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Edelbroek B, Westholm JO, Bergquist J, Söderbom F. Multi-omics analysis of aggregative multicellularity. iScience 2024; 27:110659. [PMID: 39224513 PMCID: PMC11367525 DOI: 10.1016/j.isci.2024.110659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 06/14/2024] [Accepted: 07/31/2024] [Indexed: 09/04/2024] Open
Abstract
All organisms have to carefully regulate their gene expression, not least during development. mRNA levels are often used as proxy for protein output; however, this approach ignores post-transcriptional effects. In particular, mRNA-protein correlation remains elusive for organisms that exhibit aggregative rather than clonal multicellularity. We addressed this issue by generating a paired transcriptomics and proteomics time series during the transition from uni-to multicellular stage in the social ameba Dictyostelium discoideum. Our data reveals that mRNA and protein levels correlate highly during unicellular growth, but decrease when multicellular development is initiated. This accentuates that transcripts alone cannot accurately predict protein levels. The dataset provides a useful resource to study gene expression during aggregative multicellular development. Additionally, our study provides an example of how to analyze and visualize mRNA and protein levels, which should be broadly applicable to other organisms and conditions.
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Affiliation(s)
- Bart Edelbroek
- Department of Cell and Molecular Biology, BMC, Uppsala University, 751 24 Uppsala, Sweden
| | - Jakub Orzechowski Westholm
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Jonas Bergquist
- Department of Chemistry-BMC, Analytical Chemistry and Neurochemistry, Uppsala University, Uppsala, Sweden
| | - Fredrik Söderbom
- Department of Cell and Molecular Biology, BMC, Uppsala University, 751 24 Uppsala, Sweden
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2
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Thomason PA, Corbyn R, Lilla S, Sumpton D, Gilbey T, Insall RH. Biogenesis of lysosome-related organelles complex-2 is an evolutionarily ancient proto-coatomer complex. Curr Biol 2024; 34:3564-3581.e6. [PMID: 39059394 DOI: 10.1016/j.cub.2024.06.081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 03/06/2024] [Accepted: 06/28/2024] [Indexed: 07/28/2024]
Abstract
Hermansky-Pudlak syndrome (HPS) is an inherited disorder of intracellular vesicle trafficking affecting the function of lysosome-related organelles (LROs). At least 11 genes underlie the disease, encoding four protein complexes, of which biogenesis of lysosome-related organelles complex-2 (BLOC-2) is the last whose molecular action is unknown. We find that the unicellular eukaryote Dictyostelium unexpectedly contains a complete BLOC-2, comprising orthologs of the mammalian subunits HPS3, -5, and -6, and a fourth subunit, an ortholog of the Drosophila LRO-biogenesis gene, Claret. Lysosomes from Dictyostelium BLOC-2 mutants fail to mature, similar to LROs from HPS patients, but for all endolysosomes rather than a specialized subset. They also strongly resemble lysosomes from WASH mutants. Dictyostelium BLOC-2 localizes to the same compartments as WASH, and in BLOC-2 mutants, WASH is inefficiently recruited, accounting for their impaired lysosomal maturation. BLOC-2 is recruited to endolysosomes via its HPS3 subunit. Structural modeling suggests that all four subunits are proto-coatomer proteins, with important implications for BLOC-2's molecular function. The discovery of Dictyostelium BLOC-2 permits identification of orthologs throughout eukaryotes. BLOC-2 and lysosome-related organelles, therefore, pre-date the evolution of Metazoa and have broader and more conserved functions than previously thought.
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Affiliation(s)
- Peter A Thomason
- Cancer Research UK Scotland Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK.
| | - Ryan Corbyn
- Cancer Research UK Scotland Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Sergio Lilla
- Cancer Research UK Scotland Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - David Sumpton
- Cancer Research UK Scotland Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Thomas Gilbey
- Cancer Research UK Scotland Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Robert H Insall
- School of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK; Division of Cell & Developmental Biology, University College London, London WC1E 6BT, UK.
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3
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Sen MG, Sanislav O, Fisher PR, Annesley SJ. The Multifaceted Interactions of Dictyostelium Atg1 with Mitochondrial Function, Endocytosis, Growth, and Development. Cells 2024; 13:1191. [PMID: 39056773 PMCID: PMC11274416 DOI: 10.3390/cells13141191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/04/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
Autophagy is a degradative recycling process central to the maintenance of homeostasis in all eukaryotes. By ensuring the degradation of damaged mitochondria, it plays a key role in maintaining mitochondrial health and function. Of the highly conserved autophagy proteins, autophagy-related protein 1 (Atg1) is essential to the process. The involvement of these proteins in intracellular signalling pathways, including those involving mitochondrial function, are still being elucidated. Here the role of Atg1 was investigated in the simple model organism Dictyostelium discoideum using an atg1 null mutant and mutants overexpressing or antisense-inhibiting atg1. When evaluated against the well-characterised outcomes of mitochondrial dysfunction in this model, altered atg1 expression resulted in an unconventional set of phenotypic outcomes in growth, endocytosis, multicellular development, and mitochondrial homeostasis. The findings here show that Atg1 is involved in a tightly regulated signal transduction pathway coordinating energy-consuming processes such as cell growth and multicellular development, along with nutrient status and energy production. Furthermore, Atg1's effects on energy homeostasis indicate a peripheral ancillary role in the mitochondrial signalling network, with effects on energy balance rather than direct effects on electron transport chain function. Further research is required to tease out these complex networks. Nevertheless, this study adds further evidence to the theory that autophagy and mitochondrial signalling are not opposing but rather linked, yet strictly controlled, homeostatic mechanisms.
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Affiliation(s)
| | | | | | - Sarah Jane Annesley
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, Melbourne 3086, Australia; (M.G.S.); (O.S.); (P.R.F.)
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Edelbroek B, Kjellin J, Jerlström-Hultqvist J, Koskiniemi S, Söderbom F. Chromosome-level genome assembly and annotation of the social amoeba Dictyostelium firmibasis. Sci Data 2024; 11:678. [PMID: 38909042 PMCID: PMC11193728 DOI: 10.1038/s41597-024-03513-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/12/2024] [Indexed: 06/24/2024] Open
Abstract
Dicytostelium firmibasis is a member of Dictyostelia, a group of social amoebae that upon starvation display aggregative multicellularity where the amoebae transition from uni- to multicellular life. The D. firmibasis genome assembly that is currently available is of limited use due to its low contiguity, large number of undetermined bases, and lack of annotations. Here we used Nanopore long read sequencing, complemented with Illumina sequencing, and developmental transcriptomics as well as small RNA-sequencing, to present a new, fully annotated, chromosome-level D. firmibasis genome assembly. The new assembly contains no undetermined bases, and consists mainly of six large contigs representing the chromosomes, as well as a complete mitochondrial genome. This new genome assembly will be a valuable tool, allowing comprehensive comparison to Dictyostelium discoideum, the dictyostelid genetically tractable model. Further, the new genome will be important for studies of evolutionary processes governing the transition from unicellular to multicellular organisms and will aid in the sequencing and annotation of other dictyostelids genomes, many of which are currently of poor quality.
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Affiliation(s)
- Bart Edelbroek
- Department of Cell and Molecular Biology, BMC, Uppsala University, SE-751 24, Uppsala, Sweden.
| | - Jonas Kjellin
- Department of Cell and Molecular Biology, BMC, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Jon Jerlström-Hultqvist
- Department of Cell and Molecular Biology, BMC, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Sanna Koskiniemi
- Department of Cell and Molecular Biology, BMC, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Fredrik Söderbom
- Department of Cell and Molecular Biology, BMC, Uppsala University, SE-751 24, Uppsala, Sweden.
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5
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Zhang Z, Li M, Zhang S, Qin Y, Zhao J, Li Y, Stephenson SL, Qiu J, Liu P. Diversity of Cellular Slime Molds (Dictyostelids) in the Fanjing Mountain Nature Reserve and Geographical Distribution Comparisons with Other Representative Nature Reserves in Different Climate Zones of China. Microorganisms 2024; 12:1061. [PMID: 38930443 PMCID: PMC11206006 DOI: 10.3390/microorganisms12061061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 05/13/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
Protected areas are widely considered an essential strategy for biodiversity conservation. Dictyostelids are unique protists known to have important ecological functions in promoting soil and plant health through their top-down regulation of ecosystem processes, such as decomposition, that involve bacterial populations. But the relationship between dictyostelid diversity within protected areas remains poorly understood, especially on a large scale. Herein, we report data on the distribution of dictyostelids, identified with ITS + SSU rRNA molecular and morphology-based taxonomy, from soil samples collected in the Fanjing Mountain protected area of Guizhou Province, Southwest China. We compared the biodiversity data of dictyostelids in Fanjing Mountain with similar data from previously sampled sites in four other protected areas, including Changbai Mountain (CB), Gushan Mountain (GS), Baiyun Mountain (BY), and Qinghai-Tibet Plateau (QT) in China. We identified four species of dictyostelids belonging to three genera (Dictyostelium, Heterostelium, and Polysphondylium) and herein provide information on the taxonomy of these species. Two species (Heterostelium pallidum and Dictyostelium purpureum) are common and widely distributed throughout the world, but one species (Polysphondylium fuscans) was new to China. Our data indicate that there is no distinguishable significant correlation between the dictyostelid species studied and environmental factors. Overall, the similarity index between Baiyun Mountain in Henan Province and Fanjing Mountain in Guizhou Province, located at approximately the same longitude, is the highest, and the Jaccard similarity coefficients (Jaccard index) of family, genus, and species are 100%, 100%, and 12.5%, respectively. From a species perspective, species in the same climate zone are not closely related, but obvious geographical distributions are evident in different climate zones. This preliminary study provided evidence of the ecological adaptation of dictyostelids to different biological niches.
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Affiliation(s)
- Zhaojuan Zhang
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (Z.Z.); (M.L.); (S.Z.); (Y.Q.); (J.Z.); (Y.L.)
| | - Meng Li
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (Z.Z.); (M.L.); (S.Z.); (Y.Q.); (J.Z.); (Y.L.)
| | - Shufei Zhang
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (Z.Z.); (M.L.); (S.Z.); (Y.Q.); (J.Z.); (Y.L.)
| | - Yue Qin
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (Z.Z.); (M.L.); (S.Z.); (Y.Q.); (J.Z.); (Y.L.)
| | - Jing Zhao
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (Z.Z.); (M.L.); (S.Z.); (Y.Q.); (J.Z.); (Y.L.)
| | - Yu Li
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (Z.Z.); (M.L.); (S.Z.); (Y.Q.); (J.Z.); (Y.L.)
| | - Steven L. Stephenson
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA;
| | - Junzhi Qiu
- Key Laboratory of Biopesticide and Chemical Biology, Ministry of Education, State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Pu Liu
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University, Changchun 130118, China; (Z.Z.); (M.L.); (S.Z.); (Y.Q.); (J.Z.); (Y.L.)
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Edelbroek B, Kjellin J, Biryukova I, Liao Z, Lundberg T, Noegel A, Eichinger L, Friedländer M, Söderbom F. Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity. Nucleic Acids Res 2024; 52:3121-3136. [PMID: 38375870 PMCID: PMC11014262 DOI: 10.1093/nar/gkae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/21/2024] Open
Abstract
MicroRNAs (miRNAs) are important and ubiquitous regulators of gene expression in both plants and animals. They are thought to have evolved convergently in these lineages and hypothesized to have played a role in the evolution of multicellularity. In line with this hypothesis, miRNAs have so far only been described in few unicellular eukaryotes. Here, we investigate the presence and evolution of miRNAs in Amoebozoa, focusing on species belonging to Acanthamoeba, Physarum and dictyostelid taxonomic groups, representing a range of unicellular and multicellular lifestyles. miRNAs that adhere to both the stringent plant and animal miRNA criteria were identified in all examined amoebae, expanding the total number of protists harbouring miRNAs from 7 to 15. We found conserved miRNAs between closely related species, but the majority of species feature only unique miRNAs. This shows rapid gain and/or loss of miRNAs in Amoebozoa, further illustrated by a detailed comparison between two evolutionary closely related dictyostelids. Additionally, loss of miRNAs in the Dictyostelium discoideum drnB mutant did not seem to affect multicellular development and, hence, demonstrates that the presence of miRNAs does not appear to be a strict requirement for the transition from uni- to multicellular life.
