Guest-Editorial Introduction: Converging Evolutionary Patterns in Life and Culture

The natural world demonstrates signs of spatial–temporal order, an order that appears to us through a series of recognizable, recurring and consecutive patterns, i.e. regularities in forms, functions, behaviors, events and processes. These patterns lend insight into the modes and tempos of evolution and thus into the units, levels, and mechanisms that underlie the evolutionary hierarchy. Contributors to this special issue analyze converging patterns in the biological and sociocultural realm across and beyond classic divisions between micro- and macro-evolution; horizontal/reticulate and vertical evolution; phylogeny, ontogeny and ecology; synchronic and diachronic sociocultural and linguistic research; and tree and network diagrams. Explanations are sought in complexity theory, major transitions of evolution, and process and mechanism approaches to change; and consequences for notions such as “life”, “species”, “biological individuality”, “units” and “levels” of evolution are given.     

Tracing Primordial Protein Evolution through Structurally Guided Stepwise Segment Elongation

The understanding of how primordial proteins emerged has been a fundamental and longstanding issue in biology and biochemistry. For a better understanding of primordial protein evolution, we synthesized an artificial protein on the basis of an evolutionary hypothesis, segment-based elongation starting from an autonomously foldable short peptide. A 10-residue protein, chignolin, the smallest foldable polypeptide ever reported, was used as a structural support to facilitate higher structural organization and gain-of-function in the development of an artificial protein. Repetitive cycles of segment elongation and subsequent phage display selection successfully produced a 25-residue protein, termed AF.2A1, with nanomolar affinity against the Fc region of immunoglobulin G. AF.2A1 shows exquisite molecular recognition ability such that it can distinguish conformational differences of the same molecule. The structure determined by NMR measurements demonstrated that AF.2A1 forms a globular protein-like conformation with the chignolin-derived β-hairpin and a tryptophan-mediated hydrophobic core. Using sequence analysis and a mutation study, we discovered that the structural organization and gain-of-function emerged from the vicinity of the chignolin segment, revealing that the structural support served as the core in both structural and functional development. Here, we propose an evolutionary model for primordial proteins in which a foldable segment serves as the evolving core to facilitate structural and functional evolution. This study provides insights into primordial protein evolution and also presents a novel methodology for designing small sized proteins useful for industrial and pharmaceutical applications.     

Tracing Patterns of Chloroplast Evolution in Euglenoids: Contributions from Colacium vesiculosum and Strombomonas acuminata (Euglenophyta)

The chloroplast genomes of two photosynthetic euglenoids, Colacium vesiculosum Ehrenberg (128,889 bp), and Strombomonas acuminata (Schmarda) Deflandre (144,167 bp) have been sequenced. These chloroplast genomes in combination with those of Euglena gracilis, Eutreptia viridis, and Eutreptiella gymnastica provide a snapshot of euglenoid chloroplast evolution allowing comparisons of gene content, arrangement, and expansion. The gene content of the five chloroplast genomes is very similar varying only in the presence or absence of, rrn5, roaA, psaI, psaM, rpoA, and two tRNAs. Large gene rearrangements have occurred within the C. vesiculosum and S. acuminata chloroplast genomes. Most of these rearrangements represent repositioning of entire operons rather than single genes. When compared with previously sequenced genomes, C. vesiculosum and S. acuminata chloroplast genomes more closely resemble the E. gracilis chloroplast genome in size of the genome, number of introns, and gene order than they do those of the Eutreptiales. Overall, the chloroplast genomes of these five species show an evolutionary trend toward increased intron number, a decrease in gene density, and substantial rearrangement of gene clusters.     

蛋白质新功能定向进化研究策略

利用定向进化策略改造蛋白质功能已经在农业、工业和医药等领域得到了广泛的应用.蛋白质工程的最新进展是利用定向进化策略对自然界蛋白质引入新功能,但由于其决定因素比较复杂,是研究者面临的一个重大挑战.详细介绍了国外近年发展的蛋白质新功能定向进化研究策略:对传统突变体库构建策略进行改进以及非同源重组改造技术的开发,是早期引入蛋白质新功能的常用手段,利用计算/理性设计与定向进化相结合引入蛋白质新功能是近年定向进化研究的一个重大突破,而噬菌体展示技术是蛋白质新功能筛选的主要策略.蛋白质新功能的分子进化模型已逐渐成为蛋白质工程改造的新思路.