Example Of Convergent Evolution Research Articles

Evolution of the C4 photosynthetic pathway: events at the cellular and molecular levels

The biochemistry and leaf anatomy of plants using C4 photosynthesis promote the concentration of atmospheric CO2 in leaf tissue that leads to improvements in growth and yield of C4 plants over C3 species in hot, dry, high light, and/or saline environments. C4 plants like maize and sugarcane are significant food, fodder, and bioenergy crops. The C4 photosynthetic pathway is an excellent example of convergent evolution, having evolved in multiple independent lineages of land plants from ancestors employing C3 photosynthesis. In addition to C3 and C4 species, some plant lineages contain closely related C3-C4 intermediate species that demonstrate leaf anatomical, biochemical, and physiological characteristics between those of C3 plants and species using C4 photosynthesis. These groups of plants have been extremely useful in dissecting the modifications to leaf anatomy and molecular biology, which led to the evolution of C4 photosynthesis. It is now clear that great variation exists in C4 leaf anatomy, and diverse molecular mechanisms underlie C4 biochemistry and physiology. However, all these different paths have led to the same destination-the expression of a C4 CO2 concentrating mechanism. Further identification of C4 leaf anatomical traits and molecular biological components, and understanding how they are controlled and assembled will not only allow for additional insights into evolutionary convergence, but also contribute to sustainable food and bioenergy production strategies.

An insight into the molecular basis for convergent evolution in fish antifreeze Proteins

Antifreeze proteins (AFPs) prevent the growth of ice-crystals in order to enable certain organisms to survive under sub-zero temperature surroundings. These AFPs have evolved from different types of proteins without having any significant structural and sequence similarities among them. However, all the AFPs perform the same function of anti-freeze activity and are a classical example of convergent evolution. We have analyzed fish AFPs at the sequence level, the residue level and the physicochemical property group composition to discover molecular basis for this convergent evolution. Our study on amino acid distribution does not reveal any distinctive feature among AFPs, but comparative study of the AFPs with their close non-AFP homologs based on the physicochemical property group residues revealed some useful information. In particular (a) there is a similar pattern of avoidance and preference of amino acids in Fish AFP subtypes II, III and IV—Aromatic residues are avoided whereas small residues are preferred, (b) like other psychrophilic proteins, AFPs have a similar pattern of preference/avoidance for most of the residues except for Ile, Leu and Arg, and (c) most of the computed amino acids in preferred list are the key functional residues as obtained in previous predicted model of Doxey et al. For the first time this study revealed common patterns of avoidance/preference in fish AFP subtypes II, III and IV. These avoidance/preference lists can further facilitate the identification of key functional residues and can shed more light into the mechanism of antifreeze function.

Microbes Bind Complement Inhibitor Factor H via a Common Site

To cause infections microbes need to evade host defense systems, one of these being the evolutionarily old and important arm of innate immunity, the alternative pathway of complement. It can attack all kinds of targets and is tightly controlled in plasma and on host cells by plasma complement regulator factor H (FH). FH binds simultaneously to host cell surface structures such as heparin or glycosaminoglycans via domain 20 and to the main complement opsonin C3b via domain 19. Many pathogenic microbes protect themselves from complement by recruiting host FH. We analyzed how and why different microbes bind FH via domains 19–20 (FH19-20). We used a selection of FH19-20 point mutants to reveal the binding sites of several microbial proteins and whole microbes (Haemophilus influenzae, Bordetella pertussis, Pseudomonas aeruginosa, Streptococcus pneumonia, Candida albicans, Borrelia burgdorferi, and Borrelia hermsii). We show that all studied microbes use the same binding region located on one side of domain 20. Binding of FH to the microbial proteins was inhibited with heparin showing that the common microbial binding site overlaps with the heparin site needed for efficient binding of FH to host cells. Surprisingly, the microbial proteins enhanced binding of FH19-20 to C3b and down-regulation of complement activation. We show that this is caused by formation of a tripartite complex between the microbial protein, FH, and C3b. In this study we reveal that seven microbes representing different phyla utilize a common binding site on the domain 20 of FH for complement evasion. Binding via this site not only mimics the glycosaminoglycans of the host cells, but also enhances function of FH on the microbial surfaces via the novel mechanism of tripartite complex formation. This is a unique example of convergent evolution resulting in enhanced immune evasion of important pathogens via utilization of a “superevasion site.”

