滇龙胆GrHDR基因的克隆与表达分析

龙胆苦苷(gentiopicroside)是中药龙胆中的主要药效成分,属于萜类化合物的衍生物。1-羟基-2-甲基-2-(E)-丁烯基-4-二磷酸还原酶[1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate reductase,HDR]是萜类物质合成途径中的关键酶。为探讨不同光照条件下滇龙胆HDR(GrHDR)基因的表达与龙胆苦苷含量之间的关系,该文以滇龙胆叶片cDNA为模板,采用PCR和TA克隆技术获得GrHDR基因序列,对该序列进行生物信息学分析和表达分析,并采用高效液相色谱法测定龙胆苦苷含量,对该基因表达与龙胆苦苷含量进行比较。结果表明:(1)GrHDR基因(GenBank登录号: KJ917165.1)全长1 398 bp,编码465个氨基酸,推定GrHDR蛋白是亲水且稳定的,相对分子质量是52 281.25 Da,理论等电点是5.32;(2)该蛋白属于LYTB蛋白家族,可能定位于叶绿体上,无信号肽,二级结构主要由α-螺旋(45.16%)、β-转角(6.24%)、无规卷曲(33.98%)、延伸链(14.62%)构成;(3)GrHDR蛋白序列与同属植物秦艽的HDR蛋白相似性最高(95.71%);(4)实时荧光定量PCR结果显示GrHDR基因在滇龙胆中的表达量为根 > 叶 > 茎,而在10%、30%、100%全光光照条件下各组织的表达量有很大差异;(5)高效液相色谱法结果显示,不同光照条件下龙胆苦苷含量一致,均为根 > 叶 > 茎,其中100%全光光照下,药用部位根中龙胆苦苷含量达到7.141%,约是30%、10%全光光照条件的两倍,但该结果与同一光照条件下GrHDR基因表达规律不完全一致。该研究为阐述HDR基因功能及其与龙胆苦苷含量的关系提供参考。     

Streptomyces luteolifulvus sp. nov., a novel actinomycete isolated from soil in Nanjing,China

During the investigation of exploring potential sources of novel species and natural bioactives, a novel actinomycete, designated strain HIT-DPA4^T, was isolated from a soil sample, which was collected from Nanjing, Jiangsu Province, PR China and characterized using a polyphasic approach. On the basis of 16S rRNA gene sequence similarities and the result of phylogenetic analysis, strain HIT-DPA4^T was most closely related to Streptomyces cyaneus CGMCC 4.1671 ^T, and shared the highest sequence similarity of 98.76%. In addition, the cell walls of the species HIT-DPA4^T contained LL-diaminopimelic acid as the diagnostic diamino acid and the whole-cell hydrolysates were identified as glucose and ribose, and the principal phospholipids were found to be diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannoside and phosphatidylmonomethylethanolamine. MK-9(H₆) and MK-9(H₄) were predominant menaquinones; and C_16:0, anteiso-C_15:0 and C_15:0 as major cellular fatty acids of the organism HIT-DPA4^T. Gene Ontology database analysis and antiSMASH server predicted results displayed that strain HIT-DPA4^T was a promising classification units, which has various types of functions and contains multiple biosynthetic gene clusters with the similarity more than 80%. Multilocus sequence analysis (MLSA) of five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) illustrated that Streptomyces luteolifulvus formed a separate branch in the genus Streptomyces. However, a combination of low level of DNA-DNA relatedness and physiological properties indicated that strain HIT-DPA4^T can be distinguished from its phylogenetically related species Streptomyces cyaneus CGMCC 4.1671 ^T. Moreover, gene synteny research could be further differed organism HIT-DPA4^T from similarity species. Therefore, the strain is concluded to represent a novel species of the genus Streptomyces, for which the name Streptomyces luteolifulvus sp. nov. is proposed. The type strain is HIT-DPA4^T (=?CGMCC 4.7558 ^T?=?TISTR 2751 ^T).

     

A Bayes factor approach with informative prior for rare genetic variant analysis from next generation sequencing data

The discovery of rare genetic variants through next generation sequencing is a very challenging issue in the field of human genetics. We propose a novel region‐based statistical approach based on a Bayes Factor (BF) to assess evidence of association between a set of rare variants (RVs) located on the same genomic region and a disease outcome in the context of case‐control design. Marginal likelihoods are computed under the null and alternative hypotheses assuming a binomial distribution for the RV count in the region and a beta or mixture of Dirac and beta prior distribution for the probability of RV. We derive the theoretical null distribution of the BF under our prior setting and show that a Bayesian control of the false Discovery Rate can be obtained for genome‐wide inference. Informative priors are introduced using prior evidence of association from a Kolmogorov‐Smirnov test statistic. We use our simulation program, sim1000G, to generate RV data similar to the 1000 genomes sequencing project. Our simulation studies showed that the new BF statistic outperforms standard methods (SKAT, SKAT‐O, Burden test) in case‐control studies with moderate sample sizes and is equivalent to them under large sample size scenarios. Our real data application to a lung cancer case‐control study found enrichment for RVs in known and novel cancer genes. It also suggests that using the BF with informative prior improves the overall gene discovery compared to the BF with noninformative prior.     

Correction to: lncRNA MEG3, Acting as a ceRNA,Modulates RPE Differentiation Through the miR-7-5p/Pax6 Axis

Biochemical Genetics - A correction to this paper has been published: https://doi.org/10.1007/s10528-021-10086-3