镉胁迫后旱柳转录组变化分析

随着重金属镉(Cd)应用范围的扩大,由此引发的土壤镉污染问题日益严重。以具有植物恢复潜力的旱柳Salix matsudana作为研究对象,探究不同浓度的Cd (2.5 mg/L, 50 mg/L)胁迫后旱柳无性系1 d、7 d和30 d后基因表达与代谢通路的变化。转录组测序结果表明:共获得102 595个非冗余基因(Unigenes),相同浓度不同时间的差异基因总数为26 623个和32 154个;相同时间不同浓度的差异基因总数为8 550个、3 444个和11 428个。从中筛选得到与Cd胁迫响应密切相关的基因25个,其中金属硫蛋白、ABC转运蛋白、锌和锰转运蛋白等基因的表达不仅会随着Cd胁迫浓度变化而且同时受到胁迫时间的改变而发生改变;油菜素内酯合成通路的ROT3和黄酮类化合物合成通路的FLS、F3H均明显上调。此外Cd胁迫引起旱柳在代谢过程、细胞过程、膜、细胞器、细胞、细胞部分、催化活化和结合蛋白这8个方面发生改变,参与这些GO条目的差异表达基因数随着Cd浓度和胁迫时间的增加而增加。并对转录组信息的可靠性用RT-PCR和酶活性生理实验数据进行了验证。文中通过转录组测序分析旱柳Cd胁迫后的响应机制,从而为旱柳修复土壤Cd污染提供理论指导。     

镉胁迫对拟南芥的毒害作用及自噬现象的观测

镉离子(Cd2+)具有强植物毒性,可抑制植物生长,甚至导致植物死亡。为了研究重金属镉对拟南芥的毒害作用,采用叶绿素荧光技术、流式细胞技术、激光共聚焦技术及半定量RT-PCR技术,检测光合参数的变化、活性氧(reactive oxygen species,ROS)的累积、自噬的发生,以及病原相关蛋白(pathogenesis-related protein,PR)基因表达的变化。实验结果显示,随着50μmol/L CdCl2处理时间的延长,ROS和Cd2+在细胞中大量积累。而在镉胁迫的初期,会观察到自噬的发生及PR基因表达的变化。说明植物受到外界Cd2+作用的初期,会通过自噬及增强PR基因表达来抵抗外界胁迫。但随着处理时间的延长,植物细胞内累积了大量的ROS和Cd2+,当植物不足以通过自噬途径抵抗胁迫时,就会导致生长受阻,最终对光合系统造成损伤。     

线粒体自噬基因对酿酒酵母抗氧化性能的影响

线粒体自噬是指细胞通过自噬的机制选择性地清除线粒体的过程,对维持细胞内稳态具有重要作用。为探究线粒体自噬基因对酿酒酵母(Saccharomyces cerevisiae)细胞抗氧化性能的影响,本研究分别构建了线粒体自噬相关基因ATG8、ATG11、ATG32的缺失和过表达菌株,发现在过氧化氢(H₂O₂)胁迫6 h后,过表达ATG8、ATG11基因显著降低了细胞内活性氧(reactive oxygen species,ROS)含量,分别仅为初始状态的61.23%和46.35%,并显著提高了菌株线粒体膜电位(mitochondrial membrane potential,MMP)和腺嘌呤核苷三磷酸(adenosine-triphosphate,ATP)含量,有助于提高菌株的抗氧化性能。另一方面,基因ATG8、ATG11、ATG32的缺失会导致线粒体损伤及细胞活力显著下降,同时造成胞内ROS失衡,H₂O₂胁迫6 h后,其胞内ROS含量显著升高至初始状态的174.27%、128.68%和200.92%。结果表明,ATG8、ATG11和ATG32可能是调控酵母抗氧化能力的潜在靶点。本研究为进一步研究通过调节线粒体自噬提高酵母抗氧化活性提供了新的线索。     

