Multimodal Functionalities of HIV-1 Integrase

Round 1

Reviewer 1 Report

The authors present a very interesting and timely review of HIV-1 integrase and virus particle maturation.  The HIV-1 story is very well covered and clearly presented.  They present a well-written article demonstrating a command of the HIV-1 IN field. The emphasis on association of IN mutants to the various described Classes is highly appropriate.  The classification criteria in Table 1 is interesting and should be useful in the future. They suggest that additional studies are needed to address the roles of IN-vRNA binding in virus particles maturation and reverse transcription across a variety of retroviruses.  The authors cited several MLV IN studies. There has been a significant number of earlier α-retrovirus IN studies that focus on 1) IN in ribonucleoprotein particles (RNP) derived from virus core particles, 2) the IN moiety on the β subunit of the αβ reverse transcriptase and its role in specifically binding primer tRNA^Trp, 3) the ability of IN to bind different ssRNA polymers in vitro, 4) mapping the domains of IN necessary for binding ssRNA by IN truncations, 5) IN mutants affecting gag-pol processing in virions while not affecting integration, and 6) three adjacent aptamer ssRNA (4 bases) binding pockets identified on the crystal structure of dimeric IN core (1.8 Å resolution) . Citing several of these α-retrovirus studies would be helpful to investigators as a guide for future studies on IN-RNA binding properties of different retroviruses.

Minor Points:

P1, maybe insert Fig. 1A after [3] on line 41. There is significant discussion of the virus structure thereafter without visual reference. It would be helpful to readers not familiar with the retrovirus structure.

P 3, Fig. 2 is too large to fit in the lines.

P 5, Fig. 3. The gray spheres identifying zinc are not apparent in the NTD.

P 8, Fig. 5.  It is very difficult to visualize the amino acid blue spheres with the background blue ribbon structures in both Fig. 5 A and B. The yellow spheres in 5B are excellent.  A change of color with the background or spheres would be important to better visualize and understand the Class I and II IN mutants. The different classes of IN mutant viruses makes sense.

Articles on α-retrovirus IN-RNA binding mentioned above:

1) IN in ribonucleoprotein complexes derived from virus core particles—J. Virology (1974) 13: 513-528 and Biochem. Biophys. Acta (1974) 361:53-58.

2) IN moiety on the β subunit of αβ reverse transcriptase and its role in binding the specific primer tRNA^Trp --PNAS (1975) 72: 2535-2539 and Virology (1976) 75: 26-32.

3) ability of IN to bind ssRNA -- Virology (1978) 89: 119-132; J. Virology (1988) 62: 2358-2365;

4) mapping ssRNA binding domain to C-terminus on truncated IN in vitro, J. Virology (1991) 65:1160-1167; point and deletion mutagenesis of IN (from S262 to C-terminus end) for single round infectivities —Communications Biol. (2021) 4:330.

5) IN mutants affecting gag-pol processing in virions—Virology (1984) 137:358-370 (Possibly a Class IIc mutant?).

6) three adjacent pockets identified on the crystal structure of IN dimer core (1.8 Å resolution) that have docked aptamer ssRNA (4 bases)--PLoS One (2011) 6: e23032.

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Reviewer 2 Report

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