Structurally engineered cytochromes c with novel ligand-binding properties

Semisynthesis of horse heart cytochrome c and site-directed mutagenesis of Saccharomyces cerevisiae (S. c.) iso-1-cytochrome c have been utilized to substitute Ala for the cytochrome c heme axial ligand Met80 to yield ligand-binding proteins (horse heart Ala80cyt c and S.c. Ala80cyt c) with spectroscopic properties remarkably similar to those of myoglobin. Both species of Fe(II)Ala80cyt c form exceptionally stable dioxygen complexes with autoxidation rates 10-30x smaller and O₂ binding constants ~ 3x greater than those of myoglobin. The resistance of O₂-Fe(II)Ala80cyt c to autoxidation is attributed in part to protection of the heme site from solvent as exhibited by the exceptionally slow rate of CO binding to the heme as well as the low quantum yield of CO photodissociation.

UV/vis, EPR, and paramagnetic NMR spectroscopy indicate that at pH 7 the Fe(III)Ala80cyt c heme is low-spin with axial His-OH^- coordination and that below pH ~6.5, Fe(III)Ala80cyt cis high-spin with His-H₂O heme ligation. Significant differences in the pH dependence of the ¹H NMR spectra of S.c. Fe(III)Ala80cyt c compared to wild-type demonstrate that the axial ligands influence the conformational energetics of cytochrome c.

¹H NMR spectroscopy has been utilized to determine the solution structure of the cyanide derivative of S.c. Fe(III)Ala80cyt c. 82% of the resonances in the ¹H NMR spectrum of S.c. CN-Fe(III)Ala80cyt c have been assigned through 1D and 2D experiments. The RMSD values after restrained energy minimization of the family of 17 structures obtained from distance geometry calculations are 0.68 ± 0.11 Å for the backbone and 1.32 ± 0.14 Å for all heavy atoms. The solution structure indicates that a tyrosine in the "distal" pocket of CN-Fe(III)Ala80cyt c forms a hydrogen bond with the Fe(III)-CN unit, suggesting that it may play a role analogous to that of the distal histidine in myoglobin in stabilizing the dioxygen adduct.

Developmentally regulated transcription factors in Drosophila melanogaster

During early stages of Drosophila development the heat shock response cannot be induced. It is reasoned that the adverse effects on cell cycle and cell growth brought about by Hsp70 induction must outweigh the beneficial aspects of Hsp70 induction in the early embryo. Although the Drosophila heat shock transcription factor (dHSF) is abundant in the early embryo, it does not enter the nucleus in response to heat shock. In older embryos and in cultured cells the factor is localized within the nucleus in an apparent trimeric structure that binds DNA with high affinity. The domain responsible for nuclear localization upon stress resides between residues 390 and 420 of the dHSF. Using that domain as bait in a yeast two-hybrid system we now report the identification and cloning of a nuclear transport protein Drosophila karyopherin-α3(dKap- α3). Biochemical methods demonstrate that the dKap-α3 protein binds specifically to the dHSF's nuclear localization sequence (NLS). Furthermore, the dKap-α3 protein does not associate with NLSs that contain point mutations which are not transported in vivo. Nuclear docking studies also demonstrate specific nuclear targeting of the NLS substrate by dKap-α3.Consistant with previous studies demonstrating that early Drosophila embryos are refractory to heat shock as a result of dHSF nuclear exclusion, we demonstrate that the early embryo is deficient in dKap-α3 protein through cycle 12. From cycle 13 onward the transport factor is present and the dHSF is localized within the nucleus thus allowing the embryo to respond to heat shock.

The pair-rule gene fushi tarazu (ftz) is a well-studied zygotic segmentation gene that is necessary for the development of the even-numbered parasegments in Drosophila melanogastor. During early embryogenesis, ftz is expressed in a characteristic pattern of seven stripes, one in each of the even-numbered parasegments. With a view to understand how ftz is transcriptionally regulated, cDNAs that encode transcription factors that bind to the zebra element of the ftz promoter have been cloned. Chapter Ill reports the cloning and characterization of the eDNA encoding zeb-1 (zebra element binding protein), a novel steroid receptor-like molecule that specifically binds to a key regulatory element of the ftz promoter. In transient transfection assays employing Drosophila tissue culture cells, it has been shown that zeb-1 as well as a truncated zeb-1 polypeptide (zeb480) that lacks the putative ligand binding domain function as sequencespecific trans-activators of the ftz gene.

