黄唇鱼(Bahaba flavolabiata)的全基因组测序和基因组特征研究

黄唇鱼(Bahaba flavolabiata)为国家二级重点保护野生动物、IUCN(世界自然保护联盟)红色名录的极度濒危物种(CR)。基于其样本数量极其有限,全基因组研究可以提供大量与重要性状相关的功能基因和分子标记,从而揭示其重要生命现象的遗传机制。采用二代测序技术于2018年5月完成了黄唇鱼基因组精细图的测序,分析结果表明,测序得到约202 Gb的高质量数据,总测序深度约为317×;组装得到的基因组大小为637.43 Mb,Contig N50约为88 Kb,Scaffold N50约为4.65 Mb;重复序列约142.72 Mb,占比22.39%,预测得到23743个基因、920个t RNA、85个rRNA、176个假基因;98.46%的基因可以注释到NR、GO等数据库中;有67个基因家族是黄唇鱼所特有的。本研究从单碱基错误率、核心基因完整性及二代Reads比对分析3个方面对黄唇鱼基因组精细图的组装结果进行了评估,结果显示所组装的基因区的完整性较好。黄唇鱼基因组序列图谱的绘制完成,对于黄唇鱼自然资源的保护和种质资源挖掘具有极其重要的科学意义。     

Chlamydomonas reinhardtii-derived multimer Mytichitin-CB possesses potent antibacterial properties

Mytichitin-CB was isolated from Mytilus coruscus in 2014. This antimicrobial peptide shows a weak inhibitory effect on Gram-negative bacteria but inhibits the growth of Gram-positive bacteria and fungi efficiently. Here, a C-terminal hemagglutinin and 6×Histidine (HA-6×His) double tagged three tandem repeats of Mytichitin-CB (3×Mytichitin-CB) with a molecular weight of about 21.5 kDa was expressed in Chlamydomonas reinhardtii. The recombinant 3×Mytichitin-CB was stably expressed following continuous sixth passages of cells and inhibited the growth of both Gram-negative and Gram-positive bacteria at maximum inhibitory concentration (MIC) values between 30 and 50 μg/mL. 3×Mytichitin-CB was stable in terms of its antibacterial activity when treated by a wide range of temperatures and pHs and was resistant to digestion by various proteases. C. reinhardtii-derived 3×Mytichitin-CB had low hemolytic activity and cell cytotoxicity. Moreover, 3×Mytichitin-CB efficiently caused changes on the cell morphology by destroying membrane integrity of the tested bacteria. Our data thus, for the first time, show that C. reinhardtii is a suitable host for stably expressing recombinant 3×Mytichitin-CB, which possesses potent antibacterial properties.     

Plasmid composition and the chpG gene determine the virulence level of Clavibacter capsici natural isolates in pepper

The gram-positive bacterial species Clavibacter capsici causes necrosis and canker in pepper plants. Genomic and functional analyses of C. capsici type strain PF008 have shown that multiple virulence genes exist in its two plasmids. We aimed to identify the key determinants that control the virulence of C. capsici. Pepper leaves inoculated with 54 natural isolates exhibited significant variation in the necrosis. Six isolates showed very low virulence, but their population titres in plants were not significantly different from those of the highly virulent isolates. All six isolates lacked the pCM1_Cc plasmid that carries chpG, which has been shown to be required for virulence and encodes a putative serine protease, but two of them, isolates 1,106 and 1,207, had the intact chpG elsewhere in the genome. Genomic analysis of these two isolates revealed that chpG was located in the pCM2_Cc plasmid, and two highly homologous regions were present next to the chpG locus. The chpG expression in isolate 1,106 was not induced in plants. Introduction of chpG of the PF008 strain into the six low-virulence isolates restored their virulence to that of PF008. Our findings indicate that there are at least three different variant groups of C. capsici and that the plasmid composition and the chpG gene are critical for determining the virulence level. Moreover, our findings also indicate that the virulence level of C. capsici does not directly correlate with bacterial titres in plants.     

Long‐lived electrochemiluminescence of ruthenium (II) complexes/tri‐n‐propylamine in aqueous solutions

Although the clinical use of immunoassays based on the oxidative‐reduction electrochemiluminescence (ECL) of tris(2,2′‐bipyridine)ruthenium (II)/tri‐n‐propylamine has been a great success, elucidation of the ECL generation mechanism still remains unsatisfactory. We report here our experimental observations of long‐lived luminescence that remains detectable for several seconds after termination of electrochemical heterogeneous oxidation. Long‐lived luminescence was observed in both a surfactant‐free buffer and a surfactant‐containing broadly used commercial buffer under different conditions. The slow decay of emission seems to have been unnoticed in previous ECL mechanistic studies. Within the frame of the reaction schemes so far proposed, its origin is inconclusively ascribed to the reductive‐oxidation process of ruthenium (II) complex, that is Ru(bpy)₃²⁺ → Ru(bpy)₃¹⁺ → Ru(bpy)₃²⁺* → Ru(bpy)₃²⁺ with the involvement of the tri‐n‐propylamine‐derived radical cation. It is anticipated that long‐lived ECL will suggest a research approach to separate some homogeneous reactions from the complicated reaction system and therefore help to resolve the mechanistic mystery.     

