Sequence homology between retroviral reverse transcriptase and putative polymerases of hepatitis B virus and cauliflower mosaic virus

Toh, Hiroyuki; Hayashida, Hidenori; Miyata, Takashi

doi:10.1038/305827a0

Cited by 436 publications

(198 citation statements)

References 32 publications

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“…2). These sequences have been observed to be particularly well conserved, even across kingdom boundaries (16)(17)(18)(19). These homologies are encoded near each other in the 5' half of the Bsi element, as they are in all other similar elements studied (6,10,(16)(17)(18).…”

Section: Resultsmentioning

confidence: 86%

“…These homologies are encoded near each other in the 5' half of the Bsi element, as they are in all other similar elements studied (6,10,(16)(17)(18). Without previous exception, the most conserved deduced amino acid sequence among retroposons (6,(16)(17)(18)(19) is observed in the region that encodes reverse transcriptase. Although the deAdhl duced amino acid sequence of Bs] does contain some homology with the most conserved consensus sequence of reverse transcriptase, it also specifies two nearby arginines and a cysteine, which would be incompatible with all other reverse transcriptase sequences (Fig.…”

Section: Resultsmentioning

confidence: 94%

See 1 more Smart Citation

Structure and coding properties of Bs1, a maize retrovirus-like transposon.

Jin

Bennetzen²

1989

Proc. Natl. Acad. Sci. U.S.A.

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We have sequenced Bs), an insertion element isolated from a null allele of the Adhi locus encoding alcohol dehydrogenase in maize. The Bs) element is 3203 base pairs (bp) in length, has 302-bp identical long terminal direct repeats (LTRs), and created a 5-bp flanking direct duplication oftarget AdhI DNA upon insertion. The 5' LTR is followed by a canonical primer binding site with homology to the plant initiator methionyl-tRNA, and the 3' LTR is directly preceded by a polypurine stretch like that observed in retroviruses and retrotransposons. Bs) encodes two overlapping open reading frames specifying peptides of 740 and 168 amino acids. The longer open reading frame specifies a peptide with amino acid homology to the protease and nucleic acid binding moiety of retroviruses and retrotransposons. The deduced amino acid sequence encoded by Bsl lacks convincing homology to the polymerase (reverse transcriptase) encoded by retroposons, despite the fact that this polymerase-encoding domain is routinely the most conserved region of any such element. The sequence and relatively small size of Bs) suggest that this element is a deleted retrotransposon that inserted into AdhM with the aid of a reverse transcriptase function provided in trans. In vitro transcribed Bsl complementary RNA was translated in vitro to produce both a protein of 81 kDa representing open reading frame 1 (ORF1) and one of the 95-kDa size predicted for the frame-shifted fusion of ORF1 and ORF2. As with many other retroposons, the efficiency of translational initiation at the AUG beginning ORF1 was not noticeably affected by the presence of one or more upstream, unproductive AUGs in the complementary RNA transcript.By both structural and mechanistic criteria, eukaryotic insertion sequences and transposable elements can be divided into two major categories. One class of elements is bounded by inverted terminal repeat sequences and transposes through excision (1, 2) and/or enhanced replication (3) of the integrated element. Examples of this class of transposable elements are the controlling elements of maize (4) and the P elements of Drosophila (5). A second class of eukaryotic insertion sequences, the "retroposons," integrate into the chromosome after reverse transcription of element-encoded RNA (6), are particularly abundant in animals, and are the only type of insertion sequence yet discovered in fungi. Both the retroviruses (6) and the LI elements (7) of vertebrates and the "retrotransposons" Ty of yeast (8) and copia of Drosophila (9) fall into this latter category.Despite the early discovery and characterization of numerous distinct transposable elements in maize (1, 4), a canonical retrovirus or retrotransposon has not been described in plants. The DNA caulimoviruses ofplants have the structural properties and encode the reverse transcriptase activity definitional of a retrovirus or retrotransposon but apparently do not integrate into chromosomal DNA (10). Recently, Schwarz-Sommer et al. (11) have found that the Cin4 insertion element of m...

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Section: Resultsmentioning

confidence: 86%

Section: Resultsmentioning

confidence: 94%

Structure and coding properties of Bs1, a maize retrovirus-like transposon.

Jin

Bennetzen²

1989

Proc. Natl. Acad. Sci. U.S.A.

