Catabolism of L-phenylalanine and L-tyrosine by Rhodobacter sphaeroides OU5 occurs through 3,4-dihydroxyphenylalanine

Dissolved organic matter cycling revealed from the molecular level in three coastal bays of China

As the widespread distributed and critical zones connecting the land and ocean systems, coastal bays are special units with semi-enclosed landforms to accommodate and process dissolved organic matter (DOM) in the context of increasing anthropogenic effects globally. However, compared to other common systems that have been paid much attention to (e.g., large river estuaries, wetlands), the roles of the coastal bays in coastal carbon cycling are less explored. To fill this knowledge gap, here we combined optical techniques and ultra-high-resolution mass spectrometry to systematically investigate the DOM chemistry of the three typical coastal bays in different nutrient levels, Xiangshan Bay, Jiaozhou Bay, and Sishili Bay, in China. Results show that terrestrial signals and anthropogenic imprints were observed in these three bays to various extents. Besides, Xiangshan Bay with a higher nutrient level had the DOM characterized by lower humification and aromaticity degree than Jiaozhou Bay and Sishili Bay, which not likely mainly resulted from the differences in the primary production or photochemical processing. Further examination reveals that microbial processing likely contributes to the differences in DOM chemistry among the three bays, as indicated by different proportions of potentially transformed nitrogen-containing molecules and relative abundances of the island of stability molecules. Considering the nutrient levels in different bays, we speculate that the lower nutrient concentrations would promote the efficiency of the microbial carbon pump (MCP), which hypothesized that heterotrophic microorganisms might contribute to the formation of marine recalcitrant organic carbon. Additionally, the enrichment of oxygen-rich compounds in the unique carboxyl-rich alicyclic molecule pool of Jiaozhou Bay and Sishili Bay suggests that the efficient MCP might preferentially form them in these two bays. This study emphasizes the importance of coordinating the land and ocean systems and controlling the nutrient discharge to coastal bays, thus, to potentially promote long-term marine carbon sequestration.

Characterization of dissolved organic matter processing between surface sediment porewater and overlying bottom water in the Yangtze River Estuary

Dissolved organic matter (DOM) exchange in the sediment-water interface of estuaries is essential for the global elemental cycle. To clarify the interface DOM processing, this study applies optical techniques and ultrahigh-resolution mass spectrometry to assess DOM composition of surface sediment porewater and bottom (overlying) water across the Yangtze River Estuary (YRE). Results suggested that DOM exchange in the sediment-water interface mainly followed from sediment porewater to bottom water driven by a significant dissolved organic carbon concentration gradient and hydrodynamic force. We also characterized two porewater DOM sources, including microbial production and byproducts of processed sediments. High microbial activities resulted in the enrichment of protein-like fluorescent components and N-bearing compounds in porewater, potentially decreasing the oxygen concentration of bottom water due to the high lability. And the deamination of N-bearing compounds in the sediment-water interface could likely serve as a N-bearing nutrient source to bottom water. Moreover, due to sediment-specific features in different areas driven by hydrologic sorting and local phytoplankton supply, porewater DOM of muddy areas accumulated more aromatic substances from the degradation of terrestrial organic matter. The release and oxic transformation of oxygen-deficient aromatic compounds could contribute to the refractory carbon pool of estuarine water (carboxyl-rich alicyclic molecules, CRAM), modulating the quality of organic carbon mobilized from the land to the coastal ocean. Considering strong hydrodynamic force in numerous estuaries worldwide, DOM exchange and processing at the sediment-water interface has a meaningful influence on the biogeochemistry of estuarine water columns, which warrants further studies.

Selective Biocatalytic Defunctionalization of Raw Materials

Biobased raw materials, such as carbohydrates, amino acids, nucleotides, or lipids contain valuable functional groups with oxygen and nitrogen atoms. An abundance of many functional groups of the same type, such as primary or secondary hydroxy groups in carbohydrates, however, limits the synthetic usefulness if similar reactivities cannot be differentiated. Therefore, selective defunctionalization of highly functionalized biobased starting materials to differentially functionalized compounds can provide a sustainable access to chiral synthons, even in case of products with fewer functional groups. Selective defunctionalization reactions, without affecting other functional groups of the same type, are of fundamental interest for biocatalytic reactions. Controlled biocatalytic defunctionalizations of biobased raw materials are attractive for obtaining valuable platform chemicals and building blocks. The biocatalytic removal of functional groups, an important feature of natural metabolic pathways, can also be utilized in a systemic strategy for sustainable metabolite synthesis.

