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Mohammad RM, Muqbil I, Lowe L, Yedjou C, Hsu HY, Lin LT, Siegelin MD, Fimognari C, Kumar NB, Dou QP, Yang H, Samadi AK, Russo GL, Spagnuolo C, Ray SK, Chakrabarti M, Morre JD, Coley HM, Honoki K, Fujii H, Georgakilas AG, Amedei A, Niccolai E, Amin A, Ashraf SS, Helferich WG, Yang X, Boosani CS, Guha G, Bhakta D, Ciriolo MR, Aquilano K, Chen S, Mohammed SI, Keith WN, Bilsland A, Halicka D, Nowsheen S, Azmi AS. Broad targeting of resistance to apoptosis in cancer. Semin Cancer Biol 2015; 35 Suppl:S78-S103. [PMID: 25936818 PMCID: PMC4720504 DOI: 10.1016/j.semcancer.2015.03.001] [Citation(s) in RCA: 517] [Impact Index Per Article: 57.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 03/04/2015] [Accepted: 03/04/2015] [Indexed: 12/15/2022]
Abstract
Apoptosis or programmed cell death is natural way of removing aged cells from the body. Most of the anti-cancer therapies trigger apoptosis induction and related cell death networks to eliminate malignant cells. However, in cancer, de-regulated apoptotic signaling, particularly the activation of an anti-apoptotic systems, allows cancer cells to escape this program leading to uncontrolled proliferation resulting in tumor survival, therapeutic resistance and recurrence of cancer. This resistance is a complicated phenomenon that emanates from the interactions of various molecules and signaling pathways. In this comprehensive review we discuss the various factors contributing to apoptosis resistance in cancers. The key resistance targets that are discussed include (1) Bcl-2 and Mcl-1 proteins; (2) autophagy processes; (3) necrosis and necroptosis; (4) heat shock protein signaling; (5) the proteasome pathway; (6) epigenetic mechanisms; and (7) aberrant nuclear export signaling. The shortcomings of current therapeutic modalities are highlighted and a broad spectrum strategy using approaches including (a) gossypol; (b) epigallocatechin-3-gallate; (c) UMI-77 (d) triptolide and (e) selinexor that can be used to overcome cell death resistance is presented. This review provides a roadmap for the design of successful anti-cancer strategies that overcome resistance to apoptosis for better therapeutic outcome in patients with cancer.
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Affiliation(s)
- Ramzi M Mohammad
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, United States; Interim translational Research Institute, Hamad Medical Corporation, Doha, Qatar.
| | - Irfana Muqbil
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, United States
| | - Leroy Lowe
- Getting to Know Cancer, Truro, Nova Scotia, Canada
| | - Clement Yedjou
- C-SET, [Jackson, #229] State University, Jackson, MS, United States
| | - Hsue-Yin Hsu
- Department of Life Sciences, Tzu-Chi University, Hualien, Taiwan
| | - Liang-Tzung Lin
- Department of Microbiology and Immunology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Markus David Siegelin
- Department of Pathology and Cell Biology, Columbia University, New York City, NY, United States
| | - Carmela Fimognari
- Dipartimento di Scienze per la Qualità della Vita Alma Mater Studiorum-Università di Bologna, Italy
| | - Nagi B Kumar
- Moffit Cancer Center, University of South Florida College of Medicine, Tampa, FL, United States
| | - Q Ping Dou
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, United States; Departments of Pharmacology and Pathology, Karmanos Cancer Institute, Detroit MI, United States
| | - Huanjie Yang
- The School of Life Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | | | - Gian Luigi Russo
- Institute of Food Sciences National Research Council, Avellino, Italy
| | - Carmela Spagnuolo
- Institute of Food Sciences National Research Council, Avellino, Italy
| | - Swapan K Ray
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States
| | - Mrinmay Chakrabarti
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States
| | - James D Morre
- Mor-NuCo, Inc, Purdue Research Park, West Lafayette, IN, United States
| | - Helen M Coley
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom
| | - Kanya Honoki
- Department of Orthopedic Surgery, Nara Medical University, Kashihara, Japan
| | - Hiromasa Fujii
- Department of Orthopedic Surgery, Nara Medical University, Kashihara, Japan
| | - Alexandros G Georgakilas
- Department of Physics, School of Applied Mathematical and Physical Sciences, National Technical University of Athens, Zografou 15780, Athens, Greece
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, university of florence, Italy
| | - Elena Niccolai
