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PubMed1991

Convergent evolution of similar function in two structurally divergent enzymes.

An example of two related enzymes that catalyse similar reactions but possess different active sites is provided by comparing the structure of Escherichia coli thioredoxin reductase with glutathione reductase. Both are dimeric enzymes that catalyse the reduction of disulphides by pyridine nucleotides through an enzyme disulphide and a flavin. Human glutathione reductase contains four structural domains within each molecule: the flavin-adenine dinucleotide (FAD)- and nicotinamide-adenine dinucleotide phosphate (NADPH)-binding domains, the 'central' domain and the C-terminal domain that provides the dimer interface and part of the active site. Although both enzymes share the same catalytic mechanism and similar tertiary structures, their active sites do not resemble each other. We have determined the crystal structure of E. coli thioredoxin reductase at 2 A resolution, and show that thioredoxin reductase lacks the domain that provides the dimer interface in glutathione reductase, and forms a completely different dimeric structure. The catalytically active disulphides are located in different domains on opposite sides of the flavin ring system. This suggests that these enzymes diverged from an ancestral nucleotide-binding protein and acquired their disulphide reductase activities independently.

Amino Acid Sequence↗
PubMed2005

Structure of the p115RhoGEF rgRGS domain-Galpha13/i1 chimera complex suggests convergent evolution of a GTPase activator.

p115RhoGEF, a guanine nucleotide exchange factor (GEF) for Rho GTPase, is also a GTPase-activating protein (GAP) for G12 and G13 heterotrimeric Galpha subunits. The GAP function of p115RhoGEF resides within the N-terminal region of p115RhoGEF (the rgRGS domain), which includes a module that is structurally similar to RGS (regulators of G-protein signaling) domains. We present here the crystal structure of the rgRGS domain of p115RhoGEF in complex with a chimera of Galpha13 and Galphai1. Two distinct surfaces of rgRGS interact with Galpha. The N-terminal betaN-alphaN hairpin of rgRGS, rather than its RGS module, forms intimate contacts with the catalytic site of Galpha. The interface between the RGS module of rgRGS and Galpha is similar to that of a Galpha-effector complex, suggesting a role for the rgRGS domain in the stimulation of the GEF activity of p115RhoGEF by Galpha13.

Amino Acid Motifs↗
PubMed2002

Microbat paraphyly and the convergent evolution of a key innovation in Old World rhinolophoid microbats.

Molecular phylogenies challenge the view that bats belong to the superordinal group Archonta, which also includes primates, tree shrews, and flying lemurs. Some molecular studies also challenge microbat monophyly and instead support an alliance between megabats and representative rhinolophoid microbats from the families Rhinolophidae (horseshoe bats, Old World leaf-nosed bats) and Megadermatidae (false vampire bats). Another molecular study ostensibly contradicts these results and supports traditional microbat monophyly, inclusive of representative rhinolophoids from the family Nycteridae (slit-faced bats). Resolution of the microbat paraphyly/monophyly issue is essential for reconstructing the temporal sequence and deployment of morphological character state changes associated with flight and echolocation in bats. If microbats are paraphyletic, then laryngeal echolocation either evolved more than once in different microbats or was lost in megabats after evolving in the ancestor of all living bats. To examine these issues, we used a 7.1-kb nuclear data set for nine outgroups and twenty bats, including representatives of all rhinolophoid families. Phylogenetic analyses and statistical tests rejected both Archonta and microbat monophyly. Instead, bats are in the superorder Laurasiatheria and microbats are paraphyletic. Further, the superfamily Rhinolophoidea is polyphyletic. The rhinolophoid families Rhinolophidae and Megadermatidae belong to the suborder Yinpterochiroptera along with rhinopomatids and megabats. The rhinolophoid family Nycteridae belongs to the suborder Yangochiroptera along with vespertilionoids, noctilionoids, and emballonuroids. These results resolve the apparent conflict between previous molecular studies that sampled different rhinolophoid families. An important implication of rhinolophoid polyphyly is independent evolution of key anatomical innovations associated with the nasal-emission of echolocation pulses.

Amino Acid Sequence↗
PubMed2004

Convergent evolution of behavior in an adaptive radiation of Hawaiian web-building spiders.

Species in ecologically similar habitats often display patterns of divergence that are strikingly comparable, suggesting that natural selection can lead to predictable evolutionary change in communities. However, the relative importance of selection as an agent mediating in situ diversification, versus dispersal between habitats, cannot be addressed without knowledge of phylogenetic history. We used an adaptive radiation of spiders within the Hawaiian Islands to test the prediction that species of spiders on different islands would independently evolve webs with similar architectures. Tetragnatha spiders are the only nocturnal orb-weaving spiders endemic to the Hawaiian archipelago, and multiple species of orb-weaving Tetragnatha co-occur within mesic and wet forest habitats on each of the main islands. Therefore, comparison of web architectures spun by spiders on different islands allowed study of replicated evolutionary events of past behavioral diversification. We found that species within each island construct webs with architectures that differ from one another. However, pairs of species on different islands, "ethotypes," share remarkable similarities in web architectures. Phylogenetic analysis demonstrated that the species comprising these ethotypes evolved independent of one another. Our study illustrates the high degree of predictability that can be exhibited by the evolutionary diversification of complex behaviors. However, not all web architectures were shared between islands, demonstrating that unique effects also have played an important role in the historical diversification of behavior.

