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R F Doolittle

Publications and source records attributed to R F Doolittle.

At least 73 records · Page 4Linked to original sources
PubMed1992

Characterization, primary structure, and evolution of lamprey plasma albumin.

The most abundant protein found in blood plasma from the sea lamprey (Petromyzon marinus) has the hallmarks of a plasma albumin: namely, high abundance, solubility in distilled water, a small number of tryptophans, and a high content of cysteines and charged residues. As in other vertebrate albumins, not all the cysteines are disulfide bonded. An unusual feature of this protein is its molecular weight of 175,000, roughly 2.5 times the size of other vertebrate albumins. Its amino acid sequence, deduced from a series of overlapping cDNA clones, can be aligned with other members of the gene family including plasma albumin, alpha-fetoprotein, and vitamin-D binding protein, confirming that it is indeed an oversized albumin. An unusual feature of the sequence is a 28-amino acid stretch consisting of a serine-threonine repeat with the general motif (STTT). Lamprey albumin contains a 23-amino acid putative signal peptide and a 6-residue putative propeptide, which, when cleaved, yield a mature protein of 1,394 amino acids with a calculated molecular weight of 157,000. The sequence also includes nine potential N-linked glycosylation sites (Asn-X-Ser/Thr), consistent with observation that lamprey albumin is a glycoprotein. If all the potential glycosylation sites were occupied by clusters of 2,000 molecular weight each, the total molecular weight would be 175,000. Like other members of the gene family, lamprey albumin is composed of a series of 190-amino acid repeats, there being seven such domains all together. Quantitative amino acid sequence comparisons of lamprey albumin with the other members of the gene family indicate that it diverged from an ancestral albumin prior to the gene duplications leading to this diverse group. This notion is confirmed by the pattern of amino acid insertions and deletions observed in a consideration of all domains that compose this family. Furthermore, it suggests that the invention of albumin antedates the vertebrate radiation.

Amino Acid Sequence↗
PubMed1992

A detailed consideration of a principal domain of vertebrate fibrinogen and its relatives.

Vertebrate fibrinogen is a complex multidomained protein, the structure of which has been inferred mainly from electron microscopy and amino acid sequence studies. Among its most prominent features are two terminal globules, moieties that are mostly composed of the carboxyl-terminal two-thirds of the beta and gamma chains. Sequences homologous to the latter segments are found in several other animal proteins, always as the carboxyl-terminal contributions. An alignment of 15 amino acid sequences from various fibrinogens and related proteins has been used to make judgments about secondary structure. The nature of amino acids at each position in the alignment was used to distinguish alpha helices and beta structure on the one hand from loops and turns on the other, and the resulting assignments compared with predictions of secondary structure by other methods. Additionally, constraints imposed by the locations of cystines, carbohydrate attachment residues, and proteinase-sensitive points provided further insights into the general organization of the postulated secondary structures. Other ancillary data, including the effects of bound calcium and the locations of labeled or variant residues, were also considered. An intriguing similarity to a portion of the recently reported structure of a calcium-dependent lectin is noted.

Amino Acid Sequence↗
PubMed1992

Tracing the origin of retroviruses.

Reverse transcriptase sequences, which are fundamental to retrovirus existence, are widely distributed in the living world. Phylogenies based on their sequences set vertebrate retroviruses apart as relatively modern creations. Their nearest evolutionary relatives are a large group of transposable elements that have all the standard retrovirus equipment except spliced envelope proteins. The distribution of these elements suggests a long-standing presence predating the radiation of plants, fungi, and animals. There is another large group of elements, LINEs, that also contain recognizable reverse transcriptase sequences and which likely diverged even earlier, as evidenced by their presence in trypanosomes and other protists. They lack tRNA priming sites--which they could have lost--but they do exhibit characteristic eukaryotic polyadenylation. These elements are problematic in that the sequences are so degenerate in most instances that it is not possible to identify the accessory enzymes or structural proteins with any confidence, leaving major gaps in our reconstruction of events. Even with these gaps, however, the historical beginnings of retroviruses can be traced back to events coincident with the prokaryotic invasion of primitive eukaryotes.

Biological Evolution↗
PubMed1992

A comparison of evolutionary rates of the two major kinds of superoxide dismutase.

Phylogenetic trees were constructed for 25 Cu-Zn superoxide dismutases and 31 Mn/Fe superoxide dismutases. The latter set includes seven new sequences that we determined in an effort to make the two phylogenies equally representative. We analyzed all pairwise differences in each set in an attempt to estimate rates of change. As reported by others, the Cu-Zn enzyme has experienced significant changes in its evolutionary rate. In contrast, the clock for the Mn/Fe enzyme is ticking quite regularly. The comparison of these two independently evolved superoxide dismutases that catalyze the same reaction and occur together throughout much of the biological world suggests that adaptation to environmental stress is not the basis for the erratic rate of change observed in the Cu-Zn enzyme.

