CVNH结构域的进化分析和选择压力检测

蓝藻抗病毒蛋白-N(Cyanovirin-N,CV-N)具有广谱抗病毒活性,其同源物构成CVNH(Cyanovirin-N homology)蛋白家族,并且家族成员的抗人类免疫缺陷病毒结构域在进化上非常保守。文章通过重建基因树对CVNH结构域的"零散分布"特点作了更为细致的了解,发现在黑曲霉、费氏曲菌、产黄青霉、粗糙脉孢霉、蓝杆藻和水蕨等物种中存在多份该结构域拷贝。在此基础上,分别采用机理式模型(Mechanistic model)和MEC模型(Mechanistic-empirical combination model)对CVNH结构域序列位点进行适应性进化分析,结果显示:1)两类模型均未检测到统计上显著的正选择位点;2)净化选择对CVNH起主导作用;3)MEC模型更适合所研究的数据。进一步使用"支-特异"模型和"支-位点"模型对蓝杆菌菌株7822和7424的祖先分支进行检测,发现该分支经历过适应性进化,并且鉴定出6个正选择位点(34L、63L、13H、76C、78K和80I)。     

蕨类植物rbcL基因正选择和负选择位点的鉴定

基于分支模型、位点模型及分支-位点模型对蕨类的rbcL基因所受到的选择压力进行了分析.结果显示:分支模型下检测到大部分分支处于负选择,仅4个分支处于正选择压力下,并且仅2分支具有统计上的显著性;在位点模型下,通过比较模型M1a/M2a和M7/M8,在氨基酸水平上模型M2a和模型M8均鉴定出98L位点被正选择;在模型M8下,鉴定负向选择位点共228个,占总序列的83.82%,从而揭示出负选择对rbcL基因的进化起着非常重要的作用;在分支位点-模型c下鉴定出262A被正选择.98L、262A位点分别位于rbcL羧基末端α/β桶结构域的第3和第8个α螺旋上.蕨类通过该结构域的适应性进化,适应白垩纪被子植物兴起而引发的陆地生态系统改变,研究结果为以后实验分析提供了首选位点.     

裸子植物中光敏色素PHY-PAS1结构域的适应性进化

光敏色素是一类红光／远红光受体,在植物种子萌发到成熟的整个生长发育过程中均起重要的调节作用。光敏色素PHY-PAS1结构域存在于光敏色素基因家族的所有成员中,对调节发色团的光谱特性和光信号转导非常关键。光敏色素基因家族通过基因重复产生,而基因重复可能与物种形成有关。PHYP基因是裸子植物光敏色素基因家族发生第1次重复后产生的,并且以单拷贝形式存在。为了研究不同裸子植物PHYP基因编码蛋白的PHY-PAS1结构域在进化过程中是否受到相同的选择压力以及是否发生了适应性进化,该研究利用分支模型、位点模型以及分支．位点模型对裸子植物31条PHYP基因序列编码蛋白的PHY-PAS1结构域所受到的选择压力进行了分析。结果表明,在由PHY-PAS1结构域序列构建的系统树中,多数分支处于强烈的负选择压力下（ω〈1）：有14个分支处于正选择压力下（ω〉1）,其中13个分支发生在属内种间;与之相比,在较为古老的谱系中相对缺少这种正选择压力。     

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。     

裸子植物中光敏色素PHY-PAS1 结构域的适应性进化

光敏色素是一类红光/远红光受体, 在植物种子萌发到成熟的整个生长发育过程中均起重要的调节作用。光敏色素PHYPAS1 结构域存在于光敏色素基因家族的所有成员中, 对调节发色团的光谱特性和光信号转导非常关键。光敏色素基因家族通过基因重复产生, 而基因重复可能与物种形成有关。PHYP基因是裸子植物光敏色素基因家族发生第1次重复后产生的, 并且以单拷贝形式存在。为了研究不同裸子植物PHYP基因编码蛋白的PHY-PAS1结构域在进化过程中是否受到相同的选择压力以及是否发生了适应性进化, 该研究利用分支模型、位点模型以及分支-位点模型对裸子植物31条PHYP基因序列编码蛋白的PHY-PAS1结构域所受到的选择压力进行了分析。结果表明, 在由PHY-PAS1结构域序列构建的系统树中, 多数分支处于强烈的负选择压力下 (w<1); 有14个分支处于正选择压力下 (w>1), 其中13个分支发生在属内种间; 与之相比, 在较为古老的谱系中相对缺少这种正选择压力。     

