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1.
《兽类学报》2020,(1)
鲸类是一类次生性的水生哺乳动物,其陆生祖先大约53-56Ma从陆地返回海洋。为了适应水下的弱光环境,鲸类的光感受器以视杆细胞为主,视锥细胞功能大多退化,缺乏辨别颜色的能力,然而鲸类视觉退化的分子机制尚不清楚。本文选择在视锥细胞中表达且对光传导级联反应起重要作用的GNAT2和CNGB3基因,通过PCR扩增、测序以及在数据库中下载已有的基因序列,共获得8个鲸类代表性物种的同源序列。MEGA6.0软件比对发现侏儒抹香鲸和抹香鲸的GNAT2基因分别在148位和1012位插入了1个碱基 A,而抹香鲸的CNGB3分别在554位和1407位有1个碱基的缺失,导致提前终止密码子出现;另外,小须鲸CNGB3基因在1525-1527位出现了提前终止密码子,提示鲸类的这两个基因可能为假基因。通过I-TASSER在线预测GNAT2和CNGB3蛋白的三维结构,发现出现移码突变终止密码子的位置均位于这两个基因的重要功能域。另外,运用PAML软件的Branch model分析表明发生假基因的鲸类物种GNAT2和CNGB3基因出现选择压力放松,且假基因化可能是一个近期事件。侏儒抹香鲸、抹香鲸以及小须鲸的GNAT2和CNGB3基因出现假基因可能与其深潜习性以及完全的水生生境导致其色觉功能丢失相关。此外,Free-ratio model分析发现其他鲸类的ω值接近于1,说明GNAT2和CNGB3基因出现了选择压力放松,这可能是长期适应水生生境视觉退化的结果。 相似文献
2.
《兽类学报》2021,(1)
鲸类是一类次生性的水生哺乳动物,其陆生祖先大约53-56Ma从陆地返回海洋。为了适应水下的弱光环境,鲸类的光感受器以视杆细胞为主,视锥细胞功能大多退化,缺乏辨别颜色的能力,然而鲸类视觉退化的分子机制尚不清楚。本文选择在视锥细胞中表达且对光传导级联反应起重要作用的GNAT2和CNGB3基因,通过PCR扩增、测序以及在数据库中下载已有的基因序列,共获得8个鲸类代表性物种的同源序列。MEGA6.0软件比对发现侏儒抹香鲸和抹香鲸的GNAT2基因分别在148位和1012位插入了1个碱基 A,而抹香鲸的CNGB3分别在554位和1407位有1个碱基的缺失,导致提前终止密码子出现;另外,小须鲸CNGB3基因在1525-1527位出现了提前终止密码子,提示鲸类的这两个基因可能为假基因。通过I-TASSER在线预测GNAT2和CNGB3蛋白的三维结构,发现出现移码突变终止密码子的位置均位于这两个基因的重要功能域。另外,运用PAML软件的Branch model分析表明发生假基因的鲸类物种GNAT2和CNGB3基因出现选择压力放松,且假基因化可能是一个近期事件。侏儒抹香鲸、抹香鲸以及小须鲸的GNAT2和CNGB3基因出现假基因可能与其深潜习性以及完全的水生生境导致其色觉功能丢失相关。此外,Free-ratio model分析发现其他鲸类的ω值接近于1,说明GNAT2和CNGB3基因出现了选择压力放松,这可能是长期适应水生生境视觉退化的结果。 相似文献
3.
