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Rush TA, Wymore AM, Rodríguez M, Jawdy S, Vilgalys RJ, Martin MZ, Andrews HB. Fungal elemental profiling unleashed through rapid laser-induced breakdown spectroscopy (LIBS). mSystems 2024:e0091924. [PMID: 39189771 DOI: 10.1128/msystems.00919-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Accepted: 07/30/2024] [Indexed: 08/28/2024] Open
Abstract
Elemental profiling of fungal species as a phenotyping tool is an understudied topic and is typically performed to examine plant tissue or non-biological materials. Traditional analytical techniques such as inductively coupled plasma-optical emission spectroscopy (ICP-OES) and inductively coupled plasma-mass spectrometry (ICP-MS) have been used to identify elemental profiles of fungi; however, these techniques can be cumbersome due to the difficulty of preparing samples. Additionally, the instruments used for these techniques can be expensive to procure and operate. Laser-induced breakdown spectroscopy (LIBS) is an alternative elemental analytical technique-one that is sensitive across the periodic table, easy to use on various sample types, and is cost-effective in both procurement and operation. LIBS has not been used on axenic filamentous fungal isolates grown in substrate media. In this work, as a proof of concept, we used LIBS on two genetically distinct fungal species grown on a nutrient-rich and nutrient-poor substrate media to determine whether robust elemental profiles can be detected and whether differences between the fungal isolates can be identified. Our results demonstrate a distinct correlation between fungal species and their elemental profile, regardless of the substrate media, as the same strains shared a similar uptake of carbon, zinc, phosphorus, manganese, and magnesium, which could play a vital role in their survival and propagation. Independently, each fungal species exhibited a unique elemental profile. This work demonstrates a unique and valuable approach to rapidly phenotype fungi through optical spectroscopy, and this approach can be critical in understanding these fungi's behavior and interactions with the environment. IMPORTANCE Historically, ionomics, the elemental profiling of an organism or materials, has been used to understand the elemental composition in waste materials to identify and recycle heavy metals or rare earth elements, identify the soil composition in space exploration on the moon or Mars, or understand human disorders or disease. To our knowledge, ionomic profiling of microbes, particularly fungi, has not been investigated to answer applied and fundamental biological questions. The reason is that current ionomic analytical techniques can be laborious in sample preparation, fail to measure all potential elements accurately, are cost-prohibitive, or provide inconsistent results across replications. In our previous efforts, we explored whether laser-induced breakdown spectroscopy (LIBS) could be used in determining the elemental profiles of poplar tissue, which was successful. In this proof-of-concept endeavor, we undertook a transdisciplinary effort between applied and fundamental mycology and elemental analytical techniques to address the biological question of how LIBS can used for fungi grown axenically in a nutrient-rich and nutrient-poor environment.
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Affiliation(s)
- Tomás A Rush
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Ann M Wymore
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Miguel Rodríguez
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Sara Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Rytas J Vilgalys
- Biology Department, Duke University, Durham, North Carolina, USA
| | - Madhavi Z Martin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Hunter B Andrews
- Radioisotope Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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2
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Esteves SM, Jadoul A, Iacono F, Schloesser M, Bosman B, Carnol M, Druet T, Cardol P, Hanikenne M. Natural variation of nutrient homeostasis among laboratory and field strains of Chlamydomonas reinhardtii. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:5198-5217. [PMID: 37235689 DOI: 10.1093/jxb/erad194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 05/24/2023] [Indexed: 05/28/2023]
Abstract
Natural variation among individuals and populations exists in all species, playing key roles in response to environmental stress and adaptation. Micro- and macronutrients have a wide range of functions in photosynthetic organisms, and mineral nutrition thus plays a sizable role in biomass production. To maintain nutrient concentrations inside the cell within physiological limits and prevent the detrimental effects of deficiency or excess, complex homeostatic networks have evolved in photosynthetic cells. The microalga Chlamydomonas reinhardtii (Chlamydomonas) is a unicellular eukaryotic model for studying such mechanisms. In this work, 24 Chlamydomonas strains, comprising field isolates and laboratory strains, were examined for intraspecific differences in nutrient homeostasis. Growth and mineral content were quantified in mixotrophy, as full nutrition control, and compared with autotrophy and nine deficiency conditions for macronutrients (-Ca, -Mg, -N, -P, and -S) and micronutrients (-Cu, -Fe, -Mn, and -Zn). Growth differences among strains were relatively limited. However, similar growth was accompanied by highly divergent mineral accumulation among strains. The expression of nutrient status marker genes and photosynthesis were scored in pairs of contrasting field strains, revealing distinct transcriptional regulation and nutrient requirements. Leveraging this natural variation should enable a better understanding of nutrient homeostasis in Chlamydomonas.
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Affiliation(s)
- Sara M Esteves
- InBioS-PhytoSystems, Translational Plant Biology, University of Liège, Belgium
| | - Alice Jadoul
- InBioS-PhytoSystems, Translational Plant Biology, University of Liège, Belgium
| | - Fabrizio Iacono
- InBioS-PhytoSystems, Genetics and Physiology of Microalgae, University of Liège, Belgium
| | - Marie Schloesser
- InBioS-PhytoSystems, Translational Plant Biology, University of Liège, Belgium
| | - Bernard Bosman
- InBioS-PhytoSystems, Laboratory of Plant and Microbial Ecology, University of Liège, Belgium
| | - Monique Carnol
- InBioS-PhytoSystems, Laboratory of Plant and Microbial Ecology, University of Liège, Belgium
| | - Tom Druet
- Unit of Animal Genomics (GIGA), University of Liège, Belgium
| | - Pierre Cardol
- InBioS-PhytoSystems, Genetics and Physiology of Microalgae, University of Liège, Belgium
| | - Marc Hanikenne
- InBioS-PhytoSystems, Translational Plant Biology, University of Liège, Belgium
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Wörthmüller J, Disler S, Pradervand S, Richard F, Haerri L, Ruiz Buendía GA, Fournier N, Desmedt C, Rüegg C. MAGI1 Prevents Senescence and Promotes the DNA Damage Response in ER + Breast Cancer. Cells 2023; 12:1929. [PMID: 37566008 PMCID: PMC10417439 DOI: 10.3390/cells12151929] [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: 05/09/2023] [Revised: 06/30/2023] [Accepted: 07/18/2023] [Indexed: 08/12/2023] Open
Abstract
MAGI1 acts as a tumor suppressor in estrogen receptor-positive (ER+) breast cancer (BC), and its loss correlates with a more aggressive phenotype. To identify the pathways and events affected by MAGI1 loss, we deleted the MAGI1 gene in the ER+ MCF7 BC cell line and performed RNA sequencing and functional experiments in vitro. Transcriptome analyses revealed gene sets and biological processes related to estrogen signaling, the cell cycle, and DNA damage responses affected by MAGI1 loss. Upon exposure to TNF-α/IFN-γ, MCF7 MAGI1 KO cells entered a deeper level of quiescence/senescence compared with MCF7 control cells and activated the AKT and MAPK signaling pathways. MCF7 MAGI1 KO cells exposed to ionizing radiations or cisplatin had reduced expression of DNA repair proteins and showed increased sensitivity towards PARP1 inhibition using olaparib. Treatment with PI3K and AKT inhibitors (alpelisib and MK-2206) restored the expression of DNA repair proteins and sensitized cells to fulvestrant. An analysis of human BC patients' transcriptomic data revealed that patients with low MAGI1 levels had a higher tumor mutational burden and homologous recombination deficiency. Moreover, MAGI1 expression levels negatively correlated with PI3K/AKT and MAPK signaling, which confirmed our in vitro observations. Pharmacological and genomic evidence indicate HDACs as regulators of MAGI1 expression. Our findings provide a new view on MAGI1 function in cancer and identify potential treatment options to improve the management of ER+ BC patients with low MAGI1 levels.
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Affiliation(s)
- Janine Wörthmüller
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
| | - Simona Disler
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
| | - Sylvain Pradervand
- Lausanne Genomic Technologies Facility (LGTF), University of Lausanne, 1015 Lausanne, Switzerland
| | - François Richard
- Laboratory for Translational Breast Cancer Research, KU Leuven, 3000 Leuven, Belgium
| | - Lisa Haerri
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
| | - Gustavo A. Ruiz Buendía
- Translational Data Science-Facility, AGORA Cancer Research Center, Swiss Institute of Bioinformatics (SIB), Bugnon 25A, 1005 Lausanne, Switzerland
| | - Nadine Fournier
- Translational Data Science-Facility, AGORA Cancer Research Center, Swiss Institute of Bioinformatics (SIB), Bugnon 25A, 1005 Lausanne, Switzerland
| | - Christine Desmedt
- Laboratory for Translational Breast Cancer Research, KU Leuven, 3000 Leuven, Belgium
| | - Curzio Rüegg
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology (OMI), Faculty of Science and Medicine, University of Fribourg, 1700 Fribourg, Switzerland
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Metal ion availability and homeostasis as drivers of metabolic evolution and enzyme function. Curr Opin Genet Dev 2022; 77:101987. [PMID: 36183585 DOI: 10.1016/j.gde.2022.101987] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/25/2022] [Accepted: 08/29/2022] [Indexed: 01/27/2023]
Abstract
Metal ions are potent catalysts and have been available for cellular biochemistry at all stages of evolution. Growing evidence suggests that metal catalysis was critical for the origin of the very first metabolic reactions. With approximately 80% of modern metabolic pathways being dependent on metal ions, metallocatalysis and homeostasis continue to be essential for intracellular metabolic networks and physiology. However, the genetic network that controls metal ion homeostasis and the impact of metal availability on metabolism is poorly understood. Here, we review recent work on gene and protein evolution relevant for better understanding metal ion biology and its role in metabolism. We highlight the importance of analysing the origin and evolution of enzyme catalysis in the context of catalytically relevant metal ions, summarise unanswered questions essential for developing a comprehensive understanding of metal ion homeostasis and advocate for the consideration of metal ion properties and availability in the design and directed evolution of novel enzymes and pathways.