- Department of Experimental and Clinical Medicine, university of florence, Italy
| | - Amr Amin
- Department of Biology, College of Science, UAE University, United Arab Emirates; Faculty of Science, Cairo University, Egypt
| | - S Salman Ashraf
- Department of Chemistry, College of Science, UAE University, United Arab Emirates
| | - William G Helferich
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Xujuan Yang
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Chandra S Boosani
- Department of BioMedical Sciences, School of Medicine Creighton University, Omaha NE, United States
| | - Gunjan Guha
- School of Chemical and Bio Technology, SASTRA University, Thanjavur, India
| | - Dipita Bhakta
- School of Chemical and Bio Technology, SASTRA University, Thanjavur, India
| | | | - Katia Aquilano
- Department of Biology, University of Rome "Tor Vergata", Italy
| | - Sophie Chen
- Ovarian and Prostate Cancer Research Trust Laboratory, Guildford, Surrey, United Kingdom
| | - Sulma I Mohammed
- Department of Comparative Pathobiology and Purdue University Center for Cancer Research, Purdue, West Lafayette, IN, United States
| | - W Nicol Keith
- Institute of Cancer Sciences, University of Glasgow, Glasgow, Ireland
| | - Alan Bilsland
- Institute of Cancer Sciences, University of Glasgow, Glasgow, Ireland
| | - Dorota Halicka
- Department of Pathology, New York Medical College, Valhalla, NY, United States
| | - Somaira Nowsheen
- Mayo Graduate School, Mayo Medical School, Mayo Clinic Medical Scientist Training Program, Rochester, MN, United States
| | - Asfar S Azmi
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI, United States
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Docampo R. The origin and evolution of the acidocalcisome and its interactions with other organelles. Mol Biochem Parasitol 2015; 209:3-9. [PMID: 26523947 DOI: 10.1016/j.molbiopara.2015.10.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 10/04/2015] [Accepted: 10/19/2015] [Indexed: 01/11/2023]
Abstract
Acidocalcisomes are acidic calcium stores that have been found from bacteria to human cells. They are rich in phosphorus compounds in the form of orthophosphate (Pi), pyrophosphate (PPi), and polyphosphate (polyP) and their acidity is maintained by proton pumps such as the vacuolar proton pyrophosphatase (V-H+-PPase, or VP1), the vacuolar proton ATPase (V-H+-ATPase), or both. Recent studies in trypanosomatids and in other species have revealed their role in phosphate metabolism, and cation and water homeostasis, as suggested by the presence of novel pumps, transporters, and channels. An important role in autophagy has also been described. The study of the biogenesis of acidocalcisomes as well as of the interactions of these lysosome-related organelles with other organelles have uncovered important roles in calcium signaling and osmoregulation. Significantly, despite conservation of acidocalcisomes across all of cellular life, there is evidence for intimate integration of these organelles with eukaryotic cellular functions, and which are directly relevant to parasites.
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Affiliation(s)
- Roberto Docampo
- Center for Tropical and Global Emerging Diseases and Department of Cellular Biology, University of Georgia, Athens 30602, USA; Departamento de Patología Clínica, Universidade Estadual de Campinas, São Paulo 13083-877, Brazil.
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103
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Open Questions on the Origin of Eukaryotes. Trends Ecol Evol 2015; 30:697-708. [PMID: 26455774 DOI: 10.1016/j.tree.2015.09.005] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 09/03/2015] [Accepted: 09/04/2015] [Indexed: 12/21/2022]
Abstract
Despite recent progress, the origin of the eukaryotic cell remains enigmatic. It is now known that the last eukaryotic common ancestor was complex and that endosymbiosis played a crucial role in eukaryogenesis at least via the acquisition of the alphaproteobacterial ancestor of mitochondria. However, the nature of the mitochondrial host is controversial, although the recent discovery of an archaeal lineage phylogenetically close to eukaryotes reinforces models proposing archaea-derived hosts. We argue that, in addition to improved phylogenomic analyses with more comprehensive taxon sampling to pinpoint the closest prokaryotic relatives of eukaryotes, determining plausible mechanisms and selective forces at the origin of key eukaryotic features, such as the nucleus or the bacterial-like eukaryotic membrane system, is essential to constrain existing models.
