Genomics Annotation And Comparative Studies Of Secondary Metabolite Biosynthetic Gene Clusters Of The Kingdom Bacteria

When the growth of microbes achieves a certain period, generally the stable phase, microbes will use primary metabolites as precursors to synthesize some secondary metabolites whose functions are not explicitly known for the producers themselves. This process is called secondary metabolism. Many microbial secondary metabolites have a variety of biological activities, such as anti-fungal, anti-bacterial and anti-tumour, etc. They are important sources for the development of new microbial clinical drugs. To date, antinomyces and myxobacteria are the models for the study of regulation of bacterial secondary metabolism and the major resources for the discovery of natural products. However, the sencondary metabolism potentials of bacteria have rarely been studied at the kingdom level.In this thesis, the secondary metabolism of Bacteria was studied at the kingdom level by performing systematic genomic annotation and comparative studies.A total of 635 bacteial genomes (>=4 Mb) were chosen from the NCBI (National Centre for Biotechnology Information) genome database. They are from 5 phyla, including Actinobacteria (122 strains), Bacteroidetes (52 strains), Cyanobacteria (39 strains), Firmicutes (89 strains) and Proteobacteria (333 strains). The Proteobacteria strains were from 4 classes, Alphaproteobacteria (90 strains), Betaproteobacteria (80 strains), Gammaproteobacteria (131 strains) and Deltaproteobacteria (32 strains). The secondary metabolite biosynthetic gene clusters were annotated by antiSMASH, and 40 types of secondary metabolite biosynthetic gene clusters (SMBGC) were found. Among them, biosynthetic gene clusters for NRPs, PKs, bacteriocins and terpenes were found in almost all the phyla and classes. Many types of SMBGC were mainly found in two or more phyla or classes and these gene clusters are for arylpolyenes, hserlactons, lanthipeptides, lassopeptides, T3PKs, otherks and siderophores. Other types of gene clusters were mainly found in only one phylum or class.For most types of gene clusters, the same type of gene clusters have similar lengths. At the kingdom level, there is a correlation between genome size and total length of gene clusters. Genomes of larger sizes tend to harbor longer gene clusters. Sorangium cellulosum So0157-2 (Deltaproteobacteria), with the largest genome (14.78 Mb), has 1.48 Mb gene clusters. Streptomyces bingchenggensis BCW-1 (Actinobacteria), with an 11.94 Mb geome, has the longest gene clusters (2.77 Mb).The correlation level varies among phyla/classes. Actinobacteria (R2=0.62, p-value<2.2e-16) and Deltaproteobacteria (R2=0.74, p-value=1.07e-10) have the highest relevance.Most bacterial plasmids do not carry SMBGC. However for some strains, plasmids comtribute to 50% of the SMBGC in their genomes.Gene families are constructed for genes in all clusters. For each type of secondary metabolites, their biosynthetic gene clusters were divided into different groups based on homologous genes. The largest group was chosen as a model to study the evolution and gene cluster structure. Comparative genomic results showed that, for most types of secondary metabolites, clusters in one group were distributed in different phyla/classes. Each cluster contains both genes conserved among phyla and genes specific to a particular taxonomy. Clusters from the same genus have high similaritis in the structure. On the contrary, those from different genera have low similarities.The genus Pseudoalteromonas was chosen as a model to study secondary metabolism of marine bacteria. Secondary metabolite biosynthetic gene clusters were annotated in the genomes of 26 type strains. SMBGC in non-pigmented strains are very short (mean,0.04 Mb). Both groups contain bacteriocin biosynthetic gene clusters. Non-pigmented strains have gene clusters for siderophores while pigmented strains have clusters for NRPs and PKs. Comparative analysis revealed that pigmented Pseudoalteromonas strains are among those with the longest SMBGC in the class Gammaproteobacteria.This thesis revealed the secondary metabolism capacity and features of evolution of bacteria. It also contributes to the discovery of novel natural bioactive compounds in bacteria.