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Kovár M, Navrátilová A, Kolláthová R, Trakovická A, Požgajová M. Acrylamide-Derived Ionome, Metabolic, and Cell Cycle Alterations Are Alleviated by Ascorbic Acid in the Fission Yeast. Molecules 2022; 27:molecules27134307. [PMID: 35807551 PMCID: PMC9268660 DOI: 10.3390/molecules27134307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 11/16/2022] Open
Abstract
Acrylamide (AA), is a chemical with multiple industrial applications, however, it can be found in foods that are rich in carbohydrates. Due to its genotoxic and cytotoxic effects, AA has been classified as a potential carcinogen. With the use of spectrophotometry, ICP-OES, fluorescence spectroscopy, and microscopy cell growth, metabolic activity, apoptosis, ROS production, MDA formation, CAT and SOD activity, ionome balance, and chromosome segregation were determined in Schizosaccharomyces pombe. AA caused growth and metabolic activity retardation, enhanced ROS and MDA production, and modulated antioxidant enzyme activity. This led to damage to the cell homeostasis due to ionome balance disruption. Moreover, AA-induced oxidative stress caused alterations in the cell cycle regulation resulting in chromosome segregation errors, as 4.07% of cells displayed sister chromatid non-disjunction during mitosis. Ascorbic acid (AsA, Vitamin C), a strong natural antioxidant, was used to alleviate the negative impact of AA. Cell pre-treatment with AsA significantly improved AA impaired growth, and antioxidant capacity, and supported ionome balance maintenance mainly due to the promotion of calcium uptake. Chromosome missegregation was reduced to 1.79% (44% improvement) by AsA pre-incubation. Results of our multiapproach analyses suggest that AA-induced oxidative stress is the major cause of alteration to cell homeostasis and cell cycle regulation.
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Affiliation(s)
- Marek Kovár
- Institute of Plant and Environmental Science, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia;
| | - Alica Navrátilová
- Institute of Nutrition and Genomics, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia; (A.N.); (A.T.)
| | - Renata Kolláthová
- Institute of Animal Husbandry, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia;
| | - Anna Trakovická
- Institute of Nutrition and Genomics, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia; (A.N.); (A.T.)
| | - Miroslava Požgajová
- AgroBioTech Research Center, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
- Correspondence: ; Tel.: +421-37-641-4919
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Nguyen PQ, Conesa C, Rabut E, Bragagnolo G, Gouzerh C, Fernández-Tornero C, Lesage P, Reguera J, Acker J. Ty1 integrase is composed of an active N-terminal domain and a large disordered C-terminal module dispensable for its activity in vitro. J Biol Chem 2021; 297:101093. [PMID: 34416236 PMCID: PMC8487063 DOI: 10.1016/j.jbc.2021.101093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/05/2021] [Accepted: 08/16/2021] [Indexed: 11/16/2022] Open
Abstract
Long-terminal repeat (LTR) retrotransposons are genetic elements that, like retroviruses, replicate by reverse transcription of an RNA intermediate into a complementary DNA (cDNA) that is next integrated into the host genome by their own integrase. The Ty1 LTR retrotransposon has proven to be a reliable working model to investigate retroelement integration site preference. However, the low yield of recombinant Ty1 integrase production reported so far has been a major obstacle for structural studies. Here we analyze the biophysical and biochemical properties of a stable and functional recombinant Ty1 integrase highly expressed in E.coli. The recombinant protein is monomeric and has an elongated shape harboring the three-domain structure common to all retroviral integrases at the N-terminal half, an extra folded region, and a large intrinsically disordered region at the C-terminal half. Recombinant Ty1 integrase efficiently catalyzes concerted integration in vitro, and the N-terminal domain displays similar activity. These studies that will facilitate structural analyses may allow elucidating the molecular mechanisms governing Ty1 specific integration into safe places in the genome.
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Affiliation(s)
| | - Christine Conesa
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Elise Rabut
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - Célia Gouzerh
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - Pascale Lesage
- INSERM U944, CNRS UMR 7212, Genomes and Cell Biology of Disease Unit, Institut de Recherche Saint-Louis, Université de Paris, Hôpital Saint-Louis, Paris, France
| | - Juan Reguera
- Aix-Marseille Université, CNRS, AFMB UMR 7257, Marseille, France; INSERM, AFMB UMR7257, Marseille, France.
| | - Joël Acker
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France.
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Iacovacci J, Lin W, Griffin JL, Glen RC. IonFlow: a galaxy tool for the analysis of ionomics data sets. Metabolomics 2021; 17:91. [PMID: 34562172 PMCID: PMC8464566 DOI: 10.1007/s11306-021-01841-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 09/13/2021] [Indexed: 10/28/2022]
Abstract
INTRODUCTION Inductively coupled plasma mass spectrometry (ICP-MS) experiments generate complex multi-dimensional data sets that require specialist data analysis tools. OBJECTIVE Here we describe tools to facilitate analysis of the ionome composed of high-throughput elemental profiling data. METHODS IonFlow is a Galaxy tool written in R for ionomics data analysis and is freely accessible at https://github.com/wanchanglin/ionflow . It is designed as a pipeline that can process raw data to enable exploration and interpretation using multivariate statistical techniques and network-based algorithms, including principal components analysis, hierarchical clustering, relevance network extraction and analysis, and gene set enrichment analysis. RESULTS AND CONCLUSION The pipeline is described and tested on two benchmark data sets of the haploid S. Cerevisiae ionome and of the human HeLa cell ionome.
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Affiliation(s)
- J Iacovacci
- Department of Metabolism Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK.
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
| | - W Lin
- Department of Metabolism Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
| | - J L Griffin
- Department of Metabolism Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK
- Department of Biochemistry and Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - R C Glen
- Department of Metabolism Digestion and Reproduction, Faculty of Medicine, Imperial College London, London, UK.
- Department of Chemistry, Centre for Molecular Informatics, University of Cambridge, Cambridge, UK.
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Palermo GCDL, Coutouné N, Bueno JGR, Maciel LF, dos Santos LV. Exploring metal ion metabolisms to improve xylose fermentation in Saccharomyces cerevisiae. Microb Biotechnol 2021; 14:2101-2115. [PMID: 34313008 PMCID: PMC8449651 DOI: 10.1111/1751-7915.13887] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/25/2021] [Indexed: 01/22/2023] Open
Abstract
The development of high-performance xylose-fermenting yeast is essential to achieve feasible conversion of biomass-derived sugars in lignocellulose-based biorefineries. However, engineered C5-strains of Saccharomyces cerevisiae still present low xylose consumption rates under anaerobic conditions. Here, we explore alternative metabolisms involved in metal homeostasis, which positively affect C5 fermentation and analyse the non-obvious regulatory network connection of both metabolisms using time-course transcriptome analysis. Our results indicated the vacuolar Fe2+ /Mn2+ transporter CCC1, and the protein involved in heavy metal ion homeostasis BSD2, as promising new targets for rational metabolic engineering strategies, enhancing xylose consumption in nine and 2.3-fold compared with control. Notably, intracellular metal concentration levels were affected differently by mutations and the results were compared with positive controls isu1Δ, a Fe-S cluster scaffold protein, and ssk2Δ, a component of HOG pathway. Temporal expression profiles indicate a metabolic remodelling in response to xylose, demonstrating changes in the main sugar sensing signalling pathways.
