Structural analysis and mutant growth properties reveal distinctive enzymatic and cellular roles for the three major L-alanine transaminases of Escherichia coli

The characteristics of aminotransferases gene family in Ruditapes philippinarum and its response to salinity stresses

Aminotransferase is involved in the regulation of amino acid metabolism, which can affect the balance and distribution of amino acids in the organism, help maintain the homeostasis of amino acids in the organism, and play an important role in the environmental adaptation of aquatic animals. In this study, a total of 28 aminotransferase genes were identified in the genome of R. philippinarum. The gene structure, protein structure, chromosome localization, and phylogenetic analysis of aminotransferase were conducted using bioinformatics. According to the gene structure and phylogenetic analysis of aminotransferase proteins, aminotransferase proteins can be categorized into class I and II, class III, and class V. RNA-seq data analysis showed that aminotransferase genes were differentially expressed at different developmental stages, tissues, and salinity stress. In addition, qPCR demonstrated that the expression levels of most aminotransferase genes increased significantly during salinity changes. We also measured the free amino acids content in the gills of R. philippinarum after 48 h of low and high salinity stress. The results indicated that the total free amino acids under low salinity stress (75.89 ± 3.31 mg/g) and high salinity stress (91.01 ± 3.31 mg/g) at 48 h were significantly decreased and increased compared with the control group (83.01 ± 3.12 mg/g), respectively. The results of this study provide a valuable reference for further research on the salinity adaptation of the aminotransferase gene in R. philippinarum.

Cloning and expression profile of the alanine aminotransferase gene from kuruma shrimp Penaeus japonicus exposed to different salinities

Several crustaceans including shrimps change the amount of specific free amino acids to regulate the osmotic pressure in their bodies. Kuruma shrimp Penaeus japonicus also increases the concentration of alanine (Ala) in the abdominal muscle following the increase of environmental salinity. In the present study, to elucidate the mechanisms of changes in Ala accumulation of kuruma shrimp depending on salinity, we cloned the gene encoding alanine aminotransferase (ALT), an enzyme involved in Ala biosynthesis, and examined its expression profile. It was found that the full-length kuruma shrimp ALT1 cDNA consisted of 3,301 bp, encoding 514 amino acids, and that all amino acid residues important for ALT activity were conserved. Phylogenetic analysis also indicated that the ALT gene cloned in this study was classified as ALT1. Moreover, we examined the expression levels of the ALT1 gene in the abdominal muscle and the hepatopancreas of kuruma shrimp acclimated at 17‰, 34‰, and 40‰ salinities, resulting that the mRNA levels of the ALT1 genes in both tissues of the shrimp acclimated at 40‰ were significantly higher than those at 17‰ for 12 h (p < 0.05). The mRNA levels of the ALT1 gene in the abdominal muscle of the shrimp acclimated for more than 24 h tended to increase following the increase of environmental salinity. These results indicate that ALT1 is responsible for the increase of free Ala concentration in the abdominal muscle of kuruma shrimp to regulate osmotic pressure at high salinity.

Toxic effect and inability of L-homoserine to be a nitrogen source for growth of Escherichia coli resolved by a combination of in vivo evolution engineering and omics analyses

