Table 1 Names and functions of the 57 cellular proteins identified in both the RSV and HIV-1 Gag protein interactomes

ABLIM1

Actin Binding LIM Protein 1

A LIM zinc-binding domain-containing protein that binds to actin filaments. Mediates interactions between actin and cytoplasmic targets

ACTN1

Actinin Alpha 1

A bundling F-actin cross-linking protein thought to anchor actin to a variety of intracellular structures

ATXN2

Ataxin 2

Involved in EGFR trafficking, acting as negative regulator of endocytic EGFR internalization at the plasma membrane. modulates mTOR signals, modifying ribosomal translation and mitochondrial function

BCL7B

BAF Chromatin Remodeling Complex Subunit BCL7B

Positive regulator of apoptosis. Negatively regulates the expression of Wnt signaling components CTNNB1 and HMGA1. Involved in cell cycle progression, maintenance of the nuclear structure and stem cell differentiation

CBLL1

Cbl Proto-Oncogene Like 1

E3 ubiquitin-protein ligase that mediates ubiquitination of several tyrosine-phosphorylated Src substrates. Associated component of the WMM complex, a complex that mediates N6-methyladenosine (m6A) methylation of RNAs, a modification that has a role in the efficiency of mRNA splicing and RNA processing

CDC42BPB

CDC42 Binding Protein Kinase Beta

Serine/threonine-protein kinase which is an important downstream effector of CDC42 and plays a role in the regulation of cytoskeleton reorganization and cell migration

CHTOP

Chromatin Target of PRMT1

Plays an important role in the ligand-dependent activation of estrogen receptor target genes. Binds to 5-hydroxymethylcytosine (5hmC) and associates with the methylosome complex. The CHTOP-methylosome complex associated with 5hmC is recruited to selective sites on the chromosome, where it methylates H4R3 and activates the transcription of genes involved in glioblastomagenesis. Required for effective mRNA nuclear export and is a component of the TREX complex which is thought to couple mRNA transcription, processing and nuclear export, and specifically associates with spliced mRNA and not with unspliced pre-mRNA

CYFIP1

Cytoplasmic FMR1 Interacting Protein 1

Component of the CYFIP1-EIF4E-FMR1 complex which binds to the mRNA cap and mediates translational repression. Regulates formation of membrane ruffles and lamellipodia. Plays a role in axon outgrowth. Part of the WAVE complex that regulates actin filament reorganization via its interaction with the Arp2/3 complex

EIF4G2

Eukaryotic Translation Initiation Factor 4 Gamma 2

Plays a role in the switch from cap-dependent to IRES-mediated translation during mitosis, apoptosis and viral infection

FAM120A

Family with Sequence Similarity 120A

Critical component of the oxidative stress-induced survival signaling. Activates src family kinases and acts as a scaffolding protein enabling src family kinases to phosphorylate and activate PI3-kinase. Binds RNA and promotes the secretion of IGF-II

FOXP1

Forkhead Box P1

Essential transcriptional regulator of B-cell development. Involved in regulation of cardiac muscle cell proliferation. Involved in the columnar organization of spinal motor neurons. Represses transcription of various pro-apoptotic genes and cooperates with NF-kappa B-signaling in promoting B-cell expansion by inhibition of caspase-dependent apoptosis. Involved in endothelial cell proliferation, tube formation and migration indicative for a role in angiogenesis. Involved in transcriptional regulation in embryonic stem cells (ESCs). Stimulates expression of transcription factors that are required for pluripotency and decreases expression of differentiation-associated genes

HNRNPH3

Heterogeneous nuclear ribonucleoprotein H3

Involved in the splicing process and participates in early heat shock-induced splicing arrest

IGF2BP3

Insulin Like Growth Factor 2 MRNA Binding Protein 3

RNA-binding factor that may recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs) for mRNA transport and transient storage. It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation

ING2

Inhibitor of Growth Family Member 2

Seems to be involved in p53/TP53 activation and p53/TP53-dependent apoptotic pathways, probably by enhancing acetylation of p53/TP53. Component of a mSin3A-like corepressor complex, which is probably involved in deacetylation of nucleosomal histones

IQGAP1

IQ Motif Containing GTPase Activating Protein 1

Plays a crucial role in regulating the dynamics and assembly of the actin cytoskeleton

KDM2A

Lysine Demethylase 2A

Histone demethylase that specifically demethylates 'Lys-36' of histone H3, thereby playing a central role in histone code. Required to maintain the heterochromatic state. Associates with centromeres and represses transcription of small non-coding RNAs that are encoded by the clusters of satellite repeats at the centromere. Required to sustain centromeric integrity and genomic stability, particularly during mitosis

KIAA1033 (WASHC4)