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104
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Encapsulation as a Strategy for the Design of Biological Compartmentalization. J Mol Biol 2015; 428:916-27. [PMID: 26403362 DOI: 10.1016/j.jmb.2015.09.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 08/16/2015] [Accepted: 09/03/2015] [Indexed: 02/06/2023]
Abstract
Compartmentalization is one of the defining features of life. Through intracellular spatial control, cells are able to organize and regulate their metabolism. One of the most broadly used organizational principles in nature is encapsulation. Cellular processes can be encapsulated within either membrane-bound organelles or proteinaceous compartments that create distinct microenvironments optimized for a given task. Further challenges addressed through intracellular compartmentalization are toxic or volatile pathway intermediates, slow turnover rates and competing side reactions. This review highlights a selection of naturally occurring membrane- and protein-based encapsulation systems in microbes and their recent applications and emerging opportunities in synthetic biology. We focus on examples that use engineered cellular organization to control metabolic pathway flux for the production of useful compounds and materials.
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105
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Balasubramanian K, Maeda A, Lee JS, Mohammadyani D, Dar HH, Jiang JF, St Croix CM, Watkins S, Tyurin VA, Tyurina YY, Klöditz K, Polimova A, Kapralova VI, Xiong Z, Ray P, Klein-Seetharaman J, Mallampalli RK, Bayir H, Fadeel B, Kagan VE. Dichotomous roles for externalized cardiolipin in extracellular signaling: Promotion of phagocytosis and attenuation of innate immunity. Sci Signal 2015; 8:ra95. [PMID: 26396268 PMCID: PMC4760701 DOI: 10.1126/scisignal.aaa6179] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Among the distinct molecular signatures present in the mitochondrion is the tetra-acylated anionic phospholipid cardiolipin, a lipid also present in primordial, single-cell bacterial ancestors of mitochondria and multiple bacterial species today. Cardiolipin is normally localized to the inner mitochondrial membrane; however, when cardiolipin becomes externalized to the surface of dysregulated mitochondria, it promotes inflammasome activation and stimulates the elimination of damaged or nonfunctional mitochondria by mitophagy. Given the immunogenicity of mitochondrial and bacterial membranes that are released during sterile and pathogen-induced trauma, we hypothesized that cardiolipins might function as "eat me" signals for professional phagocytes. In experiments with macrophage cell lines and primary macrophages, we found that membranes with mitochondrial or bacterial cardiolipins on their surface were engulfed through phagocytosis, which depended on the scavenger receptor CD36. Distinct from this process, the copresentation of cardiolipin with the Toll-like receptor 4 (TLR4) agonist lipopolysaccharide dampened TLR4-stimulated production of cytokines. These data suggest that externalized, extracellular cardiolipins play a dual role in host-host and host-pathogen interactions by promoting phagocytosis and attenuating inflammatory immune responses.
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Affiliation(s)
- Krishnakumar Balasubramanian
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA.
| | - Akihiro Maeda
- Division of Molecular Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Janet S Lee
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Dariush Mohammadyani
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Haider Hussain Dar
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Jian Fei Jiang
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Claudette M St Croix
- Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Simon Watkins
- Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Vladimir A Tyurin
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Yulia Y Tyurina
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Katharina Klöditz
- Division of Molecular Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Anastassia Polimova
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Valentyna I Kapralova
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Zeyu Xiong
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Prabir Ray
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | | | - Rama K Mallampalli
- Department of Internal Medicine, Acute Lung Injury Center of Excellence, University of Pittsburgh, Pittsburgh, PA 15213, USA. Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, PA 15215, USA
| | - Hülya Bayir
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA. Department of Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Bengt Fadeel
- Division of Molecular Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden.
| | - Valerian E Kagan
- Center for Free Radical and Antioxidant Health, Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15219, USA.
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106
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Expression and localization of exocytic and recycling Rabs from Magnaporthe oryzae in mammalian cells. Methods Cell Biol 2015. [PMID: 26360026 DOI: 10.1016/bs.mcb.2015.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Rab GTPases are master regulators of intracellular membrane trafficking along endocytic and exocytic pathways. In this chapter, we began to characterize the exocytic and recycling Rabs from the filamentous fungus Magnaporthe oryzae (M. oryzae) that causes the rice blast disease. Among the 11 putative Rabs identified from the M. oryzae genome database (MoRabs), MoRab1, MoRab8, and MoRab11 appear orthologs of mammalian Rab1, Rab8, and Rab11 and likely function in exocytosis and endosomal recycling. To test this contention, we cloned, expressed, and determined intracellular localization of the three MoRabs in mammalian cells, in comparison to their human counterparts (hRabs). The MoRabs were well expressed as GFP fusion proteins and colocalized with the tdTomato-labeled hRabs on exocytic and recycling organelles, as determined by immunoblot analysis and confocal fluorescence microscopy. The colocalization supports the contention that the MoRabs are indeed Rab orthologs and may play important roles in the development and pathogenicity of M. oryzae.
