Developmental mechanism and evolutionary origin of vertebrate left/right asymmetries

The systematically 'handed', or directionally asymmetrical way in which the major viscera are packed within the vertebrate body is known as situs. Other less obvious vertebrate lateralisations concern cognitive neural function, and include the human phenomena of hand-use preference and language-associated cognitive partitioning. An overview, rather than an exhaustive scholarly review, is given of recent advances in molecular understanding of the mechanism that ensures normal development of 'correct' situs. While the asymmetry itself and its left/right direction are clearly vertebrate-conserved characters, data available from various embryo types are compared in order to assess the likelihood that the developmental mechanism is evolutionarily conserved in its entirety. A conserved post-gastrular 'phylotypic' stage, with left- and right-specific cascades of key, orthologous gene expressions, clearly exists. It now seems probable that earlier steps, in which symmetry-breaking information is reliably transduced to trigger these cascades on the correct sides, are also conserved at depth although it remains unclear exactly how these steps operate. Earlier data indicated that the initiation of symmetry-breaking had been transformed, among the different vertebrate classes, as drastically as has the anatomy of pre-gastrular development itself, but it now seems more likely that this apparent diversity is deceptive. Ideas concerning the functional advantages to the vertebrate lifestyle of a systematically asymmetrical visceral packing arrangement, while untestable, are accepted because they form a plausible adaptationist 'just-so' story. Nevertheless, two contrasting beliefs are possible about the evolutionary origins of situs. Major recent advances in analysis of its developmental mechanism are largely due not to zoologists, comparative anatomists or evolutionary systematists, but to molecular geneticists, and these workers have generally assumed that the asymmetry is an evolutionary novelty imposed on a true bilateral symmetry, at or close to the origin of the vertebrate clade. A major purpose of this review is to advocate an alternative view, on the grounds of comparative anatomy and molecular systematics together with the comparative study of expressions of orthologous genes in different forms. This view is that situs represents a co-optation of a pre-existing, evolutionarily ancient non-bilaterality of the adult form in a vertebrate ancestor. Viewed this way, vertebrate or chordate origins are best understood as the novel imposition of an adaptively bilateral locomotory-skeletal-neural system, around a retained non-symmetrical 'visceral' animal. One component of neuro-anatomical asymmetry, the habenular/parapineal one that originates in the diencephalon, has recently been found (in teleosts) to be initiated from the same 'phylotypic' gene cascade that controls situs development. But the function of this particular diencephalic asymmetry is currently unclear. Other left-right partitionings of brain function, including the much more recently evolved, cerebral cortically located one associated with human language and hand-use, may be controlled entirely separately from situs even though their directionality has a particular relation to it in a majority of individuals. Finally, possible relationships are discussed between the vertebrate directional asymmetries and those that occur sporadically among protostome bilaterian forms. These may have very different evolutionary and molecular bases, such that there may have been constraints, in protostome evolution, upon any exploitation of left and right for complex organismic, and particularly cognitive neural function.     

The recent evolutionary origin of the phenylalanine-sensitive isozyme of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase in the enteric lineage of bacteria

Summary Evolutionary events that generated the three regulatory isozymes of 3-deoxy-d-arabino-heptulosonate 7-phosphate (DAHP) synthase present in contemporary strains ofEscherichia coli have been proposed recently [Ahmad et al. (1986) J Bacteriol 165:146–154]. The phylogenetic subdivision of gram-negative prokaryotes studied (Superfamily B) includes enteric bacteria, anOceanospirillum cluster, pseudomonad Group I (e.g.,Pseudomonas aeruginosa), pseudomonad Group V (e.g.,Xanthomonas), and theAcinetobacter grouping. DAHP synthase-phe, a regulatory isozyme subject to allosteric control byl-phenylalanine, was the last member of the isozyme family to evolve. Thus, DAHP synthase-phe is absent throughout Superfamily B except within the enteric lineage. Bacteria that make up the enteric lineage (Escherichia, Klebsiella, Erwinia, Serratia, Proteus, Aeromonas, andAlteromonas) were examined in detail; DAHP synthasephe was present in each of these organisms. Therefore, the isozyme originated between the separation of the enteric andOceanospirillum lineages, prior to the divergence ofAlteromonas putrefaciens (44% homology withE. coli by DNA:rRNA hybridization) from the rest of the enteric lineage. DAHP synthase-tyr and DAHP synthase-trp were uniformly present within the enteric lineage, although it was often necessary to derepress DAHP synthase-trp by physiological manipulation in order to demonstrate its presence.     

