Topological analysis of a bacterial DedA protein associated with alkaline tolerance and antimicrobial resistance

Putative Probiotic Ligilactobacillus salivarius Strains Isolated from the Intestines of Meat-Type Pigeon Squabs

This study aims to screen for potential probiotic lactic acid bacteria from the intestines of meat-type pigeon squabs. Ligilactobacillus salivarius YZU37 was identified as the best comprehensive performed strain. Being acid- and bile salt-tolerant, it displayed growth-inhibition activities against Staphylococcus aureus ATCC25923, Escherichia coli ATCC25922, and Salmonella typhimurium SL1344, exhibited sensitivity to 6 commonly used antibiotics, and endowed with good cell surface hydrophobicity, auto-aggregation property, and anti-oxidant activities. Results of in vitro experiments indicated that the bacteriostatic effects of this strain were related to the production of proteinaceous substances that depend on acidic conditions. Whole-genome sequencing of L. salivarius YZU37 was performed to elucidate the genetic basis underlying its probiotic potential. Pangenome analysis of L. salivarius YZU37 and other 212 L. salivarius strains available on NCBI database revealed a pigeon-unique gene coding choloylglycine hydrolase (CGH), which had higher enzyme-substrate binding affinity than that of the common CGH shared by L. salivarius strains of other sources. Annotation of the functional genes in the genome of L. salivarius YZU37 revealed genes involved in responses to acid, bile salt, heat, cold, heavy metal, and oxidative stresses. The whole genome analysis also revealed the absence of virulence and toxin genes and the presence of 65 genes distributed under 4 CAZymes classes, 2 CRISPR-cas regions, and 3 enterolysin A clusters which may confer the acid-dependent antimicrobial potential of L. salivarius YZU37. Altogether, our results highlighted the probiotic potential of L. salivarius YZU37. Further in vivo investigations are required to elucidate its beneficial effects on pigeons.

The Cell Envelope Integrity Protein Homologue D0Y85_RS06240 of Stenotrophomonas Confers Multiantibiotic Resistance

Background

The potential role of cell envelope integrity proteins in mediating antibiotic resistance is not well understood. In this study, we investigated whether the cell envelope integrity protein D0Y85_RS06240 from the multiantibiotic resistant strain Stenotrophomonas sp. G4 mediates antibiotic resistance.

Methods

Bioinformatics analysis was conducted to identify proteins related to the D0Y85_RS06240 protein. The D0Y85_RS06240 gene was heterologously expressed in Escherichia coli, both antibiotic MICs and the effect of efflux pump inhibitors on antibiotic MICs were determined by the broth microdilution method. A combination of antibiotic and efflux pump inhibitor was used to investigate bacterial killing kinetics, and binding of D0Y85_RS06240 to antibiotic molecules was predicted by molecular docking analysis.

Results

Sequence homology analysis revealed that D0Y85_RS06240 was related to cell envelope integrity proteins. The D0Y85_RS06240 heterologous expression strains were resistant to multiple antibiotics, including colistin, tetracycline, and cefixime. However, the efflux pump inhibitor N-methylpyrrolidone (NMP) reduced the antibiotic MICs of the D0Y85_RS06240 heterologous expression strain, and bacterial killing kinetics revealed that NMP enhanced the bactericidal rate of tetracycline to the drug-resistant bacteria. Molecular docking analysis indicated that D0Y85_RS06240 could bind colistin, tetracycline, and cefixime.

Conclusion

The cell envelope integrity protein D0Y85_RS06240 in Stenotrophomonas sp. G4 mediates multiantibiotic resistance. This study lays the foundation for an in-depth analysis of D0Y85_RS06240-mediated antibiotic resistance mechanisms and the use of D0Y85_RS06240 as a target for the treatment of multiantibiotic-resistant bacterial infections.