The Oct factors are members of the POU family of transcription factors that are shown to play important roles during development in mammals. Chapter IV reports the eDNA cloning and expression of a Drosophila Oct transcription factor. Whole mount in-situ hybridization experiments revealed that the spatial expression patterns of this gene during embryonic development have not yet been observed for any other gene. In early embryogenesis, its transcripts are transiently expressed as a wide uniform band from 20-40% of the egg length, very similar to that of gap genes. This pattern progressively resolves into a series of narrower stripes followed by expression in fourteen stripes. Subsequently, transcripts from this gene are expressed in the central nervous system and the brain. When expressed in the yeast Saccharomyces cerevisiae, this Drosophila factor functions as a strong, octamer-dependent activator of transcription. The data strongly suggest possible functions for the Oct factor in pattern formation in Drosophila that might transcend the boundaries of genetically defined segmentation genes.

稀土元素生物效应的蛋白质组学研究

蛋白质组学是研究细胞内全部蛋白的动态表达及其相互关系的新兴学科，是功能基因组学研究的重要组成部分和战略制高点，广泛应用于生命科学的各个领域，研究对象涵盖微生物、动物和植物等。 　　稀土元素（rare earth elements），亦称镧系元素（lanthanides），是性质相似的15种金属元素。随着稀土元素在工业、农牧业和医疗等领域的应用日益深入，它们对生物体的作用机制亟待研究。生物固氮作用为生命世界提供75%的绿色氮源，根瘤菌是重要的固氮微生物，具有基因组结构简单、培养周期短等特点。酿酒酵母是与人类关系最密切的一种酵母，不仅因为传统上其用于制作食品及酿酒，而且是现代分子生物学和细胞生物学中的真核模式生物。为了全面地了解稀土元素对细胞的作用，我们运用高分辨率的蛋白质双向电泳分离技术和高通量的蛋白质质谱分析手段以及生物信息学等方法，分析了稀土元素钆（Gadolinium，Gd）在原核生物费氏中华根瘤菌（Sinorhizobium fredii）USDA205和真核生物酿酒酵母（Saccharomyces cerevisiae）YM4271的生物效应。 　　结果表明，经1mM Gd(NO3)3处理12小时后，费氏中华根瘤菌USDA205中 22个蛋白质表达有差异。这些蛋白质可根据功能分为8类，包括转运蛋白、胁迫相关蛋白、代谢相关蛋白等。其中13个蛋白质表达量增加，9个蛋白质表达量下降。膜蛋白在差异蛋白中占有很大比重。另外，我们分析了不同浓度的钆处理后蛋白质表达的变化情况，发现蛋白质组的变化是与处理浓度密切相关的。研究中还发现同种浓度的钆与另一种稀土元素铒（Erbium，Er）相比，离子半径较小的铒离子对根瘤菌的抑制作用更加明显。 　　比较不同浓度的钆对酿酒酵母YM4271的影响，发现酵母对稀土元素的反应不及根瘤菌敏感，对数生长初期的酵母经钆处理12小时或24小时后均无显著变化。 　　本研究首次用蛋白质组学的方法研究稀土元素对微生物的作用，鉴定了一些有价值的蛋白质，并得到了它们的表达特点和相关数据，为更好地理解稀土元素的生物效应提供了有力的分子生物学证据。 　　

