Protein:Protein interactions in the cytoplasmic membrane apparently influencing sugar transport and phosphorylation activities of the e. coli phosphotransferase system

Genome-wide exploration: Evolution, structural characterization, molecular docking, molecular dynamics simulation and expression analysis of sugar transporter (ST) gene family in potato (Solanum tuberosum)

Sugars are the basic structural components of carbohydrates. Sugar transport is crucial for plants to ensure their optimal growth and development. Long-distance sugar transport occurs through either diffusion-based passive or active transport mediated by transporter proteins. In potatoes, STs play a vital role in sugar transport and total sugar accumulation. To better understand the roles of these transporters, in-depth structural, protein characterization, and tissue-specific expression analysis were performed. A total of 61 StSTs were identified and classified into eight sub-families (STP, PLT, ERD6L, INT, TMT, pGlcT, SUC, and VGT). The majority of StSTs were found in the plasma membrane, and all of them were dispersed throughout the 12 chromosomes. Exon and motif counts ranged from 1-18 and 1-10, respectively. In synteny analysis with four plant genomes, the highest (38) orthologous gene pair was found with S. lycopersicum (tomato). In 3D protein modeling, the alpha helix and transmembrane helices range varied from 32 % to 78 % and 53 %-57 %, respectively. During molecular docking analysis, the lowest binding energy was observed for Glu-StINT1 (ΔG: - 6.6 kcal/mol), Fru-StVGT1 (ΔG: - 6.1 kcal/mol), Gal-StSTP10 (ΔG: - 6.5 kcal/mol), and Suc-StINT2 (ΔG: - 7.5 kcal/mol), among 244 docking results. These complexes showed significant hydrogen and hydrophobic interactions, due to having significant amino acid residues. The molecular dynamics (MD) simulation of four complexes (Glu-StINT1, Fru-StVGT1, Gal-StSTP10, and Suc-StINT2) validated the ligand's stable attachment to the intended target proteins and it can be predicted that these complexes are the best sugar transporters of potato. In RNA-seq mediated expression analysis, StSTP12, StERD6L-6, 12, StpGlcT3, StVGT1, and StVGT2, were significantly upregulated in vegetative tissues/organs, revealing their significant role in vegetative organ development. In addition, stu-miRNA395 was the largest family interacting with StERD6L-1 and StTMT2 genes, demonstrating their significant role in sulfate metabolism. The detection and visualization of potential transcription factors (TFs) like ERF, Dof, MYB, BBR-BPC, LBD, and NAC in conjunction with the StSTs gene indicate their significant contribution to stress tolerance and DNA conversion and transcription into RNA. A significant interaction of StSTs in the PPI network might be due to their cumulative role in the same signaling pathways. The integration of these findings will guide the development of programming-based sugar transporter-mediated genetic circuits to improve the sugar accumulation in potatoes using synthetic biology approaches.

Engineering PTS-based glucose metabolism for efficient biosynthesis of bacterial cellulose by Komagataeibacter xylinus

Bacterial cellulose (BC) is a renewable biomaterial that has attracted significant attention due to its excellent properties and wide applications. Komagataeibacter xylinus CGMCC 2955 is an important BC-producing strain. It primarily produces BC from glucose while simultaneously generating gluconic acid as a by-product, which acidifies the medium and inhibits BC synthesis. To enhance glucose uptake and BC synthesis, we reconstructed the phosphoenolpyruvate-dependent glucose phosphotransferase system (PTSGlc) and strengthened glycolysis by introducing heterologous genes, resulting in a recombinant strain (GX08PTS03; Δgcd::ptsHIcrrE. coli::ptsGE. coli::pfkAE. coli). Strain GX08PTS03 efficiently utilized glucose for BC production without accumulating gluconic acid. Subsequently, the fermentation process was systematically optimized. Under optimal conditions, strain GX08PTS03 produced 7.74 g/L of BC after 6 days of static fermentation, with a BC yield of 0.39 g/g glucose, which were 87.41 % and 77.27 % higher than those of the wild-type strain, respectively. The BC produced by strain GX08PTS03 exhibited a longer fiber diameter along with a lower porosity, significantly higher solid content, crystallinity, tensile strength, and Young's modulus. This study is novel in reporting that the engineered PTSGlc-based glucose metabolism could effectively enhance the production and properties of BC, providing a future outlook for the biopolymer industry.

