TIMA Part 2. TIMA-based instructive evolution of macromolecules and organs and structures

In extending a previous paper (TIMA Part 1, Wassermann, 1982) “template induced molecular assembly” (TIMA) is being further explored. It is suggested that TIMA could first have evolved proteins without coevolution of mRNA-like systems, in the absence of tRNAs. Some of these early proteins could, by self-assembly, have built up ribosomes. Ribosomes jointly with amino acids could have served as assembly templates for the TIMA-based evolution of tRNAs. Once tRNAs had evolved, TIMA could have participated, via a modified Mekler (1967) mechanism, in the evolution of new proteins and the coevolution of corresponding mRNA-like strands. TIMA also requires gene duplications and/or random mutations of DNA, to produce partial matching by duplicated and/or randomized DNA sequences of TIMA-generated cDNA which is complementary to the mRNA-like strands. The cDNA could then become incorporated by crossover into the position of the partially matching DNA sequences of, say, duplicate genes in genomes of germ-line cells. Since one requires only partial matching between duplicate (and/or randomly generated) DNA and non-randomly, TIMA-generated cDNA, TIMA theory avoids the need to assume (as in the Baldwin effect) that complete genes were randomly evolved. While rejecting crude Lamarckism, TIMA equally avoids the assumption that genes evolved only by combined random events, gene duplications, and adaptive selection. The resulting theory explains typical pseudo-exogenous adaptations via TIMA. Darwinian selection—now in the guise of “molecular selection” (and favourable environmental adaptive selection where present)—combined with TIMA could account for Waddington's “genetic assimilation”, thereby conceding Lamarck's notion that the environment can help to model heredity (while rejecting crude Lamarckism).     

Novartis Medal Lecture. Antibodies: a paradigm for the evolution of molecular recognition

Novel proteins have been elaborated over evolutionary time by an iterative alternation of mutation and selection. In a similar way, the humoral immune system also uses an iterative alternation of mutation and selection to generate novel antibodies that display a high affinity for their cognate antigen -- but this is achieved in a matter of a days. Gene rearrangement is used to produce a primary repertoire of antibodies and, on entering the body, antigen triggers the clonal expansion of those B lymphocytes that express a cognate antibody, albeit one of low affinity. Rapid and specific affinity maturation is then achieved by subjecting the immunoglobulin genes in the rapidly expanding B cells to a period of intense mutation. The intensity of this mutational assault is tolerated because it is targeted specifically to the immunoglobulin genes, causing relatively little damage to other loci. Antigen-mediated selection then allows the preferential expansion of those mutants expressing antibodies displaying improved binding characteristics. Here, studies are described that have been performed to glean insight into the mechanisms of the hypermutation and selection processes. Experiments are also described in which an attempt has been made to recapitulate aspects of physiological antibody generation in vitro, allowing the development of novel approaches to the generation of proteins with high-affinity binding sites.     

Ubiquitin genes as a paradigm of concerted evolution of tandem repeats

Summary Ubiquitin is remarkable for its ubiquitous distribution and its extreme protein sequence conservation. Ubiquitin genes comprise direct repeats of the ubiquitin coding unit with no spacers. The nucleotide sequences of several ubiquitin repeats from each of humans, chicken,Xenopus, Drosophila, barley, and yeast have recently been determined. By analysis of these data we show that ubiquitin is evolving more slowly than any other known protein, and that this (together with its gene organization) contributes to an ideal situation for the occurrence of concerted evolution of tandem repeats. By contrast, there is little evidence of between-cluster concerted evolution. We deduce that in ubiquitin genes, concerted evolution involves both unequal crossover and gene conversion, and that the average time since two repeated units within the polyubiquitin locus most recently shared a common ancestor is approximately 38 million years (Myr) in mammals, but perhaps only 11 Myr inDrosophila. The extreme conservatism of ubiquitin evolution also allows the inference that certain synonymous serine codons differing at the first two positions were probably mutated at single steps.     

Vascular smooth muscle cell proliferation as a therapeutic target. Part 1: molecular targets and pathways

Cardiovascular diseases are a major cause of human death worldwide. Excessive proliferation of vascular smooth muscle cells contributes to the etiology of such diseases, including atherosclerosis, restenosis, and pulmonary hypertension. The control of vascular cell proliferation is complex and encompasses interactions of many regulatory molecules and signaling pathways. Herein, we recapitulated the importance of signaling cascades relevant for the regulation of vascular cell proliferation. Detailed understanding of the mechanism underlying this process is essential for the identification of new lead compounds (e.g., natural products) for vascular therapies.     

Dynamic diversity and small-molecule evolution: a new paradigm for ligand identification.