L-homoserine is a pivotal intermediate in the carbon and nitrogen metabolism of E. coli. However, this non-canonical amino acid cannot be used as a nitrogen source for growth. Furthermore, growth of this bacterium in a synthetic media is potently inhibited by L-homoserine. To understand this dual effect, an adapted laboratory evolution (ALE) was applied, which allowed the isolation of a strain able to grow with L-homoserine as the nitrogen source and was, at the same time, desensitized to growth inhibition by this amino acid. Sequencing of this evolved strain identified only four genomic modifications, including a 49 bp truncation starting from the stop codon of thrL. This mutation resulted in a modified thrL locus carrying a thrL* allele encoding a polypeptide 9 amino acids longer than the thrL encoded leader peptide. Remarkably, the replacement of thrL with thrL* in the original strain MG1655 alleviated L-homoserine inhibition to the same extent as strain 4E, but did not allow growth with this amino acid as a nitrogen source. The loss of L-homoserine toxic effect could be explained by the rapid conversion of L-homoserine into threonine via the thrL*-dependent transcriptional activation of the threonine operon thrABC. On the other hand, the growth of E. coli on a mineral medium with L-homoserine required an activation of the threonine degradation pathway II and glycine cleavage system, resulting in the release of ammonium ions that were likely recaptured by NAD(P)-dependent glutamate dehydrogenase. To infer about the direct molecular targets of L-homoserine toxicity, a transcriptomic analysis of wild-type MG1655 in the presence of 10 mM L-homoserine was performed, which notably identified a potent repression of locomotion-motility-chemotaxis process and of branched-chain amino acids synthesis. Since the magnitude of these effects was lower in a ΔthrL mutant, concomitant with a twofold lower sensitivity of this mutant to L-homoserine, it could be argued that growth inhibition by L-homoserine is due to the repression of these biological processes. In addition, L-homoserine induced a strong upregulation of genes in the sulfate reductive assimilation pathway, including those encoding its transport. How this non-canonical amino acid triggers these transcriptomic changes is discussed.

On the flexibility of the cellular amination network in E coli

Ammonium (NH4+) is essential to generate the nitrogenous building blocks of life. It gets assimilated via the canonical biosynthetic routes to glutamate and is further distributed throughout metabolism via a network of transaminases. To study the flexibility of this network, we constructed an Escherichia coli glutamate auxotrophic strain. This strain allowed us to systematically study which amino acids serve as amine sources. We found that several amino acids complemented the auxotrophy either by producing glutamate via transamination reactions or by their conversion to glutamate. In this network, we identified aspartate transaminase AspC as a major connector between many amino acids and glutamate. Additionally, we extended the transaminase network by the amino acids β-alanine, alanine, glycine, and serine as new amine sources and identified d-amino acid dehydrogenase (DadA) as an intracellular amino acid sink removing substrates from transaminase reactions. Finally, ammonium assimilation routes producing aspartate or leucine were introduced. Our study reveals the high flexibility of the cellular amination network, both in terms of transaminase promiscuity and adaptability to new connections and ammonium entry points.

Evolutionary Origin and Functional Diversification of Aminotransferases

Aminotransferases (ATs) are pyridoxal 5′-phosphate–dependent enzymes that catalyze the transamination reactions between amino acid donor and keto acid acceptor substrates. Modern AT enzymes constitute ∼2% of all classified enzymatic activities, play central roles in nitrogen metabolism, and generate multitude of primary and secondary metabolites. ATs likely diverged into four distinct AT classes before the appearance of the last universal common ancestor and further expanded to a large and diverse enzyme family. Although the AT family underwent an extensive functional specialization, many AT enzymes retained considerable substrate promiscuity and multifunctionality because of their inherent mechanistic, structural, and functional constraints. This review summarizes the evolutionary history, diverse metabolic roles, reaction mechanisms, and structure–function relationships of the AT family enzymes, with a special emphasis on their substrate promiscuity and multifunctionality. Comprehensive characterization of AT substrate specificity is still needed to reveal their true metabolic functions in interconnecting various branches of the nitrogen metabolic network in different organisms.

An Alanine Aminotransferase Is Required for Biofilm-Specific Resistance of Aspergillus fumigatus to Echinocandin Treatment

