99951
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Brandl L, Kirstein N, Neumann J, Sendelhofert A, Vieth M, Kirchner T, Menssen A. The c-MYC/NAMPT/SIRT1 feedback loop is activated in early classical and serrated route colorectal cancer and represents a therapeutic target. Med Oncol 2018; 36:5. [PMID: 30460421 DOI: 10.1007/s12032-018-1225-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/06/2018] [Indexed: 12/24/2022]
Abstract
We have recently identified a positive feedback loop in which c-MYC increases silent information regulator 1 (SIRT1) protein level and activity through transcriptional activation of nicotinamide phosphoribosyltransferase (NAMPT) and NAD+ increase. Here, we determined the relevance of the c-MYC-NAMPT-SIRT1 feedback loop, including the SIRT1 inhibitor deleted in breast cancer 1 (DBC1), for the development of conventional and serrated colorectal adenomas. Immunohistochemical analyses of 104 conventional adenomas with low- and high-grade dysplasia and of 157 serrated lesions revealed that elevated expression of c-MYC, NAMPT, and SIRT1 characterized all conventional and serrated adenomas, whereas DBC1 was not differentially regulated. Analyzing publicly available pharmacogenomic databases from 43 colorectal cancer cell lines demonstrated that responsiveness towards a NAMPT inhibitor was significantly associated with alterations in PTEN and TGFBR2, while features such as BRAF or RNF43 alterations, or microsatellite instability typical for serrated route colorectal cancer, showed increased sensitivities for inhibition of NAMPT and SIRT1. Our findings suggest an activation of the c-MYC-NAMPT-SIRT1 feedback loop that may crucially contribute to initiation and development of both routes to colorectal cancer. Targeting of NAMPT or SIRT1 may represent novel therapeutic strategies with putative higher sensitivity of the serrated route colorectal cancer subtype.
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Affiliation(s)
- Lydia Brandl
- Department of Pathology, Ludwig-Maximilians University (LMU), Thalkirchnerstraße 36, 80337, Munich, Germany
| | - Nina Kirstein
- Research group "Signaling pathways in colorectal cancer", Department of Pathology, Ludwig-Maximilians University (LMU), Thalkirchnerstraße 36, 80337, Munich, Germany
| | - Jens Neumann
- Department of Pathology, Ludwig-Maximilians University (LMU), Thalkirchnerstraße 36, 80337, Munich, Germany
| | - Andrea Sendelhofert
- Department of Pathology, Ludwig-Maximilians University (LMU), Thalkirchnerstraße 36, 80337, Munich, Germany
| | - Michael Vieth
- Department of Pathology, Klinikum Bayreuth, Preuschwitzer Str. 101, 95445, Bayreuth, Germany
| | - Thomas Kirchner
- Department of Pathology, Ludwig-Maximilians University (LMU), Thalkirchnerstraße 36, 80337, Munich, Germany
- German Consortium for Translational Cancer Research (DKTK), DKTK site Munich, DKFZ, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Antje Menssen
- Research group "Signaling pathways in colorectal cancer", Department of Pathology, Ludwig-Maximilians University (LMU), Thalkirchnerstraße 36, 80337, Munich, Germany.
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99952
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Lippens JL, Egea PF, Spahr C, Vaish A, Keener JE, Marty MT, Loo JA, Campuzano ID. Rapid LC-MS Method for Accurate Molecular Weight Determination of Membrane and Hydrophobic Proteins. Anal Chem 2018; 90:13616-13623. [PMID: 30335969 PMCID: PMC6580849 DOI: 10.1021/acs.analchem.8b03843] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Therapeutic target characterization involves many components, including accurate molecular weight (MW) determination. Knowledge of the accurate MW allows one to detect the presence of post-translational modifications, proteolytic cleavages, and importantly, if the correct construct has been generated and purified. Denaturing liquid chromatography-mass spectrometry (LC-MS) can be an attractive method for obtaining this information. However, membrane protein LC-MS methodology has remained relatively under-explored and under-incorporated in comparison to methods for soluble proteins. Here, systematic investigation of multiple gradients and column chemistries has led to the development of a 5 min denaturing LC-MS method for acquiring membrane protein accurate MW measurements. Conditions were interrogated with membrane proteins, such as GPCRs and ion channels, as well as bispecific antibody constructs of variable sizes with the aim to provide the community with rapid LC-MS methods necessary to obtain chromatographic and accurate MW measurements in a medium- to high-throughput manner. The 5 min method detailed has successfully produced MW measurements for hydrophobic proteins with a wide MW range (17.5 to 105.3 kDa) and provided evidence that some constructs indeed contain unexpected modifications or sequence clipping. This rapid LC-MS method is also capable of baseline separating formylated and nonformylated aquaporinZ membrane protein.
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Affiliation(s)
- Jennifer L. Lippens
- Amgen Discovery Research, Amgen, Thousand Oaks, California 91320, United States
| | - Pascal F. Egea
- Department of Biological Chemistry, University of California-Los Angeles, Los Angeles, California 90095, United States
| | - Chris Spahr
- Amgen Discovery Research, Amgen, Thousand Oaks, California 91320, United States
| | - Amit Vaish
- Amgen Discovery Research, Amgen, Thousand Oaks, California 91320, United States
| | - James E. Keener
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Michael T. Marty
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Joseph A. Loo
- Department of Biological Chemistry, University of California-Los Angeles, Los Angeles, California 90095, United States
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, California 90095, United States
| | - Iain D.G. Campuzano
- Amgen Discovery Research, Amgen, Thousand Oaks, California 91320, United States
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99953
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Prolo C, Rios N, Piacenza L, Álvarez MN, Radi R. Fluorescence and chemiluminescence approaches for peroxynitrite detection. Free Radic Biol Med 2018; 128:59-68. [PMID: 29454880 DOI: 10.1016/j.freeradbiomed.2018.02.017] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 02/07/2018] [Accepted: 02/12/2018] [Indexed: 12/23/2022]
Abstract
In the last two decades, there has been a significant advance in understanding the biochemistry of peroxynitrite, an endogenously-produced oxidant and nucleophile. Its relevance as a mediator in several pathologic states and the aging process together with its transient character and low steady-state concentration, motivated the development of a variety of techniques for its unambiguous detection and estimation. Among these, fluorescence and chemiluminescence approaches have represented important tools with enhanced sensitivity but usual limited specificity. In this review, we analyze selected examples of molecular probes that permit the detection of peroxynitrite by fluorescence and chemiluminescence, disclosing their mechanism of reaction with either peroxynitrite or peroxynitrite-derived radicals. Indeed, probes have been divided into 1) redox probes that yield products by a free radical mechanism, and 2) electrophilic probes that evolve to products secondary to the nucleophilic attack by peroxynitrite. Overall, boronate-based compounds are emerging as preferred probes for the sensitive and specific detection and quantitation. Moreover, novel strategies involving genetically-modified fluorescent proteins with the incorporation of unnatural amino acids have been recently described as peroxynitrite sensors. This review analyzes the most commonly used fluorescence and chemiluminescence approaches for peroxynitrite detection and provides some guidelines for appropriate experimental design and data interpretation, including how to estimate peroxynitrite formation rates in cells.
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Affiliation(s)
- Carolina Prolo
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Natalia Rios
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Lucia Piacenza
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - María Noel Álvarez
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Rafael Radi
- Departamento de Bioquímica, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay; Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
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99954
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Ribosome biogenesis: An emerging druggable pathway for cancer therapeutics. Biochem Pharmacol 2018; 159:74-81. [PMID: 30468711 DOI: 10.1016/j.bcp.2018.11.014] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/16/2018] [Indexed: 01/05/2023]
Abstract
Ribosomes are nanomachines essential for protein production in all living cells. Ribosome synthesis increases in cancer cells to cope with a rise in protein synthesis and sustain unrestricted growth. This increase in ribosome biogenesis is reflected by severe morphological alterations of the nucleolus, the cell compartment where the initial steps of ribosome biogenesis take place. Ribosome biogenesis has recently emerged as an effective target in cancer therapy, and several compounds that inhibit ribosome production or function, killing preferentially cancer cells, have entered clinical trials. Recent research indicates that cells express heterogeneous populations of ribosomes and that the composition of ribosomes may play a key role in tumorigenesis, exposing novel therapeutic opportunities. Here, we review recent data demonstrating that ribosome biogenesis is a promising druggable pathway in cancer therapy, and discuss future research perspectives.
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99955
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Lamont L, Eijkel GB, Jones EA, Flinders B, Ellis SR, Porta Siegel T, Heeren RMA, Vreeken RJ. Targeted Drug and Metabolite Imaging: Desorption Electrospray Ionization Combined with Triple Quadrupole Mass Spectrometry. Anal Chem 2018. [PMID: 30346139 DOI: 10.1021/acs.analchem.8b03857(2018)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Mass spectrometry imaging (MSI) has proven to be a valuable tool for drug and metabolite imaging in pharmaceutical toxicology studies and can reveal, for example, accumulation of drug candidates in early drug development. However, the lack of sample cleanup and chromatographic separation can hamper the analysis due to isobaric interferences. Multiple reaction monitoring (MRM) uses unique precursor ion-product ion transitions to add specificity which leads to higher selectivity. Here, we present a targeted imaging platform where desorption electrospray ionization is combined with a triple quadrupole (QqQ) system to perform MRM imaging. The platform was applied to visualize (i) lipids in mouse brain tissue sections and (ii) a drug candidate and metabolite in canine liver tissue. All QqQ modes were investigated to show the increased detection time provided by MRM as well as the possibility to perform dual polarity imaging. This is very beneficial for lipid imaging because some phospholipid classes ionize in opposite polarity (e.g., phosphatidylcholine/sphingomyelin in positive ion mode and phosphatidylserine/phosphatidylethanolamine in negative ion mode). Drug and metabolite images were obtained to show its strength in drug distribution studies. Multiple MRM transitions were used to confirm the local presence and selective detection of pharmaceutical compounds.
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Affiliation(s)
- Lieke Lamont
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry , Maastricht University , 6229 ER Maastricht , The Netherlands
| | - Gert B Eijkel
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry , Maastricht University , 6229 ER Maastricht , The Netherlands
| | | | - Bryn Flinders
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry , Maastricht University , 6229 ER Maastricht , The Netherlands
| | - Shane R Ellis
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry , Maastricht University , 6229 ER Maastricht , The Netherlands
| | - Tiffany Porta Siegel
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry , Maastricht University , 6229 ER Maastricht , The Netherlands
| | - Ron M A Heeren
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry , Maastricht University , 6229 ER Maastricht , The Netherlands
| | - Rob J Vreeken
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry , Maastricht University , 6229 ER Maastricht , The Netherlands
- Janssen Research & Development , B-2340 Beerse , Belgium
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99956
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Oliveira L, Campos WH, Rocha MS. Optical Trapping and Manipulation of Superparamagnetic Beads Using Annular-Shaped Beams. Methods Protoc 2018. [PMCID: PMC6481052 DOI: 10.3390/mps1040044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We propose an optical tweezers setup based on an annular-shaped laser beam that is efficient to trap 2.8 μm-diameter superparamagnetic particles. The optical trapping of such particles was fully characterized, and a direct absolute comparison with a geometrical optics model was performed. With this comparison, we were able to show that light absorption by the superparamagnetic particles is negligible for our annular beam tweezers, differing from the case of conventional Gaussian beam tweezers, in which laser absorption by the beads makes stable trapping difficult. In addition, the trap stiffness of the annular beam tweezers increases with the laser power and with the bead distance from the coverslip surface. While this first result is expected and similar to that achieved for conventional Gaussian tweezers, which use ordinary dielectric beads, the second result is quite surprising and different from the ordinary case, suggesting that spherical aberration is much less important in our annular beam geometry. The results obtained here provide new insights into the development of hybrid optomagnetic tweezers, which can apply simultaneously optical and magnetic forces on the same particles.
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99957
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Naletova I, Satriano C, Curci A, Margiotta N, Natile G, Arena G, La Mendola D, Nicoletti VG, Rizzarelli E. Cytotoxic phenanthroline derivatives alter metallostasis and redox homeostasis in neuroblastoma cells. Oncotarget 2018; 9:36289-36316. [PMID: 30555630 PMCID: PMC6284747 DOI: 10.18632/oncotarget.26346] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 11/01/2018] [Indexed: 02/06/2023] Open
Abstract
Copper homeostasis is generally investigated focusing on a single component of the metallostasis network. Here we address several of the factors controlling the metallostasis for neuroblastoma cells (SH-SY5Y) upon treatment with 2,9-dimethyl-1,10-phenanthroline-5,6-dione (phendione) and 2,9-dimethyl-1,10-phenanthroline (cuproindione). These compounds bind and transport copper inside cells, exert their cytotoxic activity through the induction of oxidative stress, causing apoptosis and alteration of the cellular redox and copper homeostasis network. The intracellular pathway ensured by copper transporters (Ctr1, ATP7A), chaperones (CCS, ATOX, COX 17, Sco1, Sco2), small molecules (GSH) and transcription factors (p53) is scrutinised.