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Affiliation(s)
- Bart Edelbroek
- Department of Cell and Molecular Biology, Uppsala Biomedical Centre, Uppsala University, 75124 Uppsala, Sweden
| | - Jonas Kjellin
- Department of Cell and Molecular Biology, Uppsala Biomedical Centre, Uppsala University, 75124 Uppsala, Sweden
| | - Inna Biryukova
- Science for Life Laboratory, The Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Zhen Liao
- Department of Cell and Molecular Biology, Uppsala Biomedical Centre, Uppsala University, 75124 Uppsala, Sweden
| | - Torgny Lundberg
- Department of Cell and Molecular Biology, Uppsala Biomedical Centre, Uppsala University, 75124 Uppsala, Sweden
| | - Angelika A Noegel
- Centre for Biochemistry, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Ludwig Eichinger
- Centre for Biochemistry, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Marc R Friedländer
- Science for Life Laboratory, The Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691 Stockholm, Sweden
| | - Fredrik Söderbom
- Department of Cell and Molecular Biology, Uppsala Biomedical Centre, Uppsala University, 75124 Uppsala, Sweden
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7
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Rojas D, Marcoleta AE, Gálvez-Silva M, Varas MA, Díaz M, Hernández M, Vargas C, Nourdin-Galindo G, Koch E, Saldivia P, Vielma J, Gan YH, Chen Y, Guiliani N, Chávez FP. Inorganic Polyphosphate Affects Biofilm Assembly, Capsule Formation, and Virulence of Hypervirulent ST23 Klebsiella pneumoniae. ACS Infect Dis 2024; 10:606-623. [PMID: 38205780 DOI: 10.1021/acsinfecdis.3c00509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
The emergence of hypervirulent Klebsiella pneumoniae (hvKP) strains poses a significant threat to public health due to high mortality rates and propensity to cause severe community-acquired infections in healthy individuals. The ability to form biofilms and produce a protective capsule contributes to its enhanced virulence and is a significant challenge to effective antibiotic treatment. Polyphosphate kinase 1 (PPK1) is an enzyme responsible for inorganic polyphosphate synthesis and plays a vital role in regulating various physiological processes in bacteria. In this study, we investigated the impact of polyP metabolism on the biofilm and capsule formation and virulence traits in hvKP using Dictyostelium discoideum amoeba as a model host. We found that the PPK1 null mutant was impaired in biofilm and capsule formation and showed attenuated virulence in D. discoideum compared to the wild-type strain. We performed a proteomic analysis to gain further insights into the underlying molecular mechanism. The results revealed that the PPK1 mutant had a differential expression of proteins involved in capsule synthesis (Wzi-Ugd), biofilm formation (MrkC-D-H), synthesis of the colibactin genotoxin precursor (ClbB), as well as proteins associated with the synthesis and modification of lipid A (ArnB-LpxC-PagP). These proteomic findings corroborate the phenotypic observations and indicate that the PPK1 mutation is associated with impaired biofilm and capsule formation and attenuated virulence in hvKP. Overall, our study highlights the importance of polyP synthesis in regulating extracellular biomolecules and virulence in K. pneumoniae and provides insights into potential therapeutic targets for treating K. pneumoniae infections.
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Affiliation(s)
- Diego Rojas
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago CP 7800003, Chile
| | - Andrés E Marcoleta
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago CP 7800003, Chile
| | - Matías Gálvez-Silva
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago CP 7800003, Chile
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago CP 7800003, Chile
| | - Macarena A Varas
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago CP 7800003, Chile
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago CP 7800003, Chile
| | - Mauricio Díaz
- Laboratorio de Comunicación Microbiana, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago CP 7800003, Chile
| | - Mauricio Hernández
- División Biotecnología, Instituto Melisa, San Pedro de la Paz CP 9660000, Chile
| | - Cristian Vargas
- División Biotecnología, Instituto Melisa, San Pedro de la Paz CP 9660000, Chile
| | | | - Elard Koch
- División Biotecnología, Instituto Melisa, San Pedro de la Paz CP 9660000, Chile
| | - Pablo Saldivia
- División Biotecnología, Instituto Melisa, San Pedro de la Paz CP 9660000, Chile
- Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción CP 4070389, Chile
| | - Jorge Vielma
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago CP 7800003, Chile
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago CP 7800003, Chile
| | - Yunn-Hwen Gan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore CP 119077, Singapore
| | - Yahua Chen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore CP 119077, Singapore
| | - Nicolás Guiliani
- Laboratorio de Comunicación Microbiana, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago CP 7800003, Chile
| | - Francisco P Chávez
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago CP 7800003, Chile
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Jaiswal P, Meena NP, Chang FS, Liao XH, Kim L, Kimmel AR. An integrated, cross-regulation pathway model involving activating/adaptive and feed-forward/feed-back loops for directed oscillatory cAMP signal-relay/response during the development of Dictyostelium. Front Cell Dev Biol 2024; 11:1263316. [PMID: 38357530 PMCID: PMC10865387 DOI: 10.3389/fcell.2023.1263316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/19/2023] [Indexed: 02/16/2024] Open
Abstract
Self-organized and excitable signaling activities play important roles in a wide range of cellular functions in eukaryotic and prokaryotic cells. Cells require signaling networks to communicate amongst themselves, but also for response to environmental cues. Such signals involve complex spatial and temporal loops that may propagate as oscillations or waves. When Dictyostelium become starved for nutrients, cells within a localized space begin to secrete cAMP. Starved cells also become chemotactic to cAMP. cAMP signals propagate as outwardly moving waves that oscillate at ∼6 min intervals, which creates a focused territorial region for centralized cell aggregation. Proximal cells move inwardly toward the cAMP source and relay cAMP outwardly to recruit additional cells. To ensure directed inward movement and outward cAMP relay, cells go through adapted and de-adapted states for both cAMP synthesis/degradation and for directional cell movement. Although many immediate components that regulate cAMP signaling (including receptors, G proteins, an adenylyl cyclase, phosphodiesterases, and protein kinases) are known, others are only inferred. Here, using biochemical experiments coupled with gene inactivation studies, we model an integrated large, multi-component kinetic pathway involving activation, inactivation (adaptation), re-activation (re-sensitization), feed-forward, and feed-back controls to generate developmental cAMP oscillations.
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Affiliation(s)
- Pundrik Jaiswal
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, The National Institutes of Health, Bethesda, MD, United States
| | - Netra Pal Meena
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, The National Institutes of Health, Bethesda, MD, United States
| | - Fu-Sheng Chang
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, The National Institutes of Health, Bethesda, MD, United States
| | - Xin-Hua Liao
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, The National Institutes of Health, Bethesda, MD, United States
| | - Lou Kim
- Department of Biological Sciences, Florida International University, Miami, FL, United States
| | - Alan R. Kimmel
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, The National Institutes of Health, Bethesda, MD, United States
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9
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Pflanze S, Mukherji R, Ibrahim A, Günther M, Götze S, Chowdhury S, Reimer L, Regestein L, Stallforth P. Nonribosomal peptides protect Pseudomonas nunensis 4A2e from amoebal and nematodal predation. Chem Sci 2023; 14:11573-11581. [PMID: 37886094 PMCID: PMC10599466 DOI: 10.1039/d3sc03335j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/01/2023] [Indexed: 10/28/2023] Open
Abstract
The rhizosphere is a highly competitive environment forcing bacteria to evolve strategies to oppose their enemies. The production of toxic secondary metabolites allows bacteria to counteract predators. In this study, we describe the anti-predator armamentarium of the soil-derived bacterium Pseudomonas nunensis 4A2e. Based on a genome mining approach, we identified several biosynthetic gene clusters coding for nonribosomal peptide synthetases. Generation of gene deletion mutants of the respective clusters shows a loss of defense capabilities. We isolated the novel lipopeptides keanumycin D and nunapeptins B and C, and fully elucidated their structures by a combination of in-depth mass spectrometry experiments, stable isotope labelling, and chemical synthesis. Additionally, investigation of the quorum sensing-dependent biosynthesis allowed us to elucidate parts of the underlying regulation of the biosynthetic machinery. Ecology-inspired bioassays highlight the role of these peptides as a defence strategy against protozoans and led us to find a previously unknown function against the bacterivorous nematode Oscheius myriophilus.
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Affiliation(s)
- Sebastian Pflanze
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Ruchira Mukherji
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Anan Ibrahim
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Markus Günther
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Sebastian Götze
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Somak Chowdhury
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Lisa Reimer
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Lars Regestein
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-HKI Beutenbergstrasse 11a 07745 Jena Germany
| | - Pierre Stallforth
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology - Leibniz-HKI Beutenbergstrasse 11a 07745 Jena Germany
- Faculty of Chemistry and Earth Sciences, Friedrich Schiller University (FSU) Jena Germany
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10
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Wood EC, Glen AK, Kvarfordt LG, Womack F, Acevedo L, Yoon TS, Ma C, Flores V, Sinha M, Chodpathumwan Y, Termehchy A, Roach JC, Mendoza L, Hoffman AS, Deutsch EW, Koslicki D, Ramsey SA. RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine. BMC Bioinformatics 2022; 23:400. [PMID: 36175836 PMCID: PMC9520835 DOI: 10.1186/s12859-022-04932-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 09/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Biomedical translational science is increasingly using computational reasoning on repositories of structured knowledge (such as UMLS, SemMedDB, ChEMBL, Reactome, DrugBank, and SMPDB in order to facilitate discovery of new therapeutic targets and modalities. The NCATS Biomedical Data Translator project is working to federate autonomous reasoning agents and knowledge providers within a distributed system for answering translational questions. Within that project and the broader field, there is a need for a framework that can efficiently and reproducibly build an integrated, standards-compliant, and comprehensive biomedical knowledge graph that can be downloaded in standard serialized form or queried via a public application programming interface (API). RESULTS To create a knowledge provider system within the Translator project, we have developed RTX-KG2, an open-source software system for building-and hosting a web API for querying-a biomedical knowledge graph that uses an Extract-Transform-Load approach to integrate 70 knowledge sources (including the aforementioned core six sources) into a knowledge graph with provenance information including (where available) citations. The semantic layer and schema for RTX-KG2 follow the standard Biolink model to maximize interoperability. RTX-KG2 is currently being used by multiple Translator reasoning agents, both in its downloadable form and via its SmartAPI-registered interface. Serializations of RTX-KG2 are available for download in both the pre-canonicalized form and in canonicalized form (in which synonyms are merged). The current canonicalized version (KG2.7.3) of RTX-KG2 contains 6.4M nodes and 39.3M edges with a hierarchy of 77 relationship types from Biolink. CONCLUSION RTX-KG2 is the first knowledge graph that integrates UMLS, SemMedDB, ChEMBL, DrugBank, Reactome, SMPDB, and 64 additional knowledge sources within a knowledge graph that conforms to the Biolink standard for its semantic layer and schema. RTX-KG2 is publicly available for querying via its API at arax.rtx.ai/api/rtxkg2/v1.2/openapi.json . The code to build RTX-KG2 is publicly available at github:RTXteam/RTX-KG2 .
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Affiliation(s)
- E C Wood
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA
| | - Amy K Glen
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA.
| | - Lindsey G Kvarfordt
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA
| | - Finn Womack
- Computer Science and Engineering, Penn State University, State College, PA, USA
| | - Liliana Acevedo
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA
| | - Timothy S Yoon
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA
| | - Chunyu Ma
- Huck Institutes of the Life Sciences, Penn State University, State College, PA, USA
| | - Veronica Flores
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA
| | - Meghamala Sinha
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA
| | | | - Arash Termehchy
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA
| | | | | | - Andrew S Hoffman
- Interdisciplinary Hub for Digitalization and Society, Radboud University, Nijmegen, The Netherlands
| | | | - David Koslicki
- Computer Science and Engineering, Penn State University, State College, PA, USA
- Huck Institutes of the Life Sciences, Penn State University, State College, PA, USA
- Department of Biology, Penn State University, State College, PA, USA
| | - Stephen A Ramsey
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, USA
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR, USA
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11
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Saito T, Whatmore P, Taylor JF, Fernandes JMO, Adam AC, Tocher DR, Espe M, Skjærven KH. Micronutrient supplementation affects DNA methylation in male gonads with potential intergenerational epigenetic inheritance involving the embryonic development through glutamate receptor-associated genes. BMC Genomics 2022; 23:115. [PMID: 35144563 PMCID: PMC8832813 DOI: 10.1186/s12864-022-08348-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 01/28/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND DNA methylation has an important role in intergenerational inheritance. An increasing number of studies have reported evidence of germline inheritance of DNA methylation induced by nutritional signals in mammals. Vitamins and minerals as micronutrients contribute to growth performance in vertebrates, including Atlantic salmon (Salmo salar), and also have a role in epigenetics as environmental factors that alter DNA methylation status. It is important to understand whether micronutrients in the paternal diet can influence the offspring through alterations of DNA methylation signatures in male germ cells. RESULTS Here, we show the effect of micronutrient supplementation on DNA methylation profiles in the male gonad through a whole life cycle feeding trial of Atlantic salmon fed three graded levels of micronutrient components. Our results strongly indicate that micronutrient supplementation affects the DNA methylation status of genes associated with cell signalling, synaptic signalling, and embryonic development. In particular, it substantially affects DNA methylation status in the promoter region of a glutamate receptor gene, glutamate receptor ionotropic, NMDA 3A-like (grin3a-like), when the fish are fed both medium and high doses of micronutrients. Furthermore, two transcription factors, histone deacetylase 2 (hdac2) and a zinc finger protein, bind to the hyper-methylated site in the grin3a-like promoter. An estimated function of hdac2 together with a zinc finger indicates that grin3a-like has a potential role in intergenerational epigenetic inheritance and the regulation of embryonic development affected by paternal diet. CONCLUSIONS The present study demonstrates alterations of gene expression patterns and DNA methylation signatures in the male gonad when Atlantic salmon are fed different levels of micronutrients. Alterations of gene expression patterns are of great interest because the gonads are supposed to have limited metabolic activities compared to other organs, whereas alterations of DNA methylation signatures are of great importance in the field of nutritional epigenetics because the signatures affected by nutrition could be transferred to the next generation. We provide extensive data resources for future work in the context of potential intergenerational inheritance through the male germline.