Right-handed penises of the earwig Labidura riparia (Insecta, Dermaptera, Labiduridae): evolutionary relationships between structural and behavioral asymmetries

The number of penises vary in the insect suborder Forficulina (order Dermaptera; earwigs). Males of the families Diplatyidae, Pigidicranidae, Anisolabididae, Apachyidae, and Labiduridae have two penises (right and left), while those of the Spongipohridae, Chelisochidae, and Forficulidae have a single penis. The proposed phylogenetic relationships among these families suggest that the single‐penis families evolved from an ancestor possessing two penises. To date, examinations of double‐penis earwig species have found that only a single penis is used per single copulation. These diversities in structural and behavioral aspects of genitalia raises the following intriguing questions: How are the two penises used? Why did a penis degenerate in several earwig families, and which one was lost? To address these questions, structural and behavioral asymmetries were examined in detail for a representative species Labidura riparia (Labiduridae). Although there was no detectable morphological differentiation between the right and left penises, male L. riparia predominantly used the right one for insemination. This significant “right‐handedness” developed without any experience of mating and was also manifested in the resting postures of the two penises when not engaged in copulation. However, surgical ablation of the right penis did not influence the insemination capacity of males. In wild‐caught males, only about 10% were left‐handed; within this group, abnormalities were frequently observed in the right penis. These lines of evidence indicate that the left penis is merely a spare intromittent organ, which most L. riparia males are likely never to use. Additional observations of five species of single‐penis families revealed that the left penis degenerated in the common ancestor of this group. Considering the proposed sister relationship between the Labiduridae and the single‐penis families, it is possible that such behavioral asymmetries in penis' use, as observed in L. riparia, are parental to the evolutionary degeneration of the infrequently used left penis. J. Morphol., 2006. © 2006 Wiley‐Liss, Inc.     

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.     

The oxidative DNA lesions 8,5'-cyclopurines accumulate with aging in a tissue-specific manner

Accumulation of DNA damage is implicated in aging. This is supported by the fact that inherited defects in DNA repair can cause accelerated aging of tissues. However, clear-cut evidence for DNA damage accumulation in old age is lacking. Numerous studies report measurement of DNA damage in nuclear and mitochondrial DNA from tissues of young and old organisms, with variable outcomes. Variability results from genetic differences between specimens or the instability of some DNA lesions. To control these variables and test the hypothesis that elderly organisms have more oxidative DNA damage than young organisms, we measured 8,5'-cyclopurine-2'-deoxynucleosides (cPu), which are relatively stable, in tissues of young and old wild-type and congenic progeroid mice. We found that cPu accumulate spontaneously in the nuclear DNA of wild-type mice with age and to a greater extent in DNA repair-deficient progeroid mice, with a similar tissue-specific pattern (liver > kidney > brain). These data, generated under conditions where genetic and environmental variables are controlled, provide strong evidence that DNA repair mechanisms are inadequate to clear endogenous lesions over the lifespan of mammals. The similar, although exaggerated, results obtained from progeroid, DNA repair-deficient mice and old normal mice support the conclusion that DNA damage accumulates with, and likely contributes to, aging.     

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.     

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.     

