Biotin and Lipoic Acid: Synthesis, Attachment, and Regulation

Biological characterization of lipoic acid- and heme-dependent Escherichia coli small colony variants isolated from sheep in Xinjiang, China

Escherichia coli (E. coli) small colony variants (SCVs) have garnered attention due to their heightened antibiotic resistance and enhanced cell retention, posing significant risks to public health and food safety. However, understanding of SCVs derived from sheep remains limited. This study aimed to detect the biological characterization of sheep-derived E. coli SCVs and investigate the factors contributing to SCV development with preliminary genomic data. In this study, a lipoic acid-dependent SCV (LA-SCV) and a wild-type (WT) strain were isolated from sheep bile. Then, a heme-dependent SCV (HD-SCV) was induced from WT using amikacin. Initially, we examined factors contributing to SCV formation via comparative genomics. Subsequent comparisons between WT and two SCV strains encompassed antibiotic resistance, hemolytic activity, biofilm formation, motility, and metabolism. Genomic analyses identified a frameshift deletion mutation in the lipA gene in LA-SCV and a stopgain mutation in the hemG gene in HD-SCV, hypothesized as potential triggers for lipoic acid- and heme-dependent SCV development, respectively. Physiological, biochemical, and cultural traits exhibited notable differences between WT and SCVs, including increased antibiotic resistance, hemolytic activity, and biofilm formation, but alongside non-fermentative acetate utilization, slow growth, reduced intracellular ATP, and decreased motility (P < 0.01). The energy and amino acid metabolism were suppressed during the logarithmic phase in LA-SCV, while both logarithmic and stable phases in HD-SCV. These alterations in biological characteristics present significant challenges in managing E. coli pathogenicity and antibiotic resistance.

Chemical shift assignments of the biotin carboxyl carrier protein domain of L. major Methylcrotonyl-CoA carboxylase

Methylcrotonyl-CoA carboxylase (MCCC) is a biotin dependent enzyme, that plays a crucial role in leucine metabolism. The enzyme comprises a biotin carboxylase (BC), a carboxyltransferase (CT), and a biotin carboxyl carrier protein (BCCP) domain. MCCC is synthesized as an apo-protein, and is posttranslationally modified at a lysine residue, conserved in the biotin carboxyl carrier protein (BCCP) domain. In order to understand the structure, function and interactions of L. major MCCC, we have expressed and characterized its domains. Here we report the complete chemical shift assignments of MCCC BCCP domain of L. major. Furthermore, we have used the assignments to generate a model of the same, using CS-Rosetta. We have also followed its chemical shift perturbations upon biotin modification. Changes were observed at the lysine 51 amide, that undergoes biotin modification, and a few others present in its immediate neighborhood.

The Multifaceted Bacterial Cysteine Desulfurases: From Metabolism to Pathogenesis

Living cells have developed a relay system to efficiently transfer sulfur (S) from cysteine to various thio-cofactors (iron-sulfur (Fe-S) clusters, thiamine, molybdopterin, lipoic acid, and biotin) and thiolated tRNA. The presence of such a transit route involves multiple protein components that allow the flux of S to be precisely regulated as a function of environmental cues to avoid the unnecessary accumulation of toxic concentrations of soluble sulfide (S2-). The first enzyme in this relay system is cysteine desulfurase (CSD). CSD catalyzes the release of sulfane S from L-cysteine by converting it to L-alanine by forming an enzyme-linked persulfide intermediate on its conserved cysteine residue. The persulfide S is then transferred to diverse acceptor proteins for its incorporation into the thio-cofactors. The thio-cofactor binding-proteins participate in essential and diverse cellular processes, including DNA repair, respiration, intermediary metabolism, gene regulation, and redox sensing. Additionally, CSD modulates pathogenesis, antibiotic susceptibility, metabolism, and survival of several pathogenic microbes within their hosts. In this review, we aim to comprehensively illustrate the impact of CSD on bacterial core metabolic processes and its requirement to combat redox stresses and antibiotics. Targeting CSD in human pathogens can be a potential therapy for better treatment outcomes.

