念珠藻属植物hetR基因的适应性进化分析

以念珠藻属(Nostoc)及其近缘类群hetR基因的51条序列为研究对象,对hetR基因的编码蛋白进行生物信息学分析和系统发育分析,并使用分支模型、位点模型和分支-位点模型进行该基因位点的适应性进化研究。系统发育分析结果显示,51条hetR基因蛋白序列可分为4个大分支。适应性进化分析结果表明,在3种进化模型中,大多数分支及藻株都没有检测到统计学上具有显著性的正选择位点,说明检测的位点大多处于负选择压力下。但在普通念珠藻(Nostoc commune,CHAB2802)中检测到正选择位点(126T),提示念珠藻属植物hetR基因发生了适应性改变。     

念珠藻属植物nifH基因的适应性进化分析

念珠藻(Nostoc)固氮过程关键在于固氮酶的催化,而固氮酶复合物中的铁蛋白(NifH)是由高度保守的nifH基因编码的,该基因是进化史上现存最古老的功能基因之一。该研究选取念珠藻属及近缘类群的nifH基因序列共40条,采用最大似然法构建系统发育树;运行PAML4.9软件,对nifH基因编码蛋白进行生物信息学分析,并使用分支模型、位点模型和分支-位点模型检测该基因的选择位点,探讨nifH基因的适应性进化特征。结果表明:(1)最大似然树显示内类群中该研究物种共分为6个分支(A、B、C、D、E和F),其中D和E是2个大的分支,每个大分支中又各包含2个特殊的小分支A、F和B、C,其中F分支包含新疆古尔班通古特沙漠采集到的9株念珠藻,A分支包含F分支及该研究测定序列的4株葛仙米,B分支包含本研究测定序列的4株地皮菜和3株未定种的念珠藻,C分支包含NCBI数据库中下载的5株念珠藻、鱼腥藻序列和本研究测定序列的1株念珠藻。(2)在所分析的3种进化模型中,仅通过分支-位点模型检测出14个统计学上显著的正选择位点,即1F、2S、3S、4T、5A、6F、7F、8I、9S、10C、17I、27Y、29D和31R位点,表明念珠藻属植物的nifH基因发生了适应性变化,分支-位点模型是研究藻类基因适应性进化较好的模型。     

念珠藻葛仙米藻蓝蛋白α与β亚基基因克隆、表达及其单体结构模拟

天然抗氧化剂对于清除人体内自由基、保障健康具有重要作用。藻蓝蛋白(phycocyanin, PC)是蓝藻等藻类细胞内的一类特殊色素蛋白,具捕获光能的功能。体外研究发现,藻蓝蛋白具有较显著的抗氧化、抑癌细胞增殖等生物活性。试验利用食源性的拟球状念珠藻葛仙米(Nostoc sphaeroides)的基因组DNA为材料,借助PCR扩增克隆葛仙米藻蓝蛋白两个重要亚基α与β基因,Ns-PC-α和Ns-PC-β。结果表明,葛仙米基因组中,Ns-PC-α和Ns-PC-β基因编码框长度分别为492 bp和522 bp;Ns-PC-α和Ns-PC-β基因以双顺反子形式存在,Ns-PC-α位于Ns-PC-β下游。Ns-PC-α和Ns-PC-β分别编码由163与173个氨基酸组成的蛋白。Ns-PC-α和Ns-PC-β亚基蛋白多肽链中共含有3个半胱氨酸残基(Ns-PC-α的第85位与Ns-PC-β中的第83位氨基酸残基和第154位氨基酸残基),很可能是藻蓝胆素的结合位点。原核表达显示Ns-PC-α和Ns-PC-β分子量为近18 kD,Ns-PC-α比Ns-PC-β略小,与预测结果一致。模拟其高级结构,发现Ns-PC-α和Ns-PC-β单亚基均含有7个α-螺旋,除N端α-螺旋外,其它几个α-螺旋进一步折叠形成疏水核心区;并且,Ns-PC-α和Ns-PC-β结构上能够较好吻合,形成一稳定而封闭的单体,弧度近2π/3。Ns-PC-α和Ns-PC-β组成的这种单体结构是其进一步建构圆盘状三聚体Ns-PC-(α/β) 3的重要基础。本研究结果为食源性念珠藻葛仙米藻蓝蛋白抗氧化功能的进一步应用提供了重要依据。     

