Environmental roles of microbial amino acid racemases

Dynamic changes in the metabolome and microbiome during Citrus depressa Hayata liquid fermentation

Citri Reticulatae Pericarpium (CRP) is a common traditional Chinese herbal medicine, valued for its multi-bioactivity. However, its processing time, environment, and microorganisms all affect its quality and bioactivity. To address this, the study replaced solid-state fermentation with liquid fermentation using microorganisms and isolated Bacillus amyloliquefaciens, respectively. This aimed to discover a more stable processing method and examine metabolite-micobiota correlations. Non-targeted metabolomics identified 70 differential metabolites, focusing on amino acids, polymethoxyflavones (PMFs), and carbohydrates. Long-read sequencing showed a shift in dominant bacterial genera from Lactobacillus to Pediococcus, then to Clostridium. Spearman analysis revealed a positive correlation between specific Clostridium species and PMFs production. B. amyloliquefaciens fermentation notably increased PMFs content without reducing hesperidin levels, suggesting its potential as an alternative processing method. This study offers valuable insights into metabolome-microbiome interactions for future biotransformation research.

Enantiomer-Specific Stable Carbon and Nitrogen Isotopic Analyses of Underivatized Individual l- and d-Amino Acids by HPLC + HPLC Separation and Nano-EA/IRMS

We developed a new method for stable carbon and nitrogen isotopic (δ13C and δ15N) analysis of underivatized amino acid (AA) enantiomers simultaneously, based on high-performance liquid chromatography (HPLC) separation and off-line isotopic measurement. l- and d-Enantiomers of each AA were isolated using a ReproSil Chiral-AA column, purified by wet chemical procedure, and analyzed for δ13C and δ15N values with a nanomol-scale elemental analyzer/isotope-ratio mass spectrometry (nano-EA/IRMS) system. We successfully achieved the separation of l- and d-enantiomers of 15 proteinogenous AAs, with all l-enantiomers eluting before respective d-enantiomers. The δ13C and δ15N values of AA enantiomers were consistent before and after HPLC separation, demonstrating that this analytical method conserves isotopic information. By coupling this column with a multidimensional HPLC system for isolating individual AAs, we analyzed l- and d-AAs in a natural sample, peptidoglycan isolated from Gram-positive bacterium Bacillus subtilis. Results show a surprisingly large 15N-depletion, up to 20‰, in d-glutamic acid relative to its l-counterpart. The first example, to our knowledge, of δ13C and δ15N analyses of underivatized AA enantiomers is expected to contribute to various research areas in the future.

Multifunctionality of a low-specificity L-threonine aldolase from the hyperthermophile Thermotoga maritima

The peptidoglycan of the hyperthermophile Thermotoga maritima contains an unusual D-lysine in addition to the typical D-alanine and D-glutamate. Previously, we identified the D-lysine and D-glutamate biosynthetic pathways of T. maritima. Additionally, we reported some multifunctional enzymes involved in amino acid metabolism. In the present study, we characterized the enzymatic properties of TM1744 (threonine aldolase) to probe both its potential multifunctionality and D-amino acid metabolizing activities. TM1744 displayed aldolase activity toward both L-allo-threonine and L-threonine, and exhibited higher activity toward L-threo-phenylserine. It did not function as an aldolase toward D-allo-threonine or D-threonine. Furthermore, TM1744 had racemase activity toward two amino acids, although its racemase activity was lower than its aldolase activity. TM1744 did not have other amino acid metabolizing activities. Therefore, TM1744 is a low-specificity L-threonine aldolase with limited racemase activity.

Phylogeny and genomic analysis of Shewanella cutis sp. nov., isolated from freshwater pufferfish

Three closely related, aerobic, Gram-stain-negative, motile, rod-shaped bacterial strains (PS-2T, PS-17, and PS-19) were isolated from the skin of freshwater pufferfish (Tetraodon cutcutia). Colonies are pinkish-colored. The optimum growth occurred at 28-30 °C, and the pH was 6.5-7. The major cellular fatty acids were C16:1 ω7c, iso-C15.0, C17:1 ω8c, C18:1 ω7c, and C16:0. The predominant polar lipids were phosphatidylglycerol, phosphatidylethanolamine, and amino lipids. The genome size of strain PS-2T is 4.8 Mbp, and the G + C content was 46.0%. The major fraction of genes were associated with biological processes (45.64%), followed by molecular function (29.86%) and cellular components (24.49%). The unique genes identified in strain PS-2T secreted cyanophycinase, UDP-N-acetylglucosamine 2-epimerase, methyltransferase, kynureninase, ADA regulatory protein, biphenyl degradation, thermostable carboxypeptidase 1, tetrathionate respiration, etc. In addition, alanine and glutamate racemases were present. The 16S rRNA gene sequences shared 98.83-99.24% similarity with the closely related type strains of Shewanella. The ANI and AAI of strain PS-2T with reference type strains of the genus Shewanella were below 95-96%, and the corresponding dDDH values were below 70%. A phylogenetic tree based on 16S rRNA gene sequences and genome-wide core genes revealed that strain PS-2T clustered with Shewanella oneidensis LMG 19005T in both phylogenetic trees. Based on the polyphasic analysis, the new isolates (PS-2T, PS-17, and PS-19) represent a novel species of Shewanella, for which Shewanella cutis sp. nov. is proposed. The type strain is PS-2T (= TBRC 15838T = NBRC 115342T).

Multifunctional enzymes related to amino acid metabolism in bacteria

In bacteria, d-amino acids are primarily synthesized from l-amino acids by amino acid racemases, but some bacteria use d-amino acid aminotransferases to synthesize d-amino acids. d-Amino acids are peptidoglycan components in the cell wall involved in several physiological processes, such as bacterial growth, biofilm dispersal, and peptidoglycan metabolism. Therefore, their metabolism and physiological roles have attracted increasing attention. Recently, we identified novel bacterial d-amino acid metabolic pathways, which involve amino acid racemases, with broad substrate specificity, as well as multifunctional enzymes with d-amino acid-metabolizing activity. Here, I review these multifunctional enzymes and their related d- and l-amino acid metabolic pathways in Escherichia coli and the hyperthermophile Thermotoga maritima.

Assessment of Protein Quality and Digestibility in Plant-Based Meat Analogues

In this first work, commercial steak-like (n = 3) and cured meat (n = 3) analogues with different legume and cereal formulations were studied and compared to their animal-based (n = 3) counterparts. Plant-based products showed lower protein content than meat controls but a good amino acidic profile even though the sum of essential amino acids of plant-cured meats does not fulfill the requirements set by the Food and Agriculture Organization for children. A comparable release of soluble proteins and peptides in the digestates after in vitro digestion was observed in meat analogues as meat products, whereas the digestibility of proteins was lower in plant-based steaks and higher in plant-based cured meats than their counterparts. The overall protein quality and digestibility of products are related to both the use of good blending of protein sources and processes applied to produce them. An adequate substitution of meat with its analogues depends mostly on the quality of raw materials used, which should be communicated to consumers.

Valorization of protein-rich waste and its application

Energy shortages present significant challenges with the rising population and dramatic urbanization development. The effective utilization of high-value products generated from massive protein-rich waste has emerged as an excellent solution for mitigating the growing energy crisis. However, the traditional disposal and treatment of protein-rich waste, have been proven to be ineffective in resource utilization, which led to high chemical oxygen demand and water eutrophication. To effectively address this issue, hydrolysate and bioconversion products from protein-rich waste have been widely investigated. Herein, we aim to provide an overview of the valorization of protein-rich waste based on a comprehensive analysis of publicly available literature. Firstly, the sources of protein-rich waste with various quantities and qualities are systematically summarized. Then, we scrutinize and analyze the hydrolysis approaches of protein-rich waste and the versatile applications of hydrolyzed products. Moreover, the main factors influencing protein biotransformation and the applications of bioconversion products are covered and extensively discussed. Finally, the potential prospects and future directions for the valorization of protein-rich waste are proposed pertinently.

