1
|
Kostenko A, Zuffa S, Zhi H, Mildau K, Raffatellu M, Dorrestein PC, Aron AT. Dietary iron intake has long-term effects on the fecal metabolome and microbiome. Metallomics 2024; 16:mfae033. [PMID: 38992131 PMCID: PMC11272056 DOI: 10.1093/mtomcs/mfae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 07/10/2024] [Indexed: 07/13/2024]
Abstract
Iron is essential for life, but its imbalances can lead to severe health implications. Iron deficiency is the most common nutrient disorder worldwide, and iron dysregulation in early life has been found to cause long-lasting behavioral, cognitive, and neural effects. However, little is known about the effects of dietary iron on gut microbiome function and metabolism. In this study, we sought to investigate the impact of dietary iron on the fecal metabolome and microbiome by using mice fed with three diets with different iron content: an iron deficient, an iron sufficient (standard), and an iron overload diet for 7 weeks. Additionally, we sought to understand whether any observed changes would persist past the 7-week period of diet intervention. To assess this, all feeding groups were switched to a standard diet, and this feeding continued for an additional 7 weeks. Analysis of the fecal metabolome revealed that iron overload and deficiency significantly alter levels of peptides, nucleic acids, and lipids, including di- and tri-peptides containing branched-chain amino acids, inosine and guanosine, and several microbial conjugated bile acids. The observed changes in the fecal metabolome persist long after the switch back to a standard diet, with the cecal gut microbiota composition and function of each group distinct after the 7-week standard diet wash-out. Our results highlight the enduring metabolic consequences of nutritional imbalances, mediated by both the host and gut microbiome, which persist after returning to the original standard diets.
Collapse
Affiliation(s)
- Anastasiia Kostenko
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, USA
| | - Simone Zuffa
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Hui Zhi
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Kevin Mildau
- Department of Analytical Chemistry, University of Vienna, Vienna, Austria
- Bioinformatics Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Manuela Raffatellu
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Chiba University, UC San Diego Center for Mucosal Immunology, Allergy, and Vaccines (CU-UCSD cMAV), La Jolla, CA, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Allegra T Aron
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO, USA
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, San Diego, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| |
Collapse
|
2
|
Lill R, Hoffmann B, Molik S, Pierik AJ, Rietzschel N, Stehling O, Uzarska MA, Webert H, Wilbrecht C, Mühlenhoff U. The role of mitochondria in cellular iron-sulfur protein biogenesis and iron metabolism. BIOCHIMICA ET BIOPHYSICA ACTA 2012; 1823:1491-508. [PMID: 22609301 DOI: 10.1016/j.bbamcr.2012.05.009] [Citation(s) in RCA: 360] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 05/07/2012] [Accepted: 05/09/2012] [Indexed: 12/21/2022]
Abstract
Mitochondria play a key role in iron metabolism in that they synthesize heme, assemble iron-sulfur (Fe/S) proteins, and participate in cellular iron regulation. Here, we review the latter two topics and their intimate connection. The mitochondrial Fe/S cluster (ISC) assembly machinery consists of 17 proteins that operate in three major steps of the maturation process. First, the cysteine desulfurase complex Nfs1-Isd11 as the sulfur donor cooperates with ferredoxin-ferredoxin reductase acting as an electron transfer chain, and frataxin to synthesize an [2Fe-2S] cluster on the scaffold protein Isu1. Second, the cluster is released from Isu1 and transferred toward apoproteins with the help of a dedicated Hsp70 chaperone system and the glutaredoxin Grx5. Finally, various specialized ISC components assist in the generation of [4Fe-4S] clusters and cluster insertion into specific target apoproteins. Functional defects of the core ISC assembly machinery are signaled to cytosolic or nuclear iron regulatory systems resulting in increased cellular iron acquisition and mitochondrial iron accumulation. In fungi, regulation is achieved by iron-responsive transcription factors controlling the expression of genes involved in iron uptake and intracellular distribution. They are assisted by cytosolic multidomain glutaredoxins which use a bound Fe/S cluster as iron sensor and additionally perform an essential role in intracellular iron delivery to target metalloproteins. In mammalian cells, the iron regulatory proteins IRP1, an Fe/S protein, and IRP2 act in a post-transcriptional fashion to adjust the cellular needs for iron. Thus, Fe/S protein biogenesis and cellular iron metabolism are tightly linked to coordinate iron supply and utilization. This article is part of a Special Issue entitled: Cell Biology of Metals.