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Affiliation(s)
| | | | - John F Taylor
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Scotland, UK
| | | | | | - Douglas R Tocher
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Scotland, UK
| | - Marit Espe
- Institute of Marine Research, Bergen, Norway
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12
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Kay RR, Lutton J, Coker H, Paschke P, King JS, Bretschneider T. The Amoebal Model for Macropinocytosis. Subcell Biochem 2022; 98:41-59. [PMID: 35378702 DOI: 10.1007/978-3-030-94004-1_3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Macropinocytosis is a relatively unexplored form of large-scale endocytosis driven by the actin cytoskeleton. Dictyostelium amoebae form macropinosomes from cups extended from the plasma membrane, then digest their contents and absorb the nutrients in the endo-lysosomal system. They use macropinocytosis for feeding, maintaining a high rate of fluid uptake that makes assay and experimentation easy. Mutants collected over the years identify cytoskeletal and signalling proteins required for macropinocytosis. Cups are organized around plasma membrane domains of intense PIP3, Ras and Rac signalling, proper formation of which also depends on the RasGAPs NF1 and RGBARG, PTEN, the PIP3-regulated protein kinases Akt and SGK and their activators PDK1 and TORC2, Rho proteins, plus other components yet to be identified. This PIP3 domain directs dendritic actin polymerization to the extending lip of macropinocytic cups by recruiting a ring of the SCAR/WAVE complex around itself and thus activating the Arp2/3 complex. The dynamics of PIP3 domains are proposed to shape macropinocytic cups from start to finish. The role of the Ras-PI3-kinase module in organizing feeding structures in unicellular organisms most likely predates its adoption into growth factor signalling, suggesting an evolutionary origin for growth factor signalling.
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Affiliation(s)
- Robert R Kay
- MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Josiah Lutton
- Department of Computer Science, University of Warwick, Coventry, UK
| | - Helena Coker
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Peggy Paschke
- MRC Laboratory of Molecular Biology, Cambridge, UK.,Cancer Research UK Beatson Institute, Garscube Estate, Glasgow, UK
| | - Jason S King
- School of Biomedical Sciences, University of Sheffield, Sheffield, UK
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13
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Bai W, Wells ML, Lai WS, Hicks SN, Burkholder AB, Perera L, Kimmel AR, Blackshear PJ. A post-transcriptional regulon controlled by TtpA, the single tristetraprolin family member expressed in Dictyostelium discoideum. Nucleic Acids Res 2021; 49:11920-11937. [PMID: 34718768 DOI: 10.1093/nar/gkab983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 10/05/2021] [Accepted: 10/12/2021] [Indexed: 12/30/2022] Open
Abstract
Post-transcriptional processes mediated by mRNA binding proteins represent important control points in gene expression. In eukaryotes, mRNAs containing specific AU-rich motifs are regulated by binding of tristetraprolin (TTP) family tandem zinc finger proteins, which promote mRNA deadenylation and decay, partly through interaction of a conserved C-terminal CNOT1 binding (CNB) domain with CCR4-NOT protein complexes. The social ameba Dictyostelium discoideum shared a common ancestor with humans more than a billion years ago, and expresses only one TTP family protein, TtpA, in contrast to three members expressed in humans. Evaluation of ttpA null-mutants identified six transcripts that were consistently upregulated compared to WT during growth and early development. The 3'-untranslated regions (3'-UTRs) of all six 'TtpA-target' mRNAs contained multiple TTP binding motifs (UUAUUUAUU), and one 3'-UTR conferred TtpA post-transcriptional stability regulation to a heterologous mRNA that was abrogated by mutations in the core TTP-binding motifs. All six target transcripts were upregulated to similar extents in a C-terminal truncation mutant, in contrast to less severe effects of analogous mutants in mice. All six target transcripts encoded probable membrane proteins. In Dictyostelium, TtpA may control an 'RNA regulon', where a single RNA binding protein, TtpA, post-transcriptionally co-regulates expression of several functionally related proteins.
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Affiliation(s)
- Wenli Bai
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Melissa L Wells
- The Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Wi S Lai
- The Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Stephanie N Hicks
- The Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Adam B Burkholder
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Lalith Perera
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Alan R Kimmel
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD 20892, USA
| | - Perry J Blackshear
- The Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.,The Departments of Medicine and Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
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14
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Katoh-Kurasawa M, Hrovatin K, Hirose S, Webb A, Ho HI, Zupan B, Shaulsky G. Transcriptional milestones in Dictyostelium development. Genome Res 2021; 31:1498-1511. [PMID: 34183452 PMCID: PMC8327917 DOI: 10.1101/gr.275496.121] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/23/2021] [Indexed: 02/02/2023]
Abstract
Dictyostelium development begins with single-cell starvation and ends with multicellular fruiting bodies. Developmental morphogenesis is accompanied by sweeping transcriptional changes, encompassing nearly half of the 13,000 genes in the genome. We performed time-series RNA-sequencing analyses of the wild type and 20 mutants to explore the relationships between transcription and morphogenesis. These strains show developmental arrest at different stages, accelerated development, or atypical morphologies. Considering eight major morphological transitions, we identified 1371 milestone genes whose expression changes sharply between consecutive transitions. We also identified 1099 genes as members of 21 regulons, which are groups of genes that remain coordinately regulated despite the genetic, temporal, and developmental perturbations. The gene annotations in these groups validate known transitions and reveal new developmental events. For example, DNA replication genes are tightly coregulated with cell division genes, so they are expressed in mid-development although chromosomal DNA is not replicated. Our data set includes 486 transcriptional profiles that can help identify new relationships between transcription and development and improve gene annotations. We show its utility by showing that cycles of aggregation and disaggregation in allorecognition-defective mutants involve dedifferentiation. We also show sensitivity to genetic and developmental conditions in two commonly used actin genes, act6 and act15, and robustness of the coaA gene. Finally, we propose that gpdA is a better mRNA quantitation standard because it is less sensitive to external conditions than commonly used standards. The data set is available for democratized exploration through the web application dictyExpress and the data mining environment Orange.
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Affiliation(s)
- Mariko Katoh-Kurasawa
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Karin Hrovatin
- Faculty of Computer and Information Science, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Shigenori Hirose
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Amanda Webb
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Hsing-I Ho
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Blaž Zupan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Faculty of Computer and Information Science, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Gad Shaulsky
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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15
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Sweeney BA, Hoksza D, Nawrocki EP, Ribas CE, Madeira F, Cannone JJ, Gutell R, Maddala A, Meade CD, Williams LD, Petrov AS, Chan PP, Lowe TM, Finn RD, Petrov AI. R2DT is a framework for predicting and visualising RNA secondary structure using templates. Nat Commun 2021; 12:3494. [PMID: 34108470 PMCID: PMC8190129 DOI: 10.1038/s41467-021-23555-5] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 05/04/2021] [Indexed: 02/05/2023] Open
Abstract
Non-coding RNAs (ncRNA) are essential for all life, and their functions often depend on their secondary (2D) and tertiary structure. Despite the abundance of software for the visualisation of ncRNAs, few automatically generate consistent and recognisable 2D layouts, which makes it challenging for users to construct, compare and analyse structures. Here, we present R2DT, a method for predicting and visualising a wide range of RNA structures in standardised layouts. R2DT is based on a library of 3,647 templates representing the majority of known structured RNAs. R2DT has been applied to ncRNA sequences from the RNAcentral database and produced >13 million diagrams, creating the world's largest RNA 2D structure dataset. The software is amenable to community expansion, and is freely available at https://github.com/rnacentral/R2DT and a web server is found at https://rnacentral.org/r2dt .
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Affiliation(s)
- Blake A Sweeney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - David Hoksza
- Department of Software Engineering, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Eric P Nawrocki
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Carlos Eduardo Ribas
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Fábio Madeira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Jamie J Cannone
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Robin Gutell
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Aparna Maddala
- School of Chemistry and Biochemistry, Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Caeden D Meade
- School of Chemistry and Biochemistry, Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Anton S Petrov
- School of Chemistry and Biochemistry, Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA, USA
| | - Patricia P Chan
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Anton I Petrov
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.
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16
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Martín‐González J, Montero‐Bullón J, Lacal J. Dictyostelium discoideum as a non-mammalian biomedical model. Microb Biotechnol 2021; 14:111-125. [PMID: 33124755 PMCID: PMC7888446 DOI: 10.1111/1751-7915.13692] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/06/2020] [Accepted: 10/11/2020] [Indexed: 02/06/2023] Open
Abstract
Dictyostelium discoideum is one of eight non-mammalian model organisms recognized by the National Institute of Health for the study of human pathology. The use of this slime mould is possible owing to similarities in cell structure, behaviour and intracellular signalling with mammalian cells. Its haploid set of chromosomes completely sequenced amenable to genetic manipulation, its unique and short life cycle with unicellular and multicellular stages, and phenotypic richness encoding many human orthologues, make Dictyostelium a representative and simple model organism to unveil cellular processes in human disease. Dictyostelium studies within the biomedical field have provided fundamental knowledge in the areas of bacterial infection, immune cell chemotaxis, autophagy/phagocytosis and mitochondrial and neurological disorders. Consequently, Dictyostelium has been used to the development of related pharmacological treatments. Herein, we review the utilization of Dictyostelium as a model organism in biomedicine.
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Affiliation(s)
- Javier Martín‐González
- Molecular Genetics of Human Diseases GroupDepartment of Microbiology and GeneticsFaculty of BiologyUniversity of SalamancaCampus Miguel de UnamunoSalamancaE‐37007Spain
| | - Javier‐Fernando Montero‐Bullón
- Metabolic Engineering GroupDepartment of Microbiology and GeneticsUniversity of SalamancaCampus Miguel de UnamunoSalamancaE‐37007Spain
| | - Jesus Lacal
- Molecular Genetics of Human Diseases GroupDepartment of Microbiology and GeneticsFaculty of BiologyUniversity of SalamancaCampus Miguel de UnamunoSalamancaE‐37007Spain
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17
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Kurakin GF, Samoukina AM, Potapova NA. Bacterial and Protozoan Lipoxygenases Could be Involved in Cell-to-Cell Signaling and Immune Response Suppression. BIOCHEMISTRY (MOSCOW) 2020; 85:1048-1071. [PMID: 33050851 DOI: 10.1134/s0006297920090059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Lipoxygenases are found in animals, plants, and fungi, where they are involved in a wide range of cell-to-cell signaling processes. The presence of lipoxygenases in a number of bacteria and protozoa has been also established, but their biological significance remains poorly understood. Several hypothetical functions of lipoxygenases in bacteria and protozoa have been suggested without experimental validation. The objective of our study was evaluating the functions of bacterial and protozoan lipoxygenases by evolutionary and taxonomic analysis using bioinformatics tools. Lipoxygenase sequences were identified and examined using BLAST, followed by analysis of constructed phylogenetic trees and networks. Our results support the theory on the involvement of lipoxygenases in the formation of multicellular structures by microorganisms and their possible evolutionary significance in the emergence of multicellularity. Furthermore, we observed association of lipoxygenases with the suppression of host immune response by parasitic and symbiotic bacteria including dangerous opportunistic pathogens.
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Affiliation(s)
- G F Kurakin
- Department of Biochemistry and Laboratory Medicine, Tver State Medical University, Ministry of Health of the Russian Federation, Tver, 170100, Russia.
| | - A M Samoukina
- Department of Microbiology, Virology, and Immunology, Tver State Medical University, Ministry of Health of the Russian Federation, Tver, 170100, Russia
| | - N A Potapova
- Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051, Russia.,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119234, Russia
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18
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Valenzuela C, Gil M, Urrutia ÍM, Sabag A, Enninga J, Santiviago CA. SopB- and SifA-dependent shaping of the Salmonella-containing vacuole proteome in the social amoeba Dictyostelium discoideum. Cell Microbiol 2020; 23:e13263. [PMID: 32945061 DOI: 10.1111/cmi.13263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 09/07/2020] [Accepted: 09/09/2020] [Indexed: 02/06/2023]
Abstract
The ability of Salmonella to survive and replicate within mammalian host cells involves the generation of a membranous compartment known as the Salmonella-containing vacuole (SCV). Salmonella employs a number of effector proteins that are injected into host cells for SCV formation using its type-3 secretion systems encoded in SPI-1 and SPI-2 (T3SS-1 and T3SS-2, respectively). Recently, we reported that S. Typhimurium requires T3SS-1 and T3SS-2 to survive in the model amoeba Dictyostelium discoideum. Despite these findings, the involved effector proteins have not been identified yet. Therefore, we evaluated the role of two major S. Typhimurium effectors SopB and SifA during D. discoideum intracellular niche formation. First, we established that S. Typhimurium resides in a vacuolar compartment within D. discoideum. Next, we isolated SCVs from amoebae infected with wild type or the ΔsopB and ΔsifA mutant strains of S. Typhimurium, and we characterised the composition of this compartment by quantitative proteomics. This comparative analysis suggests that S. Typhimurium requires SopB and SifA to modify the SCV proteome in order to generate a suitable intracellular niche in D. discoideum. Accordingly, we observed that SopB and SifA are needed for intracellular survival of S. Typhimurium in this organism. Thus, our results provide insight into the mechanisms employed by Salmonella to survive intracellularly in phagocytic amoebae.