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“…The similarity of HBV to retroviruses, its replication by reverse transcription of an RNA intermediate in particular, has been pointed out (Miller & Robinson, 1986;Summers & Mason, 1982;Toh et al, 1983). RNA viruses including retroviruses are susceptible to mutations, probably because they do not have proof-reading enzymes for correcting errors during duplication (Steinhauer & Holland, 1986).…”

Section: Discussionmentioning

confidence: 99%

Typing Hepatitis B Virus by Homology in Nucleotide Sequence: Comparison of Surface Antigen Subtypes

Okamoto

Tsuda

Sakugawa

et al. 1988

Journal of General Virology

950

774

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SUMMARYThe complete nucleotide sequences of the DNA of three hepatitis B virus (HBV) genomes of subtype adw, cloned from plasma samples of asymptomatic carriers living in the mainland and Okinawa Prefecture of Japan and Indonesia were determined. All three comprised 3215 bp and differed in sequence by only 3.9 to 5.6%. When these isolates were compared with the reported sequences of two HBV genomes of the same subtype derived from American carriers, however, the differences were greater (8.3 to 9.3%) to an extent comparable with the nucleotide divergence between an HBV genome of subtype adw and that of a heterotypic subtype, such as adr, ayw or ayr. A total of 18 HBV genomes of various subtypes, including the three described here, 10 reported previously and five unpublished ones, were classified into four groups based on an inter-group divergence in nucleotide sequence of 8 ~o or greater: group A (two adw genomes), group B (four adw), group C (three adw, four adr and one ayr) and group D (four ayw). Thus, the nine genomes of HBV subtype adw were distributed into three groups with considerably different sequences. These results indicate that the four major antigenically defined subtypes of envelope polypeptide do not reflect true genotypic variation of HBV. The fact that dtoy, as well as w to r, subtypic change can be induced by an A --, G point mutation at nucleotides 365 and 479 in the S gene, respectively, supports this view.

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“…Thyroperoxidase has a conformation similar to that of myeloperoxidase, although it contains a C- The normahzed devlatlons of the alignment scores from the mean value of the scores for the randomized sequences (the upper half of the table) and the Identity (To) of the aligned sequence (the lower half of the table). PES = prostaglandm endoperoxlde synthase and EGF = epldermal growth factor The names m the parentheses indicate the source animals of the protems The alignment used m this calculation is shown m fig 1 The score matrix MDM7s was used for the statistical test [12] The contmuous gaps were treated as single substitutions regardless of their length and a score of -60 was assigned to the gaps terminal extension: N-terminal-the region shared by 3 peroxidases-cytochrome c oxidase-like domain-C46-like domain -EGF-like domain-transmembrane-C-terminal.…”

Section: Methodsmentioning

confidence: 99%

“…The enzyme has two enzymatic activities, that is, a brs-oxygenase activity and a hydroperoxidase activity [l-5]. The former initiates the formation of the prostaglandin G and the latter is involved in the reduction of prostaglandm G to prostaglandin H. Recently, the primary structure of sheep prostaglandin endoperoxide synthase was determined and the homologies with heme proteins and the other peroxidases were reported [6-81. (release 19 0) [lo] The homology search system used m this study was described m [II] The detected homologous sequences were aligned and subJected to the statlsbcal test m order to check the slgmflcance of the slmllarlty [12] 3. RESULTS AND DISCUSSION Thus, prostaglandin endoperoxide synthase occupies an important position in the metabolism of prostanoid and the regulation of prostaglandm endoperoxide synthase controls the rate of prostanoid synthesis.…”

Section: Introductionmentioning

confidence: 99%

Prostaglandin endoperoxide synthase contains an EGF‐like domain

Toh

1989

FEBS Letters

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Prostaglandm endoperoxlde synthase was subJected to the computer-asslsted homology search m the protein pnmary structure database, m order to mvestlgate the regulation mechanism of the expresslon of prostaglandm endoperoxlde synthase As a result of that, It turned out that prostaglandm endoperoxlde synthase shares sequence homology with epldermal growth factor (EGF) m the N-termmal region The lmphcatlon of the existence of an EGF-hke domain m prostaglandm endoperoxlde synthase IS dlscussed Prostaglandm endoperoxlde synthase, Epldermal growth factor, Sequence homology

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Sequence homology between retroviral reverse transcriptase and putative polymerases of hepatitis B virus and cauliflower mosaic virus

Cited by 436 publications

References 32 publications

Structure and coding properties of Bs1, a maize retrovirus-like transposon.

Structure and coding properties of Bs1, a maize retrovirus-like transposon.

Typing Hepatitis B Virus by Homology in Nucleotide Sequence: Comparison of Surface Antigen Subtypes

Prostaglandin endoperoxide synthase contains an EGF‐like domain

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