The nucleotide sequence of blue-green algae phenylalanine-tRNA and the evolutionary origin of chloroplasts.

Phenylalanine tRNA from the blue-green alga, Agmenellum quadruplicatum, has been purified to homogeneity. The nucleotide sequence of this tRNA was determined to be: (see tests) Comparisons of the sequence and the modified nucleosides of this tRNA with those of other tRNAPhes thus far sequenced, indicate that this blue green algal tRNAPhe is typically prokaryotic and closely resembles the chloroplast tRNAPhes of higher plants and Euglena. The significance of this observation to the evolutionary origin of chloroplasts is discussed.     

Translocons on the inner and outer envelopes of chloroplasts share similar evolutionary origin in Arabidopsis thaliana

The process of importing nuclear encoded proteins into chloroplasts is mediated by the T ranslocons on the O uter/I nner Envelope of C hloroplasts (TOC and TIC complex). The ancestor of the TOC complex was formed by pre‐existing proteins from the cyanobacterial ancestor; other proteins recruited from the host cell or cyanobacterial ancestor were subsequently integrated into the complex. However, little is known about the origin of the TIC complex. In this work, the origin of the TIC complex was investigated through one of its channel proteins, AtTic21. Phylogenetic analysis suggested that AtTic21 is conserved in photosynthetic organisms. AtTic21 showed 33% sequence identity to a Synechocystis protein SynTic21. The successful genetic complementation of an AtTic21 knockout mutant by SynTic21 plus the transit peptide coding sequence of AtTic21 suggested that SynTic21 is an ortholog of AtTic21. The sequence and functional conservation between SynTic21 and AtTic21 suggested that the TIC complex shares a similar evolutionary origin to the TOC complex.     

On the evolutionary origin of aging

It is generally believed that the first organisms did not age, and that aging thus evolved at some point in the history of life. When and why this transition occurred is a fundamental question in evolutionary biology. Recent reports of aging in bacteria suggest that aging predates the emergence of eukaryotes and originated in simple unicellular organisms. Here we use simple models to study why such organisms would evolve aging. These models show that the differentiation between an aging parent and a rejuvenated offspring readily evolves as a strategy to cope with damage that accumulates due to vital activities. We use measurements of the age-specific performance of individual bacteria to test the assumptions of the model, and find evidence that they are fulfilled. The mechanism that leads to aging is expected to operate in a wide range of organisms, suggesting that aging evolved early and repeatedly in the history of life. Aging might thus be a more fundamental aspect of cellular organisms than assumed so far.     

On the evolutionary origin of the chaperonins

An analysis of the apical domain of the Group-I and Group-II chaperonins shows that they have structural similarities to two different protein folds: a "swivel-domain" phosphotransferase and a thioredoxin-like peroxiredoxin. There is no significant sequence similarity that supports either similarity and the degree of similarity based on structure is comparable but weak for both relationships. Based on possible evolutionary transitions, we deduced that a phosphotransferase origin would require both a large insertion and deletion of structure whereas a peroxiredoxin origin requires only a peripheral rearrangement, similar to an internal domain-swap. We postulate that this change could have been triggered by the insertion of a peroxiredoxin into the ATPase domain that led to the modern chaperonin domain arrangement. The peroxidoxin fold is the most highly embellished member of the thioredoxin super-family and the insertion event may have "overloaded" the core, leading to a rearrangement. A peroxiredoxin origin for the domain also provides a functional explanation, as the peroxiredoxins can act as chaperones when they adopt a multimeric ring complex, similar to the chaperonin subunit configuration. In addition, several of the GroEL apical domain hydrophobic residues which interact with the unfolded protein are located in a position that corresponds to the protein substrate binding region of the peroxiredoxin fold. We suggest that the origin of the ur-chaperonin from a thioredoxin/peroxiredoxin fold might also account for the number of thioredoxin-fold containing proteins that interact with chaperonins, such as tubulin and phosducin-like proteins.     

The evolutionary origin of glycosomes

The glycolytic pathway of the Kinetoplastida is organized in a unique manner: the majority of its enzymes are contained in organelles called glycosomes. In this article Paul Michels and Fred Opperdoes argue that the glycosomes are equivalent to the microbodies and peroxisomes identified in other eukaryotic cells. They explore the possible evolutionary origin of the glycosome by comparing many of its structural and functional properties with those of other members of the microbody family and with some features of other organelles, the mitochondria and chloroplasts, which have been studied in much more detail.     