Aerobic naphthenic acid-degrading bacteria in petroleum-coke improve oil sands process water remediation in biofilters: DNA-stable isotope probing reveals methylotrophy in Schmutzdecke

There is an increasing interest in treatment of oil sands process water (OSPW) via biofiltration with petroleum coke (PC) as a substratum. In fixed bed biofilters (FBBs) with PC, the dominance of anaerobic digestion of dissolved organics results in poor removal of naphthenic acids (NAs) along with a high degree of methanogenesis. In this study, the operation of FBBs was modified to improve OSPW remediation by supporting the filtering bed with aerobic naphthenic acid-degrading bacteria treating aerated OSPW (FBB_{bioaugmentation}). The results were compared with a biofilter operated under controlled conditions (FBB_control). To this end, a consortium of three aerobic NAs-degrading bacterial strains was immobilized on PC as a top layer (10 cm). These bacteria were pre-screened for growth on 15 different NAs surrogates as a sole carbon source, and for the presence of catabolic genes coding alkane hydroxylase (CYP153) and alkane monooxygenase (alkB) enzymes. The results illustrated that biofiltration in FBB_{bioaugmentation} removed 32% of classical NAs in 15 days; while in the FBB_control, degradation was limited to 19%. The degradation of fluorophore (aromatic) compounds was also improved from 16% to 39% for single ring (O_I), 22% to 29% for double ring (O_II), and 15% to 23% for three rings (O_III) compounds. DNA-Stable Isotope Probing revealed that potential hydrocarbons degraders such as Pseudomonas (inoculated), Pseudoxanthomonas (indigenous) were present up to 9.0% in the ¹³C-labelled DNA fraction. Furthermore, a high abundance of methylotrophs was observed in the Schmutzdecke, with Methylobacillus comprising more than two-third of the total community. This study shows that bioaugmentation rapidly improved OSPW remediation. Aeration mostly contributed to methane consumption in the top layer, thus minimizing its release into the environment.

Metabolomic strategies and biochemical analysis of the effect of processed Rehmanniae radix extract on a blood-deficient rat model

Background

Rehmanniae Radix (RR), an herb with numerous pharmacological effects, is widely used in traditional Chinese medicine for the treatment of blood deficiency syndrome, either alone or in combination with other herbs. However, the mechanism by which processed Rehmanniae Radix (PRR) improves blood enrichment efficacy has not been clearly defined.

Methods

Ultra-performance liquid chromatography coupled to quadrupole time-of-flight mass (UPLC-Q-TOF/MS) and biochemical methods were combined to explore the hematopoietic functional mechanisms of PRR on blood deficiency in a rat model, as well as the potential active ingredient for blood enrichment efficacy. The pharmacological effects of PRR were evaluated on a rat blood deficiency model induced by cyclophosphamide in combination with 1-acetyl-2-phenylhydrazine. The blood routine index, including white blood cell (WBC), red blood cell (RBC), and platelet (PLT) counts, as well as hemoglobin (HGB) level, and the changing metabolite profile based on urine and serum were assessed. Nontargeted metabolomic studies, combined with biochemical analyses, were employed to clarify pharmacological mechanisms.

Results

PRR significantly increased the blood routine index levels and reversed the levels of SOD, GSH, and ATP. The PRR group was similar to the control group, as determined from the metabolic profile. All of the 60 biomarkers, representing the typical metabolic characteristics of the blood-deficient rat model, mainly involved energy metabolism dysfunction, the peripheral circulation system, and oxidative damage in the body. This improvement may be attributed to changes in polysaccharide and sixteen non-polysaccharide compounds in PRR, which were caused by processing RR with rice wine.

Conclusions

The strategies of integrated metabolomic and biochemical analyses were combined, revealing the biological function and effective mechanism of PRR.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12906-022-03560-x.

