptor and induces type I interferon α/β production. In the bypassing action, the Ebola virus protein VP35 plays a pivotal role at multiple levels of the RIG-I cascade, masking the viral 5′-triphosphorylated dsRNA from RIG-I, and interacting with other cascade components. The VP35 type I interferon inhibition is exerted by the C-terminal domain, while the N-terminal domain, containing a coiled-coil region, is primarily required for oligomerization. However, mutations at key VP35 residues L90/93/107A (VP35-3m) in the coiled-coil region were reported to affect oligomerization and reduce type I interferon antagonism, indicating a possible but unclear role of homo-oligomerization on VP35 interaction with the RIG-I pathway components. In this work, we investigated the VP35 dimerization thermodynamics and its contribution to type I interferon antagonism by computational and biological methods. Focusing on the coiled-coil region, we combined coarse-grained and all-atom simulations on wild type VP35 and VP35-3m homo-dimerization. According to our results, wild type VP35 coiled-coil is able to self-assemble into dimers, while VP35-3m coiled-coil shows poor propensity to even dimerize. Free-energy calculations confirmed the key role of L90, L93 and L107 in stabilizing the coiled-coil homo-dimeric structure. In vitro type I interferon antagonism studies, using full-length wild type VP35 and VP35-3m, revealed that VP35 homo-dimerization is an essential preliminary step for dsRNA binding, which appears to be the main factor of the VP35 RIG-I cascade inhibition, while it is not essential to block the other steps.
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Affiliation(s)
- Francesco Di Palma
- Department of Physics, University of Cagliari, Cittadella
Universitaria, Monserrato, Italy
| | - Gian Luca Daino
- Department of Life and Environmental Sciences, University of
Cagliari, Cittadella Universitaria, Monserrato, Italy
| | | | - Angela Corona
- Department of Life and Environmental Sciences, University of
Cagliari, Cittadella Universitaria, Monserrato, Italy
| | - Aldo Frau
- Department of Life and Environmental Sciences, University of
Cagliari, Cittadella Universitaria, Monserrato, Italy
| | - Elisa Fanunza
- Department of Life and Environmental Sciences, University of
Cagliari, Cittadella Universitaria, Monserrato, Italy
| | - Attilio V Vargiu
- Department of Physics, University of Cagliari, Cittadella
Universitaria, Monserrato, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of
Cagliari, Cittadella Universitaria, Monserrato, Italy
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale
delle Ricerche (CNR), Monserrato, Italy
| | - Paolo Ruggerone
- Department of Physics, University of Cagliari, Cittadella
Universitaria, Monserrato, Italy
- Istituto Officina dei Materiali (CNR-IOM), UOS Cagliari SLACS,
Monserrato, Italy
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99981
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Cox OF, Huber PW. Developing Practical Therapeutic Strategies that Target Protein SUMOylation. Curr Drug Targets 2019; 20:960-969. [PMID: 30362419 PMCID: PMC6700758 DOI: 10.2174/1389450119666181026151802] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/19/2018] [Accepted: 10/19/2018] [Indexed: 01/02/2023]
Abstract
Post-translational modification by small ubiquitin-like modifier (SUMO) has emerged as a global mechanism for the control and integration of a wide variety of biological processes through the regulation of protein activity, stability and intracellular localization. As SUMOylation is examined in greater detail, it has become clear that the process is at the root of several pathologies including heart, endocrine, and inflammatory disease, and various types of cancer. Moreover, it is certain that perturbation of this process, either globally or of a specific protein, accounts for many instances of congenital birth defects. In order to be successful, practical strategies to ameliorate conditions due to disruptions in this post-translational modification will need to consider the multiple components of the SUMOylation machinery and the extraordinary number of proteins that undergo this modification.
