Bioinformatic identification and experimental validation of miRNAs from foxtail millet (Setariaitalica)

MiRNAs are a novel group of non-coding small RNAs that negatively regulate gene expression. Many miRNAs have been identified and investigated extensively in plant species with sequenced genomes. However, few miRNAs have been identified in foxtail millet (Setaria italica), which is an ancient cereal crop of great importance for dry land agriculture. In this study, 271 foxtail millet miRNAs belonging to 44 families were identified using a bioinformatics approach. Twenty-three pairs of sense/antisense miRNAs belonging to 13 families, and 18 miRNA clusters containing members of 8 families were discovered in foxtail millet. We identified 432 potential targets for 38 miRNA families, most of which were predicted to be involved in plant development, signal transduction, metabolic pathways, disease resistance, and environmental stress responses. Gene ontology (GO) analysis revealed that 101, 56, and 23 target genes were involved in molecular functions, biological processes, and cellular components, respectively. We investigated the expression patterns of 43 selected miRNAs using qRT-PCR analysis. All of the miRNAs were expressed ubiquitously with many exhibiting different expression levels in different tissues. We validated five predicted targets of four miRNAs using the RNA ligase mediated rapid amplification of cDNA end (5′-RLM-RACE) method.     

柯萨奇病毒B组3型基因组剪切片段的序列分析

柯萨奇病毒B组(Coxsackievirus B,CVB)感染细胞时其基因组RNA存在不稳定现象,但产生机制尚不清楚。本研究将柯萨奇病毒B组3型(CVB3)感染细胞后,利用5′ cDNA末端快速扩增技术(5′ rapid amplification of cDNA ends,5′ RACE)扩增并克隆细胞内CVB3基因组片段,并对每条序列及其5′端的二级结构进行分析。结果获得的20条CVB3基因组片段,长度为 2 067～5 547 bp,片段断端主要分布于2Apro和2C编码区。RNAfold分析显示,这些片段多数在5′断点端形成二级茎-环结构。本研究显示,CVB在宿主细胞感染时可形成大量不完整基因组RNA片段,这些片段可在5′断点端形成局部双链结构,提示片段不是随机产生,可能是RNA酶剪切产物。此发现有助于理解CVB基因组不稳定的机制。     

Isolation and characterization of a cDNA encoding a serine proteinase from the root-knot nematode Meloidogyne incognita

This report describes the first serine proteinase gene isolated from the sedentary nematode Meloidogyne incognita. Using degenerate primers, a 1372bp cDNA encoding a chymotrypsin-like serine proteinase (Mi-ser1) was amplified from total RNA of adult females by RT-PCR and 5' and 3' rapid amplification of cDNA ends. The deduced amino acid sequence of Mi-ser1 encoded a putative signal peptide and a prodomain of 22 and 33 amino acids, respectively, and a mature proteinase of 341 amino acids with a predicted molecular mass of 37,680Da. Sequence identity with the top serine proteinases matches from the databases ranged from 23 to 27%, including sequences from insects, mammals, and other nematodes. Southern blot analysis suggested that Mi-ser1 is encoded by a single or few gene copies. The pattern of developmental expression analyzed by Northern blot and RT-PCR indicated that Mi-ser1 was transcribed mainly in females. The domain architecture composed of a single chymotrypsin-like catalytic domain and the detection of a putative signal peptide suggested a digestive role for Mi-ser1.     

Molecular cloning of Daphnia magna catalase and its biomarker potential against oxidative stresses

Catalase (EC 1.11.1.6) is an important antioxidant enzyme that protects aerobic organisms against oxidative damage by degrading hydrogen peroxide to oxygen and water. Catalase mRNAs have been cloned from many species and employed as useful biomarkers of oxidative stress. In the present study, we cloned the cDNA from the catalase gene in Daphnia magna, analyzed its catalytic properties, and investigated mRNA expression patterns after the exposure to known oxidative stressors. The catalase proximal heme-ligand signature sequence, FDRERISERVVHAKGSGA, and the proximal active site signature, RLFSYTDTH, are highly conserved. The variation of catalase mRNA expression in D. magna was quantified by real-time PCR, and the results indicated that catalase expression was up-regulated after exposure to UV-B light or cadmium (Cd). The activity of catalase enzyme also showed a similar increasing pattern when exposed to these model stressors. The full-length catalase cDNA of D. magna was cloned using mixed primers by the method of 3′ and 5′ rapid amplification of cDNA ends PCR. The cDNA sequence consists of 1515 nucleotides, encoding 504 amino acids. Sequence comparison showed that the deduced amino acid sequence of D. magna shared 73%, 72%, 71% and 70% identity with that of Chlamys farreri, Fenneropenaeus chinensis, Litopenaeus vannamei and Anopheles gambiae, respectively. This study shows that the catalase mRNA from D. magna could be successfully employed as a biomarker of oxidative stress, which is a common mode of toxicity for many water contaminants.     

