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The nucleotide sequence of the unusual plasmid-mediated OXA2 beta-lactamase is presented, and compared with other beta-lactamases. The OXA2 enzyme has similar features at the presumed active site, but no other significant regions of homology with other penicillin-reactive enzymes. The active site homology may therefore represent convergent evolution of otherwise dissimilar genes.
Recent evidence indicates that in as diverse organisms as unicellular eukaryotes, higher plants and prokaryotes, anaerobic glycolysis relies on a pyrophosphate-dependent phosphofructokinase instead of the classical ATP-dependent enzyme. This difference in phosphoryl donor specificity does not necessarily reflect a primitive metabolism, as thought earlier, but could rather be the result of convergent evolution, fostered by the energetic advantage conferred to the cell when glycolysis is the sole source of ATP.
Changes in host behaviour following infection with parasites are frequently reported in the literature, and are often hypothesized to be adaptive for either host or parasite. However, investigators of such phenomena often use the "adaptation" label for host behavioural changes based on their intuition and not on rigorous criteria. Alterations in host behaviour following infection can only be considered adaptive if they satisfy certain conditions: (1) they must be complex; (2) they must show signs of a purposive design; (3) they are more likely to be adaptations if they have arisen independently in several lineages of hosts or parasites; and (4) they must be shown to increase the fitness of either the host or the parasite. A survey of published examples of host behavioural changes indicates that while some are spectacularly complex and are extremely well-fitted to their presumed function, most are simple increases or decreases in an activity performed prior to infection. There are some suggestions of convergent evolution in behavioural change in distantly related host or parasite groups but more evidence is needed. Finally, most known behavioural changes have not been demonstrated to lead to fitness gains in either hosts or parasites. Few known examples satisfy more than two of the above criteria, and, in general, the adaptive function of changes in host behaviour following infection is in need of more solid proof.
Intraproteic electrostatic potentials along the catalytic triad in serine proteinases are compared for eight enzymes for which three-dimensional co-ordinates are available. We used our bond-increment method to calculate the potential and we considered all protein atoms, including hydrogens. It was found that counter ions which may be located in the vicinity of charged surface side chains play a decisive role in determining enzymatic action. If ionizable side chains are neutralized the electrostatic potential curve across the catalytic triad is of minimum character in all investigated enzymes. It stabilizes the (-+-) charge distribution which models the Ser- -His+ -Asp- transition state structure which is formed during the catalytic process. Based on the close similarity of the electrostatic pattern in various enzymes we call attention to the possibility that convergent evolution produced not only the effective catalytic triad but also a minimum-type potential which accelerates the enzymatic reaction.
Both the A regions of diphtheria and cholera toxins contain the site of ADP-ribosyl transferase activity which is responsible for the modification of specific target proteins in mammalian cell types. The secondary structure prediction for these A regions has been made on the basis of their recently reported primary structures. In the center of both toxin A chains, the beta-structure and alpha-helix regions alternate in a manner similar to that reported for some NAD binding proteins. Other regions of alpha-helix in the A chains may be involved in the interactions with the toxin B chains. The lack of primary structure homology between these toxins indicates that the secondary structure homology is the result of convergent evolution of a NAD binding domain in each protein.
The mechanism of DNA packaging by dsDNA viruses is not well understood in any system. In bacteriophage P22 only five genes are required for successful condensation of DNA within the capsid. The products of three of these genes, the portal, scaffolding, and coat proteins, are structural components of the precursor particle, and two, the products of genes 2 and 3, are not. The scaffolding protein is lost from the structure during packaging, and only the portal and coat proteins are present in the mature virus particle. These five genes map in a contiguous cluster at the left end of the P22 genetic map. Three additional genes, 4, 10, and 26, are required for stabilizing of the condensed DNA within the capsid. In this report we present the nucleotide sequence of 7461 bp of P22 DNA that contains the five genes required for DNA condensation, as well as a nonessential open reading frame (ORF109), gene 4, and a portion of gene 10. N-terminal amino acid sequencing of the encoded proteins accurately located the translation starts of six genes in the sequence. Despite the fact that most of these proteins have striking analogs in the other dsDNA bacteriophage groups, which perform highly analogous functions, no amino acid sequence similarity between these analogous proteins has been found, indicating either that they diverged a very long time ago or that they are the products of spectacular convergent evolution.
