DNA重排及体外分子进化

ＤＮＡ重排是目前为止最简便、最有效的体外定向进化技术,可以对单一基因、质粒、代谢途径、部分甚至整个基因组进行改造。本综述了ＤＮＡ重排的基本原理、特点、与其它体外进化技术的不同,着重介绍了其在体外分子进化上的广泛应用,并对应用前景进行了展望。     

Conformational changes in the globin family during evolution

Summary Conformational restrictions imposed on the fixation of insertions and deletions by the three-dimensional structure of globins during evolution are analyzed. An evolutionary tree for the primary structure of 38 taxonomically distant globins was constructed by a computer method. Based on this tree, the calculated fixation frequency of point mutations was 50-fold higher than that established jointly for deletions and insertions, and the fixation frequency of deletions was more than three times that established for insertions. It was also found that deletions and insertions are predominantly fixed in the interhelical sections and at the ends of the -helices of the globin molecules. Conformational analysis of the packing of the -helices in the spatial structure of globins demonstrated that the fixation of deletions and insertions in the center of an -helix produces a marked distortion of their normal packing. The possible role of deletions and insertions in the evolution of protein families is discussed.     

昆虫CYP6家族多样性与进化

了解昆虫CYP6家族的多样性与进化 ,对认识昆虫细胞色素P45 0参与抗药性发生、发展的分子生物学机制具有重要的意义。作者就昆虫CYP6家族多样性的各种表现形式及其形成原因、自然进化史、内部进化关系及进化的分子机制作一综述     

杨树MIR169基因家族分子进化分析

MicroRNA(miRNA)是真核生物中普遍存在的一类参与基因表达调控的小分子RNA。ptc-MIR169基因家族有33个成员, 是杨树中规模最大的miRNA基因家族。研究MIR169基因家族的进化对揭示杨树miRNA基因的进化机制具有重要的意义。文章对毛果杨MIR169基因家族的分子系统发育、基因倍增模式、表达分化和靶基因进行了分析。结果表明, 染色体大片段重复和串联重复在毛果杨MIR169基因家族扩张中均具有重要作用; MIR169基因家族在表达方式上已经出现了较大的分化; MIR169基因家族可能在杨树中已经形成了复杂的调控网络, 对杨树的生长发育和适应性等具有重要的调控作用。文章为杨树及杨柳科相关植物中miRNA基因家族的分子进化研究提供了参考。     

AZFY-like sequence in fish,with comments on the evolution of theZFY family of genes in vertebrates

ZFY-like genes have been observed in a variety of vertebrate species. Although originally implicated as the primary testis-determining gene in humans and other placental mammals, more recent evidence indicates a role(s) outside that of testis determination. In this study, DNA from five species of fish,Carasius auratus, Rivulus marmoratus, Xiphophorus maculatus, X. milleri, andX. nigrensis was subjected to Southern blot analysis using a PCR-amplified fragment of mouseZFY-like sequence as a probe. Restriction fragment patterns were not polymorphic between sexes in any one species but showed a different pattern for each species. With one exception,Rivulus, a 3.1-kb band from theEcoRI digestion was common to all. Sequence and open reading frame analysis of this fragment showed a strong homology to other known vertebrateZFY-like genes. Of particular interest in this gene is a novel third finger domain similar to one human and one alligatorZFY-like gene. Our studies and others provide evidence for a family of vertebrateZFY genes, with those having this novel third finger being representative of the ancestral condition.     

Functional evolution in the ancestral lineage of vertebrates or when genomic complexity was wagging its morphological tail

Early vertebrate evolution is characterized by a significant increase of organismal complexity over a relatively short time span. We present quantitative evidence for a high rate of increase in morphological complexity during early vertebrate evolution. Possible molecular evolutionary mechanisms that underlie this increase in complexity fall into a small number of categories, one of which is gene duplication and subsequent structural or regulatory neofunctionalization. We discuss analyses of two gene families whose regulatory and structural evolution shed light on the connection between gene duplication and increases in organismal complexity.     

