scholarly journals Fanconi Anemia Proteins and Their Interacting Partners: A Molecular Puzzle

Anemia ◽  
2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Tagrid Kaddar ◽  
Madeleine Carreau
Keyword(s):  
Dna Repair ◽  
Fanconi Anemia ◽  
Protein Interactions ◽  
Cell Cycle Progression ◽  
Molecular Mechanisms ◽  
Protein Complexes ◽  
Repair Process ◽  
Research Field ◽  
Cross Link ◽  
Molecular Functions

In recent years, Fanconi anemia (FA) has been the subject of intense investigations, primarily in the DNA repair research field. Many discoveries have led to the notion of a canonical pathway, termed the FA pathway, where all FA proteins function sequentially in different protein complexes to repair DNA cross-link damages. Although a detailed architecture of this DNA cross-link repair pathway is emerging, the question of how a defective DNA cross-link repair process translates into the disease phenotype is unresolved. Other areas of research including oxidative metabolism, cell cycle progression, apoptosis, and transcriptional regulation have been studied in the context of FA, and some of these areas were investigated before the fervent enthusiasm in the DNA repair field. These other molecular mechanisms may also play an important role in the pathogenesis of this disease. In addition, several FA-interacting proteins have been identified with roles in these “other” nonrepair molecular functions. Thus, the goal of this paper is to revisit old ideas and to discuss protein-protein interactions related to other FA-related molecular functions to try to give the reader a wider perspective of the FA molecular puzzle.

FANCF Co-Localizes with Nonerythroid Alpha Spectrin in Nuclear Foci and Shows Enhanced Binding to It in Normal but Not Fanconi Anemia, Group A, Cells after Damage with a DNA Interstrand Cross-Linking Agent.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 838-838
Author(s):  
Deepa M. Sridharan ◽  
Laura W. McMahon ◽  
Muriel W. Lambert
Keyword(s):  
Dna Repair ◽  
Fanconi Anemia ◽  
Repair Process ◽  
Cross Linking ◽  
Cross Link ◽  
A Cells ◽  
Interstrand Cross Links ◽  
Cross Links ◽  
Normal Human ◽  
Nuclear Foci

Abstract Fanconi anemia (FA) is a genetic disorder characterized by bone marrow failure, a predisposition to cancer, congenital abnormalities and a cellular hypersensitivity to DNA interstrand cross-linking agents, which correlates with a defect in ability to repair interstrand cross-links. We have previously shown that in FA cells there is a deficiency in the structural protein nonerythroid a spectrin (aSpII), which is involved in repair of DNA interstrand cross-links and binds to cross-linked DNA. aSpII co-localizes in damage-induced nuclear foci with FANCA and the cross-link repair protein, XPF, after normal human cells are damaged with a DNA interstrand cross-linking agent. The present study was undertaken in order to get a better understanding of the relationship between aSpII and the FA proteins and the functional importance of this relationship in the repair of DNA interstrand cross-links and the repair defect in FA cells. Immunofluorescence microscopy was carried out to determine whether, after damage, additional FA proteins co-localize with aSpII in nuclear foci and whether the interaction between these proteins is enhanced after cross-link damage. The results show that in normal human cells another FA core complex protein, FANCF, co-localizes with aSpII in nuclear foci after cells are damaged with a DNA interstrand cross-linking agent, 8-methylpsoralen plus UVA light (8-MOP). Time course measurements show that these FANCF/aSpII foci are first visible between 6–8 hours after damage and the number of these foci peaks at 16 hours. By 24 hours after exposure, foci are no longer observed. This is the same time frame previously observed for formation and co-localization of FANCA and XPF foci with aSpII. In contrast, in FA-A cells, which are not deficient in FANCF, very few damage induced FANCF or aSpII foci are observed. In corrected FA-A cells, expressing the FANCA cDNA, FANCF and aSpII again co-localize in discrete foci in the nucleus after damage. Co-localization of FANCF in damage-induced foci with aSpII correlates with enhanced binding of FANCF to aSpII after damage. Co-immunoprecipitation studies show that after normal cells are damaged with 8-MOP there is enhanced binding of FANCF, as well as FANCA, to aSpII in the damaged cells compared to this binding in undamaged cells. This further indicates that there is an important interaction between FANCF, FANCA and aSpII during the repair process. These results support our model that aSpII plays a pivotal role in the recruitment of FA and DNA repair proteins to sites of damage where it acts as a scaffold aiding in their interactions with each other or with damaged DNA, thus enhancing the DNA repair process. In FA cells, where there is a deficiency in aSpII, this recruitment is defective as are the interactions of proteins at these sites. This correlates with the reduced repair of interstrand cross-links in FA cells. Thus a deficiency in the interaction of these FA proteins with aSpII may be an important factor in the defective DNA repair pathway in FA cells.

