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Imperfect DNA mirror repeats in the gag gene of HIV-1 (HXB2) identify key functional domains and coincide with protein structural elements in each of the mature proteins.

Lang DM - Virol. J. (2007)

Bottom Line: However, imperfect mirror repeats (IMRs) having > or = 50% symmetry are common in the protein coding DNA of monomeric proteins and their distribution has been found to coincide with protein structural elements - helices, beta sheets and turns.Throughout the protein, IMRs coincide with functionally significant segments of the protein.The frequency and distribution of IMRs in HIV-1 Gag indicates that DNA symmetry is a fundamental property of protein coding DNA and that different levels of symmetry are associated with different functional aspects of the gene and its protein.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Contemporary Sciences, University of Abertay-Dundee, Bell Street, Dundee DD1 1HG, Scotland, UK. dml_mail@yahoo.com

ABSTRACT

Background: A DNA mirror repeat is a sequence segment delimited on the basis of its containing a center of symmetry on a single strand, e.g. 5'-GCATGGTACG-3'. It is most frequently described in association with a functionally significant site in a genomic sequence, and its occurrence is regarded as noteworthy, if not unusual. However, imperfect mirror repeats (IMRs) having > or = 50% symmetry are common in the protein coding DNA of monomeric proteins and their distribution has been found to coincide with protein structural elements - helices, beta sheets and turns. In this study, the distribution of IMRs is evaluated in a polyprotein - to determine whether IMRs may be related to the position or order of protein cleavage or other hierarchal aspects of protein function. The gag gene of HIV-1 [GenBank:K03455] was selected for the study because its protein motifs and structural components are well documented.

Results: There is a highly specific relationship between IMRs and structural and functional aspects of the Gag polyprotein. The five longest IMRs in the polyprotein translate a key functional segment in each of the five cleavage products. Throughout the protein, IMRs coincide with functionally significant segments of the protein. A detailed annotation of the protein, which combines structural, functional and IMR data illustrates these associations. There is a significant statistical correlation between the ends of IMRs and the ends of PSEs in each of the mature proteins. Weakly symmetric IMRs (> or 33%) are related to cleavage positions and processes.

Conclusion: The frequency and distribution of IMRs in HIV-1 Gag indicates that DNA symmetry is a fundamental property of protein coding DNA and that different levels of symmetry are associated with different functional aspects of the gene and its protein. The interaction between IMRs and protein structure and function is precise and interwoven over the entire length of the polyprotein. The distribution of IMRs and their relationship to structural and functional motifs in the protein that they translate, suggest that DNA-driven processes, including the selection of mirror repeats, may be a constraining factor in molecular evolution.

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The largest mIMR in the nucleocapsid spans the two Cys-His boxes [NCBI:1F6U [18]]. Figure 3A illustrates the largest mIMR in the nucleocapsid – #6-gag. This mIMR spans both zinc knuckles and the spacer between them. Each of the next largest mIMRs in the NC, translates one of the Cys-His boxes. Figure 3B illustrates the first Cys-His box. Figure C (same polar orientation as A and B, but rotated) illustrates the two longest rdIMRs in Gag that occur in the nucleocapsid – $1-gag and $4-gag – which overlap; within the overlap region (in purple) two amino acids bind the zinc ion [19].
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Figure 3: The largest mIMR in the nucleocapsid spans the two Cys-His boxes [NCBI:1F6U [18]]. Figure 3A illustrates the largest mIMR in the nucleocapsid – #6-gag. This mIMR spans both zinc knuckles and the spacer between them. Each of the next largest mIMRs in the NC, translates one of the Cys-His boxes. Figure 3B illustrates the first Cys-His box. Figure C (same polar orientation as A and B, but rotated) illustrates the two longest rdIMRs in Gag that occur in the nucleocapsid – $1-gag and $4-gag – which overlap; within the overlap region (in purple) two amino acids bind the zinc ion [19].

Mentions: Figure 3 illustrates the two largest mIMRs in the nucleocapsid. The largest (Fig. 3A) spans the entire region connecting the two Cys-His boxes. The second largest (Fig. 3B) spans the EF1α binding site and first Cys-His box. The largest rdIMRs in the NC overlap (Fig. 3C), and a Zn ion is bound within the region translated by the overlap. The Cys-His boxes are zinc finger binding domains which enable NC to bind to nucleic acids, and the Zn ion increases the affinity of NC for nucleic acids; NC also has unwinding properties, resembling a DNA topoimerase [17].