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。     

香菇基因组中L-半胱氨酸亚砜裂解酶同源蛋白的生物信息学分析

L-半胱氨酸亚砜裂解酶（L-cysteine sulfoxide lyase,C-S lyase）是香菇中含硫风味物质生物合成途径的关键酶之一。本文基于6个不同香菇菌株的全基因组测序数据,挖掘了24个潜在的香菇L-半胱氨酸亚砜裂解酶（Lentinula edodes C-S lyase,Lecsl）同源基因,对其编码蛋白的生理生化特性、信号肽、跨膜结构域、转录活性、分子进化、保守基序和蛋白三级结构等方面进行了分析。结果发现,这24个香菇Lecsl同源蛋白含有相同的蛋白结构域（IPR015424和IPR000192）,都属于L-半胱氨酸脱巯基酶家族（PTHR43092:SF2）,都不含信号肽和跨膜结构,但它们的蛋白稳定性有所不同。对24个Lecsl同源蛋白进行聚类分析发现,其中的11个组成了新的进化分支,这一分支的Lecsl同源蛋白在香菇的菌丝体或子实体中有转录活性,且含有蒜酶和L-半胱氨酸脱硫酶的保守基序19,推测这一分支的Lecsl同源蛋白在香菇中具有催化产生含硫风味物质和内源性甲醛的活性。进一步分析发现,这一分支又分为两个亚支,其中一支包含已发现的Lecsl/LE01_CSL1,并且在香菇的菌丝体和子实体阶段都有转录活性;另一个亚支上的C-S lyase同源蛋白仅在菌丝体中有转录活性,推测这两个亚支的L-半胱氨酸亚砜裂解酶分别在香菇生长发育的不同阶段发挥催化作用。通过三维结构的解析,阐明了Lecsl中保守基序19亦是使蒜酶产生催化活性的关键结构域,并且利用分子动力学模拟的方法,预测保守基序19中的Asn3、Gln5和Ser6是香菇C-S lyase产生催化活性的关键氨基酸残基。     

西瓜含有JmjC结构域的组蛋白去甲基化酶家族的生物信息学分析

利用生物信息学方法,对西瓜（Citrullus lanatus（Thunb.）Matsum.&Nakai）JmjC基因家族的成员进行鉴定,对该基因家族的染色体定位、基因结构、蛋白结构域、选择压力和酶活位点进行分析,并对该基因家族与其它物种的系统进化及共线性关系进行研究。结果显示：西瓜全基因组含有17个JmjC候选基因,核苷酸序列长度为1209~5541 bp;这些基因均含有JmjC结构域,分别位于9条染色体上,归属8个亚族。系统进化、选择压力以及共线性分析结果表明,西瓜与黄瓜（Cucumis sativus L.）亲缘关系较近,JmjC家族基因数量相同,其中14个成员呈现一对一的共线性关系;而西瓜与拟南芥（Arabidopsis thaliana（L.）Heynh）亲缘关系较远,但西瓜和拟南芥同一亚族中JmjC基因间K_a/K_s的比值均小于1,推测西瓜各个亚族成员的编码蛋白功能与同一亚族的拟南芥成员功能极为相似。酶活位点分析结果表明西瓜JmjC基因家族中有10个成员具有潜在的组蛋白去甲基化酶活性。     

裸子植物psbA基因分子进化式样的研究

为阐明裸子植物对陆生生境生态响应的分子机制,以新近的裸子植物分类系统为指导,基于psb A基因编码全序列对4亚纲53种代表植物进行分子进化分析。首先,依据"放松分子钟"模型重建裸子植物在时间尺度下系统发育关系;其次,采用6个模型(MEC/JTT、MEC/cp REV、M5、M7、M8、M8a)估测氨基酸位点ω值,并对各模型结果进行统计检测;随后,利用Bootstrap方法检PSBA蛋白内部氨基酸位点的共进化动态。结果表明,系统树提示的物种分化历程支持前期分类结果;光合系统反应中心核心PSBA蛋白有3个氨基酸位点(13、19和243)曾经受正选择压力;PSBA蛋白内部有多对氨基酸位点间构成了共进化网络。因此,psb A基因编码序列具有作为描绘裸子植物系统发育关系标记的潜力,PSBA蛋白部分位点经历了适应性进化,通过位点间共进化网络协同作用方式辅助裸子植物响应陆生生境。     

蕨类植物psaA基因的分子进化研究

采用“放松分子钟”模型、氨基酸位点正选择模型和分子内共进化网络估算方法,对蕨类植物光合系统Ⅰ核心蛋白PSAA编码基因psaA的进化趋势进行了研究。结果显示,叶绿体基因psaA编码区全序列具备成为蕨类植物系统发育关系重建位点的潜力,与rbcL基因联合后能构建高后验概率的系统发育树;蕨类植物的PSAA蛋白中存在一些曾经历正选择的氨基酸位点,其中29个位点聚合成为16个共进化组,通过共进化网络的方式协同影响光合系统Ⅰ的内部调整,提升其在被子植物兴起后光合环境下的适应能力。本文对蕨类植物进化潜能与分子机理的研究结果为揭示蕨类植物适应新生境提供了科学依据,也为植物系统分类学研究提供了分子依据。     

Identification of a nuclease and host restriction-modification in the unicellular, aerobic nitrogen-fixing cyanobacterium Cyanothece sp.