Common pathogenic bacteria-induced reprogramming of the host proteinogenic amino acids metabolism

Apart from cancer, metabolic reprogramming is also prevalent in other diseases, such as bacterial infections. Bacterial infections can affect a variety of cells, tissues, organs, and bodies, leading to a series of clinical diseases. Common Pathogenic bacteria include Helicobacter pylori, Salmonella enterica, Mycobacterium tuberculosis, Staphylococcus aureus, and so on. Amino acids are important and essential nutrients in bacterial physiology and support not only their proliferation but also their evasion of host immune defenses. Many pathogenic bacteria or opportunistic pathogens infect the host and lead to significant changes in metabolites, especially the proteinogenic amino acids, to inhibit the host's immune mechanism to achieve its immune evasion and pathogenicity. Here, we review the regulation of host metabolism, while host cells are infected by some common pathogenic bacteria, and discuss how amino acids of metabolic reprogramming affect bacterial infections, revealing the potential adjunctive application of amino acids alongside antibiotics.

Engineering acetylation platform for the total biosynthesis of D-amino acids

Optically pure D-amino acids are key chemicals with various applications. Although the production of specific D-amino acids has been achieved by chemical synthesis or with in vitro enzyme catalysts, it is challenging to convert a simple carbon source into D-amino acids with high efficiency. Here, we design an artificial metabolic pathway by engineering bacteria to heterologously express racemase and N-acetyltransferase to produce N-acetyl-D-amino acids from L-amino acids. This new platform allows the cytotoxicity of D-amino acids to be avoided. The universal potential of this acetylation protection strategy for effectively synthesizing optically pure D-amino acids is demonstrated by testing sixteen amino acid targets. Furthermore, we combine pathway optimization and metabolic engineering in Escherichia coli and achieve practically useful efficiency with four specific examples, including N-acetyl-D-valine, N-acetyl-D-serine, N-acetyl-D-phenylalanine and N-acetyl-D-phenylglycine, with titers reaching 5.65 g/L, 5.25 g/L, 8.025 g/L and 130 mg/L, respectively. This work opens up opportunities for synthesizing D-amino acids directly from simple carbon sources, avoiding costly and unsustainable conventional approaches.

d-Amino acids in biological systems

Investigations on the occurrence and biochemical roles of free D-amino acids and D-amino acid-containing peptides and proteins in living systems have increased in frequency and significance. Their occurrence and roles may vary substantially with progression from microbiotic to evermore advanced macrobiotic systems. We now understand many of the biosynthetic and regulatory pathways, which are outlined herein. Important uses for D-amino acids in plants, invertebrates, and vertebrates are reviewed. Given its importance, a separate section on the occurrence and role of D-amino acids in human disease is presented.

Characterization of free L- and D-amino acids in size-segregated background aerosols over the Ross Sea, Antarctica

The study of airborne chemical markers is crucial for identifying sources of aerosols, and their atmospheric processes of transport and transformation. The investigation of free amino acids and their differentiation between the L- and D- enantiomers are even more important to understand their sources and atmospheric fate. Aerosol samples were collected with a high-volume sampler with cascade impactor at Mario Zucchelli Station (MZS) on the coast of the Ross Sea (Antarctica) for two summer campaigns (2018/19 and 2019/20). The total mean concentration of free amino acids in PM10 was 4 ± 2 pmol m-3 for both campaigns and most of free amino acids were distributed in fine particles. The coarse mode of airborne D-Alanine and dimethylsufoniopropionate in seawater showed a similar trend during both Antarctic campaigns. Thus, the study of D/L Ala ratio in fine, coarse and PM10 fractions indicated the microlayer as the local source. This paper demonstrated that free amino acids follow the trend of DMS and MSA release occurred in the Ross Sea, confirming their applicability as markers for phytoplankton bloom also in paleoclimatic studies.

Evaluation of Antimicrobial Activities against Various E. coli Strains of a Novel Hybrid Peptide-LENART01

Finding the ideal antimicrobial drug with improved efficacy and a safety profile that eliminates antibiotic resistance caused by pathogens remains a difficult task. Indeed, there is an urgent need for innovation in the design and development of a microbial inhibitor. Given that many promising antimicrobial peptides with excellent broad-spectrum antibacterial properties are secreted by some frog species (e.g., bombesins, opioids, temporins, etc.), our goal was to identify the antimicrobial properties of amphibian-derived dermorphin and ranatensin peptides, which were combined to produce a hybrid compound. This new chimera (named LENART01) was tested for its antimicrobial activity against E. coli strains K12 and R1-R4, which are characterized by differences in lipopolysaccharide (LPS) core oligosaccharide structure. The results showed that LENART01 had superior activity against the R2 and R4 strains compared with the effects of the clinically available antibiotics ciprofloxacin or bleomycin (MIC values). Importantly, the inhibitory effect was not concentration dependent; however, LENART01 showed a time- and dose-dependent hemolytic effect in hemolytic assays.

A sensitive and economical method for simultaneous determination of D/L- amino acids profile in foods by HPLC-UV: Application in fermented and unfermented foods discrimination

This work described a sensitive and economical HPLC-UV method with FDAA derivatization to simultaneously detect 36 D/l-amino acids, which provides higher sensitivity and lower cost than other HPLC-based methods. It was validated for linearity range (8-1000 µmol/L), limits of detection (2.68-62.44 pmol/L), limits of quantification (2.93 to 208.13 pmol/L), intraday precision (0.30 % - 5.31 %), interday precision (1.96 % - 8.04 %) and accuracy (86.53 % - 121.46 %). This method was then applied in the determination of D/L- amino acids abundance in fermented and unfermented food materials and showed the characteristics of each type of foods. The method also demonstrated good performance in another application case for the discrimination of different types of food materials based on D/L- amino acids profile. It emphasizes the ability of the method to study the characteristics, distribution and abundance of d-amino acids in foods and their potential application in food quality control.

Promising applications of D-amino acids in periprosthetic joint infection

Due to the rise in our aging population, a disproportionate demand for total joint arthroplasty (TJA) in the elderly is forecast. Periprosthetic joint infection (PJI) represents one of the most challenging complications that can occur following TJA, and as the number of primary and revision TJAs continues to rise, an increasing PJI burden is projected. Despite advances in operating room sterility, antiseptic protocols, and surgical techniques, approaches to prevent and treat PJI remain difficult, primarily due to the formation of microbial biofilms. This difficulty motivates researchers to continue searching for an effective antimicrobial strategy. The dextrorotatory-isoforms of amino acids (D-AAs) are essential components of peptidoglycan within the bacterial cell wall, providing strength and structural integrity in a diverse range of species. Among many tasks, D-AAs regulate cell morphology, spore germination, and bacterial survival, evasion, subversion, and adhesion in the host immune system. When administered exogenously, accumulating data have demonstrated that D-AAs play a pivotal role against bacterial adhesion to abiotic surfaces and subsequent biofilm formation; furthermore, D-AAs have substantial efficacy in promoting biofilm disassembly. This presents D-AAs as promising and novel targets for future therapeutic approaches. Despite their emerging antibacterial efficacy, their role in disrupting PJI biofilm formation, the disassembly of established TJA biofilm, and the host bone tissue response remains largely unexplored. This review aims to examine the role of D-AAs in the context of TJAs. Data to date suggest that D-AA bioengineering may serve as a promising future strategy in the prevention and treatment of PJI.