鲸类是一类次生性的水生哺乳动物,其陆生祖先大约53-56Ma从陆地返回海洋。为了适应水下的弱光环境,鲸类的光感受器以视杆细胞为主,视锥细胞功能大多退化,缺乏辨别颜色的能力,然而鲸类视觉退化的分子机制尚不清楚。本文选择在视锥细胞中表达且对光传导级联反应起重要作用的GNAT2和CNGB3基因,通过PCR扩增、测序以及在数据库中下载已有的基因序列,共获得8个鲸类代表性物种的同源序列。MEGA6.0软件比对发现侏儒抹香鲸和抹香鲸的GNAT2基因分别在148位和1012位插入了1个碱基 A,而抹香鲸的CNGB3分别在554位和1407位有1个碱基的缺失,导致提前终止密码子出现;另外,小须鲸CNGB3基因在1525-1527位出现了提前终止密码子,提示鲸类的这两个基因可能为假基因。通过I-TASSER在线预测GNAT2和CNGB3蛋白的三维结构,发现出现移码突变终止密码子的位置均位于这两个基因的重要功能域。另外,运用PAML软件的Branch model分析表明发生假基因的鲸类物种GNAT2和CNGB3基因出现选择压力放松,且假基因化可能是一个近期事件。侏儒抹香鲸、抹香鲸以及小须鲸的GNAT2和CNGB3基因出现假基因可能与其深潜习性以及完全的水生生境导致其色觉功能丢失相关。此外,Free-ratio model分析发现其他鲸类的ω值接近于1,说明GNAT2和CNGB3基因出现了选择压力放松,这可能是长期适应水生生境视觉退化的结果。 相似文献
4.
鲸类是一类次生性的水生哺乳动物,其陆生祖先大约53-56Ma从陆地返回海洋。为了适应水下的弱光环境,鲸类的光感受器以视杆细胞为主,视锥细胞功能大多退化,缺乏辨别颜色的能力,然而鲸类视觉退化的分子机制尚不清楚。本文选择在视锥细胞中表达且对光传导级联反应起重要作用的GNAT2和CNGB3基因,通过PCR扩增、测序以及在数据库中下载已有的基因序列,共获得8个鲸类代表性物种的同源序列。MEGA6.0软件比对发现侏儒抹香鲸和抹香鲸的GNAT2基因分别在148位和1012位插入了1个碱基 A,而抹香鲸的CNGB3分别在554位和1407位有1个碱基的缺失,导致提前终止密码子出现;另外,小须鲸CNGB3基因在1525-1527位出现了提前终止密码子,提示鲸类的这两个基因可能为假基因。通过I-TASSER在线预测GNAT2和CNGB3蛋白的三维结构,发现出现移码突变终止密码子的位置均位于这两个基因的重要功能域。另外,运用PAML软件的Branch model分析表明发生假基因的鲸类物种GNAT2和CNGB3基因出现选择压力放松,且假基因化可能是一个近期事件。侏儒抹香鲸、抹香鲸以及小须鲸的GNAT2和CNGB3基因出现假基因可能与其深潜习性以及完全的水生生境导致其色觉功能丢失相关。此外,Free-ratio model分析发现其他鲸类的ω值接近于1,说明GNAT2和CNGB3基因出现了选择压力放松,这可能是长期适应水生生境视觉退化的结果。 相似文献
5.
心率即心脏跳动的速度,不仅反映了心脏的功能,还与寿命的长短及能量代谢有关。与大多数陆生哺乳动物相比,鲸类心率显著降低。降低的心率有助于鲸类寿命的延长及能量的高效利用,便于其适应极端的海洋环境,而这一适应的分子机制尚不清楚。鉴于此,本研究采用基于最大似然法的枝模型、枝位点模型结合蛋白质功能差异分析等方法,对控制心率的环状腺苷酸结合蛋白(Epac1 和Epac2)基因进行适应性探究。分析结果表明,Epac1在长寿鲸类即须鲸类和抹香鲸(Physeter macrocephalus)组合进化支中检测到加速进化过程,且枝位点模型在须鲸类祖先支中检测到的强烈的正选择位点均位于功能重要的催化区;另外,该蛋白质在鲸类中还发生了显著的功能修饰(θ=0.5296 ± 0.1300;P<0.001)。对Epac2进行相同的分析发现,该基因在寿命长达200年之久的弓头鲸(Balaena mysticetus)中检测到的正选择位点同样位于功能重要的催化区。上述结果提示Epac1和Epac2在鲸类中均产生了适应性进化,这一方面可能有助于鲸类心率降低,另一方面也可能与其较长的寿命及高效的能量利用有关。 相似文献
6.