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107
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Frank O, Göker M, Pradella S, Petersen J. Ocean's Twelve: flagellar and biofilm chromids in the multipartite genome ofMarinovum algicola DG898 exemplify functional compartmentalization. Environ Microbiol 2015; 17:4019-34. [DOI: 10.1111/1462-2920.12947] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 06/05/2015] [Accepted: 06/05/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Oliver Frank
- Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH; Inhoffenstraße 7 B Braunschweig D-38124 Germany
| | - Markus Göker
- Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH; Inhoffenstraße 7 B Braunschweig D-38124 Germany
| | - Silke Pradella
- Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH; Inhoffenstraße 7 B Braunschweig D-38124 Germany
| | - Jörn Petersen
- Leibniz-Institut DSMZ - Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH; Inhoffenstraße 7 B Braunschweig D-38124 Germany
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108
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Schneider J, Mielich-Süss B, Böhme R, Lopez D. In vivo characterization of the scaffold activity of flotillin on the membrane kinase KinC of Bacillus subtilis. MICROBIOLOGY-SGM 2015; 161:1871-1887. [PMID: 26297017 DOI: 10.1099/mic.0.000137] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Scaffold proteins are ubiquitous chaperones that bind to proteins and facilitate the physical interaction of the components of signal transduction pathways or multi-enzymic complexes. In this study, we used a biochemical approach to dissect the molecular mechanism of a membrane-associated scaffold protein, FloT, a flotillin-homologue protein that is localized in functional membrane microdomains of the bacterium Bacillus subtilis. This study provides unambiguous evidence that FloT physically binds to and interacts with the membrane-bound sensor kinase KinC. This sensor kinase activates biofilm formation in B. subtilis in response to the presence of the self-produced signal surfactin. Furthermore, we have characterized the mechanism by which the interaction of FloT with KinC benefits the activity of KinC. Two separate and synergistic effects constitute this mechanism: first, the scaffold activity of FloT promotes more efficient self-interaction of KinC and facilitates dimerization into its active form. Second, the selective binding of FloT to KinC prevents the occurrence of unspecific aggregation between KinC and other proteins that may generate dead-end intermediates that could titrate the activity of KinC. Flotillin proteins appear to play an important role in prokaryotes in promoting effective binding of signalling proteins with their correct protein partners.
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Affiliation(s)
- Johannes Schneider
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Benjamin Mielich-Süss
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Richard Böhme
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Daniel Lopez
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
- National Center for Biotechnology (CNB), Spanish Research Council (CSIC), Madrid 28050, Spain
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
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109
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A multi-functional tubulovesicular network as the ancestral eukaryotic endomembrane system. BIOLOGY 2015; 4:264-81. [PMID: 25811639 PMCID: PMC4498299 DOI: 10.3390/biology4020264] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 03/03/2015] [Indexed: 12/31/2022]
Abstract
The origin of the eukaryotic endomembrane system is still the subject of much speculation. We argue that the combination of two recent hypotheses addressing the eukaryotic endomembrane's early evolution supports the possibility that the ancestral membranes were organised as a multi-functional tubulovesicular network. One of the potential selective advantages provided by this organisation was the capacity to perform endocytosis. This possibility is illustrated by membrane organisations observed in current organisms in the three domains of life. Based on this, we propose a coherent model of autogenous eukaryotic endomembrane system evolution in which mitochondria are involved at a late stage.