植物分子伴侣热休克蛋白90（Hsp90）的分子作用机理及抗逆基因工程研究

热激蛋白90是广泛存在于各类细菌和真核生物中的一类高度保守的分子伴侣，它对维持细胞生命是绝对必需的。对Hsp90的相关认知主要来源于对动物和酵母细胞的研究，植物Hsp90的研究甚少。由于植物的特殊性，因此对植物Hsp90的研究是对Hsp90未知功能的有力补充。拟南芥中有7个Hsp90蛋白，其中AtHsp90-1、AtHsp90-2、AtHsp90-3和AtHsp90-4定位在细胞质中，AtHsp90-5、AtHsp90-6和AtHsp90-7分别定位在叶绿体、线粒体和内质网中。本文对拟南芥中的AtHsp90-1、AtHsp90-2、AtHsp90-5、AtHsp90-6和AtHsp90-7五个基因进行了克隆，并分别利用酵母互补、双杂交和拟南芥过表达体系几个层面进行了功能分析。 我们利用酵母穿梭载体p416GPD构建了五个AtHsp90基因的酵母表达载体，将其转入Hsp90基因点突变和条件型缺失的酵母菌株iG170D和R0005中。酵母功能互补实验表明细胞质定位的AtHsp90-1和AtHsp90-2可以在各种胁迫条件下互补酵母Hsp90的功能，而定位于细胞器中的AtHsp90-5、 AtHsp90-6和AtHsp90- 7则在任何条件下都不能互补酵母Hsp90的功能。我们还对转基因酵母进行了液体培养的动态观测和细胞膜完整性检测，其结果和固体培养的结果一致。这说明细胞质Hsp90的功能具有一定的保守性，细胞器Hsp90的功能有其特殊性。 热激蛋白90在执行其生物功能时，需要和大量的辅助因子相互作用，因此我们利用酵母双杂交体系检测了AtHsp90-1、AtHsp90-2、AtHsp90-5、AtHsp90-6和AtHsp90-7五个Hsp90蛋白和Hsp70、p23、Cyp40、NOS等几个辅助因子之间的相互作用情况。双杂交结果显示AtHsp90-1和AtHsp90-2几乎不和所选的这几个辅助因子相互作用，AtHsp90-5可以和所有的辅助因子相互作用、AtHsp90-6可以和除Hsp70以外的辅助因子相互作用，AtHsp90-7也可以和所有的辅助因子相互作用但和Hsp70及Hsp70t-2和互作较其他辅助因子弱一些。可以看出胞质Hsp90和细胞器Hsp90在和辅助因子相互作用时有一定的差异。 为了进一步了解拟南芥个Hsp90基因在抗非生物逆境中的作用，我们又将AtHsp90-2、AtHsp90-5、AtHsp90-7基因插入植物表达载体pBI121，用农杆菌介导的浸蕾法将这三个基因转入拟南芥并在其中过量表达，并研究了这些基因的过表达植株的种子和幼苗对多种模拟非生物逆境的响应。结果显示，转基因种子和幼苗对ABA、盐(NaCl)、干旱(甘露醇)、高温、氧化、高钙等非生物逆境都表现出了敏感，转细胞器Hsp90的种子和幼苗比转细胞质Hsp90的更为敏感。但在高浓度钙离子胁迫下，幼苗表现情况与盐、旱和氧化等非生物逆境处理下的情况正好相反，转细胞器Hsp90的幼苗比转细胞质Hsp90的长得健壮。这些结果表明Hsp90参与了植物抵抗非生物逆境的反应，其作用可能是通过ABA和Ca2+途径实现的，然而体内Hsp90的动态平衡可能才是植物抵抗非生物逆境的关键。

FY is an RNA 3' end-processing factor that interacts with FCA to control the Arabidopsis floral transition

The nuclear RNA binding protein, FCA, promotes Arabidopsis reproductive development. FCA contains a WW protein interaction domain that is essential for FCA function. We have identified FY as a protein partner for this domain. FY belongs to a highly conserved group of eukaryotic proteins represented in Saccharomyces cerevisiae by the RNA 3' end-processing factor, Pfs2p. FY regulates RNA 3' end processing in Arabidopsis as evidenced through its role in FCA regulation. FCA expression is autoregulated through the use of different polyadenylation sites within the FCA pre-mRNA, and the FCA/FY interaction is required for efficient selection of the promoter-proximal polyadenylation site. The FCA/FY interaction is also required for the downregulation of the floral repressor FLC. We propose that FCA controls 3' end formation of specific transcripts and that in higher eukaryotes, proteins homologous to FY may have evolved as sites of association for regulators of RNA 3' end processing.

