植物光敏色素入核机理的研究进展

光敏色素是植物感受外界环境变化的重要光受体,它对植物的生长发育具有重要的调控作用。在介绍植物光敏色素分子结构的基础上,对不同光敏色素的入核机理以及核内定位进行了综述,并根据最新研究进展对光敏色素入核机理进行了展望。     

Kinetic and Thermodynamic Analysis of the Light-induced Processes in Plant and Cyanobacterial Phytochromes

The light-induced processes of the biological photoreceptor phytochrome (recombinant phyA of oat and recombinant CphA from the cyanobacterium Tolypothrix PCC7601) have been investigated in a time-resolved manner in the temperature range from 0 to 30°C. Both proteins were heterologously expressed and assembled in vitro with phycocyanobilin. The Pr state of plant phytochrome phyA is converted to the Pfr state after formation of four intermediates with an overall quantum yield of ∼18%. The reversal reaction (Pfr-to-Pr) shows several intermediates, all of which, even the first detectable one, exhibit already all spectral features of the Pr state. The canonical phytochrome CphA from Tolypothrix showed a similar intermediate sequence as its plant ortholog. Whereas the kinetics for the forward reaction (Pr-to-Pfr) was nearly identical for both proteins, the reverse process (Pr formation) in the cyanobacterial phytochrome was slower by a factor of three. As found for the Pfr-to-Pr intermediates in the plant protein, also in CphA all detectable intermediates showed the spectral features of the Pr form. For both phytochromes, activation parameters for both the forward and the backward reaction pathways were determined.     

The Role of Cryptochrome 1 and Phytochromes in the Control of Plant Photomorphogenetic Responses to Green Light

We studied the role of cryptochrome 1 (CRY1) and phytochromes in the photomorphogenetic responses of plants to the middle-wavelength region of photosynthetically active radiation. A comparison was performed of green light (GL) action on growth, GA activity and IAA and ABA contents during seedling deetiolation of two Arabidopsis thaliana (L.) Heynh lines of Landsnerg erecta ecotype (wild type Ler and mutant hy4) and of Phaseolus vulgaris L. It was shown that a growth responses of Ler hypocotyls to GL of 515 nm and Ler cotyledons to GL of 542 nm were weaker than those of the hy4 mutant defected in the CRY1 synthesis. Far-red light (730 nm) neutralized the effect of GL (533 nm) on the phytohormone balance in the primary kidney bean leaves. The data obtained permit a supposition that plants possess several photoregulatory systems functioning under GL of higher (515 nm) and lower emission energy (542–553 nm). A possible operation of GL receptors, other than cryptochrome 1 and phytochromes, is discussed.     

Cactophilic Drosophila in South America: A Model for Evolutionary Studies

The Drosophila buzzatii cluster is composed of seven cactophilic species and their known geographical distribution encompasses the open vegetation diagonal, which includes the morphoclimatic Domains of the Caatinga, Chaco and Cerrado, which are situated between the Amazon and the Atlantic forests. Besides these areas, these cactophilic species are also found in a narrow strip along the Atlantic coast from northeastern Brazil to the southern tip of the country. The hypothesis of vicariant events, defining the core areas of each species, is proposed to explain the historical diversification for the cluster. The intraspecific analysis for the cluster shows a population structure with gene flow restricted by distance, range expansion with secondary contact resulting in introgression and simpatry, especially in the limits of the species distribution, polytypic populations and assortative mating in inter population experiments. There is a variation related to these events that depends on the species and geographic origin of the population analyzed. These events are, hypothetically, described as the results of expansion and retraction of the population ranges, as a consequence of their association with cacti, which theoretically follow the expansion and retraction of dry areas during the paleoclimatic oscillations in South America, as that promoted by the glacial cycles of the Quaternary. The Drosophila buzzatii cluster is divided into two groups. The first one is composed of D. buzzatii, a species that has a broad geographic distribution and no significant differentiation between its populations. The second is the Drosophila serido sibling set, which encompasses the others species and is characterized by a significant potential for differentiation.     

