Cloning and heterologous expression of an alpha1,3-fucosyltransferase gene from the gastric pathogen Helicobacter pylori

Helicobacter pylori is an important human pathogen which causes both gastric and duodenal ulcers and is also associated with gastric cancer and lymphoma. This microorganism has been shown to express cell surface glycoconjugates including Lewis X (Lex) and Lewis Y. These bacterial oligosaccharides are structurally similar to tumor-associated carbohydrate antigens found in mammals. In this study, we report the cloning of a novel alpha1,3-fucosyltransferase gene (HpfucT) involved in the biosynthesis of Lex within H. pylori. The deduced amino acid sequence of HpfucT consists of 478 residues with the calculated molecular mass of 56,194 daltons, which is approximately 100 amino acids longer than known mammalian alpha1,3/1,4-fucosyltransferases. The approximately 52-kDa protein encoded by HpfucT was expressed in Escherichia coli CSRDE3 cells and gave rise to alpha1,3-fucosyltransferase activity but neither alpha1,4-fucosyltransferase nor alpha1,2-fucosyltransferase activity as characterized by radiochemical assays and capillary zone electrophoresis. Truncation of the C-terminal 100 amino acids of HpFuc-T abolished the enzyme activity. An approximately 72-amino acid region of HpFuc-T exhibits significant sequence identity (40-45%) with the highly conserved C-terminal catalytic domain among known mammalian and chicken alpha1,3-fucosyltransferases. These lines of evidence indicate that the HpFuc-T represents the bacterial alpha1,3-fucosyltransferase. In addition, several structural features unique to HpFuc-T, including 10 direct repeats of seven amino acids and the lack of the transmembrane segment typical for known eukaryotic alpha1,3-fucosyltransferases, were revealed. Notably, the repeat region contains a leucine zipper motif previously demonstrated to be responsible for dimerization of various basic region-leucine zipper proteins, suggesting that the HpFuc-T protein could form dimers.

The Helicobacter pylori gene encoding phosphatidylserine synthase: sequence, expression, and insertional mutagenesis

The Helicobacter pylori pss gene, coding for phosphatidylserine synthase (PSS), was cloned and sequenced in this study. A polypeptide of 237 amino acids was deduced from the PSS sequence. H. pylori PSS exhibits significant amino acid sequence identity with the PSS proteins found in the archaebacterium Methanococcus jannaschii, the gram-positive bacterium Bacillus subtilis, and the yeast Saccharomyces cerevisiae but none with its Escherichia coli counterpart. Expression of the putative pss gene in maxicells gave rise to a product of approximately 26 kDa, which is in agreement with the predicted molecular mass of 26,617 Da. A manganese-dependent PSS activity was found in the membrane fractions of the E. coli cells overexpressing the H. pylori pss gene product. This result indicates that this enzyme is a membrane-bound protein, a conclusion which is supported by the fact that the PSS protein contains several local hydrophobic segments which could form transmembrane helices. The pss gene was inactivated with a chloramphenicol acetyltransferase cassette on the plasmid. However, an isogenic pss gene-disrupted mutant of H. pylori UA802 could not be obtained, suggesting that this enzyme plays an essential role in the growth of this organism.

[Cloning and permanent expression in eukaryotic cells of rhTpo]

OBJECTIVE

To obtain recombinant human thrombopoietin (rhTpo).

METHODS

rhTpo gene was cloned from fetal liver mRNA by means of RT-PCR and subcloned into permanent expressing plasmid RC/CMV in order to form a recombinant permanent expressing plasmid RC/CMV/Tpo.

RESULTS AND CONCLUSION

After being transferred into CHO cells, the eukaryotic permanent expression of rhTpo, which can enhance murine megakaryocyte colony growth in vitro, was obtained.

Helicobacter pylori genes hpcopA and hpcopP constitute a cop operon involved in copper export

We previously reported that a gene hpcopA isolated from Helicobacter pylori is associated with copper transport. In the present study, the DNA upstream of the hpcopA was cloned and the nucleotide sequence analyzed. An open reading frame coding for 124 amino acids was predicted, which was connected in frame to the hpcopA. The deduced protein sequence exhibits striking homology with known copper-transporting P-type ATPases. Disruption of this ORF renders H. pylori hypersensitive to copper present in growth media, indicating that it encodes the N-terminal amino acid sequence of the hpCopA protein. Measurement of copper content in the wild-type and hpcopA-disrupted cells showed that the copper content was increased in the mutant cells, further supporting that the previous proposal that the gene hpcopA is involved in copper export. In addition, the cop operon consisting of the genes hpcopA and hpcopP was identified by primer extension and reverse transcription-polymerase chain reaction. Our results indicate that the genes for copper import and export are located in separate operons within H. pylori.

