Progress in the function of nucleoporin 50 and its relationship with viral infection / 中华微生物学和免疫学杂志

Nucleoporin 50 (Nup50) is a component of nuclear basket in nuclear pore complex. It includes three main domains: N domain binding to importin α, F domain binding to importin β and R domain binding to Ran. The N domain has two importin α-binding segments. There are mainly two models for explaining the role of Nup50 in nuclear import: tri-stable switch and disassemble-recycle model. Nup50 not only participates in nuclear import, but also regulates genome organization and gene expression. In addition, Nup50 is involved in the process of viral infection and replication. There is some evidence that Nup50 is related to hepatitis B virus and human immunodeficiency virus 1 infections. However, there are few researches on the relationship between Nup50 and viral infection. This article summarized the progress in the function of Nup50 and its relationship with viral infection, aiming to provide new ideas for the following in-depth study.

Tryptophan and tumor immunity / 药学学报

As an essential amino acid, tryptophan (Trp) has various physiological functions and is of great significance in the metabolic process of tumors. In the human body, tryptophan is mainly transformed through kynurenine metabolic pathway, which not only promotes the inherent malignant properties of tumor cells, but also leads to immune-suppressive tumor microenvironment. Changes in tryptophan metabolism often occur in tumors, accompanied by abnormal gene expression of tryptophan-related enzymes, among which indoleamine 2,3-bioxygenase (IDO)-related gene expression and tryptophan 2,3-dioxygenase (TDO)-related gene changes are the most significant. A large number of clinical trials on IDO inhibitors, TDO inhibitors and combination therapy have been carried out. This paper reviewed the tryptophan metabolic pathway, regulation of IDO (TDO), kynurenine (KYN) and other related genes in tumor cells, and outlined the development of therapeutic schedule targeting tryptophan-related genes. The new progress provides new ideas for the further exploration of tumor treatment options.

Metabolic regulation in constructing microbial cell factories / 生物工程学报

The regulation of the expression of genes involved in metabolic pathways, termed as metabolic regulation, is vital to construct efficient microbial cell factories. With the continuous breakthroughs in synthetic biology, the mining and artificial design of high-quality regulatory elements have substantially improved our ability to modify and regulate cellular metabolic networks and its activities. The research on metabolic regulation has also evolved from the static regulation of single genes to the intelligent and precise dynamic regulation at the systems level. This review briefly summarizes the advances of metabolic regulation technologies in the past 30 years.

Characterization of the mRNA untranslated regions [UTR] of the Trypanosoma cruzi LYT1 isoforms derived by alternative trans-splicing / Caracterización de las regiones no traducidas ARN [UTR] de las isoformas de Trypanosoma cruzi LYT1 derivadas de un trans-empalme alternativo / Caracterização das regiões não-traduzidas do RNA [UTR] das isoformas de Trypanosoma cruzi LYT1 derivadas de uma junção trans-alternativa

Abstract In trypanosomatids, gene expression is mainly regulated at posttranscriptional level, through mechanisms based on the interaction between RNA Binding Proteins [RBPs] and motifs present in the untranslated regions [UTRs] of the mRNAs, which altogether form ribonucleoproteic complexes [RNP] that define the fate of the mRNA. The pre-mRNA derived from the LYT1 gene of Trypanosoma cruzi, is processed by alternative trans-splicing, resulting in different mRNAs which code for the isoforms mLYTl and kLYTl, proteins having differential expression, cellular location and function. The aim of this study was to characterize the 5' and 3' UTRs of the LYT1 mRNAs as the initial step towards the objective of identification of the RBPs responsible for their differential expression. The presence of the two types of 5' UTRs were confirmed in two T. cruzi isolates belonging to the DTU I, thus, corroborating the occurrence of alternative trans-splicing also in the LYT1 gene of this T. cruzi DTU. In addition, for the first time, was unscovered the existence of two types of LYT1 mRNAs transcripts, differing in length by 116 nts, that are generated by alternative polyadenylation. Furthermore, an in-silico analysis of the experimentally obtained UTRs, and ten additional LYT1 sequences retrieved from TritrypDB and GenBank databases, together with a thoroughly search of structural motifs, showed a remarkable conservation of relevant structural motifs previously associated with RNA metabolism in the different UTRs; these elements might be involved in the differential stage-specific expression of each LYT1 isoform.