Collapse
Affiliation(s)
- Roland Lill
- Institut für Zytobiologie und Zytopathologie, Philipps-Universität Marburg, Robert-Koch Str. 6, 35033 Marburg, Germany.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
3
|
Vindry C, Lauwers A, Hutin D, Soin R, Wauquier C, Kruys V, Gueydan C. dTIS11 Protein-dependent polysomal deadenylation is the key step in AU-rich element-mediated mRNA decay in Drosophila cells. J Biol Chem 2012; 287:35527-35538. [PMID: 22932903 DOI: 10.1074/jbc.m112.356188] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The destabilization of AU-rich element (ARE)-containing mRNAs mediated by proteins of the TIS11 family is conserved among eukaryotes including Drosophila. Previous studies have demonstrated that Tristetraprolin, a human protein of the TIS11 family, induces the degradation of ARE-containing mRNAs through a large variety of mechanisms including deadenylation, decapping, and P-body targeting. We have previously shown that the degradation of the mRNA encoding the antimicrobial peptide Cecropin A1 (CecA1) is controlled by the TIS11 protein (dTIS11) in Drosophila cells. In this study, we used CecA1 mRNA as a model to investigate the molecular mechanism of dTIS11-mediated mRNA decay. We observed that during the biphasic deadenylation and decay process of this mRNA, dTIS11 enhances deadenylation performed by the CCR4-CAF-NOT complex while the mRNA is still associated with ribosomes. Sequencing of mRNA degradation intermediates revealed that the complete deadenylation of the mRNA triggers its decapping and decay in both the 5'-3' and the 3'-5' directions. Contrary to the observations made for its mammalian homologs, overexpression of dTIS11 does not promote the localization of ARE-containing mRNAs in P-bodies but rather decreases the accumulation of CecA1 mRNA in these structures by enhancing the degradation process. Therefore, our results suggest that proteins of the TIS11 family may have acquired additional functions in the course of evolution from invertebrates to mammals.
Collapse
Affiliation(s)
- Caroline Vindry
- Laboratoire de Biologie Moléculaire du Gène, Université Libre de Bruxelles, 12 rue Pr. Jeener et Brachet, 6041 Gosselies, Belgium
| | - Aurélien Lauwers
- Laboratoire de Biologie Moléculaire du Gène, Université Libre de Bruxelles, 12 rue Pr. Jeener et Brachet, 6041 Gosselies, Belgium
| | - David Hutin
- Laboratoire d'Immunobiologie, Université Libre de Bruxelles, 12 rue Pr. Jeener et Brachet, 6041 Gosselies, Belgium
| | - Romuald Soin
- Laboratoire de Biologie Moléculaire du Gène, Université Libre de Bruxelles, 12 rue Pr. Jeener et Brachet, 6041 Gosselies, Belgium
| | - Corinne Wauquier
- Laboratoire de Biologie Moléculaire du Gène, Université Libre de Bruxelles, 12 rue Pr. Jeener et Brachet, 6041 Gosselies, Belgium
| | - Véronique Kruys
- Laboratoire de Biologie Moléculaire du Gène, Université Libre de Bruxelles, 12 rue Pr. Jeener et Brachet, 6041 Gosselies, Belgium; Center for Microscopy and Molecular Imaging, Faculté des Sciences, Université Libre de Bruxelles, 12 rue Pr. Jeener et Brachet, 6041 Gosselies, Belgium
| | - Cyril Gueydan
- Laboratoire de Biologie Moléculaire du Gène, Université Libre de Bruxelles, 12 rue Pr. Jeener et Brachet, 6041 Gosselies, Belgium.
