Genomic Analysis Of And Transcriptomic Study Of The Effects Of Oxygen On Magnetospirillum Sp. ME-1

Magnetotactic bacteria?MTB?are polyphyletic Gram-negative bacteria that biosynthesize membrane-enveloped magnetic nanocrystals known as magnetosomes.Although MTB are widespread distribution,only a few isolates are cultivated.Oxygen is a primary factor limiting magnetosome formation and cell growth.However,the mechanisms involved in effects of oxygen on MTB growth and magnetosome formation have been poorly understood.In order to increase our understanding on these mechanisms,the genomic and transcriptomic analysis under microaerobic and aerobic conditions were performed in a novel spiral MTB strain,Magnetospirillum sp.ME-1.ME-1 was closest to Magnetospirillum sp.XM-1 according to 16S rRNA gene sequence similarity.The complete genome sequence of ME-1 was 4,551,873 bp length,and it showed the highest similarity to XM-1 genome with a pairwise average nucleotide identify value of 92.5%.Thus ME-1 was considered as a new species.A circular plasmid in ME-1 contained six genes with non-similarity to all known genes,therefore it may be a novel plasmid.The magnetosome biogenesis-specific genes of ME-1 were located at a 97,664-bp magnetosome genomic island?MAI?.MAI of ME-1 contained 96 genes including37 magnetosome specific genes,which were clustered in mamAB,mamAB-like,mamGFDC,mamXY and mms operons,respectively.Compared with the MAI of other MTB,the MAI of ME-1 possessed additional copy of mamPA and a larger mamO in mamAB-like operon,and a smaller mamJ in mamAB operon.ME-1 had an intact citric acid cycle and complete pathway models for pyruvate metabolism,ammonium assimilation and dissimilatory nitrate reduction.Potential carbon and nitrogen sources in these pathways were confirmed to be used in ME-1.The nif gene cluster coding nitrogenase was found in the ME-1 genome,thus ME-1could grow in the absence of a nitrogen source.ME-1 genome contained multiple genes coding key enzymes involved in?-oxidation.Adipate might be used to support the heterotrophic growth of ME-1 through?-oxidation.Adipate was used in the fermentation medium as a new kind of dicarboxylic acid,and the large-scale production of magnetosomes was achieved by using this medium.In the present study,we cultivated ME-1 under high and low oxygen concentrations.Aerobic ME-1 cells did not synthesize magnetosomes and had higher intracellular iron content than that of microaerobic ones.We further performed high throughput RNA sequencing of aerobic and microaerobic ME-1 cells and compared the transcriptome profiles of aerobic cells with that of the microaerobic ones.We found that expression level of mamAB operon was not influenced by high oxygen concentrations.Genes?mms and cco?responsible for the redox balance were downregulated in response to oxidative stress.The result suggested that the formation of the magnetosome was indirectly suppressed by high oxygen,probably through disturbing the redox balance.Furthermore,high oxygen stimulated the aerobic growth of ME-1 probably by upregulating genes coding oxidases aa₃ and bo₃,superoxide dismutases and other major redox proteins.The quantitative real-time polymerase chain reaction analysis of nine key magnetosome formation and aerobic growth-related genes also verified the results of transcriptomic analysis.In addition,there were 152 transcriptional factors?TFs?in ME-1,and 15 significant regulatory TFs were predicted in the regulatory network for DEGs.This possible interaction of TFs and DEGs formed the basis for the establishment of transcriptional networks that are linked to the oxidative signal in ME-1.Our study provides insights into pathway models of MTB growth and regulatory network in response to oxidative stress.The findings might lay the foundation for isolating and cultivating new MTB strains and engineering an MTB strain.