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Affiliation(s)
- Gisele Cristina de Lima Palermo
- Brazilian Biorenewable National Laboratory (LNBR)Brazilian Center for Research in Energy and Materials (CNPEM)CampinasSão Paulo13083‐100Brazil
- Genetics and Molecular Biology Graduate ProgramInstitute of BiologyUniversity of Campinas (UNICAMP)CampinasSão PauloBrazil
| | - Natalia Coutouné
- Brazilian Biorenewable National Laboratory (LNBR)Brazilian Center for Research in Energy and Materials (CNPEM)CampinasSão Paulo13083‐100Brazil
- Genetics and Molecular Biology Graduate ProgramInstitute of BiologyUniversity of Campinas (UNICAMP)CampinasSão PauloBrazil
| | - João Gabriel Ribeiro Bueno
- Brazilian Biorenewable National Laboratory (LNBR)Brazilian Center for Research in Energy and Materials (CNPEM)CampinasSão Paulo13083‐100Brazil
- Genetics and Molecular Biology Graduate ProgramInstitute of BiologyUniversity of Campinas (UNICAMP)CampinasSão PauloBrazil
| | - Lucas Ferreira Maciel
- Brazilian Biorenewable National Laboratory (LNBR)Brazilian Center for Research in Energy and Materials (CNPEM)CampinasSão Paulo13083‐100Brazil
| | - Leandro Vieira dos Santos
- Brazilian Biorenewable National Laboratory (LNBR)Brazilian Center for Research in Energy and Materials (CNPEM)CampinasSão Paulo13083‐100Brazil
- Genetics and Molecular Biology Graduate ProgramInstitute of BiologyUniversity of Campinas (UNICAMP)CampinasSão PauloBrazil
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Santos-Barriopedro I, van Mierlo G, Vermeulen M. Off-the-shelf proximity biotinylation for interaction proteomics. Nat Commun 2021; 12:5015. [PMID: 34408139 PMCID: PMC8373943 DOI: 10.1038/s41467-021-25338-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/27/2021] [Indexed: 12/15/2022] Open
Abstract
Proximity biotinylation workflows typically require CRISPR-based genetic manipulation of target cells. To overcome this bottleneck, we fused the TurboID proximity biotinylation enzyme to Protein A. Upon target cell permeabilization, the ProtA-Turbo enzyme can be targeted to proteins or post-translational modifications of interest using bait-specific antibodies. Addition of biotin then triggers bait-proximal protein biotinylation. Biotinylated proteins can subsequently be enriched from crude lysates and identified by mass spectrometry. We demonstrate this workflow by targeting Emerin, H3K9me3 and BRG1. Amongst the main findings, our experiments reveal that the essential protein FLYWCH1 interacts with a subset of H3K9me3-marked (peri)centromeres in human cells. The ProtA-Turbo enzyme represents an off-the-shelf proximity biotinylation enzyme that facilitates proximity biotinylation experiments in primary cells and can be used to understand how proteins cooperate in vivo and how this contributes to cellular homeostasis and disease.
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Affiliation(s)
- Irene Santos-Barriopedro
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Guido van Mierlo
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands.
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands.
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Ali S, Tyagi A, Bae H. Ionomic Approaches for Discovery of Novel Stress-Resilient Genes in Plants. Int J Mol Sci 2021; 22:7182. [PMID: 34281232 PMCID: PMC8267685 DOI: 10.3390/ijms22137182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 01/03/2023] Open
Abstract
Plants, being sessile, face an array of biotic and abiotic stresses in their lifespan that endanger their survival. Hence, optimized uptake of mineral nutrients creates potential new routes for enhancing plant health and stress resilience. Recently, minerals (both essential and non-essential) have been identified as key players in plant stress biology, owing to their multifaceted functions. However, a realistic understanding of the relationship between different ions and stresses is lacking. In this context, ionomics will provide new platforms for not only understanding the function of the plant ionome during stresses but also identifying the genes and regulatory pathways related to mineral accumulation, transportation, and involvement in different molecular mechanisms under normal or stress conditions. This article provides a general overview of ionomics and the integration of high-throughput ionomic approaches with other "omics" tools. Integrated omics analysis is highly suitable for identification of the genes for various traits that confer biotic and abiotic stress tolerance. Moreover, ionomics advances being used to identify loci using qualitative trait loci and genome-wide association analysis of element uptake and transport within plant tissues, as well as genetic variation within species, are discussed. Furthermore, recent developments in ionomics for the discovery of stress-tolerant genes in plants have also been addressed; these can be used to produce more robust crops with a high nutritional value for sustainable agriculture.
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Affiliation(s)
- Sajad Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea;
| | - Anshika Tyagi
- National Institute for Plant Biotechnology, New Delhi 110012, India;
| | - Hanhong Bae
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea;
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11
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Campos ACAL, van Dijk WFA, Ramakrishna P, Giles T, Korte P, Douglas A, Smith P, Salt DE. 1,135 ionomes reveal the global pattern of leaf and seed mineral nutrient and trace element diversity in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:536-554. [PMID: 33506585 DOI: 10.1111/tpj.15177] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 01/07/2021] [Accepted: 01/20/2021] [Indexed: 05/06/2023]
Abstract
Soil is a heterogeneous reservoir of essential elements needed for plant growth and development. Plants have evolved mechanisms to balance their nutritional needs based on availability of nutrients. This has led to genetically based variation in the elemental composition, the 'ionome', of plants, both within and between species. We explore this natural variation using a panel of wild-collected, geographically widespread Arabidopsis thaliana accessions from the 1001 Genomes Project including over 1,135 accessions, and the 19 parental accessions of the Multi-parent Advanced Generation Inter-Cross (MAGIC) panel, all with full-genome sequences available. We present an experimental design pipeline for high-throughput ionomic screenings and analyses with improved normalisation procedures to account for errors and variability in conditions often encountered in large-scale, high-throughput data collection. We report quantification of the complete leaf and seed ionome of the entire collection using this pipeline and a digital tool, Ion Explorer, to interact with the dataset. We describe the pattern of natural ionomic variation across the A. thaliana species and identify several accessions with extreme ionomic profiles. It forms a valuable resource for exploratory genetic mapping studies to identify genes underlying natural variation in leaf and seed ionome and genetic adaptation of plants to soil conditions.
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Affiliation(s)
- Ana Carolina A L Campos
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
| | - William F A van Dijk
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
| | - Priya Ramakrishna
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
| | - Tom Giles
- Digital Research Service and Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
| | - Pamela Korte
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
| | - Alex Douglas
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
| | - Pete Smith
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
| | - David E Salt
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
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12
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Disease Ionomics: Understanding the Role of Ions in Complex Disease. Int J Mol Sci 2020; 21:ijms21228646. [PMID: 33212764 PMCID: PMC7697569 DOI: 10.3390/ijms21228646] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/12/2020] [Accepted: 11/13/2020] [Indexed: 12/12/2022] Open
Abstract
Ionomics is a novel multidisciplinary field that uses advanced techniques to investigate the composition and distribution of all minerals and trace elements in a living organism and their variations under diverse physiological and pathological conditions. It involves both high-throughput elemental profiling technologies and bioinformatic methods, providing opportunities to study the molecular mechanism underlying the metabolism, homeostasis, and cross-talk of these elements. While much effort has been made in exploring the ionomic traits relating to plant physiology and nutrition, the use of ionomics in the research of serious diseases is still in progress. In recent years, a number of ionomic studies have been carried out for a variety of complex diseases, which offer theoretical and practical insights into the etiology, early diagnosis, prognosis, and therapy of them. This review aims to give an overview of recent applications of ionomics in the study of complex diseases and discuss the latest advances and future trends in this area. Overall, disease ionomics may provide substantial information for systematic understanding of the properties of the elements and the dynamic network of elements involved in the onset and development of diseases.
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13
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Iacovacci J, Peluso A, Ebbels T, Ralser M, Glen RC. Extraction and Integration of Genetic Networks from Short-Profile Omic Data Sets. Metabolites 2020; 10:metabo10110435. [PMID: 33137869 PMCID: PMC7693762 DOI: 10.3390/metabo10110435] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/13/2020] [Accepted: 10/23/2020] [Indexed: 01/29/2023] Open
Abstract
Mass spectrometry technologies are widely used in the fields of ionomics and metabolomics to simultaneously profile the intracellular concentrations of, e.g., amino acids or elements in genome-wide mutant libraries. These molecular or sub-molecular features are generally non-Gaussian and their covariance reveals patterns of correlations that reflect the system nature of the cell biochemistry and biology. Here, we introduce two similarity measures, the Mahalanobis cosine and the hybrid Mahalanobis cosine, that enforce information from the empirical covariance matrix of omics data from high-throughput screening and that can be used to quantify similarities between the profiled features of different mutants. We evaluate the performance of these similarity measures in the task of inferring and integrating genetic networks from short-profile ionomics/metabolomics data through an analysis of experimental data sets related to the ionome and the metabolome of the model organism S. cerevisiae. The study of the resulting ionome–metabolome Saccharomyces cerevisiae multilayer genetic network, which encodes multiple omic-specific levels of correlations between genes, shows that the proposed measures can provide an alternative description of relations between biological processes when compared to the commonly used Pearson’s correlation coefficient and have the potential to guide the construction of novel hypotheses on the function of uncharacterised genes.
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Affiliation(s)
- Jacopo Iacovacci
- Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK; (A.P.); (T.E.)
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK;
- Correspondence: (J.I.); (R.C.G.)
| | - Alina Peluso
- Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK; (A.P.); (T.E.)
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK;
| | - Timothy Ebbels
- Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK; (A.P.); (T.E.)
| | - Markus Ralser
- The Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London NW1 1AT, UK;
- Charité, Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Robert C. Glen
- Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK; (A.P.); (T.E.)
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB21EW, UK
- Correspondence: (J.I.); (R.C.G.)
