Identification and characterization of scaffold-associated region (SAR) of rRNA gene of silkworm Attacus ricini

identify the specific nuclear scaffold-bound DNA sequence in rRNA gene clusters of silkwormAttacus ricini, the detergent-like salt lithium 3′, 5′ diiodosalicylate (LIS) was used for the preparation of nuclear scaffold. Through Southern hybridization, using different DNA stretches of rRNA gene as the probe, a scaffold-associated region (SAR) in the 5-non transcribed spacer (NTS) of rRNA gene has been identified. Exonuclease III digestion was used to narrow down the sequence of matrix attachment fragment. It was defined as a specific attachment site within the SacII-EcoRI fragment. It is about 1 kb in length and AT-rich (> 70%). Computer analysis of the SAR sequencing data showed that there are topoisomerase II cleavage sites, ATATTT box, and yeast autonomously replication sequence (ARS). The d(AT)₁₈ specific DNA sequence of the SAR, which was determined previously, was an S1 nuclease hypersensitive site. It might be a cis-element of DNA-signal characteristic for SAR. Project supported by the National Natural Science Foundation of China (Grant No. 39570398).     

蓖麻蚕rRNA基因中SAR对真核基因表达的调控

蓖麻蚕核糖体RNA基因非转录间隔区（NTS）有一长约1kb所核骨架结合区（scaffold-associated region,SAR）。将这一序列克隆到含荧光素酶（luciferase）报告基因的真核表达载体pLu中,在阳离子脂质体的介导下对NIH3T3细胞进行瞬时转染（transient transfection)及稳定转化（stable transformed)株的筛选,然后检测SAR在瞬时转染及稳定整合条件下对荧光毒酶报告基因表达活性的影响。实验结果表明,在稳定转化的细胞中,该SAR对lucicerase基因的有明显的激活作用,增强基因表达活性约15倍;而在瞬时表达的条件下,SAR激活基因表达的作用不明显。说明SAR增强基因的表达可能需要整合在染色体上才能完成,我们用Southwestern印9迹法实验进一步证实了蓖麻蚕rRNA基因的SAR能特异性地与NIH3T3细胞核骨架蛋白结合,因此该SAR的作用具有非组织特异性。     

Identification and characterization of scaffold-associated region (SAR) of rRNA gene of silkwormAttacus ricini

identify the specific nuclear scaffold-bound DNA sequence in rRNA gene clusters of silkwormAttacus ricini, the detergent-like salt lithium 3′, 5′ diiodosalicylate (LIS) was used for the preparation of nuclear scaffold. Through Southern hybridization, using different DNA stretches of rRNA gene as the probe, a scaffold-associated region (SAR) in the 5-non transcribed spacer (NTS) of rRNA gene has been identified. Exonuclease III digestion was used to narrow down the sequence of matrix attachment fragment. It was defined as a specific attachment site within the SacII-EcoRI fragment. It is about 1 kb in length and AT-rich (> 70%). Computer analysis of the SAR sequencing data showed that there are topoisomerase II cleavage sites, ATATTT box, and yeast autonomously replication sequence (ARS). The d(AT)₁₈ specific DNA sequence of the SAR, which was determined previously, was an S1 nuclease hypersensitive site. It might be a cis-element of DNA-signal characteristic for SAR.     

蓖麻蚕核型多角体病毒多角体蛋白基因的克隆和核苷酸序列分析

蓖麻蚕(Attacus ricini)是我国特有蚕种,以其核多角体病毒(ArNPV)为载体有可能发展成为新的基因工程表达系统,我们建立了ArNPV基因库,并亚克隆了含多角体蛋白(Ph)基因DNA片段。对该1.1kb全长DNA片段进行序列分析,确定ArNPV Ph结构基因全长735bp,与苜蓿尺蠖NPV(AcNPV)、家蚕NPV(BmNPV)同源性分别为76%和81%,ArNPV 5'端调控结构Rohrmann box与各类NPV的Ph基因相似,但3'下游序列几无同源,显示了ArNPV Ph基因结构的特征性。同时,我们还对Ph基因启动子的其它结构特点作了剖析。     