7.
植物在进化过程中为了适应外界环境,已经具有一套完整的抵抗外界特殊环境的调控系统。但是,关于水稻抗逆相关基因的分子进化方面的研究还未见报道。文章通过Plant Tolerance Gene Database数据库,获得22个水稻抗逆相关基因。利用比较基因组学和生物信息学方法对水稻抗逆相关基因的进化动态进行研究,结果表明水稻抗逆相关基因在低等植物中比较保守;随着植物的不断进化和生存环境的改变,其基因数量也随之增加。具有相似抗性功能的基因往往具有相似的基因结构和基序(motif)结构。文章还发现4个保守motif 的存在:HRDXK、DXXSXG、LLPR和GXGXXG(X代表任意氨基酸)。在GSK1、RAN2抗逆基因中发现了3个特有的motif结构:GSK1特有的P-rich motif,RAN2特有的G-rich motif和E-rich motif。推测这些保守的motif结构与基因的抗逆功能密切相关。进化速率分析结果表明,尽管植物抗逆性相关基因在进化过程中受到较强的纯化选择作用,但是仍然有50%的抗逆性相关基因存在正选择位点。这些正选择位点的存在有可能为基因适应外界环境变化提供了重要的物质基础。 相似文献
8.
【目的】分析3个细胞核蛋白编码基因(csp1、MAT1-1-1和MAT1-2-1)在不同冬虫夏草菌株间的分子进化。【方法】从125个冬虫夏草样品中分别扩增csp1、MAT1-1-1和MAT1-2-1基因序列,比较外显子和内含子间以及2个交配型基因间的序列变异程度,比较基于不同基因或基因区域所构建的系统发育树拓扑结构的差异,分析3个基因承受的选择压力和DNA重组情况。【结果】3个蛋白编码基因外显子区的长度在不同菌株间高度保守,具有4.5%?5.7%的变异位点;内含子区的长度在不同菌株间相同或不同,具有1.8%?22%的变异位点。对于2个交配型基因,MAT1-1-1的碱基变异率低于MAT1-2-1。基于外显子与内含子构建的系统发育树的拓扑结构,以及基于2个交配型基因外显子构建的系统发育树的拓扑结构都存在明显差异。3个蛋白编码基因都经历着净化选择作用。基因内部的不同DNA位点间有重组,但3个基因片段之间没有明显的重组发生。【结论】由于冬虫夏草菌不同基因以及基因的不同区域表现出进化上的差异,所以在开展冬虫夏草菌进化相关的研究时,应该联合使用多个不同的基因片段。 相似文献
9.
《兽类学报》2020,(1)
心率即心脏跳动的速度,不仅反映了心脏的功能,还与寿命的长短及能量代谢有关。与大多数陆生哺乳动物相比,鲸类心率显著降低。降低的心率有助于鲸类寿命的延长及能量的高效利用,便于其适应极端的海洋环境,而这一适应的分子机制尚不清楚。鉴于此,本研究采用基于最大似然法的枝模型、枝位点模型结合蛋白质功能差异分析等方法,对控制心率的环状腺苷酸结合蛋白(Epac1 amp 2)基因进行适应性探究。分析结果表明,Epac1在长寿鲸类即须鲸类和抹香鲸(Physeter macrocephalus)组合进化支中检测到加速进化过程,且枝位点模型在须鲸类祖先支中检测到的强烈的正选择位点均位于功能重要的催化区;另外,该蛋白质在鲸类中还发生了显著的功能修饰(θ=0.5296 ± 0.1300;Plt;0.001)。对Epac2进行相同的分析发现,该基因在寿命长达200年之久的弓头鲸(Balaena mysticetus)中检测到的正选择位点同样位于功能重要的催化区。上述结果提示Epac1amp2在鲸类中均产生了适应性进化,这一方面可能有助于鲸类心率降低,另一方面也可能与其较长的寿命及高效的能量利用有关。 相似文献
10.