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Affiliation(s)
- Irina Naletova
- Department of Chemical Sciences, University of Catania, Catania, Italy
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici (CIRCMSB), Bari, Italy
| | - Cristina Satriano
- Department of Chemical Sciences, University of Catania, Catania, Italy
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici (CIRCMSB), Bari, Italy
| | - Alessandra Curci
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici (CIRCMSB), Bari, Italy
- Department of Chemistry, University of Bari ‘Aldo Moro’, Bari, Italy
| | - Nicola Margiotta
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici (CIRCMSB), Bari, Italy
- Department of Chemistry, University of Bari ‘Aldo Moro’, Bari, Italy
| | - Giovanni Natile
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici (CIRCMSB), Bari, Italy
- Department of Chemistry, University of Bari ‘Aldo Moro’, Bari, Italy
| | - Giuseppe Arena
- Department of Chemical Sciences, University of Catania, Catania, Italy
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici (CIRCMSB), Bari, Italy
| | - Diego La Mendola
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici (CIRCMSB), Bari, Italy
- Department of Pharmacy, University of Pisa, Pisa, Italy
| | - Vincenzo Giuseppe Nicoletti
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici (CIRCMSB), Bari, Italy
- Section of Medical Biochemistry, Department of Biomedical and Biotechnological Sciences (BIOMETEC), University of Catania, Catania, Italy
| | - Enrico Rizzarelli
- Department of Chemical Sciences, University of Catania, Catania, Italy
- Consorzio Interuniversitario di Ricerca in Chimica dei Metalli nei Sistemi Biologici (CIRCMSB), Bari, Italy
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99958
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Vergadi E, Vaporidi K, Tsatsanis C. Regulation of Endotoxin Tolerance and Compensatory Anti-inflammatory Response Syndrome by Non-coding RNAs. Front Immunol 2018; 9:2705. [PMID: 30515175 PMCID: PMC6255943 DOI: 10.3389/fimmu.2018.02705] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 11/01/2018] [Indexed: 12/17/2022] Open
Abstract
The onset and the termination of innate immune response must be tightly regulated to maintain homeostasis and prevent excessive inflammation, which can be detrimental to the organism, particularly in the context of sepsis. Endotoxin tolerance and compensatory anti-inflammatory response syndrome (CARS) describe a state of hypo-responsiveness characterized by reduced capacity of myeloid cells to respond to inflammatory stimuli, particularly those initiated by bacterial lipopolysaccharide (LPS). To achieve endotoxin tolerance, extensive reprogramming otherwise termed as “innate immune training”, is required that leads to both modifications of the intracellular components of TLR signaling and also to alterations in extracellular soluble mediators. Non-coding RNAs (ncRNAs) have been recognized as critical regulators of TLR signaling. Specifically, several microRNAs (miR-146, miR-125b, miR-98, miR-579, miR-132, let-7e and others) are induced upon TLR activation and reciprocally promote endotoxin tolerance and/or cross tolerance. Many other miRNAs have been also shown to negatively regulate TLR signaling. The long non-coding (lnc)RNAs (Mirt2, THRIL, MALAT1, lincRNA-21 and others) are also altered upon TLR activation and negatively regulate TLR signaling. Furthermore, the promotion or termination of myeloid cell tolerance is not only regulated by intracellular mediators but is also affected by other TLR-independent soluble signals that often achieve their effect via modulation of intracellular ncRNAs. In this article, we review recent evidence on the role of different ncRNAs in the context of innate immune cell tolerance and trained immunity, and evaluate their impact on immune system homeostasis.
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Affiliation(s)
- Eleni Vergadi
- Department of Paediatrics, Medical School, University of Crete, Heraklion, Greece.,Department of Clinical Chemistry, Medical School, University of Crete, Heraklion, Greece
| | - Katerina Vaporidi
- Department of Intensive Care Medicine, Medical School, University of Crete, Heraklion, Greece
| | - Christos Tsatsanis
- Department of Clinical Chemistry, Medical School, University of Crete, Heraklion, Greece
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99959
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Nordzieke DE, Medraño-Fernandez I. The Plasma Membrane: A Platform for Intra- and Intercellular Redox Signaling. Antioxidants (Basel) 2018; 7:antiox7110168. [PMID: 30463362 PMCID: PMC6262572 DOI: 10.3390/antiox7110168] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/15/2018] [Accepted: 11/17/2018] [Indexed: 02/06/2023] Open
Abstract
Membranes are of outmost importance to allow for specific signal transduction due to their ability to localize, amplify, and direct signals. However, due to the double-edged nature of reactive oxygen species (ROS)—toxic at high concentrations but essential signal molecules—subcellular localization of ROS-producing systems to the plasma membrane has been traditionally regarded as a protective strategy to defend cells from unwanted side-effects. Nevertheless, specialized regions, such as lipid rafts and caveolae, house and regulate the activated/inhibited states of important ROS-producing systems and concentrate redox targets, demonstrating that plasma membrane functions may go beyond acting as a securing lipid barrier. This is nicely evinced by nicotinamide adenine dinucleotide phosphate (NADPH)-oxidases (NOX), enzymes whose primary function is to generate ROS and which have been shown to reside in specific lipid compartments. In addition, membrane-inserted bidirectional H2O2-transporters modulate their conductance precisely during the passage of the molecules through the lipid bilayer, ensuring time-scaled delivery of the signal. This review aims to summarize current evidence supporting the role of the plasma membrane as an organizing center that serves as a platform for redox signal transmission, particularly NOX-driven, providing specificity at the same time that limits undesirable oxidative damage in case of malfunction. As an example of malfunction, we explore several pathological situations in which an inflammatory component is present, such as inflammatory bowel disease and neurodegenerative disorders, to illustrate how dysregulation of plasma-membrane-localized redox signaling impacts normal cell physiology.
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Affiliation(s)
- Daniela E Nordzieke
- Institute of Microbiology and Genetics, Department of Genetics of Eukaryotic Microorganisms, Georg August University Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany.
| | - Iria Medraño-Fernandez
- Protein Transport and Secretion Unit, Division of Genetics and Cell Biology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ospedale San Raffaele, Università Vita-Salute San Raffaele, 20132 Milan, Italy.
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99960
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Cook R, Sarker H, Fernandez-Patron C. Pathologies of matrix metalloproteinase-2 underactivity: a perspective on a neglected condition 1. Can J Physiol Pharmacol 2018; 97:486-492. [PMID: 30457883 DOI: 10.1139/cjpp-2018-0525] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A member of the matrix metalloproteinase family, matrix metalloproteinase-2 (MMP-2, gelatinase A), has been extensively studied for its role in both normal physiology and pathological processes. Whereas most research efforts in recent years have investigated the pathologies associated with MMP-2 overactivity, the pathological mechanisms elicited by MMP-2 underactivity are less well understood. Here, we distinguish between 2 states and describe their causes: (i) MMP-2 deficiency (complete loss of MMP-2 activity) and (ii) MMP-2 insufficiency (defined as MMP-2 activity below baseline levels). Further, we review the biology of MMP-2, summarizing the current literature on MMP-2 underactivity in both mice and humans, and describe research being conducted by our lab towards improving our understanding of the pathological mechanisms elicited by MMP-2 deficiency/insufficiency. We think that this research could stimulate the discovery of new therapeutic approaches for managing pathologies associated with MMP-2 underactivity. Moreover, similar concepts could apply to other members of the matrix metalloproteinase family.
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Affiliation(s)
- Ryan Cook
- a Department of Biochemistry, Faculty of Medicine and Dentistry, 3-19 Medical Sciences Building, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Hassan Sarker
- a Department of Biochemistry, Faculty of Medicine and Dentistry, 3-19 Medical Sciences Building, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Carlos Fernandez-Patron
- b Department of Biochemistry, Cardiovascular Research Centre, Mazankowski Alberta Heart Institute, Faculty of Medicine and Dentistry, 3-19 Medical Sciences Building, University of Alberta, Edmonton, AB T6G 2H7, Canada
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99961
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Quan Li P, Piper A, Schmueser I, Mount AR, Corrigan DK. Impedimetric measurement of DNA-DNA hybridisation using microelectrodes with different radii for detection of methicillin resistant Staphylococcus aureus (MRSA). Analyst 2018; 142:1946-1952. [PMID: 28492640 DOI: 10.1039/c7an00436b] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Due to their electroanalytical advantages, microelectrodes are a very attractive technology for sensing and monitoring applications. One highly important application is measurement of DNA hybridisation to detect a wide range of clinically important phenomena, including single nucleotide polymorphisms (SNPs), mutations and drug resistance genes. The use of electrochemical impedance spectroscopy (EIS) for measurement of DNA hybridisation is well established for large electrodes but as yet remains relatively unexplored for microelectrodes due to difficulties associated with electrode functionalisation and impedimetric response interpretation. To shed light on this, microelectrodes were initially fabricated using photolithography and characterised electrochemically to ensure their responses matched established theory. Electrodes with different radii (50, 25, 15 and 5 μm) were then functionalised with a mixed film of 6-mercapto-1-hexanol and a thiolated single stranded DNA capture probe for a specific gene from the antibiotic resistant bacterium MRSA. The complementary oligonucleotide target from the mecA MRSA gene was hybridised with the surface tethered ssDNA probe. The EIS response was evaluated as a function of electrode radius and it was found that charge-transfer (RCT) was more significantly affected by hybridisation of the mecA gene than the non-linear resistance (RNL) which is associated with the steady state current. The discrimination of mecA hybridisation improved as electrode radius reduced with the RCT component of the response becoming increasingly dominant for smaller radii. It was possible to utilise these findings to produce a real time measurement of oligonucleotide binding where changes in RCT were evident one minute after nanomolar target addition. These data provide a systematic account of the effect of microelectrode radius on the measurement of hybridisation, providing insight into critical aspects of sensor design and implementation for the measurement of clinically important DNA sequences. The findings open up the possibility of developing rapid, sensitive DNA based measurements using microelectrodes.
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99962
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Jiang M, Yan Y, Yang K, Liu Z, Qi J, Zhou H, Qian N, Zhou Q, Wang T, Xu X, Xiao X, Deng L. Small molecule nAS-E targeting cAMP response element binding protein (CREB) and CREB-binding protein interaction inhibits breast cancer bone metastasis. J Cell Mol Med 2018; 23:1224-1234. [PMID: 30461194 PMCID: PMC6349349 DOI: 10.1111/jcmm.14024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 09/17/2018] [Accepted: 10/20/2018] [Indexed: 11/30/2022] Open
Abstract
Bone is the most common metastatic site for breast cancer. The excessive osteoclast activity in the metastatic bone lesions often produces osteolysis. The cyclic-AMP (cAMP)-response element binding protein (CREB) serves a variety of biological functions including the transformation and immortalization of breast cancer cells. In addition, evidence has shown that CREB plays a key role in osteoclastgenesis and bone resorption. Small organic molecules with good pharmacokinetic properties and specificity, targeting CREB-CBP (CREB-binding protein) interaction to inhibit CREB-mediated gene transcription have attracted more considerations as cancer therapeutics. We recently identified naphthol AS-E (nAS-E) as a cell-permeable inhibitor of CREB-mediated gene transcription through inhibiting CREB-CBP interaction. In this study, we tested the effect of nAS-E on breast cancer cell proliferation, survival, migration as well as osteoclast formation and bone resorption in vitro for the first time. Our results demonstrated that nAS-E inhibited breast cancer cell proliferation, migration, survival and suppressed osteoclast differentiation as well as bone resorption through inhibiting CREB-CBP interaction. In addition, the in vivo effect of nAS-E in protecting against breast cancer-induced osteolysis was evaluated. Our results indicated that nAS-E could reverse bone loss induced by MDA-MB-231 tumour. These results suggest that small molecules targeting CREB-CBP interaction to inhibit CREB-mediated gene transcription might be a potential approach for the treatment of breast cancer bone metastasis.
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Affiliation(s)
- Min Jiang
- Shanghai Key Laboratory for Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yufei Yan
- Shanghai Key Laboratory for Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Kai Yang
- Shanghai Key Laboratory for Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhuochao Liu
- Shanghai Key Laboratory for Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jin Qi
- Shanghai Key Laboratory for Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Hanbing Zhou
- Shanghai Key Laboratory for Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Niandong Qian
- Shanghai Key Laboratory for Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qi Zhou
- Shanghai Key Laboratory for Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Tianqi Wang
- Shanghai Key Laboratory for Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xing Xu
- Shanghai Key Laboratory for Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiangshu Xiao
- Program in Chemical Biology, Department of Physiology and Pharmacology, Oregon Health & Science University, Portland, Oregon
| | - Lianfu Deng
- Shanghai Key Laboratory for Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Shanghai Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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99963
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Zielonka J, Kalyanaraman B. Small-molecule luminescent probes for the detection of cellular oxidizing and nitrating species. Free Radic Biol Med 2018; 128:3-22. [PMID: 29567392 PMCID: PMC6146080 DOI: 10.1016/j.freeradbiomed.2018.03.032] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 03/09/2018] [Accepted: 03/16/2018] [Indexed: 01/24/2023]
Abstract
Reactive oxygen species (ROS) have been implicated in both pathogenic cellular damage events and physiological cellular redox signaling and regulation. To unravel the biological role of ROS, it is very important to be able to detect and identify the species involved. In this review, we introduce the reader to the methods of detection of ROS using luminescent (fluorescent, chemiluminescent, and bioluminescent) probes and discuss typical limitations of those probes. We review the most widely used probes, state-of-the-art assays, and the new, promising approaches for rigorous detection and identification of superoxide radical anion, hydrogen peroxide, and peroxynitrite. The combination of real-time monitoring of the dynamics of ROS in cells and the identification of the specific products formed from the probes will reveal the role of specific types of ROS in cellular function and dysfunction. Understanding the molecular mechanisms involving ROS may help with the development of new therapeutics for several diseases involving dysregulated cellular redox status.