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Affiliation(s)
- Camila Valenzuela
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile.,Dynamics of Host-Pathogen Interactions Unit, Institut Pasteur, Paris, France.,CNRS UMR3691, Paris, France
| | - Magdalena Gil
- Dynamics of Host-Pathogen Interactions Unit, Institut Pasteur, Paris, France.,CNRS UMR3691, Paris, France
| | - Ítalo M Urrutia
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Andrea Sabag
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Jost Enninga
- Dynamics of Host-Pathogen Interactions Unit, Institut Pasteur, Paris, France.,CNRS UMR3691, Paris, France
| | - Carlos A Santiviago
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
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19
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Perrigo AL, Vadell EM, Cavender JC, Landolt JC, Liu P, Stephenson SL. Additional new species suggest high dictyostelid diversity on Madagascar. Mycologia 2020; 112:1026-1042. [PMID: 33006910 DOI: 10.1080/00275514.2020.1802641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Dictyostelids are a monophyletic group of sorocarp-forming social amoebae in the major eukaryotic division Amoebozoa. Members of this taxon, which is made up of almost 200 described species, are common in terrestrial soils globally. Still, the alpha diversity is not well known in many areas, and new species are frequently recovered. The highest species richness is found in the tropics. Here, five new species are described from soil samples collected in Madagascar. These species-Cavenderia basinodulosa, C. canoespora, Heterostelium radiatum, H. versatile, and Raperostelium stabile-are described based on both morphological characteristics and molecular data, with sequence data from the rDNA small subunit (SSU). The five new species are morphologically disparate, ranging from relatively small, robust taxa such as R. stabile to taxa with variable morphologies such as the larger H. radiatum and H. versatile and the yellow-tinted and irregularly branched species C. canoespora and C. basinulosa. These new species, together with earlier work where 13 other species were described from the island, suggest that there is a range of genetically diverse and highly morphologically variable dictyostelid taxa occurring on Madagascar, suggesting biogeographic patterns even within these very small organisms.
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Affiliation(s)
- Allison L Perrigo
- Department of Biological and Environmental Sciences, University of Gothenburg , Gothenburg, Sweden.,Gothenburg Global Biodiversity Centre , Gothenburg, Sweden
| | - Eduardo M Vadell
- Escuela de Farmacia and Bioquímica, J. F. Kennedy University Sarmiento 4564 / Museo de Historia Nat. R.S.V. Viamonte 1716 , Buenos Aires, Argentina
| | - James C Cavender
- Department of Environmental and Plant Biology, Ohio University , Athens, Ohio 45701
| | - John C Landolt
- Department of Biology, Shepherd University , Shepherdstown, West Virginia 25443
| | - Pu Liu
- Engineering Research Center of Edible and Medicinal Fungi, Ministry of Education, Jilin Agricultural University , Changchun 130118, Jilin Province, People's Republic of China
| | - Steven L Stephenson
- Department of Biological Sciences, University of Arkansas, Fayetteville , Arkansas 72701
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20
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Olmos J, Pignataro MF, Benítez dos Santos AB, Bringas M, Klinke S, Kamenetzky L, Velazquez F, Santos J. A Highly Conserved Iron-Sulfur Cluster Assembly Machinery between Humans and Amoeba Dictyostelium discoideum: The Characterization of Frataxin. Int J Mol Sci 2020; 21:E6821. [PMID: 32957566 PMCID: PMC7554988 DOI: 10.3390/ijms21186821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/05/2020] [Accepted: 09/14/2020] [Indexed: 12/17/2022] Open
Abstract
Several biological activities depend on iron-sulfur clusters ([Fe-S]). Even though they are well-known in several organisms their function and metabolic pathway were poorly understood in the majority of the organisms. We propose to use the amoeba Dictyostelium discoideum, as a biological model to study the biosynthesis of [Fe-S] at the molecular, cellular and organism levels. First, we have explored the D. discoideum genome looking for genes corresponding to the subunits that constitute the molecular machinery for Fe-S cluster assembly and, based on the structure of the mammalian supercomplex and amino acid conservation profiles, we inferred the full functionality of the amoeba machinery. After that, we expressed the recombinant mature form of D. discoideum frataxin protein (DdFXN), the kinetic activator of this pathway. We characterized the protein and its conformational stability. DdFXN is monomeric and compact. The analysis of the secondary structure content, calculated using the far-UV CD spectra, was compatible with the data expected for the FXN fold, and near-UV CD spectra were compatible with the data corresponding to a folded protein. In addition, Tryptophan fluorescence indicated that the emission occurs from an apolar environment. However, the conformation of DdFXN is significantly less stable than that of the human FXN, (4.0 vs. 9.0 kcal mol-1, respectively). Based on a sequence analysis and structural models of DdFXN, we investigated key residues involved in the interaction of DdFXN with the supercomplex and the effect of point mutations on the energetics of the DdFXN tertiary structure. More than 10 residues involved in Friedreich's Ataxia are conserved between the human and DdFXN forms, and a good correlation between mutational effect on the energetics of both proteins were found, suggesting the existence of similar sequence/function/stability relationships. Finally, we integrated this information in an evolutionary context which highlights particular variation patterns between amoeba and humans that may reflect a functional importance of specific protein positions. Moreover, the complete pathway obtained forms a piece of evidence in favor of the hypothesis of a shared and highly conserved [Fe-S] assembly machinery between Human and D. discoideum.
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Affiliation(s)
- Justo Olmos
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina; (J.O.); (M.F.P.); (A.B.B.d.S.); (L.K.)
| | - María Florencia Pignataro
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina; (J.O.); (M.F.P.); (A.B.B.d.S.); (L.K.)
| | - Ana Belén Benítez dos Santos
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina; (J.O.); (M.F.P.); (A.B.B.d.S.); (L.K.)
| | - Mauro Bringas
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE CONICET), Buenos Aires C1428EGA, Argentina;
| | - Sebastián Klinke
- Fundación Instituto Leloir, IIBBA-CONICET, and Plataforma Argentina de Biología Estructural y Metabolómica PLABEM, Av. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina;
| | - Laura Kamenetzky
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina; (J.O.); (M.F.P.); (A.B.B.d.S.); (L.K.)
- IMPaM, CONICET, Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires C1121ABG, Argentina
| | - Francisco Velazquez
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina; (J.O.); (M.F.P.); (A.B.B.d.S.); (L.K.)
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN)—(UBA/CONICET), Buenos Aires C1428EGA, Argentina
| | - Javier Santos
- Instituto de Biociencias, Biotecnología y Biología Traslacional (iB3), Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina; (J.O.); (M.F.P.); (A.B.B.d.S.); (L.K.)
- Consejo Nacional de Investigaciones Científicas y Técnicas, Rivadavia 1917, Buenos Aires C1033AAJ, Argentina
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires. Intendente Güiraldes 2160, Ciudad Universitaria, Buenos Aires C1428EGA, Argentina
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Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:91-103. [PMID: 32652120 PMCID: PMC7646089 DOI: 10.1016/j.gpb.2018.11.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 10/24/2018] [Accepted: 12/14/2018] [Indexed: 11/27/2022]
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Bioenergetics of the Dictyostelium Kinesin-8 Motor Isoform. Biomolecules 2020; 10:biom10040563. [PMID: 32272590 PMCID: PMC7226124 DOI: 10.3390/biom10040563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 03/27/2020] [Accepted: 04/02/2020] [Indexed: 12/29/2022] Open
Abstract
The functional organization of microtubules in eukaryotic cells requires a combination of their inherent dynamic properties, interactions with motor machineries, and interactions with accessory proteins to affect growth, shrinkage, stability, and architecture. In most organisms, the Kinesin-8 family of motors play an integral role in these organizations, well known for their mitotic activities in microtubule (MT) length control and kinetochore interactions. In Dictyostelium discoideum, the function of Kinesin-8 remains elusive. We present here some biochemical properties and localization data that indicate that this motor (DdKif10) shares some motility properties with other Kinesin-8s but also illustrates differences in microtubule localization and depolymerase action that highlight functional diversity.
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Lamrabet O, Melotti A, Burdet F, Hanna N, Perrin J, Nitschke J, Pagni M, Hilbi H, Soldati T, Cosson P. Transcriptional Responses of Dictyostelium discoideum Exposed to Different Classes of Bacteria. Front Microbiol 2020; 11:410. [PMID: 32210949 PMCID: PMC7078664 DOI: 10.3389/fmicb.2020.00410] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/27/2020] [Indexed: 12/19/2022] Open
Abstract
Dictyostelium discoideum amoebae feed by ingesting bacteria, then killing them in phagosomes. Ingestion and killing of different bacteria have been shown to rely on largely different molecular mechanisms. One would thus expect that D. discoideum adapts its ingestion and killing machinery when encountering different bacteria. In this study, we investigated by RNA sequencing if and how D. discoideum amoebae respond to the presence of different bacteria by modifying their gene expression patterns. Each bacterial species analyzed induced a specific modification of the transcriptome. Bacteria such as Bacillus subtilis, Klebsiella pneumoniae, or Mycobacterium marinum induced a specific and different transcriptional response, while Micrococcus luteus did not trigger a significant gene regulation. Although folate has been proposed to be one of the key molecules secreted by bacteria and recognized by hunting amoebae, it elicited a very specific and restricted transcriptional signature, distinct from that triggered by any bacteria analyzed here. Our results indicate that D. discoideum amoebae respond in a highly specific, almost non-overlapping manner to different species of bacteria. We additionally identify specific sets of genes that can be used as reporters of the response of D. discoideum to different bacteria.
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Affiliation(s)
- Otmane Lamrabet
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Astrid Melotti
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Frédéric Burdet
- Vital-IT Group, SIB, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nabil Hanna
- Department of Biochemistry, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Jackie Perrin
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Jahn Nitschke
- Department of Biochemistry, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Marco Pagni
- Vital-IT Group, SIB, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Hubert Hilbi
- Faculty of Medicine, Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Thierry Soldati
- Department of Biochemistry, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - Pierre Cosson
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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Pressure sensing through Piezo channels controls whether cells migrate with blebs or pseudopods. Proc Natl Acad Sci U S A 2020; 117:2506-2512. [PMID: 31964823 PMCID: PMC7007555 DOI: 10.1073/pnas.1905730117] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Cells migrating within the body perform vital functions in development and for defense and repair of tissues. In this dense environment, cells encounter mechanical forces and constraints not experienced when moving under buffer, and, accordingly, many change how they move. We find that gentle squashing, which mimics mechanical resistance, causes cells to move using blebs—a form of projection driven by fluid pressure—rather than pseudopods. This behavior depends on the Piezo stretch-operated ion channel in the cell membrane and calcium fluxes into the cell. Piezo is highly conserved and is required for light touch sensation; this work extends its functions into migrating cells. Blebs and pseudopods can both power cell migration, with blebs often favored in tissues, where cells encounter increased mechanical resistance. To investigate how migrating cells detect and respond to mechanical forces, we used a “cell squasher” to apply uniaxial pressure to Dictyostelium cells chemotaxing under soft agarose. As little as 100 Pa causes a rapid (<10 s), sustained shift to movement with blebs rather than pseudopods. Cells are flattened under load and lose volume; the actin cytoskeleton is reorganized, with myosin II recruited to the cortex, which may pressurize the cytoplasm for blebbing. The transition to bleb-driven motility requires extracellular calcium and is accompanied by increased cytosolic calcium. It is largely abrogated in cells lacking the Piezo stretch-operated channel; under load, these cells persist in using pseudopods and chemotax poorly. We propose that migrating cells sense pressure through Piezo, which mediates calcium influx, directing movement with blebs instead of pseudopods.