高糖环境下beclin2介导的自噬增强绒毛膜滋养层细胞凋亡

目的探讨高糖对人绒毛膜滋养层细胞早期凋亡及自噬水平的影响。方法取足月妊娠的正常及妊娠期糖尿病(gestational diabetes mellitus,GDM)患者的胎盘组织,透射电镜观察滋养层细胞超微结构的改变。体外用不同浓度的含糖培养基培养滋养层细胞系HTR8/Svneo细胞24h,分为低糖组(1.57mmol/L或LG2 2.25mmol/L),正常对照组(5.57mmol/L)和高糖组(10.57mmol/L、15.57mmol/L或40.57mmol/L);流式细胞术检测细胞早期凋亡率;q-PCR检测细胞内beclin1、beclin2和ATG7等自噬相关基因的m RNA表达水平;Western blot检测Ⅱ型自噬标志蛋白微管相关蛋白1轻链3(LC3-II)和p62蛋白表达水平。结果透射电镜下可见GDM组滋养层细胞中存在自噬小体且空泡数目明显多于正常足月妊娠组,其游离面微绒毛出现明显倒覆及坍塌现象;在体外培养的滋养层细胞中,流式细胞术检测显示1.57mmol/L低糖组及40.57mmol/L高糖组较正常对照组HTR8/SVneo细胞的早期凋亡率均明显增加;q-PCR分析发现40.57mmol/L高糖组beclin2及ATG7 m RNA表达水平较正常对照组升高,beclin1 m RNA表达无差异;Western blot检测表明,与正常对照组比较,40.57mmol/L高糖组LC3-II蛋白表达水平升高,p62蛋白表达水平降低。结论高糖可通过beclin2介导的自噬信号途径增强滋养层细胞自噬水平进而导致细胞凋亡,并可能与不良的妊娠结局相关。     

Hg2+和Cd2+胁迫对满江红生理和细胞超微结构的影响

研究了在梯度浓度Hg2+和Cd2+胁迫下,满江红(Azolla imbricata (Roxb.) Nakai)的叶绿素含量、叶绿素a/b比值、光合放氧速率、呼吸速率、抗氧化酶系(超氧化物歧化酶(SOD)、过氧化氢酶(CAT)、过氧化物酶(POD))和细胞超微结构受Hg2+和Cd2+的毒害影响.结果显示:随着胁迫程度的增大,叶绿素含量、叶绿素a/b比值、光合放氧速率明显下降,呼吸速率均在2 mg/L浓度下达到峰值,尔后下降; SOD、CAT、POD的活性均出现不同程度的应激性升高(除POD在Cd2+处理时下降),尔后下降.电镜观察发现,随着污染物浓度的增加和胁迫时间的延长,叶绿体出现膨大、破损和解体;线粒体嵴突膨胀和线粒体变形及空泡化;核染色质凝集,核仁消失,核膜破裂.实验结果表明: Hg2+和Cd2+污染不仅损害植物的生理活性,而且也破坏细胞的超微结构,最终导致植物死亡;随着Hg2+和Cd2+胁迫的增大,细胞超微结构的损伤程度和植物的生理变化是同步的;植物受毒害的程度表现出明显的剂量效应关系;在同一处理时间和浓度下,Cd2+对满江红的毒性大于Hg2+.Hg2+对满江红的致死浓度为3.5～4.0 mg/L,Cd2+为3.0～3.5 mg/L.对满江红鱼腥藻(Anabaena azollae Strasburger)细胞的超微结构变化观察表明,满江红鱼腥藻对Hg2+和Cd2+的耐受性明显高于满江红.     

茄子自噬相关基因ATG8家族鉴定及表达分析

自噬相关基因ATG8在调节植物生长发育和胁迫响应中发挥着关键作用。本研究通过生物信息学技术分析ATG8在茄子基因组中的分布、结构及进化等,并研究了其在茄子不同组织、外源激素和冷处理下的表达情况。结果表明,从茄子基因组中共鉴定到7个ATG8基因,分布在6条染色体上。理化性质分析显示茄子ATG8基因编码的蛋白包含118~166个氨基酸残基,等电点在6.29~9.16之间;基因结构和保守基序分析表明,ATG8基因家族成员具有保守的基因结构和蛋白基序;启动子区域含有多种激素响应和逆境响应的顺式作用元件;茄子中有3对ATG8基因存在共线关系;茄子与拟南芥和番茄ATG8基因家族成员间分别存在10和11对共线关系。组织表达分析表明茄子ATG8主要在不同的花器官中表达,表明其可能与茄子花发育有关;此外,表达模式分析结果显示7个茄子ATG8基因对冷胁迫和ABA、MeJA、SA等外源激素均有不同程度的响应,表明ATG8基因家族在茄子生长发育、胁迫和激素响应中具有重要的功能。     