蓖麻蚕核糖体大亚基RNA基因3‘—端序列分析及进化研究

测定了蓖麻蚕核糖体大亚基ＲＮＡ编码区３’－端ＤＮＡ序列,分析了其二级结构,并与昆虫伊蚊、果蝇;线虫;脊椎动物人、小鼠、爪蟾;低等脊索动物海鞘以及真菌酵母、毛霉相应的保守区段进行了同源比较。邻接法分析表明,昆虫核糖体大亚基ＲＮＡ在进化上与５ＳｒＲＮＡ相似,有加快的趋势。     

两株蓖麻蚕核型多角体病毒的比较研究

本文描述来源不同的两株菌麻蚕多角体病毒的形态特征和理化特性。一株为较长期饲喂马桑叶的蓖麻蚕从自然罹死的幼虫和蛹中分离的多角体病毒（简称ArscsNPV);另一株为饲喂蓖麻叶的蓖麻蚕从幼虫分离的核型多角体病毒（简称ArscsNPV);另一株为饲喂蓖麻叶的蓖麻蚕从幼虫分离的核型多角体病毒（简称ArNPV)。两株核型多角体病ArNPV多角体大小约1．2－2．0μm最大的可达2．9μm。两株NPV病毒粒子均为杆状,ArscsNPV病毒粒子大小平均为310×50nm;ArNPV病毒粒子大小为350×50nm。两株NPV均为多粒包埋型。两株NPV的多角体蛋白均为单一组分,ArscsNPV多角体蛋白分子量为27．5kd;ArNPV多角体蛋白分子量为28kd。两株NPV的病毒粒子结构多肽均含有21条多肽,其中各多肽分子量有所差异。ArscsNPV的病毒粒子多肽分子量范围为11－130kd;ArNPV病毒粒子多肽分子量范围为11－96kd,其中有11种多肽了量彼此相同包括两种主要多肽（54kd和33kd）。用SDS－苯酚提取的病毒核酸,经实验证明均为双链DNA型使用几种内切酶酶解,求得两株NPV的核酸分子量,ArscsNPV为52．4×10^6d;ArNPV为73．5×10^6d。     

An SAR sequence containing 395 bp DNA fragment mediates enhanced,gene-dosage-correlated expression of a chimaeric heat shock gene in transgenic tobacco plants

A 395 bp fragment located downstream from the soybean heat shock geneGmhsp 17.6-L exhibits several characteristics of scaffold attachment region (SAR) sequences. It contains matrix consensus elements, a topoisomerase II binding sequence and it associates with the isolated nuclear scaffold of soybeanin vitro. Chimaeric genes containing the SAR_L fragment either at one side (5 or 3) or at both sides of a heat shock promoter-regulated -glucuronidase reporter gene were constructed. A five-to nine-fold increase of heat-inducible -glucuronidase activity was observed in transgenic tobacco plants containing constructs with SAR_L fragments either at both sides or with at least one SAR_L copy located upstream from the reporter gene. The gene copy number is positively correlated with the level of heat-inducible reporter gene activity in these. plants but positional effects are not entirely eliminated. Thus, SAR sequences may potentially be used to increase gene expression, via as yet unknown mechanisms, and to reduce adverse effects on the expression of multiple gene copies in transgenic plants.     

Use of matrix attachment regions (MARs) to minimize transgene silencing

Matrix attachment regions (MARs) are operationally defined as DNA elements that bind specifically to the nuclear matrix in vitro. It is possible, although unproven, that they also mediate binding of chromatin to the nuclear matrix in vivo and alter the topology of the genome in interphase nuclei. When MARs are positioned on either side of a transgene their presence usually results in higher and more stable expression in transgenic plants or cell lines, most likely by minimizing gene silencing. Our review explores current data and presents several plausible models to explain MAR effects on transgene expression.     