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Affiliation(s)
- Jacek Zielonka
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, United States; Free Radical Research Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, United States; Cancer Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, United States.
| | - Balaraman Kalyanaraman
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, United States; Free Radical Research Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, United States; Cancer Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, United States
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99964
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Wang BD, Lee NH. Aberrant RNA Splicing in Cancer and Drug Resistance. Cancers (Basel) 2018; 10:E458. [PMID: 30463359 PMCID: PMC6266310 DOI: 10.3390/cancers10110458] [Citation(s) in RCA: 113] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 11/15/2018] [Accepted: 11/15/2018] [Indexed: 12/22/2022] Open
Abstract
More than 95% of the 20,000 to 25,000 transcribed human genes undergo alternative RNA splicing, which increases the diversity of the proteome. Isoforms derived from the same gene can have distinct and, in some cases, opposing functions. Accumulating evidence suggests that aberrant RNA splicing is a common and driving event in cancer development and progression. Moreover, aberrant splicing events conferring drug/therapy resistance in cancer is far more common than previously envisioned. In this review, aberrant splicing events in cancer-associated genes, namely BCL2L1, FAS, HRAS, CD44, Cyclin D1, CASP2, TMPRSS2-ERG, FGFR2, VEGF, AR and KLF6, will be discussed. Also highlighted are the functional consequences of aberrant splice variants (BCR-Abl35INS, BIM-γ, IK6, p61 BRAF V600E, CD19-∆2, AR-V7 and PIK3CD-S) in promoting resistance to cancer targeted therapy or immunotherapy. To overcome drug resistance, we discuss opportunities for developing novel strategies to specifically target the aberrant splice variants or splicing machinery that generates the splice variants. Therapeutic approaches include the development of splice variant-specific siRNAs, splice switching antisense oligonucleotides, and small molecule inhibitors targeting splicing factors, splicing factor kinases or the aberrant oncogenic protein isoforms.
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Affiliation(s)
- Bi-Dar Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA.
| | - Norman H Lee
- Department of Pharmacology and Physiology, School of Medicine and Health Sciences, George Washington University, GW Cancer Center, Washington, DC 20037, USA.
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99965
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Urakov VN, Mitkevich OV, Dergalev AA, Ter-Avanesyan MD. The Pub1 and Upf1 Proteins Act in Concert to Protect Yeast from Toxicity of the [PSI⁺] Prion. Int J Mol Sci 2018; 19:E3663. [PMID: 30463309 PMCID: PMC6275000 DOI: 10.3390/ijms19113663] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 11/02/2018] [Accepted: 11/14/2018] [Indexed: 12/18/2022] Open
Abstract
The [PSI⁺] nonsense-suppressor determinant of Saccharomyces cerevisiae is based on the formation of heritable amyloids of the Sup35 (eRF3) translation termination factor. [PSI⁺] amyloids have variants differing in amyloid structure and in the strength of the suppressor phenotype. The appearance of [PSI⁺], its propagation and manifestation depend primarily on chaperones. Besides chaperones, the Upf1/2/3, Siw14 and Arg82 proteins restrict [PSI⁺] formation, while Sla2 can prevent [PSI⁺] toxicity. Here, we identify two more non-chaperone proteins involved in [PSI⁺] detoxification. We show that simultaneous lack of the Pub1 and Upf1 proteins is lethal to cells harboring [PSI⁺] variants with a strong, but not with a weak, suppressor phenotype. This lethality is caused by excessive depletion of the Sup45 (eRF1) termination factor due to its sequestration into Sup35 polymers. We also show that Pub1 acts to restrict excessive Sup35 prion polymerization, while Upf1 interferes with Sup45 binding to Sup35 polymers. These data allow consideration of the Pub1 and Upf1 proteins as a novel [PSI⁺] detoxification system.
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Affiliation(s)
- Valery N Urakov
- Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 119071 Moscow, Russia.
| | - Olga V Mitkevich
- Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 119071 Moscow, Russia.
| | - Alexander A Dergalev
- Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 119071 Moscow, Russia.
| | - Michael D Ter-Avanesyan
- Bach Institute of Biochemistry, Federal Research Center "Fundamentals of Biotechnology" of the Russian Academy of Sciences, 119071 Moscow, Russia
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99966
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Pallach M, Di Lorenzo F, Duda KA, Le Pennec G, Molinaro A, Silipo A. The Lipid A Structure from the Marine Sponge Symbiont Endozoicomonas sp. HEX 311. Chembiochem 2018; 20:230-236. [PMID: 30179300 DOI: 10.1002/cbic.201800441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Indexed: 11/08/2022]
Abstract
Endozoicomonas sp. HEX311 is a Gram-negative bacterium known to establish a commensal interaction with the marine demosponge Suberites domuncula. The molecular bases of the sponge-microbe interaction events are still poorly defined. Nevertheless, it has been proved that S. domuncula possesses an innate immune system with similarities to the mammalian one and is able to recognize the main component of the Gram-negative bacteria cell wall: the lipopolysaccharide. Whether this recognition occurs in a structure-dependent manner, which is typical for mammalian immune system receptors, is still under investigation. Herein, we report the Endozoicomonas sp. HEX311 lipid A structure obtained by a combination of data attained from chemical, MALDI MS, and MS2 approaches. The lipid A is a complex family of species decorated by pyrophosphate and phosphate units and carrying (R)-3-hydroxydodecanoic acid, (R)-3-hydroxytetradecanonic acid, iso-2-hydroxyundecanoic acid, iso-(R)-3-hydroxyundecanoic acid, and iso-nonanoic acid as acyl chains.
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Affiliation(s)
- Mateusz Pallach
- Department of Chemical Sciences, University of Naples Federico II, via Cinthia 4, 80126, Naples, Italy
| | - Flaviana Di Lorenzo
- Department of Chemical Sciences, University of Naples Federico II, via Cinthia 4, 80126, Naples, Italy
| | - Katarzyna A Duda
- Research Center Borstel Leibniz Lung Center, Parkallee 4a, 23845, Borstel, Germany
| | - Gaël Le Pennec
- Laboratoire de Biotechnologie et de Chimie Marines, Université de Bretagne-Sud, Rue André Lwoff, 56000, Vannes, France
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, via Cinthia 4, 80126, Naples, Italy
| | - Alba Silipo
- Department of Chemical Sciences, University of Naples Federico II, via Cinthia 4, 80126, Naples, Italy
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99967
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Christy SF, Wernick RI, Lue MJ, Velasco G, Howe DK, Denver DR, Estes S. Adaptive Evolution under Extreme Genetic Drift in Oxidatively Stressed Caenorhabditis elegans. Genome Biol Evol 2018; 9:3008-3022. [PMID: 29069345 PMCID: PMC5714194 DOI: 10.1093/gbe/evx222] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2017] [Indexed: 12/30/2022] Open
Abstract
A mutation-accumulation (MA) experiment with Caenorhabditis elegans nematodes was conducted in which replicate, independently evolving lines were initiated from a low-fitness mitochondrial electron transport chain mutant, gas-1. The original intent of the study was to assess the effect of electron transport chain dysfunction involving elevated reactive oxygen species production on patterns of spontaneous germline mutation. In contrast to results of standard MA experiments, gas-1 MA lines evolved slightly higher mean fitness alongside reduced among-line genetic variance compared with their ancestor. Likewise, the gas-1 MA lines experienced partial recovery to wildtype reactive oxygen species levels. Whole-genome sequencing and analysis revealed that the molecular spectrum but not the overall rate of nuclear DNA mutation differed from wildtype patterns. Further analysis revealed an enrichment of mutations in loci that occur in a gas-1-centric region of the C. elegans interactome, and could be classified into a small number of functional-genomic categories. Characterization of a backcrossed four-mutation set isolated from one gas-1 MA line revealed this combination to be beneficial on both gas-1 mutant and wildtype genetic backgrounds. Our combined results suggest that selection favoring beneficial mutations can be powerful even under unfavorable population genetic conditions, and agree with fitness landscape theory predicting an inverse relationship between population fitness and the likelihood of adaptation.
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Affiliation(s)
| | | | | | | | - Dana K Howe
- Department of Integrative Biology, Oregon State University
| | - Dee R Denver
- Department of Integrative Biology, Oregon State University
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99968
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Discovery of Novel Druggable Sites on Zika Virus NS3 Helicase Using X-ray Crystallography-Based Fragment Screening. Int J Mol Sci 2018; 19:ijms19113664. [PMID: 30463319 PMCID: PMC6274715 DOI: 10.3390/ijms19113664] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/28/2018] [Accepted: 11/09/2018] [Indexed: 12/18/2022] Open
Abstract
The flavivirus family contains several important human pathogens, such as Zika virus (ZIKV), dengue, West Nile, and Yellow Fever viruses, that collectively lead to a large, global disease burden. Currently, there are no approved medicines that can target these viruses. The sudden outbreak of ZIKV infections in 2015⁻2016 posed a serious threat to global public health. While the epidemic has receded, persistent reservoirs of ZIKV infection can cause reemergence. Here, we have used X-ray crystallography-based screening to discover two novel sites on ZIKV NS3 helicase that can bind drug-like fragments. Both sites are structurally conserved in other flaviviruses, and mechanistically significant. The binding poses of four fragments, two for each of the binding sites, were characterized at atomic precision. Site A is a surface pocket on the NS3 helicase that is vital to its interaction with NS5 polymerase and formation of the flaviviral replication complex. Site B corresponds to a flexible, yet highly conserved, allosteric site at the intersection of the three NS3 helicase domains. Saturation transfer difference nuclear magnetic resonance (NMR) experiments were additionally used to evaluate the binding strength of the fragments, revealing dissociation constants (KD) in the lower mM range. We conclude that the NS3 helicase of flaviviruses is a viable drug target. The data obtained open opportunities towards structure-based design of first-in-class anti-ZIKV compounds, as well as pan-flaviviral therapeutics.
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99969
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Astumian RD. Trajectory and Cycle-Based Thermodynamics and Kinetics of Molecular Machines: The Importance of Microscopic Reversibility. Acc Chem Res 2018; 51:2653-2661. [PMID: 30346731 DOI: 10.1021/acs.accounts.8b00253] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A molecular machine is a nanoscale device that provides a mechanism for coupling energy from two (or more) processes that in the absence of the machine would be independent of one another. Examples include walking of a protein in one direction along a polymeric track (process 1, driving "force" X1 = - F⃗· l⃗) and hydrolyzing ATP (process 2, driving "force" X2 = ΔμATP); or synthesis of ATP (process 1, X1 = -ΔμATP) and transport of protons from the periplasm to the cytoplasm across a membrane (process 2, X2 = ΔμH+); or rotation of a flagellum (process 1, X1 = -torque) and transport of protons across a membrane (process 2, X2 = ΔμH+). In some ways, the function of a molecular machine is similar to that of a macroscopic machine such as a car that couples combustion of gasoline to translational motion. However, the low Reynolds number regime in which molecular machines operate is very different from that relevant for macroscopic machines. Inertia is negligible in comparison to viscous drag, and omnipresent thermal noise causes the machine to undergo continual transition among many states even at thermodynamic equilibrium. Cyclic trajectories among the states of the machine that result in a change in the environment can be broken into two classes: those in which process 1 in either the forward or backward direction ([Formula: see text]) occurs and which thereby exchange work [Formula: see text] with the environment; and those in which process 2 in either the forward or backward direction ([Formula: see text]) occurs and which thereby exchange work [Formula: see text] with the evironment. These two types of trajectories, [Formula: see text] and [Formula: see text], overlap, i.e., there are some trajectories in which both process 1 and process 2 occur, and for which the work exchanged is [Formula: see text]. The four subclasses of overlap trajectories [(+1,+2), (+1,-2), (-1,+2), (-1,-2)] are the coupled processes. The net probabilities for process 1 and process 2 are designated π+2 - π-2 and π+1 - π-1, respectively. The probabilities [Formula: see text] for any single trajectory [Formula: see text] and [Formula: see text] for its microscopic reverse [Formula: see text] are related by microscopic reversibility (MR), [Formula: see text], an equality that holds arbitrarily far from thermodynamic equilibrium, i.e., irrespective of the magnitudes of X1 and X2, and where [Formula: see text]. Using this formalism, we arrive at a remarkably simple and general expression for the rates of the processes, [Formula: see text], i = 1, 2, where the angle brackets indicate an average over the ensemble of all microscopic reverse trajectories. Stochastic description of coupling is doubtless less familiar than typical mechanical depictions of chemical coupling in terms of ATP induced violent kicks, judo throws, force generation and power-strokes. While the mechanical description of molecular machines is comforting in its familiarity, conclusions based on such a phenomenological perspective are often wrong. Specifically, a "power-stroke" model (i.e., a model based on energy driven "promotion" of a molecular machine to a high energy state followed by directional relaxation to a lower energy state) that has been the focus of mechanistic discussions of biomolecular machines for over a half century is, for catalysis driven molecular machines, incorrect. Instead, the key principle by which catalysis driven motors work is kinetic gating by a mechanism known as an information ratchet. Amazingly, this same principle is that by which catalytic molecular systems undergo adaptation to new steady states while facilitating an exergonic chemical reaction.
