<P><B>Abstract</B></P> <P>The MEP pathway genes were modulated to investigate whether there were new rate-limiting steps and toxic intermediates in this pathway. Activating IspG led to significant decrease of cell growth and β-carotene production. It was found that <I>ispG</I> overexpression led to accumulation of intermediate HMBPP, which seriously interfered with synthesis machinery of nucleotide and protein in <I>Escherichia coli</I>. Activation of the downstream enzyme IspH could solve HMBPP accumulation problem and eliminate the negative effects of <I>ispG</I> overexpression. In addition, intermediate MECPP accumulated in the starting strain, while balanced activation of IspG and IspH could push the carbon flux away from MECPP and led to 73% and 77% increase of β-carotene and lycopene titer respectively. Our work for the first time identified HMBPP to be a cytotoxic intermediate in MEP pathway and demonstrated that balanced activation of IspG and IspH could eliminate accumulation of HMBPP and MECPP and improve isoprenoids production.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Activating IspG led to decreased cell growth and β-carotene production. </LI> <LI> <I>ispG</I> overexpression led to accumulation of intermediate HMBPP. </LI> <LI> HMBPP accumulation interfered with nucleotide and protein synthesis. </LI> <LI> Balanced activation of IspG and IspH eliminated HMBPP and MECPP accumulation. </LI> <LI> β-carotene titer increased 73% by balanced activation of IspG and IspH. </LI> </UL> </P>