A de novo originated gene depresses budding yeast mating pathway and is repressed by the protein encoded by its antisense strand

Recent transcription profiling studies have revealed an unexpectedly large proportion of antisense transcripts in eukaryotic genomes. These antisense genes seem to regulate gene expression by interacting with sense genes. Previous studies have focused on the non-coding antisense genes, but the possible regulatory role of the antisense protein is poorly understood. In this study, we found that a protein encoded by the antisense gene ADF1 acts as a transcription suppressor, regulating the expression of sense gene MDF1 in Saccharomyces cerevisiae. Based on the evolutionary, genetic, cytological and biochemical evidence, we show that the protein-coding sense gene MDF1 most likely originated de novo from a previously non-coding sequence and can significantly suppress the mating efficiency of baker's yeast in rich medium by binding MAT alpha 2 and thus promote vegetative growth. These results shed new light on several important issues, including a new sense-antisense interaction mechanism, the de novo origination of a functional gene, and the regulation of yeast mating pathway.

A comparative study on effects of Immunoster and Immunowall as immunostimulants on some hematological, biochemical and growth indices of farmed great sturgeon juveniles (Huso huso)

Prebiotics are non-digestible food ingredients that profitably affect the host by selectively stimulating the growth and /or activation of one or a limited number of bacteria in the intestine that can enhance host health status. Immunoster (IS) and Immunowall (IW) are prebiotics and immunostimulants derived from the outer cell wall of brewers yeast, Saccharomyces cerevisiae. These substances contain MOS and �-glucans. After a four-week acclimatization period to rearing conditions and basal diet, 450 farmed great sturgeon juveniles weighing 95.58 ± 9.38 g were randomly distributed into 15 fiberglass tanks (2 × 2 × 0.53 m) in five treatments (Control, IS 1%, IW 1%, IS 3%, and IW 3%) in three replicates (completely randomized design) and kept at a density of 30 fish per tank for a period of 8 weeks at water temperature 20.55 ± 5.11ºC, dissolved oxygen 6.73 ± 0.35 mg L-1 and pH 7.92 ± 0.09. IS and IW were added at two levels of 1% and 3% to the basal diet in place of cellulose, except the control. At the beginning, in the middle and at the end of the trial, carcass analysis was done to determine the moisture, protein, fat, ash, and total carbohydrate. Also, blood samples were collected to measure hematological, biochemical and immune indices. At the end of the trial, final weight, final length, body weight increase (BWI), specific growth rate (SGR), average daily growth (ADG), protein efficiency ratio (PER), feed conversion ratio (FCR), and condition factor (CF) in fish fed on IS and IW in both levels 1% and 3% showed some differences. These differences were significant in IS 3% and IW 1% and 3% compared with the control (P<0.05). HSI showed no significant difference (P>0.05) and survival rate was 100% in all treatments. Crude protein of carcass in fish fed on IS and IW at 1% and 3% showed an increase in comparison with the control. There was significant difference between IS 3% and the control in crude protein of carcass (P<0.05). Fish fed on IS and IW at 1% and 3% showed various results in hematological and biochemical factors. It was observed significant difference in MCV between IW 1% and IS 3% compared with the control (P<0.05). Although there was an increase in values of hematocrit, hemoglobin (except IS 1%), WBC (except IW 3%), MCH, neutrophil, total protein, albumin (except IS 3%), K+, and lysozyme in fish fed on IS and IW compared with the control, it was no significant (P>0.05). The maximum count of WBC and the highest value of Ca2+ were seen in IW 1%. The maximum count of lymphocyte, the highest values of total protein, albumin and IgM were recorded in IW 3%. IS 1% had the maximum count of neutrophil and the highest concentration of lysozyme. Based on obtained results, it can be declared that IS and IW at two levels of 1% and 3% can enhance growth performance and feed efficiency and also improve some hematological, biochemical, and immune indices in farmed great sturgeon juveniles.

