HIV-miR-H1 evolvability during HIV pathogenesis

Abstract

The discovery of microRNAs (miRNAs) in viruses has generated considerable attention into their functional relevance in processes such as cell death, viral proliferation, and oncogenesis. Two early studies found no detectable miRNAs expressed within HIV; however, several studies have verified the existence and function of three HIV miRNAs, most notably HIV-miR-TAR, thus making the earlier results controversial. Although miRNAs are highly conserved within most species, HIV is known to have a high mutation rate, which could contribute to the opposing experimental findings and raises questions about whether all HIV miRNAs are robust enough to maintain their integrity, especially in viral regions prone to insertions and deletions. In addition, could the evolvability of HIV miRNAs contribute to the diversity in HIV disease pathogenesis? To address this question, we examined mutations in 1293 sequences in a suspect HIV miRNA, called miR-H1, derived from a large variety of tissues from seven patients. We found considerable diversity within the structures, including a patient-specific deletion and the potential for the development of new miRNAs as a result of deletions. We also note a potential disease association between a less stable miR-H1 and the development of AIDS-related lymphoma (ARL).

Fig. 1

Distance between patient sequence populations. Each patient was given a color code as shown in the figure legend. The distance between the patient on the x-axis and other patients studied is shown as a colored bar. Distances are provided as a percent with standard errors displayed on each bar. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of the article.)

Fig. 2

Distance within patient sequence populations. Distances within each patient’s sequences are provided as a percent with standard errors displayed on each bar. The number of sequences used for each patient is shown below the patient designation.

Fig. 3

Dominant stem-loop structures of the HIV-1 miR-H1 sequence for all patients. The published stem-loop structure is shown in the upper left of the figure. The mature miRNA sequence, which would be excised after dicer processing, is highlighted in blue. For each patient in the study, nucleotide changes from published structure are highlighted in red. Gaps introduced to maximize the structure’s stability are shown with dashes. Hash marks are used to indicate bulges where a different number of nucleic acids occurred on either side of the stem. Base pairing is indicated with solid lines. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of the article.)

Fig. 4

Replacement of the deletion in patient IV’s stem-loop structure with data 3′ to the deletion. Notation used for structures is identical to that in Fig. 1. The nucleotides 3′ to the deletion, which became part of a potentially new miRNA, are boxed. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of the article.)

Fig. 5

Sequences in patient CX containing deletions. Notation used in structures is identical to that in Fig. 1. The nucleotides 3′ or 5′ to the deletion, which became part of a potentially new miRNA, are boxed. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of the article.)

Fig. 6

Nucleic acid substitution patterns for each patient over all sequence groups. Notation used for structures is identical to that in Fig. 1. Sequence groups were defined in Tables 4–10. Arrows point to substitutions. Substitutions are indicated using the notation “nucleic acid substitution:group number.” In some cases a substitution occurred over multiple groups and the group numbers are separated with a comma. An “X” indicates the loss and a “∧” indicates the addition of a nucleic acid. Substitutions that would potentially alter the structure are shown in red. Patient IV contained significant variation in stomach tissue (Group 6) from other sequences in the data set. These substitutions are highlighted in green. Patient DY also contained significant variation in a subset of liver sequences (Group 3) and these are also highlighted in green. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of the article.)

Fig. 7

Nucleotide substitution probability matrix. Substitutions and probabilities were calculated over all pre-miR-H1 genomes as described in Section 2. The probability of transitions and transversions are provided in the matrix.