Sequencing, expression, and genetic characterization of the Helicobacter pylori ftsH gene encoding a protein homologous to members of a novel putative ATPase family

In this study, we isolated and sequenced a Helicobacter pylori gene, designated ftsH, coding for a 632-amino-acid protein which displayed striking similarity throughout its full length to FtsH proteins identified in Escherichia coli, Lactococcus lactis, and Bacillus subtilis. H. pylori FtsH also possessed approximately 200-amino-acid region containing a putative ATPase module which is conserved among members of the AAA protein family (AAA, ATPase associated with diverse cellular activities). The H. pylori ftsH product was overexpressed in E. coli and reacted immunologically with an anti-E. coli FtsH serum (T. Tomoyasu, K. Yamanaka, K. Murata, T. Suzaki, P. Bouloc, A. Kato, H. Niki, S. Hiraga, and T. Ogura, J. Bacteriol. 175:1352-1357, 1993). FtsH was also shown to be present in the membrane fraction of H. pylori, suggesting that it is membrane bound. Disruption of the ftsH gene led to the loss of viability of H. pylori, demonstrating that this gene is essential for cell growth. Overproduction of both H. pylori FtsH and E. coli FtsH together tremendously reduced the growth rate of the E. coli host cells, whereas the growth of the E. coli cells carrying the wild-type E. coli ftsH operon on the chromosome was not significantly affected by overproduction of H. pylori FtsH itself. This result suggests that the abnormal growth of cells results from interaction between H. pylori FtsH and E. coli FtsH.

Conservation and diversity of the Helicobacter pylori copper-transporting ATPase gene (copA) sequence among Helicobacter species and Campylobacter species detected by PCR and RFLP

BACKGROUND

Helicobacter pylori is a causative pathogen of such human stomach diseases as chronic type B gastritis, ulcer, and possibly gastric carcinoma. As a cofactor in various redox enzymes and an essential trace metal required for the synthesis of metalloproteins, copper might play a role in the pathogenesis of H. pylori. A gene, copA, associated with copper transport, has been isolated from H. pylori UA802. In this study, conservation and diversity of this gene were analyzed among some Helicobacter and Campylobacter species.

MATERIALS AND METHODS

Twenty-one clinical isolates and strains of helicobacters and campylobacters were used in this study. Methods including polymerase chain reaction (PCR) amplification, restriction fragment-length polymorphisms (RFLPs), and hybridization were employed to carry out this work.

RESULTS

The copA gene was highly conserved in all the H. pylori isolates tested (Helicobacter nemestrinae and Helicobacter felis but not in Helicobacter mustelae and the Campylobacter species), whereas the sequence downstream of the copA appears to diverge among H. pylori isolates. In addition, two restriction patterns of the PCR-amplified copA fragments from seven H. pylori isolates and H. nemestrinae were identified, and the RFLP of H. nemestrinae was identical to that of one of the H. pylori isolate group.

CONCLUSIONS

The adenosine triposphatase-derived copper-transporting mechanism is employed by various H. pylori strains, H. nemestrinae, H. felis, and perhaps by other Helicobacter species. The nucleotide mutations have risen in the copA gene. It appears that there is a genetic relatedness of the copA gene to H. pylori and H. nemestrinae.

Nucleotide sequence and mutational analysis indicate that two Helicobacter pylori genes encode a P-type ATPase and a cation-binding protein associated with copper transport

A 2.7 kb fragment of Helicobacter pylori UA802 chromosomal DNA was cloned and sequenced. Three open reading frames (designated ORF1, ORF2 and ORF3, respectively) were predicted from the DNA sequence, of which ORF1 and ORF2 appeared to be located within the same operon. The deduced 611-amino-acid sequence of ORF1, a P-type ATPase (designated hpCopA), had striking homology (29-38%) with several bacterial P-type ATPase and contained the potential functional domains conserved in P-type ATPases from various sources ranging from bacterial to human. A protein of 66 amino acids (designated hpCopP) encoded by ORF2 shared extensive sequence similarity with MerP, a periplasmic mercuric ion-transporting protein, and contains the heavy metal-binding motif. Disruption of ORF1 with a chloramphenicol-resistance cassette (CAT) rendered the H. pylori mutants more susceptible to cupric ion than their parental strains, whereas there is no significant alteration of susceptibility to Ni2+, Cd2d+ and Hg2+ between the mutants and the parental strains. The results obtained indicate that ORF1 and ORF2 comprise a cation-transporting system which is associated with copper export out of the H. pylori cells.