YgeA is involved in L- and D-homoserine metabolism in Escherichia coli

Noncanonical D-amino acids are involved in peptidoglycan and biofilm metabolism in bacteria. Previously, we identified amino acid racemases with broad substrate specificity, including YgeA from Escherichia coli, which strongly prefers homoserine as a substrate. In this study, we investigated the functions of this enzyme in vivo. When wild-type and ygeA-deficient E. coli strains were cultured in minimal medium containing D-homoserine, the D-homoserine level was significantly higher in the ygeA-deficient strain than in the wild-type strain, in which it was almost undetectable. Additionally, D-homoserine was detected in YgeA-expressed E. coli cells cultured in minimal medium containing L-homoserine. The growth of the ygeA-deficient strain was significantly impaired in minimal medium with or without supplemental D-homoserine, while L-methionine, L-threonine or L-isoleucine, which are produced via L-homoserine, restored the growth impairment. Furthermore, the wild-type strain formed biofilms significantly more efficiently than the ygeA-deficient strain. Addition of L- or D-homoserine significantly suppressed biofilm formation in the wild-type strain, whereas this addition had no significant effect in the ygeA-deficient strain. Together, these data suggest that YgeA acts as an amino acid racemase and plays a role in L- and D-homoserine metabolism in E. coli.

Diaminopimelic Acid Metabolism by Pseudomonadota in the Ocean

Diaminopimelic acid (DAP) is a unique component of the cell wall of Gram-negative bacteria. It is also an important component of organic matter and is widely utilized by microbes in the world's oceans. However, neither DAP concentrations nor marine DAP-utilizing microbes have been investigated. Here, DAP concentrations in seawater were measured and the diversity of marine DAP-utilizing bacteria and the mechanisms for their DAP metabolism were investigated. Free DAP concentrations in seawater, from surface to a 5,000 m depth, were found to be between 0.61 μM and 0.96 μM in the western Pacific Ocean. DAP-utilizing bacteria from 20 families in 4 phyla were recovered from the western Pacific seawater and 14 strains were further isolated, in which Pseudomonadota bacteria were dominant. Based on genomic and transcriptomic analyses combined with gene deletion and in vitro activity detection, DAP decarboxylase (LysA), which catalyzes the decarboxylation of DAP to form lysine, was found to be a key and specific enzyme involved in DAP metabolism in the isolated Pseudomonadota strains. Interrogation of the Tara Oceans database found that most LysA-like sequences (92%) are from Pseudomonadota, which are widely distributed in multiple habitats. This study provides an insight into DAP metabolism by marine bacteria in the ocean and contributes to our understanding of the mineralization and recycling of DAP by marine bacteria. IMPORTANCE DAP is a unique component of peptidoglycan in Gram-negative bacterial cell walls. Due to the large number of marine Gram-negative bacteria, DAP is an important component of marine organic matter. However, it remains unclear how DAP is metabolized by marine microbes. This study investigated marine DAP-utilizing bacteria by cultivation and bioinformational analysis and examined the mechanism of DAP metabolism used by marine bacteria. The results demonstrate that Pseudomonadota bacteria are likely to be an important DAP-utilizing group in the ocean and that DAP decarboxylase is a key enzyme involved in DAP metabolism. This study also sheds light on the mineralization and recycling of DAP driven by bacteria.

The conundrum in enzymatic reactions related to biosynthesis of d-amino acids in bacteria

d-Amino acids (d-AAs) are key components of the peptidoglycan matrix in bacterial cells. Various bacterial species are known to produce d-AAs by using different enzymes, such as highly specific and broad-spectrum racemases. Miyamoto et al. studied the biosynthesis of d-glutamate in the hyperthermophile and anaerobic Gram-negative bacterium, Thermotoga maritima, which does not possess a broad-spectrum racemase. The investigated TM0831 enzyme catalyzes both a d-amino acid aminotransferase reaction producing d-glutamate and an amino acid racemase activity aimed at generating d-aspartate and d-glutamate from the corresponding l-enantiomers. TM0831 represents an example of natural molecular evolution process favoring the enzyme versatility. Comment on: https://doi.org/10.1111/febs.16452.

Profiling of d-alanine production by the microbial isolates of rat gut microbiota

d-alanine (d-Ala) and several other d-amino acids (d-AAs) act as hormones and neuromodulators in nervous and endocrine systems. Unlike the endogenously synthesized d-serine in animals, d-Ala may be from exogenous sources, e.g., diet and intestinal microorganisms. However, it is unclear if the capability to produce d-Ala and other d-AAs varies among different microbial strains in the gut. We isolated individual microorganisms of rat gut microbiota and profiled their d-AA production in vitro, focusing on d-Ala. Serial dilutions of intestinal contents from adult male rats were plated on agar to obtain clonal cultures. Using MALDI-TOF MS for rapid strain typing, we identified 38 unique isolates, grouped into 11 species based on 16S rRNA gene sequences. We then used two-tier screening to profile bacterial d-AA production, combining a d-amino acid oxidase-based enzymatic assay for rapid assessment of non-acidic d-AA amount and chiral LC-MS/MS to quantify individual d-AAs, revealing 19 out of the 38 isolated strains as d-AA producers. LC-MS/MS analysis of the eight top d-AA producers showed high levels of d-Ala in all strains tested, with substantial inter- and intra-species variations. Though results from the enzymatic assay and LC-MS/MS analysis aligned well, LC-MS/MS further revealed the existence of d-glutamate and d-aspartate, which are poor substrates for this enzymatic assay. We observed large inter- and intra-species variation of d-AA production profiles from rat gut microbiome species, demonstrating the importance of chemical profiling of gut microbiota in addition to sequencing, furthering the idea that microbial metabolites modulate host physiology.

Amino Acid Configuration Affects Volatile Fatty Acid Production during Proteinaceous Waste Valorization: Chemotaxis, Quorum Sensing, and Metabolism

During proteinaceous waste valorization to produce volatile fatty acids (VFAs), protein needs to be hydrolyzed to amino acids (AAs), but the effects of the configuration of AAs on their biotransformation and VFA production have not been investigated. In this study, more residual d-AAs than their corresponding l-AAs were observed after VFAs were produced from kitchen waste in a pilot-scale bioreactor. For all AAs investigated, the VFA production from d-AAs was lower than that from corresponding l-AAs. The metagenomics and metaproteomics analyses revealed that the l-AA fermentation system exhibited greater bacterial chemotaxis and quorum sensing (QS) than d-AAs, which benefited the establishment of functional microorganisms (such as Clostridium, Sedimentibacter, and Peptoclostridium) and expression of functional proteins (e.g., substrate transportation cofactors, l-AA dehydrogenase, and acidogenic proteins). In addition, d-AAs need to be racemized to l-AAs before being metabolized, and the difference of VFA production between d-AAs and l-AAs decreased with the increase of racemization activity. The findings of the AA configuration affecting bacterial chemotaxis and QS, which altered microorganism communities and functional protein expression, provided a new insight into the reasons for higher l-AA metabolism than d-AAs and more d-AAs left during VFA production from proteinaceous wastes.

Significance of broad-spectrum racemases for the viability and pathogenicity of Aeromonas hydrophila

Aim: To investigate the function of broad-spectrum racemases in Aeromonas hydrophila (BsrA). Results: The A. hydrophila gene encoding BsrA (bsr) mutants (AHΔbsr) exhibited a significant decrease in growth, motility, extracellular protease production and biofilm formation compared with the wild-type. Furthermore, bsr gene knockout instigated cell wall damage compared with the wild-type strains. The survival rate and replication capability in the blood and organs of the AHΔbsr-infected mice were significantly decreased. The degree of tissue injury in the AHΔbsr-infected group was lower than that of the wild-type-infected group. Moreover, there was a significant decrease in the expression of 12 AHΔbsr virulence genes. Conclusion: The bsr gene is essential for the viability and virulence of A. hydrophila.

D-Amino Acids as a Biomarker in Schizophrenia

D-amino acids may play key roles for specific physiological functions in different organs including the brain. Importantly, D-amino acids have been detected in several neurological disorders such as schizophrenia, amyotrophic lateral sclerosis, and age-related disorders, reflecting the disease conditions. Relationships between D-amino acids and neurophysiology may involve the significant contribution of D-Serine or D-Aspartate to the synaptic function, including neurotransmission and synaptic plasticity. Gut-microbiota could play important roles in the brain-function, since bacteria in the gut provide a significant contribution to the host pool of D-amino acids. In addition, the alteration of the composition of the gut microbiota might lead to schizophrenia. Furthermore, D-amino acids are known as a physiologically active substance, constituting useful biomarkers of several brain disorders including schizophrenia. In this review, we wish to provide an outline of the roles of D-amino acids in brain health and neuropsychiatric disorders with a focus on schizophrenia, which may shed light on some of the superior diagnoses and/or treatments of schizophrenia.