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Affiliation(s)
- R. Dean Astumian
- Department of Physics, University of Maine, Orono, Maine 04469, United States
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99970
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Nanobody-Alkaline Phosphatase Fusion Protein-Based Enzyme-Linked Immunosorbent Assay for One-Step Detection of Ochratoxin A in Rice. SENSORS 2018; 18:s18114044. [PMID: 30463338 PMCID: PMC6263964 DOI: 10.3390/s18114044] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/14/2018] [Accepted: 11/16/2018] [Indexed: 01/23/2023]
Abstract
Ochratoxin A (OTA) has become one a focus of public concern because of its multiple toxic effects and widespread contamination. To monitor OTA in rice, a sensitive, selective, and one-step enzyme-linked immunosorbent assay (ELISA) using a nanobody-alkaline phosphatase fusion protein (Nb28-AP) was developed. The Nb28-AP was produced by auto-induction expression and retained an intact antigen-binding capacity and enzymatic activity. It exhibited high thermal stability and organic solvent tolerance. Under the optimal conditions, the developed assay for OTA could be finished in 20 min with a half maximal inhibitory concentration of 0.57 ng mL-1 and a limit of detection of 0.059 ng mL-1, which was 1.1 times and 2.7 times lower than that of the unfused Nb28-based ELISA. The Nb28-AP exhibited a low cross-reactivity (CR) with ochratoxin B (0.92%) and ochratoxin C (6.2%), and an ignorable CR (<0.10%) with other mycotoxins. The developed Nb-AP-based one-step ELISA was validated and compared with a liquid chromatography-tandem mass spectrometry method. The results show the reliability of Nb-AP-based one-step ELISA for the detection of OTA in rice.
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99971
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Kim YR, Baek JI, Kim SH, Kim MA, Lee B, Ryu N, Kim KH, Choi DG, Kim HM, Murphy MP, Macpherson G, Choo YS, Bok J, Lee KY, Park JW, Kim UK. Therapeutic potential of the mitochondria-targeted antioxidant MitoQ in mitochondrial-ROS induced sensorineural hearing loss caused by Idh2 deficiency. Redox Biol 2018; 20:544-555. [PMID: 30508699 PMCID: PMC6279977 DOI: 10.1016/j.redox.2018.11.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 11/15/2018] [Accepted: 11/18/2018] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial NADP+-dependent isocitrate dehydrogenase 2 (IDH2) is a major NADPH-producing enzyme which is essential for maintaining the mitochondrial redox balance in cells. We sought to determine whether IDH2 deficiency induces mitochondrial dysfunction and modulates auditory function, and investigated the protective potential of an antioxidant agent against reactive oxygen species (ROS)-induced cochlear damage in Idh2 knockout (Idh2−/−) mice. Idh2 deficiency leads to damages to hair cells and spiral ganglion neurons (SGNs) in the cochlea and ultimately to apoptotic cell death and progressive sensorineural hearing loss in Idh2−/− mice. Loss of IDH2 activity led to decreased levels of NADPH and glutathione causing abnormal ROS accumulation and oxidative damage, which might trigger apoptosis signal in hair cells and SGNs in Idh2−/− mice. We performed ex vivo experiments to determine whether administration of mitochondria-targeted antioxidants might protect or induce recovery of cells from ROS-induced apoptosis in Idh2-deficient mouse cochlea. MitoQ almost completely neutralized the H2O2-induced ototoxicity, as the survival rate of Idh2−/− hair cells were restored to normal levels. In addition, the lack of IDH2 led to the accumulation of mitochondrial ROS and the depolarization of ΔΨm, resulting in hair cell loss. In the present study, we identified that IDH2 is indispensable for the functional maintenance and survival of hair cells and SGNs. Moreover, the hair cell degeneration caused by IDH2 deficiency can be prevented by MitoQ, which suggests that Idh2−/− mice could be a valuable animal model for evaluating the therapeutic effects of various antioxidant candidates to overcome ROS-induced hearing loss.
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Affiliation(s)
- Ye-Ri Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea; School of Life Sciences, KNU Creative BioResearch Group (BK21 Plus Project), Kyungpook National University, Daegu, Republic of Korea
| | - Jeong-In Baek
- Department of Aroma-Applied Industry, College of Herbal Bio-industry, Daegu Haany University, Gyeongsan, Republic of Korea
| | - Sung Hwan Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea; School of Life Sciences, KNU Creative BioResearch Group (BK21 Plus Project), Kyungpook National University, Daegu, Republic of Korea
| | - Min-A Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea; School of Life Sciences, KNU Creative BioResearch Group (BK21 Plus Project), Kyungpook National University, Daegu, Republic of Korea
| | - Byeonghyeon Lee
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea; School of Life Sciences, KNU Creative BioResearch Group (BK21 Plus Project), Kyungpook National University, Daegu, Republic of Korea
| | - Nari Ryu
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea; School of Life Sciences, KNU Creative BioResearch Group (BK21 Plus Project), Kyungpook National University, Daegu, Republic of Korea
| | - Kyung-Hee Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea; School of Life Sciences, KNU Creative BioResearch Group (BK21 Plus Project), Kyungpook National University, Daegu, Republic of Korea
| | - Deok-Gyun Choi
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Hye-Min Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea; School of Life Sciences, KNU Creative BioResearch Group (BK21 Plus Project), Kyungpook National University, Daegu, Republic of Korea
| | - Michael P Murphy
- Medical Research Council (MRC)-Mitochondrial Biology Unit, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Greg Macpherson
- Antipodean Pharmaceuticals Inc, L2 14 Viaduct Harbour Rd, Auckland, New Zealand
| | - Yeon-Sik Choo
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Jinwoong Bok
- Department of Anatomy, Yonsei University College of Medicine, Seoul, Republic of Korea; BK21PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea; Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Kyu-Yup Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, School of Medicine, Kyungpook National University, Daegu, Republic of Korea.
| | - Jeen-Woo Park
- School of Life Sciences, KNU Creative BioResearch Group (BK21 Plus Project), Kyungpook National University, Daegu, Republic of Korea; Department of Biochemistry, School of Life Sciences and Biotechnology, College of Natural Sciences, Kyungpook National University, Daegu 41566, Republic of Korea.
| | - Un-Kyung Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, Republic of Korea; School of Life Sciences, KNU Creative BioResearch Group (BK21 Plus Project), Kyungpook National University, Daegu, Republic of Korea.
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99972
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Sousa SF, Neves RP, Waheed SO, Fernandes PA, Ramos MJ. Structural and mechanistic aspects of S-S bonds in the thioredoxin-like family of proteins. Biol Chem 2018; 400:575-587. [DOI: 10.1515/hsz-2018-0319] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/22/2018] [Indexed: 02/06/2023]
Abstract
Abstract
Disulfide bonds play a critical role in a variety of structural and mechanistic processes associated with proteins inside the cells and in the extracellular environment. The thioredoxin family of proteins like thioredoxin (Trx), glutaredoxin (Grx) and protein disulfide isomerase, are involved in the formation, transfer or isomerization of disulfide bonds through a characteristic thiol-disulfide exchange reaction. Here, we review the structural and mechanistic determinants behind the thiol-disulfide exchange reactions for the different enzyme types within this family, rationalizing the known experimental data in light of the results from computational studies. The analysis sheds new atomic-level insight into the structural and mechanistic variations that characterize the different enzymes in the family, helping to explain the associated functional diversity. Furthermore, we review here a pattern of stabilization/destabilization of the conserved active-site cysteine residues presented beforehand, which is fully consistent with the observed roles played by the thioredoxin family of enzymes.
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Affiliation(s)
- Sérgio F. Sousa
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade do Porto , Rua do Campo Alegre, s/n , 4169-007 Porto , Portugal
| | - Rui P.P. Neves
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade do Porto , Rua do Campo Alegre, s/n , 4169-007 Porto , Portugal
| | - Sodiq O. Waheed
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade do Porto , Rua do Campo Alegre, s/n , 4169-007 Porto , Portugal
| | - Pedro A. Fernandes
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade do Porto , Rua do Campo Alegre, s/n , 4169-007 Porto , Portugal
| | - Maria João Ramos
- UCIBIO@REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências , Universidade do Porto , Rua do Campo Alegre, s/n , 4169-007 Porto , Portugal
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99973
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Si W, Wang L, Usongo V, Zhao X. Colistin Induces S. aureus Susceptibility to Bacitracin. Front Microbiol 2018; 9:2805. [PMID: 30515145 PMCID: PMC6255926 DOI: 10.3389/fmicb.2018.02805] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 10/31/2018] [Indexed: 01/11/2023] Open
Abstract
Bacitracin has been used in topical preparations with polymyxin B for bacterial infections. Colistin belongs to the polymyxin group of antibiotics and is effective against most Gram-negative bacilli. This study investigated whether colistin could affect the susceptibility of S. aureus to bacitracin. S. aureus isolates were first incubated with colistin and the susceptibility of S. aureus to bacitracin was increased. The effect of the combination of colistin and bacitracin on S. aureus was then confirmed by the checkerboard assay and the time-kill kinetics. The Triton X-100-induced autolysis was significantly increased after S. aureus was exposed to colistin. Exposure to colistin also led to a less positive charge on the cell surface and a significant leakage of Na+, Mg2, K+, Ca2+, Mn2+, Cu2+, and Zn2+. Finally, disruptions on the cell surface and an irregular morphology were observed when the bacteria were exposed to colistin and bacitracin. Bacitracin had a stronger antibacterial activity against S. aureus in the presence of colistin. This could be due to the fact that colistin damaged the bacterial membrane. This study suggests that combination of colistin with bacitracin has a potential for treating clinical S. aureus infections.
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Affiliation(s)
- Wei Si
- Department of Animal Science, McGill University, Montreal, QC, Canada
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Liangliang Wang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Valentine Usongo
- Department of Animal Science, McGill University, Montreal, QC, Canada
| | - Xin Zhao
- Department of Animal Science, McGill University, Montreal, QC, Canada
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99974
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Berthier A, Vinod M, Porez G, Steenackers A, Alexandre J, Yamakawa N, Gheeraert C, Ploton M, Maréchal X, Dubois-Chevalier J, Hovasse A, Schaeffer-Reiss C, Cianférani S, Rolando C, Bray F, Duez H, Eeckhoute J, Lefebvre T, Staels B, Lefebvre P. Combinatorial regulation of hepatic cytoplasmic signaling and nuclear transcriptional events by the OGT/REV-ERBα complex. Proc Natl Acad Sci U S A 2018; 115:E11033-E11042. [PMID: 30397120 PMCID: PMC6255172 DOI: 10.1073/pnas.1805397115] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The nuclear receptor REV-ERBα integrates the circadian clock with hepatic glucose and lipid metabolism by nucleating transcriptional comodulators at genomic regulatory regions. An interactomic approach identified O-GlcNAc transferase (OGT) as a REV-ERBα-interacting protein. By shielding cytoplasmic OGT from proteasomal degradation and favoring OGT activity in the nucleus, REV-ERBα cyclically increased O-GlcNAcylation of multiple cytoplasmic and nuclear proteins as a function of its rhythmically regulated expression, while REV-ERBα ligands mostly affected cytoplasmic OGT activity. We illustrate this finding by showing that REV-ERBα controls OGT-dependent activities of the cytoplasmic protein kinase AKT, an essential relay in insulin signaling, and of ten-of-eleven translocation (TET) enzymes in the nucleus. AKT phosphorylation was inversely correlated to REV-ERBα expression. REV-ERBα enhanced TET activity and DNA hydroxymethylated cytosine (5hmC) levels in the vicinity of REV-ERBα genomic binding sites. As an example, we show that the REV-ERBα/OGT complex modulates SREBP-1c gene expression throughout the fasting/feeding periods by first repressing AKT phosphorylation and by epigenomically priming the Srebf1 promoter for a further rapid response to insulin. Conclusion: REV-ERBα regulates cytoplasmic and nuclear OGT-controlled processes that integrate at the hepatic SREBF1 locus to control basal and insulin-induced expression of the temporally and nutritionally regulated lipogenic SREBP-1c transcript.