On evolutionary origin of cancer

Background  

The necessary and sufficient capabilities of cancer cell have been identified. Strikingly, this list does not include one that would seem to be a key property, namely the ability of cancer cells to kill their "host". This is believed to be a self-evident consequence of the other capabilities (e.g., metastasis), although the available evidence suggests a distinct killer function. Taking into account this unlisted property can significantly affect the current paradigm of carcinogenesis.     

Romundina and the evolutionary origin of teeth

Theories on the origin of vertebrate teeth have long focused on chondrichthyans as reflecting a primitive condition—but this is better informed by the extinct placoderms, which constitute a sister clade or grade to the living gnathostomes. Here, we show that ‘supragnathal’ toothplates from the acanthothoracid placoderm Romundina stellina comprise multi-cuspid teeth, each composed of an enameloid cap and core of dentine. These were added sequentially, approximately circumferentially, about a pioneer tooth. Teeth are bound to a bony plate that grew with the addition of marginal teeth. Homologous toothplates in arthrodire placoderms exhibit a more ordered arrangement of teeth that lack enameloid, but their organization into a gnathal, bound by layers of cellular bone associated with the addition of each successional tooth, is the same. The presence of enameloid in the teeth of Romundina suggests that it has been lost in other placoderms. Its covariation in the teeth and dermal skeleton of placoderms suggests a lack of independence early in the evolution of jawed vertebrates. It also appears that the dentition—manifest as discrete gnathal ossifications—was developmentally discrete from the jaws during this formative episode of vertebrate evolution.     

On the evolutionary origin of mitochondrial DNA

Current theories of mitochondrial evolution assume that this organelle evolved either from endosymbiotic bacterial-like organisms which invaded other cells or by a gradual sequestering of functional cytoplasmic units within membranes. In either case there has been relatively little discussion of the origin of mitochondrial DNA. Because of the marked similarity in the size, physical properties, replication and sensitivity to acridine dyes and ethidium bromide of both bacterial plasmid and mitochondrial DNA, it is proposed that the plasmid of an ancestral bacterial-like organism evolved into the mitochondrial DNA of eukaryotes. This hypothesis is consistent with either theory of the whole organelle but is easier to explain if mitochondria evolved within a prokaryote by invagination of the plasma membrane.     

The evolutionary origin of the HLA-DR3 haplotype

The human HLA-DR3 haplotype consists of two functional genes (DRB1*03 and DRB3*01) and one pseudogene (DRB2), arranged in the order DRB1... DRB2... DRB3 on the chromosome. To shed light on the origin of the haplotype, we sequenced 1480 nucleotides of the HLA-DRB2 gene and aong stretches of two other genes, Gogo-DRB2 from a gorilla, Sylvia and Patr-DRB2 from a chimpanzee, Hugo. All three sequences (HLA-DRB2, Gogo-DRB2, Patr-DRB2) are pseudogenes. The HLA-DRB2 and Gogo-DRB2 pseudogenes lack exon 2 and contain a twenty-nucleotide deletion in exon 3, which destroys the correct translational reading frame and obliterates the highly conserved cysteine residue at position 173. The Patr-DRB2 pseudogene lacks exons 1 and 2; it does not contain the twenty-nucleotide deletion, but does contain a characteristic duplication of that part of exon 6 which codes for the last four amino acid residues of the cytoplasmic region. When the nucleotide sequences of these three genes are compared to those of all other known DRB genes, the HLA-DRB2 is seen as most closely related to Gogo-DRB2, indicating orthologous relationship between the two sequences. The Patr-DRB2 gene is more distantly related to these two DRB2 genes and whether it is orthologous to them is uncertain. The three genes are in turn most closely related to HLA-DRBVI (the pseudogene of the DR2 haplotype) and Patr-DRB6 (another pseudogene of the Hugo haplotype), followed by HLA-DRB4 (the functional but nonpolymorphic gene of the DR4 haplotype). These relationships suggest that these six genes evolved from a common ancestor which existed before the separation of the human, gorilla, and chimpanzee lineages. The DRB2 and DRB6 have apparently been pseudogenes for at least six million years (myr). In the human and the gorilla haplotype, the DRB2 pseudogene is flanked on each side by what appear to be related genes. Apparently, the DR3 haplotype has existed in its present form for more than six myr.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession number M86691–94.     

