Proteomic analysis of Escherichia coli detergent-resistant membranes (DRM)

Environmental adaptation and diversification of bacterial two-component systems

Bacterial two-component systems (TCS) are versatile signaling mechanisms that govern cellular responses to diverse environmental cues. These systems rely on phosphoryl-group transfers between histidine- and aspartate-containing modules of sensor histidine kinase and response regulator proteins. TCS diversity is shaped by the ecological niche of the bacterium, resulting in significant population-level variations. Consequently, orthologous TCSs can display considerable divergence throughout the signaling process. Here, we venture into the mechanisms governing the emergence of TCS variation, and explore the adaptation of orthologous TCS in bacteria with dissimilar lifestyles. The peculiar features of the bacterial adaptive response A/ultraviolet light repair Y (BarA/UvrY) and anoxic redox control B/anoxic redox control A (ArcB/ArcA) and their ortholog TCSs illustrate the remarkable capacity of TCSs to evolve and finely tune their signaling mechanisms, effectively addressing specific environmental challenges.

Theoretical study of ArcB and its dimerization, interaction with anaerobic metabolites, and activation of ArcA

The complex metabolism of Escherichia coli has been extensively studied, including its response to oxygen availability. The ArcA/B two-component system (TCS) is the key regulator for the transition between these two environmental conditions and has been thoroughly characterized using genetic and biochemical approaches. Still, to date, limited structural data is available. The breakthrough provided by AlphaFold2 in 2021 has brought a reliable tool to the scientific community for assessing the structural features of complex proteins. In this report, we analyzed the structural aspects of the ArcA/B TCS using AlphaFold2 models. The models are consistent with the experimentally determined structures of ArcB kinase. The predicted structure of the dimeric form of ArcB is consistent with the extensive genetic and biochemical data available regarding mechanistic signal perception and regulation. The predicted interaction of the dimeric form of ArcB with its cognate response regulator (ArcA) is also consistent with both the forward and reverse phosphotransfer mechanisms. The ArcB model was used to detect putative binding cavities to anaerobic metabolites, encouraging testing of these predictions experimentally. Finally, the highly accurate models of other ArcB homologs suggest that different experimental approaches are needed to determine signal perception in kinases lacking the PAS domain. Overall, ArcB is a kinase with features that need further testing, especially in determining its crystal structure under different conditions.

Escherichia coli SPFH Membrane Microdomain Proteins HflKC Contribute to Aminoglycoside and Oxidative Stress Tolerance

Many eukaryotic membrane-dependent functions are often spatially and temporally regulated by membrane microdomains (FMMs), also known as lipid rafts. These domains are enriched in polyisoprenoid lipids and scaffolding proteins belonging to the stomatin, prohibitin, flotillin, and HflK/C (SPFH) protein superfamily that was also identified in Gram-positive bacteria. In contrast, little is still known about FMMs in Gram-negative bacteria. In Escherichia coli K-12, 4 SPFH proteins, YqiK, QmcA, HflK, and HflC, were shown to localize in discrete polar or lateral inner membrane locations, raising the possibility that E. coli SPFH proteins could contribute to the assembly of inner membrane FMMs and the regulation of cellular processes. Here, we studied the determinant of the localization of QmcA and HflC and showed that FMM-associated cardiolipin lipid biosynthesis is required for their native localization pattern. Using Biolog phenotypic arrays, we showed that a mutant lacking all SPFH genes displayed increased sensitivity to aminoglycosides and oxidative stress that is due to the absence of HflKC. Our study therefore provides further insights into the contribution of SPFH proteins to stress tolerance in E. coli. IMPORTANCE Eukaryotic cells often segregate physiological processes in cholesterol-rich functional membrane microdomains. These domains are also called lipid rafts and contain proteins of the stomatin, prohibitin, flotillin, and HflK/C (SPFH) superfamily, which are also present in prokaryotes but have been mostly studied in Gram-positive bacteria. Here, we showed that the cell localization of the SPFH proteins QmcA and HflKC in the Gram-negative bacterium E. coli is altered in the absence of cardiolipin lipid synthesis. This suggests that cardiolipins contribute to E. coli membrane microdomain assembly. Using a broad phenotypic analysis, we also showed that HflKC contribute to E. coli tolerance to aminoglycosides and oxidative stress. Our study, therefore, provides new insights into the cellular processes associated with SPFH proteins in E. coli.