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Affiliation(s)
- Olivia F. Cox
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, Center for Stem Cells and Regenerative Medicine, University of Notre Dame Notre Dame, Indiana 46556, U.S.A
| | - Paul W. Huber
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, Center for Stem Cells and Regenerative Medicine, University of Notre Dame Notre Dame, Indiana 46556, U.S.A
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99982
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Heyder N, Kleinau G, Szczepek M, Kwiatkowski D, Speck D, Soletto L, Cerdá-Reverter JM, Krude H, Kühnen P, Biebermann H, Scheerer P. Signal Transduction and Pathogenic Modifications at the Melanocortin-4 Receptor: A Structural Perspective. Front Endocrinol (Lausanne) 2019; 10:515. [PMID: 31417496 PMCID: PMC6685040 DOI: 10.3389/fendo.2019.00515] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/15/2019] [Indexed: 12/19/2022] Open
Abstract
The melanocortin-4 receptor (MC4R) can be endogenously activated by binding of melanocyte-stimulating hormones (MSH), which mediates anorexigenic effects. In contrast, the agouti-related peptide (AgRP) acts as an endogenous inverse agonist and suppresses ligand-independent basal signaling activity (orexigenic effects). Binding of ligands to MC4R leads to the activation of different G-protein subtypes or arrestin and concomitant signaling pathways. This receptor is a key protein in the hypothalamic regulation of food intake and energy expenditure and naturally-occurring inactivating MC4R variants are the most frequent cause of monogenic obesity. In general, obesity is a growing problem on a global scale and is of social, medical, and economic relevance. A significant goal is to develop optimized pharmacological tools targeting MC4R without adverse effects. To date, this has not been achieved because of inter alia non-selective ligands across the five functionally different MCR subtypes (MC1-5R). This motivates further investigation of (i) the three-dimensional MC4R structure, (ii) binding mechanisms of various ligands, and (iii) the molecular transfer process of signal transduction, with the aim of understanding how structural features are linked with functional-physiological aspects. Unfortunately, experimentally elucidated structural information is not yet available for the MC receptors, a group of class A G-protein coupled receptors (GPCRs). We, therefore, generated MC4R homology models and complexes with interacting partners to describe approximate structural properties associated with signaling mechanisms. In addition, molecular insights from pathogenic mutations were incorporated to discriminate more precisely their individual malfunction of the signal transfer mechanism.
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Affiliation(s)
- Nicolas Heyder
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gunnar Kleinau
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- *Correspondence: Gunnar Kleinau
| | - Michal Szczepek
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dennis Kwiatkowski
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - David Speck
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Lucia Soletto
- Departamento de Fisiología de Peces y Biotecnología, Consejo Superior de Investigaciones Científicas, Instituto de Acuicultura Torre de la Sal, Ribera de Cabanes, Spain
| | - José Miguel Cerdá-Reverter
- Departamento de Fisiología de Peces y Biotecnología, Consejo Superior de Investigaciones Científicas, Instituto de Acuicultura Torre de la Sal, Ribera de Cabanes, Spain
| | - Heiko Krude
- Institute of Experimental Pediatric Endocrinology, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Peter Kühnen
- Institute of Experimental Pediatric Endocrinology, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Heike Biebermann
- Institute of Experimental Pediatric Endocrinology, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Patrick Scheerer
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Berlin Institute of Health, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Patrick Scheerer
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99983
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Fraser C, Ryan J, Sarosiek K. BH3 Profiling: A Functional Assay to Measure Apoptotic Priming and Dependencies. Methods Mol Biol 2019; 1877:61-76. [PMID: 30535998 DOI: 10.1007/978-1-4939-8861-7_4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Apoptosis (programmed cell death) is activated by a wide variety of cellular stresses or insults and is vital for proper mammalian development as well as the maintenance of organismal homeostasis. The apoptosis pathway is also engaged by many common types of anticancer therapies and ionizing radiation, which contributes to the regressions of tumors or the toxic side effects of treatment. Due to the importance of maintaining healthy cell survival or the efficient clearance of cancer cells, the BH3 profiling assay was developed to functionally measure the state of the apoptosis pathway in any given cells. This assay involves the exposure of cellular mitochondria, where the BCL-2 family of proteins resides and controls the commitment to apoptosis, to proapoptotic BH3 peptides that mimic the activity of endogenous proapoptotic proteins. By using either activator or sensitizer peptides, the level of mitochondrial apoptotic priming (proximity to the threshold at which a cell commits to cell death) or dependence on prosurvival BCL-2 family proteins can be determined. Described here are two methods of BH3 profiling that can enable a user to make these functional measurements, which can be useful for predicting cellular responses to proapoptotic stressors or therapeutics (BH3 mimetics) that inhibit the activity of prosurvival proteins.
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Affiliation(s)
- Cameron Fraser
- John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Jeremy Ryan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kristopher Sarosiek
- John B. Little Center for Radiation Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA. .,Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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99984
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Lin X, Yang Y, Li S, Song Y, Ma G, Su Z, Zhang S. Unique stabilizing mechanism provided by biocompatible choline-based ionic liquids for inhibiting dissociation of inactivated foot-and-mouth disease virus particles. RSC Adv 2019; 9:13933-13939. [PMID: 35519561 PMCID: PMC9063997 DOI: 10.1039/c9ra02722j] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 04/26/2019] [Indexed: 11/21/2022] Open
Abstract
Choline-based ionic liquids provide a unique stabilizing mechanism for inhibiting the dissociation of inactivated foot-and-mouth disease virus particles.
