Flavonoid evolution: an enzymic approach

Flavonoid evolution in land plants is discussed from an enzymic point of view, based on the present day distribution of the major subgroups of flavonoids in bryophytes, lower and higher vascular plants. The importance of varied functions in the origin of pathways with a series of sequential steps leading to end-products is considered; it is argued that the initial function is that of an internal regulatory agent, rather than as a filter against ultraviolet irradiation. The basic synthases, hydroxylases, and reductases of flavonoid pathways are presumed to have evolved from enzymes of primary metabolism. A speculative scheme is presented of flavonoid evolution within a primitive group of algae derived from a Charophycean rather than a Chlorophycean line, as a land environment was invaded. Flavonoid evolution was preceded by that of the phenylpropanoid and malonyl-coenzyme A pathways, but evolved prior to the lignin pathway.     

Genome evolution in an insect cell: distinct features of an ant-bacterial partnership

Bacteria that live exclusively within eukaryotic host cells include not only well-known pathogens, but also obligate mutualists, many of which occur in diverse insect groups such as aphids, psyllids, tsetse flies, and the ant genus Camponotus (Buchner, 1965; Douglas, 1998; Moran and Telang, 1998; Baumann et al., 2000; Moran and Baumann, 2000). In contrast to intracellular pathogens, these primary (P) endosymbionts of insects are required for the survival and reproduction of the host, exist within specialized host cells called bacteriocytes, and undergo stable maternal transmission through host lineages (Buchner, 1965; McLean and Houk, 1973). Due to their long-term host associations and close phylogenetic relationship with well-characterized enterobacteria (Fig. 1), P-endosymbionts of insects are ideal model systems to examine changes in genome content and architecture that occur in the context of beneficial, intracellular associations. Since these bacteria have not been cultured outside of the host cell, they are difficult to study with traditional genetic or physiological approaches. However, in recent years, molecular and computational approaches have provided important insights into their genetic diversity and ecological significance. This review describes some recent insights into the evolutionary genetics of obligate insect-bacteria symbioses, with a particular focus on an intriguing association between the bacterial endosymbiont Blochmannia and its ant hosts.     

Directionality theory: an empirical study of an entropic principle in life-history evolution

Understanding the relationship between ecological constraints and life-history properties constitutes a central problem in evolutionary ecology. Directionality theory, a model of the evolutionary process based on demographic entropy, a measure of the uncertainty in the age of the mother of a randomly chosen newborn, provides an analytical framework for addressing this problem. The theory predicts that in populations that spend the greater part of their evolutionary history in the stationary growth phase (equilibrium species), entropy will increase. Equilibrium species will be characterized by high iteroparity and strong demographic stability. In populations that spend the greater part of their evolutionary history in the exponential growth phase (opportunistic species), entropy will decrease when population size is large, and will undergo random variation when population size is small. Opportunistic species will be characterized by weak iteroparity and weak demographic stability when population size is large, and random variations in these attributes when population size is small. This paper assesses the validity of these predictions by employing a demographic dataset of 66 species of perennial plants. This empirical analysis is consistent with directionality theory and provides support for its significance as an explanatory and predictive model of life-history evolution.     

Mitochondria and G-quadruplex evolution: an intertwined relationship

G-quadruplexes (G4s) are non-canonical structures formed in guanine (G)-rich sequences through stacked G tetrads by Hoogsteen hydrogen bonding. Several studies have demonstrated the existence of G4s in the genome of various organisms, including humans, and have proposed that G4s have a regulatory role in various cellular functions. However, little is known regarding the dissemination of G4s in mitochondria. In this review, we report the observation that the number of potential G4-forming sequences in the mitochondrial genome increases with the evolutionary complexity of different species, suggesting that G4s have a beneficial role in higher-order organisms. We also discuss the possible function of G4s in mitochondrial (mt)DNA and long noncoding (lnc)RNA and their role in various biological processes.     

Directed evolution of industrial enzymes: an update

The use of enzymes in industrial processes can often eliminate the use of high temperatures, organic solvents and extremes of pH, while at the same time offering increased reaction specificity, product purity and reduced environmental impact. The growing use of industrial enzymes is dependent on constant innovation to improve performance and reduce cost. This innovation is driven by a rapidly increasing database of natural enzyme diversity, recombinant DNA and fermentation technologies that allow this diversity to be produced at low cost, and protein modification tools that enable enzymes to be tuned to fit into the industrial marketplace.     

Directed evolution: an approach to engineer enzymes

Directed evolution is being used increasingly in industrial and academic laboratories to modify and improve commercially important enzymes. Laboratory evolution is thought to make its biggest contribution in explorations of non-natural functions, by allowing us to distinguish the properties nurtured by evolution. In this review we report the significant advances achieved with respect to the methods of biocatalyst improvement and some critical properties and applications of the modified enzymes. The application of directed evolution has been elaborately demonstrated for protein solubility, stability and catalytic efficiency. Modification of certain enzymes for their application in enantioselective catalysis has also been elucidated. By providing a simple and reliable route to enzyme improvement, directed evolution has emerged as a key technology for enzyme engineering and biocatalysis.     

