Thomas H. Jukes

“Homology” in proteins and nucleic acids: A terminology muddle and a way out of it

“Homology” has the precise meaning in biology of “having a common evolutionary origin,” but it also carries the loose meaning of “possessing similarity or being matched.” Its rampant use in the loose sense is clogging the literature on protein and nucleic acid sequence comparisons with muddy writing and, in some cases, muddy thinking In its precise biological meaning, “homology” is a concept of quality. The word asserts a type of relationship between two or more things. Thus, amino acid or nucleotide sequences are either homologous or they are not. They cannot exhibit a particular “level of homology” or “percent homology.” Instead, two sequences possess a certain level of similarity. Similarity is thus a quantitative property. Homologous proteins or nucleic acid segments can range from highly similar to not recognizably similar (where similarity has disappeared through divergent evolution). If using “homology” loosely did not interfere with our thinking about evolutionary relationships, the way in which we use the term would be a rather unimportant semantic issue. The fact is, however, that loose usage in sequence comparison papers often makes it difficult to know the authors intent and can lead to confusion for the reader (and even for the author). There are three common situations in which hazards arise by using “homology” to mean similarity. The first case is the most obvious offense but perhaps the least troublesome. Here an author identifies sequence similarities (calling them homologies) but claims that the sequences being compared are not evolutionarily related. Some awkward moments occur in such a paper, since the author claims both homology (i.e., similarity) and nonhomology (i.e., lack of a common ancestor). Nonetheless, the author’s ideas are likely to be clear since arguments against common ancestry are presented explicitly. A second case is one in which an author points out similarities (again called homologies) but does not address the issue of evolutionary origins. The reader, seeing the term “homology,” may infer that the author is postulating coancestry when that is not the authors intent. The final case occurs most frequently and is the most subtle and therefore most troublesome. Here, similarities (called homologies) are used to support a hypothesis of evolutionary homology. In this case, the two meanings of homology seem to overlap, and it is almost inevitable that the thinking of author and reader alike will be intrusively distorted as follows. Similarity is relatively straightforward to document. In comparing sequences, a similarity can take the form of a numerical score (O/o amino acid or nucleotide positional identity, in the simplest approach) or of a probability associated with such a score. In comparisons of three-dimensional structures, a typical numerical description is root-mean-square positional deviation between compared atomic positions. A similarity, then, can become a fully documented, simple fact. On the other hand, a common evolutionary origin must usually remain a hypothesis, supported by a set of arguments that might include sequence or three-dimensional similarity. Not all similarity connotes homology but that can be easily overlooked if similarities are called homologies. Thus, in this third case, we can deceive ourselves into thinking we have proved something substantial (evolutionary homology) when, in actuality, we have merely established a simple fact (a similarity, mislabeled as homology). Homology among similar structures is a hypothesis that may be correct or mistaken, but a similarity itself is a fact, however it is interpreted. We believe that the concepts of evolutionary homology and sequence or three-dimensional similarity can be kept distinct only if they are referred to with different words. We therefore offer the following recommendations: *Sequence similarities (or other types of similarity) should simply be called similarities. They should be documented by appropriate statistical analysis. In writing about sequence similarities the following sorts of terms might be used: a level or degree of similarity; an alignment with optimized similarity; the % positional identity in an alignment; the probability associated with an alignment. *Homology should mean “possessing a common evolutionary origin” and in the vast majority of reports should have no other meaning. Evidence for evolutionary homology should be explicitly laid out, making it clear that the proposed relationship is based on the level of observed similarity, the statistical significance of the similarity, and possibly other lines of reasoning. One could argue that the meaning of the term “homology” is itself evolving. But if that evolution is toward vagueness and if it results in making our scientific discourse unclear, surely we should intervene. With a collective decision to mend our ways, proper usage would soon become fashionable and therefore easy. We believe that we and our scientific heirs would benefit significantly.

Evolution of the mitochondrial genetic code IV. AAA as an asparagine codon in some animal mitochondria

SummaryDifferences in assignments from those in the universal genetic code occur in codes of mitochondria. In this report, the published sequences of the mitochondrial genes for COI and ND1 in a platyhelminth (Fasciola hepatica) are examined and it is concluded that AAA may be a codon for asparagine instead of lysine, whereas AAG is the sole codon for lysine in this species.

Evolution of the mitochondrial genetic code I. Origin of AGR serine and stop codons in metazoan mitochondria

SummaryAGA and AGG (AGR) are arginine codons in the universal genetic code. These codons are read as serine or are used as stop codons in metazoan mitochondria. The arginine residues coded by AGR in yeast orTrypanosoma are coded by arginine CGN throughout metazoan mitochondria. AGR serine sites in metazoan mitochondria are occupied mainly in corresponding sites in yeast orTrypanosoma mitochondria by UCN serine, AGY serine, or codons for amino acids other than serine or arginine. Based on these observations, we propose the following evolutionary events. AGR codons became unassigned because of deletion of tRNA Arg (UCU) and elimination of AGR codons by conversion to CGN arginine codons. Upon acquisition by serine tRNA of pairing ability with AGR codons, some codons for amino acids other than arginine mutated to AGR, and were caputed by anticodon GCU in serine tRNA. During vertebrate mitochondrial evolution, AGR stop codons presumably were created from UAG stop by deletion of the first nucleotide U and by use of R as the third nucleotide that had existed next to the ancestral UAG stop.