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Affiliation(s)
- Alexandre Berthier
- University of Lille, Inserm, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, European Genomic Institute for Diabetes, U1011, Lille F-59045, France
| | - Manjula Vinod
- University of Lille, Inserm, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, European Genomic Institute for Diabetes, U1011, Lille F-59045, France
| | - Geoffrey Porez
- University of Lille, Inserm, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, European Genomic Institute for Diabetes, U1011, Lille F-59045, France
| | - Agata Steenackers
- University of Lille, CNRS, Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576, Villeneuve d'Ascq F-59655, France
| | - Jérémy Alexandre
- University of Lille, Inserm, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, European Genomic Institute for Diabetes, U1011, Lille F-59045, France
| | - Nao Yamakawa
- University of Lille, CNRS, Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576, Villeneuve d'Ascq F-59655, France
| | - Céline Gheeraert
- University of Lille, Inserm, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, European Genomic Institute for Diabetes, U1011, Lille F-59045, France
| | - Maheul Ploton
- University of Lille, Inserm, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, European Genomic Institute for Diabetes, U1011, Lille F-59045, France
| | - Xavier Maréchal
- University of Lille, Inserm, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, European Genomic Institute for Diabetes, U1011, Lille F-59045, France
| | - Julie Dubois-Chevalier
- University of Lille, Inserm, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, European Genomic Institute for Diabetes, U1011, Lille F-59045, France
| | - Agnès Hovasse
- Laboratoire de Spectrométrie de Masse BioOrganique, University of Strasbourg, CNRS, Institut Pluridisciplinaire Hubert Curien, UMR 7178, Strasbourg F-67037, France
| | - Christine Schaeffer-Reiss
- Laboratoire de Spectrométrie de Masse BioOrganique, University of Strasbourg, CNRS, Institut Pluridisciplinaire Hubert Curien, UMR 7178, Strasbourg F-67037, France
| | - Sarah Cianférani
- Laboratoire de Spectrométrie de Masse BioOrganique, University of Strasbourg, CNRS, Institut Pluridisciplinaire Hubert Curien, UMR 7178, Strasbourg F-67037, France
| | - Christian Rolando
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique, CNRS, Unité de Service et de Recherche (USR) 3290, University of Lille, Villeneuve d'Ascq F-59655, France
- Fédération de Recherche Biochimie Structurale et Fonctionnelle des Assemblages Biomoléculaires FRABio, FR 3688 CNRS, University of Lille, Villeneuve d'Ascq F-59655, France
- Institut M.-E. Chevreul, CNRS, FR 2638, University of Lille, Villeneuve d'Ascq F-59655, France
| | - Fabrice Bray
- Miniaturisation pour la Synthèse, l'Analyse & la Protéomique, CNRS, Unité de Service et de Recherche (USR) 3290, University of Lille, Villeneuve d'Ascq F-59655, France
- Fédération de Recherche Biochimie Structurale et Fonctionnelle des Assemblages Biomoléculaires FRABio, FR 3688 CNRS, University of Lille, Villeneuve d'Ascq F-59655, France
- Institut M.-E. Chevreul, CNRS, FR 2638, University of Lille, Villeneuve d'Ascq F-59655, France
| | - Hélène Duez
- University of Lille, Inserm, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, European Genomic Institute for Diabetes, U1011, Lille F-59045, France
| | - Jérôme Eeckhoute
- University of Lille, Inserm, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, European Genomic Institute for Diabetes, U1011, Lille F-59045, France
| | - Tony Lefebvre
- University of Lille, CNRS, Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576, Villeneuve d'Ascq F-59655, France
| | - Bart Staels
- University of Lille, Inserm, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, European Genomic Institute for Diabetes, U1011, Lille F-59045, France
| | - Philippe Lefebvre
- University of Lille, Inserm, Centre Hospitalier Universitaire de Lille, Institut Pasteur de Lille, European Genomic Institute for Diabetes, U1011, Lille F-59045, France;
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99975
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Mizoguchi T, Shimazawa M, Ohuchi K, Kuse Y, Nakamura S, Hara H. Impaired Cerebellar Development in Mice Overexpressing VGF. Neurochem Res 2018; 44:374-387. [PMID: 30460640 DOI: 10.1007/s11064-018-2684-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/09/2018] [Accepted: 11/15/2018] [Indexed: 12/14/2022]
Abstract
VGF nerve growth factor inducible (VGF) is a neuropeptide precursor induced by brain-derived neurotrophic factor and nerve growth factor. VGF is increased in the prefrontal cortex and cerebrospinal fluid in schizophrenia patients. In our previous study, VGF-overexpressing mice exhibited schizophrenia-like behaviors and smaller brain weights. Brain developmental abnormality is one cause of mental illness. Research on brain development is important for discovery of pathogenesis of mental disorders. In the present study, we investigated the role of VGF on cerebellar development. We performed a histological analysis with cerebellar sections of adult and postnatal day 3 mice by Nissl staining. To investigate cerebellar development, we performed immunostaining with antibodies of immature and mature granule cell markers. To understand the mechanism underlying these histological changes, we examined MAPK, Wnt, and sonic hedgehog signaling by Western blot. Finally, we performed rotarod and footprint tests using adult mice to investigate motor function. VGF-overexpressing adult mice exhibited smaller cerebellar sagittal section area. In postnatal day 3 mice, a cerebellar sagittal section area reduction of the whole cerebellum and external granule layer and a decrease in the number of mature granule cells were found in VGF-overexpressing mice. Additionally, the number of proliferative granule cell precursors was lower in VGF-overexpressing mice. Phosphorylation of Trk and Erk1 were increased in the cerebellum of postnatal day 3 VGF-overexpressing mice. Adult VGF-overexpressing mice exhibited motor disability. All together, these findings implicate VGF in the development of cerebellar granule cells via promoting MAPK signaling and motor function in the adult stage.
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Affiliation(s)
- Takahiro Mizoguchi
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, 1-25-4 Daigaku-Nishi, Gifu, 501-1196, Japan
| | - Masamitsu Shimazawa
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, 1-25-4 Daigaku-Nishi, Gifu, 501-1196, Japan
| | - Kazuki Ohuchi
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, 1-25-4 Daigaku-Nishi, Gifu, 501-1196, Japan
| | - Yoshiki Kuse
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, 1-25-4 Daigaku-Nishi, Gifu, 501-1196, Japan
| | - Shinsuke Nakamura
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, 1-25-4 Daigaku-Nishi, Gifu, 501-1196, Japan
| | - Hideaki Hara
- Molecular Pharmacology, Department of Biofunctional Evaluation, Gifu Pharmaceutical University, 1-25-4 Daigaku-Nishi, Gifu, 501-1196, Japan.
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99976
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Méndez-Ardoy A, Lostalé-Seijo I, Montenegro J. Where in the Cell Is our Cargo? Methods Currently Used To Study Intracellular Cytosolic Localisation. Chembiochem 2018; 20:488-498. [PMID: 30178574 DOI: 10.1002/cbic.201800390] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Indexed: 12/14/2022]
Abstract
The internalisation and delivery of active substances into cells is a field of growing interest for chemical biology and therapeutics. As we move from small-molecule-based drugs towards bigger cargos, such as antibodies, enzymes, nucleases or nucleic acids, the development of efficient delivery systems becomes critical for their practical application. Different strategies and synthetic carriers have been developed; these include cationic lipids, gold nanoparticles, polymers, cell-penetrating peptides (CPPs), protein surface modification etc. However, all of these methodologies still present limitations relating to the precise targeting of the different intracellular compartments and, in particular, difficulties in access to the cellular cytosol. Additionally, the precise quantification of the cellular uptake of a compound is not enough to demonstrate delivery and/or functional activity. Therefore, methods to determine cellular distributions of cargos and carriers are of critical importance for identifying the barriers that are blocking the activity. Herein we survey the different techniques that can currently be used to track and to monitor the subcellular localisation of the synthetic compounds that we deliver inside cells.
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Affiliation(s)
- Alejandro Méndez-Ardoy
- Centro Singular de Investigación en Química Biolóxica e, Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Irene Lostalé-Seijo
- Centro Singular de Investigación en Química Biolóxica e, Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
| | - Javier Montenegro
- Centro Singular de Investigación en Química Biolóxica e, Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782, Santiago de Compostela, Spain
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99977
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Yu Q, Li J, Murrell MP, Kim T. Balance between Force Generation and Relaxation Leads to Pulsed Contraction of Actomyosin Networks. Biophys J 2018; 115:2003-2013. [PMID: 30389091 PMCID: PMC6303541 DOI: 10.1016/j.bpj.2018.10.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 08/23/2018] [Accepted: 10/05/2018] [Indexed: 01/07/2023] Open
Abstract
Actomyosin contractility regulates various biological processes, including cell migration and cytokinesis. The cell cortex underlying the membrane of eukaryote cells exhibits dynamic contractile behaviors facilitated by actomyosin contractility. Interestingly, the cell cortex shows reversible aggregation of actin and myosin called "pulsed contraction" in diverse cellular phenomena, such as embryogenesis and tissue morphogenesis. Although contractile behaviors of actomyosin machinery have been studied extensively in several in vitro experiments and computational studies, none of them successfully reproduced the pulsed contraction observed in vivo. Recent experiments have suggested the pulsed contraction is dependent upon the spatiotemporal expression of a small GTPase protein called RhoA. This only indicates the significance of biochemical signaling pathways during the pulsed contraction. In this study, we reproduced the pulsed contraction with only the mechanical and dynamic behaviors of cytoskeletal elements. First, we observed that small pulsed clusters or clusters with fluctuating sizes may appear when there is subtle balance between force generation from motors and force relaxation induced by actin turnover. However, the size and duration of these clusters differ from those of clusters observed during the cellular phenomena. We found that clusters with physiologically relevant size and duration can appear only with both actin turnover and angle-dependent F-actin severing resulting from buckling induced by motor activities. We showed how parameters governing F-actin severing events regulate the size and duration of pulsed clusters. Our study sheds light on the underestimated significance of F-actin severing for the pulsed contraction observed in physiological processes.
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Affiliation(s)
- Qilin Yu
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana
| | - Jing Li
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana
| | - Michael P Murrell
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut; Systems Biology Institute, Yale University, West Haven, Connecticut
| | - Taeyoon Kim
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana.
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99978
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Computational approaches for detection and quantification of A-to-I RNA-editing. Methods 2018; 156:25-31. [PMID: 30465820 DOI: 10.1016/j.ymeth.2018.11.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 11/14/2018] [Accepted: 11/16/2018] [Indexed: 02/07/2023] Open
Abstract
Adenosine deaminases that act on RNA (ADARs) catalyze adenosine-to-inosine (A-to-I) RNA editing in double-stranded RNA. Such editing is important for protection against false activation of the immune system, but also confers plasticity on the transcriptome by generating several versions of a transcript from a single genomic locus. Recently, great efforts were made in developing computational methods for detecting editing events directly from RNA-sequencing (RNA-seq) data. These efforts have led to an improved understanding of the makeup of the editome in various genomes. Here we review recent advances in editing detection based on the data available to the researcher, with emphasis on the principles underlying the various methods and the limitations they were designed to overcome. We also discuss the available various methods for analyzing and quantifying editing levels. This review collects and organizes the available approaches for analyzing RNA editing and discuss the current status of the different A-to-I detection methods with possible directions for extending these approaches.
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99979
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Abstract
Tight regulation of cellular processes is key to the development of complex organisms but also vital for simpler ones. During evolution, different regulatory systems have emerged, among them RNA-based regulation that is carried out mainly by intramolecular and intermolecular RNA-RNA interactions. However, methods for the transcriptome-wide detection of these interactions were long unavailable. Recently, three publications described high-throughput methods to directly detect RNA duplexes in living cells. This promises to enable in-depth studies of RNA-based regulation and will narrow the gaps in our understanding of RNA structure and function. In this review, we highlight the benefits of these methods and their commonalities and differences and, in particular, point to methodological shortcomings that hamper their wider application. We conclude by presenting ideas for how to overcome these problems and commenting on the prospects we see in this area of research.
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Affiliation(s)
- Brigitte Schönberger
- Institute of Biochemical Engineering, Computational Biology Group, University of Stuttgart, Stuttgart, 70569, Germany
| | - Christoph Schaal
- Institute of Biochemical Engineering, Computational Biology Group, University of Stuttgart, Stuttgart, 70569, Germany
| | - Richard Schäfer
- Institute of Biochemical Engineering, Computational Biology Group, University of Stuttgart, Stuttgart, 70569, Germany
| | - Björn Voß
- Institute of Biochemical Engineering, Computational Biology Group, University of Stuttgart, Stuttgart, 70569, Germany
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99980
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Zuo F, Yu R, Xiao M, Khaskheli GB, Sun X, Ma H, Ren F, Zhang B, Chen S. Transcriptomic analysis of Bifidobacterium longum subsp. longum BBMN68 in response to oxidative shock. Sci Rep 2018; 8:17085. [PMID: 30459453 PMCID: PMC6244367 DOI: 10.1038/s41598-018-35286-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 10/18/2018] [Indexed: 02/08/2023] Open
Abstract
Bifidobacterium longum strain BBMN68 is sensitive to low concentrations of oxygen. A transcriptomic study was performed to identify candidate genes for B. longum BBMN68's response to oxygen treatment (3%, v/v). Expression of genes and pathways of B. longum BBMN68 involved in nucleotide metabolism, amino acid transport, protein turnover and chaperones increased, and that of carbohydrate metabolism, translation and biogenesis decreased to adapt to the oxidative stress. Notably, expression of two classes of ribonucleotide reductase (RNR), which are important for deoxyribonucleotide biosynthesis, was rapidly and persistently induced. First, the class Ib RNR NrdHIEF was immediately upregulated after 5 min oxygen exposure, followed by the class III RNR NrdDG, which was upregulated after 20 min of exposure. The upregulated expression of branched-chain amino acids and tetrahydrofolate biosynthesis-related genes occurred in bifidobacteria in response to oxidative stress. These change toward to compensate for DNA and protein damaged by reactive oxygen species (ROS). In addition, oxidative stress resulted in improved B. longum BBMN68 cell hydrophobicity and autoaggregation. These results provide a rich resource for our understanding of the response mechanisms to oxidative stress in bifidobacteria.
