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HIV Rev Assembly on the Rev Response Element (RRE): A Structural Perspective.

Rausch JW, Le Grice SF - Viruses (2015)

Bottom Line: Once in the cytoplasm, the complexes dissociate and unspliced and singly-spliced viral RNAs are packaged into nascent virions or translated into viral structural proteins and enzymes, respectively.Rev binding to the RRE is a complex process, as multiple copies of the protein assemble on the RNA in a coordinated fashion via a series of Rev-Rev and Rev-RNA interactions.Our understanding of the nature of these interactions has been greatly advanced by recent studies using X-ray crystallography, small angle X-ray scattering (SAXS) and single particle electron microscopy as well as biochemical and genetic methodologies.

View Article: PubMed Central - PubMed

Affiliation: Reverse Transcriptase Biochemistry Section, Basic Research Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA. rauschj@mail.nih.gov.

ABSTRACT
HIV-1 Rev is an ~13 kD accessory protein expressed during the early stage of virus replication. After translation, Rev enters the nucleus and binds the Rev response element (RRE), a ~350 nucleotide, highly structured element embedded in the env gene in unspliced and singly spliced viral RNA transcripts. Rev-RNA assemblies subsequently recruit Crm1 and other cellular proteins to form larger complexes that are exported from the nucleus. Once in the cytoplasm, the complexes dissociate and unspliced and singly-spliced viral RNAs are packaged into nascent virions or translated into viral structural proteins and enzymes, respectively. Rev binding to the RRE is a complex process, as multiple copies of the protein assemble on the RNA in a coordinated fashion via a series of Rev-Rev and Rev-RNA interactions. Our understanding of the nature of these interactions has been greatly advanced by recent studies using X-ray crystallography, small angle X-ray scattering (SAXS) and single particle electron microscopy as well as biochemical and genetic methodologies. These advances are discussed in detail in this review, along with perspectives on development of antiviral therapies targeting the HIV-1 RRE.

No MeSH data available.


Related in: MedlinePlus

Models for assembly of HIV-1 Rev on the RRE: (A) “Bridging” model. The first two Rev in the complex bind to IIB and IA high affinity sites on the A-like RRE, as well as to each other, thereby forming a Rev dimer that “bridges” the distance separating two sub-structures. This proposal is based largely upon the observations that the distances separating the apices of the Rev arms in the T/T dimer crystal structure and the IIB and IA motifs modeled to fit the HIV-1 RRE SAXS envelope are both approximately 55 Å. After this initial Rev dimer-RRE complex is formed, assembly is proposed to propagate in both directions along the A-like RRE structure and involve stem loops III/IV, V and more distal portions of stem I; (B) Stem I “loop-back” model. Based on analyses using SAXS and time resolved SHAPE, it has been proposed that following relatively rapid assembly of Rev dimers at R1 and R2 (R1, Region 1—IIB and stem II junction; R2, Region 2—central junction and IA), the remaining dimer in the hexameric Rev complex assembles at R3 (Region 3—a series of purine-rich bulges in a more distant segment of stem I). RNA tertiary interactions bring the stem I terminus into proximity with the RRE central junction (even in the absence of Rev), and the last Rev dimer is accommodated in the fully assembled complex by an induced fit mechanism of conformational sampling; (C) Jellyfish model. Rev initially binds to the IIB high-affinity site, after which five additional Rev molecules assemble on the RRE via a series of consecutive T/T and H/H multimerization domain interactions. These Rev-Rev interactions are facilitated by concomitant Rev ARM binding at adjacent regions on the RRE RNA, such as is observed in the T/T Rev dimer-RNA crystal structure. The six C-terminal domains in this putative Rev-RRE complex would be expected to project in a common direction, which would in turn facilitate NES binding at the Crm1 dimer interface and promote nuclear export.
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viruses-07-02760-f006: Models for assembly of HIV-1 Rev on the RRE: (A) “Bridging” model. The first two Rev in the complex bind to IIB and IA high affinity sites on the A-like RRE, as well as to each other, thereby forming a Rev dimer that “bridges” the distance separating two sub-structures. This proposal is based largely upon the observations that the distances separating the apices of the Rev arms in the T/T dimer crystal structure and the IIB and IA motifs modeled to fit the HIV-1 RRE SAXS envelope are both approximately 55 Å. After this initial Rev dimer-RRE complex is formed, assembly is proposed to propagate in both directions along the A-like RRE structure and involve stem loops III/IV, V and more distal portions of stem I; (B) Stem I “loop-back” model. Based on analyses using SAXS and time resolved SHAPE, it has been proposed that following relatively rapid assembly of Rev dimers at R1 and R2 (R1, Region 1—IIB and stem II junction; R2, Region 2—central junction and IA), the remaining dimer in the hexameric Rev complex assembles at R3 (Region 3—a series of purine-rich bulges in a more distant segment of stem I). RNA tertiary interactions bring the stem I terminus into proximity with the RRE central junction (even in the absence of Rev), and the last Rev dimer is accommodated in the fully assembled complex by an induced fit mechanism of conformational sampling; (C) Jellyfish model. Rev initially binds to the IIB high-affinity site, after which five additional Rev molecules assemble on the RRE via a series of consecutive T/T and H/H multimerization domain interactions. These Rev-Rev interactions are facilitated by concomitant Rev ARM binding at adjacent regions on the RRE RNA, such as is observed in the T/T Rev dimer-RNA crystal structure. The six C-terminal domains in this putative Rev-RRE complex would be expected to project in a common direction, which would in turn facilitate NES binding at the Crm1 dimer interface and promote nuclear export.

