The MADS and the Beauty: Genes Involved in the Development of Orchid Flowers

Since the time of Darwin, biologists have studied the origin and evolution of the Orchidaceae, one of the largest families of flowering plants. In the last two decades, the extreme diversity and specialization of floral morphology and the uncoupled rate of morphological and molecular evolution that have been observed in some orchid species have spurred interest in the study of the genes involved in flower development in this plant family. As part of the complex network of regulatory genes driving the formation of flower organs, the MADS-box represents the most studied gene family, both from functional and evolutionary perspectives. Despite the absence of a published genome for orchids, comparative genetic analyses are clarifying the functional role and the evolutionary pattern of the MADS-box genes in orchids. Various evolutionary forces act on the MADS-box genes in orchids, such as diffuse purifying selection and the relaxation of selective constraints, which sometimes reveals a heterogeneous selective pattern of the coding and non-coding regions. The emerging theory regarding the evolution of floral diversity in orchids proposes that the diversification of the orchid perianth was a consequence of duplication events and changes in the regulatory regions of the MADS-box genes, followed by sub- and neo-functionalization. This specific developmental-genetic code is termed the "orchid code."     

桃中两个MADS box基因的克隆与表达分析

为研究李属(Prunus sp．)果树生殖调控的相关基因,对国际公共数据库中的李属植物的EST(expressed sequence tags)序列进行了电子拼接,获得了8个MADS box基因的cDNA序列,并利用PCR技术从桃中克隆出其中的两个cDNA,分别命名为PpMDS4和PpMADS6,在GenBank中的登录号为AY705972和AY705973。PpMADS4基因长850bp,包含一个732bp的开放阅读框,编码243个氨基酸。PpMADS6基因长1190bp,包含1个768bp的开放阅读框,编码256个氨基酸。PpMADS4和PpMADS6在序列上分别与拟南芥中的AGAMOUS基因和矮牵牛中的PFG基因高度同源。RT-PCR分析表明,PpMADS4基因在桃的花瓣、心皮、果实及果仁中表达,应属于控制花器官发育的C类MADS box基因。PpMADS6基因在桃的叶、萼片、花瓣、心皮及果实中表达,应属于调控植物由营养生长向生殖生长过渡的A类MADSbox基因。     

Characterization and Evolution of MHC Class II B Genes in Ardeid Birds

Major histocompatibility complex (MHC) is a multi-gene family that is very suitable to investigate a wide range of open questions in evolutionary ecology. In this study, we characterized two expressed MHC class II B genes (DAB1 and DAB2) in the Grey Heron (Aves: Ardea cinerea). We further developed the primer pairs to amplify and sequence two MHC class II B loci in ten ardeid birds. Phylogenetic analysis revealed that different parts of the genes showed different evolutionary patterns. The exon 2 sequences tended to cluster two gene-specific lineages. In each lineage, exon 2 sequences from several species showed closer relationships than sequences within species, and two shared identical alleles were found between species (Egretta sacra and Nycticorax nycticorax; Egretta garzetta and Bubulcus ibis), supporting the hypothesis of trans-species polymorphism. In contrast, the species-specific intron 2 plus partial exon 3 tree suggested that DAB1 and DAB2 were subject to concerted evolution. GENECONV analyses showed the gene exchange played an important role in the ardeid MHC evolution.     

Functional Conservation of MIKC*-Type MADS Box Genes in Arabidopsis and Rice Pollen Maturation