Engineering a heterologous synthetic pathway in Escherichia coli for efficient production of biotin

OBJECTIVE

To enhance biotin production in Escherichia coli by engineering a heterologous biotin synthetic pathway.

RESULTS

Biotin operon genes from Pseudomonas putida, which consisted of a bioBFHCD cluster and a bioA gene, was engineered into Escherichia coli for biotin production. The introduction of bioW gene from Bacillus subtilis, encoding pimeloyl-CoA synthetase and sam2 gene from Saccharomyces cerevisiae, encoding S-adenosyl-L-methionine (SAM) synthetase contributed to the heterologous production of biotin in recombinant E. coli. Furthermore, biotin production was efficiently enhanced by optimization of the fermentation compositions, especially pimelic acid and L-methionine, the precursor related to the pimeloyl-CoA and SAM synthesis, respectively. The combination of overexpression of the heterologous biotin operon genes and enhanced supply of key intermediate pimeloyl-CoA and SAM increased biotin production in E. coli by more than 121-fold. With bioprocess engineering efforts, biotin was produced at a final titer of 92.6 mg/L in a shake flask and 208.7 mg/L in a fed-batch fermenter.

CONCLUSION

Through introduction of heterologous biotin synthetic pathway, increasing the supply of precursor pimeloyl-CoA and cofactor SAM can significantly enhance biotin production in E. coli.

The Effect of Alpha-Lipoic Acid on Diabetic Peripheral Neuropathy and the Upcoming Depressive Disorders of Type II Diabetics

Introduction

Peripheral neuropathy is one of the possible complications of diabetes. Alpha-lipoic acid (a-lipoic acid or ALA) is a powerful antioxidant cofactor synthesized in mitochondria that could help stimulate nerves and regenerate nerve fibers, thus preventing disease progression. Moreover, the possible feeling of oppression from the lifestyle changes needed to avoid the complications of diabetes may contribute to the development of depressive symptoms. ALA increases insulin sensitivity, which could increase serotonin synthesis and thus reduce the manifestations of depressive disorder.

Aim

The aim of this study is to investigate the therapeutic effect after oral administration of a-lipoic acid in patients with type II diabetes mellitus, regarding the possibility of developing peripheral neuropathy and the possibility of developing depressive disorder due to the existence of diabetes type II.

Methods

The study sample consisted of 148 Greek patients, type II diabetics, 68 men and 80 women, aged 50-75 years. All of them were non-smokers and did not consume alcohol. Their treatment was a combination of gliclazide, sodium-glucose-linked transporter 2 (SGLT-2) inhibitors, metformin, and glucagon-like peptide 1 (GLP-1) analogs. None of them were under insulin administration. Any other treatment received chronically from the patients for other comorbidities was not altered or paused. All patients were in regular monitoring of renal, hepatic, and ocular function, which was normal. Patients were monitored with a balanced diet, based on equivalents, in order to maintain an almost constant body mass index (BMI). All were given one tablet of 600 mg a-lipoic acid, two hours before a meal, for eight months, and the incidence of developing peripheral neuropathy and depressive disorder was assessed, using the Subjective Peripheral Neuropathy Screen Questionnaire (SPNSQ) and Beck Depression Inventory (BDI) questionnaire.

Results

ALA administration after both four and eight months resulted in statistically significant results and, specifically, the peripheral neuropathy development mean score was reduced by 4.79 at four months and 6.22 after eight months. Concerning the incidence of depressive disorder, an average decrease of 4.43 in the related depression score was observed at the four-month milestone and 7.56 at eight months, both statistically significant.

Conclusion

A-lipoic acid is a powerful antioxidant and, when used with conventional treatment, has shown to significantly decrease the incidence of depression and peripheral neuropathy in patients with type 2 diabetes mellitus.