发状念珠藻干旱胁迫响应基因NfGR的克隆与鉴定

该研究采用PCR技术,从发状念珠藻细胞中克隆了谷胱甘肽还原酶(glutathione reductase,GR)基因,命名为NfGR,其开放阅读框长1 374bp,编码458个氨基酸,蛋白相对分子量为49.42kD,理论等电点为5.49。氨基酸序列分析表明,NfGR蛋白具有NADPH结合位点超家族(NADB-Rossmann superfamily)和吡啶氧化还原酶二聚体超家族(Pyr_redox_dim superfamily)2个结构域,与点形念珠藻(Nostoc punctiforme)的相似性达93%。系统进化树分析表明,NfGR与点形念珠藻处在同一进化枝上,亲缘关系较近。qRT-PCR表达分析表明,在不同浓度PEG-6000处理下,NfGR基因均保持上调表达,其中,PEG-6000浓度为8%时,NfGR基因的相对表达量达到峰值(32.69)。研究推测,谷胱甘肽还原酶可能参与了发状念珠藻对干旱胁迫过程的响应。     

弯枝藻属rbcL基因的适应性进化分析

为探讨淡水红藻的叶绿体基因及其适应性进化特征,选取弯枝藻属(Compsopogon)及相近外类群的rbc L基因共17条,利用PAML 4.9软件,对弯枝藻属rbc L基因编码蛋白进行生物信息学分析,并分别采用分支模型、位点模型以及分支-位点模型对基因的选择位点进行检测。结果表明,弯枝藻属rbc L基因编码蛋白的二级结构主要由α螺旋和β折叠构成,结构稳定。采用最大似然法构建的系统发育树表明,内类群为单一物种,分为3个小分支,具有一定地理分布规律。在3种进化模型中均未检测到统计上显著的正选择位点,表明绝大多数位点处于负选择压力下。因此,弯枝藻属rbc L基因未发生适应性进化。     

发状念珠藻醛酮还原酶基因NfAKR的克隆与表达

以发状念珠藻细胞为试材,采用PCR技术克隆了醛酮还原酶基因的开放阅读框(ORF)序列,命名为NfAKR。对基因序列特征进行了生物信息学分析,根据其编码氨基酸序列预测了NfAKR蛋白的三维结构,同时探讨了PEG-6000胁迫下NfAKR的表达特性。结果表明:NfAKR基因的编码序列长912bp,编码304个氨基酸,预测其编码蛋白的相对分子量为33.51kD,理论等电点为4.94,具有醛酮还原酶超家族保守结构域。NfAKR蛋白主要由10个α-螺旋和11β-折叠组成,中间形成一个疏水穴,作为酶的催化活性中心。NfAKR与点形念珠藻处在同一进化枝上,具有较近的亲缘关系。qRT-PCR分析显示,PEG-6000胁迫下NfAKR基因上调表达,当PEG-6000浓度为8%时,其相对表达量为5.66并达到峰值。依据NfAKR基因响应干旱胁迫上调表达的特性,推测醛酮还原酶可能参与发状念珠藻抵御干旱胁迫过程。     

利用16S rRNA基因分析3种念珠藻的亲缘关系

通过基因克隆和序列测定,获得了地木耳、发菜和葛仙米的16S rRNA序列。以集胞藻为外类群,采用邻接法(NJ)和最大简约法(MP),对14株念珠藻的16S rRNA基因序列进行系统发育分析,两种方法得到的系统发育树基本一致。结果显示:(1)三者间的遗传距离(0.0129~0.0261,平均值0.0203)均大于普通念珠藻的种内遗传距离(0.0007~0.0118,平均值0.0074),超过了种内差异程度,在系统树中这3种念珠藻分别聚簇在不同的分支上;(2)地木耳、发菜和葛仙米与裂褶念珠藻等其它7种念珠藻间的遗传距离(0.0423~0.0996,平均值0.0561)大于三者间的遗传距离,在系统树中聚类较近,而与其它念珠藻聚类较远。据此,可将地木耳、发菜和葛仙米归为念珠藻属3个不同的种,并且它们的亲缘关系较近。     