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Affiliation(s)
- Fanglei Zuo
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China.,Key Laboratory of Functional Dairy, Department of Food Science and Engineering, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China.,Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691, Stockholm, Sweden
| | - Rui Yu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China.,Key Laboratory of Functional Dairy, Department of Food Science and Engineering, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Man Xiao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China.,Key Laboratory of Functional Dairy, Department of Food Science and Engineering, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Gul Bahar Khaskheli
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China.,Key Laboratory of Functional Dairy, Department of Food Science and Engineering, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Xiaofei Sun
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Huiqin Ma
- Department of Fruit Tree Sciences, College of Horticulture, China Agricultural University, Beijing, 100193, P. R. China
| | - Fazheng Ren
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China
| | - Bing Zhang
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, P. R. China
| | - Shangwu Chen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China. .,Key Laboratory of Functional Dairy, Department of Food Science and Engineering, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, P. R. China.
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99981
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Martyn B, Biggs CI, Gibson MI. Comparison of systematically functionalized heterogeneous and homogenous glycopolymers as toxin inhibitors. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/pola.29279] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Benjamin Martyn
- Department of ChemistryUniversity of Warwick Gibbet Hill Road Coventry CV4 7AL United Kingdom
| | - Caroline I. Biggs
- Department of ChemistryUniversity of Warwick Gibbet Hill Road Coventry CV4 7AL United Kingdom
| | - Matthew I. Gibson
- Department of ChemistryUniversity of Warwick Gibbet Hill Road Coventry CV4 7AL United Kingdom
- Warwick Medical SchoolUniversity of Warwick Gibbet Hill Road Coventry CV4 7AL United Kingdom
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99982
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Bazan B, Wiktor M, Maszczak-Seneczko D, Olczak T, Kaczmarek B, Olczak M. Lysine at position 329 within a C-terminal dilysine motif is crucial for the ER localization of human SLC35B4. PLoS One 2018; 13:e0207521. [PMID: 30458018 PMCID: PMC6245738 DOI: 10.1371/journal.pone.0207521] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 11/01/2018] [Indexed: 12/21/2022] Open
Abstract
SLC35B4 belongs to the solute carrier 35 (SLC35) family whose best-characterized members display a nucleotide sugar transporting activity. Using an experimental model of HepG2 cells and indirect immunofluorescent staining, we verified that SLC35B4 was localized to the endoplasmic reticulum (ER). We demonstrated that dilysine motif, especially lysine at position 329, is crucial for the ER localization of this protein in human cells and therefore one should use protein C-tagging with caution. To verify the importance of the protein in glycoconjugates synthesis, we generated SLC35B4-deficient HepG2 cell line using CRISPR-Cas9 approach. Our data showed that knock-out of the SLC35B4 gene does not affect major UDP-Xyl- and UDP-GlcNAc-dependent glycosylation pathways.
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Affiliation(s)
- Bożena Bazan
- Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Maciej Wiktor
- Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | | | - Teresa Olczak
- Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Beata Kaczmarek
- Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Mariusz Olczak
- Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
- * E-mail:
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99983
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Smith ER, Capo-Chichi CD, Xu XX. Defective Nuclear Lamina in Aneuploidy and Carcinogenesis. Front Oncol 2018; 8:529. [PMID: 30524960 PMCID: PMC6256246 DOI: 10.3389/fonc.2018.00529] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 10/29/2018] [Indexed: 01/05/2023] Open
Abstract
Aneuploidy, loss or gain of whole chromosomes, is a prominent feature of carcinomas, and is generally considered to play an important role in the initiation and progression of cancer. In high-grade serous ovarian cancer, the only common gene aberration is the p53 point mutation, though extensive genomic perturbation is common due to severe aneuploidy, which presents as a deviant karyotype. Several mechanisms for the development of aneuploidy in cancer cells have been recognized, including chromosomal non-disjunction during mitosis, centrosome amplification, and more recently, nuclear envelope rupture at interphase. Many cancer types including ovarian cancer have lost or reduced expression of Lamin A/C, a structural component of the lamina matrix that underlies the nuclear envelope in differentiated cells. Several recent studies suggest that a nuclear lamina defect caused by the loss or reduction of Lamin A/C leads to failure in cytokinesis and formation of tetraploid cells, transient nuclear envelope rupture, and formation of nuclear protrusions and micronuclei during the cell cycle gap phase. Thus, loss and reduction of Lamin A/C underlies the two common features of cancer—aberrations in nuclear morphology and aneuploidy. We discuss here and emphasize the newly recognized mechanism of chromosomal instability due to the rupture of a defective nuclear lamina, which may account for the rapid genomic changes in carcinogenesis.
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Affiliation(s)
- Elizabeth R Smith
- Department of Cell Biology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Callinice D Capo-Chichi
- Department of Cell Biology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, United States.,Laboratory of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, University of Abomey-Calavi, Abomey Calavi, Benin
| | - Xiang-Xi Xu
- Department of Cell Biology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, United States
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99984
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Histone acetyltransferase CBP-related H3K23 acetylation contributes to courtship learning in Drosophila. BMC DEVELOPMENTAL BIOLOGY 2018; 18:20. [PMID: 30458702 PMCID: PMC6247617 DOI: 10.1186/s12861-018-0179-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 11/05/2018] [Indexed: 12/16/2022]
Abstract
Background Histone modifications are critical in regulating neuronal processes. However, the impacts of individual histone modifications on learning and memory are elusive. Here, we investigated the contributions of histone H3 lysine modifications to learning and memory in Drosophila by using histone lysine-to-alanine mutants. Results Behavioural analysis indicated that compared to the H3WT group, mutants overexpressing H3K23A displayed impaired courtship learning. Chromatin immunoprecipitation analysis of H3K23A mutants showed that H3K23 acetylation (H3K23ac) levels were decreased on learning-related genes. Knockdown of CREB-binding protein (CBP) decreased H3K23ac levels, attenuated the expression of learning-related genes, led to a courtship learning defect and altered development of the mushroom bodies. A decline in courtship learning ability was observed in both larvae and adult treatments with ICG-001. Furthermore, treatment of Drosophila overexpressing mutated H3K23A with a CBP inhibitor did not aggravate the learning defect. Conclusions H3K23ac, catalysed by the acetyltransferases dCBP, contributes to Drosophila learning, likely by controlling the expression of specific genes. This is a novel epigenetic regulatory mechanism underlying neuronal behaviours. Electronic supplementary material The online version of this article (10.1186/s12861-018-0179-z) contains supplementary material, which is available to authorized users.
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99985
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Nguyen MT, Somogyvári M, Sőti C. Hsp90 Stabilizes SIRT1 Orthologs in Mammalian Cells and C. elegans. Int J Mol Sci 2018; 19:ijms19113661. [PMID: 30463299 PMCID: PMC6274930 DOI: 10.3390/ijms19113661] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/15/2018] [Accepted: 11/16/2018] [Indexed: 01/02/2023] Open
Abstract
Sirtuin 1 (SIRT1) othologs are ubiquitous NAD+-dependent deacetylases that act as nutrient sensors and modulate metabolism and stress responses in diverse organisms. Both mammalian SIRT1 and Caenorhabditis elegans SIR-2.1 have been implicated in dietary restriction, longevity, and healthspan. Hsp90 is an evolutionarily conserved molecular chaperone that stabilizes a plethora of signaling ’client’ proteins and regulates fundamental biological processes. Here we report that Hsp90 is required for conformational stabilization of SIRT1 and SIR-2.1. We find that inhibition of Hsp90 by geldanamycin (GA) induces the depletion of mammalian SIRT1 protein in a concentration and time dependent manner in COS-7 and HepG2 cells. In contrast to SIRT1, SIRT2 level remains unchanged by GA treatment, reflecting a specific Hsp90 SIRT1 interaction. Hsp90 inhibition leads to the destabilization and proteasomal degradation of SIRT1. Moreover, we observe a GA-sensitive physical interaction between SIRT1 and Hsp90 by immunoprecipitation. We also demonstrate that hsp-90 gene silencing also induces SIR-2.1 protein depletion and proteasomal degradation in C. elegans. Our findings identify metazoan SIRT1 orthologs as Hsp90 clients and reveal a novel crosstalk between the proteostasis and nutrient signaling networks, which may have implications in various age related diseases.
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Affiliation(s)
- Minh Tu Nguyen
- Department of Medical Chemistry, Semmelweis University, H-1094 Budapest, Hungary.
| | - Milán Somogyvári
- Department of Medical Chemistry, Semmelweis University, H-1094 Budapest, Hungary.
| | - Csaba Sőti
- Department of Medical Chemistry, Semmelweis University, H-1094 Budapest, Hungary.
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99986
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Tung QN, Linzner N, Loi VV, Antelmann H. Application of genetically encoded redox biosensors to measure dynamic changes in the glutathione, bacillithiol and mycothiol redox potentials in pathogenic bacteria. Free Radic Biol Med 2018; 128:84-96. [PMID: 29454879 DOI: 10.1016/j.freeradbiomed.2018.02.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 02/08/2018] [Accepted: 02/13/2018] [Indexed: 12/28/2022]
Abstract
Gram-negative bacteria utilize glutathione (GSH) as their major LMW thiol. However, most Gram-positive bacteria do not encode enzymes for GSH biosynthesis and produce instead alternative LMW thiols, such as bacillithiol (BSH) and mycothiol (MSH). BSH is utilized by Firmicutes and MSH is the major LMW thiol of Actinomycetes. LMW thiols are required to maintain the reduced state of the cytoplasm, but are also involved in virulence mechanisms in human pathogens, such as Staphylococcus aureus, Mycobacterium tuberculosis, Streptococcus pneumoniae, Salmonella enterica subsp. Typhimurium and Listeria monocytogenes. Infection conditions often cause perturbations of the intrabacterial redox balance in pathogens, which is further affected under antibiotics treatments. During the last years, novel glutaredoxin-fused roGFP2 biosensors have been engineered in many eukaryotic organisms, including parasites, yeast, plants and human cells for dynamic live-imaging of the GSH redox potential in different compartments. Likewise bacterial roGFP2-based biosensors are now available to measure the dynamic changes in the GSH, BSH and MSH redox potentials in model and pathogenic Gram-negative and Gram-positive bacteria. In this review, we present an overview of novel functions of the bacterial LMW thiols GSH, MSH and BSH in pathogenic bacteria in virulence regulation. Moreover, recent results about the application of genetically encoded redox biosensors are summarized to study the mechanisms of host-pathogen interactions, persistence and antibiotics resistance. In particularly, we highlight recent biosensor results on the redox changes in the intracellular food-borne pathogen Salmonella Typhimurium as well as in the Gram-positive pathogens S. aureus and M. tuberculosis during infection conditions and under antibiotics treatments. These studies established a link between ROS and antibiotics resistance with the intracellular LMW thiol-redox potential. Future applications should be directed to compare the redox potentials among different clinical isolates of these pathogens in relation to their antibiotics resistance and to screen for new ROS-producing drugs as promising strategy to combat antimicrobial resistance.
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Affiliation(s)
- Quach Ngoc Tung
- Freie Universität Berlin, Institute for Biology-Microbiology, Königin-Luise-Strasse 12-16, D-14195 Berlin, Germany
| | - Nico Linzner
- Freie Universität Berlin, Institute for Biology-Microbiology, Königin-Luise-Strasse 12-16, D-14195 Berlin, Germany
| | - Vu Van Loi
- Freie Universität Berlin, Institute for Biology-Microbiology, Königin-Luise-Strasse 12-16, D-14195 Berlin, Germany
| | - Haike Antelmann
- Freie Universität Berlin, Institute for Biology-Microbiology, Königin-Luise-Strasse 12-16, D-14195 Berlin, Germany.
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99987
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Cook M, Delbecq SP, Schweppe TP, Guttman M, Klevit RE, Brzovic PS. The ubiquitin ligase SspH1 from Salmonella uses a modular and dynamic E3 domain to catalyze substrate ubiquitylation. J Biol Chem 2018; 294:783-793. [PMID: 30459234 DOI: 10.1074/jbc.ra118.004247] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 10/17/2018] [Indexed: 11/06/2022] Open
Abstract
SspH/IpaH bacterial effector E3 ubiquitin (Ub) ligases, unrelated in sequence or structure to eukaryotic E3s, are utilized by a wide variety of Gram-negative bacteria during pathogenesis. These E3s function in a eukaryotic environment, utilize host cell E2 ubiquitin-conjugating enzymes of the Ube2D family, and target host proteins for ubiquitylation. Despite several crystal structures, details of Ube2D∼Ub binding and the mechanism of ubiquitin transfer are poorly understood. Here, we show that the catalytic E3 ligase domain of SspH1 can be divided into two subdomains: an N-terminal subdomain that harbors the active-site cysteine and a C-terminal subdomain containing the Ube2D∼Ub-binding site. SspH1 mutations designed to restrict subdomain motions show rapid formation of an E3∼Ub intermediate, but impaired Ub transfer to substrate. NMR experiments using paramagnetic spin labels reveal how SspH1 binds Ube2D∼Ub and targets the E2∼Ub active site. Unexpectedly, hydrogen/deuterium exchange MS shows that the E2∼Ub-binding region is dynamic but stabilized in the E3∼Ub intermediate. Our results support a model in which both subunits of an Ube2D∼Ub clamp onto a dynamic region of SspH1, promoting an E3 conformation poised for transthiolation. A conformational change is then required for Ub transfer from E3∼Ub to substrate.