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14
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Single cell-inductively coupled plasma-time of flight-mass spectrometry approach for ecotoxicological testing. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101964] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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15
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McKeating DR, Fisher JJ, Zhang P, Bennett WW, Perkins AV. Elemental metabolomics in human cord blood: Method validation and trace element quantification. J Trace Elem Med Biol 2020; 59:126419. [PMID: 31711786 DOI: 10.1016/j.jtemb.2019.126419] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/26/2019] [Accepted: 10/18/2019] [Indexed: 01/15/2023]
Abstract
BACKGROUND Trace elements are an essential requirement for human health and development and changes in trace element status have been associated with pregnancy complications such as gestational diabetes mellitus (GDM), pre-eclampsia (PE), fetal growth restriction (FGR), and preterm birth. Elemental metabolomics, which involves the simultaneous quantification and characterisation of multiple elements, could provide important insights into these gestational disorders. METHODS This study used an Agilent 7900 inductively coupled plasma mass spectrometer (ICP-MS) to simultaneously measure 68 elements, in 166 placental cord blood samples collected from women with various pregnancy complications (control, hypertensive, PE, GDM, FGR, pre-term, and post-term birth). RESULTS There were single element differences across gestational outcomes for elements Mg, P, Cr, Ni, Sr, Mo, I, Au, Pb, and U. Hypertensive and post-term pregnancies were significantly higher in Ni concentrations when compared to controls (control = 2.74 μg/L, hypertensive = 6.72 μg/L, post-term = 7.93 μg/L, p < 0.05), iodine concentration was significantly higher in post-term pregnancies (p < 0.05), and Pb concentrations were the lowest in pre-term pregnancies (pre-term = 2.79 μg/L, control = 4.68 μg/L, PE = 5.32 μg/L, GDM = 8.27 μg/L, p < 0.01). Further analysis was conducted using receiver operating characteristic (ROC) curves for differentiating pregnancy groups. The ratio of Sn/Pb showed the best diagnostic power in discriminating between control and pre-term birth with area under the curve (AUC) 0.86. When comparing control and post-term birth, Mg/Cr (AUC = 0.84), and Cr (AUC = 0.83) had the best diagnostic powers. In pre-term and post-term comparisons Ba was the best single element (81.5%), and P/Cu provided the best ratio (91.7%). CONCLUSIONS This study has shown that analysis of multiple elements can enable differentiation between fetal cord blood samples from control, hypertensive, PE, GDM, FGR, pre and post-term pregnancies. This data highlights the power of elemental metabolomics and provides a basis for future gestational studies.
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Affiliation(s)
- Daniel R McKeating
- School of Medical Science, Griffith University, Gold Coast Campus, Southport, 9726, Queensland, Australia
| | - Joshua J Fisher
- School of Medical Science, Griffith University, Gold Coast Campus, Southport, 9726, Queensland, Australia
| | - Ping Zhang
- School of Medical Science, Griffith University, Gold Coast Campus, Southport, 9726, Queensland, Australia
| | - William W Bennett
- School of Environmental Science, Griffith University, Gold Coast Campus, Southport, 9726, Queensland, Australia
| | - Anthony V Perkins
- School of Medical Science, Griffith University, Gold Coast Campus, Southport, 9726, Queensland, Australia.
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16
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Chen A, Hansen TH, Olsen LI, Palmgren M, Husted S, Schjoerring JK, Persson DP. Towards single-cell ionomics: a novel micro-scaled method for multi-element analysis of nanogram-sized biological samples. PLANT METHODS 2020; 16:31. [PMID: 32165911 PMCID: PMC7059671 DOI: 10.1186/s13007-020-00566-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 02/07/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND To understand processes regulating nutrient homeostasis at the single-cell level there is a need for new methods that allow multi-element profiling of biological samples ultimately only available as isolated tissues or cells, typically in nanogram-sized samples. Apart from tissue isolation, the main challenges for such analyses are to obtain a complete and homogeneous digestion of each sample, to keep sample dilution at a minimum and to produce accurate and reproducible results. In particular, determining the weight of small samples becomes increasingly challenging when the sample amount decreases. RESULTS We developed a novel method for sampling, digestion and multi-element analysis of nanogram-sized plant tissue, along with strategies to quantify element concentrations in samples too small to be weighed. The method is based on tissue isolation by laser capture microdissection (LCM), followed by pressurized micro-digestion and ICP-MS analysis, the latter utilizing a stable µL min-1 sample aspiration system. The method allowed for isolation, digestion and analysis of micro-dissected tissues from barley roots with an estimated sample weight of only ~ 400 ng. In the collection and analysis steps, a number of contamination sources were identified. Following elimination of these sources, several elements, including magnesium (Mg), phosphorus (P), potassium (K) and manganese (Mn), could be quantified. By measuring the exact area and thickness of each of the micro-dissected tissues, their volume was calculated. Combined with an estimated sample density, the sample weights could subsequently be calculated and the fact that these samples were too small to be weighed could thereby be circumvented. The method was further documented by analysis of Arabidopsis seeds (~ 20 µg) as well as tissue fractions of such seeds (~ 10 µg). CONCLUSIONS The presented method enables collection and multi-element analysis of small-sized biological samples, ranging down to the nanogram level. As such, the method paves the road for single cell and tissue-specific quantitative ionomics, which allow for future transcriptional, proteomic and metabolomic data to be correlated with ionomic profiles. Such analyses will deepen our understanding of how the elemental composition of plants is regulated, e.g. by transporter proteins and physical barriers (i.e. the Casparian strip and suberin lamellae in the root endodermis).
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Affiliation(s)
- Anle Chen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Thomas H. Hansen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Lene I. Olsen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Michael Palmgren
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Søren Husted
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Jan K. Schjoerring
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Daniel Pergament Persson
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
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17
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Pozgajova M, Navratilova A, Arvay J, Duranova H, Trakovicka A. Impact of cadmium and nickel on ion homeostasis in the yeast Schizosaccharomyces pombe. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2019; 55:166-173. [PMID: 31588841 DOI: 10.1080/03601234.2019.1673613] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Toxicity of heavy metals to living organisms is a worldwide research topic. Although, much has been discovered about cadmium and nickel impact on biological systems, a lot still remains unclear. We used inductively coupled plasma - optical emission spectroscopy to address the question of the effect of two different heavy metals nickel, and cadmium on intracellular ion balance. Increase or decrease of the content of several essential cations including Ca2+, Na+, K+, Mg2+, Cu2+, Fe3+ in the yeast Schizosaccharomyces pombe was determined. Our results revealed that the cell exposure to high nickel and cadmium concentrations led to significant elevation of Ca2+, Na+, Mg2+, Cu2+, Fe3+ levels in the yeast cell, while the content of K+ decreased. Correlation analyses showing in the presence of nickel and cadmium strong positive correlation among each tested element (Ca2+, Na+, Cu2+, Mg2+ and Fe3+) except for K+, demonstrate the significant impact of heavy metal treatment to ion homeostasis of the cell. Our data indicate that acute nickel and cadmium contamination leads to substantial ionome misbalance in yeast.
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Affiliation(s)
- Miroslava Pozgajova
- AgroBioTech Research Center, Slovak University of Agriculture, Nitra, Slovakia
| | - Alica Navratilova
- Department of Genetics and Breeding Biology, Slovak University of Agriculture, Nitra, Slovakia
| | - Julius Arvay
- Department of Chemistry, Slovak University of Agriculture, Nitra, Slovakia
| | - Hana Duranova
- AgroBioTech Research Center, Slovak University of Agriculture, Nitra, Slovakia
| | - Anna Trakovicka
- Department of Genetics and Breeding Biology, Slovak University of Agriculture, Nitra, Slovakia
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18
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Tsednee M, Castruita M, Salomé PA, Sharma A, Lewis BE, Schmollinger SR, Strenkert D, Holbrook K, Otegui MS, Khatua K, Das S, Datta A, Chen S, Ramon C, Ralle M, Weber PK, Stemmler TL, Pett-Ridge J, Hoffman BM, Merchant SS. Manganese co-localizes with calcium and phosphorus in Chlamydomonas acidocalcisomes and is mobilized in manganese-deficient conditions. J Biol Chem 2019; 294:17626-17641. [PMID: 31527081 DOI: 10.1074/jbc.ra119.009130] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 09/09/2019] [Indexed: 12/27/2022] Open
Abstract
Exposing cells to excess metal concentrations well beyond the cellular quota is a powerful tool for understanding the molecular mechanisms of metal homeostasis. Such improved understanding may enable bioengineering of organisms with improved nutrition and bioremediation capacity. We report here that Chlamydomonas reinhardtii can accumulate manganese (Mn) in proportion to extracellular supply, up to 30-fold greater than its typical quota and with remarkable tolerance. As visualized by X-ray fluorescence microscopy and nanoscale secondary ion MS (nanoSIMS), Mn largely co-localizes with phosphorus (P) and calcium (Ca), consistent with the Mn-accumulating site being an acidic vacuole, known as the acidocalcisome. Vacuolar Mn stores are accessible reserves that can be mobilized in Mn-deficient conditions to support algal growth. We noted that Mn accumulation depends on cellular polyphosphate (polyP) content, indicated by 1) a consistent failure of C. reinhardtii vtc1 mutant strains, which are deficient in polyphosphate synthesis, to accumulate Mn and 2) a drastic reduction of the Mn storage capacity in P-deficient cells. Rather surprisingly, X-ray absorption spectroscopy, EPR, and electron nuclear double resonance revealed that only little Mn2+ is stably complexed with polyP, indicating that polyP is not the final Mn ligand. We propose that polyPs are a critical component of Mn accumulation in Chlamydomonas by driving Mn relocation from the cytosol to acidocalcisomes. Within these structures, polyP may, in turn, escort vacuolar Mn to a number of storage ligands, including phosphate and phytate, and other, yet unidentified, compounds.
