دورية أكاديمية
Analyzing Iron and Oxygen-Regulated Protein Complex Formation Using Proteomic Mass Spectrometry.
| العنوان: | Analyzing Iron and Oxygen-Regulated Protein Complex Formation Using Proteomic Mass Spectrometry. |
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| المؤلفون: | Pandey V; Department of Biological Chemistry, David Geffen School of Medicine, University of California - Los Angeles, Los Angeles, CA, USA., Mayank AK; Department of Biological Chemistry, David Geffen School of Medicine, University of California - Los Angeles, Los Angeles, CA, USA., Wohlschlegel JA; Department of Biological Chemistry, David Geffen School of Medicine, University of California - Los Angeles, Los Angeles, CA, USA. jwohl@mednet.ucla.edu. |
| المصدر: | Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2023; Vol. 2648, pp. 155-166. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Humana Press Country of Publication: United States NLM ID: 9214969 Publication Model: Print Cited Medium: Internet ISSN: 1940-6029 (Electronic) Linking ISSN: 10643745 NLM ISO Abbreviation: Methods Mol Biol Subsets: MEDLINE |
| أسماء مطبوعة: | Publication: Totowa, NJ : Humana Press Original Publication: Clifton, N.J. : Humana Press, |
| مواضيع طبية MeSH: | Iron*/metabolism , Oxygen*/metabolism, Animals ; Proteomics ; Hypoxia/metabolism ; Mass Spectrometry ; Mammals/metabolism |
| مستخلص: | Multicellular organisms have evolved elaborate strategies to sense and adapt to changes in intracellular oxygen. The canonical cellular pathway responsible for oxygen sensing consists of the von Hippel-Lindau (pVHL) tumor suppressor protein, prolyl hydroxylases (PHD), and hypoxia-inducible factors (HIFs), which together regulate expression of downstream genes involved in oxygen homeostasis. In recent years, it has become increasingly clear that oxygen regulatory mechanisms are intertwined with cellular iron-sensing pathways. Key members of these networks such as prolyl-hydroxylases, E3 ubiquitin ligase adaptor protein FBXL5, iron regulatory proteins (IRPs), and Fe-S cluster proteins require both iron and oxygen for their optimal function and/or are tightly regulated by intracellular concentrations of these molecules. Monitoring how protein interactomes are remodeled as a function of intracellular oxygen and iron levels gives insights into the nature and dynamics of these pathways. We have recently described an oxygen-sensitive interaction between FBXL5 and the cytoplasmic Fe-S cluster targeting complex (CIA targeting complex) with implications in the FBXL5-dependent regulation of IRPs. Based on this work, we present a protocol describing the induction and maintenance of hypoxia in mammalian cell cultures and a mass-spectrometry-based proteomics approach aimed at interrogating changes in interactome of key proteins as a function of intracellular oxygen and iron levels. These methods are widely applicable to understanding the dynamics of iron and oxygen signaling. (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.) |
| References: | Samanta D, Prabhakar NR, Semenza GL (2017) Systems biology of oxygen homeostasis. Wiley Interdiscip Rev Syst Biol Med 9(4). https://doi.org/10.1002/wsbm.1382. Maxwell PH, Wiesener MS, Chang GW, Clifford SC, Vaux EC, Cockman ME, Wykoff CC, Pugh CW, Maher ER, Ratcliffe PJ (1999) The tumour suppressor protein VHL targets hypoxia-inducible factors for oxygen-dependent proteolysis. Nature 399(6733):271–275. (PMID: 10.1038/2045910353251) Wang GL, Semenza GL (1993) General involvement of hypoxia-inducible factor 1 in transcriptional response to hypoxia. Proc Natl Acad Sci U S A 90(9):4304–4308. (PMID: 10.1073/pnas.90.9.4304838721446495) Kaelin WG Jr, Ratcliffe PJ (2008) Oxygen sensing by metazoans: the central role of the HIF hydroxylase pathway. Mol Cell 30(4):393–402. (PMID: 10.1016/j.molcel.2008.04.00918498744) Wilson JW, Shakir D, Batie M, Frost M, Rocha S (2020) Oxygen-sensing mechanisms in cells. FEBS J 287:3888–3906. (PMID: 10.1111/febs.1537432446269) Vashisht AA, Zumbrennen KB, Huang X, Powers DN, Durazo A, Sun D, Bhaskaran N, Persson A, Uhlen M, Sangfelt O, Spruck C, Leibold EA, Wohlschlegel JA (2009) Control of iron homeostasis by an iron-regulated ubiquitin ligase. Science 326(5953):718–721. (PMID: 10.1126/science.1176333197625962929180) Salahudeen AA, Thompson JW, Ruiz JC, Ma HW, Kinch LN, Li Q, Grishin NV, Bruick RK (2009) An E3 ligase possessing an iron-responsive hemerythrin domain is a regulator of iron homeostasis. Science (New York, N.Y.) 326(5953):722–726. (PMID: 10.1126/science.117632619762597) Chollangi S, Thompson JW, Ruiz JC, Gardner KH, Bruick RK (2012) Hemerythrin-like domain within F-box and leucine-rich repeat protein 5 (FBXL5) communicates cellular iron and oxygen availability by distinct mechanisms. J Biol Chem 287(28):23710–23717. (PMID: 10.1074/jbc.M112.360404226484103390645) Mayank AK, Pandey V, Vashisht AA, Barshop WD, Rayatpisheh S, Sharma T, Haque T, Powers DN, Wohlschlegel JA (2019) An oxygen-dependent interaction between FBXL5 and the CIA-targeting complex regulates iron homeostasis. Mol Cell 75(2):382–393.e5. (PMID: 10.1016/j.molcel.2019.05.020312294046660392) Yee Koh M, Spivak-Kroizman TR, Powis G (2008) HIF-1 regulation: not so easy come, easy go. Trends Biochem Sci 33(11):526–534. (PMID: 10.1016/j.tibs.2008.08.00218809331) Jami-Alahmadi Y, Pandey V, Mayank AK, Wohlschlegel JA (2021) A robust method for packing high resolution C18 RP-nano-HPLC columns. J Vis Exp 171:e62380. Cox J, Mann M (2008) MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26(12):1367–1372. (PMID: 10.1038/nbt.151119029910) Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M (2011) Andromeda: a peptide search engine integrated into the MaxQuant environment. J Proteome Res 10(4):1794–1805. (PMID: 10.1021/pr101065j21254760) Teo G, Liu G, Zhang J, Nesvizhskii AI, Gingras AC, Choi H (2014) SAINTexpress: improvements and additional features in Significance Analysis of INTeractome software. J Proteome 100:37–43. (PMID: 10.1016/j.jprot.2013.10.023) Jimenez-Morales D, Rosa Campos A, Von Dollen J, Krogan N, Swaney D (2021) artMS: analytical R tools for mass spectrometry. R Package Version 1.12.0. http://artms.org/. |
| فهرسة مساهمة: | Keywords: Hypoxia; Iron-dependent interactions; Oxygen-sensitive interactions; Protein complexes; Proteomic mass spectrometry |
| المشرفين على المادة: | E1UOL152H7 (Iron) S88TT14065 (Oxygen) 0 (oxygen-regulated proteins) |
| تواريخ الأحداث: | Date Created: 20230411 Date Completed: 20230413 Latest Revision: 20230427 |
| رمز التحديث: | 20231215 |
| DOI: | 10.1007/978-1-0716-3080-8_10 |
| PMID: | 37039990 |
| قاعدة البيانات: | MEDLINE |
| تدمد: | 1940-6029 |
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| DOI: | 10.1007/978-1-0716-3080-8_10 |