[Preparation and application of ELISA kit for detection of G-CSF]

By adding monoclonal antibodies from BALB/c mice to the granulocyte colony-stimulating factor (G-CSF), we established a sandwich ELISA for detecting G-CSF levels in human serum samples. G-CSF was measured in 157 normal serum samples and in 153 serum samples from patients with no clinical manifestation of bacterial infection and in 269 serum samples from patients with clinical diagnosis of bacterial infection and in 31 serum samples from patients with positive bacterial infection according to cell culture. It was found that the positive rates of G-CSF were zero in normal serum samples, only 6.5% in patients with no clinical manifestation of bacterial infection, 89.2% in patients with clinical diagnosis of bacterial infection and 100% in patients with bacterial culture positive for infection. Our results reveal that the sandwich ELISA for detection of G-CSF levels in human serum samples may be useful for diagnosing patients with bacterial infection and for clinically guiding the rational use of antibiotics.

A specific orientation of RNA secondary structures is required for initiation of reverse transcription

The 5' end of avian retrovirus RNA near the primer-binding site (PBS) forms two secondary structures, the U5-inverted repeat (U5-IR) and the U5-leader stems, and contains a 7-nucleotide sequence that anneals to the T psi C loop of the tRNA(Trp) primer. Mutations that disrupt any of these base pair interactions cause defects in initiation of reverse transcription both in vivo and in vitro (D. Cobrinik, A. Aiyar, Z. Ge, M. Katzman, H. Huang, and J. Leis, J. Virol. 65:3864-3872, 1991; A. Aiyar, D. Cobrinik, Z. Ge, H.-J. Kung, and J. Leis, J. Virol. 66:2464-2472, 1992). We have now examined the effect of perturbing the non-base-paired intervening "spacer" sequences between these secondary-structure elements. Small deletions or insertions in these intervening sequences decreased initiation of reverse transcription in vitro. In contrast, base substitutions, which maintain the spacing distances between the structures, had no detectable effect. Additionally, a small deletion at the 3' end of the PBS caused a significant decrease in initiation of reverse transcription whereas substitution mutations again had no effect. Together, these results indicate that reverse transcriptase forms a complex in which the different structural elements are maintained in a specific orientation that is required for efficient initiation of reverse transcription. Specific sequence recognition of the duplex structures by reverse transcriptase is also required since mosaic RNAs that combine the human immunodeficiency virus type 1 PBS with avian sequences is not efficiently utilized for reverse transcription even though the primer used can anneal to the substituted PBS.

Vanishing De Vega annuloplasty for functional tricuspid regurgitation

Annuloplasty is performed for significant functional tricuspid regurgitation even if it is presumed that in some cases the regurgitation will regress spontaneously after correction of the left-sided lesion. In an attempt to avoid the drawbacks of a permanent annuloplasty, we used a reabsorbable De Vega annuloplasty in a selected group of patients. Of 73 patients with functional tricuspid regurgitation operated on between May 1989 and May 1991, 25 with pulmonary arteriolar resistance below 400 dyne.sec.cm-5 underwent a De Vega annuloplasty with 2-0 polydioxanone suture. The diagnosis of significant functional tricuspid regurgitation (mean 2.74 +/- 1.05) was established by transthoracic color Doppler echocardiography in all patients. The degree of functional tricuspid regurgitation and pulmonary arteriolar resistance were measured with the patients anesthetized. In 16 patients the regurgitation remained severe (3+ to 4+) and in 9 it was moderate (2+). Twenty-three patients had mitral (12 repairs, 11 replacements) and 9 had aortic (4 repairs, 5 replacements) valve operations. The immediate postbypass residual functional tricuspid regurgitation was 0 to 1+ in 23 and 0 in 2. There was 1 (4%) operative death. The maximum follow-up period was 24 months (mean 13.9 months). There were 2 (8.3%) late deaths. Six patients underwent reoperation because of mitral dysfunction. Four of them who were reoperated on between 2 and 5 weeks after the initial procedure showed no recurrence of functional tricuspid regurgitation. The other 2, reoperated on at 5 and 10 months after the first operation, had recurrence of functional tricuspid regurgitation. Visual inspection of these two tricuspid valves showed a dilated anulus with otherwise normal valves. All surviving patients are in New York Heart Association functional class I or II without significant functional tricuspid regurgitation (mean 0.78 +/- 0.56). We concluded that functional tricuspid regurgitation in patients with low pulmonary arteriolar resistance can be adequately treated by a vanishing De Vega annuloplasty, which will stent the tricuspid anulus for about 4 months.