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110
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Fu Q, Lv P, Chen Z, Ni D, Zhang L, Yue H, Yue Z, Wei W, Ma G. Programmed co-delivery of paclitaxel and doxorubicin boosted by camouflaging with erythrocyte membrane. NANOSCALE 2015; 7:4020-30. [PMID: 25653083 DOI: 10.1039/c4nr07027e] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Combination chemotherapy has been proven promising for cancer treatment, but unsatisfactory therapeutic data and increased side effects slow down the development in the clinic. In this study, we develop an effective approach to co-encapsulate a hydrophilic-hydrophobic chemotherapeutic drug pair (paclitaxel and doxorubicin) into magnetic O-carboxymethyl-chitosan nanoparticles. To endow them with the ability of programmed delivery, these carriers are further camouflaged with an Arg-Gly-Asp anchored erythrocyte membrane. Compared with the traditional polyethylene glycol coating method, this biomimetic decoration strategy is demonstrated to be superior in prolonging circulation time, improving tumor accumulation, facilitating tumor uptake, and tuning intracellular fate. These outstanding properties enable the as-designed nanodevice to exhibit greater tumor growth inhibition ability and much lower side effects than the combined use of commercial formulations.
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Affiliation(s)
- Qiang Fu
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China.
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111
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Zarra S, Wood DM, Roberts DA, Nitschke JR. Molecular containers in complex chemical systems. Chem Soc Rev 2015; 44:419-32. [DOI: 10.1039/c4cs00165f] [Citation(s) in RCA: 486] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This review discusses recent advances in the use of molecular containers in complex chemical systems, focusing on three aspects: host–guest behaviour, structural transformations and reactivity modulation.
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Affiliation(s)
| | - Daniel M. Wood
- Department of Chemistry
- University of Cambridge
- Cambridge
- UK
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112
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Metabolic pathway compartmentalization: an underappreciated opportunity? Curr Opin Biotechnol 2014; 34:73-81. [PMID: 25499800 DOI: 10.1016/j.copbio.2014.11.022] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 11/23/2014] [Indexed: 12/12/2022]
Abstract
For eukaryotic cells to function properly, they divide their intracellular space in subcellular compartments, each harboring specific metabolic activities. In recent years, it has become increasingly clear that compartmentalization of metabolic pathways is a prerequisite for certain cellular functions. This has for instance been documented for cellular migration, which relies on subcellular localization of glycolysis or mitochondrial respiration in a cell type-dependent manner. Although exciting, this field is still in its infancy, partly due to the limited availability of methods to study the directionality of metabolic pathways and to visualize metabolic processes in distinct cellular compartments. Nonetheless, advances in this field may offer opportunities for innovative strategies to target deregulated compartmentalized metabolism in disease.
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113
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Azmi AS, Bao B, Sarkar FH. Exosomes in cancer development, metastasis, and drug resistance: a comprehensive review. Cancer Metastasis Rev 2014; 32:623-42. [PMID: 23709120 DOI: 10.1007/s10555-013-9441-9] [Citation(s) in RCA: 860] [Impact Index Per Article: 86.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Trafficking of biological material across membranes is an evolutionary conserved mechanism and is part of any normal cell homeostasis. Such transport is composed of active, passive, export through microparticles, and vesicular transport (exosomes) that collectively maintain proper compartmentalization of important micro- and macromolecules. In pathological states, such as cancer, aberrant activity of the export machinery results in expulsion of a number of key proteins and microRNAs resulting in their misexpression. Exosome-mediated expulsion of intracellular drugs could be another barrier in the proper action of most of the commonly used therapeutics, targeted agents, and their intracellular metabolites. Over the last decade, a number of studies have revealed that exosomes cross-talk and/or influence major tumor-related pathways, such as hypoxia-driven epithelial-to-mesenchymal transition, cancer stemness, angiogenesis, and metastasis involving many cell types within the tumor microenvironment. Emerging evidence suggests that exosome-secreted proteins can also propel fibroblast growth, resulting in desmoplastic reaction, a major barrier in effective cancer drug delivery. This comprehensive review highlights the advancements in the understanding of the biology of exosomes secretions and the consequence on cancer drug resistance. We propose that the successful combination of cancer treatments to tackle exosome-mediated drug resistance requires an interdisciplinary understanding of these cellular exclusion mechanisms, and how secreted biomolecules are involved in cellular cross-talk within the tumor microenvironment.