Fragmentation of acetate-CoA ligase gives a clue to understand domain rearrangement history of NDP-forming acyl-CoA synthetase superfamily proteins

ABSTRACT

NDP-forming type acyl-CoA synthetase superfamily proteins are known to have six essential subdomains (1, 2, 3, a, b, c) of which partition and order are varied, suggesting yet-to-be-defined subdomain rearrangement happened in its evolution. Comparison in physicochemical and biochemical characteristics between the recombinant proteins which we made from fragmented subdomains and wild-type protein, acetate-CoA ligase in a hyperthermophilic archaeon, consisting of two distinct subunits (α1-2-3 and βa-b-c) provided a clue to the mystery of its molecular evolutionary passage. Although solubility and thermostability of each fragmented subdomain turned out to be lower than that of wild-type, mixture of the three synthetic subunits of α1-2, α3, and βa-b-c had quaternary structure, thermostability, and enzymatic activity comparable to those of the wild-type. This suggests that substantial independence and mobility of subdomain 3 have enabled rearrangement of the subdomains; and thermostability of the subdomains has constrained the composition of the subunits.     

Species-specific duplications driving the recent expansion of NBS-LRR genes in five Rosaceae species

Background

Disease resistance (R) genes from different Rosaceae species have been identified by map-based cloning for resistance breeding. However, there are few reports describing the pattern of R-gene evolution in Rosaceae species because several Rosaceae genome sequences have only recently become available.

Results

Since most disease resistance genes encode NBS-LRR proteins, we performed a systematic genome-wide survey of NBS-LRR genes between five Rosaceae species, namely Fragaria vesca (strawberry), Malus × domestica (apple), Pyrus bretschneideri (pear), Prunus persica (peach) and Prunus mume (mei) which contained 144, 748, 469, 354 and 352 NBS-LRR genes, respectively. A high proportion of multi-genes and similar Ks peaks (Ks = 0.1- 0.2) of gene families in the four woody genomes were detected. A total of 385 species-specific duplicate clades were observed in the phylogenetic tree constructed using all 2067 NBS-LRR genes. High percentages of NBS-LRR genes derived from species-specific duplication were found among the five genomes (61.81% in strawberry, 66.04% in apple, 48.61% in pear, 37.01% in peach and 40.05% in mei). Furthermore, the Ks and Ka/Ks values of TIR-NBS-LRR genes (TNLs) were significantly greater than those of non-TIR-NBS-LRR genes (non-TNLs), and most of the NBS-LRRs had Ka/Ks ratios less than 1, suggesting that they were evolving under a subfunctionalization model driven by purifying selection.

Conclusions

Our results indicate that recent duplications played an important role in the evolution of NBS-LRR genes in the four woody perennial Rosaceae species. Based on the phylogenetic tree produced, it could be inferred that species-specific duplication has mainly contributed to the expansion of NBS-LRR genes in the five Rosaceae species. In addition, the Ks and Ka/Ks ratios suggest that the rapidly evolved TNLs have different evolutionary patterns to adapt to different pathogens compared with non-TNL resistant genes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1291-0) contains supplementary material, which is available to authorized users.     

Evolution of the family of intracellular lipid binding proteins in vertebrates

Members of the family of intracellular lipid binding proteins (iLBPs) have been implicated in cytoplasmic transport of lipophilic ligands, such as long-chain fatty acids and retinoids. iLBPs are low molecular mass proteins (14–16 kDa) sharing a common structural fold. The iLBP family likely arose through duplication and diversification of an ancestral iLBP gene. Phylogenetic analysis undertaken in the present study indicates that the ancestral iLBP gene arose after divergence of animals from fungi and plants. The first gene duplication was dated around 930 millions of years ago, and subsequent duplications in the succeeding 550 millions of years gave rise to the 16 iLBP types currently recognized in vertebrates. Four clusters of proteins, each binding a characteristic range of ligands, are evident from the phylogenetic tree. Evolution of different binding properties probably allowed cytoplasmic trafficking of distinct ligands. It is speculated that recruitment of an iLBP during evolution of animals enabled the mitochondrial oxidation of long-chain fatty acids.     