Imperfect DNA mirror repeats in the gag gene of HIV-1 (HXB2) identify key functional domains and coincide with protein structural elements in each of the mature proteins.

Lang DM - Virol. J. (2007)

The largest mIMR in the nucleocapsid spans the two Cys-His boxes [NCBI:1F6U [18]]. Figure 3A illustrates the largest mIMR in the nucleocapsid – #6-gag. This mIMR spans both zinc knuckles and the spacer between them. Each of the next largest mIMRs in the NC, translates one of the Cys-His boxes. Figure 3B illustrates the first Cys-His box. Figure C (same polar orientation as A and B, but rotated) illustrates the two longest rdIMRs in Gag that occur in the nucleocapsid – $1-gag and $4-gag – which overlap; within the overlap region (in purple) two amino acids bind the zinc ion [19].
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2211468&req=5

Figure 3: The largest mIMR in the nucleocapsid spans the two Cys-His boxes [NCBI:1F6U [18]]. Figure 3A illustrates the largest mIMR in the nucleocapsid – #6-gag. This mIMR spans both zinc knuckles and the spacer between them. Each of the next largest mIMRs in the NC, translates one of the Cys-His boxes. Figure 3B illustrates the first Cys-His box. Figure C (same polar orientation as A and B, but rotated) illustrates the two longest rdIMRs in Gag that occur in the nucleocapsid – $1-gag and $4-gag – which overlap; within the overlap region (in purple) two amino acids bind the zinc ion [19].
Mentions: Figure 3 illustrates the two largest mIMRs in the nucleocapsid. The largest (Fig. 3A) spans the entire region connecting the two Cys-His boxes. The second largest (Fig. 3B) spans the EF1α binding site and first Cys-His box. The largest rdIMRs in the NC overlap (Fig. 3C), and a Zn ion is bound within the region translated by the overlap. The Cys-His boxes are zinc finger binding domains which enable NC to bind to nucleic acids, and the Zn ion increases the affinity of NC for nucleic acids; NC also has unwinding properties, resembling a DNA topoimerase [17].

Bottom Line: However, imperfect mirror repeats (IMRs) having > or = 50% symmetry are common in the protein coding DNA of monomeric proteins and their distribution has been found to coincide with protein structural elements - helices, beta sheets and turns.Throughout the protein, IMRs coincide with functionally significant segments of the protein.The frequency and distribution of IMRs in HIV-1 Gag indicates that DNA symmetry is a fundamental property of protein coding DNA and that different levels of symmetry are associated with different functional aspects of the gene and its protein.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Contemporary Sciences, University of Abertay-Dundee, Bell Street, Dundee DD1 1HG, Scotland, UK. dml_mail@yahoo.com

ABSTRACT

Background: A DNA mirror repeat is a sequence segment delimited on the basis of its containing a center of symmetry on a single strand, e.g. 5'-GCATGGTACG-3'. It is most frequently described in association with a functionally significant site in a genomic sequence, and its occurrence is regarded as noteworthy, if not unusual. However, imperfect mirror repeats (IMRs) having > or = 50% symmetry are common in the protein coding DNA of monomeric proteins and their distribution has been found to coincide with protein structural elements - helices, beta sheets and turns. In this study, the distribution of IMRs is evaluated in a polyprotein - to determine whether IMRs may be related to the position or order of protein cleavage or other hierarchal aspects of protein function. The gag gene of HIV-1 [GenBank:K03455] was selected for the study because its protein motifs and structural components are well documented.

Results: There is a highly specific relationship between IMRs and structural and functional aspects of the Gag polyprotein. The five longest IMRs in the polyprotein translate a key functional segment in each of the five cleavage products. Throughout the protein, IMRs coincide with functionally significant segments of the protein. A detailed annotation of the protein, which combines structural, functional and IMR data illustrates these associations. There is a significant statistical correlation between the ends of IMRs and the ends of PSEs in each of the mature proteins. Weakly symmetric IMRs (> or 33%) are related to cleavage positions and processes.

Conclusion: The frequency and distribution of IMRs in HIV-1 Gag indicates that DNA symmetry is a fundamental property of protein coding DNA and that different levels of symmetry are associated with different functional aspects of the gene and its protein. The interaction between IMRs and protein structure and function is precise and interwoven over the entire length of the polyprotein. The distribution of IMRs and their relationship to structural and functional motifs in the protein that they translate, suggest that DNA-driven processes, including the selection of mirror repeats, may be a constraining factor in molecular evolution.

Show MeSH