Spatiotemporal regulation of the BarA/UvrY two-component signaling system

The BarA/UvrY two-component signal transduction system mediates adaptive responses of Escherichia coli to changes in growth stage. At late exponential growth phase, the BarA sensor kinase auto-phosphorylates and transphosphorylates UvrY, which activates transcription of the CsrB and CsrC noncoding RNAs. CsrB and CsrC, in turn, sequester and antagonize the RNA binding protein CsrA, which post-transcriptionally regulates translation and/or stability of its target mRNAs. Here, we provide evidence that, during stationary phase of growth, the HflKC complex recruits BarA to the poles of the cells, and silences its kinase activity. Moreover, we show that, during the exponential phase of growth, CsrA inhibits hflK and hflC expression, thereby enabling BarA activation upon encountering its stimulus. Thus, in addition to temporal control of BarA activity, spatial regulation is demonstrated.

Plasma Membrane-Cell Wall Feedback in Bacteria

Most bacteria have cell wall peptidoglycan surrounding their plasma membranes. The essential cell wall provides a scaffold for the envelope, protection against turgor pressure and is a proven drug target. Synthesis of the cell wall involves reactions that span cytoplasmic and periplasmic compartments. Bacteria carry out the last steps of cell wall synthesis along their plasma membrane. The plasma membrane in bacteria is heterogeneous and contains membrane compartments. Here, I outline findings that highlight the emerging notion that plasma membrane compartments and the cell wall peptidoglycan are functionally intertwined. I start by providing models of cell wall synthesis compartmentalization within the plasma membrane in mycobacteria, Escherichia coli, and Bacillus subtilis. Then, I revisit literature that supports a role for the plasma membrane and its lipids in modulating enzymatic reactions that synthesize cell wall precursors. I also elaborate on what is known about bacterial lateral organization of the plasma membrane and the mechanisms by which organization is established and maintained. Finally, I discuss the implications of cell wall partitioning in bacteria and highlight how targeting plasma membrane compartmentalization serves as a way to disrupt cell wall synthesis in diverse species.

Spatiotemporal Gene Expression by a Genetic Circuit for Chemical Production in Escherichia coli

Gene expression in spatiotemporal distribution improves the ability of cells to respond to changing environments. For microbial cell factories in artificial environments, reconstruction of the target compound's biosynthetic pathway in a new spatiotemporal dimension/scale promotes the production of chemicals. Here, a genetic circuit based on the Esa quorum sensing and lac operon was designed to achieve the dynamic temporal gene expression. Meanwhile, the pathway was regulated by an l-cysteine-specific sensor and relocalized to the plasma membrane for further flux enhancement to l-cysteine and toxicity reduction on a spatial scale. Finally, the integrated spatiotemporal regulation circuit for l-cysteine biosynthesis enabled a 14.16 g/L l-cysteine yield in Escherichia coli. Furthermore, this spatiotemporal regulation circuit was also applied in our previously constructed engineered strain for pantothenic acid, methionine, homoserine, and 2-aminobutyric acid production, and the titer increased by 29, 33, 28, and 41%, respectively. These results highlighted the applicability of our spatiotemporal regulation circuit to enhance the performance of microbial cell factories.

New Antimicrobial Peptide with Two CRAC Motifs: Activity against Escherichia coli and Bacillus subtilis