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Meena NP, Jaiswal P, Chang FS, Brzostowski J, Kimmel AR. DPF is a cell-density sensing factor, with cell-autonomous and non-autonomous functions during Dictyostelium growth and development. BMC Biol 2019; 17:97. [PMID: 31791330 PMCID: PMC6889452 DOI: 10.1186/s12915-019-0714-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 10/24/2019] [Indexed: 12/20/2022] Open
Abstract
Background Cellular functions can be regulated by cell-cell interactions that are influenced by extra-cellular, density-dependent signaling factors. Dictyostelium grow as individual cells in nutrient-rich sources, but, as nutrients become depleted, they initiate a multi-cell developmental program that is dependent upon a cell-density threshold. We hypothesized that novel secreted proteins may serve as density-sensing factors to promote multi-cell developmental fate decisions at a specific cell-density threshold, and use Dictyostelium in the identification of such a factor. Results We show that multi-cell developmental aggregation in Dictyostelium is lost upon minimal (2-fold) reduction in local cell density. Remarkably, developmental aggregation response at non-permissive cell densities is rescued by addition of conditioned media from high-density, developmentally competent cells. Using rescued aggregation of low-density cells as an assay, we purified a single, 150-kDa extra-cellular protein with density aggregation activity. MS/MS peptide sequence analysis identified the gene sequence, and cells that overexpress the full-length protein accumulate higher levels of a development promoting factor (DPF) activity than parental cells, allowing cells to aggregate at lower cell densities; cells deficient for this DPF gene lack density-dependent developmental aggregation activity and require higher cell density for cell aggregation compared to WT. Density aggregation activity co-purifies with tagged versions of DPF and tag-affinity-purified DPF possesses density aggregation activity. In mixed development with WT, cells that overexpress DPF preferentially localize at centers for multi-cell aggregation and define cell-fate choice during cytodifferentiation. Finally, we show that DPF is synthesized as a larger precursor, single-pass transmembrane protein, with the p150 fragment released by proteolytic cleavage and ectodomain shedding. The TM/cytoplasmic domain of DPF possesses cell-autonomous activity for cell-substratum adhesion and for cellular growth. Conclusions We have purified a novel secreted protein, DPF, that acts as a density-sensing factor for development and functions to define local collective thresholds for Dictyostelium development and to facilitate cell-cell communication and multi-cell formation. Regions of high DPF expression are enriched at centers for cell-cell signal-response, multi-cell formation, and cell-fate determination. Additionally, DPF has separate cell-autonomous functions for regulation of cellular adhesion and growth.
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Affiliation(s)
- Netra Pal Meena
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, The National Institutes of Health, Bethesda, MD, 20892, USA
| | - Pundrik Jaiswal
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, The National Institutes of Health, Bethesda, MD, 20892, USA
| | - Fu-Sheng Chang
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, The National Institutes of Health, Bethesda, MD, 20892, USA
| | - Joseph Brzostowski
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, The National Institutes of Health, Bethesda, MD, 20892, USA.,Laboratory of Immunogenetics Twinbrook Imaging Facility, National Institute of Allergy and Infectious Diseases, The National Institutes of Health, Rockville, MD, 20852, USA
| | - Alan R Kimmel
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, The National Institutes of Health, Bethesda, MD, 20892, USA.
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Saad M, Guédin A, Amor S, Bedrat A, Tourasse NJ, Fayyad-Kazan H, Pratviel G, Lacroix L, Mergny JL. Mapping and characterization of G-quadruplexes in the genome of the social amoeba Dictyostelium discoideum. Nucleic Acids Res 2019; 47:4363-4374. [PMID: 30923812 PMCID: PMC6511855 DOI: 10.1093/nar/gkz196] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 03/08/2019] [Accepted: 03/24/2019] [Indexed: 01/25/2023] Open
Abstract
G-quadruplexes (G4) are non-canonical DNA and/or RNA secondary structures formed in guanine-rich regions. Given their over-representation in specific regions in the genome such as promoters and telomeres, they are likely to play important roles in key processes such as transcription, replication or RNA maturation. Putative G4-forming sequences (G4FS) have been reported in humans, yeast, bacteria, viruses and many organisms. Here we present the first mapping of G-quadruplex sequences in Dictyostelium discoideum, the social amoeba. ‘Dicty’ is an ameboid protozoan with a small (34 Mb) and extremely AT rich genome (78%). As a consequence, very few G4-prone motifs are expected. An in silico analysis of the Dictyostelium genome with the G4Hunter software detected 249–1055 G4-prone motifs, depending on G4Hunter chosen threshold. Interestingly, despite an even lower GC content (as compared to the whole Dicty genome), the density of G4 motifs in Dictyostelium promoters and introns is significantly higher than in the rest of the genome. Fourteen selected sequences located in important genes were characterized by a combination of biophysical and biochemical techniques. Our data show that these sequences form highly stable G4 structures under physiological conditions. Five Dictyostelium genes containing G4-prone motifs in their promoters were studied for the effect of a new G4-binding porphyrin derivative on their expression. Our results demonstrated that the new ligand significantly decreased their expression. Overall, our results constitute the first step to adopt Dictyostelium discoideum as a ‘G4-poor’ model for studies on G-quadruplexes.
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Affiliation(s)
- Mona Saad
- ARNA Laboratory, IECB, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, Bordeaux, France.,Laboratory of Cancer Biology and Molecular Immunology, Faculty of Sciences I, Lebanese University, Beirut, Al-Hadath, Lebanon, Lebanon
| | - Aurore Guédin
- ARNA Laboratory, IECB, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, Bordeaux, France
| | - Souheila Amor
- ARNA Laboratory, IECB, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, Bordeaux, France
| | - Amina Bedrat
- ARNA Laboratory, IECB, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, Bordeaux, France
| | - Nicolas J Tourasse
- ARNA Laboratory, IECB, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, Bordeaux, France
| | - Hussein Fayyad-Kazan
- Laboratory of Cancer Biology and Molecular Immunology, Faculty of Sciences I, Lebanese University, Beirut, Al-Hadath, Lebanon, Lebanon
| | | | | | - Jean-Louis Mergny
- ARNA Laboratory, IECB, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, Bordeaux, France.,Institute of Biophysics of the Czech Academy of Sciences, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
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mTORC1/AMPK responses define a core gene set for developmental cell fate switching. BMC Biol 2019; 17:58. [PMID: 31319820 PMCID: PMC6637605 DOI: 10.1186/s12915-019-0673-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 06/06/2019] [Indexed: 12/12/2022] Open
Abstract
Background Kinases mTORC1 and AMPK act as energy sensors, controlling nutrient responses and cellular growth. Changes in nutrient levels affect diverse transcriptional networks, making it challenging to identify downstream paths that regulate cellular growth or a switch to development via nutrient variation. The life cycle of Dictyostelium presents an excellent model to study the mTORC1 signaling function for growth and development. Dictyostelium grow as single cells in nutrient-rich media, but, upon nutrient withdrawal, growth ceases and cells enter a program for multi-cell development. While nearly half the genome shows gene expression changes upon nutrient removal, we hypothesized that not all of these genes are required for the switch to program development. Through manipulation of mTORC1 activity alone, without nutrient removal, we focused on a core network of genes that are required for switching between growth and development for regulation of cell fate decisions. Results To identify developmentally essential genes, we sought ways to promote development in the absence of nutrient loss. We first examined the activities of mTORC1 and AMPK in Dictyostelium during phases of rapid growth and starvation-induced development and showed they exhibited reciprocal patterns of regulation under various conditions. Using these as initial readouts, we identified rich media conditions that promoted rapid cell growth but, upon mTORC1 inactivation by rapamycin, led to a growth/development switch. Examination of gene expression during cell fate switching showed that changes in expression of most starvation-regulated genes were not required for developmental induction. Approximately 1000 genes which become downregulated upon rapamycin treatment comprise a cellular growth network involving ribosome biogenesis, protein synthesis, and cell cycle processes. Conversely, the upregulation of ~ 500 genes by rapamycin treatment defines essential signaling pathways for developmental induction, and ~ 135 of their protein products intersect through the well-defined cAMP/PKA network. Many of the rapamycin-induced genes we found are currently unclassified, and mutation analyses of 5 such genes suggest a novel gene class essential for developmental regulation. Conclusions We show that manipulating activities of mTORC1/AMPK in the absence of nutrient withdrawal is sufficient for a growth-to-developmental fate switch in Dictyostelium, providing a means to identify transcriptional networks and signaling pathways essential for early development. Electronic supplementary material The online version of this article (10.1186/s12915-019-0673-1) contains supplementary material, which is available to authorized users.
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Gomer RH. The Use of Diffusion Calculations and Monte Carlo Simulations to Understand the Behavior of Cells in Dictyostelium Communities. Comput Struct Biotechnol J 2019; 17:684-688. [PMID: 31303972 PMCID: PMC6603294 DOI: 10.1016/j.csbj.2019.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 05/25/2019] [Accepted: 06/01/2019] [Indexed: 11/01/2022] Open
Abstract
Microbial communities are the simplest possible model of multicellular tissues, allowing studies of cell-cell interactions to be done with as few extraneous factors as possible. For instance, the eukaryotic microbe Dictyostelium discoideum proliferates as single cells, and when starved, the cells aggregate together and form structures of ~20,000 cells. The cells use a variety of signals to direct their movement, inform each other of their local cell density and whether they are starving, and organize themselves into groups of ~20,000 cells. Mathematical models and computational approaches have been a key check on, and guide of, the experimental work. In this minireview, I will discuss diffusion calculations and Monte Carlo simulations that were used for Dictyostelium studies that offer general paradigms for several aspects of cell-cell communication. For instance, computational work showed that diffusible secreted cell-density sensing (quorum) factors can diffuse away so quickly from a single cell that the local concentration will not build up to incorrectly cause the cell to sense that it is in the presence of a high density of other cells secreting that signal. In another example, computation correctly predicted a mechanism that allows a group of cells to break up into subgroups. These are thus some examples of the power and necessity of computational work in biology.
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Affiliation(s)
- Richard H Gomer
- Department of Biology, Texas A&M University, College Station, TX 77843-3474, USA
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Odell J, Sikirzhytski V, Tikhonenko I, Cobani S, Khodjakov A, Koonce M. Force balances between interphase centrosomes as revealed by laser ablation. Mol Biol Cell 2019; 30:1705-1715. [PMID: 31067156 PMCID: PMC6727758 DOI: 10.1091/mbc.e19-01-0034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Numerous studies have highlighted the self-centering activities of individual microtubule (MT) arrays in animal cells, but relatively few works address the behavior of multiple arrays that coexist in a common cytoplasm. In multinucleated Dictyostelium discoideum cells, each centrosome organizes a radial MT network, and these networks remain separate from one another. This feature offers an opportunity to reveal the mechanism(s) responsible for the positioning of multiple centrosomes. Using a laser microbeam to eliminate one of the two centrosomes in binucleate cells, we show that the unaltered array is rapidly repositioned at the cell center. This result demonstrates that each MT array is constantly subject to centering forces and infers a mechanism to balance the positions of multiple arrays. Our results address the limited actions of three kinesins and a cross-linking MAP that are known to have effects in maintaining MT organization and suggest a simple means used to keep the arrays separated.
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Affiliation(s)
- Jacob Odell
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509
| | - Vitali Sikirzhytski
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509
| | - Irina Tikhonenko
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509
| | - Sonila Cobani
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509
| | - Alexey Khodjakov
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509
| | - Michael Koonce
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12201-0509
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Samba-Louaka A, Delafont V, Rodier MH, Cateau E, Héchard Y. Free-living amoebae and squatters in the wild: ecological and molecular features. FEMS Microbiol Rev 2019; 43:415-434. [DOI: 10.1093/femsre/fuz011] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/30/2019] [Indexed: 02/06/2023] Open
Abstract
ABSTRACT
Free-living amoebae are protists frequently found in water and soils. They feed on other microorganisms, mainly bacteria, and digest them through phagocytosis. It is accepted that these amoebae play an important role in the microbial ecology of these environments. There is a renewed interest for the free-living amoebae since the discovery of pathogenic bacteria that can resist phagocytosis and of giant viruses, underlying that amoebae might play a role in the evolution of other microorganisms, including several human pathogens. Recent advances, using molecular methods, allow to bring together new information about free-living amoebae. This review aims to provide a comprehensive overview of the newly gathered insights into (1) the free-living amoeba diversity, assessed with molecular tools, (2) the gene functions described to decipher the biology of the amoebae and (3) their interactions with other microorganisms in the environment.
