Journal of Molecular Evolution

Although some α-glucosidases from the α-amylase family (glycoside hydrolase family GH13) have been studied extensively, their exact number, organization on the chromosome, and orthology/paralogy relationship were unknown. This was true even for important disease vectors where gut α-glucosidase is known to be receptor for the Bin toxin used to control the population of some mosquito species. In some cases orthologs from related species were studied intensively, while potentially important paralogs were omitted. We have, therefore, used a bioinformatics approach to identify all family GH13 α-glucosidases from the selected species from Metazoa (including three mosquito species: Aedes aegypti, Anopheles gambiae, and Culex quinquefasciatus) as well as from Fungi in an effort to characterize their arrangement on the chromosome and evolutionary relationships among orthologs and among paralogs. We also searched for pseudogenes and genes coding for enzymatically inactive proteins with a possible new function. We have found GH13 α-glucosidases mostly in Arthropoda and Fungi where they form gene families, as a result of multiple lineage-specific gene duplications. In mosquito species we have identified 14 α-glucosidase (Aglu) genes of which only five have been biochemically characterized so far, two are putative pseudogenes and the rest remains uncharacterized. We also revealed quite a complex evolutionary history of the eukaryotic α-glucosidases probably involving multiple losses of genes or horizontal gene transfer from bacteria.

We have studied a number of condensation reactions involving ImpU, ImpT, ImpC, ImpA, ImpG, ImpUpG and ImpCpA as activated nucleotide donors and a variety of homo- and hetero-polynucleotides as templates. We did not obtain any evidence of a template effect with ImpU and ImpT, but observed some condensation of ImpC with GpG on appropriate templates. ImpA and ImpG take part in a number of more or less efficient template-directed reactions, as do ImpUpG and ImpCpA. Our results suggest that, on the primitive Earth, pyrimidine nucleotides could most easily have been incorporated into polymers as constituents of short oligomers, which contained one or more purine nucleotide. The linkage of the product depends strongly on the nature of the substrates; the percentage of the natural 3′-5′-linkage was, in some cases, less than 10% and, in others, as high as 70%. Wobble-pairing was often very effective in promoting condensations, suggesting that transition mutations would have been very frequent in prebiotic polynucleotide replication.

Dimeric hemoglobins in lampreys are thought to be orthologous to gnathostome hemoglobins, comprising a familiar tetrameric assembly, despite their different subunit interface. To elucidate this contradictory problem, a phylogenetic analysis of vertebrate globins was conducted. The inferred maximum-likelihood trees revealed that the cyclostome hemoglobins are closely related to STAPs, recently identified stellate cell activation-associated proteins, and are paralogous to gnathostome hemoglobins. The quaternary structural difference between cyclostome and gnathostome hemoglobins is well understandable in light of their paralogous relationship.

Electrophoretic comparisons have been made for 24 enzymes in theBergerac andBristol strains ofCaenorhabditis elegans and the related species,Caenorhabditis briggsae. No variation was detected between the two strains ofC. elegans. In contrast, the two species,C. elegans andC. briggsae exhibited electrophoretic differences in 22 of 24 enzymes. A consensus 5S rRNA sequence was determined forC. elegans and found to be identical to that fromC. briggsae. By analogy with other species with relatively well established fossil records it can be inferred that the time of divergence between the two nematode species is probably in the tens of millions of years. The limited anatomical evolution during a time period in which proteins undergo extensive changes supports the hypothesis that anatomical evolution is not dependent on overall protein changes.

κ-Caseins, involved in the milk clotting process, and human fibrinogenγ-chain, involved in the blood clotting process, show structural similarities. Several longκ-casein sections, together corresponding to 80% of the whole protein molecule, have their counterparts in theγ-chain of fibrinogen, in that 31-42% of the amino acid residues occupy identical positions. The section ofК-casein which contains the chymosin-sensitive bond has a counterpart not only in theγ but also in the Bβ-chain of fibrinogen. Furthermore, the secondary structures of theК-caseins and of theγ-chain predicted according to the method of Chou and Fasman present several common features.

If a phenotypic character is under stabilizing selection, the selective disadvantage of a nonoptimal genotype will decrease exponentially to zero as the proportion of phenotypic variation that is environmental in origin -V e /V p - increases. Under the modified mutation-drift hypothesis of genetic polymorphism, the proportion of mutations that are effectively neutral and average heterozygosity should increase with this ratio. Invertebrates, because of their small size, fast development, and low degree of homeostasis (relative to vertebrates), are expected to show a larger environmental component of phenotypic variation than vertebrates. This may help explain why invertebrates are in general more genetically variable than vertebrates and why, when laboratory populations ofDrosophila are maintained in heterogeneous environments, genetic variability is lost less rapidly than when they are kept in constant conditions.

The proposal by Schultz and Yarus is that changes in the genetic code result from ambiguous reading of codons. This is a simplistic catchall scheme. Our codon capture hypothesis was accompanied by case studies of each incident; for example, AAA changing to asparagine from lysine was preceded by all AAA lysine codons mutating to AAG under GC pressure, with disappearance of lysine anticodon UUU, followed by appearance of a new anticodon IUU for asparagine which would wobble-pair with AAU, AAC, and AAA (Ohama et al. 1990a). Ambiguous coding would not confine itself to changes in the genetic code to accommodate the proposal by Schultz and Yarus, but would extend throughout the genome if their idea is correct. Under these circumstances, much impairment of the accuracy in codon reading that is needed for maintenance of the constant sequences of amino acids in proteins would occur. Surely the net effect would be deleterious. Our conclusion is that the proposal by Schultz and Yarus is a “simple and easy answer to a complex and difficult problem,” and is not acceptable.