Resumen En los trypanosomátidos, la expresión génica se regula principalmente en el nivel post-transcripcional mediante mecanismos basados en la interacción entre las proteínas de unión del ARN [RBP] y las figuras presentes en las regiones no traducidas [UTR] de las ARN, que en conjunto forman complejos ribonucleoproteicos [RNP] que definen el destino de la ARN. El pre-ARN derivado del gen LYT1 del Trypanosoma cruzi es procesado por trans-empalme alternativo, dando como resultado diferentes ARN que codifican las isoformas mLYTl y kLYTl, proteínas con expresión diferencial, localización celular y función. El objetivo de este estudio fue caracterizar los 5' y 3' UTR de las ARN LYT1 como el paso inicial hacia la identificación de los RPB responsables de la expresión diferencial. Se confirmó la presencia de los dos tipos de 5' UTR en dos aislantes del T. cruzi pertenecientes al DTU I; de esta forma también se comprobó la ocurrencia del trans-empalme alternativo en el gen LYT1 de este T. cruzi DTU. Además, por primera vez, se pudo demostrar la existencia de dos tipos de transcripciones de ARN LYT1, que difieren en longitud por 116 nts, y son generadas por poliadenilación alternativa. Adicionalmente, se realizó un análisis in-silico de la UTR obtenida experimentalmente, y otras diez secuencias LYT1 recuperadas de las bases de datos TritrypDB y GenBank, junto con una búsqueda exhaustiva de figuras estructuradas, mostrando una notable conservación de los figuras estructurales asociadas con el metabolismo del ARN en los diferentes UTR; estos elementos podrían estar implicados en la expresión diferenciada de la etapa específica de cada isoforma LYT1.

Resumo Nos tripanossomatídeos, a expressão génica é regulada principalmente a nível pós-transcricional mediante mecanismos baseados na interação entre as proteínas de união do RNA [RBPs] e as fugiras presentes nas regiões não-traduzidas [UTRs] do RNA. O pré-RNA derivado do gene LYT1 do Trypanosoma cruzí é processado por uma junção trans-alternativa, resultando em diferentes RNA que codificam as isoformas mLYTl e kLYTl, proteínas com expressão, localização celular e função diferenciadas. O objetivo de este estudo foi caracterizar as 5' e 3' UTRs dos RNAs LYT1 como sendo o passo inicial na identificação das RBPs responsáveis pela expressão diferenciada. A presença dos dois tipos de 5' UTRs foi confirmada em dois isolados de T. cruzí pertencentes ao DTU I; corroborando assim com a ocorrência da junção trans-alternativa no gene LYT1 de este T. crují DTU. Adicionalmente, se demonstrou pela primeira vez a existência de dois tipos de transcrições de RNA LYT1, que se diferenciam em comprimento por 116 nts, e são geradas por poliadenização alternativa. Além disso, realizou-se uma análise in-sílico da UTR obtida experimentalmente e outras dez sequencias LYT1 recuperadas das bases de dados TritrypDB e GenBank, junto com uma busca exaustiva de figuras estruturadas, mostrando uma notável conservação das figuras estruturais associadas com o metabolismo do RNA nas diferentes UTRs. Estes elementos poderiam estar envolvidos na expressão estágio-específica diferenciada de cada isoforma LYT1.