Carbaryl waste-water treatment by Rhodopseudomonas sphaeroides

Carbaryl wastewater treatment and the resource recycling of biomass as sludge by Rhodopseudomonas sphaeroides (R. sphaeroides) with the assistance of starch processing wastewater (SPW) was investigated in this research. It was observed that carbaryl was not degraded under the 100, 500 mg/L COD groups. The addition of SPW assisted R. sphaeroides to degrade carbaryl efficiently. Carbaryl removal reached 100% after 5 days under the optimal group (3500 mg/L). Interestingly, carbaryl in the mixed wastewater began to be degraded after day 1. Further research indicated that cehA gene was expressed after day 1. Subsequently, carbaryl hydrolase was synthesized under gene regulation. Analysis revealed that cehA and carbaryl hydrolase were adaptive gene expressions and enzymes. Carbaryl as stimulus signal started cehA gene expression through signal transduction pathway. This process took one day for R. sphaeroides. However, organics in 100, 500 mg/L COD groups were deficient, which could not maintain R. sphaeroides growth for over one day. Organics in SPW provided sufficient carbon sources for R. sphaeroides under other groups. The method could complete the mixed (SPW and carbaryl) wastewater treatment, carbaryl removal, the resource recycling of R. sphaeroides biomass as sludge simultaneously.

Metabonomics study on the effect of Siwu Decoction for blood deficiency syndrome in rats using UPLC-Q/TOF-MS analysis

Siwu decoction (SWD), a traditional Chinese medicinal formula with over 1000 years of clinical history, is widely used for gynecological disease, especially blood deficiency syndrome, which is similar to anemia in modern medicine. In view of metabonomics being useful approach to investigate the potential mechanisms of action from the point of view of systems biology, in this study an ultra-performance liquid chromatography-quadrupole-time of flight mass spectrometry method was employed for a holistic evaluation of SWD on a blood-deficiency rat model induced by N-acetylphenylhydrazine and cyclophosphamide via plasma metabonomics study. Routine blood examination results showed that SWD could significantly improve the declining hemogram indices. Meanwhile, the plasma metabonomics profiles in different groups were analyzed and differentiating metabolites were primarily visualized through chemometric analysis. Seven biomarkers were identified in plasma samples of blood-deficiency rat model compared with the normal group. Five main metabolism pathways were suggested using the Kyoto Encyclopedia of Genes and Genomes Pathway Analysis and Pathway Activity Profiling algorithm analysis. This indicated that SWD played a therapeu role in blood deficiency by regulating the aberrant endogenous metabolites. To sum up, this study provides clear evidence that a metabonomics study could serve as a useful tool to elucidate the systematic therapeutic profiles and mechanisms for blood deficiency syndrome of Chinese herbal medicines.

Pyomelanin production: Insights into the incomplete aerobic l-phenylalanine catabolism of a photosynthetic bacterium, Rubrivivax benzoatilyticus JA2

Rubrivivax benzoatilyticus JA2 is a metabolically versatile bacterium, thrives on a wide array of organic compounds under different growth modes. Though genomic insights revealed the aromatic compound catabolic potential of strain JA2 under anaerobic/aerobic conditions, the studies are largely restricted to anaerobic metabolism. The previous study on phenylalanine metabolism in strain JA2 indicated melanin-like pigment production under aerobic conditions; however, characterization of pigment and its biosynthetic pathway is not explored. The current study aims at the characterization of pigment and elucidation of its biosynthetic pathway. Strain JA2 utilized l-phenylalanine as source of nitrogen under anaerobic/aerobic conditions but not as a carbon source. Strain JA2 produced a brown-pigment under phenylalanine-amended aerobic conditions. Spectroscopic and physicochemical analysis identified the purified brown-pigment as a melanin. Further, the genomic insights revealed the presence of a complete set of genes related to pyomelanin synthesis. Identification of key metabolites l-tyrosine, 4-hydroxyphenylpyruvic acid and homogentisic acid and their respective enzyme activities further supports the pyomelanin synthesis. Moreover, the precursors feeding, pathway specific inhibitor studies confirmed the pyomelanin synthesis in strain JA2. Our study revealed an incomplete catabolism of phenylalanine; absence of ring cleavage gene, homogentisate dioxygenase leading to homogentisate accumulation thereby pyomelanin synthesis in strain JA2.