Due to the emergence of multiple antibiotic resistance in many pathogens, the studies on new antimicrobial peptides (AMPs) have become a priority scientific direction in fundamental and applied biology. Diverse mechanisms underlie the antibacterial action of AMPs. Among them are the effects that AMPs cause on bacterial cell membranes. In this work, we studied the antibacterial activity of a peptide named P4 with the following sequence RTKLWEMLVELGNMDKAVKLWRKLKR that was constructed from two alpha-helical fragments of the influenza virus protein M1 and containing two cholesterol-recognizing amino-acid consensus (CRAC) motifs. Previously we have shown that 50 μM of peptide P4 is toxic to cultured mouse macrophages. In the present work, we have found that peptide P4 inhibits the growth of E. coli and B. subtilis strains at concentrations that are significantly lower than the cytotoxic concentration that was found for macrophages. The half-maximal inhibitory concentration (IC50) for B. subtilis and E. coli cells were 0.07 ± 0.01 μM and 1.9 ± 0.4 μM, respectively. Scramble peptide without CRAC motifs did not inhibit the growth of E. coli cells and was not cytotoxic for macrophages but had an inhibitory effect on the growth of B. subtilis cells (IC50 0.4 ± 0.2 μM). A possible involvement of CRAC motifs and membrane sterols in the mechanism of the antimicrobial action of the P4 peptide is discussed. We assume that in the case of the Gram-negative bacterium E. coli, the mechanism of the toxic action of peptide P4 is related to the interaction of CRAC motifs with sterols that are present in the bacterial membrane, whereas in the case of the Gram-positive bacterium B. subtilis, which lacks sterols, the toxic action of peptide P4 is based on membrane permeabilization through the interaction of the peptide cationic domain and anionic lipids of the bacterial membrane. Whatever the mechanism can be, we report antimicrobial activity of the peptide P4 against the representatives of Gram-positive (B. subtilis) and Gram-negative (E. coli) bacteria.

Introduction and adaptation of an emerging pathogen to olive trees in Italy

The invasive plant pathogen Xylella fastidiosa currently threatens European flora through the loss of economically and culturally important host plants. This emerging vector-borne bacterium, native to the Americas, causes several important diseases in a wide range of plants including crops, ornamentals, and trees. Previously absent from Europe, and considered a quarantine pathogen, X. fastidiosa was first detected in Apulia, Italy in 2013 associated with a devastating disease of olive trees (Olive Quick Decline Syndrome, OQDS). OQDS has led to significant economic, environmental, cultural, as well as political crises. Although the biology of X. fastidiosa diseases have been studied for over a century, there is still no information on the determinants of specificity between bacterial genotypes and host plant species, which is particularly relevant today as X. fastidiosa is expanding in the naive European landscape. We analysed the genomes of 79 X. fastidiosa samples from diseased olive trees across the affected area in Italy as well as genomes of the most genetically closely related strains from Central America. We provided insights into the ecological and evolutionary emergence of this pathogen in Italy. We first showed that the outbreak in Apulia is due to a single introduction from Central America that we estimated to have occurred in 2008 [95 % HPD: 1930–2016]. By using a combination of population genomic approaches and evolutionary genomics methods, we further identified a short list of genes that could play a major role in the adaptation of X. fastidiosa to this new environment. We finally provided experimental evidence for the adaptation of the strain to this new environment.

Regulation of the First Committed Step in Lipopolysaccharide Biosynthesis Catalyzed by LpxC Requires the Essential Protein LapC (YejM) and HslVU Protease

We previously showed that lipopolysaccharide (LPS) assembly requires the essential LapB protein to regulate FtsH-mediated proteolysis of LpxC protein that catalyzes the first committed step in the LPS synthesis. To further understand the essential function of LapB and its role in LpxC turnover, multicopy suppressors of ΔlapB revealed that overproduction of HslV protease subunit prevents its lethality by proteolytic degradation of LpxC, providing the first alternative pathway of LpxC degradation. Isolation and characterization of an extragenic suppressor mutation that prevents lethality of ΔlapB by restoration of normal LPS synthesis identified a frame-shift mutation after 377 aa in the essential gene designated lapC, suggesting LapB and LapC act antagonistically. The same lapC gene was identified during selection for mutations that induce transcription from LPS defects-responsive rpoEP3 promoter, confer sensitivity to LpxC inhibitor CHIR090 and a temperature-sensitive phenotype. Suppressors of lapC mutants that restored growth at elevated temperatures mapped to lapA/lapB, lpxC and ftsH genes. Such suppressor mutations restored normal levels of LPS and prevented proteolysis of LpxC in lapC mutants. Interestingly, a lapC deletion could be constructed in strains either overproducing LpxC or in the absence of LapB, revealing that FtsH, LapB and LapC together regulate LPS synthesis by controlling LpxC amounts.