The extent and pattern of HLA class II sequence polymorphism raise a variety of evolutionary questions, notably those concerning the genetic mechanisms for generating diversity, the rate of change and the nature of the selection pressure maintaining this variation. Phylogenetic analysis of primate MHC class II sequences suggests that the allelic lineages are ancient, having diverged long before separation of the hominoid species. For the beta-chain loci, however, considerable allelic diversification within these lineages has occurred after speciation. The striking patchwork pattern of polymorphism with different alleles containing common sequence motifs can be accounted for by common ancestry, by gene conversion or by convergent evolution, depending on the location of the shared epitope.
Although cholesterol is the predominant sterol in parasite tissue, many parasites are unable to synthesize cholesterol or longchain fatty acids, de novo, and must therefore obtain these components from the host. Of particular interest are the plasma lipoproteins, a rich and abundant source of cholesterol, and other lipids that could be used by parasites inhabiting the vascular system of their host or with access to plasma proteins at extravascular sites. It is not inconceivable that parasites may have evolved a variety of receptors for lipoproteins by convergent evolution. Here, Mark Rogers discusses evidence for the presence of lipoprotein receptors in protozoan and metazoan parasites of mammals.
A whole mount immunofluorescence method was used for the localization of immunoreactivity (IR) to four regulatory peptides and the bioamine serotonin in the nervous system of Stenostomum leucops (Turbellaria, Platyhelminthes). The flatworm S. leucops belongs to the taxon Catenulida which, according to the new phylogenetic system by Ax [2], forms a key group between the coelenterates and more advanced flatworm species. Positive IR was obtained using antisera against FMRF-amide, beta-endorphin, growth hormone releasing factor (GRF), substance P, and serotonin. The distribution patterns of these neuropeptide-like immunoreactivities differ significantly from each other. Antisera against Leu-enkephalin, bovine pancreatic polypeptide (BPP), bombesin, cholecystokinin (CCK-8), neurotensin, somatostatin, growth hormone (GH), secretin, and neurophysin II gave negative results. This primitive flatworm shows similarities with hydra in the lack of IR to anti-somatostatin, anti-Leu-enkephalin, and anti-BPP. These antisera give positive IR in more advanced flatworm species, indicating a later convergent evolution of vertebrate-like peptides within the phylum Platyhelminthes.
David P. Mindell assumes that incorporation of the holobionts (evolutionarily stable symbiotic complexes) and hybrids into phylogenetic trees necessarily distorts the hierarchical structure of cladistic classification, and must lead to reformulation of some basic cladistic concepts (BioSystems, 27, 53-62, 1992). He does not regard the Eukarya and Eubacteria as monophyletic taxa, the former being 'polyphyletic', the latter 'paraphyletic'. We attempt to show that the existence of holobionts/hybrids is not a cladistic problem. Cladistics is a systematic methodology, not a system of evolutionary hypotheses; cladograms are statements about distribution of shared characters (synapomorphies) and, consequently, the cladograms are always branching and hierarchically structured. A taxon is monophyletic if it has a single root in the cladogram, not a single ancestor 'in reality'. Cladistic methodology does not provide a clue for distinguishing whether a conflicting distribution of the potential synapomorphies is due to reticulation (e.g., symbiogenesis) or convergent evolution. Consequently, both Eubacteria and Eukarya either are or are not monophyletic taxa if they are or are not determined to be so during cladistic analysis.
