Ribosomal protein-sequence block structure suggests complex prokaryotic evolution with implications for the origin of eukaryotes

Amino acid sequence alignments of orthologous ribosomal proteins found in Bacteria, Archaea, and Eukaryota display, relative to one another, an unusual segment or block structure, with major evolutionary implications. Within each of the prokaryotic phylodomains the sequences exhibit substantial similarity, but cross-domain alignments break up into (a) universal blocks (conserved in both phylodomains), (b) bacterial blocks (unalignable with any archaeal counterparts), and (c) archaeal blocks (unalignable with any bacterial counterparts). Sequences of those eukaryotic cytoplasmic riboproteins that have orthologs in both Bacteria and Archaea, exclusively match the archaeal block structure. The distinct blocks do not correlate consistently with any identifiable functional or structural feature including RNA and protein contacts. This phylodomain-specific block pattern also exists in a number of other proteins associated with protein synthesis, but not among enzymes of intermediary metabolism. While the universal blocks imply that modern Bacteria and Archaea (as defined by their translational machinery) clearly have had a common ancestor, the phylodomain-specific blocks imply that these two groups derive from single, phylodomain-specific types that came into existence at some point long after that common ancestor. The simplest explanation for this pattern would be a major evolutionary bottleneck, or other scenario that drastically limited the progenitors of modern prokaryotic diversity at a time considerably after the evolution of a fully functional translation apparatus. The vast range of habitats and metabolisms that prokaryotes occupy today would thus reflect divergent evolution after such a restricting event. Interestingly, phylogenetic analysis places the origin of eukaryotes at about the same time and shows a closer relationship of the eukaryotic ribosome-associated proteins to crenarchaeal rather than euryarchaeal counterparts.     

Genetic divergence between cave and surface populations of Astyanax in Mexico (Characidae,Teleostei)

A study of genetic diversity at microsatellite loci and the mitochondrial DNA (mtDNA) cytochrome b gene was carried out to assess genetic relationships among four Mexican cave (Pachon, Sabinos, Tinaja, Chica) and four surface populations of Astyanax fasciatus (Characidae) from northeast Mexico and the Yucatan. With the exception of Chica, the cave populations were all characterized by extremely low microsatellite variability, which most likely resulted from bottleneck events. Population analyses of the microsatellite data indicated no measurable levels of gene flow between all cave and surface populations (F(ST) > 0.0707). Phylogenetic analyses of mtDNA data showed that only two cave populations - Sabinos and Tinaja - group together to the exclusion of surface populations. From the microsatellite data these cave populations cluster with the Pachon cave fish population. The mtDNA thus appears to have been replaced in Pachon because of introgressive hybridization. It is likely that these three cave populations have descended from a surface ancestor in common with current surface populations, rather than evolving recently from one of the extant surface populations. Like Pachon, the Chica population clustered with the surface populations according to mtDNA data, but was not clearly associated with either the surface or the other cave populations according to the microsatellite data. Our data indicate that the Chica population evolved recently from a surface population, and subsequently hybridized with a phylogenetically older cave population. In conclusion, both the microsatellite and mtDNA data suggest multiple origins of cave populations and the Chica and Sabinos/Tinaja/Pachon were founded after at least two independent invasions from surface populations.     

Evidence for a pre-restriction point Cdk3 activity

We have examined the activity of cyclin-dependent kinase 3 (cdk3) during G1-phase of the cell cycle in Chinese Hamster Ovary (CHO) fibroblasts. Histone H1 kinase activity associated with anti-cdk3 immunoprecipitates peaked during a brief window of time, 2-3 h prior to the restriction point. In vitro cdk3 activity was sensitive to roscovitine, a drug previously shown to inhibit cdks 1, 2, and 5, but not cdk4 or 6. Early G1-phase activation of cdk3 was downregulated by treatment of cells with MG132, an inhibitor of the proteasome, and by the protein synthesis inhibitor cycloheximide. These results provide evidence for a pre-restriction point cdk3 activity that requires both the synthesis of a regulatory subunit and degradation of an inhibitor.     