Recombination: an underappreciated factor in the evolution of plant genomes

Our knowledge of recombination rates and patterns in plants is far from being comprehensive. However, compelling evidence indicates a central role for recombination, through its influences on mutation and selection, in the evolution of plant genomes. Furthermore, recombination seems to be generally higher and more variable in plants than in animals, which could be one of the primary reasons for differences in genome lability between these two kingdoms. Much additional study of recombination in plants is needed to investigate these ideas further.     

The evolution of water transport in plants: an integrated approach

This review examines the evolution of the plant vascular system from its beginnings in the green algae to modern arborescent plants, highlighting the recent advances in developmental, organismal, geochemical and climatological research that have contributed to our understanding of the evolution of xylem. Hydraulic trade‐offs in vascular structure–function are discussed in the context of canopy support and drought and freeze–thaw stress resistance. This qualitative and quantitative neontological approach to palaeobotany may be useful for interpreting the water‐transport efficiencies and hydraulic limits in fossil plants. Large variations in atmospheric carbon dioxide levels are recorded in leaf stomatal densities, and may have had profound impacts on the water conservation strategies of ancient plants. A hypothesis that links vascular function with stomatal density is presented and examined in the context of the evolution of wood and/or vessels. A discussion of the broader impacts of plant transport on hydrology and climate concludes this review.     

Ribonucleotide reductases: divergent evolution of an ancient enzyme

Ribonucleotide reductases (RNRs) are uniquely responsible for converting nucleotides to deoxynucleotides in all dividing cells. The three known classes of RNRs operate through a free radical mechanism but differ in the way in which the protein radical is generated. Class I enzymes depend on oxygen for radical generation, class II uses adenosylcobalamin, and the anaerobic class III requires S-adenosylmethionine and an iron–sulfur cluster. Despite their metabolic prominence, the evolutionary origin and relationships between these enzymes remain elusive. This gap in RNR knowledge can, to a major extent, be attributed to the fact that different RNR classes exhibit greatly diverged polypeptide chains, rendering homology assessments inconclusive. Evolutionary studies of RNRs conducted until now have focused on comparison of the amino acid sequence of the proteins, without considering how they fold into space. The present study is an attempt to understand the evolutionary history of RNRs taking into account their three-dimensional structure. We first infer the structural alignment by superposing the equivalent stretches of the three-dimensional structures of representatives of each family. We then use the structural alignment to guide the alignment of all publicly available RNR sequences. Our results support the hypothesis that the three RNR classes diverged from a common ancestor currently represented by the anaerobic class III. Also, lateral transfer appears to have played a significant role in the evolution of this protein family.     

Behavioural plasticity: an interaction between evolution and experience

Animals adjust their behaviour in response to complex environmental conditions. This form of plasticity requires the formation of association between information and an appropriate behavioural response. Such a connection is the result of a complex interaction between evolutionary pre-programmed cue-response behaviour (innate behavioural response) and cumulated lifetime experience (learning). The evolution of learning and innate behavioural responses is likely to depend on their respective fitness costs and benefits. However, as natural selection will indirectly affect each form through global behavioural plasticity, it is critical to understand how each form interacts with the other. The inclusion of innate behavioural plasticity and learning in behaviour is likely to result in more than the mere sum of each plastic form. In this review we investigate the costs and benefits of learning and innate behavioural responses and the effect of one on the other in their evolution. We highlight the need for more explicit study of the interaction between innate behavioural response and learning in natural systems for a better understanding of behavioural plasticity.     

Pteridophytic evolution: an often underappreciated phytological success story

The role and success of pteridophytes in the vascular land flora from the Silurian to Recent are examined. Success is defined as the ability of plants to occupy physical and ecological space through time, and evaluated in terms of species richness and percent cover. These factors are examined for vascular plants of successively more specialized grades of life cycles. Four grades, including homospory, heterospory, extreme heterospory, and angiospermy are recognized, with angiospermy providing for the greatest species richness and percent cover in the modern flora. In terms of percent cover, gymnosperms are also relatively successful, but in terms of species richness homosporous pteridophytes are more successful than all other non-angiospermous grades combined. The diversity of growth forms and life history patterns that have helped pteridophytes become successful throughout time is examined, and evidence for rhizomatous herbs, vines, epiphytes, trees of diverse architectures, and specialized modes of growth and vegetative propagation are reviewed. Comparison of several analyses of land plant diversity through the Phanerozoic suggests that plants with pteridophytic reproduction were dominant in most floras long after the origin of seed plants, and that pteridophytes probably have continued to increase in species richness up to the present. The loss of pteridophytic dominance in terms of percent cover at the end of the Paleozoic was associated with species turnover in which arborescent pteridophytes of several clades became extinct, but some herbaceous pteridophytes may have retained dominance in many floras into the Paleogene.     

The genome: an isochore ensemble and its evolution

The genomes of eukaryotes are mosaics of isochores. These are long DNA stretches that are fairly homogeneous in base composition and that belong to a small number of families characterized by different ratios of GC to AT and different short-sequence patterns (i.e., different DNA structures that interact with different proteins). This genome organization led to two discoveries: (1) the genomic code, which refers to two correlations, that of the composition of coding and contiguous noncoding sequences, and that of coding sequences and the structural properties of the encoded proteins; and (2) the genome phenotypes, which correspond to the patterns of isochore families in the genomes. These patterns indicate that genome evolution may proceed either according to a conservative mode or to a transitional (isochore shifting) mode, apparently depending upon whether the environment is constant or shifting. According to the neoselectionist theory, natural selection is responsible for both modes.