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Affiliation(s)
- Matt Cook
- From the Departments of Biochemistry and
| | | | | | - Miklos Guttman
- Medicinal Chemistry, University of Washington, Seattle, Washington 98195
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99988
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Sokol AM, Uszczynska-Ratajczak B, Collins MM, Bazala M, Topf U, Lundegaard PR, Sugunan S, Guenther S, Kuenne C, Graumann J, Chan SSL, Stainier DYR, Chacinska A. Loss of the Mia40a oxidoreductase leads to hepato-pancreatic insufficiency in zebrafish. PLoS Genet 2018; 14:e1007743. [PMID: 30457989 PMCID: PMC6245507 DOI: 10.1371/journal.pgen.1007743] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 10/05/2018] [Indexed: 02/07/2023] Open
Abstract
Development and function of tissues and organs are powered by the activity of mitochondria. In humans, inherited genetic mutations that lead to progressive mitochondrial pathology often manifest during infancy and can lead to death, reflecting the indispensable nature of mitochondrial biogenesis and function. Here, we describe a zebrafish mutant for the gene mia40a (chchd4a), the life-essential homologue of the evolutionarily conserved Mia40 oxidoreductase which drives the biogenesis of cysteine-rich mitochondrial proteins. We report that mia40a mutant animals undergo progressive cellular respiration defects and develop enlarged mitochondria in skeletal muscles before their ultimate death at the larval stage. We generated a deep transcriptomic and proteomic resource that allowed us to identify abnormalities in the development and physiology of endodermal organs, in particular the liver and pancreas. We identify the acinar cells of the exocrine pancreas to be severely affected by mutations in the MIA pathway. Our data contribute to a better understanding of the molecular, cellular and organismal effects of mitochondrial deficiency, important for the accurate diagnosis and future treatment strategies of mitochondrial diseases. Mitochondrial pathologies which result from mutations in the nuclear DNA remain incurable and often lead to death. As mitochondria play various roles in cellular and tissue-specific contexts, the symptoms of mitochondrial pathologies can differ between patients. Thus, diagnosis and treatment of mitochondrial disorders remain challenging. To enhance this, the generation of new models that explore and define the consequences of mitochondria insufficiencies is of central importance. Here, we present a mia40a zebrafish mutant as a model for mitochondrial dysfunction, caused by an imbalance in mitochondrial protein biogenesis. This mutant shares characteristics with existing reports on mitochondria dysfunction, and has led us to identify novel phenotypes such as enlarged mitochondrial clusters in skeletal muscles. In addition, our transcriptomics and proteomics data contribute important findings to the existing knowledge on how faulty mitochondria impinge on vertebrate development in molecular, tissue and organ specific contexts.
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Affiliation(s)
- Anna M. Sokol
- International Institute of Molecular and Cell Biology, Warsaw, Poland
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- * E-mail: (AMS); (AC)
| | | | - Michelle M. Collins
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Michal Bazala
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Ulrike Topf
- International Institute of Molecular and Cell Biology, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Pia R. Lundegaard
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sreedevi Sugunan
- International Institute of Molecular and Cell Biology, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Stefan Guenther
- Bioinformatics and Deep Sequencing Platform, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Carsten Kuenne
- Bioinformatics and Deep Sequencing Platform, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Johannes Graumann
- Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Sherine S. L. Chan
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Didier Y. R. Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Agnieszka Chacinska
- International Institute of Molecular and Cell Biology, Warsaw, Poland
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
- * E-mail: (AMS); (AC)
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99989
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Kalishwaralal K, Kwon WY, Park KS. Exosomes for Non-Invasive Cancer Monitoring. Biotechnol J 2018; 14:e1800430. [PMID: 30358137 DOI: 10.1002/biot.201800430] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 10/02/2018] [Indexed: 12/17/2022]
Abstract
Exosomes, membrane-bound phospholipid vesicles having diameters of 50-200 nm, are secreted by all cell types and circulate in human body fluids. These vesicles are known to carry cellular constituents that are specific to the originating cells (e.g., cytoplasmic/membrane proteins, RNA, and DNA). Thus, exosomes, which are both structurally stable and abundant, are robust indicators of cancers and, as a result, they have been utilized to monitor this disease in a manner that is less invasive than gold standard tissue biopsies. In this review, the history of exosomes and the specific biomarkers present in exosomes that enable accurate monitoring of various diseases are described. In addition, methods for analysis of exosomes and identification of biomarkers are presented with special emphasis being given to isolation and signaling strategies. Lastly, integrated, microfluidic systems developed for exosome-based cancer diagnosis are described and future directions that research in this area will likely take are presented.
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Affiliation(s)
- Kalimuthu Kalishwaralal
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Woo Young Kwon
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Ki Soo Park
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, Republic of Korea
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99990
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Bell TA, Baker TA, Sauer RT. Hinge-Linker Elements in the AAA+ Protein Unfoldase ClpX Mediate Intersubunit Communication, Assembly, and Mechanical Activity. Biochemistry 2018; 57:6787-6796. [PMID: 30418765 DOI: 10.1021/acs.biochem.8b00907] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The ClpXP protease plays important roles in protein homeostasis and quality control. ClpX is a ring-shaped AAA+ homohexamer that unfolds target proteins and translocates them into the ClpP peptidase for degradation. AAA+ modules in each ClpX subunit-consisting of a large AAA+ domain, a short hinge-linker element, and a small AAA+ domain-mediate the mechanical activities of the ring hexamer. Here, we investigate the roles of these hinge-linker elements in ClpX function. Deleting one hinge-linker element in a single-chain ClpX pseudohexamer dramatically decreases unfolding and degradation activity, in part by compromising the formation of closed rings, protein-substrate binding, and ClpP binding. Covalently reclosing the broken hinge-linker interface rescues activity. Deleting one hinge-linker element from a single-chain dimer or trimer prevents assembly of stable hexamers. Mutationally disrupting a hinge-linker element preserves closed-ring assembly but reduces ATP-hydrolysis cooperativity and degradation activity. These results indicate that hinge-linker length and flexibility are optimized for efficient substrate unfolding and support a model in which the hinge-linker elements of ClpX facilitate efficient degradation both by maintaining proper ring geometry and facilitating subunit-subunit communication. This model informs our understanding of ClpX as well as the larger AAA+ family of motor proteins, which play diverse roles in converting chemical into mechanical energy in all cells.
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99991
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Chen M, Yin X, Lu C, Chen X, Ba H, Cai J, Sun J. Mahanine induces apoptosis, cell cycle arrest, inhibition of cell migration, invasion and PI3K/AKT/mTOR signalling pathway in glioma cells and inhibits tumor growth in vivo. Chem Biol Interact 2018; 299:1-7. [PMID: 30468732 DOI: 10.1016/j.cbi.2018.11.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/31/2018] [Accepted: 11/19/2018] [Indexed: 02/06/2023]
Abstract
Gliomas are among the most frequent types of primary malignancies in the central nervous system. The main treatment for glioma includes surgical resection followed by a combination of radiotherapy and chemotherapy. Despite the availability of several treatments, the average survival for patients with glioma at advanced stages still remains 16 months only. Therefore, there is an urgent need to look for novel and more efficient drug candidates for the treatment of glioma. In the current study the anticancer activity of Mahanine was evaluated against a panel of glioma cells. The results revealed that Mahanine exerted significant anticancer effects on the glioma HS 683 cells with an IC50 of 7.5 μM. However, the cytotoxic effects were less pronounced on the normal human astrocytes. Further the results showed that the anticancer effects were mainly due to induction of apoptosis and G2/M cell cycle arrest. Western blotting showed that Mahanine caused upregulation of Bax, cytochrome c, cleaved caspase 3 and 9 and cleaved PARP. However, the expression of cell cycle related proteins pCdc25c, Cdc25c, pCdc2, Cdc2 and cyclin B1 was significantly downregulated. The effect of Mahanine on the migration and invasion of HS 683 cells was also determined and results indicated that Mahanine inhibited the cell migration and invasion at IC50. Additionally, Mahanine-inhibited cell growth was simultaneous with suppression of p-PI3K, p-AKT and p-mTOR. Taken together these results indicate that Mahanine may prove to be an important lead molecule for the treatment of glioma and warrants further investigation.
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Affiliation(s)
- Maohua Chen
- Department of Neurosurgery, Wenzhou Central Hospital, Affiliated Dingli Clinical Institute of Wenzhou Medical University, Wenzhou, 325000, China
| | - Xiangqian Yin
- Department of Oncology, Wuhan Huangpi People's Hospital, 430300 , Wuhan, China
| | - Chuan Lu
- Department of Neurosurgery, Wenzhou Central Hospital, Affiliated Dingli Clinical Institute of Wenzhou Medical University, Wenzhou, 325000, China
| | - Xiandong Chen
- Department of Neurosurgery, Wenzhou Central Hospital, Affiliated Dingli Clinical Institute of Wenzhou Medical University, Wenzhou, 325000, China
| | - Huajun Ba
- Department of Neurosurgery, Wenzhou Central Hospital, Affiliated Dingli Clinical Institute of Wenzhou Medical University, Wenzhou, 325000, China
| | - Jianyong Cai
- Department of Neurosurgery, Wenzhou Central Hospital, Affiliated Dingli Clinical Institute of Wenzhou Medical University, Wenzhou, 325000, China
| | - Jun Sun
- Department of Neurosurgery, Wenzhou Central Hospital, Affiliated Dingli Clinical Institute of Wenzhou Medical University, Wenzhou, 325000, China.
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99992
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Cheung NJ, Yu W. De novo protein structure prediction using ultra-fast molecular dynamics simulation. PLoS One 2018; 13:e0205819. [PMID: 30458007 PMCID: PMC6245515 DOI: 10.1371/journal.pone.0205819] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 10/02/2018] [Indexed: 11/19/2022] Open
Abstract
Modern genomics sequencing techniques have provided a massive amount of protein sequences, but experimental endeavor in determining protein structures is largely lagging far behind the vast and unexplored sequences. Apparently, computational biology is playing a more important role in protein structure prediction than ever. Here, we present a system of de novo predictor, termed NiDelta, building on a deep convolutional neural network and statistical potential enabling molecular dynamics simulation for modeling protein tertiary structure. Combining with evolutionary-based residue-contacts, the presented predictor can predict the tertiary structures of a number of target proteins with remarkable accuracy. The proposed approach is demonstrated by calculations on a set of eighteen large proteins from different fold classes. The results show that the ultra-fast molecular dynamics simulation could dramatically reduce the gap between the sequence and its structure at atom level, and it could also present high efficiency in protein structure determination if sparse experimental data is available.
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Affiliation(s)
- Ngaam J. Cheung
- Department of Brain and Cognitive Science, DGIST, Daegu, South Korea
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Wookyung Yu
- Department of Brain and Cognitive Science, DGIST, Daegu, South Korea
- Core Protein Resources Center, DGIST, Daegu, South Korea
- * E-mail:
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99993
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Paudel BP, Fiorini E, Börner R, Sigel RKO, Rueda DS. Optimal molecular crowding accelerates group II intron folding and maximizes catalysis. Proc Natl Acad Sci U S A 2018; 115:11917-11922. [PMID: 30397128 PMCID: PMC6255197 DOI: 10.1073/pnas.1806685115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Unlike in vivo conditions, group II intron ribozymes are known to require high magnesium(II) concentrations ([Mg2+]) and high temperatures (42 °C) for folding and catalysis in vitro. A possible explanation for this difference is the highly crowded cellular environment, which can be mimicked in vitro by macromolecular crowding agents. Here, we combined bulk activity assays and single-molecule Förster Resonance Energy Transfer (smFRET) to study the influence of polyethylene glycol (PEG) on catalysis and folding of the ribozyme. Our activity studies reveal that PEG reduces the [Mg2+] required, and we found an "optimum" [PEG] that yields maximum activity. smFRET experiments show that the most compact state population, the putative active state, increases with increasing [PEG]. Dynamic transitions between folded states also increase. Therefore, this study shows that optimal molecular crowding concentrations help the ribozyme not only to reach the native fold but also to increase its in vitro activity to approach that in physiological conditions.