The thermal stabilities of hybrid duplexes between the DNAs from three salmonid fish species were monitored as measures of DNA homology. The chum salmon, Oncorhynchus keta, and coho salmon, Oncorhynchus kisutch, had more DNA homology with each other than either had with the rainbow trout, Salmo gairdnerii. Morphological, ecological and protein similarities between the coho salmon and the rainbow trout may be due to parallel or convergent evolution.
A cDNA clone covering the entire coding region for a glutelin subunit precursor has been identified from a library of endosperm-developing rice cDNA clones using a mixed oligodeoxynucleotide probe, and then by immunoprecipitation of hybrid-selected translation product with an antiserum against the acidic polypeptides of the glutelin. Analysis of the cDNA insert revealed that rice glutelin is synthesized as precursor polypeptides which undergo post-translational processing to form the nonrandom polypeptide pairs, like glycinin precursors of soybean. By comparing the predicted protein sequence of this precursor from monocots with that of glycinin A1aB1b precursor from dicots, it was found that the overall 32% of the amino acid positions are identical in both proteins. Because regions which show identities are dispersed throughout both molecules, the similarity is not due to convergent evolution, but to divergence evolution from a common ancestral gene.
A cochlear model is presented suggesting that the organ of Corti (OC) and the basilar membrane (BM) are both tuned resonant systems, but have different functions. The OC provides frequency filtering and amplification by means of tuned outer hair cells. The BM provides resonant absorption of excessive vibrational energy as an overload protection for vulnerable elements in the OC. Evidence supporting this model is demonstrated in dolphins, bats, and desert rodents. Specialized auditory capabilities correlate with cochlear deviations, some of them dramatically changing BM compliance. In characteristic regions along the cochlea there are BM thickenings and, on both sides of the OC, hypertrophied supporting cells. Structures of striking similarity have evolved independently across orders or families, revealing multiple events of convergent evolution. In all cases, the locations of deviating structures rule out a BM function in auditory frequency selectivity but support one in resonant absorption. Cochlear microphonics and BM responses demonstrate strongest high-level absorption in the frequency bands most vital for the tested species. The assumed cause is increased internal damping in the enlarged structures during BM motion. Species with intermediate specializations supply further evidence that resonant absorption is universally the genuine function of BM mechanics in mammals, providing complementary high-level protection of low-level sensitivity.
Ribotyping, exotoxin A genotyping (EAGP), and restriction fragment length polymorphism (RFLP) analysis of total DNA with SalI (SalI RFLP) were compared for intraspecies discrimination of 93 Pseudomonas aeruginosa isolates. Type-ability of all methods was 100% and the results of typing with each method remained unchanged during laboratory manipulation. Clonal groups defined with each molecular method were largely coincident and, in those cases where inconsistencies were detected, isolates were analyzed by transverse alternating field gel electrophoresis (TAFE) and arbitrarily primed polymerase chain reaction (AP-PCR). SalI RFLP analysis was highly discriminative so as to distinguish unrelated isolates of close lineage. However, it was not a good method to identify isolates of unrelated lineage because SalI RFLP appeared to be subjected to convergent evolution. The index of discrimination suggested by Hunter and Gaston was determined to assess the discriminatory power of the molecular methods utilized either alone or in several combinations. Combined use of ribotyping and SalI RFLP analysis reached the highest index of discrimination (0.982) and proved to be a very valuable tool for epidemiological differentiation of P. aeruginosa isolates.
The nicotinamide adenine dinucleotide (NAD)-binding domains of dehydrogenases, containing a conserved double beta-alpha-beta-alpha-beta motif, are common structural feature of many enzymes that bind NAD, nicotinamide adenine dinucleotide phosphate (NADP) and related cofactors. Features of this folding pattern that create a natural binding site for such molecules have been described. The domain continues to appear in many structures, in the form of a common core with different peripheral additions or variations. Other structures that bind NAD and related molecules use entirely different topologies, although, in many, a phosphate group appears at the N terminus of an alpha helix. Ferredoxin reductase seems to show convergent evolution, containing a single beta-alpha-beta motif that is similar both in its structure and in its interactions with the ligand to a region in dehydrogenases.