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Affiliation(s)
- Ascel Samba-Louaka
- Laboratoire Ecologie et Biologie des Interactions (EBI), Equipe Microbiologie de l'Eau, Université de Poitiers, UMR CNRS 7267, 1 rue Georges Bonnet, TSA51106, 86073 POITIERS Cedex 9, France
| | - Vincent Delafont
- Laboratoire Ecologie et Biologie des Interactions (EBI), Equipe Microbiologie de l'Eau, Université de Poitiers, UMR CNRS 7267, 1 rue Georges Bonnet, TSA51106, 86073 POITIERS Cedex 9, France
| | - Marie-Hélène Rodier
- Laboratoire Ecologie et Biologie des Interactions (EBI), Equipe Microbiologie de l'Eau, Université de Poitiers, UMR CNRS 7267, 1 rue Georges Bonnet, TSA51106, 86073 POITIERS Cedex 9, France
- Laboratoire de Parasitologie et Mycologie, CHU La Milétrie, 2 rue de la Milétrie, 86021 Poitiers Cedex, France
| | - Estelle Cateau
- Laboratoire Ecologie et Biologie des Interactions (EBI), Equipe Microbiologie de l'Eau, Université de Poitiers, UMR CNRS 7267, 1 rue Georges Bonnet, TSA51106, 86073 POITIERS Cedex 9, France
- Laboratoire de Parasitologie et Mycologie, CHU La Milétrie, 2 rue de la Milétrie, 86021 Poitiers Cedex, France
| | - Yann Héchard
- Laboratoire Ecologie et Biologie des Interactions (EBI), Equipe Microbiologie de l'Eau, Université de Poitiers, UMR CNRS 7267, 1 rue Georges Bonnet, TSA51106, 86073 POITIERS Cedex 9, France
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Urrutia ÍM, Sabag A, Valenzuela C, Labra B, Álvarez SA, Santiviago CA. Contribution of the Twin-Arginine Translocation System to the Intracellular Survival of Salmonella Typhimurium in Dictyostelium discoideum. Front Microbiol 2018; 9:3001. [PMID: 30574134 PMCID: PMC6291500 DOI: 10.3389/fmicb.2018.03001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 11/20/2018] [Indexed: 12/19/2022] Open
Abstract
The twin-arginine translocation (Tat) system is a specialized secretion pathway required for bacteria to export fully folded proteins through the cytoplasmic membrane. This system is crucial during Salmonella infection of animal hosts. In this study, we show that Salmonella enterica serovar Typhimurium (S. Typhimurium) requires the Tat system to survive and proliferate intracellularly in the social amoeba Dictyostelium discoideum. To achieve this, we developed a new infection assay to assess intracellular bacterial loads in amoeba by direct enumeration of colony forming units (CFU) at different times of infection. Using this assay we observed that a ΔtatABC mutant was internalized in higher numbers than the wild type, and was defective for intracellular survival in the amoeba at all times post infection evaluated. In addition, we assessed the effect of the ΔtatABC mutant in the social development of D. discoideum. In contrast to the wild-type strain, we observed that the mutant was unable to delay the social development of the amoeba at 2 days of co-incubation. This phenotype correlated with defects in intracellular proliferation presented by the ΔtatABC mutant in D. discoideum after 24 h of infection. All phenotypes described for the mutant were reverted by the presence of a plasmid carrying tatABC genes, indicating that abrogation of Tat system attenuates S. Typhimurium in this model organism. Overall, our results indicate that the Tat system is crucial for S. Typhimurium to survive and proliferate intracellularly in D. discoideum and for virulence in this host. To the best of our knowledge, this is the first report on the relevance of the Tat system in the interaction of any bacterial pathogen with the social amoeba D. discoideum.
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Affiliation(s)
- Ítalo M Urrutia
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Andrea Sabag
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Camila Valenzuela
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Bayron Labra
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Sergio A Álvarez
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Carlos A Santiviago
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
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32
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Liao Z, Kjellin J, Hoeppner MP, Grabherr M, Söderbom F. Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum. RNA Biol 2018; 15:937-954. [PMID: 29966484 PMCID: PMC6161686 DOI: 10.1080/15476286.2018.1481697] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Micro (mi)RNAs regulate gene expression in many eukaryotic organisms where they control diverse biological processes. Their biogenesis, from primary transcripts to mature miRNAs, have been extensively characterized in animals and plants, showing distinct differences between these phylogenetically distant groups of organisms. However, comparably little is known about miRNA biogenesis in organisms whose evolutionary position is placed in between plants and animals and/or in unicellular organisms. Here, we investigate miRNA maturation in the unicellular amoeba Dictyostelium discoideum, belonging to Amoebozoa, which branched out after plants but before animals. High-throughput sequencing of small RNAs and poly(A)-selected RNAs demonstrated that the Dicer-like protein DrnB is required, and essentially specific, for global miRNA maturation in D. discoideum. Our RNA-seq data also showed that longer miRNA transcripts, generally preceded by a T-rich putative promoter motif, accumulate in a drnB knock-out strain. For two model miRNAs we defined the transcriptional start sites (TSSs) of primary (pri)-miRNAs and showed that they carry the RNA polymerase II specific m7G-cap. The generation of the 3ʹ-ends of these pri-miRNAs differs, with pri-mir-1177 reading into the downstream gene, and pri-mir-1176 displaying a distinct end. This 3´-end is processed to shorter intermediates, stabilized in DrnB-depleted cells, of which some carry a short oligo(A)-tail. Furthermore, we identified 10 new miRNAs, all DrnB dependent and developmentally regulated. Thus, the miRNA machinery in D. discoideum shares features with both plants and animals, which is in agreement with its evolutionary position and perhaps also an adaptation to its complex lifestyle: unicellular growth and multicellular development.
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Affiliation(s)
- Zhen Liao
- a Department of Cell and Molecular Biology , Uppsala University , Uppsala , Sweden
| | - Jonas Kjellin
- a Department of Cell and Molecular Biology , Uppsala University , Uppsala , Sweden
| | - Marc P Hoeppner
- b Department of Medical Biochemistry and Microbiology , Uppsala University , Uppsala , Sweden.,c Christian-Albrechts-University of Kiel, Institute of Clinical Molecular Biology , Kiel , Germany
| | - Manfred Grabherr
- b Department of Medical Biochemistry and Microbiology , Uppsala University , Uppsala , Sweden
| | - Fredrik Söderbom
- a Department of Cell and Molecular Biology , Uppsala University , Uppsala , Sweden
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CDK5RAP2 Is an Essential Scaffolding Protein of the Corona of the Dictyostelium Centrosome. Cells 2018; 7:cells7040032. [PMID: 29690637 PMCID: PMC5946109 DOI: 10.3390/cells7040032] [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: 04/03/2018] [Revised: 04/18/2018] [Accepted: 04/20/2018] [Indexed: 01/02/2023] Open
Abstract
Dictyostelium centrosomes consist of a nucleus-associated cylindrical, three-layered core structure surrounded by a corona consisting of microtubule-nucleation complexes embedded in a scaffold of large coiled-coil proteins. One of them is the conserved CDK5RAP2 protein. Here we focus on the role of Dictyostelium CDK5RAP2 for maintenance of centrosome integrity, its interaction partners and its dynamic behavior during interphase and mitosis. GFP-CDK5RAP2 is present at the centrosome during the entire cell cycle except from a short period during prophase, correlating with the normal dissociation of the corona at this stage. RNAi depletion of CDK5RAP2 results in complete disorganization of centrosomes and microtubules suggesting that CDK5RAP2 is required for organization of the corona and its association to the core structure. This is in line with the observation that overexpressed GFP-CDK5RAP2 elicited supernumerary cytosolic MTOCs. The phenotype of CDK5RAP2 depletion was very reminiscent of that observed upon depletion of CP148, another scaffolding protein of the corona. BioID interaction assays revealed an interaction of CDK5RAP2 not only with the corona markers CP148, γ-tubulin, and CP248, but also with the core components Cep192, CP75, and CP91. Furthermore, protein localization studies in both depletion strains revealed that CP148 and CDK5RAP2 cooperate in corona organization.
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Koonce MP, Tikhonenko I. Centrosome Positioning in Dictyostelium: Moving beyond Microtubule Tip Dynamics. Cells 2018; 7:E29. [PMID: 29649097 PMCID: PMC5946106 DOI: 10.3390/cells7040029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 04/10/2018] [Accepted: 04/10/2018] [Indexed: 12/29/2022] Open
Abstract
The variability in centrosome size, shape, and activity among different organisms provides an opportunity to understand both conserved and specialized actions of this intriguing organelle. Centrosomes in the model organism Dictyostelium sp. share some features with fungal systems and some with vertebrate cell lines and thus provide a particularly useful context to study their dynamics. We discuss two aspects, centrosome positioning in cells and their interactions with nuclei during division as a means to highlight evolutionary modifications to machinery that provide the most basic of cellular services.
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Affiliation(s)
- Michael P Koonce
- Division of Translational Medicine, New York State Department of Health, Wadsworth Center, Albany, NY 12201-0509, USA.
| | - Irina Tikhonenko
- Division of Translational Medicine, New York State Department of Health, Wadsworth Center, Albany, NY 12201-0509, USA.
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Meena NP, Kimmel AR. Quantification of Live Bacterial Sensing for Chemotaxis and Phagocytosis and of Macropinocytosis. Front Cell Infect Microbiol 2018; 8:62. [PMID: 29552545 PMCID: PMC5840232 DOI: 10.3389/fcimb.2018.00062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/13/2018] [Indexed: 01/26/2023] Open
Abstract
Initial immunological defense mechanisms to pathogen invasion rely on innate pathways of chemotaxis and phagocytosis, original to ancient phagocytes. Although chemotaxis has been well-studied in mammalian and model systems using purified chemoattractants in defined conditions, directed movement toward live bacteria has been more difficult to assess. Dictyostelium discoideum is a professional phagocyte that chemotaxes toward bacteria during growth-phase in a process to locate nutrient sources. Using Dictyostelium as a model, we have developed a system that is able to quantify chemotaxis to very high sensitivity. Here, Dictyostelium can detect various chemoattractants at concentrations <1 nM. Given this exceedingly sensitive signal response, Dictyostelium will migrate directionally toward live gram positive and gram negative bacteria, in a highly quantifiable manner, and dependent upon bacterially-secreted chemoattractants. Additionally, we have developed a real-time, quantitative assay for phagocytosis of live gram positive and gram negative bacteria. To extend the analyses of endocytic functions, we further modified the system to quantify cellular uptake via macropinocytosis of smaller (<100 kDa) molecules. These various approaches provide novel means to dissect potential for identification of novel chemoattractants and mechanistic factors that are essential for chemotaxis, phagocytosis, and/or macropinocytosis and for more detailed understanding in host-pathogen interactive defenses.
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Affiliation(s)
- Netra P Meena
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, The National Institutes of Health, Bethesda, MD, United States
| | - Alan R Kimmel
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, The National Institutes of Health, Bethesda, MD, United States
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Marcoleta AE, Varas MA, Ortiz-Severín J, Vásquez L, Berríos-Pastén C, Sabag AV, Chávez FP, Allende ML, Santiviago CA, Monasterio O, Lagos R. Evaluating Different Virulence Traits of Klebsiella pneumoniae Using Dictyostelium discoideum and Zebrafish Larvae as Host Models. Front Cell Infect Microbiol 2018; 8:30. [PMID: 29479519 PMCID: PMC5811510 DOI: 10.3389/fcimb.2018.00030] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 01/23/2018] [Indexed: 01/26/2023] Open
Abstract
Multiresistant and invasive hypervirulent Klebsiella pneumoniae strains have become one of the most urgent bacterial pathogen threats. Recent analyses revealed a high genomic plasticity of this species, harboring a variety of mobile genetic elements associated with virulent strains, encoding proteins of unknown function whose possible role in pathogenesis have not been addressed. K. pneumoniae virulence has been studied mainly in animal models such as mice and pigs, however, practical, financial, ethical and methodological issues limit the use of mammal hosts. Consequently, the development of simple and cost-effective experimental approaches with alternative host models is needed. In this work we described the use of both, the social amoeba and professional phagocyte Dictyostelium discoideum and the fish Danio rerio (zebrafish) as surrogate host models to study K. pneumoniae virulence. We compared three K. pneumoniae clinical isolates evaluating their resistance to phagocytosis, intracellular survival, lethality, intestinal colonization, and innate immune cells recruitment. Optical transparency of both host models permitted studying the infective process in vivo, following the Klebsiella-host interactions through live-cell imaging. We demonstrated that K. pneumoniae RYC492, but not the multiresistant strains 700603 and BAA-1705, is virulent to both host models and elicits a strong immune response. Moreover, this strain showed a high resistance to phagocytosis by D. discoideum, an increased ability to form biofilms and a more prominent and irregular capsule. Besides, the strain 700603 showed the unique ability to replicate inside amoeba cells. Genomic comparison of the K. pneumoniae strains showed that the RYC492 strain has a higher overall content of virulence factors although no specific genes could be linked to its phagocytosis resistance, nor to the intracellular survival observed for the 700603 strain. Our results indicate that both zebrafish and D. discoideum are advantageous host models to study different traits of K. pneumoniae that are associated with virulence.