| |
Collapse
|
4
|
Canessa P, Muñoz-Guzmán F, Vicuña R, Larrondo LF. Characterization of PIR1, a GATA family transcription factor involved in iron responses in the white-rot fungus Phanerochaete chrysosporium. Fungal Genet Biol 2012; 49:626-34. [DOI: 10.1016/j.fgb.2012.05.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 05/16/2012] [Accepted: 05/26/2012] [Indexed: 01/19/2023]
|
5
|
Sanvisens N, Bañó MC, Huang M, Puig S. Regulation of ribonucleotide reductase in response to iron deficiency. Mol Cell 2012; 44:759-69. [PMID: 22152479 DOI: 10.1016/j.molcel.2011.09.021] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 08/09/2011] [Accepted: 09/10/2011] [Indexed: 11/17/2022]
Abstract
Ribonucleotide reductase (RNR) is an essential enzyme required for DNA synthesis and repair. Although iron is necessary for class Ia RNR activity, little is known about the mechanisms that control RNR in response to iron deficiency. In this work, we demonstrate that yeast cells control RNR function during iron deficiency by redistributing the Rnr2-Rnr4 small subunit from the nucleus to the cytoplasm. Our data support a Mec1/Rad53-independent mechanism in which the iron-regulated Cth1/Cth2 mRNA-binding proteins specifically interact with the WTM1 mRNA in response to iron scarcity and promote its degradation. The resulting decrease in the nuclear-anchoring Wtm1 protein levels leads to the redistribution of the Rnr2-Rnr4 heterodimer to the cytoplasm, where it assembles as an active RNR complex and increases deoxyribonucleoside triphosphate levels. When iron is scarce, yeast selectively optimizes RNR function at the expense of other non-essential iron-dependent processes that are repressed, to allow DNA synthesis and repair.
Collapse
Affiliation(s)
- Nerea Sanvisens
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas, Burjassot, Valencia 46100, Spain
| | | | | | | |
Collapse
|
6
|
Merchant SS, Helmann JD. Elemental economy: microbial strategies for optimizing growth in the face of nutrient limitation. Adv Microb Physiol 2012; 60:91-210. [PMID: 22633059 PMCID: PMC4100946 DOI: 10.1016/b978-0-12-398264-3.00002-4] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Microorganisms play a dominant role in the biogeochemical cycling of nutrients. They are rightly praised for their facility for fixing both carbon and nitrogen into organic matter, and microbial driven processes have tangibly altered the chemical composition of the biosphere and its surrounding atmosphere. Despite their prodigious capacity for molecular transformations, microorganisms are powerless in the face of the immutability of the elements. Limitations for specific elements, either fleeting or persisting over eons, have left an indelible trace on microbial genomes, physiology, and their very atomic composition. We here review the impact of elemental limitation on microbes, with a focus on selected genetic model systems and representative microbes from the ocean ecosystem. Evolutionary adaptations that enhance growth in the face of persistent or recurrent elemental limitations are evident from genome and proteome analyses. These range from the extreme (such as dispensing with a requirement for a hard to obtain element) to the extremely subtle (changes in protein amino acid sequences that slightly, but significantly, reduce cellular carbon, nitrogen, or sulfur demand). One near-universal adaptation is the development of sophisticated acclimation programs by which cells adjust their chemical composition in response to a changing environment. When specific elements become limiting, acclimation typically begins with an increased commitment to acquisition and a concomitant mobilization of stored resources. If elemental limitation persists, the cell implements austerity measures including elemental sparing and elemental recycling. Insights into these fundamental cellular properties have emerged from studies at many different levels, including ecology, biological oceanography, biogeochemistry, molecular genetics, genomics, and microbial physiology. Here, we present a synthesis of these diverse studies and attempt to discern some overarching themes.
Collapse
Affiliation(s)
- Sabeeha S. Merchant
- Institute for Genomics and Proteomics and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
| | - John D. Helmann
- Department of Microbiology, Cornell University, Ithaca, NY, 14853-8101
| |
Collapse
|
7
|
Salvail H, Massé E. Regulating iron storage and metabolism with RNA: an overview of posttranscriptional controls of intracellular iron homeostasis. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:26-36. [PMID: 21793218 DOI: 10.1002/wrna.102] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Iron (Fe) is a double-edged sword for most living organisms. Although it is essential for the catalytic activity of a large number of enzymes, ferrous iron (Fe(2+) ) becomes cytotoxic in the presence of normal respiratory by-products such as H(2) O(2) . Because of this toxicity, intracellular iron concentrations ought to be regulated by elaborated homeostasis systems that, despite decades of extensive studies, have not yet revealed all of their surprising arrays of mechanistic details. Within the last few years, our understanding of iron metabolism has revealed that posttranscriptional regulation represents a major contribution to iron homeostasis in a host of organisms. While the small RNA RyhB regulates iron homeostasis in bacteria, its functional homolog protein Cth2 performs a similar task in yeasts. Recent advances in the elucidation of the mechanism of action and functions of RyhB have been made in Escherichia coli. In addition, other RyhB-like small RNAs have been identified in several bacterial species, such as Pseudomonas aeruginosa, Salmonella enterica, Vibrio cholerae, Neisseria meningitidis, and Shigella spp. These recent findings have shed light on the complexity of iron homeostasis.