scholarly journals Mud Loss Restricts Yki-Dependent Hyperplasia in Drosophila Epithelia

2020 ◽  
Vol 8 (4) ◽  
pp. 34
Author(s):  
Amalia S. Parra ◽  
Christopher A. Johnston
Keyword(s):  
Cell Cycle Progression ◽  
Molecular Mechanisms ◽  
Chemical Exchange ◽  
Protein Complexes ◽  
Growth Dynamics ◽  
Secretory Activity ◽  
Wing Disc ◽  
Tissue Growth ◽  
Tissue Type ◽  
Mud Loss

Tissue development demands precise control of cell proliferation and organization, which is achieved through multiple conserved signaling pathways and protein complexes in multicellular animals. Epithelia are a ubiquitous tissue type that provide diverse functions including physical protection, barrier formation, chemical exchange, and secretory activity. However, epithelial cells are also a common driver of tumorigenesis; thus, understanding the molecular mechanisms that control their growth dynamics is important in understanding not only developmental mechanisms but also disease. One prominent pathway that regulates epithelial growth is the conserved Hippo/Warts/Yorkie network. Hippo/Warts inactivation, or activating mutations in Yorkie that prevent its phosphorylation (e.g., YkiS168A), drive hyperplastic tissue growth. We recently reported that loss of Mushroom body defect (Mud), a microtubule-associated protein that contributes to mitotic spindle function, restricts YkiS168A-mediated growth in Drosophila imaginal wing disc epithelia. Here we show that Mud loss alters cell cycle progression and triggers apoptosis with accompanying Jun kinase (JNK) activation in YkiS168A-expressing discs. To identify additional molecular insights, we performed RNAseq and differential gene expression profiling. This analysis revealed that Mud knockdown in YkiS168A-expressing discs resulted in a significant downregulation in expression of core basement membrane (BM) and extracellular matrix (ECM) genes, including the type IV collagen gene viking. Furthermore, we found that YkiS168A-expressing discs accumulated increased collagen protein, which was reduced following Mud knockdown. Our results suggest that ECM/BM remodeling can limit untoward growth initiated by an important driver of tumor growth and highlight a potential regulatory link with cytoskeleton-associated genes.

scholarly journals DNA-Histone Cross-Links: Formation and Repair

2020 ◽  
Vol 8 ◽  
Author(s):  
Manideep C. Pachva ◽  
Alexei F. Kisselev ◽  
Bakhyt T. Matkarimov ◽  
Murat Saparbaev ◽  
Regina Groisman
Keyword(s):  
Dna Repair ◽  
Electrostatic Interactions ◽  
Molecular Mechanisms ◽  
Genotoxic Stress ◽  
Tumor Resistance ◽  
Cross Link ◽  
Covalent Bonds ◽  
Nucleosome Core ◽  
Cross Links ◽  
Tight Association

The nucleosome is a stretch of DNA wrapped around a histone octamer. Electrostatic interactions and hydrogen bonds between histones and DNA are vital for the stable organization of nucleosome core particles, and for the folding of chromatin into more compact structures, which regulate gene expression via controlled access to DNA. As a drawback of tight association, under genotoxic stress, DNA can accidentally cross-link to histone in a covalent manner, generating a highly toxic DNA-histone cross-link (DHC). DHC is a bulky lesion that can impede DNA transcription, replication, and repair, often with lethal consequences. The chemotherapeutic agent cisplatin, as well as ionizing and ultraviolet irradiations and endogenously occurring reactive aldehydes, generate DHCs by forming either stable or transient covalent bonds between DNA and side-chain amino groups of histone lysine residues. The mechanisms of DHC repair start to unravel, and certain common principles of DNA-protein cross-link (DPC) repair mechanisms that participate in the removal of cross-linked histones from DNA have been described. In general, DPC is removed via a two-step repair mechanism. First, cross-linked proteins are degraded by specific DPC proteases or by the proteasome, relieving steric hindrance. Second, the remaining DNA-peptide cross-links are eliminated in various DNA repair pathways. Delineating the molecular mechanisms of DHC repair would help target specific DNA repair proteins for therapeutic intervention to combat tumor resistance to chemotherapy and radiotherapy.

