Current HIV Research, 2006, 4, 131-139 131

1570-162X/06 $50.00+.00 © 2006 Bentham Science Publishers Ltd.
Retrovirus Translation Initiation: Issues and Hypotheses Derived from
Study of HIV-1
Alper Yilmaz
1,4,§
, Cheryl Bolinger
1,4,§
and Kathleen Boris-Lawrie
*,1,2,3,4,5

Center for Retrovirus Research
1
, Departments of Veterinary Biosciences
2
and Molecular Virology, Immunology &
Medical Genetics
3
, Molecular, Cellular & Developmental Biology Graduate Program
4
, Comprehensive Cancer Center
5
,
The Ohio State University, Columbus, OH, USA
Abstract: Human immunodeficiency virus type 1 (HIV-1) has a small, multifunctional genome that encodes a relatively
large and complex proteome. The virus has adopted specialized post-transcriptional control mechanisms to maximize its
coding capacity while economically maintaining the information stored in cis-acting replication sequences. The conserved
features of the 5’ untranslated region of all viral transcripts suggest they are poor substrates for cap-dependent ribosome
scanning and provide a compelling rationale for internal initiation of translation. This article summarizes key
experimental results of studies that have evaluated HIV-1 translation initiation. A model is discussed in which cap-
dependent and cap-independent initiation mechanisms of HIV-1 co-exist to ensure viral protein production in the context
of 1) structured replication motifs that inhibit ribosome scanning, and 2) alterations in host translation machinery in
response to HIV-1 infection or other cellular stresses. We discuss key issues that remain to be understood and suggest
parameters to validate internal initiation activity in HIV-1 and other retroviruses.
Keywords: Retrovirus translational control, unspliced RNA, 5’ untranslated region, ribosome scanning, internal ribosome entry
site.
INTRODUCTION
Retrovirus Primary Transcription Product Can Function
as Precursor mRNA, mRNA, or Viral Genomic RNA
Retroviral genomes are multifunctional RNAs that utilize
virally encoded reverse transcriptase to replicate genomic
RNA through a proviral DNA intermediate [81]. The
provirus becomes permanently integrated into the host cell
chromosome and is expressed like a cellular gene by the host
cell transcription, RNA processing, and translation
machinery. The primary retroviral transcript interacts with
the cellular RNA processing machinery to become capped
and polyadenylated. One fraction of the retroviral transcript
behaves like a typical cellular pre-mRNA in that the
spliceosome is engaged and the intron is removed. As a
consequence, it is expected that the exon junction complex is
deposited on spliced retroviral transcripts and functions as it
does on cellular mRNAs to promote a pioneer round of
translation, followed by nuclear export and finally, steady
state translation in the cytoplasm [20, 28, 33, 50, 57, 86].
Another fraction of pre-mRNA achieves nuclear export and
translational utilization independently of splicing
commitment and this activity is trans-activated by the
essential HIV Rev protein. Rev interacts with the Rev
response element (RRE) within unspliced and incompletely
spliced viral RNAs and solicits interaction with the CRM1
nuclear export receptor [35, 65]. In the cytoplasm, the
unspliced transcript plays a dual role as mRNA template for
translation and as genomic RNA that is packaged into


*Address correspondence to this author at the Ohio State University, 1925
Coffey Road, Columbus, OH 43210, USA; Tel: 614/292-1392; Fax:
614/292-6473; E-mail: boris-lawrie.1@osu.edu