Alanine metabolism has been suggested as an adaptation strategy to oxygen limitation in organisms ranging from plants to mammals. Within the pulmonary infection microenvironment, Aspergillus fumigatus forms biofilms with steep oxygen gradients defined by regions of oxygen limitation. An alanine aminotransferase, AlaA, was observed to function in alanine catabolism and is required for several aspects of A. fumigatus biofilm physiology. Loss of alaA, or its catalytic activity, results in decreased adherence of biofilms through a defect in the maturation of the extracellular matrix polysaccharide galactosaminogalactan (GAG). Additionally, exposure of cell wall polysaccharides is also impacted by loss of alaA, and loss of AlaA catalytic activity confers increased biofilm susceptibility to echinocandin treatment, which is correlated with enhanced fungicidal activity. The increase in echinocandin susceptibility is specific to biofilms, and chemical inhibition of alaA by the alanine aminotransferase inhibitor β-chloro-l-alanine is sufficient to sensitize A. fumigatus biofilms to echinocandin treatment. Finally, loss of alaA increases susceptibility of A. fumigatus to in vivo echinocandin treatment in a murine model of invasive pulmonary aspergillosis. Our results provide insight into the interplay of metabolism, biofilm formation, and antifungal drug resistance in A. fumigatus and describe a mechanism of increasing susceptibility of A. fumigatus biofilms to the echinocandin class of antifungal drugs. IMPORTANCE Aspergillus fumigatus is a ubiquitous filamentous fungus that causes an array of diseases depending on the immune status of an individual, collectively termed aspergillosis. Antifungal therapy for invasive pulmonary aspergillosis (IPA) or chronic pulmonary aspergillosis (CPA) is limited and too often ineffective. This is in part due to A. fumigatus biofilm formation within the infection environment and the resulting emergent properties, particularly increased antifungal resistance. Thus, insights into biofilm formation and mechanisms driving increased antifungal drug resistance are critical for improving existing therapeutic strategies and development of novel antifungals. In this work, we describe an unexpected observation where alanine metabolism, via the alanine aminotransferase AlaA, is required for several aspects of A. fumigatus biofilm physiology, including resistance of A. fumigatus biofilms to the echinocandin class of antifungal drugs. Importantly, we observed that chemical inhibition of alanine aminotransferases is sufficient to increase echinocandin susceptibility and that loss of alaA increases susceptibility to echinocandin treatment in a murine model of IPA. AlaA is the first gene discovered in A. fumigatus that confers resistance to an antifungal drug specifically in a biofilm context.

Highly efficient production of L-homoserine in Escherichia coli by engineering a redox balance route

L-Homoserine is a nonessential chiral amino acid and the precursor of L-threonine and L-methionine. It has great potential to be used in the pharmaceutical, agricultural, cosmetic, and fragrance industries. However, the current low efficiency in the fermentation process of L-homoserine drives up the cost and therefore limits applications. Here, we systematically analyzed the L-homoserine production network in Escherichia coli to design a redox balance route for L-homoserine fermentation from glucose. Production of L-homoserine from L-aspartate via reduction of the tricarboxylic acid cycle intermediate oxaloacetate lacks reducing power. This deficiency could be corrected by activating the glyoxylate shunt and driving the flux from fumarate to L-aspartate with excess reducing power. This redox balance route decreases cell growth pressure and the theoretical yield of L-homoserine is 1.5 mol/mol of glucose without carbon loss. We fine-tuned the flux from fumarate to L-aspartate, deleted competitive and degradative pathways, enhanced L-homoserine efflux, and generated 84.1 g/L L-homoserine with 1.96 g/L/h productivity and 0.50 g/g glucose yield in a fed-batch fermentation. This study proposes a novel balanced redox metabolic network strategy for highly efficient production of L-homoserine and its derivative amino acids.