Earliest record of megaphylls and leafy structures, and their initial diversification

Evolutionary changes in the structure of leaves have had far-reaching effects on the anatomy and physiology of vascular plants, resulting in morphological diversity and species expansion. People have long been interested in the question of the nature of the morphology of early leaves and how they were attained. At least five lineages of euphyllophytes can be recognized among the Early Devonian fossil plants (Pragian age, ca. 410 Ma ago) of South China. Their different leaf precursors or “branch-leaf complexes” are believed to foreshadow true megaphylls with different venation patterns and configurations, indicating that multiple origins of megaphylls had occurred by the Early Devonian, much earlier than has previously been recognized. In addition to megaphylls in euphyllophytes, the laminate leaf-like appendages (sporophylls or bracts) occurred independently in several distantly related Early Devonian plant lineages, probably as a response to ecological factors such as high atmospheric CO2 concentrations. This is a typical example of convergent evolution in early plants.

Neuron and beta‐cell evolution: Learning about neurons is learning about beta‐cells

Neurons and insulin-producing pancreatic beta-cells share multiple common features although they arise from different germ layers 1. In analogy to neurons, beta-cells release insulin by membrane depolarization reminiscent of synaptic neurotransmitter release in neurons and produce the neurotransmitter gamma aminobutyric acid (GABA) in synaptic-like vesicles. Although expression of many individual genes has been shown in neurons and beta-cells, an estimation of the total amount of genes commonly expressed in these cell types has just been addressed recently 2, 3. In a genome-wide mRNA expression scan, profiles of human and rodent beta-cells were compared to non-beta-cell tissues to find genes selectively expressed in beta-cells 2. Interestingly, 15% of these conserved beta-cell markers were also expressed in neuronal tissue coding for proteins involved in neurotransmitter transport, synaptic vesicle formation and brain development 2. To explain why ectodermal-derived neurons and endodermal-derived beta-cells share many common features, Arntfield and van der Kooy have recently speculated that beta-cells may have “borrowed from the brain”, i.e. their ancestors have deployed parts of the neuronal developmental program thereby creating an example of convergent evolution 1. This idea is consistent with the fact that multiple transcription factors are expressed in the neuronal and the pancreatic endocrine lineage including Neurogenin 3 (Ngn3) and NeuroD, both essential for brain and pancreas development. Arntfield et al. have further suggested that the evolution of (modern) beta-cells may have resulted from stochastic effects, i.e. mutation, activating neuronal master transcription factors in gut cells 1. However it remains unclarified which cell type may have first adopted the neuronal program, i.e. a more unspecified gut cell or a pre-differentiated endocrine cell. Recently it has been suggested that beta-cell progenitors co-opt the neural program rather late during their differentiation based on observations on the level of epigenetics 3. Interestingly, neuronal genes are still repressed in multipotent pancreatic progenitors that can give rise to exo- or endocrine tissue suggesting that an activation of neuronal gene activity occured later in the endocrine lineage 3. This would indicate that a pre-differentiated multipotent pancreatic progenitor adopted the neuronal program rather than a more unspecified cell. The notion that neurons and beta-cells are similar has stimulated scientists to transfer principles from neurobiology to understand beta-cell function and to find drugs to support beta-cell function under stress conditions as observed in type 2 diabetes mellitus. For example, screening of a chemical library for neurogenic activators has recently led to the identification of a potent inducer of NeuroD, supporting insulin production in pancreatic beta-cells 4. Moreover, known neuroprotective mechanisms may also be essential in beta-cells as observed in the case of the Parkinson-related antioxidant protein DJ-1 5. DJ-1 preserves mitochondrial integrity in dopaminergic neurons that are vulnerable to reactive oxygen species. In analogy to neurons, DJ-1 also protects the mitochondrial function of beta-cells suggesting that beta-cells and neurons share similar oxidative stress defence mechanisms. Thus, the study of common principles in neurons and beta-cells may provide a basis for prevention and treatment of diabetes mellitus and neurodegenerative diseases.