A dynamic history of gene duplications and losses characterizes the evolution of the SPARC family in eumetazoans

The vertebrates share the ability to produce a skeleton made of mineralized extracellular matrix. However, our understanding of the molecular changes that accompanied their emergence remains scarce. Here, we describe the evolutionary history of the SPARC (secreted protein acidic and rich in cysteine) family, because its vertebrate orthologues are expressed in cartilage, bones and teeth where they have been proposed to bind calcium and act as extracellular collagen chaperones, and because further duplications of specific SPARC members produced the small calcium-binding phosphoproteins (SCPP) family that is crucial for skeletal mineralization to occur. Both phylogeny and synteny conservation analyses reveal that, in the eumetazoan ancestor, a unique ancestral gene duplicated to give rise to SPARC and SPARCB described here for the first time. Independent losses have eliminated one of the two paralogues in cnidarians, protostomes and tetrapods. Hence, only non-tetrapod deuterostomes have conserved both genes. Remarkably, SPARC and SPARCB paralogues are still linked in the amphioxus genome. To shed light on the evolution of the SPARC family members in chordates, we performed a comprehensive analysis of their embryonic expression patterns in amphioxus, tunicates, teleosts, amphibians and mammals. Our results show that in the chordate lineage SPARC and SPARCB family members were recurrently recruited in a variety of unrelated tissues expressing collagen genes. We propose that one of the earliest steps of skeletal evolution involved the co-expression of SPARC paralogues with collagenous proteins.     

The Xenopus FcR family demonstrates continually high diversification of paired receptors in vertebrate evolution

Background  

Recent studies have revealed an unexpected diversity of domain architecture among FcR-like receptors that presumably fulfill regulatory functions in the immune system. Different species of mammals, as well as chicken and catfish have been found to possess strikingly different sets of these receptors. To better understand the evolutionary history of paired receptors, we extended the study of FcR-like genes in amphibian representatives Xenopus tropicalis and Xenopus laevis.     

Molecular evolution of the ankyrin gene family

Ankyrins are membrane adaptor molecules that play important roles in coupling integral membrane proteins to the spectrin-based cytoskeleton network. Human mutations of ankyrin genes lead to severe genetic diseases such as fatal cardiac arrhythmias and hereditary spherocytosis. To elucidate the evolutionary history of ankyrins, we have identified novel ankyrin sequences in insect, fish, frog, chicken, dog, and chimpanzee genomes and explored the phylogenetic relationships of the ankyrin gene family. Our data demonstrate that duplication of ankyrin genes occurred at two different stages. The first duplication resulted from an independent evolution event specific in Arthropoda after its divergence from Chordata. Following the separation from Urochordata, expansion of ankyrins in vertebrates involved ancestral genome duplications. We did not find evidence of coordinated arrangements of gene families of ankyrin-associated membrane proteins on paralogous chromosomes. In addition, evolution of the 24 ANK-repeats strikingly correlated with the exon boundary sites of ankyrin genes, which might have occurred before its duplication in vertebrates. Such correlation is speculated to bring functional diversity and complexity. Moreover, based on the phylogenetic analysis of the ANK-repeat domain, we put forward a novel model for the putative primordial ankyrin that contains the fourth six-ANK-repeat subdomain and the spectrin-binding domain. These findings will provide guides for future studies concerning structure, function, evolutionary origins of ankyrins, and possibly other cytoskeletal proteins.     