Collapse
Affiliation(s)
- Hubert Salvail
- RNA Group, Department of Biochemistry, University of Sherbrooke, Sherbrooke, Québec, Canada
| | | |
Collapse
|
8
|
Nevitt T. War-Fe-re: iron at the core of fungal virulence and host immunity. Biometals 2011; 24:547-58. [PMID: 21399939 DOI: 10.1007/s10534-011-9431-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Accepted: 02/22/2011] [Indexed: 12/21/2022]
Abstract
Iron acquisition is a bona fide virulence determinant. The successful colonization of the mammalian host requires that microorganisms overcome the Fe aridity of this milieu in which the levels of circulating Fe are maintained exceedingly low both through the compartmentalization of this nutrient within cells as well as the tight binding of Fe to host circulating proteins and ligands. Microbes notoriously employ multiple strategies for high affinity Fe acquisition from the host that rely either on the expression of receptors for host Fe-binding proteins and ligands, its reduction by cell surface reductases or the utilization of siderophores, small organic molecules with very high affinity for Fe(3+). This review will discuss the multiple mechanisms deployed by fungal pathogens in Fe acquisition focusing on the role of siderophore utilization in virulence as well as host immune strategies of iron withholding and emerging clinical evidence that human disorders of Fe homeostasis can act as modifiers of infectious disease.
Collapse
Affiliation(s)
- Tracy Nevitt
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27710, USA.
| |
Collapse
|
9
|
Early recruitment of AU-rich element-containing mRNAs determines their cytosolic fate during iron deficiency. Mol Cell Biol 2010; 31:417-29. [PMID: 21135132 DOI: 10.1128/mcb.00754-10] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The yeast Cth2 protein is a CX(8)CX(5)CX(3)H tandem zinc finger protein that binds AU-rich element (ARE)-containing transcripts to enhance their decay in response to iron (Fe) deficiency. Mammalian members of this family of proteins are known to undergo nucleocytoplasmic shuttling, but little is known about the role of shuttling in the mechanism of ARE-dependent mRNA decay. Here we demonstrate that, like its mammalian homologues, Cth2 is a nucleocytoplasmic shuttling protein whose nuclear export depends on mRNA transport to the cytosol. The nuclear import information of Cth2 is contained within its tandem zinc finger domain, but it is independent of mRNA-binding function. Moreover, we also demonstrate that nucleocytoplasmic shuttling of Cth2 requires active transcription and that disruption of shuttling leads to defects in Cth2 function in mRNA decay under Fe deficiency. Taken together, our data suggest that under conditions of Fe deficiency Cth2 travels into the nucleus to recruit target mRNAs, perhaps cotranscriptionally, that are destined for cytosolic degradation as part of the mechanism of adaptation to growth under Fe limitation. These data also suggest an important role for nucleocytoplasmic shuttling in this conserved family of proteins in the mechanism of ARE-mediated mRNA decay.
Collapse
|
10
|
Mühlenhoff U, Molik S, Godoy JR, Uzarska MA, Richter N, Seubert A, Zhang Y, Stubbe J, Pierrel F, Herrero E, Lillig CH, Lill R. Cytosolic monothiol glutaredoxins function in intracellular iron sensing and trafficking via their bound iron-sulfur cluster. Cell Metab 2010; 12:373-385. [PMID: 20889129 PMCID: PMC4714545 DOI: 10.1016/j.cmet.2010.08.001] [Citation(s) in RCA: 220] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Revised: 05/06/2010] [Accepted: 06/16/2010] [Indexed: 11/18/2022]
Abstract
Iron is an essential nutrient for cells. It is unknown how iron, after its import into the cytosol, is specifically delivered to iron-dependent processes in various cellular compartments. Here, we identify an essential function of the conserved cytosolic monothiol glutaredoxins Grx3 and Grx4 in intracellular iron trafficking and sensing. Depletion of Grx3/4 specifically impaired all iron-requiring reactions in the cytosol, mitochondria, and nucleus, including the synthesis of Fe/S clusters, heme, and di-iron centers. These defects were caused by impairment of iron insertion into proteins and iron transfer to mitochondria, indicating that intracellular iron is not bioavailable, despite highly elevated cytosolic levels. The crucial task of Grx3/4 is mediated by a bridging, glutathione-containing Fe/S center that functions both as an iron sensor and in intracellular iron delivery. Collectively, our study uncovers an important role of monothiol glutaredoxins in cellular iron metabolism, with a surprising connection to cellular redox and sulfur metabolisms.