A simultaneous study of Doppler-echo and catheterization in noninvasive assessment of the left ventricular dp/dt

To confirm the feasibility and accuracy of the method for the noninvasive measurement of the left ventricular dp/dt, 53 patients with mitral regurgitation underwent simultaneous determination of left ventricular dp/dt by continuous-wave Doppler echocardiography and cardiac catheterization. Doppler-determined left ventricular dp/dt is derived from the Doppler mitral regurgitant spectrum by dividing the magnitude of the left ventricular-atrial pressure gradient rise between 1 and 3 m/s of the mitral regurgitant velocity signal by the time taken for this change. Left ventricular dp/dt by Doppler ranged from 629 to 3494 mmHg/s (mean +/- SD, 1971 +/- 785 mmHg/s), and that by catheterization varied between 716 and 3650 mmHg/s (mean +/- SD, 1974 +/- 727 mmHg/s). There was a high correlation (r = 0.93, y = 0.862x + 274.77, SEE = 271 mmHg/s, p < 0.001) of left ventricular dp/dt between the two techniques. It is concluded that left ventricular dp/dt is one of the most commonly used parameters for the evaluation of left ventricular systolic function and that Doppler echocardiography provides a new, accurate and noninvasive method of evaluation.

Nucleotide sequence of sweet clover necrotic mosaic dianthovirus RNA-1

The complete nucleotide sequence of sweet clover necrotic mosaic dianthovirus (SCNMV) RNA-1 has been determined. RNA-1 consists of 3876 nucleotides in length, containing three large open reading frames (ORFs). The 5'-proximal, internal and 3'-terminal ORFs potentially encode 27-kDa, 57-kDa and 37-kDa proteins, respectively. The frameshift event between the C-terminus of the 27-kDa protein and extension of the N-terminus of the 57-kDa protein may result in the formation of a 88-kDa protein which is presumed to be a replicase. The 37-kDa coat protein ORF is located immediately downstream of the 57-kDa ORF. The same genome organization and high similarity (80-92%) of both the nucleotide sequences and the deduced amino acid sequences between red clover necrotic mosaic dianthovirus and SCNMV suggest that they originate from a common progenitor, but have divergent evolution later. Striking similarity was detected between the putative RNA-dependent RNA polymerase of SCNMV and that of the tombus-, carmo-, necro-, machlomo- and luteoviruses, supporting a proposal that they belong to the same virus supergroup although there is a relatively low degree of coat protein sequence similarity in these viruses.

Noninvasive evaluation of right ventricular and pulmonary artery systolic pressures in patients with ventricular septal defects: simultaneous study of Doppler and catheterization data

The method for evaluating right ventricular and pulmonary artery systolic pressures by subtracting the systolic pressure gradient across the ventricular septal defect from the cuff systolic blood pressure is documented. To confirm the reliability and accuracy of this method, simultaneous continuous wave Doppler echocardiography and left and right cardiac catheterization were performed in 66 patients with congenital ventricular septal defects. The comparisons between the Doppler-derived right ventricular or pulmonary artery systolic pressures and those measured by catheterization yielded an excellent correlation (r = 0.969, y = 1.035x - 3.627, SEE = 8.2 mm Hg, p < 0.001 and r = 0.972, y = 1.012x - 2.904, SEE = 7.6 mm Hg, p < 0.001), respectively. There was a close agreement between the Doppler-derived right ventricular or pulmonary artery systolic pressures and those measured by catheters, and the differences between the two measurements did not differ significantly from zero. It is concluded that Doppler echocardiography offers a reliable and accurate method for noninvasive assessment of right ventricular and pulmonary artery systolic pressures in patients with ventricular septal defects.