Experimental design and metabolic flux analysis tools to optimize industrially relevant Haemophilus influenzae type b growth medium

Haemophilus influenzae type b (Hib), a Gram-negative capsulated bacterium, is a causative agent of meningitis worldwide. The capsular polysaccharide, a high molecular mass polymer consisting of the repeated units of the polyribosyl-ribitol-phosphate, is considered the main virulence factor and it is used as an antigen to vaccines, conjugated to a carrier protein. The industrial production of the polysaccharide requires the cultivation of Hib in rich medium, which impacts process costs and product recovery. In this study, a central composite rotational experimental design strategy was used to access the influence of key components of culture medium (soy peptone, yeast extract and glucose) on biomass formation and polysaccharide production in shake-flasks. The optimized medium formulation, containing half of the usual yeast extract and soytone concentrations, was further validated in batch bioreactor cultivations. High polysaccharide production (∼500 mg/L) was obtained in a cheaper and more competitive production process for use in Hib vaccine production. In addition, simulations of a metabolic model describing Hib central metabolism were used to assess the role of key amino acids on growth. A chemically defined medium supplemented only with amino acids from α-ketoglutarate and oxaloacetate families as well as phenylalanine was suggested as a promising alternative for reduced acetate accumulation and enhanced polysaccharide production in Hib cultures. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1508-1519, 2017.

Systematic variations associated with renal disease uncovered by parallel metabolomics of urine and serum

Background

Membranous nephropathy is an important glomerular disease characterized by podocyte injury and proteinuria, but no metabolomics research was reported as yet. Here, we performed a parallel metabolomics study, based on human urine and serum, to comprehensively profile systematic metabolic variations, identify differential metabolites, and understand the pathogenic mechanism of membranous nephropathy.

Results

There were obvious metabolic distinctions between the membranous nephropathy patients with urine protein lower than 3.5 g/24 h (LUPM) and those higher than 3.5 g/24 h (HUPM) by Partial Least Squares Discriminant Analysis (PLS-DA) model analysis. In total, 26 urine metabolites and 9 serum metabolites were identified to account for such differences, and the majority of metabolites were significantly increased in HUPM patients for both urines and serums. Combining the results of urine with serum, all differential metabolites were classified to 5 classes. This classification helps globally probe the systematic metabolic alterations before and after blood flowing through kidney. Citric acid and 4 amino acids were markedly increased only in the serum samples of HUPM patients, implying more impaired filtration function of kidneys of HUPM patients than LUPM patients. The dicarboxylic acids, phenolic acids, and cholesterol were significantly elevated only in urines of HUPM patients, suggesting more severe oxidative attacks than LUPM patients.

Conclusions

Parallel metabolomics of urine and serum revealed the systematic metabolic variations associated with LUPM and HUPM patients, where HUPM patients suffered more severe injury of kidney function and oxidative stresses than LUPM patients. This research exhibited a promising application of parallel metabolomics in renal diseases.

Diagenetic transformation of dissolved organic nitrogen compounds under contrasting sedimentary redox conditions in the Black Sea

Remineralization of organic matter in reactive marine sediments releases nutrients and dissolved organic matter (DOM) into the ocean. Here we focused on the molecular-level characterization of DOM by high-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) in sediment pore waters and bottom waters from contrasting redox regimes in the northern Black Sea with particular emphasis on nitrogen-bearing compounds to derive an improved understanding of the molecular transformations involved in nitrogen release. The number of nitrogen-bearing molecules is generally higher in pore waters than in bottom waters. This suggests intensified degradation of nitrogen-bearing precursor molecules such as proteins in anoxic sediments: No significant difference was observed between sediments deposited under oxic vs anoxic conditions (average O/C ratios of 0.55) suggesting that the different organic matter quality induced by contrasting redox conditions does not impact protein diagenesis in the subseafloor. Compounds in the pore waters were on average larger, less oxygenated, and had a higher number of unsaturations. Applying a mathematical model, we could show that the assemblages of nitrogen-bearing molecular formulas are potential products of proteinaceous material that was transformed by the following reactions: (a) hydrolysis and deamination, both reducing the molecular size and nitrogen content of the products and intermediates; (b) oxidation and hydration of the intermediates; and (c) methylation and dehydration.

