Table 3.

Previously discovered viral proteins with a known role in HIV-1 Replication^a

Proteinb	Gene namec	Score in virion cores fromd			Known role in HIV-1 replicatione
		Sup-T1	Act. THP1	N-Act. THP1
DNA Binding: Chromatin Organization, Replication, Topoisomerases
Regulator of chromosome condensation 2	RCC2	3.32	1.78	-	RCC proteins interact with Rac1 and Arf6 subnetworks and limit signaling required for membrane protrusion and delivery [99]; RCC2 acts as a Rac1 guanine nucleotide exchange factor (GEF); RCC1 is involved in HIV-1 RNA nuclear export through activation of RanGAP [100] and hence facilitates dissociation of RNA nuclear export complex [101].
RNA Binding: Structure Organization, Modification, Splicing, Transport
Helicase like protein 2 - DEAD/H box polypeptide 3	DDX3X	2.05	-	-	Member of DEAD box RNA helicases that is implicated in alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. RNAi knockdown of DDX3 suppresses HIV-1 viral replication [102]; interaction of DDX3 with Rev/CRM1 is important for nuclear export of non-spliced HIV-1 RNA [103].
RNA-dependent helicase p72 - DEAD box polypeptide 17 isoform 1	DDX17	6.36	-	-	Members of ATP-dependent DEAD box RNA helicases, potentially involved in interaction with HIV-1 RNA.
RNA helicase II/Gu protein - DEAD box polypeptide 21	DDX21	-	2.07	-
ATP-dependent RNA helicase A - DEAD box protein 9	DHX9	6.36	6.09	27.18	RNA helicases that catalyze ATP-dependent unwinding of double-stranded RNA and DNA-RNA complexes; localize in both nucleus and cytoplasm and function as transcriptional regulators; may also be involved in expression and nuclear export of retroviral RNAs, particularly in post-transcriptional regulation of HIV-1 [104]. DHX9 is packaged in HIV-1 particles and contributes to particle assembly and reverse transcription [10]; it also facilitates tRNALys3 binding and initiation of reverse transcription [73]
Heterogeneous nuclear ribonucleoprotein A1	HNRNPA1	-	1.92	-	RNA binding proteins that complex with heterogeneous nuclear RNA (hnRNA) and are involved in pre-mRNA processing in the nucleus: alternative splicing regulation, polyadenylation, nucleo-cytoplasmic transport and other aspects of mRNA metabolism and transport; hnRNP-A1 is involved in HIV-1 mRNA splicing [105,106]; hnRNP-A2 is found to be important for trafficking of HIV-1 mRNA out of the nucleus and through the cytoplasm [105]; hnRNP H and hnRNP K interact directly with HIV-1 RNA and are involved in alternative splicing [107].
Heterogeneous nuclear ribonucleoprotein F	HNRNPF	3.47	-	-
Heterogeneous nuclear ribonucleoprotein H1	HNRNPH1	3.04	-	8.26
Heterogeneous nuclear ribonucleoprotein M isoform b	HNRNPM	1.9	-	--
Heterogeneous nuclear ribonucleoprotein R	HNRNPR	6.31	-	--
Nonsense-mediated decay (NMD) factor	UPF1	5.65	6.48	6.32	ATP-dependent RNA helicase, the HIV-1 RNP component, positively influences HIV-1 RNA translatability. Important for stability of unspliced viral RNA and translation of Gag polypeptide in producer cells [108]
Cytoskeleton
β Actin	ACTBL2	60.12	35.05	99.59	Actin microfilaments are important for RTC formation and RTC transport in cytoplasm [1]; interaction with NC domain of Gag is required for HIV-1 assembly [109].
Tubulin α 1	TUBA1A	69.39	58.56	66.49	Microtubules are shown to be important for RTC cytoplasmic trafficking [18,110]assembly of Gag polyprotein molecules [111] and viral genomic RNA trafficking [112].
Tubulin α 6	TUBA1C	57.11	41.39	61.72
Tubulin β 5	TUBB	29.82	27.85	49.68
Tubulin β 3	TUBB3	13.84	9.07	30.56
Tubulin β 1	TUBB1	13.3	-	22.5
Tubulin γ 1	TUBG1	-	-	4.96
Dynein	DYNC1H1	-	11.68	10.11	Dynein motor and late endosomes are involved in viral RNA trafficking [112] and transport of RTC toward the nucleus [18].
Cytoskeleton Regulation
ARP3 actin-related protein 3 homolog (yeast)	ACTR3	-	9.52	-	Major constituent of the ARP2/3, a 7 subunit complex, responsible for actin polymerization [113]. The complex is required for early phase of HIV-1 replication [114].