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Affiliation(s)
- Andrés E Marcoleta
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Macarena A Varas
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Javiera Ortiz-Severín
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Leonardo Vásquez
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Camilo Berríos-Pastén
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Andrea V Sabag
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Francisco P Chávez
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Miguel L Allende
- Departamento de Biología, Facultad de Ciencias, Centro FONDAP de Regulación del Genoma, Universidad de Chile, Santiago, Chile
| | - Carlos A Santiviago
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Octavio Monasterio
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Rosalba Lagos
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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Varas MA, Riquelme-Barrios S, Valenzuela C, Marcoleta AE, Berríos-Pastén C, Santiviago CA, Chávez FP. Inorganic Polyphosphate Is Essential for Salmonella Typhimurium Virulence and Survival in Dictyostelium discoideum. Front Cell Infect Microbiol 2018; 8:8. [PMID: 29441327 PMCID: PMC5797601 DOI: 10.3389/fcimb.2018.00008] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 01/09/2018] [Indexed: 01/26/2023] Open
Abstract
Inorganic polyphosphate (polyP) deficiency in enteric bacterial pathogens reduces their ability to invade and establish systemic infections in different hosts. For instance, inactivation of the polyP kinase gene (ppk) encoding the enzyme responsible for polyP biosynthesis reduces invasiveness and intracellular survival of Salmonella enterica serovar Typhimurium (S. Typhimurium) in epithelial cells and macrophages in vitro. In addition, the virulence in vivo of a S. Typhimurium Δppk mutant is significantly reduced in a murine infection model. In spite of these observations, the role played by polyP during the Salmonella-host interaction is not well understood. The social amoeba Dictyostelium discoideum has proven to be a useful model for studying relevant aspects of the host-pathogen interaction. In fact, many intracellular pathogens can survive within D. discoideum cells using molecular mechanisms also required to survive within macrophages. Recently, we established that S. Typhimurium is able to survive intracellularly in D. discoideum and identified relevant genes linked to virulence that are crucial for this process. The aim of this study was to determine the effect of a polyP deficiency in S. Typhimurium during its interaction with D. discoideum. To do this, we evaluated the intracellular survival of wild-type and Δppk strains of S. Typhimurium in D. discoideum and the ability of these strains to delay the social development of the amoeba. In contrast to the wild-type strain, the Δppk mutant was unable to survive intracellularly in D. discoideum and enabled the social development of the amoeba. Both phenotypes were complemented using a plasmid carrying a copy of the ppk gene. Next, we simultaneously evaluated the proteomic response of both S. Typhimurium and D. discoideum during host-pathogen interaction via global proteomic profiling. The analysis of our results allowed the identification of novel molecular signatures that give insight into Salmonella-Dictyostelium interaction. Altogether, our results indicate that inorganic polyP is essential for S. Typhimurium virulence and survival in D. discoideum. In addition, we have validated the use of global proteomic analyses to simultaneously evaluate the host-pathogen interaction of S. Typhimurium and D. discoideum. Furthermore, our infection assays using these organisms can be exploited to screen for novel anti-virulence molecules targeting inorganic polyP biosynthesis.
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Affiliation(s)
- Macarena A Varas
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Sebastián Riquelme-Barrios
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Camila Valenzuela
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Andrés E Marcoleta
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Camilo Berríos-Pastén
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Carlos A Santiviago
- Laboratorio de Microbiología, Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Francisco P Chávez
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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Dunn JD, Bosmani C, Barisch C, Raykov L, Lefrançois LH, Cardenal-Muñoz E, López-Jiménez AT, Soldati T. Eat Prey, Live: Dictyostelium discoideum As a Model for Cell-Autonomous Defenses. Front Immunol 2018; 8:1906. [PMID: 29354124 PMCID: PMC5758549 DOI: 10.3389/fimmu.2017.01906] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/13/2017] [Indexed: 12/11/2022] Open
Abstract
The soil-dwelling social amoeba Dictyostelium discoideum feeds on bacteria. Each meal is a potential infection because some bacteria have evolved mechanisms to resist predation. To survive such a hostile environment, D. discoideum has in turn evolved efficient antimicrobial responses that are intertwined with phagocytosis and autophagy, its nutrient acquisition pathways. The core machinery and antimicrobial functions of these pathways are conserved in the mononuclear phagocytes of mammals, which mediate the initial, innate-immune response to infection. In this review, we discuss the advantages and relevance of D. discoideum as a model phagocyte to study cell-autonomous defenses. We cover the antimicrobial functions of phagocytosis and autophagy and describe the processes that create a microbicidal phagosome: acidification and delivery of lytic enzymes, generation of reactive oxygen species, and the regulation of Zn2+, Cu2+, and Fe2+ availability. High concentrations of metals poison microbes while metal sequestration inhibits their metabolic activity. We also describe microbial interference with these defenses and highlight observations made first in D. discoideum. Finally, we discuss galectins, TNF receptor-associated factors, tripartite motif-containing proteins, and signal transducers and activators of transcription, microbial restriction factors initially characterized in mammalian phagocytes that have either homologs or functional analogs in D. discoideum.
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Affiliation(s)
- Joe Dan Dunn
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Cristina Bosmani
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Caroline Barisch
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Lyudmil Raykov
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Louise H Lefrançois
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Elena Cardenal-Muñoz
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | | | - Thierry Soldati
- Faculty of Sciences, Department of Biochemistry, University of Geneva, Geneva, Switzerland
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Mlecnik B, Galon J, Bindea G. Comprehensive functional analysis of large lists of genes and proteins. J Proteomics 2018; 171:2-10. [DOI: 10.1016/j.jprot.2017.03.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/13/2017] [Accepted: 03/19/2017] [Indexed: 01/16/2023]
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40
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Chen S, Annesley SJ, Jasim RAF, Musco VJ, Sanislav O, Fisher PR. The Parkinson's disease-associated protein DJ-1 plays a positive nonmitochondrial role in endocytosis in Dictyostelium cells. Dis Model Mech 2017; 10:1261-1271. [PMID: 28819044 PMCID: PMC5665451 DOI: 10.1242/dmm.028084] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 08/14/2017] [Indexed: 01/01/2023] Open
Abstract
The loss of function of DJ-1 caused by mutations in DJ1 causes a form of familial Parkinson's disease (PD). However, the role of DJ-1 in healthy and in PD cells is poorly understood. Even its subcellular localization in mammalian cells is uncertain, with both cytosolic and mitochondrial locations having been reported. We show here that DJ-1 is normally located in the cytoplasm in healthy Dictyostelium discoideum cells. With its unique life cycle, straightforward genotype-phenotype relationships, experimental accessibility and genetic tractability, D.discoideum offers an attractive model to investigate the roles of PD-associated genes. Furthermore, the study of mitochondrial biology, mitochondrial genome transcription and AMP-activated protein kinase-mediated cytopathologies in mitochondrial dysfunction have been well developed in this organism. Unlike mammalian systems, Dictyostelium mitochondrial dysfunction causes a reproducible and readily assayed array of aberrant phenotypes: defective phototaxis, impaired growth, normal rates of endocytosis and characteristic defects in multicellular morphogenesis. This makes it possible to study whether the underlying cytopathological mechanisms of familial PD involve mitochondrial dysfunction. DJ-1 has a single homologue in the Dictyostelium genome. By regulating the expression level of DJ-1 in D. discoideum, we show here that in unstressed cells, DJ-1 is required for normal rates of endocytic nutrient uptake (phagocytosis and, to a lesser extent, pinocytosis) and thus growth. Reduced expression of DJ-1 had no effect on phototaxis in the multicellular migratory ‘slug’ stage of the life cycle, but resulted in thickened stalks in the final fruiting bodies. This pattern of phenotypes is distinct from that observed in Dictyostelium to result from mitochondrial dyfunction. Direct measurement of mitochondrial respiratory function in intact cells revealed that DJ-1 knockdown stimulates whereas DJ-1 overexpression inhibits mitochondrial activity. Together, our results suggest positive roles for DJ-1 in endocytic pathways and loss-of-function cytopathologies that are not associated with impaired mitochondrial function. Editor's choice: The Dictyostelium homologue of the Parkinson's disease-associated protein DJ-1 is located in the cytosol, and its loss causes cytopathological defects in endocytic and autophagic cell death pathways, but stimulates respiration by functionally normal mitochondrial respiratory complexes.
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Affiliation(s)
- Suwei Chen
- Department of Microbiology, Faculty of Science, Technology and Engineering, La Trobe University, VIC 3086, Australia.,School of Modern Agriculture and Biological Science and Technology, Ankang University, Shaanxi 725000, PRC
| | - Sarah J Annesley
- Department of Microbiology, Faculty of Science, Technology and Engineering, La Trobe University, VIC 3086, Australia
| | - Rasha A F Jasim
- Department of Microbiology, Faculty of Science, Technology and Engineering, La Trobe University, VIC 3086, Australia.,Department of Laboratory and Clinical Sciences, College of Pharmacy, University of Babylon, PO Box 4, Hilla, Iraq
| | - Vanessa J Musco
- Department of Microbiology, Faculty of Science, Technology and Engineering, La Trobe University, VIC 3086, Australia
| | - Oana Sanislav
- Department of Microbiology, Faculty of Science, Technology and Engineering, La Trobe University, VIC 3086, Australia
| | - Paul R Fisher
- Department of Microbiology, Faculty of Science, Technology and Engineering, La Trobe University, VIC 3086, Australia
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41
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Galperin MY, Fernández-Suárez XM, Rigden DJ. The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes. Nucleic Acids Res 2017; 45:D1-D11. [PMID: 28053160 PMCID: PMC5210597 DOI: 10.1093/nar/gkw1188] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 11/16/2016] [Indexed: 12/23/2022] Open
Abstract
This year's Database Issue of Nucleic Acids Research contains 152 papers that include descriptions of 54 new databases and update papers on 98 databases, of which 16 have not been previously featured in NAR As always, these databases cover a broad range of molecular biology subjects, including genome structure, gene expression and its regulation, proteins, protein domains, and protein-protein interactions. Following the recent trend, an increasing number of new and established databases deal with the issues of human health, from cancer-causing mutations to drugs and drug targets. In accordance with this trend, three recently compiled databases that have been selected by NAR reviewers and editors as 'breakthrough' contributions, denovo-db, the Monarch Initiative, and Open Targets, cover human de novo gene variants, disease-related phenotypes in model organisms, and a bioinformatics platform for therapeutic target identification and validation, respectively. We expect these databases to attract the attention of numerous researchers working in various areas of genetics and genomics. Looking back at the past 12 years, we present here the 'golden set' of databases that have consistently served as authoritative, comprehensive, and convenient data resources widely used by the entire community and offer some lessons on what makes a successful database. The Database Issue is freely available online at the https://academic.oup.com/nar web site. An updated version of the NAR Molecular Biology Database Collection is available at http://www.oxfordjournals.org/nar/database/a/.
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Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | | | - Daniel J Rigden
- Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
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Meena NP, Kimmel AR. Chemotactic network responses to live bacteria show independence of phagocytosis from chemoreceptor sensing. eLife 2017; 6. [PMID: 28541182 PMCID: PMC5476428 DOI: 10.7554/elife.24627] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 05/24/2017] [Indexed: 12/21/2022] Open
Abstract
Aspects of innate immunity derive from characteristics inherent to phagocytes, including chemotaxis toward and engulfment of unicellular organisms or cell debris. Ligand chemotaxis has been biochemically investigated using mammalian and model systems, but precision of chemotaxis towards ligands being actively secreted by live bacteria is not well studied, nor has there been systematic analyses of interrelationships between chemotaxis and phagocytosis. The genetic/molecular model Dictyostelium and mammalian phagocytes share mechanistic pathways for chemotaxis and phagocytosis; Dictyostelium chemotax toward bacteria and phagocytose them as food sources. We quantified Dictyostelium chemotaxis towards live gram positive and gram negative bacteria and demonstrate high sensitivity to multiple bacterially-secreted chemoattractants. Additive/competitive assays indicate that intracellular signaling-networks for multiple ligands utilize independent upstream adaptive mechanisms, but common downstream targets, thus amplifying detection at low signal propagation, but strengthening discrimination of multiple inputs. Finally, analyses of signaling-networks for chemotaxis and phagocytosis indicate that chemoattractant receptor-signaling is not essential for bacterial phagocytosis. DOI:http://dx.doi.org/10.7554/eLife.24627.001
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Affiliation(s)
- Netra Pal Meena
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, The National Institutes of Health, Bethesda, United States
| | - Alan R Kimmel
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, The National Institutes of Health, Bethesda, United States
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Blewett NH, Iben JR, Gaidamakov S, Maraia RJ. La Deletion from Mouse Brain Alters Pre-tRNA Metabolism and Accumulation of Pre-5.8S rRNA, with Neuron Death and Reactive Astrocytosis. Mol Cell Biol 2017; 37:e00588-16. [PMID: 28223366 PMCID: PMC5477551 DOI: 10.1128/mcb.00588-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 12/01/2016] [Accepted: 02/06/2017] [Indexed: 12/20/2022] Open
Abstract
Human La antigen (Sjögren's syndrome antigen B [SSB]) is an abundant multifunctional RNA-binding protein. In the nucleoplasm, La binds to and protects from 3' exonucleases, the ends of precursor tRNAs, and other transcripts synthesized by RNA polymerase III and facilitates their maturation, while a nucleolar isoform has been implicated in rRNA biogenesis by multiple independent lines of evidence. We showed previously that conditional La knockout (La cKO) from mouse cortex neurons results in defective tRNA processing, although the pathway(s) involved in neuronal loss thereafter was unknown. Here, we demonstrate that La is stably associated with a spliced pre-tRNA intermediate. Microscopic evidence of aberrant nuclear accumulation of 5.8S rRNA in La cKO is supported by a 10-fold increase in a pre-5.8S rRNA intermediate. To identify pathways involved in subsequent neurodegeneration and loss of brain mass in the cKO cortex, we employed mRNA sequencing (mRNA-Seq), immunohistochemistry, and other approaches. This revealed robust enrichment of immune and astrocyte reactivity in La cKO cortex. Immunohistochemistry, including temporal analyses, demonstrated neurodegeneration, followed by astrocyte invasion associated with immune response and decreasing cKO cortex size over time. Thus, deletion of La from postmitotic neurons results in defective pre-tRNA and pre-rRNA processing and progressive neurodegeneration with loss of cortical brain mass.