The hepatic ectonucleotide pyrophosphatase/phosphodiesterase 1 gene mRNA abundance is reduced by insulin and induced by dexamethasone

Hormones regulate hepatic gene expressions to maintain metabolic homeostasis. Ectonucleotide pyrophosphatase/phosphodiesterase 1 has been thought to interfere with insulin signaling. To determine its potential role in the regulation of metabolism, we analyzed its gene (Enpp1) expression in the liver of rats experiencing fasting and refeeding cycles, and in primary rat hepatocytes and human hepatoma HepG2 cells treated with insulin and dexamethasone using northern blot and real-time PCR techniques. Hepatic Enpp1 expression was induced by fasting and reduced by refeeding in the rat liver. In primary rat hepatocytes and HepG2 hepatoma cells, insulin reduced Enpp1 mRNA abundance, whereas dexamethasone induced it. Dexamethasone disrupted the insulin-reduced Enpp1 expression in primary hepatocytes. This is in contrast to the responses of the expression of the cytosolic form of phosphoenolpyruvate carboxykinase gene to the same hormones, where insulin reduced it significantly in the process. In addition, the dexamethasone-induced Enpp1 gene expression was attenuated in the presence of 8-Br-cAMP. In conclusion, we demonstrated for the first time that hepatic Enpp1 is regulated in the cycle of fasting and refeeding, a process that might be attributed to insulin-reduced Enpp1 expression. This insulin-reduced Enpp1 expression might play a role in the development of complications in diabetic patients.

G-quadruplex Structures in Promoters of MET Proto-oncogene / 中国医科大学学报

Objective To identify G?quadruplex structures in the promoter region of MET. Methods CD spectroscopy,UV spectroscopy,non?denatured electrophoresis and PCR stop assay were applied to indicate the G?quadruplex structure and its function. Results The Pu23WT se?quence in the promoter of MET adopted an intramolecular parallel G?quadruplex structure under physiological conditions in vitro,which can stop the extension of Pmet. Conclusion G?quadruplex structure in the promoter might inhibit MET gene expression in vivo.

A new understanding of Pax6, a master regulator in eye and brain development / 中华实验眼科杂志

Background Paired box gene 6 (Pax6) is a master regulator for eye and brain development.Pax6 mutations or changes in its expression cause a series of ocular diseases including absence of iris,corneal opacity,cataract,glaucoma,abnormal fovea,retinoblastoma,and Wilm's tumor-aniridia-qenital ahormalies-retardation (WAGR).As a transcription factor,it is expressed in the region of anterior surface ectoderm corresponding to the future adenohypophyseal,olfactory and lens placodes,optic vesicle and other parts of the future brain and thus control the development of eye,brain,pituitary grand,nose and pancreas.Pax6 exists in 4 different isoforms,whose functions are subjected to regulation by different post-translation modifications.A complete understanding of the structure and functions of Pax6 and its associations with relevant diseases is helpful for ophthalmologists to investigate the pathogenesis and treatment of implicated ocular diseases caused by Pax6 gene mutation or changing in its expression.

From basic studies to clinical application: Advances in novel oncogene ATAD2 and tumors / 肿瘤

AT Pase family, AAA domain containing 2 (ATAD2) is a newly uncovered oncogene playing an important role in occurrence and development of prostate cancer, breast cancer and other human malignancies. It is a coactivator of a variety of transcription factors, and it can also modulate genes through epigenetic modifications, resulting in overexpression of its downstream oncogenes, and in turn changing the phenotypes of tumor cells; what's more, the expression of ATAD2 is associated with histological grade of cancer, metastasis, disease recurrence and the survival, indicating that it can be used as a molecular marker for prognosis of cancer and has remarkable value in clinical application. Furthermore, ATAD2 contains bromodomain (BRD) and also functions as cellular activity-associated ATPase, which means that ATAD2 may be a potential target for drug therapy. This review summarizes the recent findings and discusses the prospect of this field.