Fecal Microbiome Alteration May Be a Potential Marker for Gastric Cancer

Although intestinal microbial dysbiosis was confirmed to be associated with many chronic diseases and health status through complicated interaction with the host, the effect on gastric cancer was less studied. In this study, we sequenced the 16S rRNA and 18S rRNA genes of fecal bacteria and fungi, respectively, in 134 gastric cancer patients and 58 healthy controls matched by age and gender. Propensity score matching (PSM) was adopted for adjusting diet habits and lifestyle, and 44 patients and 44 healthy controls (matching population) were enrolled. Serum antibody to H. pylori and metabolites of the matching population were detected. The positive rates of antibody to H. pylori between the patients and the control group did not reach the statistical difference. LEfSe analysis indicated that bacteria were more stable than fungi when adjusting diet and lifestyle. Veillonella, Megasphaera, and Prevotella 7 genus and Streptococcus salivarius subsp. Salivarius, Bifidobacterium dentium, and Lactobacillus salivarius species in bacteria were related to the risk of gastric cancer and showed a good diagnostic value in distinguishing the patients from healthy controls. Streptococcus mitis showed a risk effect for gastric cancer; however, the effect turned into be protective after PSM. Serum L-alanine, L-threonine, and methionol were positively associated with Veillonella and Streptococcus and several fungi genus. Overall, our findings indicated that fecal microbiome constitution alteration may be associated with gastric cancer through influencing the amino acid metabolism.

RidA Proteins Protect against Metabolic Damage by Reactive Intermediates

The Rid (YjgF/YER057c/UK114) protein superfamily was first defined by sequence homology with available protein sequences from bacteria, archaea, and eukaryotes (L. Parsons, N. Bonander, E. Eisenstein, M. Gilson, et al., Biochemistry 42:80-89, 2003, https://doi.org/10.1021/bi020541w). The archetypal subfamily, RidA (reactive intermediate deaminase A), is found in all domains of life, with the vast majority of free-living organisms carrying at least one RidA homolog. In over 2 decades, close to 100 reports have implicated Rid family members in cellular processes in prokaryotes, yeast, plants, and mammals. Functional roles have been proposed for Rid enzymes in amino acid biosynthesis, plant root development and nutrient acquisition, cellular respiration, and carcinogenesis. Despite the wealth of literature and over a dozen high-resolution structures of different RidA enzymes, their biochemical function remained elusive for decades. The function of the RidA protein was elucidated in a bacterial model system despite (i) a minimal phenotype of ridA mutants, (ii) the enzyme catalyzing a reaction believed to occur spontaneously, and (iii) confusing literature on the pleiotropic effects of RidA homologs in prokaryotes and eukaryotes. Subsequent work provided the physiological framework to support the RidA paradigm in Salmonella enterica by linking the phenotypes of mutants lacking ridA to the accumulation of the reactive metabolite 2-aminoacrylate (2AA), which damaged metabolic enzymes. Conservation of enamine/imine deaminase activity of RidA enzymes from all domains raises the likelihood that, despite the diverse phenotypes, the consequences when RidA is absent are due to accumulated 2AA (or a similar reactive enamine) and the diversity of metabolic phenotypes can be attributed to differences in metabolic network architecture. The discovery of the RidA paradigm in S. enterica laid a foundation for assessing the role of Rid enzymes in diverse organisms and contributed fundamental lessons on metabolic network evolution and diversity in microbes. This review describes the studies that defined the conserved function of RidA, the paradigm of enamine stress in S. enterica, and emerging studies that explore how this paradigm differs in other organisms. We focus primarily on the RidA subfamily, while remarking on our current understanding of the other Rid subfamilies. Finally, we describe the current status of the field and pose questions that will drive future studies on this widely conserved protein family to provide fundamental new metabolic information.

Metabolomics reveals impact of seven functional foods on metabolic pathways in a gut microbiota model

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Metabolomics was employed to assess 7 functional foods impact on gut microbiota.

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Insights regarding how functional foods alter gut metabolic pathways is presented.

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Increased GABA production was observed in polyphenol rich functional food.

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Purine alkaloids served as direct substrate in microbiota metabolism.