植物细胞自噬基因的功能与转录调控机制

自噬(autophagy)是真核生物长期进化形成的一种高度保守的细胞内物质降解和周转途径, 通过形成双层膜结构的自噬体将包裹其中的待降解大分子物质, 如受损伤的蛋白质、蛋白质复合物和细胞器, 运送至液泡或溶酶体进行降解并产生可循环利用的降解产物。细胞自噬在植物生长发育和环境应答等过程中发挥重要作用。在拟南芥(Arabidopsis thaliana)和水稻(Oryza sativa)等模式植物中已鉴定到40多个自噬基因, 并发现其中多个基因在植物叶片衰老、种子成熟等发育阶段以及营养饥饿、干旱和病原菌侵染等逆境胁迫响应过程中显著上调表达, 但具体的转录激活或抑制机制有待阐明。该文综述了自噬基因在植物生长发育和胁迫应答过程中的功能与转录调控网络。     

塞内卡病毒A结构蛋白VP2诱导PK-15细胞自噬的研究

本研究在塞内卡病毒A(Senecavirus A,SVA)诱导自噬的基础上,着重探究VP2蛋白在细胞自噬过程中的作用。构建VP2基因真核表达载体pcDNA3.1-VP2,将其转染至PK-15细胞,通过检测自噬蛋白和相关基因的表达情况,明确VP2蛋白对细胞自噬的影响。结果显示,本研究成功构建了pcDNA3.1-VP2真核表达载体,且SVA VP2基因在PK-15细胞中正常表达;与对照组相比,VP2蛋白显著上调LC3蛋白的表达水平（P<0.01）;同时,自噬基因LC3、Beclin-1和ATG5转录水平均显著提高（P<0.01）。综上所述,本研究证实SVA VP2蛋白可诱导PK-15细胞自噬,且VP2蛋白与自噬蛋白和基因表达水平呈正相关,为进一步研究病毒感染与致病机制打下基础。     

基于基因芯片技术的转Slnac2基因拟南芥差异表达基因分析

NAC转录因子,对植物的生长发育及抵御逆境胁迫起着重要的作用。实验室前期克隆了辽宁碱蓬(Suaeda liaotungensis)Slnac2基因,转Slnac2拟南芥(Arabidopsis thaliana)提高了抵御盐胁迫的能力。本研究利用基因芯片技术筛选转SlNAC2拟南芥差异表达基因,共筛选出差异表达2倍以上的基因1 258个。GO富集度分析结果显示,分子功能相关基因占34.06%,细胞组分相关基因占33.13%,生物学过程相关基因占32.81%。KEGG分析表明,差异表达基因涉及63个信号通路,主要有植物激素信号转导、核糖体、植物病原物相互作用和抗坏血酸代谢等。通过实时荧光定量PCR对部分差异基因进行验证,所得结果与基因芯片结果一致。本研究揭示,SlNAC2可调控多个下游基因的表达,提高植物在逆境胁迫下的生存能力。     

Notch信号及自噬在三氧化矿化聚合物促人牙髓细胞体外增殖中的作用

目的:探讨Notch信号及自噬在三氧化矿化聚合物(MTA)促人牙髓细胞(h DPCs)体外增殖中的作用。方法:取临床上完整拔除的健康第三磨牙,通过酶消化法获得原代培养h DPCs。采用CCK-8比色法检测不同浓度(0.5、1.0、2.0、5.0、10.0 mg/m L)MTA对h DPCs增殖的影响,筛选出最佳促增殖作用浓度和作用时间。通过Western Blot法检测MTA作用下h DPCs Notch信号及自噬相关蛋白表达的变化。结果:1.0 mg/m L MTA对体外培养h DPCs促增殖作用最显著,高浓度MTA(10 mg/m L)则具有一定的细胞毒性。与未处理h DPCs相比,MTA处理组h DPCs的Notch1、Hes1表达(P0.05)及自噬相关蛋白P62及LC3II/I表达(P0.01)均显著增高。平衡盐溶液(EBSS)饥饿实验诱导自噬发生后Notch1表达水平显著下降。结论:MTA可显著促进h DPCs的体外增殖,其作用机制可能与Notch1-Hes1信号转导途径激活及自噬抑制有关。     