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Affiliation(s)
- Xuan Lin
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- PR China
| | - Yanli Yang
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- PR China
| | - Shuai Li
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- PR China
| | - Yanmin Song
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- PR China
| | - Guanghui Ma
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- PR China
| | - Zhiguo Su
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- PR China
| | - Songping Zhang
- State Key Laboratory of Biochemical Engineering
- Institute of Process Engineering
- Chinese Academy of Sciences
- Beijing 100190
- PR China
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99985
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Li CC, Hung CL, Yeh PS, Li CE, Chiang YW. Doubly spin-labeled nanodiscs to improve structural determination of membrane proteins by ESR. RSC Adv 2019; 9:9014-9021. [PMID: 35517660 PMCID: PMC9062051 DOI: 10.1039/c9ra00896a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 03/14/2019] [Indexed: 11/30/2022] Open
Abstract
Pulsed dipolar spectroscopy (PDS) is a powerful tool to explore conformational changes of membrane proteins (MPs). However, the MPs suffer from relatively weak dipolar signals due to their complex nature in membrane environments, which consequently reduces the interspin distance resolution obtainable by PDS. Here we report the use of nanodiscs (NDs) to improve the distance resolution. Two genetically engineered membrane scaffold protein mutants are introduced, each of which is shown to form double-labeled ND efficiently and with high homogeneity. The resultant interspin distance distribution is featured by a small distribution width, suggesting high resolution. When PDS is performed on a binary mixture of the double-labeled ND devoid of MPs and the un-labeled ND with incorporated double-labeled MPs, the overall amplitude of dipolar signals is increased, leading to a critical enhancement of the distance resolution. A theoretical foundation is provided to validate the analysis. With this approach, the determination of MP structures can be studied at high resolution in NDs. Spin-labeled nanodiscs improve DEER distance measurement of membrane proteins.![]()
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Affiliation(s)
- Chieh-Chin Li
- Department of Chemistry
- Frontier Research Center on Fundamental and Applied Sciences of Matters
- National Tsing Hua University
- Hsinchu 30013
- Taiwan
| | - Chien-Lun Hung
- Department of Chemistry
- Frontier Research Center on Fundamental and Applied Sciences of Matters
- National Tsing Hua University
- Hsinchu 30013
- Taiwan
| | - Pei-Shan Yeh
- Department of Chemistry
- Frontier Research Center on Fundamental and Applied Sciences of Matters
- National Tsing Hua University
- Hsinchu 30013
- Taiwan
| | - Chi-En Li
- Department of Chemistry
- Frontier Research Center on Fundamental and Applied Sciences of Matters
- National Tsing Hua University
- Hsinchu 30013
- Taiwan
| | - Yun-Wei Chiang
- Department of Chemistry
- Frontier Research Center on Fundamental and Applied Sciences of Matters
- National Tsing Hua University
- Hsinchu 30013
- Taiwan
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99986
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Viola TW, Wearick-Silva LE, Creutzberg KC, Kestering-Ferreira É, Orso R, Centeno-Silva A, Albrechet-Souza L, Marshall PR, Li X, Bredy TW, Riva MA, Grassi-Oliveira R. Postnatal impoverished housing impairs adolescent risk-assessment and increases risk-taking: A sex-specific effect associated with histone epigenetic regulation of Crfr1 in the medial prefrontal cortex. Psychoneuroendocrinology 2019; 99:8-19. [PMID: 30172072 DOI: 10.1016/j.psyneuen.2018.08.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/21/2018] [Accepted: 08/24/2018] [Indexed: 01/01/2023]
Abstract
While increasing evidence posits poor decision-making as a central feature of mental disorders, very few studies investigated the effects of early-life stress (ELS) on specific components of reward-related choice behaviors. Risk-taking (RT) involves the exposure to some danger, or negative consequences, in order to achieve a goal-directed behavior. Such behaviors are likely to be preceded by risk-assessment (RA), which is a dynamic cognitive process involving the acquisition of information in potentially dangerous situations. Here, we investigated the effects of being raised in impoverished housing conditions during early life (P2-P9) on RT, RA and dopaminergic and corticotrophinergic gene expression of adolescent male and female mice. Phenotypes were assessed by two protocols: the elevated plus-maze (EPM) and the predator-odor risk-taking (PORT). We found decreased RA in mice exposed to impoverished housing in the absence of a reward (EPM), with a more pronounced effect among females. Moreover, when exposed to a predatory olfactory cue, increased RT was observed in these females in a reward-related task (PORT), as well as decreased HPA axis responsivity. This sex-specific behavioral effect was associated with increased Crfr1 mRNA expression in the medial prefrontal cortex (mPFC) and higher levels of the histone mark H3R2me2s, a histone modification known to be involved in transcriptional activation, within the promoter of the Crfr1 gene. These findings revealed that ELS exposure can impair the acquisition of environmental information in dangerous situations and increase RT in reward-related scenarios among females, with an important role regarding epigenetic regulation of the Crfr1 gene.