Biotin, a universal and essential cofactor: Synthesis, ligation and regulation

Biotin is a covalently attached enzyme cofactor required for intermediary metabolism in all three domains of life. Several important human pathogens (e.g. Mycobacterium tuberculosis) require biotin synthesis for pathogenesis. Humans lack a biotin synthetic pathway hence bacterial biotin synthesis is a prime target for new therapeutic agents. The biotin synthetic pathway is readily divided into early and late segments. Although pimelate, a seven carbon α,ω-dicarboxylic acid that contributes seven of the ten biotin carbons atoms, was long known to be a biotin precursor, its biosynthetic pathway was a mystery until the E. coli pathway was discovered in 2010. Since then, diverse bacteria encode evolutionarily distinct enzymes that replace enzymes in the E. coli pathway. Two new bacterial pimelate synthesis pathways have been elucidated. In contrast to the early pathway the late pathway, assembly of the fused rings of the cofactor, was long thought settled. However, a new enzyme that bypasses a canonical enzyme was recently discovered as well as homologs of another canonical enzyme that functions in synthesis of another protein-bound coenzyme, lipoic acid. Most bacteria tightly regulate transcription of the biotin synthetic genes in a biotin-responsive manner. The bifunctional biotin ligases which catalyze attachment of biotin to its cognate enzymes and repress biotin gene transcription are best understood regulatory system.

Activity Mapping the Acyl Carrier Protein: Elongating Ketosynthase Interaction in Fatty Acid Biosynthesis

Elongating ketosynthases (KSs) catalyze carbon-carbon bond-forming reactions during the committed step for each round of chain extension in both fatty acid synthases (FASs) and polyketide synthases (PKSs). A small α-helical acyl carrier protein (ACP) shuttles fatty acyl intermediates between enzyme active sites. To accomplish this task, the ACP relies on a series of dynamic interactions with multiple partner enzymes of FAS and associated FAS-dependent pathways. Recent structures of the Escherichia coli FAS ACP, AcpP, in covalent complexes with its two cognate elongating KSs, FabF and FabB, provide high-resolution details of these interfaces, but a systematic analysis of specific interfacial interactions responsible for stabilizing these complexes has not yet been undertaken. Here, we use site-directed mutagenesis with both in vitro and in vivo activity analyses to quantitatively evaluate these contacting surfaces between AcpP and FabF. We delineate the FabF interface into three interacting regions and demonstrate the effects of point mutants, double mutants, and region deletion variants. Results from these analyses reveal a robust and modular FabF interface capable of tolerating seemingly critical interface mutations with only the deletion of an entire region significantly compromising activity. Structure and sequence analyses of FabF orthologs from related type II FAS pathways indicate significant conservation of type II FAS KS interface residues and, overall, support its delineation into interaction regions. These findings strengthen our mechanistic understanding of molecular recognition events between ACPs and FAS enzymes and provide a blueprint for engineering ACP-dependent biosynthetic pathways.

Surface Grafted MSI-78A Antimicrobial Peptide has High Potential for Gastric Infection Management

As we approach the end of the antibiotic era, newer therapeutic options, such as antimicrobial peptides (AMPs), are in urgent demand. AMP surface grafting onto biomaterials has been described as a good strategy to overcome problems associated with their in vivo stability. Helicobacter pylori is among the bacteria that pose greatest threat to human health, being MSI-78A one of the few bactericidal AMPs against this bacterium. Here, we report that MSI-78A grafted onto model surfaces (Self-Assembled Monolayers –SAMs), in a concentration of 30.3 ± 1.2 ng/cm² determined by quartz crystal microbalance with dissipation (QCM-D), was able to kill, by contact, 98% of planktonic H. pylori in only 2 h. This fact was not verified against the control bacteria (Staphylococcus epidermidis), although the minimal inhibitory concentration (MIC) of MSI-78A in solution is much lower for S. epidermidis (2 μg/mL) than for H. pylori (64 μg/mL). Our results also demonstrated that, in opposite to other bacteria, H. pylori cells were attracted to ethylene glycol terminated (antiadhesive) surfaces, which can explain the high bactericidal potential of grafted MSI-78A. This proof of concept study establishes the foundations for development of MSI-78A grafted nanoparticles for gastric infection management within a targeted nanomedicine concept.