雨生红球藻己糖激酶基因的克隆和生物信息学分析

本研究以雨生红球藻(Haematococcus pluvialis)为研究对象,利用同源克隆和cDNA末端快速扩增技术(RACE)相结合的方法获得了雨生红球藻己糖激酶(HaeHK)基因的cDNA全长序列,并进行了序列分析。结果表明,HaeHK的cDNA全长为2 047 bp,其中开放阅读框的长度为1 716 bp,编码571个氨基酸。该蛋白预测的等电点(pI)为6.49,理论分子量为60.61 kD。经在线BLAST同源比对分析发现,其与团藻(Volvox carteri)和莱茵衣藻(Chlamydomonas reinhardtii)来源HKs的相似性分别达到50%和46%。通过序列比对和结构域分析可知,HaeHK蛋白存在与高等植物来源HKs相似的结构域,且具有HK家族的显著特征。高级结构同源建模表明其具有典型的“蝴蝶”结构。系统进化分析显示,高等植物和真核绿藻(Chlorophyta)来源HKs可能来自共同的祖先。本文首次从雨生红球藻中获得编码HaeHK的基因序列,为雨生红球藻中HK的表达和功能研究奠定基础,同时为解析雨生红球藻己糖利用及代谢的分子机制提供线索。     

棕色棉DFR基因的克隆与生物信息学分析

花色素苷是影响花色的主要色素,二氢黄酮醇4-还原酶(DFR)基因是花色素苷生物合成途径的关键酶基因。通过同源克隆策略,以新彩棉6号(XC-6)纤维的RNA以及DNA为模板克隆得到GhDFR基因的CDS全长编码序列及带有内含子的基因组序列,并进行了生物信息学分析。序列分析结果显示,该基因含有6个外显子,5个内含子结构,其cDNA包含一个1 020 bp的开放阅读框,编码355个氨基酸,其氨基酸序列包含具有高度保守性的NADP(H)的结合位点以及底物特异性结合位点。推定的GhDFR蛋白质分子量为39.65 kD,等电点为5.67。该蛋白氨基酸序列同毛果杨、葡萄、天竺葵等物种DFR蛋白显示出较高同源性,而系统进化分析结果表明其与天竺葵、芍药DFR亲缘关系较近。氨基酸序列分析预测表明,GhDFR基因所编码的蛋白不具备信号肽区段,无明显跨膜区域,不属于分泌蛋白,可能为亲水性蛋白,定位于细胞质的可能性最高,其主要二级结构元件为α-螺旋和无规则卷曲。GhDFR属于NADB-Rossmann superfamily。     

甜荞FeFUL2基因的克隆与表达分析

为了探索甜荞FUL同源基因参与花与籽粒发育调控的分子机制,该文采用同源克隆的方法从甜荞(Fagopyrum esculentum)长花柱和长雄蕊突变体(lpls)中克隆到1个长837 bp的FeFUL2基因(GenBank登录号为MG779493.1),其包含长690 bp的完整开放阅读框,编码1个由229个氨基酸残基组成的MADS-box转录因子。通过对FeFUL2进行分子系统发生、同源蛋白比对与转录因子结构分析,结果显示FeFUL2与核心真双子叶植物AP1/FUL亚家族转录因子中的euFUL进化系聚于1个进化分支,属甜荞euFUL型MADS-box转录因子,且包含1个57个氨基酸残基长的高度保守的MADS结构域、1个69个氨基酸残基长的次级保守的K结构域,其C末端转录激活区在序列长度和氨基酸残基组成上与其他euFUL型转录因子差异较大,但仍含有2个euFUL型转录因子特有的保守基元:FUL motif和paleo AP1 motif。用qPCR检测基因表达的组织特异性显示:FeFUL2基因在甜荞lpls突变体的根、茎、叶、花被片、雄蕊、雌蕊和发育4 d的幼果中均有表达,但其在花被片中表达量极显著高于该基因在其他器官中的表达量(LSD,P0.01)。综合转录因子的结构与基因的表达模式推测,FeFUL2基因与其他euFUL型基因的功能可能存在一定差异,其在花发育过程中可能主要参与甜荞花被片的发育调控。     

