Fig. 2

Overview of the stress responses induced by (over)expression of (heterologous) proteins. The top figure shows the situation in unstressed cells: (i) Protein synthesis; (ii) Charging of tRNA with their cognate amino acid; (iii) Degradation of \(\sigma ^{\textrm{S}}\) and \(\sigma ^{\textrm{H}}\) by ClpXP and FtsH respectively; (iv) AC bound to ACP. The bottom figure gives an overview of how (over)expression of (heterologous) proteins induces stress and how different stress mechanisms are connected. Effect on the cell: (1) Depletion of amino acids due to increased protein synthesis; (2) Depletion of specific amino acids because of a different amino acid composition; (3) Recharging of tRNAs compromised due to a lack of (specific) amino acids; (4) Depletion of tRNAs because of an over-use of rare codons; (5) Uncharged tRNAs present in the ribosomal A-site; (6) Translation errors occur due to long waiting times for the ribosome for the correct charged tRNA to arrive; (7) Codon optimised sequences result in misfolding of proteins; (8) Changed mRNA sequence influences its stability. Stress mechanisms: (a) RelA (stringent response) produces ppGpp in response to uncharged tRNAs in the ribosomal A-site; (b) SpoT (stringent response) produces ppGpp because of fatty acid starvation; (c) ppGpp transcriptionally activates several genes; (d) Transcription of iraP only happens under phosphate starvation in the presence of SpoT; (e) sRNA dsrA binds to rpoS, frees the RBS and allows translation; (f) IraP and IraD are anti-adaptor proteins, inhibiting the function of RssB to deliver \(\sigma ^{\textrm{S}}\) to ClpXP for degradation; (g) DnaK/J are sequestered by misfolded proteins for refolding and degradation; (h) Proteases assist in degrading misfolded proteins, resulting in reduced degradation of \(\sigma ^{\textrm{S}}\) and \(\sigma ^{\textrm{H}}\); (i) \(\sigma ^{\textrm{S}}\) involved in activating the heat shock response via an unknown mechanism. ppGpp guanosine tetra- and pentaphosphate, AC Acyl chain, ACP Acyl carrier protein, RBS ribosome binding site, tRNA transfer RNA, mRNA messenger RNA, sRNA small RNA. Gene structures are displayed according to the SBOL guidelines [6]