A longstanding goal of organic, medicinal and bioorganic chemists has been the discovery of efficient methods for designing or identifying biologically active compounds. Recently, several groups have reported using the directed evolution of combinatorial libraries as a new method of identifying compounds capable of binding tightly to a target molecule. Although significant development remains to be done, the initial results suggest that dynamic diversity and associated selection methods will prove to be valuable additions to the drug-discovery process.     

The mosasaur tooth attachment apparatus as paradigm for the evolution of the gnathostome periodontium

SUMMARY Vertebrate teeth are attached to jaws by a variety of mechanisms, including acrodont, pleurodont, and thecodont modes of attachment. Recent studies have suggested that various modes of attachment exist within each subcategory. Especially squamates feature a broad diversity of modes of attachment. Here we have investigated tooth attachment tissues in the late cretaceous mosasaur Clidastes and compared mosasaur tooth attachment with modes of attachment found in other extant reptiles. Using histologic analysis of ultrathin ground sections, four distinct mineralized tissues that anchor mosasaur teeth to the jaw were identified: (i) an acellular cementum layer at the interface between root and cellular cementum, (ii) a massive cone consisting of trabecular cellular cementum, (iii) the mineralized periodontal ligament containing mineralized Sharpey's fibers, and (iv) the interdental ridges connecting adjacent teeth. The complex, multilayered attachment apparatus in mosasaurs was compared with attachment tissues in extant reptiles, including Iguana and Caiman . Based on our comparative analysis we postulate the presence of a quadruple-layer tissue architecture underlying reptilian tooth attachment, comprised of acellular cementum, cellular cementum, mineralized periodontal ligament, and interdental ridge (alveolar bone). We propose that the mineralization status of the periodontal ligament is a dynamic feature in vertebrate evolution subject to functional adaptation.     

Towards a new paradigm linking virus molecular evolution and pathogenesis: experimental design and phylodynamic inference

Phylogenetic analysis has become a powerful tool for the investigation of evolution at a molecular level. During the last three decades, statistical phylogenetics has increasingly been applied to the study of microbial pathogens. The new field of phylodynamics was formally introduced in 2004 and encompasses the interaction between evolutionary and ecological processes that shape the spatiotemporal and phylogenetic patterns of infectious disease dynamics. This novel framework has significantly enhanced the study of measurable evolving pathogen populations, in particular RNA viruses and retroviruses. One of the major challenges in phylodynamic studies, however, is the generation of data in the form of dense coverage in sequence sampling coupled with high quality epidemiological and/or accurate clinical information. This review focuses specifically on experimental and data assembling strategies that are required to test multi-level phylodynamic hypotheses, ranging from intra-host viral evolution to population dynamics of infectious disease pandemics. Ultimately, bridging the gap between rational experimental design and phylodynamic inference will prove to be essential to take full advantage of this new exciting area of research.     

A basic molecular model for the H2 histamine receptor. Part 1

A 3D model of the canine H2 receptor was built and analysed. This model was constructed using primary sequence comparisons and three-dimensional homology building with bacteriorhodopsin serving as a template. The energy analysis of the interaction between the N3H⁺ form and the N1H⁺ form of histamine with the receptor shows that both have the same binding affinity for the H2 receptor, but only the N3H⁺ form provokes structural changes. The calculated potential energies are consistent with the published binding data and suggest that Asp 98 is the principal residue for ligand recognition. On the basis of sequence alignment studies we postulate that Glu 270 in helix 7 may be important for activation of the H2 receptor. Docking studies of the N3H⁺ folded conformation in our model show that an intramolecular hydrogen bond between N3 and the amino group of the histamine molecule is broken, and the histamine then adopts a conformation similar to the N3H⁺ extended form to interact optimally with the H2 receptor. Mutations were made in the H2 receptor model to mimic published experimental point mutations. The interactions of the mutated receptor models with histamine are consistent with the experimental data.     

New mini-ColE1 as a molecular cloning vehicle.

A new mini-ColE1 plasmid, designated pAC105, was isolated. It has a molecular weight of 1.6 X 10(6) and carries information for its self-replication as well as information for conferring colicin E1 immunity upon its host. Furthermore, pAC105 undergoes replication in the presence of chloramphenicol even when a foreign deoxyribonucleic acid (pSC101) is inserted into its single EcoRI restriction site. Studies in minicell-producing strains demonstrate that pAC105 codes for only two or three polypeptides of low molecular weight. The advantages of using it as a molecular cloning vehicle are discussed.     