心率即心脏跳动的速度,不仅反映了心脏的功能,还与寿命的长短及能量代谢有关。与大多数陆生哺乳动物相比,鲸类心率显著降低。降低的心率有助于鲸类寿命的延长及能量的高效利用,便于其适应极端的海洋环境,而这一适应的分子机制尚不清楚。鉴于此,本研究采用基于最大似然法的枝模型、枝位点模型结合蛋白质功能差异分析等方法,对控制心率的环状腺苷酸结合蛋白(Epac1 amp 2)基因进行适应性探究。分析结果表明,Epac1在长寿鲸类即须鲸类和抹香鲸(Physeter macrocephalus)组合进化支中检测到加速进化过程,且枝位点模型在须鲸类祖先支中检测到的强烈的正选择位点均位于功能重要的催化区;另外,该蛋白质在鲸类中还发生了显著的功能修饰(θ=0.5296 ± 0.1300;Plt;0.001)。对Epac2进行相同的分析发现,该基因在寿命长达200年之久的弓头鲸(Balaena mysticetus)中检测到的正选择位点同样位于功能重要的催化区。上述结果提示Epac1amp2在鲸类中均产生了适应性进化,这一方面可能有助于鲸类心率降低,另一方面也可能与其较长的寿命及高效的能量利用有关。 相似文献
11.
Day blindness is a progressive and specific degeneration of cone photoreceptors in the retina of young dogs. This disorder has been associated with a breed-specific non-synonymous substitution in exon 6 of the cyclic nucleotide gated channel beta3 (CNGB3) gene in German Shorthaired Pointer dogs and a genomic deletion removing the entire gene in Alaskan Malamute dogs from the USA. To further investigate this disorder, we characterized CNGB3 in a three-generation pedigree of Alaskan Malamute dogs from Australia segregating for day blindness. Fifteen of the dogs showed clinical signs of day blindness. Four of these were definitively diagnosed by standardized electroretinography. Polymerase chain reaction amplification of exon 6 of CNGB3 was attempted, and as expected, amplification was successful in the 18 unaffected or carrier dogs. However, a non-mutated exon 6 was also amplified and sequenced in six of the 15 affected dogs. On sequencing each exon and exon/intron boundary in two such affected individuals and two unaffected individuals, three exonic substitutions and 12 intronic changes were noted. These sequence variations in affected individuals were also present in one or both unaffected dogs and so appear to have no obvious effect on the protein's function. Hence, day blindness shows genetic heterogeneity within the Alaskan Malamute population of Australia, a result that is somewhat unexpected given the relatively small effective population size of this breed. 相似文献
12.
Emanuela Nizi Alessio Sferrazza Danilo Fabbrini Valentina Nardi Matteo Andreini Rita Graziani Nadia Gennari Alberto Bresciani Giacomo Paonessa Steven Harper 《Bioorganic & medicinal chemistry letters》2018,28(9):1540-1544
Falcipain-2 (FP2) is an essential enzyme in the lifecycle of malaria parasites such as Plasmodium falciparum, and its inhibition is viewed as an attractive mechanism of action for new anti-malarial agents. Selective inhibition of FP2 with respect to a family of human cysteine proteases (that include cathepsins B, K, L and S) is likely to be required for the development of agents targeting FP2. Here we describe a series of P2-modified aminonitrile based inhibitors of FP2 that provide a clear strategy toward addressing selectivity for the P. falciparum and show that it can provide potent FP2 inhibitors with strong selectivity against all four of these human cathepsin isoforms. 相似文献
13.