大鼠前列腺甾体结合蛋白基因表达的种族专一性研究

以大鼠ＰＳＢＰ基因ｃＤＮＡ为探针,用Ｎｏｒｔｈｅｒｎ印迹法测定ｍＲＮＡ,Ｓｏｕｔｈｅｒｎ印迹法测定ＤＮＡ,明确了只在大鼠腹侧前列腺表达的ＰＳＢＰ基因,在其他种族,如小鼠、兔和人的前裂腺中不仅不表达,而且基因也不存在?澄清了文献中的混乱。     

文昌鱼—研究脊柱动物起源和进化的模式动物

长久以来,文昌鱼一直被认为和生活在约5亿年前的脊椎动物的直接祖先相似。由于文昌鱼在进化上的重要性,它在动物学研究史上发挥着关键作用,近100多年来,文昌鱼作为研究对象曾数次受到动物学界青睐或冷落,大约10年前,随着分子生物学技术应用于文昌鱼研究,又激发了动物学家对文昌鱼的研究兴趣,又一次出现在文昌鱼研究的高潮,并且一直持续至今,分子生物学研究结果表明,文昌鱼样生物可能是环节动物样动物和最早的脊椎动物之间的进化中间体,因此,文昌鱼在动物学研究史上好像绕了个大圈又回到了原处,在被忽视一段时间之后,又重新占据脊椎动物起源和进化研究中心舞台的位置,成为研究脊椎动物起源和进化的模式动物。     

Genomic assessment of the evolution of the prion protein gene family in vertebrates

Prion diseases are devastating neurological disorders caused by the propagation of particles containing an alternative β?sheet-rich form of the prion protein (PrP). Genes paralogous to PrP, called Doppel and Shadoo, have been identified, that also have neuropathological relevance. To aid in the further functional characterization of PrP and its relatives, we annotated completely the PrP gene family (PrP-GF), in the genomes of 42 vertebrates, through combined strategic application of gene prediction programs and advanced remote homology detection techniques (such as HMMs, PSI-TBLASTN and pGenThreader). We have uncovered several previously undescribed paralogous genes and pseudogenes. We find that current high-quality genomic evidence indicates that the PrP relative Doppel, was likely present in the last common ancestor of present-day Tetrapoda, but was lost in the bird lineage, since its divergence from reptiles. Using the new gene annotations, we have defined the consensus of structural features that are characteristic of the PrP and Doppel structures, across diverse Tetrapoda clades. Furthermore, we describe in detail a transcribed pseudogene derived from Shadoo that is conserved across primates, and that overlaps the meiosis gene, SYCE1, thus possibly regulating its expression.In addition, we analysed the locus of PRNP/PRND for significant conservation across the genomic DNA of eleven mammals, and determined the phylogenetic penetration of non-coding exons. The genomic evidence indicates that the second PRNP non-coding exon found in even-toed ungulates and rodents, is conserved in all high-coverage genome assemblies of primates (human, chimp, orang utan and macaque), and is, at least, likely to have fallen out of use during primate speciation. Furthermore, we have demonstrated that the PRNT gene (at the PRNP human locus) is conserved across at least sixteen mammals, and evolves like a long non-coding RNA, fashioned from fragments of ancient, long, interspersed elements.These annotations and evolutionary analyses will be of further use for functional characterisation of the PrP-GF, and will be updatable in a semi-automated fashion as more genomes accumulate.     

Elimination of a tandem repeat of telomeric heterochromatin during the evolution of wheat

 An analysis of accessions of Triticum and Aegilops species (86 diploid, 91 tetraploid and 109 hexaploid) was performed using squash-dot hybridization with the tandem repeat Spelt1 sequence as a probe. The Spelt1 sequence is a highly species-specific repeat associated with the telomeric heterochromatin of Aegilops speltoides Boiss. in which its copy numbers vary from 1.5×10⁵ to 5.3×10⁵. The amounts of Spelt1 are sharply decreased in tetraploid and hexaploid species and vary widely from less than 10² to 1.2×10⁴. Two tetraploid wheats, Triticum timopheevii Zhuk. and T. carthlicum Nevski, are exceptional endemic species and within their restricted geographical distributions maintain the amounts of Spelt1 unaltered. The Spelt1 repetitive sequence was localized on the 6BL chromosome of tetraploid wheat Triticum durum Desf. cv ‘Langdon’ by dot-hybridization using D-genome disomic substitution lines. The possible causes of the loss of the telomere-associated tandem repeat Spelt1 in the process of wheat evolution and polyploidization are discussed. Received: 5 March 1998 / Accepted: 28 May 1998