scholarly journals Optimization of light harvesting and photoprotection: molecular mechanisms and physiological consequences

2012 ◽  
Vol 367 (1608) ◽  
pp. 3455-3465 ◽  
Author(s):  
Peter Horton
Keyword(s):  
Protein Interactions ◽  
Thylakoid Membrane ◽  
Molecular Mechanisms ◽  
Light Harvesting ◽  
Protein Complexes ◽  
Efficient Energy Transfer ◽  
Light Harvesting Complexes ◽  
Functional Flexibility ◽  
Jan Anderson ◽  
Repulsive Forces

The distinctive lateral organization of the protein complexes in the thylakoid membrane investigated by Jan Anderson and co-workers is dependent on the balance of various attractive and repulsive forces. Modulation of these forces allows critical physiological regulation of photosynthesis that provides efficient light-harvesting in limiting light but dissipation of excess potentially damaging radiation in saturating light. The light-harvesting complexes (LHCII) are central to this regulation, which is achieved by phosphorylation of stromal residues, protonation on the lumen surface and de-epoxidation of bound violaxanthin. The functional flexibility of LHCII derives from a remarkable pigment composition and configuration that not only allow efficient absorption of light and efficient energy transfer either to photosystem II or photosystem I core complexes, but through subtle configurational changes can also exhibit highly efficient dissipative reactions involving chlorophyll–xanthophyll and/or chlorophyll–chlorophyll interactions. These changes in function are determined at a macroscopic level by alterations in protein–protein interactions in the thylakoid membrane. The capacity and dynamics of this regulation are tuned to different physiological scenarios by the exact protein and pigment content of the light-harvesting system. Here, the molecular mechanisms involved will be reviewed, and the optimization of the light-harvesting system in different environmental conditions described.

Control of genome stability by Slx protein complexes

2009 ◽  
Vol 37 (3) ◽  
pp. 495-510 ◽  
Author(s):  
John Rouse
Keyword(s):  
Dna Damage ◽  
Dna Replication ◽  
Protein Interactions ◽  
Cellular Response ◽  
Genome Stability ◽  
Molecular Mechanisms ◽  
Excision Repair ◽  
Protein Complexes ◽  
Alkylating Agents ◽  
Strand Break

The six Saccharomyces cerevisiae SLX genes were identified in a screen for factors required for the viability of cells lacking Sgs1, a member of the RecQ helicase family involved in processing stalled replisomes and in the maintenance of genome stability. The six SLX gene products form three distinct heterodimeric complexes, and all three have catalytic activity. Slx3–Slx2 (also known as Mus81–Mms4) and Slx1–Slx4 are both heterodimeric endonucleases with a marked specificity for branched replication fork-like DNA species, whereas Slx5–Slx8 is a SUMO (small ubiquitin-related modifier)-targeted E3 ubiquitin ligase. All three complexes play important, but distinct, roles in different aspects of the cellular response to DNA damage and perturbed DNA replication. Slx4 interacts physically not only with Slx1, but also with Rad1–Rad10 [XPF (xeroderma pigmentosum complementation group F)–ERCC1 (excision repair cross-complementing 1) in humans], another structure-specific endonuclease that participates in the repair of UV-induced DNA damage and in a subpathway of recombinational DNA DSB (double-strand break) repair. Curiously, Slx4 is essential for repair of DSBs by Rad1–Rad10, but is not required for repair of UV damage. Slx4 also promotes cellular resistance to DNA-alkylating agents that block the progression of replisomes during DNA replication, by facilitating the error-free mode of lesion bypass. This does not require Slx1 or Rad1–Rad10, and so Slx4 has several distinct roles in protecting genome stability. In the present article, I provide an overview of our current understanding of the cellular roles of the Slx proteins, paying particular attention to the advances that have been made in understanding the cellular roles of Slx4. In particular, protein–protein interactions and underlying molecular mechanisms are discussed and I draw attention to the many questions that have yet to be answered.

scholarly journals MaXLinker: Proteome-wide Cross-link Identifications with High Specificity and Sensitivity

2019 ◽  
Vol 19 (3) ◽  
pp. 554-568 ◽  
Author(s):  
Kumar Yugandhar ◽  
Ting-Yi Wang ◽  
Alden King-Yung Leung ◽  
Michael Charles Lanz ◽  
Ievgen Motorykin ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Search Engine ◽  
Protein Interactions ◽  
Molecular Mechanisms ◽  
Cross Linking ◽  
Interaction Patterns ◽  
Protein Protein Interactions ◽  
Cross Link ◽  
Wide Cross ◽  
Cross Links

