Advance in research of characteristics and action mechanism of microRNAs from prokaryotes / 中国人兽共患病学报

microRNAs is a group of small non-coding RNAs that play a negative regulation role in expression of target genes at post-transcriptional level by inhibition or degradation of target mRNAs after combination of the seed sequence (SS) in microRNAs with the SS-binding sequences usually located at 5'ends of target mRNAs.microRNAs was firstly found in Caenorhabditis elegans.Subsequently,many different microRNAs in eukaryocytes were revealed.In eukaryocytes,microRNA precursors are transcribed at first and then become functional microRNAs with 21-23 nt in size after splice.Most of eukaryocytic microRNAs combime with the sequences at 3'end of target mRNAs that cause the translation inhibition or degradation of the mRNAs.In the recent years,many different prokaryocytes,such as bacteria,have been confirmed to possess microRNAs.However,the microRNAs in prokaryotes such as bacteria are 50-400 nt in size and have the biological activity without splice.Moreover,the characteristics,action sites and mechanisms of the prokaryotic microRNAs have some certain diversity compared to the eukaryotic microRNAs.Our review briefly introduce the major regulation mechanisms of gene expression as well as the general characteristics of microRNAs and their regulation mechanisms of gene expression in prokaryocytes and eukaryocytes,which will provide a basis for further and profound study on the gene expression regulation and pathogenic mechanisms of prokaryotic microbial pathogens.

ANALIZANDO DATOS DE RNA-Seq EN PROCARIOTAS: UNA REVISIÓN PARA NO EXPERTOS: A Review for Non-experts / RNA-Seq Data Analysis in Prokaryotes

La secuenciación de transcritos con RNA-Seq es hoy en día una de las técnicas más populares en los estudios transcriptómicos. Relativamente reciente, esta técnica ha permitido la secuenciación de transcritos de RNA en una escala y profundidad no alcanzada por otras técnicas anteriores. Sin embargo, el alcance de las conclusiones que se pueden sacar depende estrictamente de un proceso adecuado, desde el diseño experimental hasta el análisis bioinformático de los datos. Dadas las diferencias en el proceso transcripcional de las células eucariotas y procariotas, el análisis de RNA-Seq deberá tener ciertas consideraciones dependiendo del tipo de organismo estudiado. En esta revisión se exponen los principales factores a tener en cuenta para lograr un análisis de RNA-Seq consistente, replicable y concluyente, enfocándose específicamente en organismos procariotas.

RNA-Seq is nowadays the method of choice for the sequencing of transcripts and transcriptomes in the field of molecular biology and gene expression assays. Until recently, this technique has allowed for the sequencing of RNA transcripts in an unprecedented scale and depth never reached in previous years; nevertheless, the reach and validity of the conclusions generated will depend strictly on an adequate experimental design and a robust analysis of the data. Given the inherent differences between prokaryotes and eukaryotes, the RNA-Seq analysis should take into account the type of organism studied. In this review we present the main factors to take into consideration when designing a consistent analysis for this type of data in prokaryotes, from the experimental design to the in silico analysis of the generated data.

Intrinsically bent DNA in replication origins and gene promoters

Intrinsically bent DNA is an alternative conformation of the DNA molecule caused by the presence of dA/dT tracts, 2 to 6 bp long, in a helical turn phase DNA or with multiple intervals of 10 to 11 bp. Other than flexibility, intrinsic bending sites induce DNA curvature in particular chromosome regions such as replication origins and promoters. Intrinsically bent DNA sites are important in initiating DNA replication, and are sometimes found near to regions associated with the nuclear matrix. Many methods have been developed to localize bent sites, for example, circular permutation, computational analysis, and atomic force microscopy. This review discusses intrinsically bent DNA sites associated with replication origins and gene promoter regions in prokaryote and eukaryote cells. We also describe methods for identifying bent DNA sites for circular permutation and computational analysis.

Update of microbial genome programs for bacteria and archaea

Since the Haemophilus influenzae genome sequence was completed in 1995, 172 other prokaryotic genomes have been completely sequenced, while 508 projects are underway. Besides pathogens, organisms important in several other fields, such as biotechnology and bioremediation, have also been sequenced. Institutions choose the organisms they wish to sequence according to the importance that these species represent to them, the availability of the microbes, and based on the similarity of a species of interest with others that have been sequenced previously. Improvements in sequencing techniques and in associated methodologies have been achieved; however, scientists need to continue working on the development of this field. In Brazil, a multicentered, centrally coordinated and research-focused network was adopted and successfully used for the sequencing of several important organisms. We analyzed the current status of microbial genomes, the trends for criteria used to choose new sequencing projects, the future of microbial sequencing, and the Brazilian genome network.