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Affiliation(s)
- Nathan H Blewett
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Rockville, Maryland, USA
| | - James R Iben
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Rockville, Maryland, USA
| | - Sergei Gaidamakov
- Intramural Research Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Rockville, Maryland, USA
| | - Richard J Maraia
- Commissioned Corps, U.S. Public Health Service, Rockville, Maryland, USA
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Platt JL, Kent NA, Kimmel AR, Harwood AJ. Regulation of nucleosome positioning by a CHD Type III chromatin remodeler and its relationship to developmental gene expression in Dictyostelium. Genome Res 2017; 27:591-600. [PMID: 28330902 PMCID: PMC5378177 DOI: 10.1101/gr.216309.116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 02/27/2017] [Indexed: 01/14/2023]
Abstract
Nucleosome placement and repositioning can direct transcription of individual genes; however, the precise interactions of these events are complex and largely unresolved at the whole-genome level. The Chromodomain-Helicase-DNA binding (CHD) Type III proteins are a subfamily of SWI2/SNF2 proteins that control nucleosome positioning and are associated with several complex human disorders, including CHARGE syndrome and autism. Type III CHDs are required for multicellular development of animals and Dictyostelium but are absent in plants and yeast. These CHDs can mediate nucleosome translocation in vitro, but their in vivo mechanism is unknown. Here, we use genome-wide analysis of nucleosome positioning and transcription profiling to investigate the in vivo relationship between nucleosome positioning and gene expression during development of wild-type (WT) Dictyostelium and mutant cells lacking ChdC, a Type III CHD protein ortholog. We demonstrate major nucleosome positional changes associated with developmental gene regulation in WT. Loss of chdC caused an increase of intragenic nucleosome spacing and misregulation of gene expression, affecting ∼50% of the genes that are repositioned during WT development. These analyses demonstrate active nucleosome repositioning during Dictyostelium multicellular development, establish an in vivo function of CHD Type III chromatin remodeling proteins in this process, and reveal the detailed relationship between nucleosome positioning and gene regulation, as cells transition between developmental states.
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Affiliation(s)
- James L Platt
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, United Kingdom.,Laboratory of Cellular and Developmental Biology, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Nicholas A Kent
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, United Kingdom
| | - Alan R Kimmel
- Laboratory of Cellular and Developmental Biology, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Adrian J Harwood
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, United Kingdom.,Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, CF24 4HQ, United Kingdom
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Liao XH, Kimmel AR. A Unique High-Throughput Assay to Identify Novel Small Molecule Inhibitors of Chemotaxis and Migration. ACTA ACUST UNITED AC 2017; 74:12.11.1-12.11.13. [PMID: 28256720 DOI: 10.1002/cpcb.17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chemotaxis and cell migration play pivotal roles in normal physiological processes such as embryogenesis, inflammation, and wound healing, as well as in pathological processes including chronic inflammatory disease and cancer metastasis. Novel chemotaxis/migration inhibitors are desirable for developing effective therapeutics and probing molecular mechanisms. We describe a fluorescence-based phenotypic assay in a 1536-well plate format for high-throughput screening of novel inhibitors of chemotaxis/migration within complex libraries of thousands of compounds. Although the assay utilizes the unique cellular response properties of Dictyostelium, the compounds identified are able to inhibit chemotaxis of mammalian cells. In addition, a parallel cell cytotoxicity counter-screen with an ATP content assay is described that eliminates cytotoxic compounds from the screen. This novel compound screening approach enables rapid identification of novel lead compounds that inhibit chemotaxis in human and other cells for drug development and research tools. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Xin-Hua Liao
- Fujian Key Laboratory for Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, and Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, Fujian, China
| | - Alan R Kimmel
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
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The Long Noncoding RNA Transcriptome of Dictyostelium discoideum Development. G3-GENES GENOMES GENETICS 2017; 7:387-398. [PMID: 27932387 PMCID: PMC5295588 DOI: 10.1534/g3.116.037150] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Dictyostelium discoideum live in the soil as single cells, engulfing bacteria and growing vegetatively. Upon starvation, tens of thousands of amoebae enter a developmental program that includes aggregation, multicellular differentiation, and sporulation. Major shifts across the protein-coding transcriptome accompany these developmental changes. However, no study has presented a global survey of long noncoding RNAs (ncRNAs) in D. discoideum To characterize the antisense and long intergenic noncoding RNA (lncRNA) transcriptome, we analyzed previously published developmental time course samples using an RNA-sequencing (RNA-seq) library preparation method that selectively depletes ribosomal RNAs (rRNAs). We detected the accumulation of transcripts for 9833 protein-coding messenger RNAs (mRNAs), 621 lncRNAs, and 162 putative antisense RNAs (asRNAs). The noncoding RNAs were interspersed throughout the genome, and were distinct in expression level, length, and nucleotide composition. The noncoding transcriptome displayed a temporal profile similar to the coding transcriptome, with stages of gradual change interspersed with larger leaps. The transcription profiles of some noncoding RNAs were strongly correlated with known differentially expressed coding RNAs, hinting at a functional role for these molecules during development. Examining the mitochondrial transcriptome, we modeled two novel antisense transcripts. We applied yet another ribosomal depletion method to a subset of the samples to better retain transfer RNA (tRNA) transcripts. We observed polymorphisms in tRNA anticodons that suggested a post-transcriptional means by which D. discoideum compensates for codons missing in the genomic complement of tRNAs. We concluded that the prevalence and characteristics of long ncRNAs indicate that these molecules are relevant to the progression of molecular and cellular phenotypes during development.
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Meyer I, Peter T, Batsios P, Kuhnert O, Krüger-Genge A, Camurça C, Gräf R. CP39, CP75 and CP91 are major structural components of the Dictyostelium centrosome's core structure. Eur J Cell Biol 2017; 96:119-130. [PMID: 28104305 DOI: 10.1016/j.ejcb.2017.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 12/13/2016] [Accepted: 01/09/2017] [Indexed: 12/11/2022] Open
Abstract
The acentriolar Dictyostelium centrosome is a nucleus-associated body consisting of a core structure with three plaque-like layers, which are surrounded by a microtubule-nucleating corona. The core duplicates once per cell cycle at the G2/M transition, whereby its central layer disappears and the two outer layers form the mitotic spindle poles. Through proteomic analysis of isolated centrosomes, we have identified CP39 and CP75, two essential components of the core structure. Both proteins can be assigned to the central core layer as their centrosomal presence is correlated to the disappearance and reappearance of the central core layer in the course of centrosome duplication. Both proteins contain domains with centrosome-binding activity in their N- and C-terminal halves, whereby the respective N-terminal half is required for cell cycle-dependent regulation. CP39 is capable of self-interaction and GFP-CP39 overexpression elicited supernumerary microtubule-organizing centers and pre-centrosomal cytosolic clusters. Underexpression stopped cell growth and reversed the MTOC amplification phenotype. In contrast, in case of CP75 underexpression of the protein by RNAi treatment elicited supernumerary MTOCs. In addition, CP75RNAi affects correct chromosome segregation and causes co-depletion of CP39 and CP91, another central core layer component. CP39 and CP75 interact with each other directly in a yeast two-hybrid assay. Furthermore, CP39, CP75 and CP91 mutually interact in a proximity-dependent biotin identification (BioID) assay. Our data indicate that these three proteins are all required for proper centrosome biogenesis and make up the major structural components of core structure's central layer.
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Affiliation(s)
- Irene Meyer
- University of Potsdam, Institute for Biochemistry and Biology, Dept. of Cell Biology, Karl-Liebknecht-Straße 24-25, Haus 26, D-14476 Potsdam-Golm, Germany.
| | - Tatjana Peter
- University of Potsdam, Institute for Biochemistry and Biology, Dept. of Cell Biology, Karl-Liebknecht-Straße 24-25, Haus 26, D-14476 Potsdam-Golm, Germany
| | - Petros Batsios
- University of Potsdam, Institute for Biochemistry and Biology, Dept. of Cell Biology, Karl-Liebknecht-Straße 24-25, Haus 26, D-14476 Potsdam-Golm, Germany
| | - Oliver Kuhnert
- University of Potsdam, Institute for Biochemistry and Biology, Dept. of Cell Biology, Karl-Liebknecht-Straße 24-25, Haus 26, D-14476 Potsdam-Golm, Germany
| | - Anne Krüger-Genge
- University of Potsdam, Institute for Biochemistry and Biology, Dept. of Cell Biology, Karl-Liebknecht-Straße 24-25, Haus 26, D-14476 Potsdam-Golm, Germany
| | - Carl Camurça
- University of Potsdam, Institute for Biochemistry and Biology, Dept. of Cell Biology, Karl-Liebknecht-Straße 24-25, Haus 26, D-14476 Potsdam-Golm, Germany
| | - Ralph Gräf
- University of Potsdam, Institute for Biochemistry and Biology, Dept. of Cell Biology, Karl-Liebknecht-Straße 24-25, Haus 26, D-14476 Potsdam-Golm, Germany.
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Petrov AI, Kay SJE, Kalvari I, Howe KL, Gray KA, Bruford EA, Kersey PJ, Cochrane G, Finn RD, Bateman A, Kozomara A, Griffiths-Jones S, Frankish A, Zwieb CW, Lau BY, Williams KP, Chan PP, Lowe TM, Cannone JJ, Gutell R, Machnicka MA, Bujnicki JM, Yoshihama M, Kenmochi N, Chai B, Cole JR, Szymanski M, Karlowski WM, Wood V, Huala E, Berardini TZ, Zhao Y, Chen R, Zhu W, Paraskevopoulou MD, Vlachos IS, Hatzigeorgiou AG, Ma L, Zhang Z, Puetz J, Stadler PF, McDonald D, Basu S, Fey P, Engel SR, Cherry JM, Volders PJ, Mestdagh P, Wower J, Clark MB, Quek XC, Dinger ME. RNAcentral: a comprehensive database of non-coding RNA sequences. Nucleic Acids Res 2017; 45:D128-D134. [PMID: 27794554 PMCID: PMC5210518 DOI: 10.1093/nar/gkw1008] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 10/13/2016] [Accepted: 10/18/2016] [Indexed: 12/12/2022] Open
Abstract
RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides a single entry point for accessing ncRNA sequences of all ncRNA types from all organisms. Since its launch in 2014, RNAcentral has integrated twelve new resources, taking the total number of collaborating database to 22, and began importing new types of data, such as modified nucleotides from MODOMICS and PDB. We created new species-specific identifiers that refer to unique RNA sequences within a context of single species. The website has been subject to continuous improvements focusing on text and sequence similarity searches as well as genome browsing functionality. All RNAcentral data is provided for free and is available for browsing, bulk downloads, and programmatic access at http://rnacentral.org/.
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Abstract
Many publicly available data repositories and resources have been developed to support protein-related information management, data-driven hypothesis generation, and biological knowledge discovery. To help researchers quickly find the appropriate protein-related informatics resources, we present a comprehensive review (with categorization and description) of major protein bioinformatics databases in this chapter. We also discuss the challenges and opportunities for developing next-generation protein bioinformatics databases and resources to support data integration and data analytics in the Big Data era.
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Affiliation(s)
- Chuming Chen
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA.
| | - Hongzhan Huang
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA
| | - Cathy H Wu
- Center for Bioinformatics and Computational Biology, Department of Computer and Information Sciences, University of Delaware, Newark, DE, 19711, USA
- Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC, 20007, USA
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50
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Gong M, Zhu Q, Tan Q. Evolutionary analyses of mitochondrial carrier family of dictyostelids. SPRINGERPLUS 2016; 5:1465. [PMID: 27652040 PMCID: PMC5007236 DOI: 10.1186/s40064-016-3146-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 08/24/2016] [Indexed: 11/25/2022]
Abstract
The transportation of solutes across the inner membrane of the mitochondria is catalyzed by a nuclear-coded family of transport proteins called mitochondrial carriers (MCs). Sequences from dictyostelid genome projects have facilitated analysis of the evolution of the dictyostelid mitochondrial carrier family (MCF). The average evolutionary distances between various regions in the MCF shows that the transmembrane region (TR) and conical pit region (CPR) are the only two conserved structural regions. A phylogenetic tree built using the concatenated orthologous TR and CPR sequences of 7 MCs showed that dictyostelids are similar to metazoans in this way. A close evolutionary relationship was observed between dictyostelids and metazoans in 4 MCs known to be related to ADP/ATP transport (MAA). This was further evidenced by the fact that dictyostelids have undergone gene expansion similar to that of metazoans during the evolution of MAA. Sequence logo analysis of CPR in MAA showed that dictyostelids have motifs similar to those of Metazoa. Combined with the conserved substrate binding site of 7 MCs in eukaryotes, it is postulated that dictyostelids are closely related to Metazoa with respect to the evolution of MAA.
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Affiliation(s)
- Ming Gong
- National Engineering Research Center of Edible Fungi; Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture; Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403 People's Republic of China ; Department of Computer Science, University of Nebraska at Omaha, Omaha, NE 68182 USA
| | - Qiuming Zhu
- Department of Computer Science, University of Nebraska at Omaha, Omaha, NE 68182 USA
| | - Qi Tan
- National Engineering Research Center of Edible Fungi; Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture; Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai, 201403 People's Republic of China
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