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Affiliation(s)
- Asfar S Azmi
- Department of Pathology, Wayne State University School of Medicine, 4100 John R, HWCRC 740, Detroit, MI, 48201, USA,
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114
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Warszawski S, Netzer R, Tawfik DS, Fleishman SJ. A "fuzzy"-logic language for encoding multiple physical traits in biomolecules. J Mol Biol 2014; 426:4125-4138. [PMID: 25311857 PMCID: PMC4270444 DOI: 10.1016/j.jmb.2014.10.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 09/21/2014] [Accepted: 10/02/2014] [Indexed: 12/16/2022]
Abstract
To carry out their activities, biological macromolecules balance different physical traits, such as stability, interaction affinity, and selectivity. How such often opposing traits are encoded in a macromolecular system is critical to our understanding of evolutionary processes and ability to design new molecules with desired functions. We present a framework for constraining design simulations to balance different physical characteristics. Each trait is represented by the equilibrium fractional occupancy of the desired state relative to its alternatives, ranging from none to full occupancy, and the different traits are combined using Boolean operators to effect a "fuzzy"-logic language for encoding any combination of traits. In another paper, we presented a new combinatorial backbone design algorithm AbDesign where the fuzzy-logic framework was used to optimize protein backbones and sequences for both stability and binding affinity in antibody-design simulation. We now extend this framework and find that fuzzy-logic design simulations reproduce sequence and structure design principles seen in nature to underlie exquisite specificity on the one hand and multispecificity on the other hand. The fuzzy-logic language is broadly applicable and could help define the space of tolerated and beneficial mutations in natural biomolecular systems and design artificial molecules that encode complex characteristics.
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Affiliation(s)
- Shira Warszawski
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ravit Netzer
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Dan S Tawfik
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sarel J Fleishman
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel.
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115
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Abstract
Bacteria are polarized cells with many asymmetrically localized proteins that are regulated temporally and spatially. This spatiotemporal dynamics is critical for several fundamental cellular processes including growth, division, cell cycle regulation, chromosome segregation, differentiation, and motility. Therefore, understanding how proteins find their correct location at the right time is crucial for elucidating bacterial cell function. Despite the diversity of proteins displaying spatiotemporal dynamics, general principles for the dynamic regulation of protein localization to the cell poles and the midcell are emerging. These principles include diffusion-capture, self-assembling polymer-forming landmark proteins, nonpolymer forming landmark proteins, matrix-dependent self-organizing ParA/MinD ATPases, and small Ras-like GTPases.
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Affiliation(s)
- Anke Treuner-Lange
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Lotte Søgaard-Andersen
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
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116
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The relative ages of eukaryotes and akaryotes. J Mol Evol 2014; 79:228-39. [PMID: 25179144 DOI: 10.1007/s00239-014-9643-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 08/18/2014] [Indexed: 12/22/2022]
Abstract
The Last Eukaryote Common Ancestor (LECA) appears to have the genetics required for meiosis, mitosis, nucleus and nuclear substructures, an exon/intron gene structure, spliceosomes, many centres of DNA replication, etc. (and including mitochondria). Most of these features are not generally explained by models for the origin of the Eukaryotic cell based on the fusion of an Archeon and a Bacterium. We find that the term 'prokaryote' is ambiguous and the non-phylogenetic term akaryote should be used in its place because we do not yet know the direction of evolution between eukaryotes and akaryotes. We use the term 'protoeukaryote' for the hypothetical stem group ancestral eukaryote that took up a bacterium as an endosymbiont that formed the mitochondrion. It is easier to make detailed models with a eukaryote to an akaryote transition, rather than vice versa. So we really are at a phylogenetic impasse in not being confident about the direction of change between eukaryotes and akaryotes.
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117
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McHugh CA, Fontana J, Nemecek D, Cheng N, Aksyuk AA, Heymann JB, Winkler DC, Lam AS, Wall JS, Steven AC, Hoiczyk E. A virus capsid-like nanocompartment that stores iron and protects bacteria from oxidative stress. EMBO J 2014; 33:1896-911. [PMID: 25024436 DOI: 10.15252/embj.201488566] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Living cells compartmentalize materials and enzymatic reactions to increase metabolic efficiency. While eukaryotes use membrane-bound organelles, bacteria and archaea rely primarily on protein-bound nanocompartments. Encapsulins constitute a class of nanocompartments widespread in bacteria and archaea whose functions have hitherto been unclear. Here, we characterize the encapsulin nanocompartment from Myxococcus xanthus, which consists of a shell protein (EncA, 32.5 kDa) and three internal proteins (EncB, 17 kDa; EncC, 13 kDa; EncD, 11 kDa). Using cryo-electron microscopy, we determined that EncA self-assembles into an icosahedral shell 32 nm in diameter (26 nm internal diameter), built from 180 subunits with the fold first observed in bacteriophage HK97 capsid. The internal proteins, of which EncB and EncC have ferritin-like domains, attach to its inner surface. Native nanocompartments have dense iron-rich cores. Functionally, they resemble ferritins, cage-like iron storage proteins, but with a massively greater capacity (~30,000 iron atoms versus ~3,000 in ferritin). Physiological data reveal that few nanocompartments are assembled during vegetative growth, but they increase fivefold upon starvation, protecting cells from oxidative stress through iron sequestration.