Protein-protein interactions play a vital role in nearly all cellular functions. Hence, understanding their interaction patterns and three-dimensional structural conformations can provide crucial insights about various biological processes and underlying molecular mechanisms for many disease phenotypes. Cross-linking mass spectrometry (XL-MS) has the unique capability to detect protein-protein interactions at a large scale along with spatial constraints between interaction partners. The inception of MS-cleavable cross-linkers enabled the MS2-MS3 XL-MS acquisition strategy that provides cross-link information from both MS2 and MS3 level. However, the current cross-link search algorithm available for MS2-MS3 strategy follows a “MS2-centric” approach and suffers from a high rate of mis-identified cross-links. We demonstrate the problem using two new quality assessment metrics [“fraction of mis-identifications” (FMI) and “fraction of interprotein cross-links from known interactions” (FKI)]. We then address this problem, by designing a novel “MS3-centric” approach for cross-link identification and implementing it as a search engine named MaXLinker. MaXLinker outperforms the currently popular search engine with a lower mis-identification rate, and higher sensitivity and specificity. Moreover, we performed human proteome-wide cross-linking mass spectrometry using K562 cells. Employing MaXLinker, we identified a comprehensive set of 9319 unique cross-links at 1% false discovery rate, comprising 8051 intraprotein and 1268 interprotein cross-links. Finally, we experimentally validated the quality of a large number of novel interactions identified in our study, providing a conclusive evidence for MaXLinker's robust performance.

scholarly journals Evidence for subcomplexes in the Fanconi anemia pathway

Blood ◽  
2006 ◽  
Vol 108 (6) ◽  
pp. 2072-2080 ◽  
Author(s):  
Annette L. Medhurst ◽  
El Houari Laghmani ◽  
Jurgen Steltenpool ◽  
Miriam Ferrer ◽  
Chantal Fontaine ◽  
...  
Keyword(s):  
Fanconi Anemia ◽  
Protein Interactions ◽  
Congenital Abnormalities ◽  
Bone Marrow Failure ◽  
Direct Interaction ◽  
Molecular Architecture ◽  
Cross Link ◽  
Core Complex ◽  
Downstream Target ◽  
Nuclear Complex

AbstractFanconi anemia (FA) is a genomic instability disorder, clinically characterized by congenital abnormalities, progressive bone marrow failure, and predisposition to malignancy. Cells derived from patients with FA display a marked sensitivity to DNA cross-linking agents, such as mitomycin C (MMC). This observation has led to the hypothesis that the proteins defective in FA are involved in the sensing or repair of interstrand cross-link lesions of the DNA. A nuclear complex consisting of a majority of the FA proteins plays a crucial role in this process and is required for the monoubiquitination of a downstream target, FANCD2. Two new FA genes, FANCB and FANCL, have recently been identified, and their discovery has allowed a more detailed study into the molecular architecture of the FA pathway. We demonstrate a direct interaction between FANCB and FANCL and that a complex of these proteins binds FANCA. The interaction between FANCA and FANCL is dependent on FANCB, FANCG, and FANCM, but independent of FANCC, FANCE, and FANCF. These findings provide a framework for the protein interactions that occur “upstream” in the FA pathway and suggest that besides the FA core complex different subcomplexes exist that may have specific functions other than the monoubiquitination of FANCD2.

scholarly journals SECAT: Quantifying differential protein-protein interaction states by network-centric analysis

2019 ◽  
Author(s):  
George Rosenberger ◽  
Moritz Heusel ◽  
Isabell Bludau ◽  
Ben Collins ◽  
Claudia Martelli ◽  
...  
Keyword(s):  
Protein Interaction ◽  
Protein Interactions ◽  
Molecular Mechanisms ◽  
Protein Complexes ◽  
Mass Spectrometric ◽  
Mass Spectrometric Analysis ◽  
Size Exclusion ◽  
Spectrometric Analysis ◽  
Differential Analysis ◽  
Ppi Networks