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Affiliation(s)
- Thiago Wendt Viola
- Pontifical Catholic University of Rio Grande do Sul (PUCRS), Brain Institute (InsCer), Developmental Cognitive Neuroscience Lab, Porto Alegre, RS, Brazil
| | - Luis Eduardo Wearick-Silva
- Pontifical Catholic University of Rio Grande do Sul (PUCRS), Brain Institute (InsCer), Developmental Cognitive Neuroscience Lab, Porto Alegre, RS, Brazil
| | - Kerstin C Creutzberg
- Pontifical Catholic University of Rio Grande do Sul (PUCRS), Brain Institute (InsCer), Developmental Cognitive Neuroscience Lab, Porto Alegre, RS, Brazil
| | - Érika Kestering-Ferreira
- Pontifical Catholic University of Rio Grande do Sul (PUCRS), Brain Institute (InsCer), Developmental Cognitive Neuroscience Lab, Porto Alegre, RS, Brazil
| | - Rodrigo Orso
- Pontifical Catholic University of Rio Grande do Sul (PUCRS), Brain Institute (InsCer), Developmental Cognitive Neuroscience Lab, Porto Alegre, RS, Brazil
| | - Anderson Centeno-Silva
- Pontifical Catholic University of Rio Grande do Sul (PUCRS), Brain Institute (InsCer), Developmental Cognitive Neuroscience Lab, Porto Alegre, RS, Brazil
| | - Lucas Albrechet-Souza
- Louisiana State University, Health Sciences Center, Department of Physiology, New Orleans, United States
| | - Paul R Marshall
- University of Queensland, Queensland Brain Institute, Brisbane, Australia
| | - Xiang Li
- University of Queensland, Queensland Brain Institute, Brisbane, Australia
| | - Timothy W Bredy
- University of Queensland, Queensland Brain Institute, Brisbane, Australia
| | - Marco A Riva
- Università degli Studi di Milano, Department of Pharmacological and Biomolecular Sciences, Milan, Italy
| | - Rodrigo Grassi-Oliveira
- Pontifical Catholic University of Rio Grande do Sul (PUCRS), Brain Institute (InsCer), Developmental Cognitive Neuroscience Lab, Porto Alegre, RS, Brazil.
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99987
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Schüßler A, Herwig S, Kleinschmidt JH. Kinetics of Insertion and Folding of Outer Membrane Proteins by Gel Electrophoresis. Methods Mol Biol 2019; 2003:145-162. [PMID: 31218617 DOI: 10.1007/978-1-4939-9512-7_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
To examine the mechanisms of folding and insertion of TMPs into membranes, kinetic studies are instrumental, for example, for the analysis of folding steps and involved intermediates or for the determination of activation energies. For many β-barrel transmembrane proteins (β-TMPs) it has been shown that the folded, functional form can be separated from the unfolded form by a simple electrophoretic mobility assay. The only requirements for a separation by SDS-polyacrylamide gel electrophoresis (SDS-PAGE) are that the folded form is sufficiently stable and that the samples are not heat-denatured before the electrophoresis is performed. Many folded β-TMPs resist the treatment with SDS at room temperature and are stable against forces during electrophoresis. On the other side, SDS also binds to unfolded forms of β-TMPs and prevents their folding into β-barrel structure. These observations have been used to develop a simple assay to monitor the kinetics of β-barrel tertiary structure formation in a membrane environment by electrophoresis. A folding reaction of a β-TMP is initiated by dilution of the denaturant in the presence of preformed lipid bilayers, proteoliposomes or membrane vesicles. At selected times, samples are taken from the reaction. In these samples, folding is stopped by addition of SDS. At the end of the entire folding reaction, all samples are analyzed by SDS-PAGE and the fractions of folded β-TMP that they contain are determined by densitometry.An advantage of this kinetic assay is that it not only allows a direct determination of fractions of folded and unfolded forms at a selected time during folding of the β-TMP into a membrane, but also facilitates the determination of the impact of folding factors (e.g., molecular chaperones) or folding machinery that most often have a different molecular mass and electrophoretic mobility. The assay has been very useful to examine how folding and insertion is affected by the structure of the phospholipids in the lipid bilayer and how folding machinery compensates for the presence of membrane lipids that retard folding and insertion of β-TMPs.
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Affiliation(s)
- Andre Schüßler
- Department of Biophysics, Institute of Biology, FB10 and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Kassel, Germany
| | - Sascha Herwig
- Department of Biophysics, Institute of Biology, FB10 and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Kassel, Germany
| | - Jörg H Kleinschmidt
- Department of Biophysics, Institute of Biology, FB10 and Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), University of Kassel, Kassel, Germany.