Protein intake and outcome of critically ill patients: analysis of a large international database using piece-wise exponential additive mixed models

Background

Proteins are an essential part of medical nutrition therapy in critically ill patients. Guidelines almost universally recommend a high protein intake without robust evidence supporting its use.

Methods

Using a large international database, we modelled associations between the hazard rate of in-hospital death and live hospital discharge (competing risks) and three categories of protein intake (low: < 0.8 g/kg per day, standard: 0.8–1.2 g/kg per day, high: > 1.2 g/kg per day) during the first 11 days after ICU admission (acute phase). Time-varying cause-specific hazard ratios (HR) were calculated from piece-wise exponential additive mixed models. We used the estimated model to compare five different hypothetical protein diets (an exclusively low protein diet, a standard protein diet administered early (day 1 to 4) or late (day 5 to 11) after ICU admission, and an early or late high protein diet).

Results

Of 21,100 critically ill patients in the database, 16,489 fulfilled inclusion criteria for the analysis. By day 60, 11,360 (68.9%) patients had been discharged from hospital, 4,192 patients (25.4%) had died in hospital, and 937 patients (5.7%) were still hospitalized. Median daily low protein intake was 0.49 g/kg [IQR 0.27–0.66], standard intake 0.99 g/kg [IQR 0.89– 1.09], and high intake 1.41 g/kg [IQR 1.29–1.60]. In comparison with an exclusively low protein diet, a late standard protein diet was associated with a lower hazard of in-hospital death: minimum 0.75 (95% CI 0.64, 0.87), and a higher hazard of live hospital discharge: maximum HR 1.98 (95% CI 1.72, 2.28). Results on hospital discharge, however, were qualitatively changed by a sensitivity analysis. There was no evidence that an early standard or a high protein intake during the acute phase was associated with a further improvement of outcome.

Conclusions

Provision of a standard protein intake during the late acute phase may improve outcome compared to an exclusively low protein diet. In unselected critically ill patients, clinical outcome may not be improved by a high protein intake during the acute phase.

Study registration ID number ISRCTN17829198

Supplementary Information

The online version contains supplementary material available at 10.1186/s13054-021-03870-5.

Acetylornithine aminotransferase TM1785 performs multiple functions in the hyperthermophile Thermotoga maritima

The hyperthermophilic bacterium Thermotoga maritima peptidoglycan contains unusual d-lysine alongside typical d-alanine and d-glutamate. We previously identified lysine racemase and threonine dehydratase, but knowledge of d-amino acid metabolism remains limited. Herein, we identified and characterized T. maritima acetylornithine aminotransferase TM1785. The enzyme was most active towards acetyl-l-ornithine, but also utilized l-glutamate, l-ornithine and acetyl-l-lysine as amino donors, and 2-oxoglutarate was the preferred amino acceptor. TM1785 also displayed racemase activity towards four amino acids and lyase activity towards l-cysteine, but no dehydratase activity towards l-serine, l-threonine or corresponding d-amino acids. Catalytic efficiency (k_cat /K_m ) was highest for aminotransferase activity and lowest for racemase activity. TM1785 is a novel acetylornithine aminotransferase associated with l-arginine biosynthesis that possesses two additional distinct activities.

Production of both l- and d- N-acyl-homoserine lactones by Burkholderia cepacia and Vibrio fischeri

Quorum sensing (QS) is a complex process in which molecules, such as l-N-acyl-homoserine lactones (l-AHLs), are produced as essential signaling molecules allowing bacteria to detect and respond to cell population density by gene regulation. Few studies have considered the natural production and role of the opposite enantiomers, d-AHLs. In this work, production of d,l-AHLs by Burkholderia cepacia and Vibrio fischeri was monitored over time, with significant amounts of d-AHLs detected. Bioluminescence of V. fischeri was observed with maximum bioluminescence correlating with the maximum concentrations of both l- and d- octanoyl-homoserine lactones (l- and d-OHL). l-Methionine, a precursor to l-AHLs, was examined via supplementation studies conducted by growing three parallel cultures of B. cepacia in M9 minimal media with added l-, d-, or d,l-methionine and observing their effect on the production of d,l-AHL by B. cepacia. The results show that addition of any methionine (l-, d-, or d,l-) does not affect the overall ratio of l- to d-AHLs, that is d-AHL production was not selectively enhanced by d-methionine addition. However, the overall AHL (l- and d-) concentration does increase with the addition of any methionine supplement. These findings indicate the possibility of a distinct biosynthetic pathway for d-AHL production, possibly exposing a new dimension within bacterial communication.

Cell Wall Biology of Vibrio cholerae

Most bacteria are protected from environmental offenses by a cell wall consisting of strong yet elastic peptidoglycan. The cell wall is essential for preserving bacterial morphology and viability, and thus the enzymes involved in the production and turnover of peptidoglycan have become preferred targets for many of our most successful antibiotics. In the past decades, Vibrio cholerae, the gram-negative pathogen causing the diarrheal disease cholera, has become a major model for understanding cell wall genetics, biochemistry, and physiology. More than 100 articles have shed light on novel cell wall genetic determinants, regulatory links, and adaptive mechanisms. Here we provide the first comprehensive review of V. cholerae's cell wall biology and genetics. Special emphasis is placed on the similarities and differences with Escherichia coli, the paradigm for understanding cell wall metabolism and chemical structure in gram-negative bacteria.

The Rhizobacterium Pseudomonas alcaligenes AVO110 Induces the Expression of Biofilm-Related Genes in Response to Rosellinia necatrix Exudates

The rhizobacterium Pseudomonas alcaligenes AVO110 exhibits antagonism toward the phytopathogenic fungus Rosellinia necatrix. This strain efficiently colonizes R. necatrix hyphae and is able to feed on their exudates. Here, we report the complete genome sequence of P. alcaligenes AVO110. The phylogeny of all available P. alcaligenes genomes separates environmental isolates, including AVO110, from those obtained from infected human blood and oyster tissues, which cluster together with Pseudomonas otitidis. Core and pan-genome analyses showed that P. alcaligenes strains encode highly heterogenic gene pools, with the AVO110 genome encoding the largest and most exclusive variable region (~1.6 Mb, 1795 genes). The AVO110 singletons include a wide repertoire of genes related to biofilm formation, several of which are transcriptionally modulated by R. necatrix exudates. One of these genes (cmpA) encodes a GGDEF/EAL domain protein specific to Pseudomonas spp. strains isolated primarily from the rhizosphere of diverse plants, but also from soil and water samples. We also show that CmpA has a role in biofilm formation and that the integrity of its EAL domain is involved in this function. This study contributes to a better understanding of the niche-specific adaptations and lifestyles of P. alcaligenes, including the mycophagous behavior of strain AVO110.

Characterization of a novel moderate-substrate specificity amino acid racemase from the hyperthermophilic archaeon Thermococcus litoralis

The amino acid sequence of the OCC_10945 gene product from the hyperthermophilic archaeon Thermococcus litoralis DSM5473, originally annotated as γ-aminobutyrate aminotransferase, is highly similar to that of the uncharacterized pyridoxal 5'-phosphate (PLP)-dependent amino acid racemase from Pyrococcus horikoshii. The OCC_10945 enzyme was successfully overexpressed in Escherichia coli by coexpression with a chaperone protein. The purified enzyme demonstrated PLP-dependent amino acid racemase activity primarily toward Met and Leu. Although PLP contributed to enzyme stability, it only loosely bound to this enzyme. Enzyme activity was strongly inhibited by several metal ions, including Co2+ and Zn2+, and nonsubstrate amino acids such as l-Arg and l-Lys. These results suggest that the underlying PLP-binding and substrate recognition mechanisms in this enzyme are significantly different from those of the other archaeal and bacterial amino acid racemases. This is the first description of a novel PLP-dependent amino acid racemase with moderate substrate specificity in hyperthermophilic archaea.

