As is the case for some other RNA viruses, the amino acid sequences of retroviral proteins change at an astonishing rate. For example, the proteases of the human immunodeficiency virus (HIV) and the visna lentivirus with which it is often compared are as different as the proteases of fungi and mammals, and those of the human type I leukemia virus are as different from HIV or visna as are the proteins of humans and bacteria. That the sequences of retrovirus proteins can be recognized as sharing common ancestry with non-retroviral proteins implies that the vastly accelerated change has begun only recently or occurs very sporadically. Only a scheme whereby exogenous retroviruses exist as short-lived bursts upon a backdrop of germline-encoded endogenous viruses is consistent with the sequence data. Retroviruses are related to many other reverse transcriptase-bearing entities present in the genomes of eukaryotes. They also have proteins that are homologous with those of some plant and animal DNA viruses, and their reverse transcriptase is recognizably similar to sequences found in the introns of some fungal mitochondria. Computer alignment of all these sequences allows an overall phylogeny to be constructed that chronicles the history of events leading to infectious retroviruses.

A computer analysis of the amino acid sequences from the putative gene products of retroviral pol genes has revealed a 150-residue segment that is homologous with the ribonuclease H of Escherichia coli. The segment occurs at the carboxyl terminus of the region assigned to the 90-kDa reverse transcriptase polypeptide. In contrast, a section nearer the amino terminus of this sequence can be aligned with nonretroviral polymerases. (5), and an endonuclease ("integrase") that is essential for the integration of the newly synthesized DNA into the host genome (6).The pol gene of retroviruses is expressed initially as a gag-pol precursor that is proteolytically processed to a number of small gag proteins, an approximately 90-kDa protein encompassing both RNA-directed DNA polymerase (reverse transcriptase) and ribonuclease H activities, and, finally, a 40-kDa fragment with endonuclease activity (7). Several reports have presented evidence that the ribonuclease H activity of the 90-kDa reverse transcriptase portion is associated with the amino-terminal end of that protein, and by implication, that the DNA polymerase activity is at the carboxyl-terminal end. These conclusions are based on experiments involving deletion mutants (2), on the one hand, and antibodies to synthetic peptides modeled on the putative sequences, on the other (3).We now suggest that the opposite must be true: the ribonuclease H activity should be situated at the carboxyl terminus, and the DNA polymerase, at the amino terminus. We draw this conclusion on the basis of comparisons of the retroviral sequences with those of nonviral enzymes of similar function. In this regard, we have uncovered a significant resemblance between a 150-residue segment at the carboxyl-terminal end of the 90-kDa fragment and the reported sequence of a ribonuclease H from Escherichia coli. We also provide an alignment of a segment near the amino terminus of the 90-kDa polypeptide with highly conserved sequences from many other polymerases, including the a subunit of E. coli DNA-directed RNA polymerase. Finally, there is a distinctive sequence in the endonuclease sequence that is characteristic of a zinc-binding segment. METHODSThe sequences used were taken from the 1985 version of NEWAT (8) identical (Fig. 1). Binary comparison of each of the retroviral sequences with the E. coliribonuclease H sequence, followed by statistical evaluation by a randomization method, gave authentic alignment scores from 4 to 10 standard deviations above the means of the jumbled comparisons. The cumulative weight of the multiple alignment (Fig. 2) further bears out the significance of the overall relationship. That the polymerase portion of the viral reverse transcriptase system must encompass the amino-terminal portion of the 90-kDa fragment is established by the alignment shown in Fig. 3. The key region here involves a sector previously shown by Kamer and Argos (20) to be present in a number of nonretroviral polymerases; these consistently have two aspartic acid residues surrounded by...

The polypeptide encoded in URF6, the last unassigned reading frame of human mitochondrial DNA, has been identified with antibodies to peptides predicted from the DNA sequence. Antibodies prepared against highly purified respiratory chain NADH dehydrogenase from beef heart or against the cytoplasmically synthesized 49-kilodalton iron-sulfur subunit isolated from this enzyme complex, when added to a deoxycholate or a Triton X-100 mitochondrial lysate of HeLa cells, specifically precipitated the URF6 product together with the six other URF products previously identified as subunits of NADH dehydrogenase. These results strongly point to the URF6 product as being another subunit of this enzyme complex. Thus, almost 60% of the protein coding capacity of mammalian mitochondrial DNA is utilized for the assembly of the first enzyme complex of the respiratory chain. The absence of such information in yeast mitochondrial DNA dramatizes the variability in gene content of different mitochondrial genomes.

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The ABC excision nuclease of Escherichia coli is an ATP-dependent DNA repair enzyme composed of three protein subunits, UvrA, UvrB and UvrC. The DNA sequences of all three genes have been reported. UvrA, the component that binds directly to the DNA, and UvrB, which attaches itself to the UvrA-DNA complex, both contain consensus sequences though to be diagnostic of ATP-binding sites, although the UvrC sequence does not. We now report that a computer analysis of the UvrA sequence has revealed an unusual series of internal duplications centering around putative metal-binding sites which may be involved in the interaction with DNA. We also find a strong evolutionary relationship to a family of prokaryotic membrane-associated active-transport proteins.