LCI1, a Chlamydomonas reinhardtii plasma membrane protein,functions in active CO2 uptake under low CO2

In response to high CO₂ environmental variability, green algae, such as Chlamydomonas reinhardtii, have evolved multiple physiological states dictated by external CO₂ concentration. Genetic and physiological studies demonstrated that at least three CO₂ physiological states, a high CO₂ (0.5–5% CO₂), a low CO₂ (0.03–0.4% CO₂) and a very low CO₂ (< 0.02% CO₂) state, exist in Chlamydomonas. To acclimate in the low and very low CO₂ states, Chlamydomonas induces a sophisticated strategy known as a CO₂‐concentrating mechanism (CCM) that enables proliferation and survival in these unfavorable CO₂ environments. Active uptake of C_i from the environment is a fundamental aspect in the Chlamydomonas CCM, and consists of CO₂ and HCO₃^– uptake systems that play distinct roles in low and very low CO₂ acclimation states. LCI1, a putative plasma membrane C_i transporter, has been linked through conditional overexpression to active C_i uptake. However, both the role of LCI1 in various CO₂ acclimation states and the species of C_i, HCO₃^– or CO₂, that LCI1 transports remain obscure. Here we report the impact of an LCI1 loss‐of‐function mutant on growth and photosynthesis in different genetic backgrounds at multiple pH values. These studies show that LCI1 appears to be associated with active CO₂ uptake in low CO₂, especially above air‐level CO₂, and that any LCI1 role in very low CO₂ is minimal.     

ABC转运蛋白及其在合成生物学中的应用

ABC转运蛋白(ATP-binding cassette transporter,ABC transporter)作为一种超大膜转运蛋白家族,在大多数生物体中发挥着重要作用。文中从结构特征、转运机制以及生理功能等方面论述了ABC转运蛋白的研究进展,进而着重综述了近些年来ABC转运蛋白在合成生物学领域中的应用,并为今后进一步的研究提出了展望,希望为扩展其应用提供指导。     

果胶甲酯酶的结构与功能研究进展

果胶甲酯酶(PME)是一种重要的果胶酶,其水解果胶中的甲酯基从而释放甲醇并降低果胶的甲酯化程度。目前在食品加工、茶饮料、造纸等生产工艺中有着广泛的应用前景。随着对PME的深入研究,已报道了几种不同来源的酶晶体结构,对这些已获得的晶体结构进行分析发现,PME属于右手平行β-螺旋结构,其催化残基为2个保守的天冬氨酸和1个谷氨酰胺残基,并且在催化过程中分别起到了一般酸碱、亲核试剂以及稳定中间体的作用。同时对其底物特异性进行分析,初步了解其底物与活性位点的识别机制。文中针对这几个相关方面进行了系统的综述。     

氮代谢参与植物逆境抵抗的作用机理研究进展

近年来,植物所受到的诸如干旱、盐、高温、低氧、重金属胁迫和营养元素缺乏等环境胁迫越来越多,严重影响了植物的生长发育及作物的质量和产量。氮素是植物生长发育所需的必需营养元素,同时也是核酸、蛋白质和叶绿素的重要组成成分,其代谢过程与植物抵抗逆境的能力息息相关。氮代谢是指植物对氮素的吸收、同化和利用的全过程,是植物体内基础代谢途径之一。氮代谢主要从氮素吸收、同化及氨基酸代谢等方面参与植物的抗逆性,并通过调节离子吸收和转运、稳定细胞形态和蛋白质结构、维持激素平衡和细胞代谢水平、减少体内活性氧(reactive oxygen species,ROS)生成以及促进叶绿素合成等生理机制来影响植物抵抗非生物胁迫的能力。因此,提高植物在逆境下的氮代谢水平是减轻外界胁迫对其损伤的一种潜在途径。该文从氮素同化的基本途径出发,分别阐述了氮代谢在干旱胁迫、盐胁迫和高温胁迫等多个方面的逆境抵抗过程中的作用机理,为氮代谢参与植物抗逆性研究提供了有利参考。     

黄土区土质与土石质塿土堆积体水力侵蚀过程差异

利用室内模拟降雨试验,研究了不同雨强及坡度条件下黄土区土质(不含砾石)与土石质(砾石质量分数30%)塿土堆积体的水动力学特征、侵蚀特征及侵蚀动力机制的差异。结果表明: 砾石存在改变了堆积体坡面的水动力学特性,与土质坡面相比,土石质坡面的流速、弗汝德数、单位径流功率和过水断面单位能分别减少1.7%～49.7%、6.7%～60.6%、2.0%～44.6%和1.0%～26.7%;曼宁糙率系数、径流剪切力分别增加6.2%～169.4%、5.7%～79.3%。2.0、2.5 mm·min^-1雨强下,土石质坡面侵蚀速率较土质坡面降低26.2%～89.9%,砾石的减沙效益显著。2种堆积体的侵蚀速率与水动力学参数间均可用线性函数拟合,与土质坡面相比,土石质坡面的可蚀性参数均降低,降幅为56.1%～73.3%;而临界水动力学参数中径流剪切力增加11.1%,径流功率、单位径流功率和过水断面单位能分别减少25.4%、64.0%和5.0%。砾石的存在一定程度上控制了工程堆积体坡面降雨侵蚀过程。