In the process of developing a gene transfer system for the marine, unicellular, nitrogen-fixing cyanobacterium Cyanothece sp. strain BH68K, two major restriction barriers have been identified. A cell wall-associated nuclease exhibited non-site-specific degradation of covalently closed circular and linear double-stranded DNA molecules, including Cyanothece sp. strain BH68K chromosomal DNA. The nuclease is easily released from intact cells by using water or buffer containing Triton X-100. Nuclease activity was undetectable in cell extracts prepared from water-washed cells. Comparison of the restriction endonuclease susceptibility of Cyanothece sp. strain BH68K DNA to that of Anabaena sp. strain PCC 7120 revealed that these organisms have a nearly identical pattern of restriction and therefore may contain similar systems for DNA methylation. Restriction by DpnI, MboI, and Sau3AI indicated the presence of adenine methylation. Cyanothece sp. strain BH68K cell extracts contain a type II restriction endonuclease, Csp68KI. The activity of Csp68KI was easily detected in cell extracts without extensive purification. Csp68KI is an isoschizomer of AvaII and recognizes the nucleotide sequence 5'-GG(A/T)CC-3'. Cleavage occurs between the guanosine nucleotides producing 3-bp 5' overhang ends.     

Pattern of cyanophycin accumulation in nitrogen-fixing and non-nitrogen-fixing cyanobacteria

The temporal and spatial accumulation of cyanophycin was studied in two unicellular strains of cyanobacteria, the diazotrophic Cyanothece sp. strain ATCC 51142 and the non-diazotrophic Synechocystis sp. strain PCC 6803. Biochemistry and electron microscopy were used to monitor the dynamics of cyanophycin accumulation under nitrogen-sufficient and nitrogen-deficient conditions. In Cyanothece sp. ATCC 51142 grown under 12 h light/12 h dark nitrogen-fixing conditions, cyanophycin was temporally regulated relative to nitrogenase activity and accumulated in granules after nitrogenase activity commenced. Cyanophycin granules reached a maximum after the peak of nitrogenase activity and eventually were utilized completely. Knock-out mutants were constructed in Synechocystis sp. PCC 6803 cphA and cphB genes to analyze the function of these genes and cyanophycin accumulation under nitrogen-deficient growth conditions. The mutants grew under such conditions, but needed to degrade phycobilisomes as a nitrogen reserve. Granules could be seen in some wild-type cells after treatment with chloramphenicol, but were never found in Delta cphA and Delta cphB mutants. These results led to the conclusion that cyanophycin is temporally and spatially regulated in nitrogen-fixing strains such as Cyanothece sp. ATCC 51142 and represents a key nitrogen reserve in these organisms. However, cyanophycin appeared to play a less important role in the non-diazotrophic unicellular strains and phycobilisomes appeared to be the main nitrogen reserve.     

Positive selection drives rapid evolution of certain amino acid residues in an evolutionarily highly conserved interferon-inducible antiviral protein of fishes

Viperin, an evolutionarily highly conserved interferon-inducible multifunctional protein, has previously been reported to exhibit antiviral activity against a wide range of DNA and RNA viruses. Utilizing the complete nucleotide coding sequence data of fish viperin antiviral genes, and employing the maximum likelihood-based codon substitution models, the present study reports the pervasive role of positive selection in the evolution of viperin antiviral protein in fishes. The overall rate of nonsynonymous (dN) to synonymous (dS) substitutions (dN/dS) for the three functional domains of viperin (N-terminal, central domain and C-terminal) were 1.1, 0.12, and 0.24, respectively. Codon-by-codon substitution analyses have revealed that while most of the positively selected sites were located at the N-terminal amphipathic α-helix domain, few amino acid residues at the C-terminal domain were under positive selection. However, none of the sites in the central domain were under positive selection. These results indicate that, although viperin is evolutionarily highly conserved, the three functional domains experienced differential selection pressures. Taken together with the results of previous studies, the present study suggests that the persistent antagonistic nature of surrounding infectious viral pathogens might be the likely cause for such adaptive evolutionary changes of certain amino acids in fish viperin antiviral protein.     