An evolutionary scenario for the origin of flowers

The Mostly Male theory is the first to use evidence from gene phylogenies, genetics, modern plant morphology and fossils to explain the evolutionary origin of flowers. It proposes that flower organization derives more from the male structures of ancestral gymnosperms than from female structures. The theory arose from a hypothesis-based study. Such studies are the most likely to generate testable evolutionary scenarios, which should be the ultimate goal of evo-devo.     

Metabolic integration during the evolutionary origin of mitochondria

Although mitochondria provide eukaryotic cells with certain metabolic advantages, in other ways they may be disadvantageous. For example, mitochondria produce reactive oxygen species that damage both nucleocytoplasm and mitochondria, resulting in mutations, diseases, and aging. The relationship of mito-chondria to the cytoplasm is best understood in the context of evolutionary history. Although it is clearthat mitochondria evolved from symbiotic bacteria, the exact nature of the initial symbiosis is a matter of continuing debate. The exchange of nutrients between host and symbiont may have differed from that be-tween the cytoplasm and mitochondria in modern cells. Speculations about the initial relationships includethe following. (1) The pre-mitochondrion may have been an invasive, parasitic bacterium. The host did notbenefit. (2) The relationship was a nutritional syntrophy based upon transfer of organic acids from host tosymbiont. (3) The relationship was a syntrophy based upon H2 transfer from symbiont to host, where thehost was a methanogen. (4) There was a syntrophy based upon reciprocal exchange of sulfur compounds.The last conjecture receives support from our detection in eukaryotic cells of substantial H2S-oxidizing activity in mitochondria, and sulfur-reducing activity in the cytoplasm.     

Development and evolutionary origin of feathers

Avian feathers are a complex evolutionary novelty characterized by structural diversity and hierarchical development. Here, I propose a functionally neutral model of the origin and evolutionary diversification of bird feathers based on the hierarchical details of feather development. I propose that feathers originated with the evolution of the first feather follicle-a cylindrical epidermal invagination around the base of a dermal papilla. A transition series of follicle and feather morphologies is hypothesized to have evolved through a series of stages of increasing complexity in follicle structure and follicular developmental mechanisms. Follicular evolution proceeded with the origin of the undifferentiated collar (stage I), barb ridges (stage II), helical displacement of barb ridges, barbule plates, and the new barb locus (stage III), differentiation of pennulae of distal and proximal barbules (stage IV), and diversification of barbule structure and the new barb locus position (stage V). The model predicts that the first feather was an undifferentiated cylinder (stage I), which was followed by a tuft of unbranched barbs (stage II). Subsequently, with the origin of the rachis and barbules, the bipinnate feather evolved (stage III), followed then by the pennaceous feather with a closed vane (stage IV) and other structural diversity (stages Va-f). The model is used to evaluate the developmental plausibility of proposed functional theories of the origin of feathers. Early feathers (stages I, II) could have functioned in communication, defense, thermal insulation, or water repellency. Feathers could not have had an aerodynamic function until after bipinnate, closed pennaceous feathers (stage IV) had evolved. The morphology of the integumental structures of the coelurisaurian theropod dinosaurs Sinosauropteryx and Beipiaosaurus are congruent with the model's predictions of the form of early feathers (stage I or II). Additional research is required to examine whether these fossil integumental structures developed from follicles and are homologous with avian feathers. J. Exp. Zool. (Mol. Dev. Evol.) 285:291-306, 1999.Copyright 1999 Wiley-Liss, Inc.     

The evolutionary origin of orphan genes

Gene evolution has long been thought to be primarily driven by duplication and rearrangement mechanisms. However, every evolutionary lineage harbours orphan genes that lack homologues in other lineages and whose evolutionary origin is only poorly understood. Orphan genes might arise from duplication and rearrangement processes followed by fast divergence; however, de novo evolution out of non-coding genomic regions is emerging as an important additional mechanism. This process appears to provide raw material continuously for the evolution of new gene functions, which can become relevant for lineage-specific adaptations.