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99988
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SubCellBarCode: Proteome-wide Mapping of Protein Localization and Relocalization. Mol Cell 2019; 73:166-182.e7. [DOI: 10.1016/j.molcel.2018.11.035] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 09/28/2018] [Accepted: 11/27/2018] [Indexed: 11/22/2022]
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99989
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Abstract
Histone deacetylases (HDACs) modulate chromatin structure by removing acetyl groups from histones. Upon DNA double-strand breaks (DSBs), deacetylation of H3K56 and H4K16 by HDACs occurs immediately at break sites, and is crucial for DSB repair. Here we describe two assays that examine defective DSB repair caused by HDAC inhibition in primary cortical neurons: single-cell gel electrophoresis to assay DNA integrity (the comet assay) and western blot analysis for γH2AX, a phosphorylated histone variant associated with DSBs.
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Affiliation(s)
- Ping-Chieh Pao
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jay Penney
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA.
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99990
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Saltzberg D, Greenberg CH, Viswanath S, Chemmama I, Webb B, Pellarin R, Echeverria I, Sali A. Modeling Biological Complexes Using Integrative Modeling Platform. Methods Mol Biol 2019; 2022:353-377. [PMID: 31396911 DOI: 10.1007/978-1-4939-9608-7_15] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Integrative structure modeling provides 3D models of macromolecular systems that are based on information from multiple types of experiments, physical principles, statistical inferences, and prior structural models. Here, we provide a hands-on realistic example of integrative structure modeling of the quaternary structure of the actin, tropomyosin, and gelsolin protein assembly based on electron microscopy, solution X-ray scattering, and chemical crosslinking data for the complex as well as excluded volume, sequence connectivity, and rigid atomic X-ray structures of the individual subunits. We follow the general four-stage process for integrative modeling, including gathering the input information, converting the input information into a representation of the system and a scoring function, sampling alternative model configurations guided by the scoring function, and analyzing the results. The computational aspects of this approach are implemented in our open-source Integrative Modeling Platform (IMP), a comprehensive and extensible software package for integrative modeling ( https://integrativemodeling.org ). In particular, we rely on the Python Modeling Interface (PMI) module of IMP that provides facile mixing and matching of macromolecular representations, restraints based on different types of information, sampling algorithms, and analysis including validations of the input data and output models. Finally, we also outline how to deposit an integrative structure and corresponding experimental data into PDB-Dev, the nascent worldwide Protein Data Bank (wwPDB) resource for archiving and disseminating integrative structures ( https://pdb-dev.wwpdb.org ). The example application provides a starting point for a user interested in using IMP for integrative modeling of other biomolecular systems.
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Affiliation(s)
- Daniel Saltzberg
- California Institute for Quantitative Biosciences, University of California, San Francisco, CA, USA
| | - Charles H Greenberg
- California Institute for Quantitative Biosciences, University of California, San Francisco, CA, USA
| | - Shruthi Viswanath
- California Institute for Quantitative Biosciences, University of California, San Francisco, CA, USA
| | - Ilan Chemmama
- California Institute for Quantitative Biosciences, University of California, San Francisco, CA, USA
| | - Ben Webb
- California Institute for Quantitative Biosciences, University of California, San Francisco, CA, USA
| | - Riccardo Pellarin
- Structural Bioinformatics Unit, Institut Pasteur, CNRS UMR 3528, Paris, France
| | - Ignacia Echeverria
- California Institute for Quantitative Biosciences, University of California, San Francisco, CA, USA
| | - Andrej Sali
- California Institute for Quantitative Biosciences, University of California, San Francisco, CA, USA.
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99991
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Chen H, Sun H, Zhang S, Yan W, Li Q, Guan A, Xiang J, Liu M, Tang Y. Monitoring autophagy in live cells with a fluorescent light-up probe for G-quadruplex structures. Chem Commun (Camb) 2019; 55:5060-5063. [DOI: 10.1039/c9cc01263j] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Monitoring autophagy in live cells with a fluorescent light-up probe for G-quadruplex structures.