Detection of Laribacter hongkongensis using species-specific duplex PCR assays targeting the 16S rRNA gene and the 16S-23S rRNA intergenic spacer region (ISR)

Aims: For the rapid detection of Laribacter hongkongensis, which is associated with human community‐acquired gastroenteritis and traveller’s diarrhoea, we developed a duplex species‐specific PCR assay. Methods and Results: Full‐length of the 16S–23S rRNA intergenic spacer region (ISR) sequences of 52 L. hongkongensis isolates were obtained by PCR‐based sequencing. Two species‐specific primer pairs targeting 16S rRNA gene and ISR were designed for duplex PCR detection of L. hongkongensis. The L. hongkongensis species‐specific duplex PCR assay showed 100% specificity, and the minimum detectable level was 2·1 × 10^?2 ng μl^?1 genomic DNA which corresponds to 5000 CFU ml^?1. Conclusions: The high specificity and sensitivity of the assay make it suitable for rapid detection of L. hongkongensis. Significance and Impact of the Study: This species‐specific duplex PCR method provides a rapid, simple, and reliable alternative to conventional methods to identify L. hongkongensis and may have applications in both clinical and environmental microbiology.     

Molecular characterization of Fasciola flukes using mitochondrial 28S rRNA gene in Naimi Saudi sheep

Fasciolosis is a parasitic disease of medical and economic importance. This retrospective study was conducted on 110 Fasciola flukes collected from livers of 14 infected Naimi sheep slaughtered at Riyadh abattoir in Saudi Arabia during winter season of 2016. Collected specimens were analyzed for their species identification on the basis of partial sequences of mitochondrial 28S rRNA gene. Results have shown the presence of both Fasciola hepatica (F. hepatica) and Fasciola gigantica (F. gigantica) species. Where Fasciola hepatica was predominate (80%). Both intra-species and interspecies genetic distance was studied and results showed that the intraspecific variability among individuals of both species i.e., F. hepatica and F. gigantica, ranging between 0 and 1% while the interspecific diversity between F. hepatica and F. gigantica was only 1%. In conclusion, mitochondrial 28S rRNA gene is a proved as a good marker in identifying Fasciola of different species. Where, the F. hepatica and F. gigantica are present in sheep breed in Riyadh region, Saudi Arabia.     

Analysis of oral infection and helicase gene of the nucleopolyhedroviruses isolated from Philosamia cynthia ricini and Antheraea pernyi

Philosamia cynthia ricini is an important commercial silkworm in Asia. In this report, a nucleopolyhedrovirus isolated from P. cynthia ricini (PhcyNPV) larva was purified and compared with Antheraea pernyi nucleopolyhedrovirus (AnpeNPV), a pathogen of A. pernyi, another commercial silkworm in China. The two viruses had similar polyhedral morphology and shared high sequence homologue of viral fragments including the p143 gene. However, the restriction fragments, digested with SalI, XhoI, HindIII and PstI, respectively, were different. The cross-infectivity of the two viruses was also tested. AnpeNPV caused 57% mortality in larvae of P. cynthia rici, whereas PcrNPV did not kill larvae of A. pernyi. Results indicated that PhcyNPV and AnpeNPV had closed relatedness, and that PhcyNPV might be a variant of AnpeNPV.     

Study on fibroin heavy chain of the silkworm Bombyx mori by fluorescence in situ hybridization (FISH)

The sericulture industry plays a very important role in our national economy. Silkworm (Bombyx mori) is always regarded as a model animal and biological reactor. There have been detailed studies on the structure, expression and control and molecular evolution of silk genes. However, few, if any, reports are available on the localization of structural genes in silkworm by molecular cytogenetics. The present experiment has tentatively localized the Fib-H gene at the distal end of the 25th linkage group, namely at the 25-0.0 position, and verified that Fib-H has only one locus, thus providing a temporary solution to the problem about its localization.     

家蚕组织蛋白酶基因家族的鉴定及表达特征分析

家蚕是鳞翅目完全变态昆虫,在其变态过程中伴随着巨大的形态变化,包括旧组织的解离和新组织的形成,在这过程中有多种组织蛋白酶参与。组织蛋白酶是一类细胞内蛋白酶,广泛存在于各个物种中,包括组织蛋白酶B、H、L等几个亚家族。对家蚕组织蛋白酶的研究将有利于阐明家蚕变态发育的详细过程。通过对家蚕基因组数据库进行筛选,共在家蚕中鉴定到13种组织蛋白酶,并对这13种组织蛋白酶的基本信息和表达模式进行了分析。另外,利用家蚕基因芯片数据和荧光定量PCR分析,鉴定编号为BGIBMGA004622的基因为卵巢特异表达的组织蛋白酶L亚家族基因。该基因全长1 209 bp,编码402个氨基酸。经过序列分析,该酶与其他物种的组织蛋白酶L具有较高的同源性,其活性位点高度保守,且与鳞翅目的组织蛋白酶L在进化上聚为一支。同时,对该基因进行克隆并原核表达,结果显示重组蛋白以包涵体的形式表达。定量PCR结果显示,该酶在蛹发育初期表达量逐渐升高,至蛹3 d达到最高值,推测其可能参与卵巢与卵母细胞的发育过程。     