On the generation of information as motive power for molecular evolution

Molecular evolution can be described as a learning process during which previously inanimate matter developed the ability to organize all the reaction pathways that establish a living system. Common to all natural self-organizing procedures is the ability of matter to store, process and evaluate the information achieved by learning. Genetic information which is stored in RNA or DNA is the object of natural evolution. With the recognition of nature's concepts, evolutionary optimization was applied to biopolymers that are not optimally adapted for particular technical or medical purposes. Information can also be stored in molecules with structures and chemical properties that are completely different from nucleic acids. Therefore, optimization processes that mimic the natural evolutionary strategies can also be applied to small organic molecules. Much effort has been made theoretically and practically to find a certain optimized species within the (hyper)astronomical number of possible sequence alternatives. From a series of computer experiments it can be concluded that it is not necessary to search the entire sequence space in order to find a particular structure; this is advantageous because the diversity of mutant libraries that can realistically be achieved in the laboratory never extends to the number of theoretically possible sequences. Molecular mutant libraries that serve as starting populations for in vitro selection have been constructed for nucleic acids, proteins, peptides and small organic molecules.     

The Croonian lecture, 1989. Antibodies: a paradigm for the biology of molecular recognition

The hallmark of the antibody response to antigenic challenge is its remarkable specificity. In his Croonian Lecture in 1905, Ehrlich recognized it as a biological puzzle, but considered it inconceivable that animals could produce substances capable of specific recognition of toxins that the species had never encountered before. It took the largest part of the following 70 years to begin to understand the chemical base of the biological puzzle. Even more recently, the genetic base of the underlying events has been clarified. Unique genetic rearrangements of the DNA initiate the biological diversity of somatic cells; this provides an initial source of antigen recognition. The remarkable specificity is the result of an antigen-driven Darwinian selection of proliferating clones, operating on further diversity that is generated by a high rate of point mutations in specific genes. Although the complexity of the biological events underlying the process remain largely unknown, the knowledge gained so far provides insights into alternative approaches to the production of new antibodies.     

Suspension array technology: evolution of the flat-array paradigm.

Suspension arrays of microspheres analyzed using flow cytometry offer a new approach to multiplexed assays for large-scale screening applications. By optically encoding micron-sized polymer particles, suspension microarrays can be created to enable highly multiplexed analysis of complex samples. Each element in the array is comprised of a subpopulation of particles with distinct optical properties and each array element bears a different surface receptor. Nucleic acids, proteins, lipids or carbohydrates can serve as receptors to support the analysis of a wide range of biomolecular assemblies, and applications in genomic and proteomic research are being developed. Coupled with recent innovations for rapid serial analysis of samples, molecular analysis with microsphere arrays holds significant potential as a general analysis platform for both research and clinical applications.     

The evolution of sexual reproduction as a repair mechanism. Part I. A model for self-repair and its biological implications

Summary The theory is presented that the sexual process is a repair mechanism which maintains redundancy within the sub-structure of hierarchical, self-reproducing organisms. In order to keep the problems within mathematically tractable limits (see Part II), a simple model is introduced: a wheel with 6 spokes, 3 of them vital and 3 redundant, symbolizes the individual (cell or organism). Random accidents destroy spokes; the wheels replicate at regular cycles and engage periodically in pairing and repair phases during which missing spokes are copy-reproduced along the intact spokes of the partner wheel.The hierarchical structure of such a system is analysed and an autonomous unit is defined: this is the unit of minimal hierarchical complexity which is capable of perpetuating autonomously all higher and all lower levels of the hierarchy; this is the central unit of selection.Four basic, physical parameters are isolated which determine the essential features of any eucaryotic life cycle: 1. The number of levels of the hierarchy (unicellular, multicellular, colonial, etc.); 2. the relation between the phases of replication (asexual generations) and repair (sexual generations); 3. the duration of potential repair (haplo- diplo-phases); 4. the position of the sexual partners within the hierarchy (selfing, monecy, dioecy, reproductive individuals within colonies, etc.).The evaluation of fitness components is considered in relation to trends of reproductive patterns in evolution.     

Elements for a theory of molecular evolution

Biological evolution is known to be driven by the availability of genetic variants. Spontaneous genetic variation can be the result of a number of specific molecular mechanisms. These can be grouped into three qualitatively different natural strategies of generating genetic variations, namely local sequence changes, DNA rearrangement within the genome and horizontal gene transfer, which is referred to here as DNA acquisition. All of these strategies bring about alterations in the DNA sequences of the genome, thus corresponding to the molecular genetic definition of the term mutation. A detailed inspection of specific mechanisms of mutagenesis reveals on the one hand the impact of non-genetic internal and environmental factors, and on the other hand the specific involvement of gene products. The underlying so-called evolution genes can be classified into generators of genetic variations and into modulators of the frequency of genetic variation. These evolution genes are postulated to have themselves undergone biological evolution under the pressure of second-order selection. On the basis of a few selected examples of mutagenesis, elements for a theory of molecular evolution are collected without a claim for completeness. Philosophical dimensions as well as practical aspects of the advanced knowledge on specific molecular mechanisms involved in molecular evolution are also briefly discussed.