Mentions: From the 3D structure of a 232-nt RRE obtained using molecular modeling in conjunction with SAXS, a model for Rev assembly was proposed in which 8 Rev molecules are coaxially arranged along one face of the A-like structure of the truncated RRE (Figure 6A) [51]. Support from this proposal comes primarily from observations that the high affinity Rev binding sites on IIB and stem-loop I are separated by ~55 Å, matching the approximate separation between distal portions of the ARMs in the T/T Rev dimer crystal structure [39]. However, the model also suggests direct binding of Rev to stem loops III/IV and V in higher order complexes and does not involve distal regions of stem I in Rev assembly. Both of these suppositions are inconsistent with prior nuclease protection analysis [32]. The high resolution Rev-dimer-RNA co-crystal structure [27], in which tandem NLS/RBSs bind at adjacent sites on the same helix likewise does not support the IIB-I bridging model of Rev assembly suggested by Wang and colleagues.


HIV Rev Assembly on the Rev Response Element (RRE): A Structural Perspective.

Rausch JW, Le Grice SF - Viruses (2015)

Models for assembly of HIV-1 Rev on the RRE: (A) “Bridging” model. The first two Rev in the complex bind to IIB and IA high affinity sites on the A-like RRE, as well as to each other, thereby forming a Rev dimer that “bridges” the distance separating two sub-structures. This proposal is based largely upon the observations that the distances separating the apices of the Rev arms in the T/T dimer crystal structure and the IIB and IA motifs modeled to fit the HIV-1 RRE SAXS envelope are both approximately 55 Å. After this initial Rev dimer-RRE complex is formed, assembly is proposed to propagate in both directions along the A-like RRE structure and involve stem loops III/IV, V and more distal portions of stem I; (B) Stem I “loop-back” model. Based on analyses using SAXS and time resolved SHAPE, it has been proposed that following relatively rapid assembly of Rev dimers at R1 and R2 (R1, Region 1—IIB and stem II junction; R2, Region 2—central junction and IA), the remaining dimer in the hexameric Rev complex assembles at R3 (Region 3—a series of purine-rich bulges in a more distant segment of stem I). RNA tertiary interactions bring the stem I terminus into proximity with the RRE central junction (even in the absence of Rev), and the last Rev dimer is accommodated in the fully assembled complex by an induced fit mechanism of conformational sampling; (C) Jellyfish model. Rev initially binds to the IIB high-affinity site, after which five additional Rev molecules assemble on the RRE via a series of consecutive T/T and H/H multimerization domain interactions. These Rev-Rev interactions are facilitated by concomitant Rev ARM binding at adjacent regions on the RRE RNA, such as is observed in the T/T Rev dimer-RNA crystal structure. The six C-terminal domains in this putative Rev-RRE complex would be expected to project in a common direction, which would in turn facilitate NES binding at the Crm1 dimer interface and promote nuclear export.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4488727&req=5