Structural Insights into the Evolution of the Adaptive Immune System

The adaptive immune system, which is based on highly diverse antigen receptors that are generated by somatic recombination, arose approximately 500 Mya at the dawn of vertebrate evolution. In jawed vertebrates, adaptive immunity is mediated by antibodies and T cell receptors (TCRs), which are composed of immunoglobulin (Ig) domains containing hypervariable loops that bind antigen. In striking contrast, the adaptive immune receptors of jawless vertebrates, termed variable lymphocyte receptors (VLRs), are constructed from leucine-rich repeat (LRR) modules. Structural studies of VLRs have shown that these LRR-based receptors bind antigens though their concave surface, in addition to a unique hypervariable loop in the C-terminal LRR capping module. These studies have revealed a remarkable example of convergent evolution in which jawless vertebrates adopted the LRR scaffold to recognize as broad a spectrum of antigens as the Ig-based antibodies and TCRs of jawed vertebrates, with altogether comparable affinity and specificity.

Using evolution as a guide to engineer kranz-type c4 photosynthesis.

Kranz-type C4 photosynthesis has independently and rapidly evolved over 60 times to dramatically increase radiation use efficiency in both monocots and eudicots. Indeed, it is one of the most exceptional examples of convergent evolution in the history of life. The repeated and rapid evolution of Kranz-type C4 suggests that it may be a derivative of a conserved developmental pathway that is present in all angiosperms. Here, I argue that the Kranz-type C4 photosynthetic system is an extension of the endodermis/starch sheath, that is normally only found in the roots and stems, into photosynthetic structures such as leaves. Support for this hypothesis was recently provided by a study that showed that the same genetic pathway that gives rise to the endodermis in roots, the SCARECROW/SHORT-ROOT radial patterning system, also regulates the development of Kranz anatomy and C4 physiology in leaves. This new hypothesis for the evolution of Kranz-type C4 photosynthesis has opened new opportunities to explore the underlying genetic networks that regulate the development and physiology of C4 and provides new potential avenues for the engineering of the mechanism into C3 crops.

G6f-Like Is an ITAM-Containing Collagen Receptor in Thrombocytes

Collagen activates mammalian platelets through a complex of the immunoglobulin (Ig) receptor GPVI and the Fc receptor γ-chain, which has an immunoreceptor tyrosine-based activation motif (ITAM). Cross-linking of GPVI mediates activation through the sequential activation of Src and Syk family kinases and activation of PLCγ2. Nucleated thrombocytes in fish are activated by collagen but lack an ortholog of GPVI. In this study we show that collagen activates trout thrombocytes in whole blood and under flow conditions through a Src kinase driven pathway. We identify the Ig receptor G6f-like as a collagen receptor and demonstrate in a cell line assay that it signals through its cytoplasmic ITAM. Using a morpholino for in vivo knock-down of G6f-like levels in zebrafish, we observed a marked delay or absence of occlusion of the venous and arterial systems in response to laser injury. Thus, G6f-like is a physiologically relevant collagen receptor in fish thrombocytes which signals through the same ITAM-based signalling pathway as mammalian GPVI, providing a novel example of convergent evolution.