Screening and identification of autophagy-related biomarkers for oral squamous cell carcinoma (OSCC) via integrated bioinformatics analysis

Increasing evidences have showed that autophagy played a significant role in oral squamous cell carcinoma (OSCC). Purpose of our study was to explore the prognostic value of autophagy-related genes (ATGs) and screen autophagy-related biomarkers for OSCC. RNA-seq and clinical data were downloaded from The Cancer Genome Atlas (TCGA) database following extracting ATG expression profiles. Then, differentially expressed analysis was performed in R software and a risk score model according to ATGs was established. Moreover, comprehensive bioinformatics analyses were used to screen autophagy-related biomarkers which were later verified in OSCC tissues and cell lines. A total of 232 ATGs were extracted, and 37 genes were differentially expressed in OSCC. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that these genes were mainly located in autophagosome membrane and associated with autophagy. Furthermore, the risk score on basis of ATGs was identified as potential independent prognostic biomarker. Moreover, ATG12 and BID were identified as potential autophagy-related biomarkers of OSCC. This study successfully constructed a risk model, and the risk score could predict the prognosis of OSCC patients accurately. Moreover, ATG12 and BID were identified as two potential independent prognostic autophagy-related biomarkers and might provide new OSCC therapeutic targets.     

Cheating on ubiquitin with Atg8

Macroautophagy sequesters superflous cytosol and organelles into double-membraned autophagosomes. Over 30 autophagy-related (ATG) genes have been identified without elucidating the molecular details of autophagosome biogenesis. All proposed models for autophagosome formation require membrane fusion events (Fig. 1). Previous studies assumed that the autophagic machinery mediates these membrane fusions in a SNARE-independent manner and identified the ubiquitin-like protein Atg8 as a key component especially for elongation of the forming autophagosome. However, if and how Atg8 mediates membrane fusion and why a ubiquitin-like protein is needed for autophagosome biogenesis remained open questions. Since nuclear envelope growth and fusion of Golgi fragments are topologically similar to autophagosome formation and depend on the AAA (+) ATPase p97/VCP and p47 we analyzed the involvement of their yeast homologues Cdc48 and Shp1 in macroautophagy.     

PAQR3 controls autophagy by integrating AMPK signaling to enhance ATG14L‐associated PI3K activity

The Beclin1–VPS34 complex is recognized as a central node in regulating autophagy via interacting with diverse molecules such as ATG14L for autophagy initiation and UVRAG for autophagosome maturation. However, the underlying molecular mechanism that coordinates the timely activation of VPS34 complex is poorly understood. Here, we identify that PAQR3 governs the preferential formation and activation of ATG14L‐linked VPS34 complex for autophagy initiation via two levels of regulation. Firstly, PAQR3 functions as a scaffold protein that facilitates the formation of ATG14L‐ but not UVRAG‐linked VPS34 complex, leading to elevated capacity of PI(3)P generation ahead of starvation signals. Secondly, AMPK phosphorylates PAQR3 at threonine 32 and switches on PI(3)P production to initiate autophagosome formation swiftly after glucose starvation. Deletion of PAQR3 leads to reduction of exercise‐induced autophagy in mice, accompanied by a certain degree of disaggregation of ATG14L‐associated VPS34 complex. Together, this study uncovers that PAQR3 can not only enhance the capacity of pro‐autophagy class III PI3K due to its scaffold function, but also integrate AMPK signal to activation of ATG14L‐linked VPS34 complex upon glucose starvation.     

Molecular machinery of autophagosome formation in yeast, Saccharomyces cerevisiae

Autophagy is a degradation process accompanied by dynamic membrane organization. In the yeast, Saccharomyces cerevisiae, about 30 ATG (autophagy-related) genes have been identified as important genes for autophagy. Among them, 17 are indispensable for formation of the autophagosome, an organelle enclosed by a double lipid bilayer during starvation-induced autophagy. Recently, a central structure for autophagosome generation, termed the pre-autophagosomal structure, was identified. Despite intensive study, many questions regarding the mechanisms underlying autophagosome formation remain unanswered. In this review, we will give an overview of recent studies on the mechanisms of autophagosome formation and discuss these unresolved questions.     