There are two groups of MADS intervening keratin-like and C-terminal (MIKC)-type MADS box genes, MIKC^C type and MIKC* type. In seed plants, the MIKC^C type shows considerable diversity, but the MIKC* type has only two subgroups, P- and S-clade, which show conserved expression in the gametophyte. To examine the functional conservation of MIKC*-type genes, we characterized all three rice (Oryza sativa) MIKC*-type genes. All three genes are specifically expressed late in pollen development. The single knockdown or knockout lines, respectively, of the S-clade MADS62 and MADS63 did not show a mutant phenotype, but lines in which both S-clade genes were affected showed severe defects in pollen maturation and germination, as did knockdown lines of MADS68, the only P-clade gene in rice. The rice MIKC*-type proteins form strong heterodimeric complexes solely with partners from the other subclade; these complexes specifically bind to N10-type C-A-rich-G-boxes in vitro and regulate downstream gene expression by binding to N10-type promoter motifs. The rice MIKC* genes have a much lower degree of functional redundancy than the Arabidopsis thaliana MIKC* genes. Nevertheless, our data indicate that the function of heterodimeric MIKC*-type protein complexes in pollen development has been conserved since the divergence of monocots and eudicots, roughly 150 million years ago.     

Characterization,Polymorphism, and Evolution of MHC Class II B Genes in Birds of Prey

During the last decade, the major histocompatibility complex (MHC) has received much attention in the fields of evolutionary and conservation biology because of its potential implications in many biological processes. New insights into the gene structure and evolution of MHC genes can be gained through study of additional lineages of birds not yet investigated at the genomic level. In this study, we characterized MHC class II B genes in five families of birds of prey (Accipitridae, Pandionidae, Strigidae, Tytonidae, and Falconidae). Using PCR approaches, we isolated genomic MHC sequences up to 1300 bp spanning exons 1 to 3 in 26 representatives of each raptor lineage, finding no stop codons or frameshift mutations in any coding region. A survey of diversity across the entirety of exon 2 in the lesser kestrel Falco naumanni reported 26 alleles in 21 individuals. Bayesian analysis revealed 21 positively selected amino acid sites, which suggests that the MHC genes described here are functional and probably expressed. Finally, through interlocus comparisons and phylogenetic analysis, we also discuss genetic evidence for concerted and transspecies evolution in the raptor MHC.     

Possible Mechanism for Formation and Regulation of the Palmitate-Induced Cyclosporin A-Insensitive Mitochondrial Pore

The mechanism of the palmitate-induced opening of the mitochondrial Ca2+-dependent cyclosporin A (CsA)-insensitive pore was studied, as well as the influence on this process of well-known modulators of the CsA-sensitive Ca2+-dependent pore. Palmitic acid, which can bind Ca2+ with high affinity, induced the cyclosporin A-insensitive swelling of mitochondria, whereas palmitoleic and 2-bromopalmitic acids, which have no such affinity for Ca2+, failed to induce the pore opening. The palmitate-induced Ca2+-dependent swelling of mitochondria was not affected by a well-known inhibitor of the CsA-sensitive pore (ADP) and an activator of this pore (inorganic phosphate, P(i)). However, this swelling was inhibited by physiological concentrations of ATP ([I]50 = 1.3 mM), but 100 microM ATP increased by 30% the rate of mitochondria swelling if Ca2+ had been added earlier. The effects of ATP (inhibition and activation) manifested themselves from different sides of the inner mitochondrial membrane. Mg2+ inhibited the palmitate-induced Ca2+-dependent swelling of mitochondria with [I]50 = 0.8 mM. It is concluded that palmitic acid induces the opening of the CsA-insensitive pore due to its ability for complexing with Ca2+. A possible mechanism of the pore formation and the influence of some modulators on this process are discussed.     

风信子HoMADS2基因的克隆及表达分析

利用同源克隆策略,从风信子中分离出一个MADS box基因,命名为HoMADS2。序列比较分析表明,HoMADS2与B类MADS box蛋白具有较高的同源性。分子进化树分析显示,HoMADS2与PI家族类聚在一起。同时,在HoMADS2的Kbox和C末端区域均具有PI家族的特征序列。以上序列分析结果表明,HOMADS2可能是尸,的一个同源基因。RNA分子杂交结果显示,HoMADS2在四轮花器官中均表达,其表达模式不同于双子叶植物中尸,同源基因。利用风信子离体花器官再生系统研究表明,HoMADS2在再生花芽中的表达不同于HoMADS1和HAG1,该基因在再生花芽发育过程中组成型表达,不受外源细胞分裂素和生长素的影响。     

Characterization of Nodal/TGF-Lefty Signaling Pathway Gene Variants for Possible Roles in Congenital Heart Diseases

Background

Nodal/TGF-Lefty signaling pathway has important effects at early stages of differentiation of human embryonic stem cells in directing them to differentiate into different embryonic lineages. LEFTY, one of transforming growth factors in the Nodal/TGF-Lefty signaling pathway, plays an important role in the development of heart. The aim of this work was to find evidence on whether Lefty variations are associated with congenital heart diseases (CHD).