Evolutionary constraints and the neutral theory

SummaryThe neutral theory of molecular evolution postulates that nucleotide substitutions inherently take place in DNA as a result of point mutations followed by random genetic drift. In the absence of selective constraints, the substitution rate reaches the maximum value set by the mutation rate. The rate in globin pseudogenes is about 5 × 10−9 substitutions per site per year in mammals. Rates slower than this indicate the presence of constraints imposed by negative (natural) selection, which rejects and discards deleterious mutations.

Biological Implications of the Viking Mission to Mars

A central purpose of Viking was to search for evidence that life exists on Mars or may have existed in the past. The missions carried three biology experiments the prime purpose of which was to seek for existing microbial life. In addition the results of a number of the other experiments have biological implications: (1) The elemental analyses of the atmosphere and the regolith showed or implied that the elements generally considered essential to terrestrial biology are present. (2) But unexpectedly, no organic compounds were detected in Martian samples by an instrument that easily detected organic materials in the most barren of terrestrial soils. (3) Liquid water is believed to be an absolute requisite for life. Viking obtained direct evidence for the presence of water vapor and water ice, and it obtained strong inferential evidence for the existence of large amounts of subsurface permafrost now and in the Martain past. However it obtained no evidence for the current existence of liquid water possessing the high chemical potential required for at least terrestrial life, a result that is consistent with the known pressure-temperature relations on the planets surface. On the other hand, the mission did obtain strong indications from both atmospheric analyses and orbital photographs that large quantities of liquid water flowed episodically on the Martian surface 0.5 to 2.5 G years ago.The three biology experiments produced clear evidence of chemical reactivity in soil samples, but it is becoming increasingly clear that the chemical reactions were nonbiological in origin. The unexpected release of oxygen by soil moistened with water vapor in the Gas Exchange experiment together with the negative findings of the organic analysis experiment lead to the conclusion that the surface contains powerful oxidants. This conclusion is consistent with models of the atmosphere. The oxidants appear also to have been responsible for the decarboxylation of the organic nutrients that were introduced in the Label Release experiment. The major results of the GEX and LR experiments have been simulated at least qualitatively on Earth. The third, Pyrolytic Release, experiment obtained evidence for organic synthesis by soil samples. Although the mechanism of the synthesis is obscure, the thermal stability of the reaction makes a biological explanation most unlikely. Furthermore, the response of soil samples in all three experiments to the addition of water is not consistent with a biological interpretation.The conditions now known to exist at and below the Martian surface are such that no known terrestrial organism could grow and function. Although the evidence does not absolutely rule out the existence of favourable oases, it renders their existence extremely unlikely. The limiting conditions for the functioning of terrestrial organisms are not the limits for conceivable life elsewhere, and accordingly one cannot exclude the possibility that indigenous life forms may currently exist somewhere on Mars or may have existed sometime in the past. Nevertheless, the available information about the present Martian environment puts severe constraints and presents formidable challenges to any putative Martian organisms. The Martian environment in the past, on the other hand, appears to have been considerably less hostile biologically, and it might possibly have permitted the origin and transient establishment of a biota.

Evolution of the mitochondrial genetic code. III : Reassignment of CUN codons from leucine to threonine during evolution of yeast mitochondria

SummaryYeast mitochondria use UUR as the sole leucine codons. CUN, universal leucine codons, are read as threonine by aberrant threonine tRNA with anticodon sequence (UAG).The reassignment of CUN codons to threonine during yeast mitochondrial evolution could have proceeded by the disappearance of CUN codons from the reading frames of messenger RNA, through mutation mainly to UUR leucine codons as a result of AT pressure. We suggest that this was accompanied by a loss of leucine-accepting ability of tRNA Leu(UAG). This tRNA could have then acquired threonine-accepting activity through the appearance of an additional threonyl-tRNA synthetase. CUN codons that subsequently appeared from mutations of various other codons would have been translated as threonine. This change in the yeast mitochondrial genetic code is likely to have evolved through a series of nondisruptive nucleotide substitutions that produced no widespread replacement of leucine by threonine in proteins as a consequence.

Early Development of the Neutral Theory

The neutral theory of molecular evolution has become well known and widely discussed. As defined by Jukes and Kimura [1], it postulates that nucleotide substitutions inherently take place in DNA as a result of point mutations followed by random genetic drift. In the absence of selective constraints, the substitution rate reaches the maximum value set by the mutation rate, for example, about 5 x 10 ~9 substitutions per site per year. Rates slower than this occur when constraints are imposed by natural selection. This brief communication will review the history of the neutral theory during the 1960s, when it was proposed. Before this, genetic drift was often discussed; but not until sequences of amino acids in proteins became known was it possible to perceive neutral changes in molecular evolution. In 1961, differences in amino acid content of total protein in bacteria were found to be related to base composition of DNA. This will be discussed below. Later, sequences of nucleic acids became available and provided further evidence for neutral changes. Two proposals were made independently, one through biochemistry and one through population genetics.