viruses-07-02760-f006: Models for assembly of HIV-1 Rev on the RRE: (A) “Bridging” model. The first two Rev in the complex bind to IIB and IA high affinity sites on the A-like RRE, as well as to each other, thereby forming a Rev dimer that “bridges” the distance separating two sub-structures. This proposal is based largely upon the observations that the distances separating the apices of the Rev arms in the T/T dimer crystal structure and the IIB and IA motifs modeled to fit the HIV-1 RRE SAXS envelope are both approximately 55 Å. After this initial Rev dimer-RRE complex is formed, assembly is proposed to propagate in both directions along the A-like RRE structure and involve stem loops III/IV, V and more distal portions of stem I; (B) Stem I “loop-back” model. Based on analyses using SAXS and time resolved SHAPE, it has been proposed that following relatively rapid assembly of Rev dimers at R1 and R2 (R1, Region 1—IIB and stem II junction; R2, Region 2—central junction and IA), the remaining dimer in the hexameric Rev complex assembles at R3 (Region 3—a series of purine-rich bulges in a more distant segment of stem I). RNA tertiary interactions bring the stem I terminus into proximity with the RRE central junction (even in the absence of Rev), and the last Rev dimer is accommodated in the fully assembled complex by an induced fit mechanism of conformational sampling; (C) Jellyfish model. Rev initially binds to the IIB high-affinity site, after which five additional Rev molecules assemble on the RRE via a series of consecutive T/T and H/H multimerization domain interactions. These Rev-Rev interactions are facilitated by concomitant Rev ARM binding at adjacent regions on the RRE RNA, such as is observed in the T/T Rev dimer-RNA crystal structure. The six C-terminal domains in this putative Rev-RRE complex would be expected to project in a common direction, which would in turn facilitate NES binding at the Crm1 dimer interface and promote nuclear export.
Mentions: From the 3D structure of a 232-nt RRE obtained using molecular modeling in conjunction with SAXS, a model for Rev assembly was proposed in which 8 Rev molecules are coaxially arranged along one face of the A-like structure of the truncated RRE (Figure 6A) [51]. Support from this proposal comes primarily from observations that the high affinity Rev binding sites on IIB and stem-loop I are separated by ~55 Å, matching the approximate separation between distal portions of the ARMs in the T/T Rev dimer crystal structure [39]. However, the model also suggests direct binding of Rev to stem loops III/IV and V in higher order complexes and does not involve distal regions of stem I in Rev assembly. Both of these suppositions are inconsistent with prior nuclease protection analysis [32]. The high resolution Rev-dimer-RNA co-crystal structure [27], in which tandem NLS/RBSs bind at adjacent sites on the same helix likewise does not support the IIB-I bridging model of Rev assembly suggested by Wang and colleagues.

Bottom Line: Once in the cytoplasm, the complexes dissociate and unspliced and singly-spliced viral RNAs are packaged into nascent virions or translated into viral structural proteins and enzymes, respectively.Rev binding to the RRE is a complex process, as multiple copies of the protein assemble on the RNA in a coordinated fashion via a series of Rev-Rev and Rev-RNA interactions.Our understanding of the nature of these interactions has been greatly advanced by recent studies using X-ray crystallography, small angle X-ray scattering (SAXS) and single particle electron microscopy as well as biochemical and genetic methodologies.

View Article: PubMed Central - PubMed

Affiliation: Reverse Transcriptase Biochemistry Section, Basic Research Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA. rauschj@mail.nih.gov.

ABSTRACT
HIV-1 Rev is an ~13 kD accessory protein expressed during the early stage of virus replication. After translation, Rev enters the nucleus and binds the Rev response element (RRE), a ~350 nucleotide, highly structured element embedded in the env gene in unspliced and singly spliced viral RNA transcripts. Rev-RNA assemblies subsequently recruit Crm1 and other cellular proteins to form larger complexes that are exported from the nucleus. Once in the cytoplasm, the complexes dissociate and unspliced and singly-spliced viral RNAs are packaged into nascent virions or translated into viral structural proteins and enzymes, respectively. Rev binding to the RRE is a complex process, as multiple copies of the protein assemble on the RNA in a coordinated fashion via a series of Rev-Rev and Rev-RNA interactions. Our understanding of the nature of these interactions has been greatly advanced by recent studies using X-ray crystallography, small angle X-ray scattering (SAXS) and single particle electron microscopy as well as biochemical and genetic methodologies. These advances are discussed in detail in this review, along with perspectives on development of antiviral therapies targeting the HIV-1 RRE.

No MeSH data available.


Related in: MedlinePlus