Comparison of apo- and heme-bound crystal structures of a truncated human heme oxygenase-2

Heme oxygenase (HO) catalyzes the first step in the heme degradation pathway. The crystal structures of apo- and heme-bound truncated human HO-2 reveal a primarily alpha-helical architecture similar to that of human HO-1 and other known HOs. Proper orientation of heme in HO-2 is required for the regioselective oxidation of the alpha-mesocarbon. This is accomplished by interactions within the heme binding pocket, which is made up of two helices. The iron coordinating residue, His(45), resides on the proximal helix. The distal helix contains highly conserved glycine residues that allow the helix to flex and interact with the bound heme. Tyr(154), Lys(199), and Arg(203) orient the heme through direct interactions with the heme propionates. The rearrangements of side chains in heme-bound HO-2 compared with apoHO-2 further elucidate HO-2 heme interactions.     

Crystal structure of human heme oxygenase-1.

Heme oxygenase catalyzes the first step in the oxidative degradation of heme. The crystal structure of heme oxygenase-1 (HO-1) reported here reveals a novel helical fold with the heme sandwiched between two helices. The proximal helix provides a heme iron ligand, His 25. Conserved glycines in the distal helix near the oxygen binding site allow close contact between the helix backbone and heme in addition to providing flexibility for substrate binding and product release. Regioselective oxygenation of the alpha-meso heme carbon is due primarily to steric influence of the distal helix.     

Crystal structure of rat apo-heme oxygenase-1 (HO-1): mechanism of heme binding in HO-1 inferred from structural comparison of the apo and heme complex forms

Heme oxygenase (HO) catalyzes the oxidative cleavage of heme to biliverdin by utilizing O(2) and NADPH. HO (apoHO) was crystallized as twinned P3(2) with three molecules per asymmetric unit, and its crystal structure was determined at 2.55 A resolution. Structural comparison of apoHO and its complex with heme (HO-heme) showed three distinct differences. First, the A helix of the eight alpha-helices (A-H) in HO-heme, which includes the proximal ligand of heme (His25), is invisible in apoHO. In addition, the B helix, a portion of which builds the heme pocket, is shifted toward the heme pocket in apoHO. Second, Gln38 is shifted toward the position where the alpha-meso carbon of heme is located in HO-heme. Nepsilon of Gln38 is hydrogen-bonded to the carbonyl group of Glu29 located at the C-terminal side of the A helix in HO-heme, indicative that this hydrogen bond restrains the angle between the A and B helices in HO-heme. Third, the amide group of Gly143 in the F helix is directed outward from the heme pocket in apoHO, whereas it is directed toward the distal ligand of heme in HO-heme. This means that the F helix around Gly143 must change its conformation to accommodate heme binding. The apoHO structure has the characteristic that the helix on one side of the heme pocket fluctuates, whereas the rest of the structure is similar to that of HO-heme, as observed in such hemoproteins as myoglobin and cytochromes b(5) and b(562). These structural features of apoHO suggest that the orientation of the proximal helix and the position of His25 are fixed upon heme binding.     

Comparison of the heme-free and -bound crystal structures of human heme oxygenase-1

Heme oxygenase (HO) catalyzes the degradation of heme to biliverdin. The crystal structure of human HO-1 in complex with heme reveals a novel helical structure with conserved glycines in the distal helix, providing flexibility to accommodate substrate binding and product release (Schuller, D. J., Wilks, A., Ortiz de Montellano, P. R., and Poulos, T. L. (1999) Nat. Struct. Biol. 6, 860-867). To structurally understand the HO catalytic pathway in more detail, we have determined the crystal structure of human apo-HO-1 at 2.1 A and a higher resolution structure of human HO-1 in complex with heme at 1.5 A. Although the 1.5-A heme.HO-1 model confirms our initial analysis based on the 2.08-A model, the higher resolution structure has revealed important new details such as a solvent H-bonded network in the active site that may be important for catalysis. Because of the absence of the heme, the distal and proximal helices that bracket the heme plane in the holo structure move farther apart in the apo structure, thus increasing the size of the active-site pocket. Nevertheless, the relative positioning and conformation of critical catalytic residues remain unchanged in the apo structure compared with the holo structure, but an important solvent H-bonded network is missing in the apoenzyme. It thus appears that the binding of heme and a tightening of the structure around the heme stabilize the solvent H-bonded network required for proper catalysis.     