A Novel Gene Contributing to the Initiation of Fatty Acid Biosynthesis in Escherichia coli

Type II fatty acid biosynthesis in bacteria can be broadly classified into the initiation and elongation phases. The biochemical functions defining each step in the two phases have been studied in vitro Among the β-ketoacyl-acyl carrier protein (ACP) synthases, FabH catalyzes the initiation reaction, while FabB and FabF, which primarily catalyze the elongation reaction, can also drive initiation as side reactions. A role for FabB and FabF in the initiation of fatty acid biosynthesis would be supported by the viability of the ΔfabH mutant. In this study, we show that the ΔfabH and ΔyiiD mutations were synthetically lethal and that ΔfabH ΔrelA ΔspoT and ΔfabH ΔdksA synthetic lethality was rescued by the heterologous expression of yiiD In the ΔfabH mutant, the expression of yiiD was positively regulated by (p)ppGpp. The growth defect, reduced cell size, and altered fatty acid profile of the ΔfabH mutant and the growth defect of the ΔfabH ΔfabF fabB15(Ts) mutant in oleate- and palmitate-supplemented medium at 42°C were rescued by the expression of yiiD from a multicopy plasmid. Together, these results indicate that the yiiD-encoded function supported initiation of fatty acid biosynthesis in the absence of FabH. We have renamed yiiD as fabY IMPORTANCE Fatty acid biosynthesis is an essential process conserved across life forms. β-Ketoacyl-ACP synthases are essential for fatty acid biosynthesis. FabH is a β-ketoacyl-ACP synthase that contributes to the initiation of fatty acid biosynthesis in Escherichia coli In this study, we present genetic and biochemical evidence that the yiiD (renamed fabY)-encoded function contributes to the biosynthesis of fatty acid in the absence of FabH activity and that under these conditions, the expression of FabY was regulated by the stringent response factors (p)ppGpp and DksA. Combined inactivation of FabH and FabY resulted in growth arrest, possibly due to the loss of fatty acid biosynthesis. A molecule(s) that inhibits the two activities can be an effective microbicide.

Engineering an Artificial Membrane Vesicle Trafficking System (AMVTS) for the Excretion of β-Carotene in Escherichia coli

Large hydrophobic molecules, such as carotenoids, cannot be effectively excreted from cells by natural transportation systems. These products accumulate inside the cells and affect normal cellular physiological functions, which hinders further improvement of carotenoid production by microbial cell factories. In this study, we proposed to construct a novel artificial transport system utilizing membrane lipids to carry and transport hydrophobic molecules. Membrane lipids allow the physiological mechanism of membrane dispersion to be reconstructed and amplified to establish a novel artificial membrane vesicle transport system (AMVTS). Specifically, a few proteins in E. coli were reported or proposed to be related to the formation mechanism of outer membrane vesicles, and were individually knocked out or overexpressed to test their physiological functions. The effects on tolR and nlpI were the most significant. Knocking out both tolR and nlpI resulted in a 13.7% increase of secreted β-carotene with a 35.6% increase of specific production. To supplement the loss of membrane components of the cells due to the increased membrane vesicle dispersion, the synthesis pathway of phosphatidylethanolamine was engineered. While overexpression of AccABCD and PlsBC in TW-013 led to 15% and 17% increases of secreted β-carotene, respectively, the overexpression of both had a synergistic effect and caused a 53-fold increase of secreted β-carotene, from 0.2 to 10.7 mg/g dry cell weight (DCW). At the same time, the specific production of β-carotene increased from 6.9 to 21.9 mg/g DCW, a 3.2-fold increase. The AMVTS was also applied to a β-carotene hyperproducing strain, CAR025, which led to a 24-fold increase of secreted β-carotene, from 0.5 to 12.7 mg/g DCW, and a 61% increase of the specific production, from 27.7 to 44.8 mg/g DCW in shake flask fermentation. The AMVTS built in this study establishes a novel artificial transport mechanism different from natural protein-based cellular transport systems, which has great potential to be applied to various cell factories for the excretion of a wide range of hydrophobic compounds.

