Physiological response in E. coli to YdgR overexpression depends on whether the protein has an intact function

Area of Science:

• Biochemistry
• Molecular Biology
• Systems Biology

Background:

• Membrane transport proteins are crucial for cellular homeostasis, facilitating molecule transport across cell membranes.
• Overexpression of these proteins in host cells (bacteria, yeast, mammalian) is known to impact global metabolomic and proteomic profiles.
• Investigating these physiological alterations can provide insights into cellular functions and gene roles.

Purpose of the Study:

• To investigate the physiological consequences of overexpressing the E. coli membrane transport protein YdgR.
• To compare the effects of a functional YdgR with an attenuated mutant (YdgR-E33Q) on host cell 'omics' profiles.
• To explore the potential of using protein overexpression studies for deorphanizing y-gene transportome.

Main Methods:

• Utilized the E. coli lab strain BL21 (DE3)pLysS for protein overexpression.
• Employed metabolomic and proteomic analyses to compare host cells expressing functional YdgR versus YdgR-E33Q.
• Performed molecular network analysis to identify metabolic pathway alterations.

Main Results:

• Significant differences were observed in the metabolomic and proteomic profiles between cells expressing functional YdgR and the attenuated mutant.
• Upregulation of uncharacterized y-proteins and enzymes involved in peptide and amino acid metabolism was noted in cells with functional YdgR.
• Molecular network analysis indicated a higher abundance of proline-containing tripeptides in cells expressing functional YdgR.

Conclusions:

• Overexpression of the YdgR membrane transport protein induces distinct physiological changes in host cells.
• The observed metabolic and proteomic shifts, particularly in amino acid and peptide metabolism, highlight the functional impact of YdgR.
• Further investigation into these overexpression-induced alterations may aid in identifying the functions of uncharacterized y-genes and their associated transport systems.