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Affiliation(s)
- Hongbo Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
- China
| | - Hongxia Sun
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
- China
| | - Suge Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
- China
| | - Wenpeng Yan
- Technical Institute of Physics and Chemistry
- Chinese Academy of Sciences
- Beijing
- China
| | - Qian Li
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
- China
| | - Aijiao Guan
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
- China
| | - Junfeng Xiang
- Center for Physiochemical Analysis & Measurement
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
- China
| | - Meirong Liu
- Center for Physiochemical Analysis & Measurement
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
- China
| | - Yalin Tang
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species
- Institute of Chemistry Chinese Academy of Sciences
- Beijing
- China
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99992
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Ilicic M, Zakar T, Paul JW. Epigenetic regulation of progesterone receptors and the onset of labour. Reprod Fertil Dev 2019; 31:1035-1048. [DOI: 10.1071/rd18392] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/29/2019] [Indexed: 01/09/2023] Open
Abstract
Progesterone plays a crucial role in maintaining pregnancy by promoting myometrial quiescence. The withdrawal of progesterone action signals the end of pregnancy and, in most mammalian species, this is achieved by a rapid fall in progesterone concentrations. However, in humans circulating progesterone concentrations remain high up to and during labour. Efforts to understand this phenomenon led to the ‘functional progesterone withdrawal’ hypothesis, whereby the pro-gestation actions of progesterone are withdrawn, despite circulating concentrations remaining elevated. The exact mechanism of functional progesterone withdrawal is still unclear and in recent years has been the focus of intense research. Emerging evidence now indicates that epigenetic regulation of progesterone receptor isoform expression may be the crucial mechanism by which functional progesterone withdrawal is achieved, effectively precipitating human labour despite high concentrations of circulating progesterone. This review examines current evidence that epigenetic mechanisms play a role in determining whether the pro-gestation or pro-contractile isoform of the progesterone receptor is expressed in the pregnant human uterus. We explore the mechanism by which these epigenetic modifications are achieved and, importantly, how these underlying epigenetic mechanisms are influenced by known regulators of uterine physiology, such as prostaglandins and oestrogens, in order to phenotypically transform the pregnant uterus and initiate labour.
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99993
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De la Rosa C, Covarrubias AA, Reyes JL. A dicistronic precursor encoding miR398 and the legume-specific miR2119 coregulates CSD1 and ADH1 mRNAs in response to water deficit. PLANT, CELL & ENVIRONMENT 2019; 42:133-144. [PMID: 29626361 DOI: 10.1111/pce.13209] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/23/2018] [Accepted: 03/26/2018] [Indexed: 05/07/2023]
Abstract
Plant microRNAs are commonly encoded in transcripts containing a single microRNA precursor. Processing by DICER-LIKE 1 and associated factors results in the production of a small RNA, followed by its incorporation into an AGO-containing protein complex to guide silencing of an mRNA possessing a complementary target sequence. Certain microRNA loci contain more than one precursor stem-loop structure, thus encoding more than one microRNA in the same transcript. Here, we describe a unique case where the evolutionary conserved miR398a is encoded in the same transcript as the legume-specific miR2119. The dicistronic arrangement found in common bean was also observed in other legumes. In Phaseolus vulgaris, mature miR398 and miR2119 are repressed in response to water deficit, and we demonstrate that both are functional as they target the mRNAs for CSD1 and ADH1, respectively. Our results indicate that the repression of miR398 and miR2119 leads to coordinated up-regulation of CSD1 and ADH1 mRNAs in response to water deficit in common bean and possibly in other legumes. Furthermore, we show that miRNA directed CSD1 and ADH1 mRNAs up-regulation also occurs when common bean plants are exposed to flooding, suggesting that plant redox status and fermentation metabolism must be closely coordinated under different adverse conditions.
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Affiliation(s)
- Carlos De la Rosa
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos, 62210, Mexico
| | - Alejandra Alicia Covarrubias
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos, 62210, Mexico
| | - José Luis Reyes
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Cuernavaca, Morelos, 62210, Mexico
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99994
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Paleček JJ, Vondrová L, Zábrady K, Otočka J. Multicomponent Yeast Two-Hybrid System: Applications to Study Protein-Protein Interactions in SMC Complexes. Methods Mol Biol 2019; 2004:79-90. [PMID: 31147911 DOI: 10.1007/978-1-4939-9520-2_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Analysis of protein-protein interactions (PPI) is key for the understanding of most protein assemblies including structural maintenance of chromosomes (SMC) complexes. SMC complexes are composed of SMC proteins, kleisin, and kleisin-interacting subunits. These subunits interact in specific ways to constitute and regulate the closed structure of the complexes. Specifically, kleisin molecules bridge the SMC dimers and the kleisin-interacting subunits modulate stability of the bridge. Here we describe a multicomponent version of a yeast two-hybrid (Y2H) method and its application for analysis of the bridging role of the Nse4 kleisin in the SMC5/6 complex. Using this technique, we also show a stabilizing effect of KITE (kleisin-interacting tandem winged-helix element) proteins on SMC5/6.