XdfA, a novel membrane-associated DedA family protein of Xanthomonas campestris, is required for optimum virulence, maintenance of magnesium, and membrane homeostasis

Xanthomonas campestris is an important member of the Xanthomonas group of phytopathogens that causes diseases in crucifers. In X. campestris, several virulence-associated functions, including some belonging to unknown predicted functions, have been implicated in the colonization and disease processes. However, the role of many of these unknown predicted proteins in Xanthomonas-host interaction and their exact physiological function is not clearly known. In this study, we identified a novel membrane-associated protein belonging to the DedA super family, XdfA, which is required for virulence in X. campestris. The DedA family of proteins are generally ubiquitous in bacteria; however, their function and actual physiological role are largely elusive. Characterization of ∆xdfA by homology modeling, membrane localization, and physiological studies indicated that XdfA is a membrane-associated protein that plays a role in the maintenance of membrane integrity. Furthermore, functional homology modeling analysis revealed that the XdfA exhibits structural similarity to a CorA-like magnesium transporter and is required for optimum growth under low magnesium ion concentration. We report for the first time that a putative DedA family of protein in Xanthomonas is required for optimum virulence and plays a role in the maintenance of membrane-associated functions and magnesium homeostasis. IMPORTANCE Bacterial DedA family proteins are involved in a range of cellular processes such as ion transport, signal transduction, and cell division. Here, we have discussed about a novel DedA family protein XdfA in Xanthomonas campestris pv. campestris that has a role in membrane homeostasis, magnesium transport, and virulence. Understanding membrane and magnesium homeostasis will aid in our comprehension of bacterial physiology and eventually will help us devise effective antimicrobial strategies to safeguard horticulturally and agriculturally important crop plants.

Three Bacterial DedA Subfamilies with Distinct Functions and Phylogenetic Distribution

Recent studies in bacteria have suggested that the broadly conserved but enigmatic DedA proteins function as undecaprenyl-phosphate (UndP) flippases, recycling this essential lipid carrier. To determine whether all DedA proteins have UndP flippase activity, we performed a phylogenetic analysis and correlated our findings to previously published experimental results and predicted structures. We uncovered three major DedA subfamilies: one contains UndP flippases, the second contains putative phospholipid flippases and is associated with aerobic metabolism, and the third is found only in specific Gram-negative phyla. IMPORTANCE DedA family proteins are highly conserved and nearly ubiquitous integral membrane proteins found in archaea, bacteria, and eukaryotes. Recent work revealed that eukaryotic DedA proteins are phospholipid scramblases and that some bacterial DedA proteins are undecaprenyl phosphate flippases. We performed a phylogenetic analysis of this protein family in bacteria that revealed 3 DedA subfamilies with distinct phylogenetic distributions, genomic contexts, and putative functions. Our bioinformatic analysis lays the groundwork for future experimental studies on the role of DedA proteins in maintaining and modifying the membrane.

Three bacterial DedA subfamilies with distinct functions and phylogenetic distribution

Recent studies in bacteria suggested that the broadly conserved but enigmatic DedA proteins function as undecaprenyl-phosphate (UndP) flippases, recycling this essential lipid carrier. To determine whether all DedA proteins have UndP flippase activity, we performed a phylogenetic analysis and correlated it to previously published experimental results and predicted structures. We uncovered three major DedA subfamilies: one contains UndP flippases, the second contains putative phospholipid flippases and is associated with aerobic metabolism, and the third is found only in specific Gram-negative phyla.

IMPORTANCE

DedA-family proteins are highly conserved and nearly ubiquitous integral membrane proteins found in Archaea, Bacteria, and Eukaryotes. Recent work revealed that eukaryotic DedA proteins are phospholipid scramblases and some bacterial DedA proteins are undecaprenyl phosphate flippases. We perform a phylogenetic analysis of this protein family in Bacteria revealing 3 DedA subfamilies with distinct phylogenetic distributions, genomic contexts, and putative functions. Our analysis lays the groundwork for a deeper understanding of DedA proteins and their role in maintaining and modifying the membrane.

Regulation of ER-derived membrane dynamics by the DedA domain-containing proteins VMP1 and TMEM41B

The endoplasmic reticulum (ER) is a central hub for the biogenesis of various organelles and lipid-containing structures. Recent studies suggest that vacuole membrane protein 1 (VMP1) and transmembrane protein 41B (TMEM41B), multispanning ER membrane proteins, regulate the formation of many of these ER-derived structures, including autophagosomes, lipid droplets, lipoproteins, and double-membrane structures for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication. VMP1 and TMEM41B possess a DedA domain that is widely distributed not only in eukaryotes but also in prokaryotes and predicted to adopt a characteristic structure containing two reentrant loops. Furthermore, recent studies show that both proteins have lipid scrambling activity. Based on these findings, the potential roles of VMP1 and TMEM41B in the dynamic remodeling of ER membranes and the biogenesis of ER-derived structures are discussed.