Nuclear Import
Transportin 3; importin-SR; importin 12; transportin SR2	TNPO3	1.0	-	-	Impotin-β family member, binds catalytic core domain close to the N terminus of IN and promotes nuclear entry of PICs [115,116]; might serve as a chaperone that associates with PIC post-entry to guide it through nuclear pore [117].
Karyopherin α2; importin α1)	KPNA2	-	-	7.91	Directly interacts with central core domain of HIV-1 integrase, facilitates PIC nuclear import [118-120].
Karyopherin β2; importin β2	TNPO1	-	3.63	1.95	Importin α/β heterodimer interacts with HIV-1 integrase and probably MA protein and Vpr to translocate PIC into the nucleus [121]
Karyopherin β1; nuclear factor p97; importin 90	KPNB1	-	-	8.02
Nuclear Export
RANBP21/exportin 5 (Exp5)	XPO5	5.5	-	6.87	Association of RanBP1 and 2 with Rev-CRM1-RanGTP complex has been shown [122], thus RanBP is required for dissociation of nuclear export complex during HIV-1 RNA nuclear export [101].
Vesicular Transport
CLTC protein - clathrin	CLTC	37.6	7.7	7	Clathrin is incorporated in HIV-1 particles probably through interaction with Pol, especially IN domain [32]; it facilitates the accurate morphogenesis of infectious particles probably by contribution to spatial organization of Gag and Pol proteins and proteolytic processing of virion components during particle assembly [5].
Rab5C GTP protease	RAB5C	-	6.78	6.58	Rab GTP proteases are important for vesicular trafficking. They are activated by guanine nucleotide exchange factor (GEF), RCC2 protein revealed in HIV-1 cores can act as a GEF. Rab11 is important for HIV-1 production [123]; Rab1 potentially associates with HIV-1 Rev and is involved in nuclear export of viral RNA [124]; Rab9 is required for Gag trafficking to the site of assembly [123]; Rab7-interacting lysosomal protein promotes vRNA clustering at the MTOC [112]; Rab6 is probably involved in viral entry [58].
Rab7A GTP protease	RAB7A	8.89	9.08	21.97
Rab8A GTP protease	RAB8A	7.91	6.78	6.58
Rab11A GTP protease	RAB11A	-	-	9.31
Programmed cell death 6 interacting protein; HP95; AIP1/ALIX	PDCD6IP	6.43	13.62	29.94	Alix/HP95 is a protein implicated in endosomal organization and virus budding; overexpression results in cytoplasmic vacuolization, which may be partially responsible for protection against cell death. AIP1/ALIX is a binding partner for HIV-1 Gag L-domain and other budding network proteins (Tsg101) functioning in virus budding [125].
Intracellular Trafficking
TNFAIP3 interacting protein 1; HIV-1 Nef interacting protein; NAF1	TNIP1	1.0	-	-	An ERK2 binding protein, Naf1, attenuates EGF/ERK2 nuclear signaling, binds HIV-1 Nef and increases cell surface CD4 expression [126]. ERK2 interacts with HIV-1 matrix, packaged into virions and responsible for MA phosphorylation [24].
Chaperones/Molecular Folding
Hsp70 protein 8	HSPA8	7.85	26.4	31.35	Heat shock protein 70 family members are shown to be incorporated in HIV-1 particles. This is important for subsequent viral cDNA synthesis [11,127]; they can also interfere with Vpr in HIV-1 nuclear import in macrophages [128,129].
Hsp70 protein 9 (mortalin)	HSPA9	-	5.75	-
Cyclophilin A, CyPA	PPIA	22.35	20.00	7.68	incorporates into virions via binding to the CA domain of Pr55Gag [23]. The role of CA-bound CyPA is still unclear [48] It is critical for protection and stabilization of HIV-1 cores as a chaperone [49] and is probably involved in PIC nuclear transport [31]

^a Proteins are listed by function category.

^b Full Protein name as listed in NCBI Protein database (http://www.ncbi.nlm.nih.gov/protein).

^c Official Gene Symbol as listed by HGNC.

^d The Xcorr values of each protein in different viral core samples are shown; if protein was not present in the virion core from a specific producer cell type, the Xcorr is not shown.

^e Protein function within the cell is listed, along with known implicated function(s) in HIV-1 replication.