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Affiliation(s)
| | - Madeli Castruita
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095
| | - Patrice A Salomé
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095.,Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095
| | - Ajay Sharma
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Brianne E Lewis
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201
| | - Stefan R Schmollinger
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095.,Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095
| | - Daniela Strenkert
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095.,Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095
| | - Kristen Holbrook
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095
| | - Marisa S Otegui
- Departments of Botany and Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Kaustav Khatua
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Sayani Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Ankona Datta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Si Chen
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439
| | - Christina Ramon
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550
| | - Martina Ralle
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon 97239
| | - Peter K Weber
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550
| | - Timothy L Stemmler
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan 48201
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry, UCLA, Los Angeles, California 90095 .,Institute for Genomics and Proteomics, UCLA, Los Angeles, California 90095
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19
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Courbet G, Gallardo K, Vigani G, Brunel-Muguet S, Trouverie J, Salon C, Ourry A. Disentangling the complexity and diversity of crosstalk between sulfur and other mineral nutrients in cultivated plants. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:4183-4196. [PMID: 31055598 DOI: 10.1093/jxb/erz214] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 04/29/2019] [Indexed: 05/02/2023]
Abstract
A complete understanding of ionome homeostasis requires a thorough investigation of the dynamics of the nutrient networks in plants. This review focuses on the complexity of interactions occurring between S and other nutrients, and these are addressed at the level of the whole plant, the individual tissues, and the cellular compartments. With regards to macronutrients, S deficiency mainly acts by reducing plant growth, which in turn restricts the root uptake of, for example, N, K, and Mg. Conversely, deficiencies in N, K, or Mg reduce uptake of S. TOR (target of rapamycin) protein kinase, whose involvement in the co-regulation of C/N and S metabolism has recently been unravelled, provides a clue to understanding the links between S and plant growth. In legumes, the original crosstalk between N and S can be found at the level of nodules, which show high requirements for S, and hence specifically express a number of sulfate transporters. With regards to micronutrients, except for Fe, their uptake can be increased under S deficiency through various mechanisms. One of these results from the broad specificity of root sulfate transporters that are up-regulated during S deficiency, which can also take up some molybdate and selenate. A second mechanism is linked to the large accumulation of sulfate in the leaf vacuoles, with its reduced osmotic contribution under S deficiency being compensated for by an increase in Cl uptake and accumulation. A third group of broader mechanisms that can explain at least some of the interactions between S and micronutrients concerns metabolic networks where several nutrients are essential, such as the synthesis of the Mo co-factor needed by some essential enzymes, which requires S, Fe, Zn and Cu for its synthesis, and the synthesis and regulation of Fe-S clusters. Finally, we briefly review recent developments in the modelling of S responses in crops (allocation amongst plant parts and distribution of mineral versus organic forms) in order to provide perspectives on prediction-based approaches that take into account the interactions with other minerals such as N.
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Affiliation(s)
- Galatéa Courbet
- Normandie Université, UNICAEN, INRA, UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, Esplanade de la Paix, Caen Cedex, France
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne, Franche-Comté, Dijon, France
| | - Karine Gallardo
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne, Franche-Comté, Dijon, France
| | - Gianpiero Vigani
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Sophie Brunel-Muguet
- Normandie Université, UNICAEN, INRA, UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, Esplanade de la Paix, Caen Cedex, France
| | - Jacques Trouverie
- Normandie Université, UNICAEN, INRA, UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, Esplanade de la Paix, Caen Cedex, France
| | - Christophe Salon
- Agroécologie, AgroSup Dijon, INRA, Université Bourgogne, Franche-Comté, Dijon, France
| | - Alain Ourry
- Normandie Université, UNICAEN, INRA, UMR 950 Ecophysiologie Végétale, Agronomie et Nutritions N, C, S, Esplanade de la Paix, Caen Cedex, France
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20
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Lee AR, Lee SJ, Lee M, Nam M, Lee S, Choi J, Lee HJ, Kim DU, Hoe KL. Editor's Highlight: A Genome-wide Screening of Target Genes Against Silver Nanoparticles in Fission Yeast. Toxicol Sci 2019; 161:171-185. [PMID: 29294138 PMCID: PMC5837777 DOI: 10.1093/toxsci/kfx208] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
To identify target genes against silver nanoparticles (AgNPs), we screened a genome-wide gene deletion library of 4843 fission yeast heterozygous mutants covering 96% of all protein encoding genes. A total of 33 targets were identified by a microarray and subsequent individual confirmation. The target pattern of AgNPs was more similar to those of AgNO3 and H2O2, followed by Cd and As. The toxic effect of AgNPs on fission yeast was attributed to the intracellular uptake of AgNPs, followed by the subsequent release of Ag+, leading to the generation of reactive oxygen species (ROS). Next, we focused on the top 10 sensitive targets for further studies. As described previously, 7 nonessential targets were associated with detoxification of ROS, because their heterozygous mutants showed elevated ROS levels. Three novel essential targets were related to folate metabolism or cellular component organization, resulting in cell cycle arrest and no induction in the transcriptional level of antioxidant enzymes such as Sod1 and Gpx1 when 1 of the 2 copies was deleted. Intriguingly, met9 played a key role in combating AgNP-induced ROS generation via NADPH production and was also conserved in a human cell line.
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Affiliation(s)
- Ah-Reum Lee
- Department of New Drug Discovery and Development, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Sook-Jeong Lee
- Department of Bioactive Material Science, Chonbuk National University, Jeonju 54896, Republic of Korea
| | - Minho Lee
- Catholic Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Miyoung Nam
- Department of New Drug Discovery and Development, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Sol Lee
- Department of New Drug Discovery and Development, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jian Choi
- Department of New Drug Discovery and Development, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Hye-Jin Lee
- Department of New Drug Discovery and Development, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Dong-Uk Kim
- Department of Aging Research Center, KRIBB, Daejeon 34141, Republic of Korea
| | - Kwang-Lae Hoe
- Department of New Drug Discovery and Development, Chungnam National University, Daejeon 34134, Republic of Korea
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21
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McKeating DR, Fisher JJ, Perkins AV. Elemental Metabolomics and Pregnancy Outcomes. Nutrients 2019; 11:E73. [PMID: 30609706 PMCID: PMC6356574 DOI: 10.3390/nu11010073] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 12/26/2018] [Accepted: 01/01/2019] [Indexed: 01/22/2023] Open
Abstract
Trace elements are important for human health and development. The body requires specific micronutrients to function, with aberrant changes associated with a variety of negative health outcomes. Despite this evidence, the status and function of micronutrients during pregnancy are relatively unknown and more information is required to ensure that women receive optimal intakes for foetal development. Changes in trace element status have been associated with pregnancy complications such as gestational diabetes mellitus (GDM), pre-eclampsia (PE), intrauterine growth restriction (IUGR), and preterm birth. Measuring micronutrients with methodologies such as elemental metabolomics, which involves the simultaneous quantification and characterisation of multiple elements, could provide insight into gestational disorders. Identifying unique and subtle micronutrient changes may highlight associated proteins that are affected underpinning the pathophysiology of these complications, leading to new means of disease diagnosis. This review will provide a comprehensive summary of micronutrient status during pregnancy, and their associations with gestational disorders. Furthermore, it will also comment on the potential use of elemental metabolomics as a technique for disease characterisation and prediction.
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Affiliation(s)
- Daniel R McKeating
- School of Medical Science, Menzies Health Institute Queensland, Griffith University, Southport 9726, Queensland, Australia.
| | - Joshua J Fisher
- School of Medical Science, Menzies Health Institute Queensland, Griffith University, Southport 9726, Queensland, Australia.
| | - Anthony V Perkins
- School of Medical Science, Menzies Health Institute Queensland, Griffith University, Southport 9726, Queensland, Australia.
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22
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Trace Elements and Healthcare: A Bioinformatics Perspective. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1005:63-98. [PMID: 28916929 DOI: 10.1007/978-981-10-5717-5_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Biological trace elements are essential for human health. Imbalance in trace element metabolism and homeostasis may play an important role in a variety of diseases and disorders. While the majority of previous researches focused on experimental verification of genes involved in trace element metabolism and those encoding trace element-dependent proteins, bioinformatics study on trace elements is relatively rare and still at the starting stage. This chapter offers an overview of recent progress in bioinformatics analyses of trace element utilization, metabolism, and function, especially comparative genomics of several important metals. The relationship between individual elements and several diseases based on recent large-scale systematic studies such as genome-wide association studies and case-control studies is discussed. Lastly, developments of ionomics and its recent application in human health are also introduced.
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23
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Ziegler G, Nelson R, Granada S, Krishnan HB, Gillman JD, Baxter I. Genomewide association study of ionomic traits on diverse soybean populations from germplasm collections. PLANT DIRECT 2018; 2:e00033. [PMID: 31245681 PMCID: PMC6508489 DOI: 10.1002/pld3.33] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/06/2017] [Accepted: 11/14/2017] [Indexed: 05/17/2023]
Abstract
The elemental content of a soybean seed is a determined by both genetic and environmental factors and is an important component of its nutritional value. The elemental content is chemically stable, making the samples stored in germplasm repositories an intriguing source of experimental material. To test the efficacy of using samples from germplasm banks for gene discovery, we analyzed the elemental profile of seeds from 1,653 lines in the USDA Soybean Germplasm Collection. We observed large differences in the elemental profiles based on where the lines were grown, which lead us to break up the genetic analysis into multiple small experiments. Despite these challenges, we were able to identify candidate single nucleotide polymorphisms (SNPs) controlling elemental accumulation as well as lines with extreme elemental accumulation phenotypes. Our results suggest that elemental analysis of germplasm samples can identify SNPs in linkage disequilibrium to genes, which can be leveraged to assist in crop improvement efforts.