§
These authors contributed equally to this article.
assembling virions [17]. Experiments with metabolic
inhibitors to address the relationship between HIV-1 RNA
packaging and translation have determined that unspliced
HIV-1 RNA does not segregate into separate pools for
translation and packaging, as has been identified for murine
leukemia virus [16, 43, 54]. Lack of translation is not a
prerequisite to qualify HIV-1 unspliced RNA for packaging
into progeny virions [16]. Instead, unspliced HIV-1 RNA
functions interchangeably as an mRNA template for
translation and as genomic RNA that is packaged [16]. A
similar conclusion was reached for Rous sarcoma virus
(RSV) in a study that evaluated the relationship between
translation-dependent nonsense mediated decay and RNA
packaging [48].
Barriers Posed Against Efficient Translation of All HIV-
1 Transcripts
While translation and packaging are not mutually
exclusive processes for HIV-1, the packaging signal and
other structural motifs in the 5’ untranslated regions (UTRs)
have been demonstrated to inhibit ribosome scanning and
translation initiation [29, 55, 59]. The 5’ UTR is the most
conserved region in HIV-1 [7] and contains several cis-
acting replication sequences, including the Tat trans-
activation response element (TAR), poly(A) signal, primer
binding site, dimerization signal, splice donor site and the
packaging signal. Some of the same structural motifs are
maintained in spliced HIV-1 transcripts. HIV-1 encodes over
30 distinct spliced transcripts as a result of alternative
splicing of the primary transcription product [66, 73]. All of
the spliced transcripts and the unspliced gag mRNA share
the same 289 nt 5’ noncoding exon (Fig. 1). Because this 5’
UTR contains several of the highly conserved structured
replication motifs, ribosome scanning of the spliced HIV-1
mRNAs is likewise expected to be inefficient. In addition,

132 Current HIV Research, 2006, Vol. 4, No. 2 Yilmaz et al.
ligation to various distal exons produces a collection of 5’
UTRs that are ~350 to 775 nt in length and contain
degenerate Kozak consensus sequences and upstream AUG
or CUG initiator codons (Fig. 1).
CUG can be recognized as a non-AUG initiator codon
[34] and the recognition of an upstream CUG or AUG
typically decreases initiation at downstream initiator codon
[23]. The efficiency of non-AUG initiation can be modulated
by the context surrounding the codon, the secondary
structure of the transcript, and in response to changes in the
growth status of the cells. The observation that the efficiency
of non-AUG initiation in growth-regulatory mRNAs changes
in response to changes in cellular growth conditions
indicates that the scanning preinitiation complex can be
regulated to affect the recognition of such a non-AUG codon
[34].
The conservation of a relatively long 5’ UTR that harbors
complex structural motifs and upstream initiator codons
implies that both the unspliced gag mRNA and the
alternatively spliced HIV-1 transcripts are poor substrates for
ribosome scanning and efficient cap-dependent translation.
Because the replication strategy of this virus family
necessitates conservation of a long and highly structured 5’
UTR, the ribosome scanning and initiation of cap-dependent
translation is expected to be inefficient for retroviruses in
general.
























Fig. (1). Organization and features of the 5’ untranslated regions of the major HIV-1 transcripts. Structure of the predominant
transcript for each open reading frame is shown from among the ~30 alternatively spliced transcripts that are detectable by RT-PCR [66].
Colored lines highlight sequences that comprise the various 5’ UTRs. The blue line depicts the first noncoding exon, which is 289 nts in
length and is present in all HIV-1 transcripts. The black line denotes the additional 47 nts that are maintained in the unspliced transcript,
which is mRNA template for translation to Gag and Gag-Pol protein and is genomic RNA that is packaged into progeny virions. The gray
lines represent coding regions and dashed lines denote introns. AUG indicates the translation initiation codon. Also indicated is the number
of CUG and AUG codons that are present upstream of actual initiation codon. Translation to Vpu and Env is achieved from the same
transcript. The vpu AUG is subject to leaky scanning and scanning may continue until recognition of the downstream env AUG. The unused
AUG in this bicistronic transcript is labeled in parenthesis. Depiction of predicted secondary structure of replication motifs is adapted from
[7]; the motifs include the trans-activation responsive sequence; primer binding site; dimer initiation site; 5’ splice site; and core RNA
packaging signal. Alternatively spliced exons, which are depicted in color, may induce variations in the folding of the upstream region,
which are not shown. Free energy predictions were calculated using Mfold [51, 87]. Deviations from Kozak consensus are indicated in
lowercase letters; underlined nts indicate those most critical for efficient cap-dependent translation initiation.