Adaptation, Physiological↗
PubMed1990

Convergent evolution of the red- and green-like visual pigment genes in fish, Astyanax fasciatus, and human.

We have isolated and sequenced genes from the blind cave fish, Astyanax fasciatus, that are homologous to the human red and green visual pigment genes. The data strongly suggest that, like human, these fish have one red-like visual pigment gene and multiple green-like visual pigment genes. By comparing the DNA sequences of the human and fish visual pigment genes and knowing their phylogenetic relationship, one can infer the direction of amino acid substitutions in the red and green visual pigments. The results indicate that the red pigments in human and fish evolved from the green pigment independently by identical amino acid substitutions in only a few key positions.

Amino Acid Sequence↗
PubMed1999

Convergent evolution of Trichomonas vaginalis lactate dehydrogenase from malate dehydrogenase.

Lactate dehydrogenase (LDH) is present in the amitochondriate parasitic protist Trichomonas vaginalis and some but not all other trichomonad species. The derived amino acid sequence of T. vaginalis LDH (TvLDH) was found to be more closely related to the cytosolic malate dehydrogenase (MDH) of the same species than to any other LDH. A key difference between the two T. vaginalis sequences was that Arg91 of MDH, known to be important in coordinating the C-4 carboxyl of oxalacetate/malate, was replaced by Leu91 in LDH. The change Leu91Arg by site-directed mutagenesis converted TvLDH into an MDH. The reverse single amino acid change Arg91Leu in TvMDH, however, gave a product with no measurable LDH activity. Phylogenetic reconstructions indicate that TvLDH arose from an MDH relatively recently.

Amino Acid Sequence↗
PubMed1996

Histological convergent evolution of the accessory submandibular glands in four species of frog-eating bats.

The accessory submandibular glands in four species of bats were examined by electron microscopy. These four species represent two independently evolved lineages. The fringe-lipped bat, Trachops cirrhosis, is a Neotropical phyllostomid species, whereas the false vampire bats of southeast Asia, Megaderma lyra and M. spasma, and the heart-nosed bat, Cardioderma cor, of East Africa are megadermatid species. These glands show extreme deviation from typical salivary gland histology: their secretory endpieces are in the form of follicles and their ducts lack the cytological details that permit identification of diverse duct segments. Despite their unusual histology, the secretory endpieces in M. lyra, M. spasma, and C. cor consist of secretory cells that conform to typical secretory cell morphology. In contrast, secretion by follicular cells in T. cirrhosis involves unusual cytoplasmic bodies, and their mitochondria frequently have intracristal crystalloids. Ducts in all four species consist of simple cuboidal to columnar epithelium without basal striations. Follicles and ducts in all four bats are surrounded by numerous myoepithelial cells and are heavily innervated by hypolemmal nerve terminals. Despite their widely separated geographical ranges, all four bat species consume frogs and other vertebrates. Frogs and toads often possess toxic cutaneous glands that provide a chemical defense against predation. It is postulated that the unusual accessory glands in the four frog-eating species secrete toxin-neutralizing salivary factors. The follicular form of the endpieces permits storage of preformed saliva and their coterie of myoepithelial cells and hypolemmal nerve terminals facilitates the sudden and rapid expulsion of saliva into the oral cavity during the consumption of noxious amphibians.

Animals↗
PubMed2005

Divergent and convergent evolution after a common-source outbreak of hepatitis C virus.

The genomic sequences of viruses that are highly mutable and cause chronic infection tend to diverge over time. We report that these changes represent both immune-driven selection and, in the absence of immune pressure, reversion toward an ancestral consensus. Sequence changes in hepatitis C virus (HCV) structural and nonstructural genes were studied in a cohort of women accidentally infected with HCV in a rare common-source outbreak. We compared sequences present in serum obtained 18-22 yr after infection to sequences present in the shared inoculum and found that HCV evolved along a distinct path in each woman. Amino acid substitutions in known epitopes were directed away from consensus in persons having the HLA allele associated with that epitope (immune selection), and toward consensus in those lacking the allele (reversion). These data suggest that vaccines for genetically diverse viruses may be more effective if they represent consensus sequence, rather than a human isolate.

Alleles↗
PubMed1994

Convergent evolution of TEM-26, a beta-lactamase with extended-spectrum activity.