Estudo da função do gene kerV de Pseudomonas aeruginosa / Function of Pseudomonas aeruginosa kerV gene

P. aeruginosa PA14 é uma linhagem isolada de queimadura que apresenta vários fatores de patogenicidade comuns no quadro de infecção de hospedeiros filogeneticamente distintos (plantas, mamíferos ou invertebrados). O gene kerV foi revelado numa busca por mutantes atenuados em virulência em uma biblioteca de mutantes por transposons da linhagem PA14 (Rahme et al., 1997). A caracterização da linhagem D12, mutante em kerV, confirmou sua virulência atenuada (Apidianakis et al., 2005 e An et al., 2009) e resultados do transcriptoma mostraram alteração na expressão de mais de 500 genes, sendo alguns relacionados com o sistema de "quorum sensing" (Rahme et al, dados não publicados). O gene kerV está próximo à montante ao gene gloB, envolvido em detoxificação de metilglioxal, e à jusante aos genes rnhA e dnaQ, que codificam proteínas envolvidas na replicação e reparo do DNA. Este trabalho teve como objetivo estudar a função molecular do produto de kerV e a expressão dos genes do lócus kerV-rnhA-dnaQ. Análises de bioinformática indicam que a proteína KerV é uma metiltransferase dependente de S-adenosil-metionina (SAM), apresentando um domínio conservado de ligação a SAM e uma arquitetura de domínio compatível com a organização em fitas-beta e hélices-alfa alternadas descritas para a família das metiltransferases dependentes de SAM. Ela não apresenta outros domínios conservados que indiquem seu substrato de metilação. A expressão heteróloga desta proteína em E. coli, mostrou que ela é expressa de maneira parcialmente solúvel quando co-expressa com as chaperoninas GroEL/GroES em baixas temperaturas ou quando fusionada a MBP ou GST. A purificação desta proteína mostra que ela é co-eluída com a chaperonina GroEL sugerindo que para atingir sua conformação nativa ela necessita dessas proteínas acessórias. MBP-KerV purificado foi usado para ensaios "in vitro" de atividade de metiltransferase e ligação a SAM, que não foram conclusivos, pois não há certeza do seu ...

P. aeruginosa PA14 is a burn isolate multi-host pathogen strain. The screening for virulence attenuated mutants in a PA14 transposon mutant library revealed the kerV gene (Rahme et al., 1997). The characterization of D12 strain, a kerV mutant, confirmed the attenuated virulence phenotype (Apidianakis et al., 2005 and An et al., 2009) and transcriptome analysis showed the expression of more than 500 genes are affected in D12, some of these genes are related with quorum sensing (Rahme et al, unpublished data). kerV is upstream of the gloB gene, related with methylglioxal detoxification and downstream of the rnhA and dnaQ genes, both related with DNA replication and repair. The purpose of this work was to study the molecular function of KerV product and the expression of kerV-rnhA-dnaQ locus. Bioinformatics analysis indicated that KerV is a SAM dependent methyltransferase that have a conserved SAM binding domain with architecture compatible with classic alternating β-stranded and α-helical regions. KerV does not show any other conserved motif that could indicate its methylation substrate. Heterologous expression in E. coli showed that KerV is partially soluble only when co-expressed with GroeL/GroES chaperones at low temperatures or when KerV is in fusion with MBP or GST tag. During the purification process KerV was copurified with GroEL chaperone suggesting that this association may be required for the correct folding of KerV. Methyltransferase activity and SAM binding assays were done with purified MBPKerV and the results were not conclusive since the proper conformation of MBP-KerV cannot be verified. Yeast two-hybrid assays indicated that RNaseH and DnaQ are not interaction partners of KerV, suggesting that their functions are not directly related. The mutation frequency of D12 strain increased only about four times in relation to PA14, suggesting that KerV is not directly involved with DNA mismatch repair. The assays to detect methylation...

Exploration on the Teaching Method of Regulation of Gene Expression / 中华医学教育探索杂志

To analyze the problems in teaching regulation of gene expression in biochemistry and investigate the teaching method which can improve the teaching of the contents.