Simultaneous measurement of left atrial pressure by Doppler echocardiography and catheterization

Simultaneous, continuous wave Doppler echocardiography, left ventricular systolic and mean pulmonary capillary wedge pressure measurements were performed during cardiac catheterization in 54 patients with mitral regurgitation. Doppler-derived left atrial pressure, which was calculated by subtracting mitral regurgitant gradient from brachial artery systolic pressure, correlated well with mean pulmonary capillary wedge pressure by catheter (r = 0.933, SEE = 2.9 mmHg, P < 0.001); a comparison between non-invasive and invasive systolic gradients across the mitral valve yielded a high correlation (r = 0.91, SEE = 6.0 mmHg, P < 0.001); and there was also a high correlation between brachial artery and left ventricular systolic pressures (r = 0.93, SEE = 4.9 mmHg, P < 0.01). It is concluded that Doppler echocardiography provides a reliable and accurate method for complete non-invasive assessment of left atrial pressure in patients with mitral regurgitation.

Pulmonary artery diastolic pressure: a simultaneous Doppler echocardiography and catheterization study

Pulmonary hypertension is an important determinant of the clinical presentation of and surgical approach to patients with heart disease. To confirm the utility of continuous wave Doppler echocardiography in assessing the pulmonary artery diastolic pressure in patients with pulmonary regurgitation, 51 patients representing the wide hemodynamic spectrum of pulmonary artery pressure underwent simultaneous determination of pulmonary artery diastolic pressure by continuous wave Doppler echocardiography and cardiac catheterization. Pulmonary artery diastolic pressure was estimated from the Doppler recordings by the end-diastolic pressure gradient obtained by the modified Bernoulli equation plus the estimated right atrial pressure. A correlation was observed (r = 0.935, SEE = 7.4 mmHg) between Doppler and catheterization pulmonary artery diastolic pressure. In addition, comparison between the mean diastolic pressure gradient across the pulmonary valve by Doppler and pulmonary artery diastolic pressure at catheterization yielded a high correlation (r = 0.947, SEE = 5.1 mmHg). These data demonstrate that continuous wave Doppler echocardiography is a useful noninvasive technique for evaluating the pulmonary artery diastolic pressure in patients with pulmonary regurgitation.

A comparative study of the RNA-2 nucleotide sequences of two sweet clover necrotic mosaic virus strains

The nucleotide sequences of the RNA-2s of two strains of sweet clover necrotic mosaic virus (SCNMV-38 and -59) have been determined. The RNA-2s of SCNMV-38 and -59 consist of 1446 and 1449 nucleotides, respectively, and both contain one major open reading frame (ORF) which potentially can encode polypeptides of 326 amino acid residues (about 36.5K), designated SC38P2 and SC59P2, respectively. The nucleotide sequences of SCNMV-38 and -59 RNA-2s show 93.2% similarity, and the amino acid sequences of SC38P2 and SC59P2 are 91.7% identical, although the identical nucleotides and amino acids are not distributed uniformly in RNA-2 and the encoded proteins. Two highly conserved regions (from positions 23 to 221 and 297 to 326) and a relatively divergent region (from positions 222 to 296) are found in the P2 proteins of these strains. A similar pattern is apparent on comparison of the nucleotide and deduced amino acid sequences of RNA-2 of these SCNMV strains with those of the Australian and Czechoslovakian isolates of red clover necrotic mosaic virus.

Requirement for a conserved serine in both processing and joining activities of retroviral integrase

Retroviruses encode a protein, the integrase (IN), that is required for insertion of the viral DNA into the host cell chromosome. IN alone can carry out the integration reaction in vitro. The reaction involves endonucleolytic cleavage near the 3' ends of both viral DNA strands (the processing step), followed by joining of these new viral DNA ends to host DNA (the joining step). Based on their evolutionary conservation, we have previously identified at least 11 amino acid residues of IN that may be essential for the reaction. Here we report that even conservative replacements of one of these residues, an invariant serine, produce severe reductions in both the processing and joining activities of Rous sarcoma virus IN in vitro. Replacement of the analogous serine of the type 1 human immunodeficiency virus IN had similar effects on processing activity. These results suggest that this single conserved serine is a component of the active site and that one active site is used for both processing and joining. Replacement of this serine with certain amino acids resulted in a loss or reduction in DNA binding activities, while other replacements at this position appeared to affect later steps in catalysis. All of the defective Rous sarcoma virus INs were able to compete with the wild-type protein, which supports a model in which IN functions in a multimeric complex.