Carbonic anhydrases of anaerobic microbes

Carbonic anhydrases (CAs) catalyze the reversible hydration of carbon dioxide to bicarbonate and are abundantly distributed in prokaryotes and eukaryotes. There are five classes (α,β,γ,δ,ζ) with no significant sequence or structural identity among them, a remarkable example of convergent evolution. The β and γ classes predominate in anaerobic microbes, living without O2, that comprise a substantial portion of the living protoplasm on Earth. Anaerobes reside in the lower intestinal tract of humans, one of many O2-free environments on Earth, where they convert complex biomass to methane and CO2 contributing an essential link in the global carbon cycle. Carbon dioxide is a universal metabolite of anaerobes necessitating CA for a diversity of proposed functions.

A fish-specific transposable element shapes the repertoire of p53 target genes in zebrafish.

Transposable elements, as major components of most eukaryotic organisms' genomes, define their structural organization and plasticity. They supply host genomes with functional elements, for example, binding sites of the pleiotropic master transcription factor p53 were identified in LINE1, Alu and LTR repeats in the human genome. Similarly, in this report we reveal the role of zebrafish (Danio rerio) EnSpmN6_DR non-autonomous DNA transposon in shaping the repertoire of the p53 target genes. The multiple copies of EnSpmN6_DR and their embedded p53 responsive elements drive in several instances p53-dependent transcriptional modulation of the adjacent gene, whose human orthologs were frequently previously annotated as p53 targets. These transposons define predominantly a set of target genes whose human orthologs contribute to neuronal morphogenesis, axonogenesis, synaptic transmission and the regulation of programmed cell death. Consistent with these biological functions the orthologs of the EnSpmN6_DR-colonized loci are enriched for genes expressed in the amygdala, the hippocampus and the brain cortex. Our data pinpoint a remarkable example of convergent evolution: the exaptation of lineage-specific transposons to shape p53-regulated neuronal morphogenesis-related pathways in both a hominid and a teleost fish.

Escherichia coli RecG functionally suppresses human Bloom syndrome phenotypes

Defects in the human BLM gene cause Bloom syndrome, notable for early development of tumors in a broad variety of tissues. On the basis of sequence similarity, BLM has been identified as one of the five human homologs of RecQ from Escherichia coli. Nevertheless, biochemical characterization of the BLM protein indicates far greater functional similarity to the E. coli RecG protein and there is no known RecG homolog in human cells. To explore the possibility that the shared biochemistries of BLM and RecG may represent an example of convergent evolution of cellular function where in humans BLM has evolved to fulfill the genomic stabilization role of RecG, we determined whether expression of RecG in human BLM-deficient cells could suppress established functional cellular Bloom syndrome phenotypes. We found that RecG can indeed largely suppress both the definitive elevated sister chromatid exchange phenotype and the more recently demonstrated gene cluster instability phenotype of BLM-deficient cells. In contrast, expression of RecG has no impact on either of these phenotypes in human cells with functional BLM protein. These results suggest that the combination of biochemical activities shared by RecG and BLM fill the same evolutionary niche in preserving genomic integrity without requiring exactly identical molecular mechanisms.

Insects converge on resistance

In a remarkable example of convergent evolution, insect species spanning 300 million years of divergence have evolved identical single-amino-acid substitutions that confer resistance to plant cardenolide toxins.

MULTIPLE EVOLUTIONARY PATHWAYS TO DECREASED LATERAL PLATE COVERAGE IN FRESHWATER THREESPINE STICKLEBACKS

Adaptation to novel environments can be based either on standing genetic variation or variation attributable to new mutations. When standing genetic variation for a functional adaptation is lacking, and variation due to new mutations is not yet available, adaptation is possible only through alternative functional solutions. Reduction in the number of bony lateral plates as an adaptation to freshwater colonization by marine threespine sticklebacks (Gasterosteus aculeatus) has occurred in numerous independent cases through allelic substitution in the ectodysplasin-a (Eda) gene. Studying the phenotypic and genetic variation in plate number and size in five marine and six freshwater threespine stickleback populations, we found that when variation in Eda was limiting (i.e., alleles associated with the low-plate morph were missing or in extremely low frequency), plate number reduction did not take place in freshwater populations, but reduced lateral plate coverage was achieved by a reduction in the size of lateral plates. Our results suggest that this phenotypically and genetically discrete "small-plated" threespine stickleback-which is the dominant form in three northern European freshwater populations-may be functionally equivalent to the low-plated morph and hence, serve as an example of convergent evolution toward functional similarity in the face of genetic constraints.