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Affiliation(s)
- Greg Ziegler
- USDA‐ARS Plant Genetics Research UnitSt. LouisMOUSA
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | - Randall Nelson
- Soybean/Maize Germplasm, Pathology and Genetics Research Unit and Department of Crop SciencesUSDA‐ARSUniversity of IllinoisUrbanaILUSA
| | | | - Hari B. Krishnan
- USDA‐ARS Plant Genetics Research UnitColumbiaMOUSA
- Plant Science DivisionUniversity of MissouriColumbiaMOUSA
| | - Jason D. Gillman
- USDA‐ARS Plant Genetics Research UnitColumbiaMOUSA
- Plant Science DivisionUniversity of MissouriColumbiaMOUSA
| | - Ivan Baxter
- USDA‐ARS Plant Genetics Research UnitSt. LouisMOUSA
- Donald Danforth Plant Science CenterSt. LouisMOUSA
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Abstract
Most biological mechanisms involve more than one type of biomolecule, and hence operate not solely at the level of either genome, transcriptome, proteome, metabolome or ionome. Datasets resulting from single-omic analysis are rapidly increasing in throughput and quality, rendering multi-omic studies feasible. These should offer a comprehensive, structured and interactive overview of a biological mechanism. However, combining single-omic datasets in a meaningful manner has so far proved challenging, and the discovery of new biological information lags behind expectation. One reason is that experiments conducted in different laboratories can typically not to be combined without restriction. Second, the interpretation of multi-omic datasets represents a significant challenge by nature, as the biological datasets are heterogeneous not only for technical, but also for biological, chemical, and physical reasons. Here, multi-layer network theory and methods of artificial intelligence might contribute to solve these problems. For the efficient application of machine learning however, biological datasets need to become more systematic, more precise - and much larger. We conclude our review with basic guidelines for the successful set-up of a multi-omic experiment.
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25
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Golla U, Swagatika S, Chauhan S, Tomar RS. A systematic assessment of chemical, genetic, and epigenetic factors influencing the activity of anticancer drug KP1019 (FFC14A). Oncotarget 2017; 8:98426-98454. [PMID: 29228701 PMCID: PMC5716741 DOI: 10.18632/oncotarget.21416] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 08/28/2017] [Indexed: 12/11/2022] Open
Abstract
KP1019 ([trans-RuCl4(1H-indazole)2]; FFC14A) is one of the promising ruthenium-based anticancer drugs undergoing clinical trials. Despite the pre-clinical and clinical success of KP1019, the mode of action and various factors capable of modulating its effects are largely unknown. Here, we used transcriptomics and genetic screening approaches in budding yeast model and deciphered various genetic targets and plethora of cellular pathways including cellular signaling, metal homeostasis, vacuolar transport, and lipid homeostasis that are primarily targeted by KP1019. We also demonstrated that KP1019 modulates the effects of TOR (target of rapamycin) signaling pathway and induces accumulation of neutral lipids (lipid droplets) in both yeast and HeLa cells. Interestingly, KP1019-mediated effects were found augmented with metal ions (Al3+/Ca2+/Cd2+/Cu2+/Mn2+/Na+/Zn2+), and neutralized by Fe2+, antioxidants, osmotic stabilizer, and ethanolamine. Additionally, our comprehensive screening of yeast histone H3/H4 mutant library revealed several histone residues that could significantly modulate the KP1019-induced toxicity. Altogether, our findings in both the yeast and HeLa cells provide molecular insights into mechanisms of action of KP1019 and various factors (chemical/genetic/epigenetic) that can alter the therapeutic efficiency of this clinically important anticancer drug.
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Affiliation(s)
- Upendarrao Golla
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462066, India
| | - Swati Swagatika
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462066, India
| | - Sakshi Chauhan
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462066, India
| | - Raghuvir Singh Tomar
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Bhopal 462066, India
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26
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Huang CW, Walker ME, Fedrizzi B, Gardner RC, Jiranek V. Yeast genes involved in regulating cysteine uptake affect production of hydrogen sulfide from cysteine during fermentation. FEMS Yeast Res 2017; 17:3934655. [PMID: 28810701 DOI: 10.1093/femsyr/fox046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/04/2017] [Indexed: 11/13/2022] Open
Abstract
An early burst of hydrogen sulfide (H2S) produced by Saccharomyces cerevisiae during fermentation could increase varietal thiols and therefore enhance desirable tropical aromas in varieties such as Sauvignon Blanc. Here we attempted to identify genes affecting H2S formation from cysteine by screening yeast deletion libraries via a colony colour assay on media resembling grape juice. Both Δlst4 and Δlst7 formed lighter coloured colonies and produced significantly less H2S than the wild type on high concentrations of cysteine, likely because they are unable to take up cysteine efficiently. We then examined the nine known cysteine permeases and found that deletion of AGP1, GNP1 and MUP1 led to reduced production of H2S from cysteine. We further showed that deleting genes involved in the SPS-sensing pathway such as STP1 and DAL81 also reduced H2S from cysteine. Together, this study indirectly confirms that Agp1p, Gnp1p and Mup1p are the major cysteine permeases and that they are regulated by the SPS-sensing and target of rapamycin pathways under the grape juice-like, cysteine-supplemented, fermentation conditions. The findings highlight that cysteine transportation could be a limiting factor for yeast to generate H2S from cysteine, and therefore selecting wine yeasts without defects in cysteine uptake could maximise thiol production potential.
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Affiliation(s)
- Chien-Wei Huang
- Department of Wine and Food Science, University of Adelaide, Adelaide, SA 5064, Australia
| | - Michelle E Walker
- Department of Wine and Food Science, University of Adelaide, Adelaide, SA 5064, Australia
| | - Bruno Fedrizzi
- Wine Science Programme, School of Chemical Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Richard C Gardner
- Wine Science Programme, School of Biological Sciences, University of Auckland, Auckland 1142, New Zealand
| | - Vladimir Jiranek
- Department of Wine and Food Science, University of Adelaide, Adelaide, SA 5064, Australia
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27
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Sun C, Zhou B. The antimalarial drug artemisinin induces an additional, Sod1-supressible anti-mitochondrial action in yeast. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:1285-1294. [DOI: 10.1016/j.bbamcr.2017.04.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 04/21/2017] [Accepted: 04/24/2017] [Indexed: 12/01/2022]
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Jeyasingh PD, Goos JM, Thompson SK, Godwin CM, Cotner JB. Ecological Stoichiometry beyond Redfield: An Ionomic Perspective on Elemental Homeostasis. Front Microbiol 2017; 8:722. [PMID: 28487686 PMCID: PMC5403914 DOI: 10.3389/fmicb.2017.00722] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/07/2017] [Indexed: 11/13/2022] Open
Abstract
Elemental homeostasis has been largely characterized using three important elements that were part of the Redfield ratio (i.e., carbon: nitrogen: phosphorus). These efforts have revealed substantial diversity in homeostasis among taxonomic groups and even within populations. Understanding the evolutionary basis, and ecological consequences of such diversity is a central challenge. Here, we propose that a more complete understanding of homeostasis necessitates the consideration of other elements beyond C, N, and P. Specifically, we posit that physiological complexity underlying maintenance of elemental homeostasis along a single elemental axis impacts processing of other elements, thus altering elemental homeostasis along other axes. Indeed, transcriptomic studies in a wide variety of organisms have found that individuals differentially express significant proportions of the genome in response to variability in supply stoichiometry in order to maintain varying levels of homeostasis. We review the literature from the emergent field of ionomics that has established the consequences of such physiological trade-offs on the content of the entire suite of elements in an individual. Further, we present experimental data on bacteria exhibiting divergent phosphorus homeostasis phenotypes demonstrating the fundamental interconnectedness among elemental quotas. These observations suggest that physiological adjustments can lead to unexpected patterns in biomass stoichiometry, such as correlated changes among suites of non-limiting microelements in response to limitation by macroelements. Including the entire suite of elements that comprise biomass will foster improved quantitative understanding of the links between chemical cycles and the physiology of organisms.