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Affiliation(s)
- Bishnu P Paudel
- Molecular Virology, Department of Medicine, Imperial College London, London W12 0NN, United Kingdom
- Single Molecule Imaging, Medical Research Council London Institute of Medical Sciences, London W12 0NN, United Kingdom
| | - Erica Fiorini
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Richard Börner
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Roland K O Sigel
- Department of Chemistry, University of Zurich, 8057 Zurich, Switzerland
| | - David S Rueda
- Molecular Virology, Department of Medicine, Imperial College London, London W12 0NN, United Kingdom;
- Single Molecule Imaging, Medical Research Council London Institute of Medical Sciences, London W12 0NN, United Kingdom
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99994
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Reichard A, Asosingh K. The role of mitochondria in angiogenesis. Mol Biol Rep 2018; 46:1393-1400. [PMID: 30460535 DOI: 10.1007/s11033-018-4488-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 11/09/2018] [Indexed: 12/19/2022]
Abstract
Angiogenesis extends pre-existing blood vessels to improve oxygen and nutrient delivery to inflamed or otherwise hypoxic tissues. Mitochondria are integral in this process, controlling cellular metabolism to regulate the proliferation, migration, and survival of endothelial cells which comprise the inner lining of blood vessels. Mitochondrial Complex III senses hypoxic conditions and generates mitochondrial reactive oxygen species which stabilize hypoxia-inducible factor (HIF-1α) protein. HIF-1α induces the transcription of the vegfa gene, allowing the translation of vascular endothelial growth factor protein, which interacts with mature and precursor endothelial cells, mobilizing them to form new blood vessels. This cascade can be inhibited at specific points by means of gene knockdown, enzyme treatment, and introduction of naturally occurring small molecules, providing insight into the relationship between mitochondria and angiogenesis. This review focuses on current knowledge of the overall role of mitochondria in controlling angiogenesis and outlines known inhibitors that have been used to elucidate this pathway which may be useful in future research to control angiogenesis in vivo.
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Affiliation(s)
- Andrew Reichard
- Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, NC22 9500 Euclid Ave., Cleveland, OH, 44195, USA
| | - Kewal Asosingh
- Department of Inflammation and Immunity, Lerner Research Institute, The Cleveland Clinic, NC22 9500 Euclid Ave., Cleveland, OH, 44195, USA. .,Flow Cytometry Core, Lerner Research Institute, The Cleveland Clinic, Cleveland, OH, USA.
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99995
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Pouget JP, Georgakilas AG, Ravanat JL. Targeted and Off-Target (Bystander and Abscopal) Effects of Radiation Therapy: Redox Mechanisms and Risk/Benefit Analysis. Antioxid Redox Signal 2018; 29:1447-1487. [PMID: 29350049 PMCID: PMC6199630 DOI: 10.1089/ars.2017.7267] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
SIGNIFICANCE Radiation therapy (from external beams to unsealed and sealed radionuclide sources) takes advantage of the detrimental effects of the clustered production of radicals and reactive oxygen species (ROS). Research has mainly focused on the interaction of radiation with water, which is the major constituent of living beings, and with nuclear DNA, which contains the genetic information. This led to the so-called target theory according to which cells have to be hit by ionizing particles to elicit an important biological response, including cell death. In cancer therapy, the Poisson law and linear quadratic mathematical models have been used to describe the probability of hits per cell as a function of the radiation dose. Recent Advances: However, in the last 20 years, many studies have shown that radiation generates "danger" signals that propagate from irradiated to nonirradiated cells, leading to bystander and other off-target effects. CRITICAL ISSUES Like for targeted effects, redox mechanisms play a key role also in off-target effects through transmission of ROS and reactive nitrogen species (RNS), and also of cytokines, ATP, and extracellular DNA. Particularly, nuclear factor kappa B is essential for triggering self-sustained production of ROS and RNS, thus making the bystander response similar to inflammation. In some therapeutic cases, this phenomenon is associated with recruitment of immune cells that are involved in distant irradiation effects (called "away-from-target" i.e., abscopal effects). FUTURE DIRECTIONS Determining the contribution of targeted and off-target effects in the clinic is still challenging. This has important consequences not only in radiotherapy but also possibly in diagnostic procedures and in radiation protection.
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Affiliation(s)
- Jean-Pierre Pouget
- 1 Institut de Recherche en Cancérologie de Montpellier (IRCM) , INSERM, Université de Montpellier, Institut Régional du Cancer de Montpellier (ICM), Montpellier, France
| | - Alexandros G Georgakilas
- 2 DNA Damage Laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens , Athens, Greece
| | - Jean-Luc Ravanat
- 3 Univ. Grenoble Alpes , CEA, CNRS INAC SyMMES UMR 5819, Grenoble, France
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99996
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Tomás RF, Martyn B, Bailey TL, Gibson MI. Engineering Cell Surfaces by Covalent Grafting of Synthetic Polymers to Metabolically-Labeled Glycans. ACS Macro Lett 2018; 7:1289-1294. [PMID: 30533278 PMCID: PMC6281312 DOI: 10.1021/acsmacrolett.8b00675] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/09/2018] [Indexed: 12/16/2022]
Abstract
Re-engineering mammalian cell surfaces enables modulation of their phenotype, function, and interactions with external markers and may find application in cell-based therapies. Here we use metabolic glycan labeling to install azido groups onto the cell surface, which can act as anchor points to enable rapid, simple, and robust "click" functionalization by the addition of a polymer bearing orthogonally reactive functionality. Using this strategy, new cell surface functionality was introduced by using telechelic polymers with fluorescence or biotin termini, demonstrating that recruitment of biomacromolecules is possible. This approach may enable the attachment of payloads and modulation of cell function and fate, as well as providing a tool to interface synthetic polymers with biological systems.
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Affiliation(s)
- Ruben
M. F. Tomás
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
- MAS
CDT, Senate House, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Benjamin Martyn
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
| | - Trisha L. Bailey
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
| | - Matthew I. Gibson
- Department
of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
- Warwick
Medical School, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
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Pearson CS, Nemati R, Liu B, Zhang J, Scalabrin M, Li Z, Li H, Fabris D, Belfort M, Belfort G. Structure of an engineered intein reveals thiazoline ring and provides mechanistic insight. Biotechnol Bioeng 2018; 116:709-721. [PMID: 30450538 DOI: 10.1002/bit.26875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/18/2018] [Accepted: 10/26/2018] [Indexed: 11/08/2022]
Abstract
We have engineered an intein which spontaneously and reversibly forms a thiazoline ring at the native N-terminal Lys-Cys splice junction. We identified conditions to stablize the thiazoline ring and provided the first crystallographic evidence, at 1.54 Å resolution, for its existence at an intein active site. The finding bolsters evidence for a tetrahedral oxythiazolidine splicing intermediate. In addition, the pivotal mutation maps to a highly conserved B-block threonine, which is now seen to play a causative role not only in ground-state destabilization of the scissile N-terminal peptide bond, but also in steering the tetrahedral intermediate toward thioester formation, giving new insight into the splicing mechanism. We demonstrated the stability of the thiazoline ring at neutral pH as well as sensitivity to hydrolytic ring opening under acidic conditions. A pH cycling strategy to control N-terminal cleavage is proposed, which may be of interest for biotechnological applications requiring a splicing activity switch, such as for protein recovery in bioprocessing.
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Affiliation(s)
- C Seth Pearson
- Howard P Isermann Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
| | - Reza Nemati
- Department of Chemistry, State University of New York, Albany, New York
| | - Binbin Liu
- Laboratory of Computational & Structural Biology, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Jing Zhang
- Laboratory of Computational & Structural Biology, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Matteo Scalabrin
- Department of Chemistry, State University of New York, Albany, New York
| | - Zhong Li
- Laboratory of Computational & Structural Biology, Wadsworth Center, New York State Department of Health, Albany, New York
| | - Hongmin Li
- Laboratory of Computational & Structural Biology, Wadsworth Center, New York State Department of Health, Albany, New York.,Department of Biomedical Sciences, School of Public Health, Albany, State University of New York, Albany, New York
| | - Dan Fabris
- Department of Chemistry, State University of New York, Albany, New York
| | - Marlene Belfort
- Department of Biomedical Sciences, School of Public Health, Albany, State University of New York, Albany, New York.,Department of Biological Sciences, Albany, State University of New York, Albany, New York
| | - Georges Belfort
- Howard P Isermann Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
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99998
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Chan SHH, Chan JYH. Phosphodiesterase 2 as a Therapeutic Target for Heart Failure: Is Upregulation an Option? Circ Res 2018; 120:13-16. [PMID: 28057782 DOI: 10.1161/circresaha.116.310250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Samuel H H Chan
- From the Institute for Translational Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Taiwan, Republic of China
| | - Julie Y H Chan
- From the Institute for Translational Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Taiwan, Republic of China.
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Apo-Opsin Exists in Equilibrium Between a Predominant Inactive and a Rare Highly Active State. J Neurosci 2018; 39:212-223. [PMID: 30459230 DOI: 10.1523/jneurosci.1980-18.2018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/30/2018] [Accepted: 11/04/2018] [Indexed: 12/17/2022] Open
Abstract
Bleaching adaptation in rod photoreceptors is mediated by apo-opsin, which activates phototransduction with effective activity 105- to 106-fold lower than that of photoactivated rhodopsin (meta II). However, the mechanism that produces such low opsin activity is unknown. To address this question, we sought to record single opsin responses in mouse rods. We used mutant mice lacking efficient calcium feedback to boosts rod responses and generated a small fraction of opsin by photobleaching ∼1% of rhodopsin. The bleach produced a dramatic increase in the frequency of discrete photoresponse-like events. This activity persisted for hours, was quenched by 11-cis-retinal, and was blocked by uncoupling opsin from phototransduction, all indicating opsin as its source. Opsin-driven discrete activity was also observed in rods containing non-activatable rhodopsin, ruling out transactivation of rhodopsin by opsin. We conclude that bleaching adaptation is mediated by opsin that exists in equilibrium between a predominant inactive and a rare meta II-like state.SIGNIFICANCE STATEMENT Electrophysiological analysis is used to show that the G-protein-coupled receptor opsin exists in equilibrium between a predominant inactive and a rare highly active state that mediates bleaching adaptation in photoreceptors.
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100000
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Wu SM, Liu H, Huang PJ, Chang IYF, Lee CC, Yang CY, Tsai WS, Tan BCM. circlncRNAnet: an integrated web-based resource for mapping functional networks of long or circular forms of noncoding RNAs. Gigascience 2018; 7:1-10. [PMID: 29194536 PMCID: PMC5765557 DOI: 10.1093/gigascience/gix118] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 11/22/2017] [Indexed: 12/26/2022] Open
Abstract
Background Despite their lack of protein-coding potential, long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) have emerged as key determinants in gene regulation, acting to fine-tune transcriptional and signaling output. These noncoding RNA transcripts are known to affect expression of messenger RNAs (mRNAs) via epigenetic and post-transcriptional regulation. Given their widespread target spectrum, as well as extensive modes of action, a complete understanding of their biological relevance will depend on integrative analyses of systems data at various levels. Findings While a handful of publicly available databases have been reported, existing tools do not fully capture, from a network perspective, the functional implications of lncRNAs or circRNAs of interest. Through an integrated and streamlined design, circlncRNAnet aims to broaden the understanding of ncRNA candidates by testing in silico several hypotheses of ncRNA-based functions, on the basis of large-scale RNA-seq data. This web server is implemented with several features that represent advances in the bioinformatics of ncRNAs: (1) a flexible framework that accepts and processes user-defined next-generation sequencing–based expression data; (2) multiple analytic modules that assign and productively assess the regulatory networks of user-selected ncRNAs by cross-referencing extensively curated databases; (3) an all-purpose, information-rich workflow design that is tailored to all types of ncRNAs. Outputs on expression profiles, co-expression networks and pathways, and molecular interactomes, are dynamically and interactively displayed according to user-defined criteria. Conclusions In short, users may apply circlncRNAnet to obtain, in real time, multiple lines of functionally relevant information on circRNAs/lncRNAs of their interest. In summary, circlncRNAnet provides a “one-stop” resource for in-depth analyses of ncRNA biology. circlncRNAnet is freely available at http://app.cgu.edu.tw/circlnc/.
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Affiliation(s)
- Shao-Min Wu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Guishan, Taoyuan, Taiwan
| | - Hsuan Liu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Guishan, Taoyuan, Taiwan.,Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Guishan, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, Taiwan.,Division of Colon and Rectal Surgery, Department of Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Po-Jung Huang
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, Taiwan.,Department of Biomedical Sciences, College of Medicine, Chang Gung University, Guishan, Taoyuan, Taiwan.,Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Ian Yi-Feng Chang
- Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, Taiwan
| | - Chi-Ching Lee
- Department of Computer Science and Information Engineering, College of Engineering, Chang Gung University, Guishan, Taoyuan, Taiwan
| | - Chia-Yu Yang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Guishan, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, Taiwan.,Division of Colon and Rectal Surgery, Department of Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan.,Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Guishan, Taoyuan, Taiwan
| | - Wen-Sy Tsai
- Division of Colon and Rectal Surgery, Department of Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Bertrand Chin-Ming Tan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Guishan, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang Gung University, Guishan, Taoyuan, Taiwan.,Department of Biomedical Sciences, College of Medicine, Chang Gung University, Guishan, Taoyuan, Taiwan.,Department of Neurosurgery, Linkou Medical Center, Chang Gung Memorial Hospital, Linkou, Taiwan
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