两株希木龙假丝酵母14α-去甲基化酶基因(ERG11)的克隆及其功能初步验证

为探讨希木龙假丝酵母(假丝酵母又称念珠菌)的耐药机制,首先克隆出两株希木龙念珠菌ERG11基因,初步验证其功能,从而为后续研究奠定基础。从美国国家生物技术信息中心(National Center of Biotechnology Information,NCBI)基因数据库中获取白念珠菌、热带念珠菌、近平滑念珠菌和光滑念珠菌Erg11蛋白的保守序列,设计简并引物,聚合酶链反应(polymerase chain reaction,PCR)扩增获得希木龙念珠菌ERG11cDNA部分片段;用快速cDNA末端扩增法(rapid amplification of cDNA ends,RACE)分别扩增其5′和3′端,获得完整的ERG11编码序列(coding sequence,CDS);将CDS克隆到pYES2表达载体中,在尿嘧啶营养缺陷型酿酒酵母中过表达ERG11;用微量液基稀释法检测转化后的酿酒酵母对氟康唑的敏感性,初步验证其功能。结果显示,简并PCR扩增获得预期708bp片段,5′RACE和3′RACE分别获得385bp和1 336bp片段,经纯化、克隆、测序、比对分析,获得两株菌的ERG11CDS;比对其编码的蛋白,与其他念珠菌的Erg11蛋白高度同源;分别检测克隆了这两株希木龙念珠菌ERG11CDS表达载体的酿酒酵母对氟康唑的敏感性,发现过表达ERG11明显降低其对氟康唑的敏感性。结果提示,简并PCR联合RACE能准确有效地克隆出希木龙念珠菌ERG11基因,用pYES2酿酒酵母表达系统能初步验证其功能。     

Molecular cloning and characterization of the sheep α-TTP gene and its expression in response to different vitamin E status

The α-tocopherol transfer protein (α-TTP) is a ~ 32 kDa protein that exhibits a marked ligand specificity and selectively recognizes of α-tocopherol, which is the most active form of vitamin E. The α-TTP gene has been cloned and its physiological functions have been studied in numbers of species, however, the understanding of sheep α-TTP is still in his infancy. In this study, the full-length cDNA of sheep α-TTP gene was cloned from sheep liver by using of rapid amplification of complementary DNA ends (RACE). As a result, the sheep α-TTP gene was 1098 bp in nucleotide which contained 23 bp 5'-untranslated region (UTR), 226 bp 3'-UTR and 849 bp open reading frame (ORF) that encoded a basic protein of 282 amino acids. Further bioinformatic analysis indicated that the sheep α-TTP gene had a high homologous of both nucleotide and amino acid sequences compared with that of other species and had a Sec14p-like lipid-binding domain which called the CRAL-TRIO domain. Moreover, the expression of sheep α-TTP mRNA and protein in response to different vitamin E supplemented levels were observed according to quantitative real-time PCR (qRT-PCR) and Western blotting analysis. The results showed that dietary vitamin E levels did not affect α-TTP mRNA expression significantly while the low vitamin E supplemented level groups of sheep had significantly higher α-TTP protein compared to high-vitamin E groups.     

Extraction of High-Quality RNA from Rubber Tree Leaves

A specific technique capable of producing high-quality RNA for rapid amplification of cDNA ends (RACE) was established for challenging tissues: leaves of the rubber tree. Total RNA was extracted by cetyltrimethylammonium bromide (CTAB)-LiCl combined with TRIzol reagent. The isolated RNA was highly intact. With RNA as template, full-length cDNA was obtained (NCBI, AY461413) by RACE.     

Versican 3′-untranslated region (3′UTR) promotes dermal wound repair and fibroblast migration by regulating miRNA activity

Versican is an extracellular chondroitin sulfate proteoglycan which functions as a structural molecule but can also regulate a variety of cellular activities. This study was designed to explore the roles of versican in the process of dermal wound repair. To elevate levels of versican, we ectopically expressed the versican 3′-untranslated region (3′UTR) as a competitive endogenous RNA to modulate expression of versican. We demonstrated that wounds closed faster in transgenic mice expressing the versican 3′UTR, as compared to those in wildtype mice. We stably expressed versican 3′UTR in NIH3T3 fibroblasts and found that the 3′UTR-transfected cells showed increased migratory capacity relative to vector-transfected cells. Interestingly, we found that the 3′UTRs of versican and β-catenin shared common microRNAs (miRNAs) including miR-185, miR-203*, miR-690, miR-680, and miR-434-3p. Luciferase assays showed that all of these miRNAs could target the 3′UTRs of both versican and β-catenin, when the luciferase constructs contained fragments harboring the miRNA binding sites. As a consequence, expression of both versican and β-catenin was up-regulated, which was confirmed in vitro and in vivo. Transfection with small interfering RNAs (siRNAs) targeting the versican 3′UTR abolished the 3′UTR's effects on cell migration and invasion. Taken together, these results demonstrate that versican plays important roles in wound repair and that versican messenger RNAs (mRNAs) could compete with endogenous RNAs for regulating miRNA functions.     

MicroRNA profile analysis of a feline kidney cell line before and after infection with mink enteritis virus

MicroRNAs (miRNAs) are small regulatory RNAs that play a significant role in eukaryotes by targeting mRNAs for cleavage or translational repression. Recent studies have also shown them to be associated with cellular changes following viral infection. Mink enteritis virus (MEV) is one of the most important viral pathogens in the mink industry. To study the involvement of miRNAs in the MEV infection process, we used Illumina's ultrahigh throughput approach to sequencing miRNA libraries from the feline kidney (F81) cell line before and after infection with MEV. Using this bioinformatics approach we identified 196 known mammalian miRNA orthologs belonging to 152 miRNA families in F81 cells. Additionally, 97 miRNA*s of these miRNAs were detected. As well as known miRNAs, 384 and 398 novel miRNA precursor candidates were identified in uninfected and MEV-infected F81 cells respectively that have not been reported in other mammals. In MEV-infected cells 3 miRNAs were significantly down-regulated and 4 up-regulated including 3 significantly. The majority (12 of 16) of randomly selected miRNA expression profiles by qRT-PCR were consistent with those identified by deep sequencing. A total of 88 miRNAs were predicted to target interferon-associated genes; 6 appear to target the 3′UTR of MEV-specific receptor transferring receptor mRNAs; and 8 to target the MEV mRNA coding region. No miRNAs coded by MEV itself were detected.