Two Permeases Associated with the Multifunctional CtaP Cysteine Transport System in Listeria monocytogenes Play Distinct Roles in Pathogenesis

The soil-dwelling bacterium Listeria monocytogenes survives a multitude of conditions when residing in the outside environment and as a pathogen within host cells. Key to survival within the infected mammalian host is the expression of bacterial gene products necessary for nutrient acquisition. Similar to many bacteria, L. monocytogenes uses peptide import to acquire amino acids. Peptide transport systems play an important role in nutrient uptake as well as in additional functions that include bacterial quorum sensing and signal transduction, recycling of peptidoglycan fragments, adherence to eukaryotic cells, and alterations in antibiotic susceptibility. It has been previously described that CtaP, encoded by lmo0135, is a multifunctional protein associated with activities that include cysteine transport, resistance to acid, membrane integrity, and bacterial adherence to host cells. ctaP is located next to two genes predicted to encode membrane-bound permeases lmo0136 and lmo0137, termed CtpP1 and CtpP2, respectively. Here, we show that CtpP1 and CtpP2 are required for bacterial growth in the presence of low concentrations of cysteine and for virulence in mouse infection models. Taken together, the data identify distinct nonoverlapping roles for two related permeases that are important for the growth and survival of L. monocytogenes within host cells. IMPORTANCE Bacterial peptide transport systems are important for nutrient uptake and may additionally function in a variety of other roles, including bacterial communication, signal transduction, and bacterial adherence to eukaryotic cells. Peptide transport systems often consist of a substrate-binding protein associated with a membrane-spanning permease. The environmental bacterial pathogen Listeria monocytogenes uses the substrate-binding protein CtaP not only for cysteine transport but also for resistance to acid, maintenance of membrane integrity, and bacterial adherence to host cells. In this study, we demonstrate complementary yet distinct functional roles for two membrane permeases, CtpP1 and CtpP2, that are encoded by genes linked to ctaP and that contribute to bacterial growth, invasion, and pathogenicity.

Omics analysis coupled with gene editing revealed potential transporters and regulators related to levoglucosan metabolism efficiency of the engineered Escherichia coli

Background

Bioconversion of levoglucosan, a promising sugar derived from the pyrolysis of lignocellulose, into biofuels and chemicals can reduce our dependence on fossil-based raw materials. However, this bioconversion process in microbial strains is challenging due to the lack of catalytic enzyme relevant to levoglucosan metabolism, narrow production ranges of the native strains, poor cellular transport rate of levoglucosan, and inhibition of levoglucosan metabolism by other sugars co-existing in the lignocellulose pyrolysate. The heterologous expression of eukaryotic levoglucosan kinase gene in suitable microbial hosts like Escherichia coli could overcome the first two challenges to some extent; however, no research has been dedicated to resolving the last two issues till now.

Results

Aiming to resolve the two unsolved problems, we revealed that seven ABC transporters (XylF, MalE, UgpB, UgpC, YtfQ, YphF, and MglA), three MFS transporters (KgtP, GntT, and ActP), and seven regulatory proteins (GalS, MhpR, YkgD, Rsd, Ybl162, MalM, and IraP) in the previously engineered levoglucosan-utilizing and ethanol-producing E. coli LGE2 were induced upon exposure to levoglucosan using comparative proteomics technique, indicating these transporters and regulators were involved in the transport and metabolic regulation of levoglucosan. The proteomics results were further verified by transcriptional analysis of 16 randomly selected genes. Subsequent gene knockout and complementation tests revealed that ABC transporter XylF was likely to be a levoglucosan transporter. Molecular docking showed that levoglucosan can bind to the active pocket of XylF by seven H-bonds with relatively strong strength.

Conclusion

This study focusing on the omics discrepancies between the utilization of levoglucosan and non-levoglucosan sugar, could provide better understanding of levoglucosan transport and metabolism mechanisms by identifying the transporters and regulators related to the uptake and regulation of levoglucosan metabolism. The protein database generated from this study could be used for further screening and characterization of the transporter(s) and regulator(s) for downstream enzymatic/genetic engineering work, thereby facilitating more efficient microbial utilization of levoglucosan for biofuels and chemicals production in future.