The catalytic subunit, gamma, of phosphorylase kinase contains two calmodulin-binding sequences that define a domain in gamma that is homologous to the troponin-C-binding domain in troponin I. The homology is based on both sequence and functional similarities. To account for this homology, it has been proposed that the calmodulin-binding sequences in gamma and the troponin-C-binding domain in troponin I have evolved from a common ancestor. We investigated this possibility by comparing the exon structure of the gamma gene with that of troponin-I gene over their homologous domains. In the quail troponin-I gene, it is known that the entire troponin-C-binding domain is encoded by a single exon. However, two exons are found to encode the calmodulin-binding domain in the gamma gene from mouse. This result indicates that convergent evolution may be responsible for the sequence and functional similarities between the homologous domains in troponin I and gamma.
Molecular systematic analysis of the annexin gene superfamily characterized the evolutionary origin, frequency and range of structural variation in calcium interaction domains that are considered intrinsic for membrane targeting and ion channel function. Approximately 36% of annexin repeat domains in an estimated 100 distinct subfamilies contained amino acid changes consistent with the functional loss of type two calcium-binding sites. At least 11% of annexin domains contained a novel K/H/RGD motif conserved in particular subfamilies and manifest in all phyla, apparently via convergent evolution. The first yeast annexin from Yarrowia lipolytica was classified in the ANXC1 subfamily with fungal and mycetozoan representatives. This clade had intact calcium-binding sites but disruption of the normally well-conserved, mid-repeat 4 region implicated in calcium channel regulation. Conversely, a tandem pair of novel annexins from the amphioxus Branchiostoma floridae resembled annexin A13 in gene structure and conserved the charged amino acids associated with the internal hydrophilic pore, but were devoid of external type 2 calcium-binding sites and incorporated K/RGD motifs instead, like annexin A9. The selective erosion of calcium-binding sites in annexin domains and the occurrence of alternate ligands in the same exposed, interhelical loops are pervasive features of the superfamily. This suggests greater complexity than previously appreciated in the mechanisms controlling annexin membrane interaction and calcium channel operation.
Nitric oxide synthase (NOS) is amongst a family of evolutionarily conserved enzymes, involved in a multi-turnover process that results in NO as a product. The significant role of NO in various pathological and physiological processes has created an interest in this enzyme from several perspectives. This study describes for the first time, cloning and expression of a NOS-like protein, baNOS, from Bacillus anthracis, a pathogenic bacterium responsible for causing anthrax. baNOS was expressed in Escherichia coli as a soluble and catalytically active enzyme. Homology models generated for baNOS indicated that the key structural features that are involved in the substrate and active site interaction have been highly conserved. Further, the behavior of baNOS in terms of heme-substrate interactions and heme-transitions was studied in detail. The optical perturbation spectra of the heme domain demonstrated that the ligands perturb the heme site in a ligand specific manner. baNOS forms a five-coordinate, high-spin complex with l-arginine analogs and a six-coordinate low-spin complex with inhibitor imidazole. Studies indicated that the binding of l-arginine, N(omega)-hydroxy-l-arginine, and imidazole produces various spectroscopic species that closely correspond to the equivalent complexes of mammalian NOS. The values of spectral binding constants further corroborated these results. The overall conservation of the key structural features and the correlation of heme-substrate interactions in baNOS and mammalian NOS, thus, point towards an interesting phenomenon of convergent evolution. Importantly, the NO generated by NOS of mammalian macrophages plays a potent role in antimicrobicidal activity. Because of the existence of high structural and behavioral similarity between mammalian NOS and baNOS, we propose that NO produced by B. anthracis may also have a pivotal pathophysiological role in anthrax infection. Therefore, this first report of characterization of a NOS-like protein from a pathogenic bacterium opens up avenues for further studies in understanding the importance of this protein in pathogenicity.