Publications

2018
Beltran, PM Jean, et al.Infection-Induced Peroxisome Biogenesis Is a Metabolic Strategy for Herpesvirus Replication”. Cell Host Microbe (2018). Print.
EA, Rowland, Snowden CK, and Cristea IM. “Protein lipoylation: an evolutionarily conserved metabolic regulator of health and disease”. Curr Opin Chem Biol. 42 (2018): , 42, 76-85. Print.
2017
EA, Rowland, et al.Sirtuin Lipoamidase Activity Is Conserved in Bacteria as a Regulator of Metabolic Enzyme Complexes”. mBio 85 (2017). Print.
PM, Jean Beltran, Cook KC, and Cristea IM. “Exploring and Exploiting Proteome Organization during Viral Infection”. J Virol 91.18 (2017). Print.
VJ, Carabetta, and Cristea IM. “Regulation, Function, and Detection of Protein Acetylation in Bacteria”. J Bacteriol. 199.16 (2017). Print.
R, Alfonso-Dunn, et al.Transcriptional Elongation of HSV Immediate Early Genes by the Super Elongation Complex Drives Lytic Infection and Reactivation from Latency”. Cell Host Microbe 21.4 (2017): , 21, 4, 507-517. Print.
PM, Jean Beltran, et al.Proteomics and integrative omic approaches for understanding host-pathogen interactions and infectious diseases”. Mol Syst Biol. 13.3 (2017): , 13, 3, 922. Print.
IM, Cristea. “The Host-Pathogen Ecosystem Viewed Through the Prism of Proteomics”. Mol Cell Proteomics 16.4 (2017): , 16, 4, S1-4. Print.
TM, Greco, and Cristea IM. “Proteomics Tracing the Footsteps of Infectious Disease”. Mol Cell Proteomics 16.4 (2017): , 16, 4, S5-14. Print.
MS, Crow, and Cristea IM. “Human Antiviral Protein IFIX Suppresses Viral Gene Expression during Herpes Simplex Virus 1 (HSV-1) Infection and Is Counteracted by Virus-induced Proteasomal Degradation”. Mol Cell Proteomics 16.4 (2017): , 16, 4, S200-214. Print.
2016
BA, Diner, et al.Viral DNA Sensors IFI16 and Cyclic GMP-AMP Synthase Possess Distinct Functions in Regulating Viral Gene Expression, Immune Defenses, and Apoptotic Responses during Herpesvirus Infection”. mBio 76 (2016). Print.
PM, Jean Beltran, Mathias RA, and Cristea IM. “A Portrait of the Human Organelle Proteome In Space and Time during Cytomegalovirus Infection”. Cell Syst. 34 (2016): , 3, 4, 361-373. Print.
MS, Crow, et al.Diverse mechanisms evolved by DNA viruses to inhibit early host defenses.”. Crit Rev Biochem Mol Biol. 51.6 (2016): , 51, 6, 452-481. Print.
HG, Budayeva, and Cristea IM. “Human Sirtuin 2 Localization, Transient Interactions, and Impact on the Proteome Point to Its Role in Intracellular Trafficking”. Mol Cell Proteomics 15.10 (2016): , 15, 10, 3107-3125. Print.
RA, Mathias, Greco TM, and Cristea IM. “Identification of Sirtuin4 (SIRT4) Protein Interactions: Uncovering Candidate Acyl-Modified Mitochondrial Substrates and Enzymatic Regulators”. Methods Mol Biol 1436.213-39 (2016). Print.
AJ, Guise, and Cristea IM. “Approaches for Studying the Subcellular Localization, Interactions, and Regulation of Histone Deacetylase 5 (HDAC5)”. Methods Mol Biol 1436 (2016): , 1436, 47-84. Print.
TM, Greco, and Cristea IM. “The Biochemical Evolution of Protein Complexes.”. Trends Biochem Sci. 41.1 (2016): , 41, 1, 4-6. Web. PubMedAbstract

Over the past decade, it became evident that proteins perform critical functions as components of specialized macromolecular complexes. Here, we discuss a recent study by Wan and colleagues, which highlights the significance of protein complexes by studying their conservation in organisms separated by up to a billion years of evolution. 

L, Waldron, et al.The Cardiac TBX5 Interactome Reveals a Chromatin Remodeling Network Essential for Cardiac Septation.”. Dev Cell 36.3 (2016): , 36, 3, 262-75. Web. PubMedAbstract

Human mutations in the cardiac transcription factor gene TBX5 cause congenital heart disease (CHD), although the underlying mechanism is unknown. We report characterization of the endogenous TBX5 cardiac interactome and demonstrate that TBX5, long considered a transcriptional activator, interacts biochemically and genetically with the nucleosome remodeling and deacetylase (NuRD) repressor complex. Incompatible gene programs are repressed by TBX5 in the developing heart. CHD mis-sense mutations that disrupt the TBX5-NuRD interaction cause depression of a subset of repressed genes. Furthermore, the TBX5-NuRD interaction is required for heart development. Phylogenetic analysis showed that the TBX5-NuRD interaction domain evolved during early diversification of vertebrates, simultaneous with the evolution of cardiac septation. Collectively, this work defines a TBX5-NuRD interaction essential to cardiac development and the evolution of the mammalian heart, and when altered may contribute to human CHD. 

TM, Greco, Guise AJ, and Cristea IM. “Determining the Composition and Stability of Protein Complexes Using an Integrated Label-Free and Stable Isotope Labeling Strategy.”. Methods Mol Biol (2016). Web. PubMedAbstract

In biological systems, proteins catalyze the fundamental reactions that underlie all cellular functions, including metabolic processes and cell survival and death pathways. These biochemical reactions are rarely accomplished alone. Rather, they involve a concerted effect from many proteins that may operate in a directed signaling pathway and/or may physically associate in a complex to achieve a specific enzymatic activity. Therefore, defining the composition and regulation of protein complexes is critical for understanding cellular functions. In this chapter, we describe an approach that uses quantitative mass spectrometry (MS) to assess the specificity and the relative stability of protein interactions. Isolation of protein complexes from mammalian cells is performed by rapid immunoaffinity purification, and followed by in-solution digestion and high-resolution mass spectrometry analysis. We employ complementary quantitative MS workflows to assess the specificity of protein interactions using label-free MS and statistical analysis, and the relative stability of the interactions using a metabolic labeling technique. For each candidate protein interaction, scores from the two workflows can be correlated to minimize nonspecific background and profile protein complex composition and relative stability. 

KK, Lum, and Cristea IM. “Proteomic approaches to uncovering virus-host protein interactions during the progression of viral infection.”. Expert Rev Proteomics 13.3 (2016): , 13, 3, 325-40. Web. PubMedAbstract

The integration of proteomic methods to virology has facilitated a significant breadth of biological insight into mechanisms of virus replication, antiviral host responses and viral subversion of host defenses. Throughout the course of infection, these cellular mechanisms rely heavily on the formation of temporally and spatially regulated virus-host protein-protein interactions. Reviewed here are proteomic-based approaches that have been used to characterize this dynamic virus-host interplay. Specifically discussed are the contribution of integrative mass spectrometry, antibody-based affinity purification of protein complexes, cross-linking and protein array techniques for elucidating complex networks of virus-host protein associations during infection with a diverse range of RNA and DNA viruses. The benefits and limitations of applying proteomic methods to virology are explored, and the contribution of these approaches to important biological discoveries and to inspiring new tractable avenues for the design of antiviral therapeutics is highlighted. 

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