Functional food defined as dietary supplements that in addition to their nutritional values, can beneficially modulate body functions becomes more and more popular but the reaction of the intestinal microbiota to it is largely unknown. In order to analyse the impact of functional food on the microbiota itself it is necessary to focus on the physiology of the microbiota, which can be assessed in a whole by untargeted metabolomics. Obtaining a detailed description of the gut microbiota reaction to food ingredients can be a key to understand how these organisms regulate and bioprocess many of these food components. Extracts prepared from seven chief functional foods, namely green tea, black tea, Opuntia ficus-indica (prickly pear, cactus pear), black coffee, green coffee, pomegranate, and sumac were administered to a gut consortium culture encompassing 8 microbes which are resembling, to a large extent, the metabolic activities found in the human gut. Samples were harvested at 0.5 and 24 h post addition of functional food extract and from blank culture in parallel and analysed for its metabolites composition using gas chromatography coupled to mass spectrometry detection (GC-MS). A total of 131 metabolites were identified belonging to organic acids, alcohols, amino acids, fatty acids, inorganic compounds, nitrogenous compounds, nucleic acids, phenolics, steroids and sugars, with amino acids as the most abundant class in cultures. Considering the complexity of such datasets, multivariate data analyses were employed to classify samples and investigate how functional foods influence gut microbiota metabolisms. Results from this study provided a first insights regarding how functional foods alter gut metabolism through either induction or inhibition of certain metabolic pathways, i.e. GABA production in the presence of higher acidity induced by functional food metabolites such as polyphenols. Likewise, functional food metabolites i.e., purine alkaloids acted themselves as direct substrate in microbiota metabolism.

Denitrifying sulfide removal by Pseudomonas sp. C27 at excess carbon supply: mechanisms

Pseudomonas sp. C27 can effectively conduct mixotrophic denitrifying sulfide removal (DSR) reactions using both organic matters and sulfide as electron donors. This study conducted DSR tests using C27 and quantitatively analyzed the protein abundances at C/N=1.26, 1.63 and 3.0. At C/N=1.26, C27 principally adopted autotrophic denitrification pathway in DSR reaction. As C/N ratio was increased to 1.63, C27 enhanced heterotrophic denitrification pathway for removing nitrous compounds. As the C/N ratio was further increased to 3.0, C27 accelerated metabolism via coupled-cycles pathway. The C/N ratio for coupled-cycles pathway was estimated ranging 2.0-2.3 in the studied medium. Optimal C/N ratio of traditional DSR processes ranged 1.05-1.26. With the coupled-cycles pathway, the accessible C/N/S regime for C27 on DSR reactions is enlarged. Minor revision of the coupled-cycles pathway considering production of ammonium step was made.

Crystal structure and enzymatic properties of a broad substrate-specificity psychrophilic aminotransferase from the Antarctic soil bacterium Psychrobacter sp. B6

Aminotransferases (ATs) are enzymes that are commonly used in the chemical and pharmaceutical industries for the synthesis of natural and non-natural amino acids by transamination reactions. Currently, the easily accessible enzymes from mesophilic organisms are most commonly used; however, for economical and ecological reasons the utilization of aminotransferases from psychrophiles would be more advantageous, as their optimum reaction temperature is usually significantly lower than for the mesophilic ATs. Here, gene isolation, protein expression, purification, enzymatic properties and structural studies are reported for the cold-active aromatic amino-acid aminotransferase (PsyArAT) from Psychrobacter sp. B6, a psychrotrophic, Gram-negative strain from Antarctic soil. Preliminary computational analysis indicated dual functionality of the enzyme through the ability to utilize both aromatic amino acids and aspartate as substrates. This postulation was confirmed by enzymatic activity tests, which showed that it belonged to the class EC 2.6.1.57. The first crystal structures of a psychrophilic aromatic amino-acid aminotransferase have been determined at resolutions of 2.19 Å for the native enzyme (PsyArAT) and 2.76 Å for its complex with aspartic acid (PsyArAT/D). Both types of crystals grew in the monoclinic space group P21 under slightly different crystallization conditions. The PsyArAT crystals contained a dimer (90 kDa) in the asymmetric unit, which corresponds to the active form of this enzyme, whereas the crystals of the PsyArAT/D complex included four dimers showing different stages of the transamination reaction.