Identification and biochemical characterization of threonine dehydratase from the hyperthermophile Thermotoga maritima

The peptidoglycan of the hyperthermophile Thermotoga maritima contains an unusual component, D-lysine (D-Lys), in addition to the typical D-alanine (D-Ala) and D-glutamate (D-Glu). In a previous study, we identified a Lys racemase that is presumably associated with D-Lys biosynthesis. However, our understanding of D-amino acid metabolism in T. maritima and other bacteria remains limited, although D-amino acids in the peptidoglycan are crucial for preserving bacterial cell structure and resistance to environmental threats. Herein, we characterized enzymatic and structural properties of TM0356 that shares a high amino acid sequence identity with serine (Ser) racemase. The results revealed that TM0356 forms a tetramer with each subunit containing a pyridoxal 5'-phosphate as a cofactor. The enzyme did not exhibit racemase activity toward various amino acids including Ser, and dehydratase activity was highest toward L-threonine (L-Thr). It also acted on L-Ser and L-allo-Thr, but not on the corresponding D-amino acids. The catalytic mechanism did not follow typical Michaelis-Menten kinetics; it displayed a sigmoidal dependence on substrate concentration, with highest catalytic efficiency (k_cat/K_0.5) toward L-Thr. Interestingly, dehydratase activity was insensitive to allosteric regulators L-valine and L-isoleucine (L-Ile) at low concentrations, while these L-amino acids are inhibitors at high concentrations. Thus, TM0356 is a biosynthetic Thr dehydratase responsible for the conversion of L-Thr to α-ketobutyrate and ammonia, which is presumably involved in the first step of the biosynthesis of L-Ile.

Understanding the Interactions between Staphylococcus aureus and the Raw-Meat-Processing Environment Isolate Klebsiella oxytoca in Dual-Species Biofilms via Discovering an Altered Metabolic Profile

In a raw-meat-processing environment, members of the Enterobacteriaceae family can coexist with Staphylococcus aureus to form dual-species biofilms, leading to a higher risk of food contamination. However, very little is known about the effect of inter-species interactions on dual-species biofilm formation. The aim of this study was to investigate the interactions between S. aureus and raw-meat-processing environment isolates of Klebsiella oxytoca in dual-species biofilms, by employing an untargeted metabolomics tool. Crystal violet staining assay showed that the biomass of the dual-species biofilm significantly increased and reached its maximum after incubation for 21 h, compared with that of single species grown alone. The number of K. oxytoca in the dual-species biofilm was significantly higher than that of S. aureus. Field emission scanning electron microscopy (FESEM) revealed that both species were evenly distributed, and were tightly wrapped by extracellular polymeric substances in the dual-species biofilms. Ultra-high-pressure liquid chromatography equipped with a quadrupole-time-of-flight mass spectrometer (UHPLC-Q-TOF MS) analysis exhibited a total of 8184 positive ions, and 6294 negative ions were obtained from all test samples. Multivariate data analysis further described altered metabolic profiling between mono- and dual-species biofilms. Further, 18 and 21 different metabolites in the dual-species biofilm were screened as biomarkers by comparing the mono-species biofilms of S. aureus and K. oxytoca, respectively. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways that were exclusively upregulated in the dual-species biofilm included ABC transporters, amino acid metabolism, and the two-component signal transduction system. Our results contribute to a better understanding of the interactive behavior of inter-species biofilm communities, by discovering altered metabolic profiling.

TK1211 Encodes an Amino Acid Racemase towards Leucine and Methionine in the Hyperthermophilic Archaeon Thermococcus kodakarensis

Members of Thermococcales harbor a number of genes encoding putative aminotransferase class III enzymes. Here, we characterized the TK1211 protein from the hyperthermophilic archaeon Thermococcus kodakarensis The TK1211 gene was expressed in T. kodakarensis under the control of the strong, constitutive promoter of the cell surface glycoprotein gene TK0895 (P _csg ). The purified protein did not display aminotransferase activity but exhibited racemase activity. An examination of most amino acids indicated that the enzyme was a racemase with relatively high activity toward Leu and Met. Kinetic analysis indicated that Leu was the most preferred substrate. A TK1211 gene disruption strain (ΔTK1211) was constructed and grown on minimal medium supplemented with l- or d-Leu or l- or d-Met. The wild-type T. kodakarensis is not able to synthesize Leu and displays Leu auxotrophy, providing a direct means to examine the Leu racemase activity of the TK1211 protein in vivo When we replaced l-Leu with d-Leu in the medium, the host strain with an intact TK1211 gene displayed an extended lag phase but displayed cell yield similar to that observed in medium with l-Leu. In contrast, the ΔTK1211 strain displayed growth in medium with l-Leu but could not grow with d-Leu. The results indicate that TK1211 encodes a Leu racemase that is active in T. kodakarensis cells and that no other protein exhibits this activity, at least to an extent that can support growth. Growth experiments with l- or d-Met also confirmed the Met racemase activity of the TK1211 protein in T. kodakarensis IMPORTANCE Phylogenetic analysis of aminotransferase class III proteins from all domains of life reveals numerous groups of protein sequences. One of these groups includes a large number of sequences from Thermococcales species and can be divided into four subgroups. Representatives of three of these subgroups have been characterized in detail. This study reveals that a representative from the remaining uncharacterized subgroup is an amino acid racemase with preference toward Leu and Met. Taken together with results of previous studies on enzymes from Pyrococcus horikoshii and Thermococcus kodakarensis, members of the four subgroups now can be presumed to function as a broad-substrate-specificity amino acid racemase (subgroup 1), alanine/serine racemase (subgroup 2), ornithine ω-aminotransferase (subgroup 3), or Leu/Met racemase (subgroup 4).

Binding of non-canonical peptidoglycan controls Vibrio cholerae broad spectrum racemase activity

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Cell wall muropeptides bind Vibrio cholerae's broad spectrum racemase BsrV and inhibit its activity.

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BsrV activity is regulated by polymeric peptidoglycan.

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Muropeptides modified with non-canonical D-amino acids show the strongest inhibitory activity of BsrV.

Broad-spectrum amino acid racemases (Bsrs) enable bacteria to generate non-canonical D-amino acids (NCDAAs), whose roles and impact on microbial physiology, including modulation of cell wall structure and dissolution of biofilms, are just beginning to be appreciated. Here we used a diverse array of structural, biochemical and molecular simulation studies to define and characterize how BsrV is post-translationally regulated. We discovered that contrary to Vibrio cholerae alanine racemase AlrV highly compacted active site, BsrV’s is broader and can be occupied by cell wall stem peptides. We found that peptidoglycan peptides modified with NCDAAs are better stabilized by BsrV’s catalytic cavity and show better inhibitory capacity than canonical muropeptides. Notably, BsrV binding and inhibition can be recapitulated by undigested peptidoglycan sacculi as it exists in the cell. Docking simulations of BsrV binding the peptidoglycan polymer generate a model where the peptide stems are perfectly accommodated and stabilized within each of the dimeŕs active sites. Taking these biochemical and structural data together, we propose that inhibition of BsrV by peptidoglycan peptides underlies a negative regulatory mechanism to avoid excessive NCDAA production. Our results collectively open the door to use “à la carte” synthetic peptides as a tool to modulate DAAs production of Bsr enzymes.