Molecular Evolution of the Primate Antiviral Restriction Factor Tetherin

Background

Tetherin is a recently identified antiviral restriction factor that restricts HIV-1 particle release in the absence of the HIV-1 viral protein U (Vpu). It is reminiscent of APOBEC3G and TRIM5a that also antagonize HIV. APOBEC3G and TRIM5a have been demonstrated to evolve under pervasive positive selection throughout primate evolution, supporting the red-queen hypothesis. Therefore, one naturally presumes that Tetherin also evolves under pervasive positive selection throughout primate evolution and supports the red-queen hypothesis. Here, we performed a detailed evolutionary analysis to address this presumption.

Methodology/Principal Findings

Results of non-synonymous and synonymous substitution rates reveal that Tetherin as a whole experiences neutral evolution rather than pervasive positive selection throughout primate evolution, as well as in non-primate mammal evolution. Sliding-window analyses show that the regions of the primate Tetherin that interact with viral proteins are under positive selection or relaxed purifying selection. In particular, the sites identified under positive selection generally focus on these regions, indicating that the main selective pressure acting on the primate Tetherin comes from virus infection. The branch-site model detected positive selection acting on the ancestral branch of the New World Monkey lineage, suggesting an episodic adaptive evolution. The positive selection was also found in duplicated Tetherins in ruminants. Moreover, there is no bias in the alterations of amino acids in the evolution of the primate Tetherin, implying that the primate Tetherin may retain broad spectrum of antiviral activity by maintaining structure stability.

Conclusions/Significance

These results conclude that the molecular evolution of Tetherin may be attributed to the host–virus arms race, supporting the Red Queen hypothesis, and Tetherin may be in an intermediate stage in transition from neutral to pervasive adaptive evolution.     

Nonribosomal peptide synthetase genes occur in most cyanobacterial genera as evidenced by their distribution in axenic strains of the PCC

Previous studies largely carried out with environmental samples or axenic and non-axenic cultures suggested that cyanobacteria may be a rich source of hitherto unexplored bioactive compounds. This has been confirmed in the present study by a screening of 146 axenic strains from the Pasteur Culture Collection (PCC) of cyanobacteria. Use of degenerate PCR primers, designed on the basis of conserved sequence motifs in the aminoacyl-adenylation domain of peptide synthetases, revealed the presence of the corresponding genes in the majority (75.3%) of the strains examined. Among unicellular cyanobacteria, only Chamaesiphon sp. strain PCC 6605, two strains of Gloeocapsa and most Microcystis isolates (22 out of 24) contained these genes; no amplicons were detected for any members of the genera Cyanothece, Gloeobacter and Gloeothece and the genetically diverse representatives of Synechococcus and Synechocystis. By contrast, eight out of ten pleurocapsalean members, 16 out of 25 oscillatorian strains, and all but two of the 63 filamentous heterocystous cyanobacteria tested gave positive amplification results. This information will be highly valuable for further exploring the corresponding cyanobacterial peptides and for elucidating the bioactivity of such non-ribosomally synthesized molecules.     

Solution and crystal structures of a sugar binding site mutant of cyanovirin-N: no evidence of domain swapping

The cyanobacterial lectin Cyanovirin-N (CV-N) exhibits antiviral activity against HIV at a low nanomolar concentration by interacting with high-mannose oligosaccharides on the virus surface envelope glycoprotein gp120. Atomic structures of wild-type CV-N revealed a monomer in solution and a domain-swapped dimer in the crystal, with the monomer comprising two independent carbohydrate binding sites that individually bind with micromolar affinity to di- and trimannoses. In the mutant CVN(mutDB), the binding site on domain B was abolished and the protein was found to be completely inactive against HIV. We determined the solution NMR and crystal structures of this variant and characterized its sugar binding properties. In solution and the crystal, CVN(mutDB) is a monomer and no domain-swapping was observed. The protein binds to Man-3 and Man-9 with similar dissociation constants ( approximately 4 muM). This confirms that the nanomolar activity of wild-type CV-N is related to the multisite nature of the protein carbohydrate interaction.     

Solution structure of CyanoP from Synechocystis sp. PCC 6803: New insights on the structural basis for functional specialization amongst PsbP family proteins

The structure of the CyanoP subunit of photosystem II from the cyanobacterium Synechocystis sp. PCC 6803 has been determined in solution by Nuclear Magnetic Resonance spectroscopy. Combined with homology modeling of PsbP-like structures we have identified distinct structural differences between PsbP homologues which may account for the functional differences apparent between members of this protein family. A surface cleft containing a large number of conserved residues found only in CyanoP and PsbP-like homologues has been identified and our findings suggest that one of the potential cation binding sites found in CyanoP may be functionally significant. Evidence for the evolution and divergence of the PsbP super family is presented from a structural perspective including identification of residues which distinguish the PsbP family from unrelated proteins with a similar domain fold. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.