Crystal structure of heme oxygenase-1 from cyanobacterium Synechocystis sp. PCC 6803 in complex with heme.

Heme oxygenase (HO) catalyzes the oxidative degradation of heme utilizing molecular oxygen and reducing equivalents. In photosynthetic organisms, HO functions in the biosynthesis of such open-chain tetrapyrroles as phyto-chromobilin and phycobilins, which are involved in the signal transduction for light responses and light harvesting for photosynthesis, respectively. We have determined the first crystal structure of a HO-1 from a photosynthetic organism, Synechocystis sp. PCC 6803 (Syn HO-1), in complex with heme at 2.5 A resolution. Heme-Syn HO-1 shares a common folding with other heme-HOs. Although the heme pocket of heme-Syn HO-1 is, for the most part, similar to that of mammalian HO-1, they differ in such features as the flexibility of the distal helix and hydrophobicity. In addition, 2-propanol derived from the crystallization solution occupied the hydrophobic cavity, which is proposed to be a CO trapping site in rat HO-1 that suppresses product inhibition. Although Syn HO-1 and mammalian HO-1 are similar in overall structure and amino acid sequence (57% similarity vs. human HO-1), their molecular surfaces differ in charge distribution. The surfaces of the heme binding sides are both positively charged, but this patch of Syn HO-1 is narrow compared to that of mammalian HO-1. This feature is suited to the selective binding of ferredoxin, the physiological redox partner of Syn HO-1; the molecular size of ferredoxin is approximately 10 kDa whereas the size of NADPH-cytochrome P450 reductase, a reducing partner of mammalian HO-1, is approximately 77 kDa. A docking model of heme-Syn HO-1 and ferredoxin suggests indirect electron transfer from an iron-sulfur cluster in ferredoxin to the heme iron of heme-Syn HO-1.     

利用序列比较寻找胰岛素基因表达启动区与DNA结合蛋白的结合位点

NDFl、IPFl和HNF4是与胰岛素基因表达有关的DNA结合蛋白,通过比较SWISSPROT蛋白质数据库中人类、小鼠、大鼠这三种核蛋白氨基酸一级序列、模体和结构域,发现其结构十分相似,根据蛋白质结构和功能的关系,推测这些DNA结合蛋白与胰岛素基因结合的核苷酸序列相似;从GenBanl(核酸数据库中获得人类、小鼠、大鼠胰岛素DNA序列,用ClustalW比较三者Promoter区的核苷酸序列,显示有一段核苷酸序列较为相似,同时搜索TRANSFAC基因转录数据库中NDFl、IPFl和NHF4蛋白核苷酸结合位点,发现核酸比对保守的部分序列与TRANSFAC数据库中这三个转录因子的DNA结合位点一致,另外一些核酸保守序列可能为其他未知DNA结合蛋白的结合位点。这种核酸序列比对设计为分子生物学实验寻找和验证胰岛素DNA结合蛋白与核苷酸的结合位点提供了简单而实用的方法。     

Expression of heme oxygenase and its RNA in mouse liver after injection of heme and splenectomy.

Heme is known to activate the HO (heme oxygenase) gene in cultured cells, but little is known about the effect of heme on the HO gene in intact organisms. The expressions of HO and its RNA in mouse liver were measured using mouse HO cDNA and HO antibody after injection of heme or splenectomy. The antibody was prepared against a beta-galactosidase-HO hybrid protein made in Escherichia coli. The HO mRNA level increased to a maximum 15 h after heme injection. In contrast, expression of HO was maximal about 45 h after heme injection. Essentially the same results were obtained in mice after splenectomy. These results suggest that the HO gene in mouse liver was activated by the injection of heme and splenectomy.