Amino Acid Sequence↗
PubMed1992

Evolution by acquisition: the case for horizontal gene transfers.

One of the most debated questions in the field of molecular evolution is the possible role of horizontal transfer in evolution. Of all the claims that have been made over the years, those reporting transfers between eukaryotes and prokaryotes are the most controversial. Here we present the cases for and against several such possible gene acquisitions.

Animals↗
PubMed1991

Evolution and relatedness in two aminoacyl-tRNA synthetase families.

Sequence segments of about 140 amino acids in length, each containing a selected consensus region, were used in alignments of the aminoacyl-tRNA synthetases with the aim of discerning their evolutionary relationships. In all cases tested, enzymes specific for the same amino acid from a variety of organisms grouped together, reinforcing the supposition that the aminoacyl-tRNA synthetases are very ancient enzymes that evolved to include the full complement of 20 amino acids long before the divergence leading to prokaryotes and eukaryotes. The enzymes are divided into two mutually exclusive groups that appear to have evolved from independent roots. Group I, for which two sequence segments were analyzed, contains the enzymes specific for glutamic acid, glutamine, tryptophan, tyrosine, valine, leucine, isoleucine, methionine, and arginine. Group II enzymes include those activating threonine, proline, serine, lysine, aspartic acid, asparagine, histidine, alanine, glycine, and phenylalanine. Both groups contain a spectrum of amino acid types, suggesting the possibility that each could have once supported an independent system for protein synthesis. Within each group, enzymes specific for chemically similar amino acids tend to cluster together, indicating that a major theme of synthetase evolution involved the adaptation of binding sites to accommodate related amino acids with subsequent specialization to a single amino acid. In a few cases, however, synthetases activating dissimilar amino acids are grouped together.

Amino Acid Sequence↗
PubMed1990

The structure and evolution of vertebrate fibrinogen: a comparison of the lamprey and mammalian proteins.

The blood plasmas of all vertebrate animals contain a six-chained fibrinogen molecule that is polymerized into fibrin upon the thrombin-catalyzed removal of fibrinopeptides. In all cases, also, the polymerization reaction is inhibited by Gly-Pro-Arg-ending peptides. The complete amino acid sequences of human, rat and lamprey fibrinogens are known, permitting an assessment of just which sequence features are essential for polymerization. To an extent, the same approach can also be applied to the associated phenomena of fibrin cross-linking by factor XIII, plasminogen and plasminogen activator binding, and vessel wall-fibrinogen interactions.

Amino Acid Sequence↗
PubMed1990

Retrovirus phylogeny and evolution.

The elucidation of complete genomic sequences from a wide variety of retroviruses and retrotransposons has allowed the construction of sequence-based phylogenies that reveal their evolutionary history. True retroviruses, whether exogenous or endogenous, tend to cluster into four major groups. Not only is there no distinction between exogenous and endogenous viruses, but their evolutionary limb lengths on the phylogenetic trees are comparable. This can be taken as evidence favoring a dynamic equilibrium balancing a constant invasion of germlines by infectious retroviruses on the one hand, with subsequent escape of endogenous viruses to alternative hosts on the other. Retroviruses share a common ancestry with a wide variety of retrotransposons and other reverse transcriptase-bearing entities. One of these retrotransposon groups, the Gypsy group, resembles the Moloney mouse group of retroviruses much more closely than it does other retroviruses. The simplest explanation is that the evolutionary rate of the retrotransposon is much slower than the retrovirus rate and that among the retroviruses the Moloney mouse group has been evolving more slowly than the other three groups, leaving the two short-limbed taxa more similar. The alternative explanation that these two groups actually shared a common ancestor more recently than has either with the other retrovirus groups is not supported by residue-by-residue character assessment.

Animals↗
PubMed1990

A naturally occurring horizontal gene transfer from a eukaryote to a prokaryote.

Naturally occurring horizontal gene transfers between nonviral organisms are difficult to prove. Only with the availability of sequence data from a wide variety of organisms can a convincing case be made. In the case of putative gene transfers between prokaryotes and eukaryotes, the minimum requirements for inferring such an event include (1) sequences of the transferred gene or its product from several appropriately divergent eukaryotes and several prokaryotes, and (2) a similar set of sequences from the same (or closely related organisms) for another gene or genes. Given these criteria, we believe that a strong case can be made for Escherichia coli having acquired a second glyceraldehyde-3-phosphate dehydrogenase gene from some eukaryotic host. Ancillary observations on the general rate of change and the time of the prokaryote-eukaryote divergence support the notion.

Amino Acid Sequence↗