Estimation of the age of extant Ephedra using chloroplast rbcL sequence data

The distinctive gymnosperm genus Ephedra is sometimes considered to have originated over 200 million years (Myr) ago on the basis of "ephedroid" fossil pollen. In this article we estimate the age of extant Ephedra using chloroplast rbcL gene sequences. Relative rate tests fail to reject the null hypothesis of equal rates of nucleotide substitution of the rbcL sequences among three landmark lineages (Gnetales, Pinaceae, and Ginkgo). The most divergent sequences we have found in Ephedra differ by only 7 bp for an 1,110 bp region of rbcL sequence, whereas the differences among genera range from 92 to 107 bp in Gnetales and from 35 to 92 bp in Pinaceae. Using three landmark events, the age of extant Ephedra is estimated to be approximately 8-32 Myr. Our result is consistent with the current distribution of many Ephedra species in geologically recent habitats and points out difficulties in the identification of older ephedroid pollen fossils with the modern genus Ephedra.     

The Lyon and the LINE hypothesis

X-chromosome inactivation (XCI) was first suggested as an explanation for the variegated phenotypes in mice heterozygous for X-linked colour genes or for X-autosome translocations involving autosomal coat colour genes. The effects seen in X-autosome translocations led to the suggestion of an X-inactivation centre (Xic) from which the inactivation was initiated, and this suggestion has led to major advances in understanding. Another feature of X-autosome translocations is incomplete inactivation of the attached autosomal segment, implying that the X-chromosome is enriched in features favouring inactivation. Interspersed repeat elements, and in particular long interspersed elements (LINEs), have been suggested as the relevant enriching features. Recent evidence concerning this hypothesis is discussed.     

Allozyme Variation Patterns and Multiple Hybridization Origins: Clonal Variation Among Four Sibling Parthenogenetic Caucasian Rock Lizards

Allozyme electrophoresis of four sibling parthenogenetic Caucasian rock lizards Darevskia unisexualis, D.uzzelli, D.sapphirina, and D.bendimahiensis found seven clones and five variable loci. The data supported the hypothesis that D.raddei and D.valentini are the parental species of all four parthenogens. Variation patterns in Darevskia were summarized. Species that originated from a single F₁ typically consisted of one widespread clone with a few rare clones. Species with multiple origins displayed variation only slightly higher than species with a single origin. This is contrary to other genera of parthenogenetic lizards, in which cases massive clonal variations were observed. This revised version was published online in August 2006 with corrections to the Cover Date.     

ORIGIN AND BIOGEOGRAPHY OF AESCULUS L. (HIPPOCASTANACEAE): A MOLECULAR PHYLOGENETIC PERSPECTIVE

Sequences of chloroplast gene matK and internal transcribed spacers of nuclear ribosomal RNA genes were used for phylogenetic analyses of Aesculus, a genus currently distributed in eastern Asia, eastern and western North America, and southeastern Europe. Phylogenetic relationships inferred from these molecular data are highly correlated with the geographic distributions of species. The identified lineages closely correspond to the five sections previously recognized on the basis of morphology. Ancestral character-state reconstruction, a molecular clock, and fossil evidence were used to infer the origin and biogeographic history of the genus within a phylogenetic framework. Based on the molecular phylogenetic reconstruction of the genus, sequence divergence, and paleontological evidence, we infer that the genus originated during the transition from the Cretaceous to the Tertiary (~65 M.Y.B.P.) at a high latitude in eastern Asia and spread into North America and Europe as an element of the “boreotropical flora”; the current disjunct distribution of the genus resulted from geological and climatic changes during the Tertiary.     

The use of zinc(II) to probe iron binding and oxidation by the ferritin (EcFtnA) of Escherichia coli

 The ferritin of Escherichia coli (EcFtnA) is similar to human H-chain ferritin (HuHF) in having 24 subunits, each containing a dinuclear site at which two iron atoms can be oxidised (the diiron centre). In EcFtnA, unlike HuHF, fluorescence quenching of Trp122, located near site A of the dinuclear centre, can be used to monitor metal binding (this tryptophan is absent from HuHF). Metal binding also perturbs the UV absorbance spectrum of Trp122 and that of Tyr24 (a conserved residue near site B of the dinuclear centre). Using UV-difference spectroscopy and fluorescence quenching it is shown that Fe(II) and Zn(II) bind at the same sites, A and B. Sequential stopped-flow studies of Fe(II) binding and oxidation also show that Zn(II) is an effective competitor of Fe(II) binding and an inhibitor of its oxidation. Received: 10 June 1998 / Accepted: 18 September 1998     

The origin of prokaryotic life and molecular evolution

The origin of prokaryotic life is discussed with an emphasis on the self-assembly of early life in a microscale environment where ordered cellular structures and integrated functions evolved from disorder. Early molecular evolution may have been due to both molecular chaos and evolving molecular order.