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Affiliation(s)
- Punidan D Jeyasingh
- Department of Integrative Biology, Oklahoma State UniversityStillwater, OK, USA
| | - Jared M Goos
- Department of Biology, University of Texas at ArlingtonArlington, TX, USA
| | - Seth K Thompson
- Water Resources Science Program, University of MinnesotaSt. Paul, MN, USA
| | - Casey M Godwin
- School of Natural Resources and Environment, University of MichiganAnn Arbor, MI, USA
| | - James B Cotner
- Department of Ecology, Evolution, and Behavior, University of MinnesotaSt. Paul, MN, USA
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29
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Verhoeven MD, Lee M, Kamoen L, van den Broek M, Janssen DB, Daran JMG, van Maris AJA, Pronk JT. Mutations in PMR1 stimulate xylose isomerase activity and anaerobic growth on xylose of engineered Saccharomyces cerevisiae by influencing manganese homeostasis. Sci Rep 2017; 7:46155. [PMID: 28401919 PMCID: PMC5388867 DOI: 10.1038/srep46155] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 03/09/2017] [Indexed: 01/04/2023] Open
Abstract
Combined overexpression of xylulokinase, pentose-phosphate-pathway enzymes and a heterologous xylose isomerase (XI) is required but insufficient for anaerobic growth of Saccharomyces cerevisiae on d-xylose. Single-step Cas9-assisted implementation of these modifications yielded a yeast strain expressing Piromyces XI that showed fast aerobic growth on d-xylose. However, anaerobic growth required a 12-day adaptation period. Xylose-adapted cultures carried mutations in PMR1, encoding a Golgi Ca2+/Mn2+ ATPase. Deleting PMR1 in the parental XI-expressing strain enabled instantaneous anaerobic growth on d-xylose. In pmr1 strains, intracellular Mn2+ concentrations were much higher than in the parental strain. XI activity assays in cell extracts and reconstitution experiments with purified XI apoenzyme showed superior enzyme kinetics with Mn2+ relative to other divalent metal ions. This study indicates engineering of metal homeostasis as a relevant approach for optimization of metabolic pathways involving metal-dependent enzymes. Specifically, it identifies metal interactions of heterologous XIs as an underexplored aspect of engineering xylose metabolism in yeast.
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Affiliation(s)
- Maarten D Verhoeven
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Misun Lee
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Lycka Kamoen
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Dick B Janssen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Jean-Marc G Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Antonius J A van Maris
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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30
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The New Role for an Old Kinase: Protein Kinase CK2 Regulates Metal Ion Transport. Pharmaceuticals (Basel) 2016; 9:ph9040080. [PMID: 28009816 PMCID: PMC5198054 DOI: 10.3390/ph9040080] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 12/13/2016] [Accepted: 12/16/2016] [Indexed: 12/27/2022] Open
Abstract
The pleiotropic serine/threonine protein kinase CK2 was the first kinase discovered. It is renowned for its role in cell proliferation and anti-apoptosis. The complexity of this kinase is well reflected by the findings of past decades in terms of its heterotetrameric structure, subcellular location, constitutive activity and the extensive catalogue of substrates. With the advent of non-biased high-throughput functional genomics such as genome-wide deletion mutant screening, novel aspects of CK2 functionality have been revealed. Our recent discoveries using the model organism Saccharomyces cerevisiae and mammalian cells demonstrate that CK2 regulates metal toxicity. Extensive literature search reveals that there are few but elegant works on the role of CK2 in regulating the sodium and zinc channels. As both CK2 and metal ions are key players in cell biology and oncogenesis, understanding the details of CK2’s regulation of metal ion homeostasis has a direct bearing on cancer research. In this review, we aim to garner the recent data and gain insights into the role of CK2 in metal ion transport.
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31
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Navarro-Arias MJ, Defosse TA, Dementhon K, Csonka K, Mellado-Mojica E, Dias Valério A, González-Hernández RJ, Courdavault V, Clastre M, Hernández NV, Pérez-García LA, Singh DK, Vizler C, Gácser A, Almeida RS, Noël T, López MG, Papon N, Mora-Montes HM. Disruption of Protein Mannosylation Affects Candida guilliermondii Cell Wall, Immune Sensing, and Virulence. Front Microbiol 2016; 7:1951. [PMID: 27994582 PMCID: PMC5133257 DOI: 10.3389/fmicb.2016.01951] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 11/21/2016] [Indexed: 11/13/2022] Open
Abstract
The fungal cell wall contains glycoproteins that interact with the host immune system. In the prominent pathogenic yeast Candida albicans, Pmr1 acts as a Golgi-resident ion pump that provides cofactors to mannosyltransferases, regulating the synthesis of mannans attached to glycoproteins. To gain insight into a putative conservation of such a crucial process within opportunistic yeasts, we were particularly interested in studying the role of the PMR1 homolog in a low-virulent species that rarely causes candidiasis, Candida guilliermondii. We disrupted C. guilliermondii PMR1 and found that loss of Pmr1 affected cell growth and morphology, biofilm formation, susceptibility to cell wall perturbing agents, mannan levels, and the wall composition and organization. Despite the significant increment in the amount of β1,3-glucan exposed at the wall surface, this positively influenced only the ability of the mutant to stimulate IL-10 production by human monocytes, suggesting that recognition of both mannan and β1,3-glucan, is required to stimulate strong levels of pro-inflammatory cytokines. Accordingly, our results indicate C. guilliermondii sensing by monocytes was critically dependent on the recognition of N-linked mannans and β1,3-glucan, as reported in other Candida species. In addition, chemical remotion of cell wall O-linked mannans was found to positively influence the recognition of C. guilliermondii by human monocytes, suggesting that O-linked mannans mask other cell wall components from immune cells. This observation contrasts with that reported in C. albicans. Finally, mice infected with C. guilliermondii pmr1Δ null mutant cells had significantly lower fungal burdens compared to animals challenged with the parental strain. Accordingly, the null mutant showed inability to kill larvae in the Galleria mellonella infection model. This study thus demonstrates that mannans are relevant for the C. guilliermondii-host interaction, with an atypical role for O-linked mannans.
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Affiliation(s)
- María J Navarro-Arias
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato Guanajuato, Mexico
| | - Tatiana A Defosse
- Biomolécules et Biotechnologies Végétales, Université François-Rabelais de ToursTours, France; Groupe d'Etude des Interactions Hôte-Pathogène, Université d'AngersAngers, France
| | - Karine Dementhon
- Laboratoire de Microbiologie Fondamentale et Pathogénicité, Université Bordeaux 2, UMR-Centre National de la Recherche Scientifique 5234 Bordeaux, France
| | - Katalin Csonka
- Department of Microbiology, University of Szeged Szeged, Hungary
| | - Erika Mellado-Mojica
- Centro de Investigaciones y de Estudios Avanzados del Instituto Politécnico Nacional (IPN) Guanajuato, Mexico
| | - Aline Dias Valério
- Departamento de Microbiologia, Centro de Ciências Biológicas, Universidade Estadual de Londrina Londrina, Brazil
| | - Roberto J González-Hernández
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato Guanajuato, Mexico
| | - Vincent Courdavault
- Biomolécules et Biotechnologies Végétales, Université François-Rabelais de Tours Tours, France
| | - Marc Clastre
- Biomolécules et Biotechnologies Végétales, Université François-Rabelais de Tours Tours, France
| | - Nahúm V Hernández
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato Guanajuato, Mexico
| | - Luis A Pérez-García
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato Guanajuato, Mexico
| | | | - Csaba Vizler
- Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences Szeged, Hungary
| | - Attila Gácser
- Department of Microbiology, University of Szeged Szeged, Hungary
| | - Ricardo S Almeida
- Departamento de Microbiologia, Centro de Ciências Biológicas, Universidade Estadual de Londrina Londrina, Brazil
| | - Thierry Noël
- Laboratoire de Microbiologie Fondamentale et Pathogénicité, Université Bordeaux 2, UMR-Centre National de la Recherche Scientifique 5234 Bordeaux, France
| | - Mercedes G López
- Centro de Investigaciones y de Estudios Avanzados del Instituto Politécnico Nacional (IPN) Guanajuato, Mexico
| | - Nicolas Papon
- Groupe d'Etude des Interactions Hôte-Pathogène, Université d'Angers Angers, France
| | - Héctor M Mora-Montes
- División de Ciencias Naturales y Exactas, Departamento de Biología, Universidad de Guanajuato Guanajuato, Mexico
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32
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Huang XY, Salt DE. Plant Ionomics: From Elemental Profiling to Environmental Adaptation. MOLECULAR PLANT 2016; 9:787-97. [PMID: 27212388 DOI: 10.1016/j.molp.2016.05.003] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 05/12/2016] [Accepted: 05/16/2016] [Indexed: 05/03/2023]
Abstract
Ionomics is a high-throughput elemental profiling approach to study the molecular mechanistic basis underlying mineral nutrient and trace element composition (also known as the ionome) of living organisms. Since the concept of ionomics was first introduced more than 10 years ago, significant progress has been made in the identification of genes and gene networks that control the ionome. In this update, we summarize the progress made in using the ionomics approach over the last decade, including the identification of genes by forward genetics and the study of natural ionomic variation. We further discuss the potential application of ionomics to the investigation of the ecological functions of ionomic alleles in adaptation to the environment.
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Affiliation(s)
- Xin-Yuan Huang
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen AB24 3UU, UK
| | - David E Salt
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, St Machar Drive, Aberdeen AB24 3UU, UK.