L-Tryptophan catabolism by Rubrivivax benzoatilyticus JA2 occurs through indole 3-pyruvic acid pathway

Rubrivivax benzoatilyticus JA2 utilizes L: -tryptophan as the sole source of nitrogen for growth, and it has a doubling time of approximately 11 h (compared to 8 h with ammonium chloride). With cell free extracts in the presence of 2-oxoglutarate, indole-3-pyruvic acid, indole-3-acetaldehyde, indole-3-acetic acid, isatin, benzaldehyde, gallic acid and pyrogallol were identified using high performance liquid chromatography (HPLC) and liquid chromatography-mass spectroscopy (LC-MS) analysis. The conversion of L: -tryptophan into indole 3-pyruvic acid and glutamate by an enzyme aminotransferase was confirmed and the catabolism of indole-3-pyruvic acid via side chain oxidation followed by ring oxidation, gallic acid and pyrogallol were confirmed as metabolites. In addition, the proposed pathway sequential conversion of indole-3-pyruvic acid to the end product of pyrogallol was identified, including an enzymatic step that would convert isatin to benzaldehyde by an enzyme yet to be identified. At this stage of the study, the enzyme tryptophan aminotransferase in R. benzoatilyticus JA2 was demonstrated.

Identification and characterization of the PhhR regulon in Pseudomonas putida

Pseudomonas putida is a soil microorganism that utilizes aromatic amino acids present in root exudates as a nitrogen source. We have previously shown that the PhhR transcriptional regulator induces phhAB genes encoding a phenylalanine hydroxylase. In this study we show, using microarray assays and promoter fusions, that PhhR is a global regulator responsible for the activation of genes essential for phenylalanine degradation, phenylalanine homeostasis and other genes of unknown function. Recently, it has been shown that phenylalanine catabolism occurs through more than one pathway. One of these possible pathways involves the metabolism of phenylalanine via tyrosine, p-hydroxyphenylpyruvate, and homogentisate. We identified two genes within this pathway that encode an acyl-CoA transferase involved in the metabolism of acetoacetate. All genes in this pathway were induced in response to phenylalanine in a PhhR-proficient background. The second potential degradative pathway involves the degradation of phenylalanine to produce phenylpyruvate, which seems to be degraded via phenylacetyl-CoA. A number of mutants in the paa genes encoding phenylacetyl-CoA degradation enzymes fail to grow on phenylpyruvate or phenylacetate, further supporting the existence of this second pathway. We found that the PhhR regulon also includes genes involved in the biosynthesis of aromatic amino acids that are repressed in the presence of phenylalanine, suggesting the possibility of feedback at the transcriptional level. In addition, we found that PhhR modulates the level of expression of the broad-substrate-specificity MexEF/OprN efflux pump. Expression from this pump is under the control of mexT gene product because phenylalanine-dependent transcription from the mexE promoter does not occur in a mexT mutant background. These results place PhhR as an important regulator in the control of bacterial responses to aromatic amino acids.

Purification and characterization of 3,4-dihydroxyphenylalanine oxidative deaminase fromRhodobacter sphaeroidesOU5

An enzyme involved in the catabolism of 3,4-dihydroxyphenylalanine (DOPA) was isolated from Rhodobacter sphaeroides OU5. The enzyme catalyzes the formation of 3,4-dihydroxyphenylpyruvic acid (DOPP) and ammonia from DOPA. Formation of ammonia by DOPA oxidative deaminase was O2dependent and the enzyme isolated to its homogeneity has 100% affinity for DOPA. DOPA oxidative deaminase is functional at low concentrations of the substrate (<100 μmol·L–1) and is independent of NADH. The molecular mass of the purified enzyme is ~190 kDa and the enzyme could be a pentamer of 54, 42, 34, 25, and 23 kDa subunits as determined by SDS–PAGE.