数量遗传学理论框架下的进化生态学研究：以动物模型的运用为例

目前,生态学家越来越关注深入的生物学问题,例如,1)理解生态和进化过程的互作和关系;2)种群中一个重要的表型特征,受遗传基因影响多大?即其可遗传程度,表示该性状的进化潜能;3)基因是怎样影响表型性状,及其对应的个体适合度以及种群动态?4)决定多个重要表型性状的基因之间关系和互作如何?随着生物统计软件尤其是线性混合模型的发展,结合经典数量遗传学的理论,发展出了针对上述问题的动物模型(Animal Model),使得我们可以对野外种群进行上述研究。本文首先介绍了经典数量遗传学的重要概念,随后在其理论框架下,举例介绍了动物模型的操作和使用,最后探讨和展望了利用数量遗传学方法进行进化生态学研究的前景。     

Functional Analyses of Resurrected and Contemporary Enzymes Illuminate an Evolutionary Path for the Emergence of Exolysis in Polysaccharide Lyase Family 2

Family 2 polysaccharide lyases (PL2s) preferentially catalyze the β-elimination of homogalacturonan using transition metals as catalytic cofactors. PL2 is divided into two subfamilies that have been generally associated with secretion, Mg²⁺ dependence, and endolysis (subfamily 1) and with intracellular localization, Mn²⁺ dependence, and exolysis (subfamily 2). When present within a genome, PL2 genes are typically found as tandem copies, which suggests that they provide complementary activities at different stages along a catabolic cascade. This relationship most likely evolved by gene duplication and functional divergence (i.e. neofunctionalization). Although the molecular basis of subfamily 1 endolytic activity is understood, the adaptations within the active site of subfamily 2 enzymes that contribute to exolysis have not been determined. In order to investigate this relationship, we have conducted a comparative enzymatic analysis of enzymes dispersed within the PL2 phylogenetic tree and elucidated the structure of VvPL2 from Vibrio vulnificus YJ016, which represents a transitional member between subfamiles 1 and 2. In addition, we have used ancestral sequence reconstruction to functionally investigate the segregated evolutionary history of PL2 progenitor enzymes and illuminate the molecular evolution of exolysis. This study highlights that ancestral sequence reconstruction in combination with the comparative analysis of contemporary and resurrected enzymes holds promise for elucidating the origins and activities of other carbohydrate active enzyme families and the biological significance of cryptic metabolic pathways, such as pectinolysis within the zoonotic marine pathogen V. vulnificus.     

Rethinking the Synthesis Period in Evolutionary Studies

I propose we abandon the unit concept of “the evolutionary synthesis”. There was much more to evolutionary studies in the 1920s and 1930s than is suggested in our commonplace narratives of this object in history. Instead, four organising threads capture much of evolutionary studies at this time. First, the nature of species and the process of speciation were dominating, unifying subjects. Second, research into these subjects developed along four main lines, or problem complexes: variation, divergence, isolation, and selection. Some calls for ‹synthesis’ focused on these problem complexes (sometimes on one of these; other times, all). In these calls, comprehensive and pluralist compendia of plausibly relevant elements were preferred over reaching consensus about the value of particular formulae. Third, increasing confidence in the study of common problems coincided with methodological and epistemic changes associated with experimental taxonomy. Finally, the surge of interest in species problems and speciation in the 1930s is intimately tied to larger trends, especially a shifting balance in the life sciences towards process-based biologies and away from object-based naturalist disciplines. Advocates of synthesis in evolution supported, and were adapting to, these larger trends.     