Structure and Functions of Nuclear Matrix Associated Regions (S/MARs)

Modern concepts on the chromatin loop–domain organization and the role of the DNA regions specifically binding the nuclear matrix or nuclear scaffold (S/MARs) during its formation, maintenance, and regulation are discussed. Some S/MAR structural features, properties of binding the nuclear matrix, and probable mechanisms of their involvement in the gene regulation of activity are considered.     

Identification of a novel mutation affecting domain V of the 23S rRNA gene in Helicobacter pylori

BACKGROUND: This study analyzes clarithromycin resistance status and 23S rRNA gene mutations in Helicobacter pylori strains from Central Italian patients. MATERIALS AND METHODS: H. pylori strains from 235 dyspeptic patients (205 with no history of clarithromycin exposure and 30 referred for failure of eradication therapy) were tested for clarithromycin resistance by screening agar method and E-test. Resistant strains were analyzed for mutations of the 23S rRNA gene by PCR-RFLP and sequencing. RESULTS: Primary resistance was observed in strains from 43/205 (21%) patients with no history of clarithromycin exposure and secondary resistance in 30/30 (100%) strains from previously treated patients. A single mutant strain was detected in 54/73 (74%) cases, a mixture of one or more mutant(s) plus the wild type in the remaining 19/73 (26%) cases. One 23S rRNA gene mutation (A-->T transversion at nucleotide 2144) in the peptidyltransferase region of domain V was novel. CONCLUSIONS: This study shows: (a) a high prevalence of H. pylori strains with primary or secondary clarithromycin resistance in an urban area of Central Italy; (b) colonization by both mutant and wild-type H. pylori in the same patient; (c) a novel variant of the H. pylori 23S rRNA gene.     

Complete sequence and gene organization of the Nosema spodopterae rRNA gene

By sequencing the entire ribosomal RNA (rRNA) gene of Nosema spodopterae, we show here that its gene organization follows a pattern similar to the Nosema type species, Nosema bombycis, i.e. 5'-large subunit rRNA (2,497 bp)-internal transcribed spacer (185 bp)-small subunit rRNA (1,232 bp)-intergenic spacer (277 bp)-5S rRNA (114 bp)-3'. Gene sequences and the secondary structures of large subunit rRNA, small subunit rRNA, and 5S rRNA are compared with the known corresponding sequences and structures of closely related microsporidia. The results suggest that the Nosema genus may be heterogeneous and that the rRNA gene organization may be a useful characteristic for determining which species are closely related to the type species.     

Ecdysteroid as a mediator in the regulation of silk protein synthesis and its influence on silkworm (Bom., Lepidoptera) genome

Abstract:  Ecdysteroid is one of the two most important insect hormones, which controls growth and developmental activities of insect. In silkworm, Bombyx mori L., basically ecdysteroid induces molting and metamorphosis in larvae and exogenous administration hastens the silk synthetic activity and cocoon spinning process but it strictly depends on the time of administration. In the present study, we administered phytogenous ecdysteroid to the 48-h-old 5th instar silkworm, B. mori at a single dose of 2  μ g per larva to study its effects on the larval growth, cocoon and silk variables. The possible role of ecdysteroid in altering the developmental sequence of silkworm and thereby its effect on cocoon and silk production at molecular level have been tried to get elucidated. The genomic DNA was isolated from the posterior silk gland on day 5 and 7 of the 5th instar from the ecdysteroid treated and the control larvae and was randomly amplified with arbitrary primers. The result presented notable variation in the amplified product suggesting the participation of ecdysteroid in regulating the silk gene. The feeding period of treated larvae was unaffected while the cocoon characters exhibited considerable improvement. The filament traits also were improved notably in the treated larvae. The participation of ecdysteroid in the silk biosynthetic process with its physiological and molecular implications was discussed.