Enterococcus faecalis Encodes an Atypical Auxiliary Acyl Carrier Protein Required for Efficient Regulation of Fatty Acid Synthesis by Exogenous Fatty Acids

Acyl carrier proteins (ACPs) play essential roles in the synthesis of fatty acids and transfer of long fatty acyl chains into complex lipids. The Enterococcus faecalis genome contains two annotated acp genes, called acpA and acpB AcpA is encoded within the fatty acid synthesis (fab) operon and appears essential. In contrast, AcpB is an atypical ACP, having only 30% residue identity with AcpA, and is not essential. Deletion of acpB has no effect on E. faecalis growth or de novo fatty acid synthesis in media lacking fatty acids. However, unlike the wild-type strain, where growth with oleic acid resulted in almost complete blockage of de novo fatty acid synthesis, the ΔacpB strain largely continued de novo fatty acid synthesis under these conditions. Blockage in the wild-type strain is due to repression of fab operon transcription, leading to levels of fatty acid synthetic proteins (including AcpA) that are insufficient to support de novo synthesis. Transcription of the fab operon is regulated by FabT, a repressor protein that binds DNA only when it is bound to an acyl-ACP ligand. Since AcpA is encoded in the fab operon, its synthesis is blocked when the operon is repressed and acpA thus cannot provide a stable supply of ACP for synthesis of the acyl-ACP ligand required for DNA binding by FabT. In contrast to AcpA, acpB transcription is unaffected by growth with exogenous fatty acids and thus provides a stable supply of ACP for conversion to the acyl-ACP ligand required for repression by FabT. Indeed, ΔacpB and ΔfabT strains have essentially the same de novo fatty acid synthesis phenotype in oleic acid-grown cultures, which argues that neither strain can form the FabT-acyl-ACP repression complex. Finally, acylated derivatives of both AcpB and AcpA were substrates for the E. faecalis enoyl-ACP reductases and for E. faecalis PlsX (acyl-ACP; phosphate acyltransferase).IMPORTANCE AcpB homologs are encoded by many, but not all, lactic acid bacteria (Lactobacillales), including many members of the human microbiome. The mechanisms regulating fatty acid synthesis by exogenous fatty acids play a key role in resistance of these bacteria to those antimicrobials targeted at fatty acid synthesis enzymes. Defective regulation can increase resistance to such inhibitors and also reduce pathogenesis.

FabG: from a core to circumstantial catalyst

Core biochemical pathways such as Fatty-acid synthesis II (FAS II) is ascribed to the synthesis of fatty-acids, biotin and lipoic acid in prokaryotes. It has two dehydrogenases namely, FabG and FabI which interact with the fatty-acid chain bound to Acyl-carrier protein (ACP), a well-studied enzyme which binds to substrates of varying lengths. This protein-protein interaction 'broadens' the active site of these dehydrogenases thus, contributing to their flexible nature. This property is exploited for catalysing numerous chiral synthons, alkanes, long-chain alcohols and secondary metabolites in industries especially with FabG. FASI relegates FASII in eukaryotes making it a 'relic gene pool' and an antibacterial drug target with diverse inhibitor and substrate markush. FabG often substitutes other dehydrogenases for producing secondary metabolites in nature. This redundancy is probably due to gene duplication or addition events possibly making FabG, a progenitor to some of the complex short-chain dehydrogenases used in organisms and industries today.