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Affiliation(s)
- Jan Josef Paleček
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic. .,Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
| | - Lucie Vondrová
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Kateřina Zábrady
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
| | - Jakub Otočka
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
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99995
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Xu C, Zhou J, Wang Y, Wang A, Su L, Liu S, Kang X. Inhibition of malignant human bladder cancer phenotypes through the down-regulation of the long non-coding RNA SNHG7. J Cancer 2019; 10:539-546. [PMID: 30719150 PMCID: PMC6360294 DOI: 10.7150/jca.25507] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 10/16/2018] [Indexed: 12/29/2022] Open
Abstract
There is abundant evidence that long non-coding RNAs play important roles in the development of tumors. In the present study, our main aim was to explore the relationship between lncRNA SNHG7 and human bladder cancer cells, thus finding a novel target for bladder cancer therapy and diagnosis. Expression of lncRNA SNHG7 was evaluated using real-time quantitative polymerase chain reaction in bladder tumor tissues and paired adjacent normal tissues from 72 patients diagnosed with urothelial bladder carcinoma. We analyzed the differences in expression according to grading and staging. Human bladder cancer cell lines UMUC, 5637, T24 and SW780 were transiently transfected with lncRNA SNHG7-specific siRNA and negative control siRNA. The changes in malignant phenotypes in transfected bladder cancer cells were determined using CCK-8 assay, wound-healing assay and ELISA. We found that lncRNA SNHG7 was correlated with human bladder cancer. lncRNA SNHG7 was overexpressed in bladder cancer tissues compared to paired normal tissues and expression of SNHG7 was higher in high-grade than low-grade tumors. The malignant phenotypes were significantly inhibited when we inhibited expression of lncRNA SNHG7 in several bladder cell lines. SNHG7 plays an oncogenic role in human bladder cancer and may be a potential novel therapeutic target for treating bladder cancer.
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Affiliation(s)
- Congjie Xu
- Hainan General Hospital, Haikou 570311, China
| | | | - Yang Wang
- Hainan General Hospital, Haikou 570311, China
| | - Anfang Wang
- Hainan General Hospital, Haikou 570311, China
| | - Liangju Su
- Hainan General Hospital, Haikou 570311, China
| | - Shuan Liu
- Hainan General Hospital, Haikou 570311, China
| | - Xinli Kang
- Hainan General Hospital, Haikou 570311, China
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99996
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Wilkinson RA, Martin C, Nemudryi AA, Wiedenheft B. CRISPR RNA-guided autonomous delivery of Cas9. Nat Struct Mol Biol 2019; 26:14-24. [PMID: 30598555 PMCID: PMC7703833 DOI: 10.1038/s41594-018-0173-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/13/2018] [Indexed: 02/06/2023]
Abstract
Cas9 is an endonuclease that can be programed to autonomously deliver diverse effectors to specified genetic addresses. High-resolution structures of this protein and its associated CRISPR RNA guide explain the molecular mechanisms of CRISPR-RNA-guided DNA recognition and provide a molecular blueprint that has facilitated structure-guided functional remodeling. Here we retrace events that led from early efforts to understand the central role of Cas9 in CRISPR-mediated adaptive immunity to contemporary efforts aimed at developing and deploying this enzyme for programmable genetic editing.
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Affiliation(s)
- Royce A Wilkinson
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
| | - Coleman Martin
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
| | - Artem A Nemudryi
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA
| | - Blake Wiedenheft
- Department of Microbiology and Immunology, Montana State University, Bozeman, Montana, USA.
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99997
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Mockly S, Seitz H. Inconsistencies and Limitations of Current MicroRNA Target Identification Methods. Methods Mol Biol 2019; 1970:291-314. [PMID: 30963499 DOI: 10.1007/978-1-4939-9207-2_16] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
MicroRNAs and their Argonaute protein partners constitute the RISC complex, which can repress specific target mRNAs. The identification of microRNA targets is of central importance, and various experimental and computational methods have been developed over the last 15 years. Most experimental methods are based on the assumption that mRNAs which interact physically with the RISC complex constitute regulatory targets and, similarly, some computational methods only aim at predicting physical interactors for RISC. Besides specific limitations, which we discuss for each method, the mere concept of assuming a functional role for every detected molecular event is likely to identify many deceptive interactions (i.e., interactions that really exist at the molecular scale, but without controlling any biological function at the macroscopic scale).In order to select biologically important interactions, some computational tools interrogate the phylogenetic conservation of microRNA/mRNA interactions, thus theoretically selecting only biologically relevant targets. Yet even comparative genomics can yield false positives.Conceptual and technical limitations for all these techniques tend to be overlooked by the scientific community. This review sums them up, emphasizing on the implications of these issues on our understanding of microRNA biology.
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Affiliation(s)
- Sophie Mockly
- IGH (CNRS and University of Montpellier), Montpellier, France
| | - Hervé Seitz
- IGH (CNRS and University of Montpellier), Montpellier, France.
