Transcriptome And DAP-seq Study Of Transcription Factors In Salt Tolerance Response Of Halotolerant Bacteria From Chaka Salt Lake

Bacillus licheniformis strain CSL2 is a strain with salt tolerance that was collected and isolated from Chaka Salt Lake.In order to better explore the transcriptional regulation mechanism of this strain under salt stress conditions,the Next Generation Sequencing based on Illumina Hiseq 2500 platform and long single molecular sequencing based on Nanopore were carried out to analysis the whole genome of strain CSL2;according to the growth curve of the cultured strains,13 groups of cells under different culture conditions were selected for transcriptome sequencing analysis to predict salt tolerance-related transcription factors;DNA affinity purification sequencing technology?DAP-seq?was applied to capture the regulatory region of transcription factors,excavate target genes regulated by salt-tolerant transcription factors,and analyze their functions to provide a basis for the construction of a salt-tolerant transcription regulation network of strain CSL2.The main results of thesis are as follows:The genome of Bacillus licheniformis strain CSL2 was a set of circular plasmid-free molecule with a chromosome number of 1.The total length of the genome sequence was 4,280,457 bp,and the G + C content was 45.92%.It contains 4246 coding genes,81 tRNAs,24 5S-16S-23 S rRNA operons and 5 other non-coding RNAs.By comparing and analyzing the COG database,the coding genes were considered to be mainly involved in functional classification such as general function prediction only,transcription,amino acid transportation and metabolism,and carbohydrate transport and metabolism.The strain CSL2 genome contains a variety of salt-tolerant genes,allowing it to survive in hypertonic environments.Its genomic information also contains enzymes related to sugar metabolism and cellulose degradation,so that salt-tolerant bacteria have good viability and research value.Specific genomic data information has been submitted to the NCBI database,GenBank number is CP041154.Thirteen sets of transcriptome data were analyzed by TopHat and Cufflinks software,and 3940 differentially expressed genes were obtained,including 3388 up-regulated genes and 552 down-regulated genes.By comparing and analyzing the GO database,it was found that the differential genes are mainly involved in metabolic process,single-organism process,cellular process,membrane,catalytic activity,and binding.By comparing and analyzing the COG database,it was found that the differential genes were mainly concentrated in functional classification such as general function prediction only,transcription,amino acid transportation and metabolism,and carbohydrate transport and metabolism.Combining PFAM biological information prediction with differentially expressed genes,this study predicts a total of 6 transcription factors?5 families?: gene-BLCSL₀1560?PadR-like family?? gene-BLCSL₀3550?TetR_C family?? gene-BLCSL₀6300?CitT family?? gene-BLCSL₁0835?TetR_C family?? gene-BLCSL₁8415?Trns_repr_metal family??gene-BLCSL₂1000?IclR family??DAP-seq technology was used to enrich DNA fragments bound to transcription factors.After sequencing,bioinformatics was used to analyze the enrichment region of binding sites.The results showed that gene-BLCSL₀1560 detected 633 peaks,found 3 long fragments and 8 short fragment motif;gene-BLCSL₀3550 detected 518 peaks,found 2 long fragment and 7 short fragment motif;gene-BLCSL₀6300 detected 14 peaks,found 1 long fragment motif;gene-BLCSL₁0835 detected 50 peak and no motif was found;no reliable peaks were detected for gene-BLCSL₁8415 and gene-BLCSL₂1000.GO enrichment analysis of samples detected with peaks found that the four groups of target genes regulated by transcription factors are mainly involved in single-organism process,cellular process,metabolic process,membrane,membrane part,catalytic activity,binding and other biology process,it is speculated that the regulatory mechanisms of these four transcription factors may be similar.