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 durophagous pelagic stingray ecomorph

Studies of the origin of evolutionary novelties (novel traits, feeding modes, behaviours, ecological niches, etc.) have considered a number of taxa experimenting with new body plans, allowing them to occupy new habitats and exploit new trophic resources. In the marine realm, colonization of pelagic environments by marine fishes occurred recurrently through time. Stingrays (Myliobatiformes) are a diverse clade of batoid fishes commonly known to possess venomous tail stings. Current hypotheses suggest that stingrays experimented with a transition from a benthic to a pelagic/benthopelagic habitat coupled with a transition from a non-durophagous diet to extreme durophagy. However, there is no study detailing macroevolutionary patterns to understand how and when habitat shift and feeding specialization arose along their evolutionary history. A new exquisitely preserved fossil stingray from the Eocene Konservat-Lagerstätte of Bolca (Italy) exhibits a unique mosaic of plesiomorphic features of the rajobenthic ecomorph, and derived traits of aquilopelagic taxa, that helps to clarify the evolutionary origin of durophagy and pelagic lifestyle in stingrays. A scenario of early evolution of the aquilopelagic ecomorph is proposed based on new data, and the possible adaptive meaning of the observed evolutionary changes is discussed. The body plan of †Dasyomyliobatis thomyorkei gen. et sp. nov. is intermediate between the rajobenthic and more derived aquilopelagic stingrays, supporting its stem phylogenetic position and the hypothesis that the aquilopelagic body plan arose in association with the evolution of durophagy and pelagic lifestyle from a benthic, soft-prey feeder ancestor.     

Tissue specificity of senescent cell accumulation during physiologic and accelerated aging of mice

Senescent cells accumulate with age in vertebrates and promote aging largely through their senescence‐associated secretory phenotype (SASP). Many types of stress induce senescence, including genotoxic stress. ERCC1‐XPF is a DNA repair endonuclease required for multiple DNA repair mechanisms that protect the nuclear genome. Humans or mice with reduced expression of this enzyme age rapidly due to increased levels of spontaneous, genotoxic stress. Here, we asked whether this corresponds to an increased level of senescent cells. p16^Ink4a and p21^Cip1 mRNA were increased ~15‐fold in peripheral lymphocytes from 4‐ to 5‐month‐old Ercc1^?/? and 2.5‐year‐old wild‐type (WT) mice, suggesting that these animals exhibit a similar biological age. p16^Ink4a and p21^Cip1 mRNA were elevated in 10 of 13 tissues analyzed from 4‐ to 5‐month‐old Ercc1^?/? mice, indicating where endogenous DNA damage drives senescence in vivo. Aged WT mice had similar increases of p16^Ink4a and p21^Cip1 mRNA in the same 10 tissues as the mutant mice. Senescence‐associated β–galactosidase activity and p21^Cip1 protein also were increased in tissues of the progeroid and aged mice, while Lamin B1 mRNA and protein levels were diminished. In Ercc1^?/Δ mice with a p16^Ink4a luciferase reporter, bioluminescence rose steadily with age, particularly in lung, thymus, and pancreas. These data illustrate where senescence occurs with natural and accelerated aging in mice and the relative extent of senescence among tissues. Interestingly, senescence was greater in male mice until the end of life. The similarities between Ercc1^?/? and aged WT mice support the conclusion that the DNA repair‐deficient mice accurately model the age‐related accumulation of senescent cells, albeit six‐times faster.     

Delayed kinetics of DNA double-strand break processing in normal and pathological aging

