INI1/SMARCB1 Rpt1 domain mimics TAR RNA in binding to integrase to facilitate HIV-1 replication

Abstract

INI1/SMARCB1 binds to HIV-1 integrase (IN) through its Rpt1 domain and exhibits multifaceted role in HIV-1 replication. Determining the NMR structure of INI1-Rpt1 and modeling its interaction with the IN-C-terminal domain (IN-CTD) reveal that INI1-Rpt1/IN-CTD interface residues overlap with those required for IN/RNA interaction. Mutational analyses validate our model and indicate that the same IN residues are involved in both INI1 and RNA binding. INI1-Rpt1 and TAR RNA compete with each other for IN binding with similar IC50 values. INI1-interaction-defective IN mutant viruses are impaired for incorporation of INI1 into virions and for particle morphogenesis. Computational modeling of IN-CTD/TAR complex indicates that the TAR interface phosphates overlap with negatively charged surface residues of INI1-Rpt1 in three-dimensional space, suggesting that INI1-Rpt1 domain structurally mimics TAR. This possible mimicry between INI1-Rpt1 and TAR explains the mechanism by which INI1/SMARCB1 influences HIV-1 late events and suggests additional strategies to inhibit HIV-1 replication.

Multimodal Functionalities of HIV-1 Integrase

“…Typified by changes of the DDE active site residues, class I IN mutant viruses contain the normal complement of virion proteins, harbor a vRNA-binding competent IN, and generally appear phenotypically normal and display the WT level of reverse transcription; in certain studies, subtle reverse transcription (at most 2-fold) and particle morphology defects have also been noted [ 50 , 51 , 52 , 54 , 56 , 75 , 114 , 117 , 118 , 119 , 120 , 121 , 122 , 123 , 124 , 125 ]. Class I IN mutant viruses accordingly behave as expected for viruses that are specifically blocked at the integration step of the HIV-1 lifecycle.…”

“…INI1-dependent incorporation of Sin3a-associated protein 18 kD (SAP18) and histone deacetylase 1 (HDAC1) into virus particles was reported to underlie the role of INI1 in HIV-1 reverse transcription, as virions engineered to harbor catalytically inactive H141A HDAC1 were defective for vDNA synthesis [ 169 ]. Class I IN mutant W235E protein is also defective for INI1 binding, and IN mutant W235E particles accordingly lacked INI1, seemingly dispensing critical roles for the IN-INI1 interaction in HIV-1 particle production and reverse transcription [ 125 ].…”

“…The vRNP is the most electron-dense material observed via TEM [ 7 , 175 ]. Under these conditions, WT HIV-1 reveals a large proportion of mature particles with minor populations of eccentric and immature particles [ 7 , 53 , 56 , 58 , 125 , 176 , 177 ] ( Figure 1 ). Class II IN mutant virus preparations by contrast harbor qualitatively reversed proportions of these respective virion populations, yielding a predominance of eccentric and immature particles [ 7 , 53 , 56 , 58 , 112 , 125 , 177 ].…”

“…Under these conditions, WT HIV-1 reveals a large proportion of mature particles with minor populations of eccentric and immature particles [ 7 , 53 , 56 , 58 , 125 , 176 , 177 ] ( Figure 1 ). Class II IN mutant virus preparations by contrast harbor qualitatively reversed proportions of these respective virion populations, yielding a predominance of eccentric and immature particles [ 7 , 53 , 56 , 58 , 112 , 125 , 177 ]. Although less routinely categorized, class II IN mutant viruses can also harbor increased frequencies of particles with non-conical/malformed capsid shells [ 7 , 51 ] as well as particles that lack electron density altogether [ 51 , 53 ].…”

“…Although less routinely categorized, class II IN mutant viruses can also harbor increased frequencies of particles with non-conical/malformed capsid shells [ 7 , 51 ] as well as particles that lack electron density altogether [ 51 , 53 ]. Interestingly, class I IN mutant W235E virions harbored a higher percentage of eccentric particles than the WT, though appeared more similar to the WT than did a class II IN mutant control virus [ 125 ].…”