Molecular Basis for Olefin Rearrangement in the Gephyronic Acid Polyketide Synthase

Polyketide synthases (PKS) are a rich source of natural products of varied chemical composition and biological significance. Here, we report the characterization of an atypical dehydratase (DH) domain from the PKS pathway for gephyronic acid, an inhibitor of eukaryotic protein synthesis. Using a library of synthetic substrate mimics, the reaction course, stereospecificity, and tolerance to non-native substrates of GphF DH1 are probed via LC-MS analysis. Taken together, the studies establish GphF DH1 as a dual-function dehydratase/isomerase that installs an odd-to-even double bond and yields a product consistent with the isobutenyl terminus of gephyronic acid. The studies also reveal an unexpected C2 epimerase function in catalytic turnover with the native substrate. A 1.55-Å crystal structure of GphF DH1 guided mutagenesis experiments to elucidate the roles of key amino acids in the multistep DH1 catalysis, identifying critical functions for leucine and tyrosine side chains. The mutagenesis results were applied to add a secondary isomerase functionality to a nonisomerizing DH in the first successful gain-of-function engineering of a PKS DH. Our studies of GphF DH1 catalysis highlight the versatility of the DH active site and adaptation for a specific catalytic outcome with a specific substrate.

Evaluation of E. coli inhibition by plain and polymer-coated silver nanoparticles

Escherichia coli causes various ailments such as septicemia, enteritis, foodborne illnesses, and urinary tract infections which are of concern in the public health field due to antibiotic resistance. Silver nanoparticles (AgNP) are known for their biocompatibility and antibacterial activity, and may prove to be an alternative method of treatment, especially as wound dressings. In this study, we compared the antibacterial efficacy of two polymer-coated silver nanoparticles either containing 10% Ag (Ag 10% + Polymer), or 99% Ag (AgPVP) in relation to plain uncoated silver nanoparticles (AgNP). Atomic force microscopy was used to characterize the nanoparticles, and their antibacterial efficacy was compared by the minimum inhibitory concentration (MIC) and bacterial growth curve assays, followed by molecular studies using scanning electron microscopy (SEM) and (qRT- PCR). AgNP inhibited the growth of E. coli only at 0.621 mg/mL, which was double the concentration required for both coated nanoparticles (0.312 mg/mL). Similarly, bacterial growth was impeded as early as 8 h at 0.156 mg/mL of both coated nanoparticles as compared to 0.312 mg/mL for plain AgNP. SEM data showed that nanoparticles damaged the cell membrane, resulting in bacterial cell lysis, expulsion of cellular contents, and complete disintegration of some cells. The expression of genes associated with the TCA cycle (aceF and frdB) and amino acid metabolism (gadB, metL, argC) were substantially downregulated in E. coli treated with nanoparticles. The reduction in the silver ion (Ag+) concentration of polymer-coated AgNP did not affect their antibacterial efficacy against E. coli.

Successful conversion of the Bacillus subtilis BirA Group II biotin protein ligase into a Group I ligase

Group II biotin protein ligases (BPLs) are characterized by the presence of an N-terminal DNA binding domain that allows transcriptional regulation of biotin biosynthetic and transport genes whereas Group I BPLs lack this N-terminal domain. The Bacillus subtilis BPL, BirA, is classified as a Group II BPL based on sequence predictions of an N-terminal helix-turn-helix motif and mutational alteration of its regulatory properties. We report evidence that B. subtilis BirA is a Group II BPL that regulates transcription at three genomic sites: bioWAFDBI, yuiG and yhfUTS. Moreover, unlike the paradigm Group II BPL, E. coli BirA, the N-terminal DNA binding domain can be deleted from Bacillus subtilis BirA without adverse effects on its ligase function. This is the first example of successful conversion of a Group II BPL to a Group I BPL with retention of full ligase activity.