Accumulation of DNA damage may play an essential role in both cellular senescence and organismal aging. The ability of cells to sense and repair DNA damage declines with age. However, the underlying molecular mechanism for this age-dependent decline is still elusive. To understand quantitative and qualitative changes in the DNA damage response during human aging, DNA damage-induced foci of phosphorylated histone H2AX (γ-H2AX), which occurs specifically at sites of DNA double-strand breaks (DSBs) and eroded telomeres, were examined in human young and senescing fibroblasts, and in lymphocytes of peripheral blood. Here, we show that the incidence of endogenous γ-H2AX foci increases with age. Fibroblasts taken from patients with Werner syndrome, a disorder associated with premature aging, genomic instability and increased incidence of cancer, exhibited considerably higher incidence of γ-H2AX foci than those taken from normal donors of comparable age. Further increases in γ-H2AX focal incidence occurred in culture as both normal and Werner syndrome fibroblasts progressed toward senescence. The rates of recruitment of DSB repair proteins to γ-H2AX foci correlated inversely with age for both normal and Werner syndrome donors, perhaps due in part to the slower growth of γ-H2AX foci in older donors. Because genomic stability may depend on the efficient processing of DSBs, and hence the rapid formation of γ-H2AX foci and the rapid accumulation of DSB repair proteins on these foci at sites of nascent DSBs, our findings suggest that decreasing efficiency in these processes may contribute to genome instability associated with normal and pathological aging.     

Sickle cell disease as an accelerated aging syndrome

Sickle cell disease (SCD) is characterized by vaso-occlusion, hemolysis, and systemic manifestations that form the hallmark of the disease. Apart from morbidity, SCD is also associated with increased mortality and decreased quality of life. Aging is a natural phenomenon that is associated with changes at cellular, tissue, and organ levels, in addition to the loss of physical fitness, increased susceptibility to diseases, and a higher likelihood of mortality. Some of the cellular mechanisms involved in normal (or physiological) aging include abnormalities of sphingolipids (ceramides) and reduced length of the telomere. These changes have also been documented in SCD. Cellular, organs, and physical manifestations of SCD resemble an accelerated aging syndrome. Sickle erythrocytes also acquire morphological features similar to that of aged normal erythrocytes and are thus picked up early by the macrophages for destruction. Brain, kidney, heart, innate and adaptive immune system, and musculoskeletal system of patients with SCD exhibit morphological and functional changes that are ordinarily seen in the elderly in the general population. Stroke, silent cerebral infarcts, cardiomegaly, heart failure, pulmonary hypertension, nephropathy with proteinuria, osteopenia, osteoporosis, osteonecrosis, gout, and infections are exceedingly common in SCD. In this review, we have attempted to draw parallels between SCD and accelerated aging syndromes.     

Genetics and epigenetics of aging and longevity

Evolutionary theories of aging predict the existence of certain genes that provide selective advantage early in life with adverse effect on lifespan later in life (antagonistic pleiotropy theory) or longevity insurance genes (disposable soma theory). Indeed, the study of human and animal genetics is gradually identifying new genes that increase lifespan when overexpressed or mutated: gerontogenes. Furthermore, genetic and epigenetic mechanisms are being identified that have a positive effect on longevity. The gerontogenes are classified as lifespan regulators, mediators, effectors, housekeeping genes, genes involved in mitochondrial function, and genes regulating cellular senescence and apoptosis. In this review we demonstrate that the majority of the genes as well as genetic and epigenetic mechanisms that are involved in regulation of longevity are highly interconnected and related to stress response.     

Bloom syndrome patients and mice display accelerated epigenetic aging

Bloom syndrome (BSyn) is an autosomal recessive disorder caused by variants in the BLM gene, which is involved in genome stability. Patients with BSyn present with poor growth, sun sensitivity, mild immunodeficiency, diabetes, and increased risk of cancer, most commonly leukemias. Interestingly, patients with BSyn do not have other signs of premature aging such as early, progressive hair loss and cataracts. We set out to determine epigenetic age in BSyn, which can be a better predictor of health and disease over chronological age. Our results show for the first time that patients with BSyn have evidence of accelerated epigenetic aging across several measures in blood lymphocytes, as compared to carriers. Additionally, homozygous Blm mice exhibit accelerated methylation age in multiple tissues, including brain, blood, kidney, heart, and skin, according to the brain methylation clock. Overall, we find that Bloom syndrome is associated with accelerated epigenetic aging effects in multiple tissues and more generally a strong effect on CpG methylation levels.