Statistical analysis of sequence features of introns with positive transcriptional regulation in yeast genes

A great deal of experimental studies have shown that many introns of eukaryotic genes function as regulators of transcription. However, comprehensive studies of this problem have not yet been conducted. After checking the transcription frequencies of some Saccharomyces cerevisiae (yeast), genes and their introns, a remarkable phenomenon was discovered that generally the introns of the genes with higher transcription frequencies are longer, and the introns of the genes with lower transcription frequencies are shorter. This suggests that the longer introns of genes with higher transcription frequencies may contain some characteristic sequence structures, which could enhance the transcription of genes. Therefore, two sets of introns of yeast genes were chosen for further study. The transcription frequencies of the first set of genes are higher (>30), and those of the second set of genes are lower (less than or equal to10). Some oligonucleotides are detected by statistically comparative analyses of the occurrence frequencies of oligonucleotides (mainly tetranucleotides and pentanucleotides), whose occurrence frequencies in the first set of introns; are significantly higher than those in the second set of introns, and are also significantly higher than those in the exons flanking the introns of the first set. Some of these extracted oligonucleotides are the same as the regulatory elements of transcription revealed by experimental analyses. Besides, the distributions of these extracted oligonucleotides in the two sets of introns and the exons show that the sequence structures of the first set of introns are favorable for transcription of genes.

Bayesian correlated clustering to integrate multiple datasets.

MOTIVATION: The integration of multiple datasets remains a key challenge in systems biology and genomic medicine. Modern high-throughput technologies generate a broad array of different data types, providing distinct-but often complementary-information. We present a Bayesian method for the unsupervised integrative modelling of multiple datasets, which we refer to as MDI (Multiple Dataset Integration). MDI can integrate information from a wide range of different datasets and data types simultaneously (including the ability to model time series data explicitly using Gaussian processes). Each dataset is modelled using a Dirichlet-multinomial allocation (DMA) mixture model, with dependencies between these models captured through parameters that describe the agreement among the datasets. RESULTS: Using a set of six artificially constructed time series datasets, we show that MDI is able to integrate a significant number of datasets simultaneously, and that it successfully captures the underlying structural similarity between the datasets. We also analyse a variety of real Saccharomyces cerevisiae datasets. In the two-dataset case, we show that MDI's performance is comparable with the present state-of-the-art. We then move beyond the capabilities of current approaches and integrate gene expression, chromatin immunoprecipitation-chip and protein-protein interaction data, to identify a set of protein complexes for which genes are co-regulated during the cell cycle. Comparisons to other unsupervised data integration techniques-as well as to non-integrative approaches-demonstrate that MDI is competitive, while also providing information that would be difficult or impossible to extract using other methods.

Influence of specific HSP70 domains on fibril formation of the yeast prion protein Ure2.

Ure2p is the protein determinant of the Saccharomyces cerevisiae prion state [URE3]. Constitutive overexpression of the HSP70 family member SSA1 cures cells of [URE3]. Here, we show that Ssa1p increases the lag time of Ure2p fibril formation in vitro in the presence or absence of nucleotide. The presence of the HSP40 co-chaperone Ydj1p has an additive effect on the inhibition of Ure2p fibril formation, whereas the Ydj1p H34Q mutant shows reduced inhibition alone and in combination with Ssa1p. In order to investigate the structural basis of these effects, we constructed and tested an Ssa1p mutant lacking the ATPase domain, as well as a series of C-terminal truncation mutants. The results indicate that Ssa1p can bind to Ure2p and delay fibril formation even in the absence of the ATPase domain, but interaction of Ure2p with the substrate-binding domain is strongly influenced by the C-terminal lid region. Dynamic light scattering, quartz crystal microbalance assays, pull-down assays and kinetic analysis indicate that Ssa1p interacts with both native Ure2p and fibril seeds, and reduces the rate of Ure2p fibril elongation in a concentration-dependent manner. These results provide new insights into the structural and mechanistic basis for inhibition of Ure2p fibril formation by Ssa1p and Ydj1p.

Influence of specific HSP70 domains on fibril formation of the yeast prion protein Ure2.