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99998
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Abstract
The transport of specific molecules across lipid membranes is an essential function of all living organisms. The processes are usually mediated by specific transporters. One of the largest transporter families is the ATP-binding cassette (ABC) family. More than 40 ABC transporters have been identified in human, which are divided into 7 subfamilies (ABCA to ABCG) based on their gene structure, amino acid sequence, domain organization, and phylogenetic analysis. Of them, at least 11 ABC transporters including P-glycoprotein (P-GP/ABCB1), multidrug resistance-associated proteins (MRPs/ABCCs), and breast cancer resistance protein (BCRP/ABCG2) are involved in multidrug resistance (MDR) development. These ABC transporters are expressed in various tissues such as the liver, intestine, kidney, and brain, playing important roles in absorption, distribution, and excretion of drugs. Some ABC transporters are also involved in diverse cellular processes such as maintenance of osmotic homeostasis, antigen processing, cell division, immunity, cholesterol, and lipid trafficking. Several human diseases such as cystic fibrosis, sitosterolemia, Tangier disease, intrahepatic cholestasis, and retinal degeneration are associated with mutations in corresponding transporters. This chapter will describe function and expression of several ABC transporters (such as P-GP, BCRP, and MRPs), their substrates and inhibitors, as well as their clinical significance.
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Affiliation(s)
- Xiaodong Liu
- China Pharmaceutical University, Nanjing, China.
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99999
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Gerstman BS, Chapagain PP, Gc J, Steckmann T. Molecular Dynamics Simulations of Conformational Conversions in Transformer Proteins. Methods Mol Biol 2019; 1958:297-311. [PMID: 30945225 DOI: 10.1007/978-1-4939-9161-7_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A relatively recently discovered class of proteins known as transformer proteins undergo large-scale conformational conversions that change their supersecondary structure. These structural transformations lead to different configurations that perform different functions. We describe computational methods using molecular dynamics simulations that allow the determination of the specific amino acids that facilitate the conformational transformations. These investigations provide guidance on the location and type of amino acid mutations that can either enhance or inhibit the structural transitions that allow transformer proteins to perform multiple functions.
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Affiliation(s)
- Bernard S Gerstman
- Department of Physics, Florida International University, Miami, FL, USA.
| | - Prem P Chapagain
- Department of Physics, Florida International University, Miami, FL, USA
| | - Jeevan Gc
- Department of Physics, Florida International University, Miami, FL, USA
| | - Timothy Steckmann
- Department of Physics, Florida International University, Miami, FL, USA
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100000
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Mo ZQ, Han R, Wang JL, Ni LY, Su YL, Lai XL, He ZC, Chen HP, Li YW, Sun HY, Luo XC, Dan XM. Characterization and functional analysis of grouper (Epinephelus coioides) MEK1 and MEK2. FISH & SHELLFISH IMMUNOLOGY 2019; 84:1090-1097. [PMID: 30419398 DOI: 10.1016/j.fsi.2018.11.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/02/2018] [Accepted: 11/05/2018] [Indexed: 06/09/2023]
Abstract
MEK dual-specificity protein kinases are a group of mitogen-activated protein kinase kinases, which act as an integration point by transferring extracellular signals to the nucleus. To investigate the function of MEK in teleost fish, we cloned MEK1 and MEK2 cDNA sequences from the orange-spotted grouper (Epinephelus coioides). EcMEK1 and EcMEK2 shared 80% amino acid identity with each other. EcMEK1 had 89-99% amino acid identity with teleosts or mammals, whereas EcMEK2 shared 85-97% amino acid identity. The exon structures of the grouper MEK1/2 genes were conserved with zebrafish and human MEK1/2. Tissue distribution analysis showed that EcMEK1 and EcMEK2 had a similar expression pattern in grouper tissues and was mainly transcribe in systemic immune organs. Both EcMEK1 and EcMEK2 were distributed throughout the cytoplasm of transfected GS or HEK293T cells. Overexpression of EcMEK1 or EcMEK2 activated Activator protein 1 dependent luciferase. The phosphorylation levels of EcMEK1/2 and EcERK1/2 were significantly increased in head kidney leukocytes by stimulation with PMA treatment. The grouper MEK1/2-ERK1/2 axis was activated in Cryptocaryon irritans infection and showed an enhanced phosphorylation after immunization.
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Affiliation(s)
- Ze-Quan Mo
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China
| | - Rui Han
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China
| | - Jiu-Le Wang
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China
| | - Lu-Yun Ni
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China
| | - Yu-Ling Su
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China
| | - Xue-Li Lai
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China
| | - Zhi-Chang He
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China
| | - Hong-Ping Chen
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China
| | - Yan-Wei Li
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China
| | - Hong-Yan Sun
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China
| | - Xiao-Chun Luo
- School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, 510006, PR China.
| | - Xue-Ming Dan
- Joint Laboratory of Guangdong Province and Hong Kong Regions on Marine Bioresource Conservation and Exploitation, College of Marine Sciences, South China Agricultural University, Guangzhou, 510642, Guangdong Province, PR China.
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