Reorganization of gene network of Bacillus subtilis for amylase production and secretion under different conditions


Shaomin Yan;Guang Wu;


As an important cell factory,B.subtilis can produce large amounts of designed proteins,for which many efforts have been made to improve its properties in order to meet the demand for industrial application.B.subtilis has a sophisticated genetic system to regulate and control its protein production and secretion.In B.subtilis,about 150 genes have been identified in response to amylase overproduction and super-secretion,meanwhile these genes can function differently under different conditions because no single gene acts alone without interaction with other genes.Therefore it is necessary to study how these genes behave under different conditions in order to better understand this sophisticated genetic system.One way to study how genes behave under different conditions is to conduct the transcriptome studies,whose data have been documented in Gene Expression Omnibus(GEO).In this study,we apply network analysis to investigating the transcriptome data of B.subtilis from GEO including platforms GPL 188,GPL343,GPL6257,GPL 15025,GPL 19890,etc.under different conditions,and construct gene networks focusing on the abovementioned genes related to amylase production and secretion.The results show that gene networks are different under different experimental conditions in terms of gene clusters,which consequently lead the genes related to amylase production and secretion to change their memberships.Such changes do not act alone but are associated with different genes,thus the network analysis reveals what types of genes are more likely to follow amylase production and secretion genes to change their memberships.Furthermore,gene hierarchical structures are built,and relevant implications are discussed.To our knowledge,this is the first study to use network analysis to integrate all B.subtilis genes together to get a whole picture of the gene relationships for amylase production and secretion,which provides information on better understanding of the mechanisms as suggested by Big Data to Knowledge(BD2K)initiative.This study can shed light on enzyme engineering to enhance protein production.


Amylase;;Bacillus subtilis;;Gene;;Network analysis;;Overproduction;;Reorganization;;Hyper-secretion


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