Ure2p is the protein determinant of the Saccharomyces cerevisiae prion state [URE3]. Constitutive overexpression of the HSP70 family member SSA1 cures cells of [URE3]. Here, we show that Ssa1p increases the lag time of Ure2p fibril formation in vitro in the presence or absence of nucleotide. The presence of the HSP40 co-chaperone Ydj1p has an additive effect on the inhibition of Ure2p fibril formation, whereas the Ydj1p H34Q mutant shows reduced inhibition alone and in combination with Ssa1p. In order to investigate the structural basis of these effects, we constructed and tested an Ssa1p mutant lacking the ATPase domain, as well as a series of C-terminal truncation mutants. The results indicate that Ssa1p can bind to Ure2p and delay fibril formation even in the absence of the ATPase domain, but interaction of Ure2p with the substrate-binding domain is strongly influenced by the C-terminal lid region. Dynamic light scattering, quartz crystal microbalance assays, pull-down assays and kinetic analysis indicate that Ssa1p interacts with both native Ure2p and fibril seeds, and reduces the rate of Ure2p fibril elongation in a concentration-dependent manner. These results provide new insights into the structural and mechanistic basis for inhibition of Ure2p fibril formation by Ssa1p and Ydj1p.

Cell surface display of functionally active lipases from Yarrowia lipolytica in Pichia pastoris

The lipase genes of Yarrowia lipolytica, LIPY7 and LIPY8, fused with FLO-flocculation domain sequence from Saccharomyces cerevisiae at their N-termini, were expressed in Pichia pastoris KM71. Following the induction with methanol, the recombinant proteins were displayed on the cell surface of P. pastoris, as confirmed by the confocal laser scanning microscopy. The LipY7p and LipY8p were anchored on P. pastoris via the flocculation functional domain of Flo 1 p. The surface-displayed lipases were characterized for their application as the whole-cell biocatalyst. These lipases can also be cleaved off from their anchor by enterokinase treatment to yield functionally active proteins in the supernatant offering an alternative purification method for LipY7p and LipY8p. (c) 2007 Elsevier Inc. All rights reserved.

酵母基因组进化中一些重要新性状的产生及其效应

本论文用生物信息学的方法对酵母基因组进化中产生的新性状进行了系统 深入的研究。首先，在大多数的真核生物中，线粒体是生物能量生成所必需的细 胞器。但当葡萄糖的含量丰富的时候，即使是在有氧条件下，经过基因组重复 （WGD，whole genome duplication）后的大多酵母也都可以不需要线粒体而执行 发酵过程，而且甚至在线粒体基因组缺陷的情况下仍可以生存。在本次研究中， 我们揭示核编码的线粒体相关基因的进化速率在基因组重复后的物种中比其在 基因组重复前的物种中显著加快。而且这些基因的密码子使用偏好也在基因组重 复后的物种中减弱。密码子使用偏好的模式和一个特殊转录调控因子的分布显示 在基因组重复后的进化支系中，有效的有氧发酵过程的起源时间大致是在 Kluyveromyces polysporus 和 Saccharomyces castellii 从它们的共同祖先分化之 后。根据上述结果我们得出结论，可能正是这种新的能量策略的产生导致了线粒 体相关基因的功能在基因组重复后的物种中选择性放松。 其次，我们系统地研究了一个多细胞真菌Ashbya gossypii 和九个单细胞酵母 之间密码子使用偏好性的差异。细胞周期调控基因一直被认为是它们形态差异的 关键基因。由于A. gossypii 和典型的单细胞酵母Saccharomyces cerevisiae 有几乎 完全一样的细胞周期调控基因，因此形态上的差异可能是由于直系同源基因的表 达调控差异造成的。我们发现在A. gossypii 中细胞周期基因的翻译效率比在其他 单细胞酵母中显著增高，同时也发现单细胞酵母中的新陈代谢基因比其在A. gossypii 中有显著增高的翻译效率。因为基因的翻译效率和该基因在物种中的重 要性密切相关，所以我们观察到的这些基因翻译效率的显著差异可能可以阐明 A. gossypii 和单细胞酵母的形态差异的原因。同时我们的结果对理解真核生物多 细胞的起源过程也有提示意义。