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Affiliation(s)
- Colleen A McHugh
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Juan Fontana
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Daniel Nemecek
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Naiqian Cheng
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Anastasia A Aksyuk
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - J Bernard Heymann
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Dennis C Winkler
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Alan S Lam
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Joseph S Wall
- Department of Biology, Brookhaven National Laboratory, Upton, NY, USA
| | - Alasdair C Steven
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, Bethesda, MD, USA
| | - Egbert Hoiczyk
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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118
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Van Roey K, Uyar B, Weatheritt RJ, Dinkel H, Seiler M, Budd A, Gibson TJ, Davey NE. Short Linear Motifs: Ubiquitous and Functionally Diverse Protein Interaction Modules Directing Cell Regulation. Chem Rev 2014; 114:6733-78. [DOI: 10.1021/cr400585q] [Citation(s) in RCA: 293] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Kim Van Roey
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Bora Uyar
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Robert J. Weatheritt
- MRC
Laboratory of Molecular Biology (LMB), Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Holger Dinkel
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Markus Seiler
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Aidan Budd
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Toby J. Gibson
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Norman E. Davey
- Structural
and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
- Department
of Physiology, University of California, San Francisco, San Francisco, California 94143, United States
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119
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Aumiller WM, Davis BW, Hashemian N, Maranas C, Armaou A, Keating CD. Coupled enzyme reactions performed in heterogeneous reaction media: experiments and modeling for glucose oxidase and horseradish peroxidase in a PEG/citrate aqueous two-phase system. J Phys Chem B 2014; 118:2506-17. [PMID: 24517887 PMCID: PMC3983363 DOI: 10.1021/jp501126v] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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The
intracellular environment in which biological reactions occur
is crowded with macromolecules and subdivided into microenvironments
that differ in both physical properties and chemical composition.
The work described here combines experimental and computational model
systems to help understand the consequences of this heterogeneous
reaction media on the outcome of coupled enzyme reactions. Our experimental
model system for solution heterogeneity is a biphasic polyethylene
glycol (PEG)/sodium citrate aqueous mixture that provides coexisting
PEG-rich and citrate-rich phases. Reaction kinetics for the coupled
enzyme reaction between glucose oxidase (GOX) and horseradish peroxidase
(HRP) were measured in the PEG/citrate aqueous two-phase system (ATPS).
Enzyme kinetics differed between the two phases, particularly for
the HRP. Both enzymes, as well as the substrates glucose and H2O2, partitioned to the citrate-rich phase; however,
the Amplex Red substrate necessary to complete the sequential reaction
partitioned strongly to the PEG-rich phase. Reactions in ATPS were
quantitatively described by a mathematical model that incorporated
measured partitioning and kinetic parameters. The model was then extended
to new reaction conditions, i.e., higher enzyme concentration. Both
experimental and computational results suggest mass transfer across
the interface is vital to maintain the observed rate of product formation,
which may be a means of metabolic regulation in vivo. Although outcomes
for a specific system will depend on the particulars of the enzyme
reactions and the microenvironments, this work demonstrates how coupled
enzymatic reactions in complex, heterogeneous media can be understood
in terms of a mathematical model.
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Affiliation(s)
- William M Aumiller
- Department of Chemistry and ‡Department of Chemical Engineering, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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120
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Cornejo E, Abreu N, Komeili A. Compartmentalization and organelle formation in bacteria. Curr Opin Cell Biol 2014; 26:132-8. [PMID: 24440431 DOI: 10.1016/j.ceb.2013.12.007] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 12/17/2013] [Accepted: 12/17/2013] [Indexed: 12/19/2022]
Abstract
A number of bacterial species rely on compartmentalization to gain specific functionalities that will provide them with a selective advantage. Here, we will highlight several of these modes of bacterial compartmentalization with an eye toward describing the mechanisms of their formation and their evolutionary origins. Spore formation in Bacillus subtilis, outer membrane biogenesis in Gram-negative bacteria and protein diffusion barriers of Caulobacter crescentus will be used to demonstrate the physical, chemical, and compositional remodeling events that lead to compartmentalization. In addition, magnetosomes and carboxysomes will serve as models to examine the interplay between cytoskeletal systems and the subcellular positioning of organelles.