Vetting MW Bareich DC Yu M Blanchard JS 《Protein science : a publication of the Protein Society》2008,17(10):1781-1790
The three ribosomal proteins L7, S5, and S18 are included in the rare subset of prokaryotic proteins that are known to be N(alpha)-acetylated. The GCN5-related N-acetyltransferase (GNAT) protein RimI, responsible for the N(alpha)-acetylation of the ribosomal protein S18, was cloned from Salmonella typhimurium LT2 (RimI(ST)), overexpressed, and purified to homogeneity. Steady-state kinetic parameters for RimI(ST) were determined for AcCoA and a peptide substrate consisting of the first six amino acids of the target protein S18. The crystal structure of RimI(ST) was determined in complex with CoA, AcCoA, and a CoA-S-acetyl-ARYFRR bisubstrate inhibitor. The structures are consistent with a direct nucleophilic addition-elimination mechanism with Glu103 and Tyr115 acting as the catalytic base and acid, respectively. The RimI(ST)-bisubstrate complex suggests that several residues change conformation upon interacting with the N terminus of S18, including Glu103, the proposed active site base, facilitating proton exchange and catalysis. 相似文献
14.
Jyoti Singh Tomar 《Journal of biomolecular structure & dynamics》2017,35(5):1115-1126
In the current scenario, widespread multidrug resistivity in ESKAPE pathogens demands identification of novel drug targets to keep their infections at bay. For this purpose, we have identified a novel target Hpa2 of A. baumannii, a member of GNAT superfamily of HATs. But due to sequence identity of equal or less than 35%, the correct sequence alignment and construction of 3D monomeric and dimeric models of Hpa2 having optimal structural parameters is a troublesome task. To circumvent these problems, we have designed an easy and optimized protocol for Hpa2 monomer modeling, and for generation of dimeric Hpa2 model using data-driven protein–protein docking experiment. Improvement in the structural features of generated model is an onerous process and generally achieved by paying time and computational cost. Herein, it is achieved by reconciliation of FoldX commands which takes less time in execution. Evaluations performed to validate structural parameters and stability of monomeric and dimeric Hpa2 attests to its quality. Analysis of interfacial residues, energy terms and RMSD values indicated a clear correlation between experimental and theoretical interface properties of the dimers, corroborating to the regime used for Hpa2 dimer generation. Structural information from the refined models was used for virtual screening of substrate-derived library and polyamines to achieve a new platform for developing A. baumannii inhibitory molecules. Molecules showing preferential binding at the dimer interface could be used as allosteric inhibitors. Binding of polyamines with model illustrated the same binding pattern as described experimentally in case of yeast Hpa2. 相似文献
15.
Stiborová M Borek-Dohalská L Hodek P Mráz J Frei E 《Archives of biochemistry and biophysics》2002,403(1):41-49
2-Isopropenyl-2-methyladamantane (2-PMADA) and 3-isopropenyl-3-methyldiamantane (3-PMDIA) showed potent and selective inhibition of cytochrome P450 (CYP) 2B6-mediated reactions with K(i) values of 5.27 and 2.17 microM, respectively. No effect on activities of other human CYP was found even at concentrations 100-fold higher than those inhibiting CYP2B6. These results indicate that 2-PMADA and 3-PMDIA belong among the most potent CYP2B6-selective inhibitors discovered to date. Both compounds also inhibited reactions catalyzed by CYP2B2 and CYP2B4 with K(i) values ranging between 0.23 and 2 microM. They are competitive inhibitors of all CYP2B. The activation of the anticancer drug tamoxifen by human and rabbit microsomes generating tamoxifen-DNA adducts, which are responsible for carcinogenic side effects of this drug, was strongly inhibited by both compounds. 2-PMADA and 3-PMDIA are very potent for inhibition of formation of these DNA adducts and warrant consideration as candidates for preventing endometrial cancer development by tamoxifen in humans treated with this anticancer drug. 相似文献
16.