Evolutionary Diversification of Plant Shikimate Kinase Gene Duplicates

Shikimate kinase (SK; EC 2.7.1.71) catalyzes the fifth reaction of the shikimate pathway, which directs carbon from the central metabolism pool to a broad range of secondary metabolites involved in plant development, growth, and stress responses. In this study, we demonstrate the role of plant SK gene duplicate evolution in the diversification of metabolic regulation and the acquisition of novel and physiologically essential function. Phylogenetic analysis of plant SK homologs resolves an orthologous cluster of plant SKs and two functionally distinct orthologous clusters. These previously undescribed genes, shikimate kinase-like 1 (SKL1) and -2 (SKL2), do not encode SK activity, are present in all major plant lineages, and apparently evolved under positive selection following SK gene duplication over 400 MYA. This is supported by functional assays using recombinant SK, SKL1, and SKL2 from Arabidopsis thaliana (At) and evolutionary analyses of the diversification of SK-catalytic and -substrate binding sites based on theoretical structure models. AtSKL1 mutants yield albino and novel variegated phenotypes, which indicate SKL1 is required for chloroplast biogenesis. Extant SKL2 sequences show a strong genetic signature of positive selection, which is enriched in a protein–protein interaction module not found in other SK homologs. We also report the first kinetic characterization of plant SKs and show that gene expression diversification among the AtSK inparalogs is correlated with developmental processes and stress responses. This study examines the functional diversification of ancient and recent plant SK gene duplicates and highlights the utility of SKs as scaffolds for functional innovation.     

模式植物二穗短柄草研究进展与展望

二穗短柄草(Brachypodium distachyon)是一种温带禾本科植物,其植株矮小,自花授粉,生活周期短,生长条件简单,基因组小,易于进行遗传转化,与小麦、柳枝稷同属禾本科早熟禾亚科,是研究小麦、大麦等经济作物以及柳枝稷等能源植物的比较适合的模式植物。最近,二穗短柄草基因组测序及注释正式完成,有必要对其研究进展进行全面的总结。综述了二穗短柄草的基因组特征、基因表达模式、遗传转化等方面的最新研究进展,并对今后的研究方向作了展望,以促进对禾谷类经济作物和能源植物的深入研究。     

在植物考据研究中应用进化思想的探讨

探讨了在植物考据研究中如何应用进化思想。我们认为在确定中国古籍文献中记载植物的学名时,对部分植物宜采用集合种（或复合种）的概念。     

Evolutionary History of the Plant Pathogenic Bacterium Xanthomonas axonopodis

Deciphering mechanisms shaping bacterial diversity should help to build tools to predict the emergence of infectious diseases. Xanthomonads are plant pathogenic bacteria found worldwide. Xanthomonas axonopodis is a genetically heterogeneous species clustering, into six groups, strains that are collectively pathogenic on a large number of plants. However, each strain displays a narrow host range. We address the question of the nature of the evolutionary processes – geographical and ecological speciation – that shaped this diversity. We assembled a large collection of X. axonopodis strains that were isolated over a long period, over continents, and from various hosts. Based on the sequence analysis of seven housekeeping genes, we found that recombination occurred as frequently as point mutation in the evolutionary history of X. axonopodis. However, the impact of recombination was about three times greater than the impact of mutation on the diversity observed in the whole dataset. We then reconstructed the clonal genealogy of the strains using coalescent and genealogy approaches and we studied the diversification of the pathogen using a model of divergence with migration. The suggested scenario involves a first step of generalist diversification that spanned over the last 25 000 years. A second step of ecology-driven specialization occurred during the past two centuries. Eventually, secondary contacts between host-specialized strains probably occurred as a result of agricultural development and intensification, allowing genetic exchanges of virulence-associated genes. These transfers may have favored the emergence of novel pathotypes. Finally, we argue that the largest ecological entity within X. axonopodis is the pathovar.     