Comparative expression analysis of heavy metal ATPase subfamily genes between Cd-tolerant and Cd-sensitive turnip landraces

The heavy metal ATPase(HMA)subfamily is mainly involved in heavy metal(HM)tolerance and transport in plants,but an understanding of the definite roles and mechanisms of most HMA members are still limited.In the present study,we identified 14 candidate HMA genes named BrrHMAl—BrrHMA8 from the turnip genome and analyzed the phylogeny,gene structure,chromosome distribution,and conserved domains and motifs of HMAs in turnip(Brassica rapa var.rapa).According to our phylogenetic tree,the BrrHMAs are divided into a Zn/Cd/Co/Pb subclass and Cu/Ag subclass.The BrrHMA members show similar structural characteristics within subclasses.To explore the roles of BrrHMAs in turnip,we compared the gene sequences and expression patterns of the BrrHMA genes between a Cd-tolerant landrace and a Cd-sensitive landrace.Most BrrHMA genes showed similar spatial expression patterns in both Cd-tolerant and Cd-sensitive turnip landraces;some BrrHMA genes,however,were differentially expressed in specific tissue in Cd-tolerant and Cd-sensitive turnip.Specifically,BrrHMA genes in the Zn/Cd/Co/Pb subclass shared the same coding sequence but were differentially expressed in Cd-tolerant and Cd-sensitive turnip landraces under Cd stress.Our findings suggest that the stable expression and up-regulated expression of BrrHMA Zn/Cd/Co/Pb subclass genes under Cd stress may contribute to the higher Cd tolerance of turnip landraces.     

Oculopharyngeal muscular dystrophy mutations link the RNA-binding protein HNRNPQ to autophagosome biogenesis

Autophagy is an intracellular degradative process with an important role in cellular homeostasis. Here, we show that the RNA binding protein (RBP), heterogeneous nuclear ribonucleoprotein Q (HNRNPQ)/SYNCRIP is required to stimulate early events in autophagosome biogenesis, in particular the induction of VPS34 kinase by ULK1-mediated beclin 1 phosphorylation. The RBPs HNRNPQ and poly(A) binding protein nuclear 1 (PABPN1) form a regulatory network that controls the turnover of distinct autophagy-related (ATG) proteins. We also show that oculopharyngeal muscular dystrophy (OPMD) mutations engender a switch from autophagosome stimulation to autophagosome inhibition by impairing PABPN1 and HNRNPQ control of the level of ULK1. The overexpression of HNRNPQ in OPMD patient-derived cells rescues the defective autophagy in these cells. Our data reveal a regulatory mechanism of autophagy induction that is compromised by PABPN1 disease mutations, and may thus further contribute to their deleterious effects.     

FKBP8 is a novel molecule that participates in the regulation of the autophagic pathway

Autophagy is a homeostatic process by which misfolded proteins, organelles and cytoplasmic material are engulfed in autophagosomal vesicles and degraded through a lisosomal pathway. FKBP8 is a member of the FK506-binding proteins family (FKBP) usually found in mitochondria and the endoplasmic reticulum. This protein plays a critical role in cell functions such as protein trafficking and folding. In the present report we demonstrate that the depletion of FKBP8 abrogated autophagy activation induced by starvation, whereas the overexpression of this protein triggered the autophagy cascade. We found that FKBP8 co-localizes with ATG14L and BECN1, both members of the VPS34 lipid kinase complex, which regulates the initial steps in the autophagosome formation process. We have also demonstrated that FKBP8 is necessary for VPS34 activity. Our findings indicate that the regulatory function of FKBP8 in the autophagy process depends of its transmembrane domain. Surprisingly, this protein was not found in autophagosomal vesicles, which reinforces the notion that the FKBP8 only participates in the initial steps of the autophagosome formation process. Taken together, our data provide evidence that FKBP8 modulates the early steps of the autophagosome formation event by interacting with the VPS34 lipid kinase complex.SummaryIn this article, the protein FKBP38 is reported to be a novel modulator of the initial steps of the autophagic pathway, specifically in starvation-induced autophagy. FKBP38 interacts with the VPS34 lipid kinase complex, with the transmembrane domain of FKBP38 being critical for its biological function.     