Alanine metabolism in Bacillus subtilis

Both isomeric forms of alanine play a crucial role in bacterial growth and viability; the L-isomer of this amino acid is one of the building blocks for protein synthesis, and the D-isomer is incorporated into the bacterial cell wall. Despite a long history of genetic manipulation of Bacillus subtilis using auxotrophic markers, the genes involved in alanine metabolism have not been characterized fully. In this work, we genetically characterized the major enzymes involved in B. subtilis alanine biosynthesis and identified an alanine permease, AlaP (YtnA), which we show has a major role in the assimilation of D-alanine from the environment. Our results provide explanations for the puzzling fact that growth of B. subtilis does not result in the significant accumulation of extracellular D-alanine. Interestingly, we find that in B. subtilis, unlike E. coli where multiple enzymes have a biochemical activity that can generate alanine, the primary synthetic enzyme for alanine is encoded by alaT, although a second gene, dat, can support slow growth of an L-alanine auxotroph. However, our results also show that Dat mediates the synthesis of D-alanine and its activity is influenced by the abundance of L-alanine. This work provides valuable insights into alanine metabolism that suggests that the relative abundance of D- and L-alanine might be linked with cytosolic pool of D and L-glutamate, thereby coupling protein and cell envelope synthesis with the metabolic status of the cell. The results also suggest that, although some of the purified enzymes involved in alanine biosynthesis have been shown to catalyze reversible reactions in vitro, most of them function unidirectionally in vivo.

Differences in bioavailability of canonical and non-canonical D-amino acids for marine microbes

Dissolved organic matter (DOM) accounts for >95% of total marine organic matter, and >95% of marine DOM is refractory to biodegradation. The recalcitrancy of DOM determines its residence time and thus is of great concern regarding to carbon sequestration in the ocean. However, the recalcitrancy of DOM not only varies among different compounds but also within different conformations of a same molecule such as L-amino acids (L-AAs) and D-amino acids (D-AAs). While the former is labile, the latter is refractory and used as a proxy for estimation of bacterial refractory DOM in the ocean. However, some D-AAs are also reported to be bioavailable. To clarify the controversy, we examined the bioavailability of two types of D-AAs: canonical D-AAs, which mainly present as bacterial cell wall components, and non-canonical D-AAs (NCDAAs), which are secreted by various bacteria as signaling molecules in bacterial physiology. Bioassay experiments were conducted with nine marine bacterial strains and a natural microbial community. D-AAs were poorly utilized by the strains as sole carbon or nitrogen sources compared with L-AAs, in addition, NCDAAs were barely used compared with canonical D-AAs. In comparison, the microbial community consumed all three canonical D-AAs (D-alanine, D-aspartic acid and D-glutamic acid) as efficiently as their corresponding L-AAs when supplied separately; however, L-AAs were preferentially used over D-AAs when both forms were provided simultaneously. Remarkably, two NCDAAs, D-methionine and D-leucine, were poorly utilized regardless of the presence of the L-enantiomers. It was found for the first time that NCDAAs are relatively more refractory than canonical D-AAs to microbial utilization. This novel recognition of difference in recalcitrancy between NCDAAs and canonical D-AAs lays the foundation for a better understanding of carbon cycling and more accurate estimation of carbon storage in the ocean.

Enzymatic properties and physiological function of glutamate racemase from Thermus thermophilus

d-Amino acids are physiologically important components of peptidoglycan in the bacterial cell wall, maintaining cell structure and aiding adaptation to environmental changes through peptidoglycan remodelling. Therefore, the biosynthesis of d-amino acids is essential for bacteria to adapt to different environmental conditions. The peptidoglycan of the extremely thermophilic bacterium Thermus thermophilus contains d-alanine (d-Ala) and d-glutamate (d-Glu), but its d-amino acid metabolism remains poorly understood. Here, we investigated the enzyme activity and function of the product of the TTHA1643 gene, which is annotated to be a Glu racemase in the T. thermophilus HB8 genome. Among 21 amino acids tested, TTHA1643 showed highly specific activity toward Glu as the substrate. The catalytic efficiency (k_cat/K_m) of TTHA1643 toward d- and l-Glu was comparable; however, the k_cat value was 18-fold higher for l-Glu than for d-Glu. Temperature and pH profiles showed that the racemase activity of TTHA1643 is high under physiological conditions for T. thermophilus growth. To assess physiological relevance, we constructed a TTHA1643-deficient strain (∆TTHA1643) by replacing the TTHA1643 gene with the thermostable hygromycin resistance gene. Growth of the ∆TTHA1643 strain in synthetic medium without d-Glu was clearly diminished relative to wild type, although the TTHA1643 deletion was not lethal, suggesting that alternative d-Glu biosynthetic pathways may exist. The deterioration in growth was restored by adding d-Glu to the culture medium, showing that d-Glu is required for normal growth of T. thermophilus. Collectively, our findings show that TTHA1643 is a Glu racemase and has the physiological function of d-Glu production in T. thermophilus.

Metabolic versatility of freshwater sedimentary archaea feeding on different organic carbon sources

Members of the phylum Bathyarchaeota and the class Thermoplasmata are widespread in marine and freshwater sediments where they have been recognized as key players in the carbon cycle. Here, we tested the responsiveness of archaeal communities on settled plant debris and sediment from a karstic lake to different organic carbon amendments (amino acids, plant-derived carbohydrates, and aromatics) using a lab-scale microcosm. Changes in the composition and abundance of sediment and biofilm archaeal communities in both DNA and RNA fractions were assessed by 16S rRNA gene amplicon sequencing and qPCR, respectively, after 7 and 30 days of incubation. Archaeal communities showed compositional changes in terms of alpha and beta diversity in relation to the type of carbon source (amino acids vs. plant-derived compounds), the nucleic acid fraction (DNA vs. RNA), and the incubation time (7 vs. 30 days). Distinct groups within the Bathyarchaeota (Bathy-15 and Bathy-6) and the Thermoplasmata (MBG-D) differently reacted to carbon supplements as deduced from the analysis of RNA libraries. Whereas Bathyarchaeota in biofilms showed a long-term positive response to humic acids, their counterparts in the sediment were mainly stimulated by the addition of tryptophan, suggesting the presence of different subpopulations in both habitats. Overall, our work presents an in vitro assessment of the versatility of archaea inhabiting freshwater sediments towards organic carbon and introduces settled leaf litter as a new habitat for the Bathyarchaeota and the Thermoplasmata.

Involvement of penicillin-binding proteins in the metabolism of a bacterial peptidoglycan containing a non-canonical D-amino acid

Bacteria produce various D-amino acids, including non-canonical D-amino acids, to adapt to environmental changes and overcome a variety of threats. These D-amino acids are largely utilized as components of peptidoglycan, and they promote peptidoglycan remodeling and biofilm disassembly. The biosynthesis, maturation, and recycling of peptidoglycan are catalyzed by penicillin-binding proteins (PBPs). However, although non-canonical D-amino acids are known to be incorporated into peptidoglycan, the maturation and recycling of peptidoglycan containing such residues remain uncharacterized. Therefore, we investigated whether PBP4 and PBP5, low molecular mass (LMM) PBPs from Escherichia coli and Bacillus subtilis, are involved in these events of peptidoglycan metabolism. Enzyme assays using p-nitroaniline (pNA)-derivatized D-amino acids and peptidoglycan-mimicking peptides revealed that PBP4 and PBP5 from both species have peptidase activity toward substrates containing D-Asn, D-His, or D-Trp. These D-amino acids slowed the growth of dacA- or dacB-deficient E. coli (∆dacA or ∆dacB) relative to the wild-type strain. Additionally, these D-amino acids affected biofilm formation by the ∆dacB strain. Collectively, PBP4 and PBP5 are involved in the cleavage of peptidoglycan containing non-canonical D-amino acids, and these properties affect growth and biofilm formation.