WASH Complex Subunit 4

Acts as a component of the WASH core complex that functions as a nucleation-promoting factor (NPF) at the surface of endosomes, where it recruits and activates the Arp2/3 complex to induce actin polymerization, playing a key role in the fission of tubules that serve as transport intermediates during endosome sorting

KLC1

Kinesin Light Chain 1

Kinesin is a microtubule-associated force-producing protein that may play a role in organelle transport. The light chain may function in coupling of cargo to the heavy chain or in the modulation of its ATPase activity

KLC2

Kinesin Light Chain 2

See above

LEO1

LEO1 Homolog, Paf1/RNA Polymerase II Complex Component

Component of the PAF1 complex (PAF1C) which has multiple functions during transcription by RNA polymerase II and is implicated in regulation of development and maintenance of embryonic stem cell pluripotency. PAF1C associates with RNA polymerase II through interaction with POLR2A CTD non-phosphorylated and 'Ser-2'- and 'Ser-5'- phosphorylated forms and is involved in transcriptional elongation

MAP2

Microtubule Associated Protein 2

The exact function of MAP2 is unknown but MAPs may stabilize the microtubules against depolymerization

MAPRE2

Microtubule Associated Protein RP/EB Family Member 2

May be involved in microtubule polymerization, and spindle function by stabilizing microtubules and anchoring them at centrosomes

MED26

Mediator Complex Subunit 26

Component of the Mediator complex, a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery

NDUFA9

NADH:Ubiquinone Oxidoreductase Subunit A9

Accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I). Complex I functions in the transfer of electrons from NADH to the respiratory chain

OGT

O-Linked N-Acetylglucosamine (GlcNAc) Transferase

Catalyzes the transfer of a single N-acetylglucosamine from UDP-GlcNAc to a serine or threonine residue in cytoplasmic and nuclear proteins resulting in their modification with a beta-linked N-acetylglucosamine (O-GlcNAc). Glycosylates a large and diverse number of proteins and can regulate their cellular processes via cross-talk between glycosylation and phosphorylation or by affecting proteolytic processing. Component of a THAP1/THAP3-HCFC1-OGT complex that is required for the regulation of the transcriptional activity of RRM1. Plays a key role in chromatin structure by mediating O-GlcNAcylation of 'Ser-112' of histone H2B: recruited to CpG-rich transcription start sites of active genes via its interaction with TET proteins

ORC5

Origin Recognition Complex Subunit 5

Component of the origin recognition complex (ORC) that binds origins of replication. ORC is required to assemble the pre-replication complex necessary to initiate DNA replication

PDCD11

Programmed Cell Death 11

Essential for the generation of mature 18S rRNA. Directly interacts with U3 snoRNA. Involved in the biogenesis of rRNA

PDLIM5

PDZ And LIM Domain 5

May play an important role in the heart development by scaffolding PKC to the Z-disk region. May play a role in the regulation of cardiomyocyte expansion. Contributes to the regulation of dendritic spine morphogenesis in neurons

PLOD2

Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase 2

Forms hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens. These hydroxylysines serve as sites of attachment for carbohydrate units and are essential for the stability of the intermolecular collagen cross-links

POLR2B

RNA Polymerase II Subunit B

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit

PPIB

Peptidylprolyl Isomerase B

PPIase that catalyzes the cis–trans isomerization of proline imidic peptide bonds in oligopeptides and may therefore assist protein folding

PRPF40A

Pre-MRNA Processing Factor 40 Homolog A

Binds to WASL/N-WASP and suppresses its translocation from the nucleus to the cytoplasm, thereby inhibiting its cytoplasmic function. Plays a role in the regulation of cell morphology and cytoskeletal organization

PTBP1

Polypyrimidine Tract Binding Protein 1

Plays a role in pre-mRNA splicing and in the regulation of alternative splicing events. May promote RNA looping when bound to two separate polypyrimidine tracts in the same pre-mRNA. May promote the binding of U2 snRNP to pre-mRNA

RAD21

RAD21 Cohesin Complex Component

A member of the cohesin complex, involved in sister chromatid cohesion from the time of DNA replication in S phase to their segregation in mitosis, a function that is essential for proper chromosome segregation, post-replicative DNA repair, and the prevention of inappropriate recombination between repetitive regions

RBM33

RNA Binding Motif Protein 33

*Could not find a clear function associated with the protein

RFC1

Replication Factor C Subunit 1

The elongation of primed DNA templates by DNA polymerase delta and epsilon requires the action of the accessory proteins PCNA and activator 1. This subunit binds to the primer-template junction. Can bind single- or double-stranded DNA. 5' phosphate residue is required for binding of the N-terminal DNA-binding domain to duplex DNA, suggesting a role in recognition of non-primer template DNA structures during replication and/or repair