RNA-binding protein,human antigen R regulates hypoxia-induced autophagy by targeting ATG7/ATG16L1 expressions and autophagosome formation

Autophagy, a prosurvival mechanism offers a protective role during acute kidney injury. We show novel findings on the functional role of RNA binding protein, HuR during hypoxia-induced autophagy in renal proximal tubular cells-2 (HK-2). HK-2 cells showed upregulated expressions of HuR and autophagy-related proteins such as autophagy related 7 (ATG7), autophagy related 16 like 1 (ATG16L1), and LC3II under hypoxia. Increased autophagosome formation was visualized as LC3 puncta in hypoxic cells. Further, short hairpin-RNA-mediated loss of HuR function in HK-2 cells significantly decreased ATG7 and ATG16L1 protein expressions. Bioinformatics prediction revealed HuR motif binding on the coding region of ATG7 and AU-rich element at 3′UTR ATG16L1 messnger RNA (mRNA). The RNA immunoprecipitation study showed that HuR was predominantly associated with ATG7 and ATG16L1 mRNAs under hypoxia. In addition, HuR enhanced autophagosome formation by regulating LC3II expressions. These results show that HuR regulates ATG7 and ATG16L1 expressions and thereby mediate autophagy in HK-2 cells. Importantly, HuR knockdown cells underwent apoptosis during hypoxia as observed through the terminal deoxynucleotidyl transferase dUTP nick end labeling assay. Collectively, these findings show the crucial role of HuR under hypoxia by regulating autophagy and suppressing apoptosis in renal tubular cells.     

Effects of Mycobacterium tuberculosis ESAT-6/CFP-10 fusion protein on the autophagy function of mouse macrophages

Autophagy plays specific roles in host innate and adaptive immune responses to numerous intracellular pathogens, including Mycobacterium tuberculosis. The ESAT-6 and CFP-10 proteins are secreted by M. tuberculosis and play important roles in pathogenesis. We hypothesized that these two proteins may affect the autophagy function of host macrophages during infection with M. tuberculosis, thereby shaping the immune reaction toward the pathogen. Interestingly, we found that rapamycin-induced autophagy of macrophages infected with M. tuberculosis H37Rv enhanced localization of mycobacteria with autophagosomes and lysosomes. Ectopic expression of the ESAT-6/CFP-10 fusion in macrophages dramatically inhibited autophagosome formation, and M. tuberculosis survival inside infected macrophages was significantly affected as well. Further, M. tuberculosis viability was increased by the fusion protein. Expression levels of autophagy-related genes (ATG), especially atg8, also decreased (p<0.05). These results suggested that ESAT-6 and CFP-10 proteins play significant roles in autophagy formation in M. tuberculosis infection and that autophagosome formation is regulated through the expression of ATG.     

肝细胞癌患者自噬相关基因的预后作用

构建由自噬相关基因组成的预后模型,预测肝细胞癌(HCC)患者的生存预后情况,为其个性化诊疗和临床研究提供依据。利用TCGA数据库中HCC的测序信息与人类自噬数据库联合,筛选差异表达的自噬相关基因,对其进行GO富集与KEGG通路分析;通过单因素与多因素Cox分析筛选与患者生存预后明显相关的风险基因,构建预后风险评分模型;根据模型计算患者风险值并验证模型,利用GEPIA2.0网页工具与HPA数据库对风险基因在HCC中的表达情况以及与生存预后的关系进行验证。结果发现,HCC肿瘤组织相较正常组织共筛选到61个差异表达的自噬相关基因(表达上调57个,下调4个),GO富集与KEGG通路分析显示均与自噬有关;单因素Cox分析共筛选到12个与患者生存预后相关的基因,多因素Cox分析后共有4个基因被纳入预后风险评分模型,分别是SQSTM1、HDAC1、RHEB和ATIC,计算公式为:风险值(risk score)=SQSTM1表达量×0.185+HDAC1表达量×0.382+RHEB表达量×0.423+ATIC表达量×0.438;K-M生存曲线显示高风险组生存率低于低风险组,风险曲线提示4个基因与不良预后密切相关,ROC曲线证明模型具有预测意义;GEPIA2.0网页工具以及HPA数据库表明高表达4个基因均导致患者生存率降低。所构建预后风险评分模型可有效预测HCC患者生存预后情况,并提供个性化诊疗策略。