TEM-26, an extended-spectrum beta-lactamase has been characterized in clinical isolates of Klebsiella pneumoniae and Escherichia coli derived from patients on the Paediatric Oncology Unit of St James's University Hospital, Leeds. The nucleotide sequence of this beta-lactamase gene (blaTEM26b) was determined, and compared with the nucleotide sequences of other TEM-type beta-lactamases. The blaTEM26b gene was found to differ from blaTEM12b by a single nucleotide. This difference causes the substitution of glutamic acid in blaTEM12b for lysine in blaTEM26b at position 102 in the predicted amino acid sequence. The blaTEM12b gene was first described in an isolate of Klebsiella oxytoca from a patient nursed on the same unit that yielded the strains that carry blaTEM26b. However, the blaTEM26b gene differs at no less than six nucleotides from the nucleotide sequence encoding the TEM-26 beta-lactamase that was first described in isolates from cancer patients nursed in the Children's Hospital, Stanford, California, USA. This indicates that the genes encoding TEM-26 have evolved from different progenitors.

Amino Acid Sequence↗
PubMed1997

Phylogenetic analyses of DNA and allozyme data suggest that Gonioctena leaf beetles (Coleoptera; Chrysomelidae) experienced convergent evolution in their history of host-plant family shifts.

A phylogenetic analysis of the genus Gonioctena (Coleoptera, Chrysomelidae) based on allozyme data (17 loci) and mitochondrial DNA sequence data (three gene fragments, 1,391 sites) was performed to study the evolutionary history of host-plant shifts among these leaf beetles. This chrysomelid genus is characteristically associated with a high number of different plant families. The diverse molecular data gathered in this study are to a large extent congruent, and the analyses provide a well-supported phylogenetic hypothesis to address questions about the evolution of host-plant shifts in the genus Gonioctena. The most-parsimonious reconstruction of the ancestral host-plant associations, based on the estimated phylogeny, suggests that the Fabaceae was the ancestral host-plant family of the genus. Although most of the host-plant shifts (between different host species) in Gonioctena have occurred within the same plant family or within the same plant genus, at least eight shifts have occurred between hosts belonging to distantly related and chemically dissimilar plant families. In these cases, host shifts may have been simply directed toward plant species available in the environment. Yet, given that two Gonioctena lineages have independently colonized the same three new plant families (Salicaceae, Betulaceae, Rosaceae), including four of the same new genera (Salix, Alnus, Prunus, Sorbus), some constraints are likely to have limited the different possibilities of interfamilial host-plant shifts.

Animals↗
PubMed1996

Neuronal nitric oxide synthase, a modular enzyme formed by convergent evolution: structure studies of a cysteine thiolate-liganded heme protein that hydroxylates L-arginine to produce NO. as a cellular signal.

The nitric oxide synthases (NOS-I, neuronal, NOS-II, inducible, and NOS-III, endothelial) are the most recent additions to the large number of heme proteins that contain cysteine thiolate-liganded protoporphyrin IX heme prosthetic groups. This group of oxygenating enzymes also includes one of the largest gene families, that of the cytochromes P450, which have been demonstrated to be involved in the hydroxylation of a variety of substrates, including endogenous compounds (steroids, fatty acids, and prostaglandins) and exogenous compounds (therapeutic drugs, environmental toxicants, and carcinogens). The substrates for cytochromes P450 are universally hydrophobic while the physiological substrate for the nitric oxide synthases is the amino acid L-arginine, a hydrophilic compound. This review will discuss the approaches being used to study the structure and mechanism of neuronal nitric oxide synthase in the context of its known prosthetic groups and regulation by Ca(2+)-calmodulin and/or tetrahydrobiopterin (BH4).

Animals↗
PubMed2026

SARS-CoV-2 intra-host variation shows evidence of transmission and convergent evolution in a university surveillance cohort.

Monitoring and understanding the transmission and evolution of SARS-CoV-2 remains a significant public health priority. Within-host genetic variation provides insight into viral evolution during infection and may help infer transmission events. In this study, we analysed intra-host variation in SARS-CoV-2 genome sequences from Boston University's testing mandate. Focusing on intra-host single nucleotide variants (iSNVs), we inferred transmission events and assessed the selective forces shaping within-host viral evolution. To minimize false-positive iSNVs resulting from systematic biases, we implemented stringent data filtering and developed a heuristic to exclude contamination-derived artefacts arising from batched sequencing. We find that intra-host variation is limited and infrequently transmitted during acute infections, suggesting that shared iSNVs serve as highly specific but insensitive markers of transmission. We also observed incomplete purifying selection shaping within-host diversity, with the loci most affected changing among variants of concern. Finally, we identified a highly recurrent iSNV (G11083T) which may represent a site of positive selection. Our results highlight that within-host variation provides insight into within-host pathogen evolution, in spite of its limited use in genomic epidemiology.

SARS-CoV-2↗