Transcriptome response of a new serotype of avian type Klebsiella varicella strain to chicken sera

Klebsiella variicola is a newly discovered pathogen of zoonotic importance, commonly causing serious systemic infection via the bloodstream route. However, the mechanism by which K. variicola survives and grows in the bloodstream is poorly understood. In a previous study, a strain of Klebsiella causing chicken bloodstream infection was obtained, and whole genome sequencing showed that it was a new ST174 type K. variicola. Therefore, the present study aimed to determine the molecular mechanism underlying the survival and development of K. variicola in host serum. First, we compared the transcriptomes of K. variicola grown in Luria-Bertani broth and chicken serum. We sequenced six RNA libraries from the two groups, each library had three repeats. A total of 1046 differentially expressed genes were identified. Functional annotation analysis showed that the differentially expressed genes are mainly involved in adaptive metabolism, biosynthesis pathways (including biosynthesis of siderophore group nonribosomal peptides and lipopolysaccharide (LPS) biosynthesis), stress resistance, and several known virulence regulatory systems (including the ABC transporter system, the two-component signal transduction system and the quorum sensing system). These genes are expected to contribute to the adaptation and growth of K. variicola in host birds. This analysis provides a new insight into the pathogenesis of K. variicola.

Protein-Protein Interactions in the Cytoplasmic Membrane of Escherichia coli: Influence of the Overexpression of Diverse Transporter-Encoding Genes on the Activities of PTS Sugar Uptake Systems

The prokaryotic phosphoenolpyruvate (PEP):sugar phosphotransferase system (PTS) concomitantly transports and phosphorylates its substrate sugars. In a recent publication, we provided evidence that protein-protein interactions of the fructose-specific integral membrane transporter (FruAB) with other PTS sugar group translocators regulate the activities of the latter systems in vivo and sometimes in vitro. In this communication, we examine the consequences of the overexpression of several different transport systems on the activities of selected PTS and non-PTS permeases. We report that high levels of these transport systems enhance the in vivo activities of several other systems in a fairly specific fashion. Thus, (1) overexpression of ptsG (glucose porter) selectively enhanced mannitol, N-acetylglucosamine, and 2-deoxyglucose (2DG) uptake rates; (2) overexpression of mtlA (mannitol porter) promoted methyl α-glucoside (αMG) and 2DG uptake; (3) manYZ (but not manY alone) (mannose porter) overexpression enhanced αMG uptake; (4) galP (galactose porter) overexpression enhanced mannitol and αMG uptake; and (5) ansP (asparagine porter) overexpression preferentially enhanced αMG and 2DG uptake, all presumably as a result of direct protein-protein interactions. Thus, it appears that high level production of several integral membrane permeases enhances sugar uptake rates, with the PtsG and ManXYZ systems being most consistently stimulated, but the MtlA and NagE systems being more selectively stimulated and to a lesser extent. Neither enhanced expression nor in vitro PEP-dependent phosphorylation activities of the target PTS systems were appreciably affected. The results are consistent with the suggestion that integral membrane transport proteins form an interacting network in vivo with physiological consequences, dependent on specific transporters and their concentrations in the membrane.

Phosphotransferase System Uptake and Metabolism of the β-Glucoside Salicin Impact Group A Streptococcal Bloodstream Survival and Soft Tissue Infection

Streptococcus pyogenes (group A Streptococcus [GAS]), a major human-specific pathogen, relies on efficient nutrient acquisition for successful infection within its host. The phosphotransferase system (PTS) couples the import of carbohydrates with their phosphorylation prior to metabolism and has been linked to GAS pathogenesis. In a screen of an insertional mutant library of all 14 annotated PTS permease (EIIC) genes in MGAS5005, the annotated β-glucoside PTS transporter (bglP) was found to be crucial for GAS growth and survival in human blood and was validated in another M1T1 GAS strain, 5448. In 5448, bglP was shown to be in an operon with a putative phospho-β-glucosidase (bglB) downstream and a predicted antiterminator (licT) upstream. Using defined nonpolar mutants of the β-glucoside permease (bglP) and β-glucosidase enzyme (bglB) in 5448, we showed that bglB, not bglP, was important for growth in blood. Furthermore, transcription of the licT-blgPB operon was found to be repressed by glucose and induced by the β-glucoside salicin as the sole carbon source. Investigation of the individual bglP and bglB mutants determined that they influence in vitro growth in the β-glucoside salicin; however, only bglP was necessary for growth in other non-β-glucoside PTS sugars, such as fructose and mannose. Additionally, loss of BglP and BglB suggests that they are important for the regulation of virulence-related genes that control biofilm formation, streptolysin S (SLS)-mediated hemolysis, and localized ulcerative lesion progression during subcutaneous infections in mice. Thus, our results indicate that the β-glucoside PTS transports salicin and its metabolism can differentially influence GAS pathophysiology during soft tissue infection.