从头起源的酵母新基因的功能和正反链编码的基因相互作用的新机制的研究

基因从头起源一直被传统观念认为是近乎不可能的事件。虽然近年来有一些 基因起源于非编码序列的实例的报道，但所有这些从头起源的基因都没有确凿的 编码蛋白的能力的证据。在本工作的前半部分，我们在酿酒酵母Saccharomyces cerevisiae 中发现了一个从头起源的蛋白编码基因MDF1。通过全面的遗传学、 细胞生物学和分子生物学等研究手段，我们细致地揭示了MDF1 在酿酒酵母中 获得的新功能。在营养充足的情况下，MDF1 编码的蛋白质Mdf1p 通过与一个 S. cerevisiae 交配型决定因子MATα2 结合抑制了酿酒酵母交配通路，从而极大程 度上抑制了S. cerevisiae 的交配行为，使S. cerevisiae 节省下更多的能量用于快速 的无性繁殖。我们的工作首次为从头起源的基因提供了确凿的蛋白编码能力的证 据，而且证明年轻的新基因也可以像保守的老基因一样在一些基本的生命过程发 挥关键的作用，为提高物种的适应性作出重要贡献。同时我们的工作在机制上阐 明一个新进化出的基因如何被一个已有的信号通路募集，这为更深刻理解信号通 路的进化提供了有益参考。 在本工作的后半部分，我们发现了一种新的正反链编码的基因对相互作用的 分子机制。最近全基因组转录谱的研究提示：在很多真核生物的基因组中，很大 一部分双链DNA 链都有编码能力，这些分别由正反两条链编码的基因之间可能 存在的相互作用已被公认为一种基因调控的重要方式。现在已知的正反链基因相 互作用的分子机制包括RNAi, 转录干扰，RNA-诱导的组蛋白去乙酰化，RNA 编辑等，所有这些反链基因对正链基因的调控机制都依赖于非编码的反链RNA 的存在，但编码蛋白的反链基因能否对正链基因行使调节功能还是未知。在本工 作中，我们发现编码新基因MDF1 的同一座位的反链基因可以编码一个保守的 基因ADF1, 而且MDF1 和ADF1 对酿酒酵母生长产生相反的影响（MDF1 可以 促进生长，但ADF1 抑制生长）提示MDF1 和ADF1 之间存在相互作用。对这种 相互作用的分子机制的深入研究揭示ADF1 编码的蛋白Adf1p 以转录抑制因子的 方式结合在MDF1 的启动子区，从而抑制MDF1 的转录。这种相互作用需要反 链编码的蛋白而不是RNA 参与，所以不同于任何一种已知的正反链相互作用机 制。我们还进一步发掘出这种抑制效应在S. cerevisiae 中起作用的生理条件。当 营养丰富时，Mdf1p 抑制性地结合非发酵碳源代谢的控制因子Snf1p, 从而促进可发酵碳源被快速利用，使S. cerevisiae 获得最快的生长速度。当营养减少时， Adf1p 抑制MDF1 表达，从而促进非发酵碳源的利用。我们前后两部分的工作还 为生殖代价提供了一种机制上的解释。有性生殖和无性繁殖是两种负相关的过 程，有性生殖总会以生长速度减慢为代价，但至今没有一种分子机制能把这两个 拮抗的过程联系起来。Mdf1p 同时处在有性生殖和无性繁殖两条信号通路中，抑 制交配行为而加速生长，所以Mdf1p 实现了两条信号通路之间的对话。

Global transposable characteristics in the complete DNA sequence of the yeast

Global transposable characteristics in the complete DNA sequence of the Saccharomyces cevevisiae yeast is determined by using the metric representation and recurrence plot methods. On the basis of the correlation distance of nucleotide strings, 16 chromosome sequences of the yeast, which are divided into 5 groups, display 4 kinds of the fundamental transposable characteristics: a short increasing period, a long increasing quasi-period, a long major value and hardly relevant.