SRL pathogenicity island contributes to the metabolism of D-aspartate via an aspartate racemase in Shigella flexneri YSH6000

In recent years, multidrug resistance of Shigella strains associated with genetic elements like pathogenicity islands, have become a public health problem. The Shigella resistance locus pathogenicity island (SRL PAI) of S. flexneri 2a harbors a 16Kbp region that contributes to the multidrug resistance phenotype. However, there is not much information about other functions such as metabolic, physiologic or ecological ones. For that, wild type S. flexneri YSH6000 strain, and its spontaneous SRL PAI mutant, 1363, were used to study the contribution of the island in different growth conditions. Interestingly, when both strains were compared by the Phenotype Microarrays, the ability to metabolize D-aspartic acid as a carbon source was detected in the wild type strain but not in the mutant. When D-aspartate was added to minimal medium with other carbon sources such as mannose or mannitol, the SRL PAI-positive strain was able to metabolize it, while the SRL PAI-negative strain did not. In order to identify the genetic elements responsible for this phenotype, a bioinformatic analysis was performed and two genes belonging to SRL PAI were found: orf8, coding for a putative aspartate racemase, and orf9, coding for a transporter. Thus, it was possible to measure, by an indirect analysis of racemization activity in minimal medium supplemented only with D-aspartate, that YSH6000 strain was able to transform the D-form into L-, while the mutant was impaired to do it. When the orf8-orf9 region from SRL island was transformed into S. flexneri and S. sonnei SRL PAI-negative strains, the phenotype was restored. Although, when single genes were cloned into plasmids, no complementation was observed. Our results strongly suggest that the aspartate racemase and the transporter encoded in the SRL pathogenicity island are important for bacterial survival in environments rich in D-aspartate.

Heterologous expression, purification and biochemical characterization of a glutamate racemase (MurI) from Streptococcus mutans UA159

Background

Glutamate racemase (MurI) is a cofactor-independent enzyme that is essential to the bacterial peptidoglycan biosynthesis pathway and has therefore been considered an attractive target for the development of antimicrobial drugs. While in our previous study the essentiality of the murI gene was shown in Streptococcus mutans, the primary aetiologic agent of human dental caries, studies on S. mutans MurI have not yet provided definitive results. This study aimed to produce and characterize the biochemical properties of the MurI from the S. mutans UA159 genome.

Methods

Structure characterization prediction and multiple sequence alignment were performed by bioinformatic analysis. Recombinant His₆-tagged S. mutans MurI was overexpressed in the expression vector pColdII and further purified using a Ni²⁺ affinity chromatography method. Protein solubility, purity and aggregation state were analyzed by SDS–PAGE, Western blotting, native PAGE and SEC-HPLC. Kinetic parameters were assessed by a circular dichroism (CD) assay. Kinetic constants were calculated based on the curve fit for the Michaelis–Menten equation. The effects of temperature and pH on enzymatic activity were determined by a series of coupled enzyme reaction mixtures.

Results

The glutamate racemase gene from S. mutans UA159 was amplified by PCR, cloned and expressed in Escherichia coli BL21 (DE3). The 264-amino-acid protein, as a mixture of dimeric and monomeric enzymes, was purified to electrophoretic homogeneity. In the CD assay, S. mutans MurI displayed unique kinetic parameters (K_{m, d-Glu→l-Glu} = 0.3631 ± 0.3205 mM, V_{max, d-Glu→l-Glu} = 0.1963 ± 0.0361 mM min⁻¹, k_{cat, d-Glu→l-Glu} = 0.0306 ± 0.0065 s⁻¹, k_cat/K_{m,d-Glu→l-Glu} = 0.0844 ± 0.0128 s⁻¹ mM⁻¹, with d-glutamate as substrate; K_{m, l-Glu→d-Glu} = 0.8077 ± 0.5081 mM, V_{max, l-Glu→d-Glu} = 0.2421 ± 0.0418 mM min⁻¹, k_{cat,l-Glu→d-Glu} = 0.0378 ± 0.0056 s⁻¹, k_cat/K_{m,l-Glu→d-Glu} = 0.0468 ± 0.0176 s⁻¹ mM⁻¹, with l-glutamate as substrate). S. mutans MurI possessed an assay temperature optimum of 37.5 °C and its optimum pH was 8.0.

Conclusion

The findings of this study provide insight into the structure and biochemical traits of the glutamate racemase in S. mutans and supply a conceivable guideline for employing glutamate racemase in anti-caries drug design.

d-amino Acids in Health and Disease: A Focus on Cancer

d-amino acids, the enantiomeric counterparts of l-amino acids, were long considered to be non-functional or not even present in living organisms. Nowadays, d-amino acids are acknowledged to play important roles in numerous physiological processes in the human body. The most commonly studied link between d-amino acids and human physiology concerns the contribution of d-serine and d-aspartate to neurotransmission. These d-amino acids and several others have also been implicated in regulating innate immunity and gut barrier function. Importantly, the presence of certain d-amino acids in the human body has been linked to several diseases including schizophrenia, amyotrophic lateral sclerosis, and age-related disorders such as cataract and atherosclerosis. Furthermore, increasing evidence supports a role for d-amino acids in the development, pathophysiology, and treatment of cancer. In this review, we aim to provide an overview of the various sources of d-amino acids, their metabolism, as well as their contribution to physiological processes and diseases in man, with a focus on cancer.

Effect of D-cysteine on dual-species biofilms of Streptococcus mutans and Streptococcus sanguinis

Dental caries is a highly prevalent disease worldwide. It is caused by the cariogenic biofilms composed of multiple dynamic bacteria on dental surface. Streptococcus mutans and Streptococcus sanguinis are resident members within the biofilms and an antagonistic relationship has been shown between these two species. S. mutans, as the major causative microorganism of dental caries, has been reported to be inhibited by free D-cysteine (D-Cys). However, whether D-Cys could affect S. sanguinis and the interspecies relationship between S. mutans and S. sanguinis remains unknown. The aim of the current study was to investigate the effect of D-Cys on the growth and cariogenicity of dual-species biofilms formed by S. mutans and S. sanguinis. We measured dual-species biofilms biomass, metabolic activity, lactate production. We also detected the biofilms structure, the ratio of live/dead bacteria, extracellular polysaccharide (EPS) synthesis and bacterial composition in the dual-species biofilms. We found that D-Cys could reduce the metabolic activity and lactic acid production of dual-species biofilms (p < 0.05). In addition, biofilms formation, the proportion of S. mutans in dual-species biofilms, and EPS synthesis were decreased with D-Cys treatment. The results suggested that D-Cys could inhibit the growth and cariogenic virulence of dual-species biofilms formed by S. mutans and S. sanguinis, indicating the potential of D-Cys in clinical application for caries prevention and treatment.

Elucidation of the d-lysine biosynthetic pathway in the hyperthermophile Thermotoga maritima

Various d-amino acids are involved in peptidoglycan and biofilm metabolism in bacteria, suggesting that these compounds are necessary for successful adaptation to environmental changes. In addition to the conventional d-alanine (d-Ala) and d-glutamate, the peptidoglycan of the hyperthermophilic bacterium Thermotoga maritima contains both l-lysine (l-Lys) and d-Lys, but not meso-diaminopimelate (meso-Dpm). d-Lys is an uncommon component of peptidoglycan, and its biosynthetic pathway remains unclear. In this study, we identified and characterized a novel Lys racemase (TM1597) and Dpm epimerase (TM1522) associated with the d-Lys biosynthetic pathway in T. maritima. The Lys racemase had a dimeric structure containing pyridoxal 5'-phosphate as a cofactor. Among the amino acids, it exhibited the highest racemase activity toward d- and l-Lys, and also had relatively high activity toward d- and l-enantiomers of ornithine and Ala. The Dpm epimerase had the highest epimerization activity toward ll- and meso-Dpm, and also measurably racemized certain amino acids, including Lys. These results suggest that Lys racemase contributes to production of d-Lys and d-Ala for use as peptidoglycan components, and that Dpm epimerase converts ll-Dpm to meso-Dpm, a precursor in the l-Lys biosynthetic pathway.