Collapse
Affiliation(s)
- Ulrich Mühlenhoff
- Institut für Zytobiologie und Zytopathologie, 35032 Marburg, Germany
| | - Sabine Molik
- Institut für Zytobiologie und Zytopathologie, 35032 Marburg, Germany
| | - José R Godoy
- Institut für Zytobiologie und Zytopathologie, 35032 Marburg, Germany
| | - Marta A Uzarska
- Institut für Zytobiologie und Zytopathologie, 35032 Marburg, Germany
| | - Nadine Richter
- Institut für Zytobiologie und Zytopathologie, 35032 Marburg, Germany
| | - Andreas Seubert
- Fachbereich Chemie, Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Yan Zhang
- Chemistry Department, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - JoAnne Stubbe
- Chemistry Department, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Fabien Pierrel
- Laboratoire de Chimie et Biologie des Métaux, CEA Grenoble, 38054 Grenoble Cedex 9, France
| | - Enrique Herrero
- Departament de Ciències Mèdiques Bàsiques, IRB Lleida, Universitat de Lleida, Lleida 25198, Spain
| | | | - Roland Lill
- Institut für Zytobiologie und Zytopathologie, 35032 Marburg, Germany.
| |
Collapse
|
11
|
Vega VL, Charles W, De Maio A. A new feature of the stress response: increase in endocytosis mediated by Hsp70. Cell Stress Chaperones 2010; 15:517-27. [PMID: 20043217 PMCID: PMC3006637 DOI: 10.1007/s12192-009-0165-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Revised: 11/19/2009] [Accepted: 11/23/2009] [Indexed: 11/26/2022] Open
Abstract
The expression of heat shock proteins (HSP) is a conserved cellular response to a variety of stresses. These proteins have been found to refold denatured polypeptides and stabilize critical cellular processes. In this study, we introduce a new component of the stress response: the increase of receptor-mediated uptake of macromolecules from the external environment. We observed that endocytosis of transferrin, which is involved in the delivery of iron to the cell, was increased after stress induced by heat shock or after incubation with inhibitors of Hsp90 function. In both cases, the increase in endocytosis was reverted by inhibition of transcription, suggesting that gene expression is required. Transfection of cells with Hsp70 gene or inhibition of its expression by siRNA confirmed the role of this HSP in the increase of endocytosis. The mechanism for the enhancement of transferrin uptake was related to an accelerated internalization of the ligand-receptor complex as well as an increase in receptor recycling. These observations constitute a new paradigm for the cellular protection induced by HSP.
Collapse
Affiliation(s)
- Virginia L. Vega
- UCSD Department of Surgery, University of California San Diego, 9500 Gilman Drive, 0739, La Jolla, CA 92093-0739 USA
| | - Wisler Charles
- UCSD Department of Surgery, University of California San Diego, 9500 Gilman Drive, 0739, La Jolla, CA 92093-0739 USA
| | - Antonio De Maio
- UCSD Department of Surgery, University of California San Diego, 9500 Gilman Drive, 0739, La Jolla, CA 92093-0739 USA
| |
Collapse
|
12
|
Gutteridge A, Pir P, Castrillo JI, Charles PD, Lilley KS, Oliver SG. Nutrient control of eukaryote cell growth: a systems biology study in yeast. BMC Biol 2010; 8:68. [PMID: 20497545 PMCID: PMC2895586 DOI: 10.1186/1741-7007-8-68] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 05/24/2010] [Indexed: 01/21/2023] Open
Abstract
Background To elucidate the biological processes affected by changes in growth rate and nutrient availability, we have performed a comprehensive analysis of the transcriptome, proteome and metabolome responses of chemostat cultures of the yeast, Saccharomyces cerevisiae, growing at a range of growth rates and in four different nutrient-limiting conditions. Results We find significant changes in expression for many genes in each of the four nutrient-limited conditions tested. We also observe several processes that respond differently to changes in growth rate and are specific to each nutrient-limiting condition. These include carbohydrate storage, mitochondrial function, ribosome synthesis, and phosphate transport. Integrating transcriptome data with proteome measurements allows us to identify previously unrecognized examples of post-transcriptional regulation in response to both nutrient and growth-rate signals. Conclusions Our results emphasize the unique properties of carbon metabolism and the carbon substrate, the limitation of which induces significant changes in gene regulation at the transcriptional and post-transcriptional level, as well as altering how many genes respond to growth rate. By comparison, the responses to growth limitation by other nutrients involve a smaller set of genes that participate in specific pathways. See associated commentary http://www.biomedcentral.com/1741-7007/8/62
Collapse
Affiliation(s)
- Alex Gutteridge