Methods

We sequenced the Lefty gene for 230 Chinese Han CHD patients and evaluated SNPs rs2295418, rs360057 and g.G169A, which are located within the translated regions of the genes. The statistical analyses were conducted using Chi-Square Tests as implemented in SPSS (version 13.0). The Hardy-Weinberg equilibrium test of the population was carried out using online software OEGE, and multiple-sequence alignments of LEFTY proteins were carried out using the Vector NTI software.

Results

Two heterozygous variants in Lefty1 gene, g.G169A and g.A1035C, and one heterozygous variant in Lefty2 gene, g.C925A, were identified. Statistical analyses showed that the rs2295418 (g.C925A) variant in Lefty2 gene was obviously associated with the risk of CHD (P value = 0.016<0.05). The genotype frequency of rs360057 (g.A1035C) variant in Lefty1 gene was associated with the risk of CHD (P value = 0.007<0.05), but the allele frequency was not (P value = 0.317>0.05).

Conclusions

The SNP rs2295418 in the Lefty2 gene is associated with CHD in Chinese Han populations.     

Characterization and Phylogenetic Relationship of Prosimian MHC Class I Genes

MHC class I cDNA sequences from the most divergent primate group of extant primates compared to human, the suborder Strepsirrhini (prosimians), are described. The sequences are derived from the gray mouse lemur (Microcebus murinus) and the ring-tailed lemur (Lemur catta), which are members of the malagasy Lemuriformes, as well as from the pygmy slow loris (Nycticebus pygmaeus), a prosimian from East Asia. The M. murinus sequences have been analyzed in detail. Analysis of the expression level, G/C content, and synonymous vs. nonsynonymous substitution rates in the peptide-binding region codons suggests that these cDNA clones represent classical class I (class Ia) genes. According to Southern blot analysis, the genome of the gray mouse lemur might contain about 10 class I genes. In gene tree analysis, the strepsirrhine class Ia genes described here cluster significantly separately from the known class I genes of Catarrhini (humans, apes, Old World monkeys) and Platyrrhini (New World monkeys) species, suggesting that the class I loci of Simiiformes arose by gene duplications which occurred after the divergence of prosimians.     

两种国兰C类花发育MADS基因的克隆与表达研究

该研究以蕙兰(Cymbidium faberi)和墨兰(Cymbidium sinense)为材料,利用RT-PCR对AGAMOUS (AG)基因进行克隆,并利用qRT-PCR进行组织表达.结果 表明:(1)获得3个AG基因均属于植物特有的C类MIKC型MADS-box基因,其中2个蕙兰AG基因命名为CfAG1(登录号...     

A Class of Genes Affecting B Factor-Regulated Development in SCHIZOPHYLLUM COMMUNE

Twelve mutations affecting nuclear migration, a major developmental phase in Schizophyllum commune, display a complex pattern of complementation and recombination. They are expressed only when a genetic factor controlling this phase of development, the B incompatibility factor, is operative. All twelve mutations are linked to the B factor, nine in a cluster and three in distinct loci outside the cluster. A linear map cannot be constructed from the frequency of recombination. Complementation maps are not linear. There is little correlation between the complementation groups and the groups based on recombination. Many pairs of mutations that do not complement recombine with frequencies of 1.1% to 26.9%. The genes represented by the twelve mutations are located in a linked group of about 18 known genes involved in the specific phase of development controlled by the B factor.