Enzymatic characterization and crystal structure of biosynthetic alanine racemase from Pseudomonas aeruginosa PAO1

Alanine racemase is a pyridoxal-5'-phosphate (PLP)-dependent enzyme that reversibly catalyzes the conversion of l-alanine to d-alanine. d-alanine is an essential constituent in many prokaryotic cell structures. Inhibition of alanine racemase is lethal to prokaryotes, creating an attractive target for designing antibacterial drugs. Here we report the crystal structure of biosynthetic alanine racemase (Alr) from a pathogenic bacteria Pseudomonas aeruginosa PAO1. Structural studies showed that P. aeruginosa Alr (PaAlr) adopts a conserved homodimer structure. A guest substrate d-lysine was observed in the active site and refined to dual-conformation. Two buffer ions, malonate and acetate, were bound in the proximity to d-lysine. Biochemical characterization revealed the optimal reaction conditions for PaAlr.

Vibrio fischeri DarR Directs Responses to d-Aspartate and Represents a Group of Similar LysR-Type Transcriptional Regulators

Mounting evidence suggests that d-amino acids play previously underappreciated roles in diverse organisms. In bacteria, even d-amino acids that are absent from canonical peptidoglycan (PG) may act as growth substrates, as signals, or in other functions. Given these proposed roles and the ubiquity of d-amino acids, the paucity of known d-amino-acid-responsive transcriptional control mechanisms in bacteria suggests that such regulation awaits discovery. We found that DarR, a LysR-type transcriptional regulator (LTTR), activates transcription in response to d-Asp. The d-Glu auxotrophy of a Vibrio fischerimurI::Tn mutant was suppressed, with the wild-type PG structure maintained, by a point mutation in darR This darR mutation resulted in the overexpression of an adjacent operon encoding a putative aspartate racemase, RacD, which compensated for the loss of the glutamate racemase encoded by murI Using transcriptional reporters, we found that wild-type DarR activated racD transcription in response to exogenous d-Asp but not upon the addition of l-Asp, l-Glu, or d-Glu. A DNA sequence typical of LTTR-binding sites was identified between darR and the divergently oriented racD operon, and scrambling this sequence eliminated activation of the reporter in response to d-Asp. In several proteobacteria, genes encoding LTTRs similar to DarR are linked to genes with predicted roles in d- and/or l-Asp metabolism. To test the functional similarities in another bacterium, darR and racD mutants were also generated in Acinetobacter baylyi In V. fischeri and A. baylyi, growth on d-Asp required the presence of both darR and racD Our results suggest that multiple bacteria have the ability to sense and respond to d-Asp.IMPORTANCE d-Amino acids are prevalent in the environment and are generated by organisms from all domains of life. Although some biological roles for d-amino acids are understood, in other cases, their functions remain uncertain. Given the ubiquity of d-amino acids, it seems likely that bacteria will initiate transcriptional responses to them. Elucidating d-amino acid-responsive regulators along with the genes they control will help uncover bacterial uses of d-amino acids. Here, we report the discovery of DarR, a novel LTTR in V. fischeri that mediates a transcriptional response to environmental d-Asp and underpins the catabolism of d-Asp. DarR represents the founding member of a group of bacterial homologs that we hypothesize control aspects of aspartate metabolism in response to d-Asp and/or to d-Asp-containing peptides.

A Novel PLP-Dependent Alanine/Serine Racemase From the Hyperthermophilic Archaeon Pyrococcus horikoshii OT-3

We recently identified and characterized a novel broad substrate specificity amino acid racemase (BAR) from the hyperthermophilic archaeon Pyrococcus horikoshii OT-3. Three genes, PH0782, PH1423, and PH1501, encoding homologs exhibiting about 45% sequence identity with BAR were present in the P. horikoshii genome. In this study, we detected pyridoxal 5′-phosphate (PLP)-dependent amino acid racemase activity in the protein encoded by PH0782. The enzyme showed activity toward Ala, Ser, Thr, and Val, but the catalytic efficiency with Thr or Val was much lower than with Ala or Ser. The enzyme was therefore designated Ala/Ser racemase (ASR). Like BAR, ASR was highly stable at high temperatures and over a wide range of pHs, though its hexameric structure differed from the dimeric structure of BAR. No activity was detected in K291A or D234A ASR mutants. This suggests that, as in Ile 2-epimerase (ILEP) from Lactobacillus buchneri JCM1115, these residues are involved in Schiff base formation and substrate interaction, respectively. Unlike BAR, enhanced ASR activity was not detected in P. horikoshii cells cultivated in the presence of D-Ala or D-Ser. This is the first description of a PLP-dependent fold type I ASR in archaea.

Cystathionine β-lyase is involved in d-amino acid metabolism

Non-canonical d-amino acids play important roles in bacteria including control of peptidoglycan metabolism and biofilm disassembly. Bacteria appear to produce non-canonical d-amino acids to adapt to various environmental changes, and understanding the biosynthetic pathways is important. We identified novel amino acid racemases possessing the ability to produce non-canonical d-amino acids in Escherichia coli and Bacillus subtilis in our previous study, whereas the biosynthetic pathways of these d-amino acids still remain unclear. In the present study, we demonstrated that two cystathionine β-lyases (MetC and MalY) from E. coli produce non-canonical d-amino acids including non-proteinogenic amino acids. Furthermore, MetC displayed d- and l-serine (Ser) dehydratase activity. We characterised amino acid racemase, Ser dehydratase and cysteine lyase activities, and all were higher for MetC. Interestingly, all three activities were at a comparable level for MetC, although optimal conditions for each reaction were distinct. These results indicate that MetC and MalY are multifunctional enzymes involved in l-methionine metabolism and the production of d-amino acids, as well as d- and l-Ser metabolism. To our knowledge, this is the first evidence that cystathionine β-lyase is a multifunctional enzyme with three different activities.

Function of alanine racemase in the physiological activity and cariogenicity of Streptococcus mutans

The enzyme alanine racemase (Alr) has been a new target for the development of antibacterial drugs based on the involvement of D-Ala in bacterial cell wall biosynthesis. Our previous study noted that Alr is essential for the growth and interspecies competitiveness of S. mutans, the major causative organism of dental caries. However, physiological activity and cariogenicity of S. mutans affected by Alr remains unknown. The current study examined the biofilm biomass, biofilm structure, extracellular polysaccharide (EPS) synthesis, glucosyltransferase (gtf) gene expression, acid production and acid tolerance in the alr-mutant strain. We found that biofilm formation, biofilm structure, and EPS synthesis was in a D-Ala dose-dependent manner. Biofilm structure was loose in alr-mutant group and the ratio of EPS/bacteria was also elevated. Additionally, the expression levels of multiple gtfs were up-regulated, and acid tolerance was decreased. We also established in vivo models of dental caries and found that the incidence and severity of the caries were decreased in the alr-mutant group in comparison to the parental S. mutans group. Our in vivo and in vitro experiments demonstrate that Alr is essential for the cariogenicity of S. mutans and that Alr might be a potential target for the prevention and treatment of caries.

d-Amino Acids Are Exuded by Arabidopsis thaliana Roots to the Rhizosphere

Proteinogenic l-amino acids (l-AAs) are essential in all kingdoms as building blocks of proteins. Their d-enantiomers are also known to fulfill important functions in microbes, fungi, and animals, but information about these molecules in plants is still sparse. Previously, it was shown that d-amino acids (d-AAs) are taken up and utilized by plants, but their ways to reduce excessive amounts of them still remained unclear. Analyses of plant d-AA content after d-Ala and d-Glu feeding opened the question if exudation of d-AAs into the rhizosphere takes place and plays a role in the reduction of d-AA content in plants. The exudation of d-Ala and d-Glu could be confirmed by amino acid analyses of growth media from plants treated with these d-AAs. Further tests revealed that other d-AAs were also secreted. Nevertheless, treatments with d-Ala and d-Glu showed that plants are still able to reduce their contents within the plant without exudation. Further exudation experiments with transport inhibitors revealed that d-AA root exudation is rather passive and comparable to the secretion of l-AAs. Altogether, these observations argued against a dominant role of exudation in the regulation of plant d-AA content, but may influence the composition of the rhizosphere.