In this work, we present, to our knowledge, the first demonstration of the utility of iron oxide magnetic microspheres coated with gallium oxide for the highly selective enrichment of phosphopeptide prior to mass spectrometric analysis. These microspheres that we prepared not only have a shell of gallium oxide, giving them a high-trapping capacity for the phosphopeptides, but also their magnetic property enables easy isolation by positioning an external magnetic field. Tryptic digest products of phosphoproteins including beta-casein, ovalbumin, casein, as well as five protein mixtures were used as the samples to exemplify the feasibility of this approach. In very short time (only 0.5 min), phosphopeptides sufficient for characterization by MALDI-TOF-MS were selectively enriched by the Ga(2)O(3)-coated Fe(3)O(4) microspheres. The performance of the Ga(2)O(3)-coated Fe(3)O(4) microspheres were further compared with Fe(3+)-immobilized magnetic silica microspheres, commercial Fe(3+)-IMAC resin, and TiO2 beads for enrichment of peptides originating from tryptic digestion of beta-casein and BSA with a molar ratio of 1:50, and the results proved a stronger selective ability of Ga(2)O(3)-coated Fe(3)O(4) microspheres over the other materials. Finally, the Ga(2)O(3)-coated Fe(3)O(4) microspheres were successfully utilized for enrichment of phosphopeptides from digestion products of rat liver extract. All results show that Ga(2)O(3)-coated Fe(3)O(4) microsphere is an effective material for selective isolation and concentration of phosphopeptides. 相似文献
17.
Zhang Zhang 《基因组蛋白质组与生物信息学报(英文版)》2022,20(3):536-540
KaKs_Calculator 3.0 is an updated toolkit that is capable of calculating selective pressure on both coding and non-coding sequences. Similar to the nonsynonymous/synonymous substitution rate ratio for coding sequences, selection on non-coding sequences can be quantified as the ratio of non-coding nucleotide substitution rate to synonymous substitution rate of adjacent coding sequences. As testified on empirical data, KaKs_Calculator 3.0 shows effectiveness to detect the strength and mode of sele... 相似文献
18.
以thyA基因为选择压力非抗性质粒载体的构建 总被引:8,自引:0,他引:8
以干酷乳杆菌L.casei34103染色体DNA为模板,利用PCR技术扩增胸苷酸合成酶(Thymidylatesynthase,thyA)基因,回收纯化,选择以红霉素抗性为选择压力的可以在大肠杆菌和乳酸菌中穿梭表达的质粒pW425e为基本质粒,以thyA基因取代红霉素基因,获得重组载体并鉴定,此重组载体可以对thyA基因缺陷的大肠杆菌E.coli X51和嗜酸乳杆菌DOMLaS 107进行功能弥补,进而构建了以thyA基因为地选择压力的非抗生素抗性穿梭表达载体,其大小为3716bp,并命名为pW425t。 相似文献
19.
D2蛋白是植物光系统Ⅱ复合体(PSⅡ)核心蛋白之一,由叶绿体psbD基因编码。为了深入理解核心薄囊蕨类植物在阴生环境下的“辐射”式演化,我们对12种蕨类植物的psbD基因进行了克隆和测序,然后联合已公布的其他8种蕨类植物的psbD序列,基于ω值(非同义替换率ds和同义替换率ds的比值)探讨了该基因经受的选择压力。发现D2蛋白在大多数分支和位点受到强烈的负选择,但是树蕨类分支的psbD进化速率低且ω值较高。借助多种模型进行的共进化分析显示,树蕨类D2蛋白的168R、245H和272M两两组成具有共进化关系的氨基酸位点对。 相似文献
20.
《Genomics》2020,112(6):3862-3870
To investigate the molecular evolution of mitochondrial genomes among the family Odontobutidae, the complete mitochondrial genomes of Neodontobutis hainanensis and Perccottus glenii were sequenced and compared with seven odontobutids species. The genome organization, base composition, codon usage, and gene arrangement of N. hainanensis exhibited high similarity to P. glenii compared to those of other Odontobutidae species. Reconstructed phylogenetic analyses of Odontobutidae strongly supported that Neodontobutis and Perccottus formed a unifying group sister to Odontobutis. Our molecular dating time revealed that the two species diverged approximately 21.7 Ma during Miocene, later than that of Odontobutis. Selection analyses showed stronger selective constraints in mitochondrial genes for P. glenii. However, two positively selected sites in NADH4 and NADH6 genes were respectively detected in N. hainanensis and P. glenii, indicating that they might evolve different metabolic performance in response to the contrasting environments. 相似文献