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33
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Klukovich R, Courchesne WE. Functions of Saccharomyces cerevisiae Ecm27p, a putative Na+/Ca2+ exchanger, in calcium homeostasis, carbohydrate storage and cell cycle reentry from the quiescent phase. Microbiol Res 2016; 186-187:81-9. [DOI: 10.1016/j.micres.2016.03.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 03/25/2016] [Accepted: 03/31/2016] [Indexed: 01/13/2023]
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Slavic K, Krishna S, Lahree A, Bouyer G, Hanson KK, Vera I, Pittman JK, Staines HM, Mota MM. A vacuolar iron-transporter homologue acts as a detoxifier in Plasmodium. Nat Commun 2016; 7:10403. [PMID: 26786069 PMCID: PMC4735874 DOI: 10.1038/ncomms10403] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 12/07/2015] [Indexed: 01/03/2023] Open
Abstract
Iron is an essential micronutrient but is also highly toxic. In yeast and plant cells, a key detoxifying mechanism involves iron sequestration into intracellular storage compartments, mediated by members of the vacuolar iron-transporter (VIT) family of proteins. Here we study the VIT homologue from the malaria parasites Plasmodium falciparum (PfVIT) and Plasmodium berghei (PbVIT). PfVIT-mediated iron transport in a yeast heterologous expression system is saturable (Km ∼ 14.7 μM), and selective for Fe(2+) over other divalent cations. PbVIT-deficient P. berghei lines (Pbvit(-)) show a reduction in parasite load in both liver and blood stages of infection in mice. Moreover, Pbvit(-) parasites have higher levels of labile iron in blood stages and are more sensitive to increased iron levels in liver stages, when compared with wild-type parasites. Our data are consistent with Plasmodium VITs playing a major role in iron detoxification and, thus, normal development of malaria parasites in their mammalian host.
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Affiliation(s)
- Ksenija Slavic
- Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - Sanjeev Krishna
- Institute for Infection & Immunity, St. George's, University of London, London SW17 0RE, UK
| | - Aparajita Lahree
- Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - Guillaume Bouyer
- Institute for Infection & Immunity, St. George's, University of London, London SW17 0RE, UK
- Sorbonne Universités, UPMC Univ Paris 6, CNRS, UMR 8227, Comparative Physiology of Erythrocytes, Station Biologique de Roscoff, CS 90074, 29688 Roscoff, France
| | - Kirsten K. Hanson
- Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, 1649-028 Lisbon, Portugal
- Present address: University of Texas at San Antonio, Department of Biology and STCEID, San Antonio, Texas 78249, USA
| | - Iset Vera
- Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - Jon K. Pittman
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
| | - Henry M. Staines
- Institute for Infection & Immunity, St. George's, University of London, London SW17 0RE, UK
| | - Maria M. Mota
- Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, 1649-028 Lisbon, Portugal
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35
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Yenush L. Potassium and Sodium Transport in Yeast. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 892:187-228. [DOI: 10.1007/978-3-319-25304-6_8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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36
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Malinouski M, Hasan NM, Zhang Y, Seravalli J, Lin J, Avanesov A, Lutsenko S, Gladyshev VN. Genome-wide RNAi ionomics screen reveals new genes and regulation of human trace element metabolism. Nat Commun 2015; 5:3301. [PMID: 24522796 PMCID: PMC5578452 DOI: 10.1038/ncomms4301] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 01/23/2014] [Indexed: 11/09/2022] Open
Abstract
Trace elements are essential for human metabolism and dysregulation of their homoeostasis is associated with numerous disorders. Here we characterize mechanisms that regulate trace elements in human cells by designing and performing a genome-wide high-throughput siRNA/ionomics screen, and examining top hits in cellular and biochemical assays. The screen reveals high stability of the ionomes, especially the zinc ionome, and yields known regulators and novel candidates. We further uncover fundamental differences in the regulation of different trace elements. Specifically, selenium levels are controlled through the selenocysteine machinery and expression of abundant selenoproteins; copper balance is affected by lipid metabolism and requires machinery involved in protein trafficking and post-translational modifications; and the iron levels are influenced by iron import and expression of the iron/haeme-containing enzymes. Our approach can be applied to a variety of disease models and/or nutritional conditions, and the generated data set opens new directions for studies of human trace element metabolism.
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Affiliation(s)
- Mikalai Malinouski
- 1] Genetics Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA [2] Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - Nesrin M Hasan
- Department of Physiology, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Yan Zhang
- 1] Genetics Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA [2] Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Javier Seravalli
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - Jie Lin
- 1] Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China [2] Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Andrei Avanesov
- Genetics Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Svetlana Lutsenko
- Department of Physiology, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Vadim N Gladyshev
- Genetics Division, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
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37
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Baxter I. Should we treat the ionome as a combination of individual elements, or should we be deriving novel combined traits? JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2127-31. [PMID: 25711709 PMCID: PMC4986723 DOI: 10.1093/jxb/erv040] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 12/12/2014] [Accepted: 01/12/2015] [Indexed: 05/18/2023]
Abstract
It has been more than 10 years since the concept of the ionome, all of the mineral nutrients in a cell tissue or organism, was introduced. In the intervening years, ionomics, high throughput elemental profiling, has been used to analyse over 400,000 samples from at least 10 different organisms. There are now multiple published examples where an ionomics approach has been used to find genes of novel function, find lines or environments that produce foods with altered nutritional profiles, or define gene by environmental effects on elemental accumulation. In almost all of these studies, the ionome has been treated as a collection of independent elements, with the analysis repeated on each measured element. However, many elements share chemical properties, are known to interact with each other, or have been shown to have similar interactions with biological molecules. Accordingly, there is strong evidence from ionomic studies that the elements of the ionome do not behave independently and that combinations of elements should be treated as the phenotypes of interest. In this review, I will consider the evidence that we have for the interdependence of the ionome, some of its causes, methods for incorporating this interdependence into analyses and the benefits, drawbacks, and challenges of taking these approaches.
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Affiliation(s)
- Ivan Baxter
- United States Department of Agriculture-Agricultural Research Service Plant Genetics Research Unit, Donald Danforth Plant Science Center, St Louis, MO 63132, USA
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Schuldiner M, Zalckvar E. Peroxisystem: Harnessing systems cell biology to study peroxisomes. Biol Cell 2015; 107:89-97. [DOI: 10.1111/boc.201400091] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 01/05/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Maya Schuldiner
- Department of Molecular Genetics; Weizmann Institute of Science; Rehovot 7610001 Israel
| | - Einat Zalckvar
- Department of Molecular Genetics; Weizmann Institute of Science; Rehovot 7610001 Israel
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Yoshida S, Date Y, Akama M, Kikuchi J. Comparative metabolomic and ionomic approach for abundant fishes in estuarine environments of Japan. Sci Rep 2014; 4:7005. [PMID: 25387575 PMCID: PMC4228347 DOI: 10.1038/srep07005] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 09/17/2014] [Indexed: 12/23/2022] Open
Abstract
Environmental metabolomics or ionomics is widely used to characterize the effects of environmental stressors on the health of aquatic organisms. However, most studies have focused on liver and muscle tissues of fish, and little is known about how the other organs are affected by environmental perturbations and effects such as metal pollutants or eutrophication. We examined the metabolic and mineral profiles of three kinds of abundant fishes in estuarine ecosystem, yellowfin goby, urohaze-goby, and juvenile Japanese seabass sampled from Tsurumi River estuary, Japan. Multivariate analyses, including nuclear magnetic resonance-based metabolomics and inductively coupled plasma optical emission spectrometry-based ionomics approaches, revealed that the profiles were clustered according to differences among body tissues rather than differences in body size, sex, and species. The metabolic and mineral profiles of the muscle and fin tissues, respectively, suggest that these tissues are most appropriate for evaluating environmental perturbations. Such analyses will be highly useful in evaluating the environmental variation and diversity in aquatic ecosystems.
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Affiliation(s)
- Seiji Yoshida
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yasuhiro Date
- 1] Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan [2] RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Makiko Akama
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Jun Kikuchi
- 1] Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan [2] RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan [3] RIKEN Biomass Engineering Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan [4] Graduate School of Bioagricultural Sciences, Nagoya University, 1 Furo-cho, Chikusa-ku, Nagoya, Aichi 464-0810, Japan
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Jones AM, Grossmann G, Danielson JÅ, Sosso D, Chen LQ, Ho CH, Frommer WB. In vivo biochemistry: applications for small molecule biosensors in plant biology. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:389-95. [PMID: 23587939 PMCID: PMC3679211 DOI: 10.1016/j.pbi.2013.02.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 02/22/2013] [Accepted: 02/22/2013] [Indexed: 05/02/2023]
Abstract
Revolutionary new technologies, namely in the areas of DNA sequencing and molecular imaging, continue to impact new discoveries in plant science and beyond. For decades we have been able to determine properties of enzymes, receptors and transporters in vitro or in heterologous systems, and more recently been able to analyze their regulation at the transcriptional level, to use GFP reporters for obtaining insights into cellular and subcellular localization, and tp measure ion and metabolite levels with unprecedented precision using mass spectrometry. However, we lack key information on the location and dynamics of the substrates of enzymes, receptors and transporters, and on the regulation of these proteins in their cellular environment. Such information can now be obtained by transitioning from in vitro to in vivo biochemistry using biosensors. Genetically encoded fluorescent protein-based sensors for ion and metabolite dynamics provide highly resolved spatial and temporal information, and are complemented by sensors for pH, redox, voltage, and tension. They serve as powerful tools for identifying missing processes (e.g., glucose transport across ER membranes), components (e.g., SWEET sugar transporters for cellular sugar efflux), and signaling networks (e.g., from systematic screening of mutants that affect sugar transport or cytosolic and vacuolar pH). Combined with the knowledge of properties of enzymes and transporters and their interactions with the regulatory machinery, biosensors promise to be key diagnostic tools for systems and synthetic biology.
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Affiliation(s)
- Alexander M Jones
- Carnegie Institution for Science, Department of Plant Biology, 260 Panama St., Stanford, CA 94305, USA
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