RFC5

Replication Factor C Subunit 5

See above

SAFB

Scaffold Attachment Factor B

Binds to scaffold/matrix attachment region (S/MAR) DNA and forms a molecular assembly point to allow the formation of a 'transcriptosomal' complex (consisting of SR proteins and RNA polymerase II) coupling transcription and RNA processing. Can function as an estrogen receptor corepressor and can also bind to the HSP27 promoter and decrease its transcription. Can inhibit cell proliferation

SAFB2

Scaffold Attachment Factor B2

See above with S/MAR DNA. Is involved in cell cycle regulation, apoptosis, differentiation, the stress response, and regulation of immune genes

SCAF8

SR-Related CTD Associated Factor 8

Anti-terminator protein required to prevent early mRNA termination during transcription. Mechanistically, associates with the phosphorylated C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit (POLR2A), and subsequently binds nascent RNA upstream of early polyadenylation sites to prevent premature mRNA transcript cleavage and polyadenylation. Independently of SCAF4, also acts as a positive regulator of transcript elongation

SEPT7

Septin 7

Filament-forming cytoskeletal GTPase. Required for normal organization of the actin cytoskeleton. Required for normal progress through mitosis

SERBP1

SERPINE1 MRNA Binding Protein 1

May play a role in the regulation of mRNA stability. Seems to play a role in PML-nuclear bodies formation

SLC25A3

Solute Carrier Family 25 Member 3

Transport of phosphate groups from the cytosol to the mitochondrial matrix

SMAD2

SMAD Family Member 2

Receptor-regulated SMAD (R-SMAD) that is an intracellular signal transducer and transcriptional modulator activated by TGF-beta (transforming growth factor) and activin type 1 receptor kinases

SMC1A

Structural Maintenance of Chromosomes 1A

Involved in chromosome cohesion during cell cycle and in DNA repair. Involved in DNA repair via its interaction with BRCA1 and its related phosphorylation by ATM, or via its phosphorylation by ATR

SMC4

Structural Maintenance of Chromosomes 4

Central component of the condensin complex, a complex required for conversion of interphase chromatin into mitotic-like condense chromosomes

SURF4

Surfeit 4

May play a role in the maintenance of the architecture of the endoplasmic reticulum-Golgi intermediate compartment and of the Golgi

THOC3

THO Complex 3

Required for efficient export of polyadenylated RNA and spliced mRNA. Acts as component of the THO subcomplex of the TREX complex which is thought to couple mRNA transcription, processing and nuclear export, and which specifically associates with spliced mRNA and not with unspliced pre-mRNA

TJP1

Tight Junction Protein 1

TJP1, TJP2, and TJP3 are closely related scaffolding proteins that link tight junction (TJ) transmembrane proteins such as claudins, junctional adhesion molecules, and occludin to the actin cytoskeleton

TPM1

Tropomyosin 1

Binds to actin filaments in muscle and non-muscle cells. Plays a central role, in association with the troponin complex, in the calcium dependent regulation of vertebrate striated muscle contraction. In non-muscle cells is implicated in stabilizing cytoskeleton actin filaments

TPM3

Tropomyosin 3

Binds to actin filaments in muscle and non-muscle cells. Plays a central role, in association with the troponin complex, in the calcium dependent regulation of vertebrate striated muscle contraction. Smooth muscle contraction is regulated by interaction with caldesmon. In non-muscle cells is implicated in stabilizing cytoskeleton actin filaments

TRA2B

Transformer 2 Beta Homolog

Sequence-specific RNA-binding protein which participates in the control of pre-mRNA splicing. Can either activate or suppress exon inclusion. Binds to pre-mRNA

TRIP12

Thyroid Hormone Receptor Interactor 12

E3 ubiquitin-protein ligase involved in ubiquitin fusion degradation pathway and regulation of DNA repair. Acts as a key regulator of DNA damage

U2AF1

U2 Small Nuclear RNA Auxiliary Factor 1

Plays a critical role in both constitutive and enhancer-dependent splicing by mediating protein–protein interactions and protein-RNA interactions required for accurate 3'-splice site selection. Recruits U2 snRNP to the branch point. Directly mediates interactions between U2AF2 and proteins bound to the enhancers

VWA9 (INTS14)

Integrator Complex Subunit 14

Probable component of the Integrator (INT) complex, a complex involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing

ZEB1

Zinc Finger E-Box Binding Homeobox 1

Acts as a transcriptional repressor

ZFC3H1

Zinc Finger C3H1-Type Containing

Subunit of the trimeric poly(A) tail exosome targeting (PAXT) complex, a complex that directs a subset of long and polyadenylated poly(A) RNAs for exosomal degradation