AbstractProtein-protein interactions (PPIs) play critical functional and regulatory roles in virtually all cellular processes. They are essential for the formation of macromolecular complexes, which in turn constitute the basis for extended protein interaction networks that determine the functional state of a cell. We and others have previously shown that chromatographic fractionation of native protein complexes in combination with bottom-up mass spectrometric analysis of consecutive fractions supports the multiplexed characterization and detection of state-specific changes of protein complexes.In this study, we describe a computational approach that extends the analysis of data from the co-fractionation / mass spectrometric analysis of native complexes to the level of PPI networks, thus enabling a qualitative and quantitative comparison of the proteome organization between samples and states. The Size-Exclusion Chromatography Algorithmic Toolkit (SECAT) implements a novel, network-centric strategy for the scalable and robust differential analysis of PPI networks. SECAT and its underlying statistical framework elucidate differential quantitative abundance and stoichiometry attributes of proteins in the context of their PPIs. We validate algorithm predictions using publicly available datasets and demonstrate that SECAT represents a more scalable and effective methodology to assess protein-network state and that our approach thus obviates the need to explicitly infer individual protein complexes. Further, by differential analysis of PPI networks of HeLa cells in interphase and mitotic state, respectively, we demonstrate the ability of the algorithm to detect PPI network differences and to thus suggest molecular mechanisms that differentiate cellular states.

scholarly journals CELL SYSTEMS BIOLOGY OF TRANSLATION FACTORS AND PROTEASOME-TARGETED PROTEIN COMPLEXES ASSOCIATED WITH AGC KINASE SCH9

2020 ◽  
Author(s):  
Alex Sobko
Keyword(s):  
Protein Synthesis ◽  
Protein Kinase ◽  
Protein Interactions ◽  
Cell Cycle Progression ◽  
Protein Complexes ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Protein Protein Interactions ◽  
Functional Connections ◽  
Translation Factors

Sch9 appears to be the Saccharomyces cerevisiae homolog of protein kinase B and S6 kinase and is involved in the control of numerous nutrient-sensitive processes, including regulation of cell size, cell cycle progression, and stress resistance. Sch9 has also been implicated in the regulation of replicative and chronological life span. The availability of data from global studies of protein-protein interactions now makes it possible to predict and validate functional connections between Sch9, its putative substrates, and other proteins. Sch9 appears to be involved in control of biosynthetic and catabolic pathways. Thus, the analysis of Sch9-associated proteins indicates that this kinase may be involved in regulation of protein synthesis. Sch9 forms a complex with, and, presumably, phosphorylates starvation- and stress-induced protein kinase GCN2, which, in turn, phosphorylates translation initiation factor eIF2alpha. Sch9 also interacts with translation factors Arc1, Pab1 and prion-like protein Sup35. Thus, Sch9 may be part of the mechanism that relays availability of nutrients to utilization of glucose and to the rates of protein synthesis. One of the interesting outcomes of the proteome-wide analysis of protein-protein interactions in yeast is the finding that Sch9 associates with Shp1, Cdc48, and Ufd1, which form a complex responsible for the recognition and targeting of ubiquitinated proteins to the proteasome for degradation. It is unknown and remains to be elucidated, whether mammalian homologues of Sch9 are also associated with the proteins involved in translation/protein synthesis and proteasomal degradation.

scholarly journals Towards a structurally resolved human protein interaction network

2021 ◽  
Author(s):  
David F Burke ◽  
Patrick Bryant ◽  
Inigo Barrio-Hernandez ◽  
Danish Memon ◽  
Gabriele Pozzati ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Cell Biology ◽  
Molecular Mechanisms ◽  
Protein Complexes ◽  
Interaction Network ◽  
Protein Protein Interactions ◽  
Cellular Functions ◽  
Human Interactions ◽  
Pathogenic Variants ◽  
Binary Complexes

All cellular functions are governed by complex molecular machines that assemble through protein-protein interactions. Their atomic details are critical to the study of their molecular mechanisms but fewer than 5% of hundreds of thousands of human interactions have been structurally characterized. Here, we test the potential and limitations of recent progress in deep-learning methods using AlphaFold2 to predict structures for 65,484 human interactions. We show that higher confidence models are enriched in interactions supported by affinity or structure based methods and can be orthogonally confirmed by spatial constraints defined by cross-link data. We identify 3,137 high confidence models, of which 1,371 have no homology to a known structure, from which we identify interface residues harbouring disease mutations, suggesting potential mechanisms for pathogenic variants. We find groups of interface phosphorylation sites that show patterns of co-regulation across conditions, suggestive of coordinated tuning of multiple interactions as signalling responses. Finally, we provide examples of how the predicted binary complexes can be used to build larger assemblies. Accurate prediction of protein complexes promises to greatly expand our understanding of the atomic details of human cell biology in health and disease.

Sign in / Sign up

Export Citation Format

Share Document