Noninvasive evaluation of interventricular pressure gradient across ventricular septal defect: a simultaneous study of Doppler echocardiography and cardiac catheterization

Simultaneous continuous-wave Doppler echocardiography and left- and right-sided cardiac pressure measurements were performed during cardiac catheterization in 64 patients with a congenital ventricular septal defect (VSD). The peak-to-peak pressure gradient across the VSD on cardiac catheterization ranged from 0 to 109 mm Hg (61 +/- 31.7 mm Hg). The peak shunt velocity and peak pressure gradient across the VSD on Doppler ultrasound imaging ranged from 0.96 to 5.21 m/sec (3.75 +/- 1.16 m/sec) and from 4 to 105 mm Hg (62 +/- 29.8 mm Hg), respectively. Doppler measurements of the peak interventricular pressure gradient correlated well with measurements obtained by cardiac catheterization (r = 0.98, standard error of estimate = 6.3 mm Hg, p less than 0.001). Doppler ultrasound imaging yielded information comparable to that obtained by catheterization and provided an accurate method of measuring the pressure gradient across the VSD, which is a useful parameter for the assessment of pulmonary artery systolic pressure in patients with a VSD, without a left or right ventricular outflow tract obstruction.

Interaction between retroviral U5 RNA and the T psi C loop of the tRNA(Trp) primer is required for efficient initiation of reverse transcription

The 5' end of avian sarcoma and leukosis virus RNA near the primer binding site forms two RNA secondary structures, U5-inverted repeat (U5-IR) and U5-leader stems, which are required for efficient initiation of reverse transcription. Lying between these two secondary structures is a 7-base sequence that can anneal to the T psi C loop of the tRNA(Trp) primer. Base substitutions in U5 RNA which disrupt this potential interaction result in a defect in the initiation of reverse transcription both in vivo and in vitro. The defect can be complemented in vitro by base substitutions in the primer. The U5 RNA-T psi C interaction is also dependent upon the presence of both the U5-IR and the U5-leader structures. These RNA secondary structures and primer interactions are conserved in other type C and D retroviruses, suggesting that there is a common mechanism for the initiation of reverse transcription in all of these retroviruses.

[Validation of Doppler-derived interventricular pressure gradients in patients with ventricular septal defect comparing with catheterization study]

To evaluate the accuracy of Doppler echocardiography for measuring the interventricular pressure gradient in patients with ventricular septal defect (VSD), Doppler echocardiography and dual catheters were performed simultaneously in 31 cases with VSD ranging from 9 to 40 years old. The systolic jet velocities through VSD were recorded by the continuous-wave Doppler technique and converted to the peak instantaneous pressure gradient (delta Pp) and the mean pressure gradient (delta Pm) using a modified Bernoulli's equation with the aid of computer system. Both left and right heart catheters were performed to record the left (LVSP) and the right (RVSP) ventricular systolic pressure simultaneously. Guided by the color flow image Doppler technique, the tip of the right heart catheter was carefully placed within the jet area of the right ventricle. The following parameters were measured from the ventricular pressure curves, the peak instantaneous pressure gradient (IPG), the peak to peak pressure gradient (PPG) and the mean pressure gradient (MPG). The comparison between delta Pp and PPG yielded an excellent correlation (r = 0.99, SEE = 0.69 kPa). There was a close agreement between delta Pp and IPG (r = 0.99, SEE = 0.64 kPa). However, the correlation between delta Pm and MPG was also high (r = 0.98, SEE = 0.67 kPa). We conclude that Doppler echocardiography offers a reliable technique for measuring the interventricular pressure gradient in patients with VSD.

Overlapping retrovirus U5 sequence elements are required for efficient integration and initiation of reverse transcription

A secondary structure in the 5' noncoding region of avian retrovirus RNA, called the U5-leader stem, was shown previously to have a role in initiation of reverse transcription (D. Cobrinik, L. Soskey, and J. Leis, J. Virol. 62:3622-3630, 1988). We now show that an additional RNA secondary structure near the U5 terminus, called the U5-IR stem, is also important for reverse transcription. Mutations that disrupt the U5-IR stem cause a replication defect associated with both a decrease in synthesis of viral DNA in infected cells and a decrease in initiation of reverse transcription in melittin-permeabilized virions. Structure-compensating base substitutions in the U5-IR restore reverse transcription efficiency. In viral DNA, U5-IR sequences are included in the U5 terminal region that functions as a viral integration donor site. When base substitutions are introduced into these sequences, a reduced efficiency of integration in vitro and in vivo is observed. These observations indicate that U5-IR sequences have a structural role in reverse transcription of viral RNA and a sequence-specific role in the integration of viral DNA.