The structure and evolution of angiosperm nuclear genomes

Despite several decades of investigation, the organization of angiosperm genomes remained largely unknown until very recently. Data describing the sequence composition of large segments of genomes, covering hundreds of kilobases of contiguous sequence, have only become available in the past two years. Recent results indicate commonalities in the characteristics of many plant genomes, including in the structure of chromosomal components like telomeres and centromeres, and in the order and content of genes. Major differences between angiosperms have been associated mainly with repetitive DNAs, both gene families and mobile elements. Intriguing new studies have begun to characterize the dynamic three-dimensional structures of chromosomes and chromatin, and the relationship between genome structure and co-ordinated gene function.     

Crystal structure of Bacillus subtilis YckF: structural and functional evolution

The crystal structure of the YckF protein from Bacillus subtilis was determined with MAD phasing and refined at 1.95A resolution. YckF forms a tight tetramer both in crystals and in solution. Conservation of such oligomerization in other phosphate sugar isomerases indicates that the crystallographically observed tetramer is physiologically relevant. The structure of YckF was compared to with its ortholog from Methanococcus jannaschii, MJ1247. Both of these proteins have phosphate hexulose isomerase activity, although neither of the organisms can utilize methane or methanol as source of energy and/or carbon. Extensive sequence and structural similarities with MJ1247 and with the isomerase domain of glucosamine-6-phosphate synthase from Escherichia coli allowed us to group residues contributing to substrate binding or catalysis. Few notable differences among these structures suggest possible cooperativity of the four active sites of the tetramer. Phylogenetic relationships between obligatory and facultative methylotrophs along with B. subtilis and E. coli provide clues about the possible evolution of genes as they loose their physiological importance.     

The evolution of nuclear genome structure in seed plants

Plant nuclear genomes exhibit extensive structural variation in size, chromosome number, number and arrangement of genes, and number of genome copies per nucleus. This variation is the outcome of a set of highly active processes, including gene duplication and deletion, chromosomal duplication followed by gene loss, amplification of retrotransposons separating genes, and genome rearrangement, the latter often following hybridization and/or polyploidy. While these changes occur continuously, it is not surprising that some of them should be fixed evolutionarily and come to mark major clades. Large-scale duplications pre-date the radiation of Brassicaceae and Poaceae and correlate with the origin of many smaller clades as well. Nuclear genomes are largely colinear among closely related species, but more rearrangements are observed with increasing phylogenetic distance; however, the correlation between amount of rearrangement and time since divergence is not perfect. By changing patterns of gene expression and triggering genome rearrangements, novel combinations of genomes (hybrids) may be a driving force in evolution.     

Evolution of the PEBP gene family in plants: functional diversification in seed plant evolution

The phosphatidyl ethanolamine-binding protein (PEBP) gene family is present in all eukaryote kingdoms, with three subfamilies identified in angiosperms (FLOWERING LOCUS T [FT], MOTHER OF FT AND TFL1 [MFT], and TERMINAL FLOWER1 [TFL1] like). In angiosperms, PEBP genes have been shown to function both as promoters and suppressors of flowering and to control plant architecture. In this study, we focus on previously uncharacterized PEBP genes from gymnosperms. Extensive database searches suggest that gymnosperms possess only two types of PEBP genes, MFT-like and a group that occupies an intermediate phylogenetic position between the FT-like and TFL1-like (FT/TFL1-like). Overexpression of Picea abies PEBP genes in Arabidopsis (Arabidopsis thaliana) suggests that the FT/TFL1-like genes (PaFTL1 and PaFTL2) code for proteins with a TFL1-like function. However, PaFTL1 and PaFTL2 also show highly divergent expression patterns. While the expression of PaFTL2 is correlated with annual growth rhythm and mainly confined to needles and vegetative and reproductive buds, the expression of PaFTL1 is largely restricted to microsporophylls of male cones. The P. abies MFT-like genes (PaMFT1 and PaMFT2) show a predominant expression during embryo development, a pattern that is also found for many MFT-like genes from angiosperms. P. abies PEBP gene expression is primarily detected in tissues undergoing physiological changes related to growth arrest and dormancy. A first duplication event resulting in two families of plant PEBP genes (MFT-like and FT/TFL1-like) seems to coincide with the evolution of seed plants, in which independent control of bud and seed dormancy was required, and the second duplication resulting in the FT-like and TFL1-like clades probably coincided with the evolution of angiosperms.     

Comprehensive structure and functional adaptations of the yeast nuclear pore complex

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地下啮齿动物视觉系统的形态结构与机能进化

感觉系统的适应进化机制一直是动物行为学研究的焦点。生活在特殊环境中的动物,其感觉系统在进化过程中表现出的显著差异更是引人注目。由于适应地下黑暗生活环境,地下啮齿动物感觉系统在各个组织水平都表现出进化和退化镶嵌的形态特征,其视觉系统表现得最为突出：视觉器官退化,有关图象分析结构、由视觉诱导产生行为反应的脑区及视觉投射严重退化,有关感受光周期的“非成像” 视觉通路结构高度发达。本文综述了地下啮齿动物视觉系统的结构、功能、进化与发育等方面的研究进展,旨在阐明地下啮齿动物视觉系统的特点,有助于开展地下啮齿动物视觉系统适应进化机制的研究。     

The two tempos of nuclear pore complex evolution: highly adapting proteins in an ancient frozen structure

Background  

The origin of the nuclear compartment has been extensively debated, leading to several alternative views on the evolution of the eukaryotic nucleus. Until recently, too little phylogenetic information was available to address this issue by using multiple characters for many lineages.     

Matrix representation of cell structure,functional processes and evolution: Part V of a general theory

The purpose of this paper is to formulate a compact analytical representation of cell structure, functional processes and evolution. In this formulation, the individual molecular structures are represented by their force-field surfaces. Complementary active sites on these surfaces permit molecular interactions. In cells, these interactions are further regulated by barrier systems in time, space, specificity, and energy. In terms of these parameters, evolution can be represented (modeled) as a random walk in a multi-dimensional space, subject to constraints. In this paper, the various parameters are integrated into a single compact matrix (stack) representation (a three index array). Cell life cycle and functional processes can be represented as a sequence of quantized, time-dependent changes in the representation matrix, subject to specified constraints. Cell evolution can be modeled by generating allowed matrix combinations. This theoretical approach has applications in: (1) ordering and interpreting experimental findings into the matrix representation. Missing matrix elements can be predicted, to be confirmed experimentally; (2) theoretical analysis and prediction of cell regulatory processes and the possible pathological failures; (3) theoretical derivation of the possible biological structures and functional processes, modeling possible pathways of cell and molecular evolution in terms of the matrix representation.     

The impact of nonlinear functional responses on the long-term evolution of food web structure

We investigate the long-term web structure emerging in evolutionary food web models when different types of functional responses are used. We find that large and complex webs with several trophic layers arise only if the population dynamics is such that it allows predators to focus on their best prey species. This can be achieved using modified Lotka-Volterra or Holling/Beddington functional responses with effective couplings that depend on the predator's efficiency at exploiting the prey, or a ratio-dependent functional response with adaptive foraging. In contrast, if standard Lotka-Volterra or Holling/Beddington functional responses are used, long-term evolution generates webs with almost all species being basal, and with additionally many links between these species. Interestingly, in all cases studied, a large proportion of weak links result naturally from the evolution of the food webs.