Bioinformatic Researches On Genomic Structure, Function And Regulatory Mode In Cyanobacteria

Cyanobacteria is known as one of the simplest and oldest species on the earth. The structure and function of cyanobacteria is studied easier and faster than other species due to its smaller genome, and the related information can be used in drug production and disease prevention. sRNAs participate in various biological processes such as transcription regulation, chromosome replication, RNA processing and modification, protein translation and degradation. The study on sRNA in cyanobacteria can give us a thorough understanding of complicated regulatory mechanism, and help us make RNAi fragment for gene silencing, which is meaningful in human embryonic development and tumor suppressor. Cyanobacteria can adapt various habitats and take an interaction with the surrounding ecosystem. pH is an environmental signal that can affect the physiological process and toxin synthesis of cyanobacteria. The related researches provide theoretical basis for antibiotics development. In this study, we systematically analyzed the genomic structure of the latest sequenced strain by bioinformatic algorithms and tools, and determined the function of key genes and proteins. Then we discussed the structure、function and regulatory mode of sRNA. At last, we constructed the gene network under acid stress and elaborated the response mechanism.The thesis mainly includes the following three parts:1. Analyze the genomic structure of Synechococcus PCC7336. We constructed local blast database and local annotation database to decipher the new sequenced genome of Synechococcus PCC7336. The number of coding genes, core RNAs and repetitive sequences were predicted, GC content and GC skew were canculated. Comparision with other strains showed the difference between Synechococcus PCC7336 and other strains. Then we analyzed and summarized the gene function involved in photosynthesis, signal transduction and metabolism. Phylogenetic tree based on 16 S rRNA showed the significant differences between Synechococcus PCC7336 and other Synechococcus strains. We inferred that Synechococcus PCC7336 is an independent branch.2. Study the non-coding RNA and genomic islands. So far, 20 members have been found in Yfr family while the further researches on these members are rare. We picked Yfr1 and Yfr7 as the targets and did their sequence blast first. The results showed both of them have a very conservative region, independent promoter and terminator. Their secondary structure presented the arrangement of stem-loop-stem. Then we combined classic Waterman algorithm and hybrid energy to predict the targets of Yfr7, and described the targets from cellular component, molecular function and biological process. Phylogenetic tree analysis showed their evolution has the correlation with species and habitats. We also made a general analysis and summary for other Yfr members. At last, we predicted the specific location of 11 genomic islands and classified them according to their practical roles.3. Construct the gene network under the acid stress. We firstly collected many confirmed genes from Escherichia coli, Lactococcus lactis and Salmonella enterica for the acid stress response and mapped them to Synechocystis PCC6803. Using the 85 collected genes, the initial template was constructed. Then the new genes were predicted through co-regulation, global regulator, protein-protein interactions and phylogenetic profiles, and 264 genes were obtained to form a complete template. All the genes were divided into 6 categories according to their functions. The enrichment analysis and the results from the existing literatures were used to confirm the reliability of the predicted results, and the connection relationships beween all the genes were constructed. At last, we summarized the key steps of acid stress response for Synechocystis PCC6803, and it is clearly seen that the productions of some genes can participate in multiple metabolic reactions.We analyzed the genomes of cyanobacteria by bioinformatic methods from the individual to the group, which include the sequence, the structure, the regulation and the evolution. The useful information obtained not only coveres some blank of this field, but also provides guidance value for applications of cyanobacteria in biofuel, agricultural and food production.