- Cambridge Systems Biology Centre & Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | | | | | | | | | | |
Collapse
|
13
|
Smith DP, Kitner JB, Norbeck AD, Clauss TR, Lipton MS, Schwalbach MS, Steindler L, Nicora CD, Smith RD, Giovannoni SJ. Transcriptional and translational regulatory responses to iron limitation in the globally distributed marine bacterium Candidatus pelagibacter ubique. PLoS One 2010; 5:e10487. [PMID: 20463970 PMCID: PMC2864753 DOI: 10.1371/journal.pone.0010487] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 04/11/2010] [Indexed: 11/19/2022] Open
Abstract
Iron is recognized as an important micronutrient that limits microbial plankton productivity over vast regions of the oceans. We investigated the gene expression responses of Candidatus Pelagibacter ubique cultures to iron limitation in natural seawater media supplemented with a siderophore to chelate iron. Microarray data indicated transcription of the periplasmic iron binding protein sfuC increased by 16-fold, and iron transporter subunits, iron-sulfur center assembly genes, and the putative ferroxidase rubrerythrin transcripts increased to a lesser extent. Quantitative peptide mass spectrometry revealed that sfuC protein abundance increased 27-fold, despite an average decrease of 59% across the global proteome. Thus, we propose sfuC as a marker gene for indicating iron limitation in marine metatranscriptomic and metaproteomic ecological surveys. The marked proteome reduction was not directly correlated to changes in the transcriptome, implicating post-transcriptional regulatory mechanisms as modulators of protein expression. Two RNA-binding proteins, CspE and CspL, correlated well with iron availability, suggesting that they may contribute to the observed differences between the transcriptome and proteome. We propose a model in which the RNA-binding activity of CspE and CspL selectively enables protein synthesis of the iron acquisition protein SfuC during transient growth-limiting episodes of iron scarcity.
Collapse
Affiliation(s)
- Daniel P. Smith
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America
| | - Joshua B. Kitner
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
| | - Angela D. Norbeck
- Biological and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Therese R. Clauss
- Biological and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Mary S. Lipton
- Biological and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Michael S. Schwalbach
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
| | - Laura Steindler
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
| | - Carrie D. Nicora
- Biological and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Richard D. Smith
- Biological and Computational Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Stephen J. Giovannoni
- Department of Microbiology, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
| |
Collapse
|
14
|
Iron regulation through the back door: iron-dependent metabolite levels contribute to transcriptional adaptation to iron deprivation in Saccharomyces cerevisiae. EUKARYOTIC CELL 2009; 9:460-71. [PMID: 20008079 DOI: 10.1128/ec.00213-09] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Budding yeast (Saccharomyces cerevisiae) responds to iron deprivation both by Aft1-Aft2-dependent transcriptional activation of genes involved in cellular iron uptake and by Cth1-Cth2-specific degradation of certain mRNAs coding for iron-dependent biosynthetic components. Here, we provide evidence for a novel principle of iron-responsive gene expression. This regulatory mechanism is based on the modulation of transcription through the iron-dependent variation of levels of regulatory metabolites. As an example, the LEU1 gene of branched-chain amino acid biosynthesis is downregulated under iron-limiting conditions through depletion of the metabolic intermediate alpha-isopropylmalate, which functions as a key transcriptional coactivator of the Leu3 transcription factor. Synthesis of alpha-isopropylmalate involves the iron-sulfur protein Ilv3, which is inactivated under iron deficiency. As another example, decreased mRNA levels of the cytochrome c-encoding CYC1 gene under iron-limiting conditions involve heme-dependent transcriptional regulation via the Hap1 transcription factor. Synthesis of the iron-containing heme is directly correlated with iron availability. Thus, the iron-responsive expression of genes that are downregulated under iron-limiting conditions is conferred by two independent regulatory mechanisms: transcriptional regulation through iron-responsive metabolites and posttranscriptional mRNA degradation. Only the combination of the two processes provides a quantitative description of the response to iron deprivation in yeast.
Collapse
|
15
|
Current awareness on yeast. Yeast 2009. [DOI: 10.1002/yea.1619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
|