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Affiliation(s)
- Elias Cornejo
- Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720-3102, United States
| | - Nicole Abreu
- Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720-3102, United States
| | - Arash Komeili
- Department of Plant and Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720-3102, United States.
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121
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Schreiber A, Schiller SM. Nanobiotechnology of protein-based compartments: steps toward nanofactories. BIOINSPIRED BIOMIMETIC AND NANOBIOMATERIALS 2013. [DOI: 10.1680/bbn.13.00008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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122
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Saier MH. Microcompartments and protein machines in prokaryotes. J Mol Microbiol Biotechnol 2013; 23:243-69. [PMID: 23920489 DOI: 10.1159/000351625] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The prokaryotic cell was once thought of as a 'bag of enzymes' with little or no intracellular compartmentalization. In this view, most reactions essential for life occurred as a consequence of random molecular collisions involving substrates, cofactors and cytoplasmic enzymes. Our current conception of a prokaryote is far from this view. We now consider a bacterium or an archaeon as a highly structured, nonrandom collection of functional membrane-embedded and proteinaceous molecular machines, each of which serves a specialized function. In this article we shall present an overview of such microcompartments including (1) the bacterial cytoskeleton and the apparati allowing DNA segregation during cell division; (2) energy transduction apparati involving light-driven proton pumping and ion gradient-driven ATP synthesis; (3) prokaryotic motility and taxis machines that mediate cell movements in response to gradients of chemicals and physical forces; (4) machines of protein folding, secretion and degradation; (5) metabolosomes carrying out specific chemical reactions; (6) 24-hour clocks allowing bacteria to coordinate their metabolic activities with the daily solar cycle, and (7) proteinaceous membrane compartmentalized structures such as sulfur granules and gas vacuoles. Membrane-bound prokaryotic organelles were considered in a recent Journal of Molecular Microbiology and Biotechnology written symposium concerned with membranous compartmentalization in bacteria [J Mol Microbiol Biotechnol 2013;23:1-192]. By contrast, in this symposium, we focus on proteinaceous microcompartments. These two symposia, taken together, provide the interested reader with an objective view of the remarkable complexity of what was once thought of as a simple noncompartmentalized cell.
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Affiliation(s)
- Milton H Saier
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, Calif. 92093-0116, USA.
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123
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Klinger CM, Nisbet RE, Ouologuem DT, Roos DS, Dacks JB. Cryptic organelle homology in apicomplexan parasites: insights from evolutionary cell biology. Curr Opin Microbiol 2013; 16:424-31. [PMID: 23932202 PMCID: PMC4513074 DOI: 10.1016/j.mib.2013.07.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 07/18/2013] [Accepted: 07/23/2013] [Indexed: 12/21/2022]
Abstract
The economic and clinical significance of apicomplexan parasites drives interest in their many evolutionary novelties. Distinctive intracellular organelles play key roles in parasite motility, invasion, metabolism, and replication, and understanding their relationship with the organelles of better-studied eukaryotic systems suggests potential targets for therapeutic intervention. Recent work has demonstrated divergent aspects of canonical eukaryotic components in the Apicomplexa, including Golgi bodies and mitochondria. The apicoplast is a relict plastid of secondary endosymbiotic origin, harboring metabolic pathways distinct from those of host species. The inner membrane complex (IMC) is derived from the cortical alveoli defining the superphylum Alveolata, but in apicomplexans functions in parasite motility and replication. Micronemes and rhoptries are associated with establishment of the intracellular niche, and define the apical complex for which the phylum is named. Morphological, cell biological and molecular evidence strongly suggest that these organelles are derived from the endocytic pathway.
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Affiliation(s)
| | - R. Ellen Nisbet
- Department of Biochemistry, Cambridge University, Cambridge UK and School of Pharmacy and Medical Sciences, University of South Australia, Adelaide SA, Australia
- Department of Biology, University of Pennsylvania, Philadelphia PA USA
| | | | | | - Joel B. Dacks
- Department of Cell Biology, University of Alberta, Edmonton AB, Canada
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