The genus Melanophloea, an example of convergent evolution towards polyspory

AbstractThe species described in or referred to the genus Melanophloea, traditionally referred to the Thelocarpaceae, are discussed. Detailed observations on two species, including the type species, show that they have not much more in common than their polysporous ascus. Melanophloea is reduced to the type species, M. pacifica. It shows a close resemblance to Aptrootia in the Trypetheliaceae, and it is therefore tentatively referred to this family. Melanophloea americana is shown to be close to Thelenella in the Thelenellaceae. The latter species and the related M. montana are newly combined into this genus as Thelenella americana and T. montana. Thelocarpon nigrum, which was recently compared to Melanophloea, is retained in Thelocarpon in the Thelocarpaceae. Polyspory is suggested to facilitate dispersion, especially when compared to parent taxa that produce large muriform ascospores. Based on the current classification, polyspory originated at least 57 times within the lichenized ascomycetes, a clear example of convergent evolution.

Thoughts on the diversity of convergent evolution of bioluminescence on earth

AbstractThe widespread independent evolution of analogous bioluminescent systems is one of the most impressive and diverse examples of convergent evolution on earth. There are roughly 30 extant bioluminescent systems that have evolved independently on Earth, with each system likely having unique enzymes responsible for catalysing the bioluminescent reaction. Bioluminescence is a chemical reaction involving a luciferin molecule and a luciferase or photoprotein that results in the emission of light. Some independent systems utilize the same luciferin, such as the use of tetrapyrrolic compounds by krill and dinoflagellates, and the wide use of coelenterazine by marine organisms, while the enzymes involved are unique. One common thread among all the different bioluminescent systems is the requirement of molecular oxygen. Bioluminescence is found in most forms of life, especially marine organisms.Bioluminescence in known to benefit the organism by: attraction, repulsion, communication, camouflage, and illumination. The marine ecosystem is significantly affected by bioluminescence, the only light found in the pelagic zone and below is from bioluminescent organisms.Transgenic bioluminescent organisms have revolutionized molecular research, medicine and the biotechnology industry. The use of bioluminescence in studying molecular pathways and disease allows for non-invasive and real-time analysis. Bioluminescence-based assays have been developed for several analytes by coupling luminescence to many enzyme-catalysed reactions.

Divergent role of the Hox gene Antennapedia in spiders is responsible for the convergent evolution of abdominal limb repression

Evolution often results in morphologically similar solutions in different organisms, a phenomenon known as convergence. However, there is little knowledge of the processes that lead to convergence at the genetic level. The genes of the Hox cluster control morphology in animals. They may also be central to the convergence of morphological traits, but whether morphological similarities also require similar changes in Hox gene function is disputed. In arthropods, body subdivision into a region with locomotory appendages ("thorax") and a region with reduced appendages ("abdomen") has evolved convergently in several groups, e.g., spiders and insects. In insects, legs develop in the expression domain of the Hox gene Antennapedia (Antp), whereas the Hox genes Ultrabithorax (Ubx) and abdominal-A mediate leg repression in the abdomen. Here, we show that, unlike Antp in insects, the Antp gene in the spider Achaearanea tepidariorum represses legs in the first segment of the abdomen (opisthosoma), and that Antp and Ubx are redundant in the following segment. The down-regulation of Antp in A. tepidariorum leads to a striking 10-legged phenotype. We present evidence from ectopic expression of the spider Antp gene in Drosophila embryos and imaginal tissue that this unique function of Antp is not due to changes in the Antp protein, but likely due to divergent evolution of cofactors, Hox collaborators or target genes in spiders and flies. Our results illustrate an interesting example of convergent evolution of abdominal leg repression in arthropods by altering the role of distinct Hox genes at different levels of their action.