A New Appraisal of the Prokaryotic Origin of Eukaryotic Phytochromes

The evolutionary origin of the phytochromes of eukaryotes is controversial. Three cyanobacterial proteins have been described as ``phytochrome-like' and have been suggested to be potential ancestors of these essential photoreceptors: Cph1 from Synechocystis PCC 6803, showing homology to phytochromes along its entire length and known to attach a chromophore; and PlpA from Synechocystis PCC 6803 and RcaE from Fremyella diplosiphon, both showing homology to phytochromes most strongly only in the C-terminal region and not known to bind a chromophore. We have reexamined the evolution of the photoreceptors using for PCR amplification a highly conserved region encoding the chromophore-binding domain in both Cph1 and phytochromes of plants and have identified genes for phytochrome-like proteins (PLP) in 11 very diverse cyanobacteria. The predicted gene products contain either a Cys, Arg, Ile, or Leu residue at the putative chromophore binding site. In 10 of the strains examined only a single gene was found, but in Calothrix PCC 7601 two genes (cphA and cphB) were identified. Phylogenetic analysis revealed that genes encoding PLP are homologues that share a common ancestor with the phytochromes of eukaryotes and diverged before the latter. In contrast, the putative sensory/regulatory proteins, including PlpA and RcaE, that lack a part of the chromophore lyase domain essential for chromophore attachment on the apophytochrome, are only distantly related to phytochromes. The Ppr protein of the anoxygenic photosynthetic bacterium Rhodospirillum centenum and the bacterial phytochrome-like proteins (BphP) of Deinococcus radiodurans and Pseudomonas aeruginosa fall within the cluster of cyanobacterial phytochromes. Received: 9 December 1999 / Accepted: 10 May 2000     

The Pleiomorphic Plant MTOC： An Evolutionary Perspective

γ-Tubulin is an essential component of the microtubule organizing center （MTOC） responsible for nucleating microtubules in both plants and animals. Whereas γ-tubulin is tightly associated with centrosomes that are inheritable organelles in cells of animals and most algae, it appears at different times and places to organize the myriad specialized microtubule systems that characterize plant cells. We have traced the distribution of γ-tubulin through the cell cycle in representative land plants （embryophytes） and herein present data that have led to a concept of the pleiomorphic and migratory MTOC. The many forms of the plant MTOC at spindle organization constitute pleiomorphism, and stage-specific “migration” is suggested by the consistent pattern of redistribution of γ-tubulin during mitosis. Mitotic spindles may be organized at centriolar centrosomes （only in final divisions of spermatogenesis）, polar organizers （POs）, plastid MTOCs, or nuclear envelope MTOCs （NE-MTOCs）. In all cases, with the possible exception of centrosomes in spermatogenesis, the γ-tubulin migrates to broad polar regions and along the spindle fibers, even when it is initially a discrete polar entity. At anaphase it moves poleward, and subsequently migrates from polar regions （distal nuclear surfaces） into the interzone （proximal nuclear surfaces） where interzonal microtubule arrays and phragmoplasts are organized. Following cytokinesis, γ-tubulin becomes associated with nuclear envelopes and organizes radial microtubule systems （RMSs）. These may exist only briefly, before establishment of hoop-like cortical arrays in vegetative tissues, or they may be characteristic of interphase in syncytial systems where they serve to organize the common cytoplasm into nuclear cytoplasmic domains （NCDs）.     

Adaptive Evolution in the GAF Domain of Phytochromes in Gymnosperms

The GAF domain of phytochrome is essential for photoconversion and signal transduction. In gymnosperms, it exists in all members of the phytochrome family that experience gene duplication. Maximum-likelihood models of codon substitution can provide a framework for constructing likelihood ratio tests of changes in selective pressure and make clear predictions about patterns of genetic change following gene duplication. In this study, 68 gymnosperm GAF sequences were analyzed to identify lineages and sites under positive selection. Our results indicate that (1) positive selection at a few sites (3.6%), rather than relaxation of selective constraints, has played a major role in the evolution of the gymnosperm GAF domain; (2) strong positive selective pressure tends to occur in the recent PHYP lineages of cogeneric species, but is absent in old lineages consisting of distantly related species; and (3) the selective pressure indicated by the ω ratio varies greatly among lineages and sites in the GAF domain.