Crystal Structure of Novel Metallocarboxypeptidase Inhibitor from Marine Mollusk Nerita versicolor in Complex with Human Carboxypeptidase A4

NvCI is a novel exogenous proteinaceous inhibitor of metallocarboxypeptidases from the marine snail Nerita versicolor. The complex between human carboxypeptidase A4 and NvCI has been crystallized and determined at 1.7 Å resolution. The NvCI structure defines a distinctive protein fold basically composed of a two-stranded antiparallel β-sheet connected by three loops and the inhibitory C-terminal tail and stabilized by three disulfide bridges. NvCI is a tight-binding inhibitor that interacts with the active site of the enzyme in a substrate-like manner. NvCI displays an extended and novel interface with human carboxypeptidase A4, responsible for inhibitory constants in the picomolar range for some members of the M14A subfamily of carboxypeptidases. This makes NvCI the strongest inhibitor reported so far for this family. The structural homology displayed by the C-terminal tails of different carboxypeptidase inhibitors represents a relevant example of convergent evolution.

Transmission of Cyanobacterial Symbionts During Embryogenesis in the Coral Reef Ascidians Trididemnum nubilum and T. clinides (Didemnidae, Ascidiacea, Chordata)

Vertical transmission of cyanobacterial symbionts occurs in didemnid ascidians harboring Prochloron as an obligate symbiont; the photosymbionts are transferred from the parental ascidian colony to the offspring in various ways depending on host species. Although several didemnids harbor non-Prochloron cyanobacteria in their tunics, few studies have reported the processes of vertical transmission in these didemnids. Here we describe the histological processes of the transmission of cyanobacteria in two didemnids, Trididemnum nubilum harboring Synechocystis and T. clinides harboring three cyanobacterial species. In both species, the photosymbionts in the tunic of the parent colony were apparently captured by the tunic cells of the host and transferred to the embryos brooded in the tunic. The symbiont cells were then incorporated into the inner tunic of the embryo. This mode of transmission is essentially the same as that of T. miniatum harboring Prochloron in the tunic, although there are some differences among species in the timing of the release of the symbionts from the tunic cells. We suggest that the similar modes of vertical transmission are an example of convergent evolution caused by constraints in the distribution patterns of symbiont cells in the host colony.

On the Limits of Diversity

On the Limits of Diversity

Human NKG2D-ligands: cell biology strategies to ensure immune recognition

Immune recognition mediated by the activating receptor NKG2D plays an important role for the elimination of stressed cells, including tumors and virus-infected cells. On the other hand, the ligands for NKG2D can also be shed into the sera of cancer patients where they weaken the immune response by downmodulating the receptor on effector cells, mainly NK and T cells. Although both families of NKG2D-ligands, major histocompatibility complex class I-related chain (MIC) A/B and UL16 binding proteins (ULBPs), are related to MHC molecules and their expression is increased after stress, many differences are observed in terms of their biochemical properties and cell trafficking. In this paper, we summarize the variety of NKG2D-ligands and propose that selection pressure has driven evolution of diversity in their trafficking and shedding, but not receptor binding affinity. However, it is also possible to identify functional properties common to individual ULBP molecules and MICA/B alleles, but not generally conserved within the MIC or ULBP families. These characteristics likely represent examples of convergent evolution for efficient immune recognition, but are also attractive targets for pathogen immune evasion strategies. Categorization of NKG2D-ligands according to their biological features, rather than their genetic family, may help to achieve a better understanding of NKG2D-ligand association with disease.