Amino Acid Fingerprint Research Articles

Toxicometabolomics-based cardiotoxicity evaluation of Thiazolidinedione exposure in human-derived cardiomyocytes

IntroductionThiazolidinediones (TZDs), represented by pioglitazone and rosiglitazone, are a class of cost-effective oral antidiabetic agents posing a marginal hypoglycaemia risk. Nevertheless, observations of heart failure have hindered the clinical use of both therapies.ObjectiveSince the mechanism of TZD-induced heart failure remains largely uncharacterised, this study aimed to explore the as-yet-unidentified mechanisms underpinning TZD cardiotoxicity using a toxicometabolomics approach.MethodsThe present investigation included an untargeted liquid chromatography–mass spectrometry-based toxicometabolomics pipeline, followed by multivariate statistics and pathway analyses to elucidate the mechanism(s)of TZD-induced cardiotoxicity using AC16 human cardiomyocytes as a model, and to identify the prognostic features associated with such effects.ResultsAcute administration of either TZD agent resulted in a significant modulation in carnitine content, reflecting potential disruption of the mitochondrial carnitine shuttle. Furthermore, perturbations were noted in purine metabolism and amino acid fingerprints, strongly conveying aberrations in cardiac energetics associated with TZD usage. Analysis of our findings also highlighted alterations in polyamine (spermine and spermidine) and amino acid (L-tyrosine and valine) metabolism, known modulators of cardiac hypertrophy, suggesting a potential link to TZD cardiotoxicity that necessitates further research. In addition, this comprehensive study identified two groupings – (i) valine and creatine, and (ii) L-tryptophan and L-methionine – that were significantly enriched in the above-mentioned mechanisms, emerging as potential fingerprint biomarkers for pioglitazone and rosiglitazone cardiotoxicity, respectively.ConclusionThese findings demonstrate the utility of toxicometabolomics in elaborating on mechanisms of drug toxicity and identifying potential biomarkers, thus encouraging its application in the toxicological sciences. (245 words)

Traces of dietary patterns in saliva of hominids: Profiling salivary amino acid fingerprints in great apes and humans

Herbivorous animals that regularly consume tannin-rich food are known to secrete certain tannin-binding salivary proteins (TBSPs), especially proline-rich proteins and histidine-rich proteins, as an effective measure to counteract the antinutritive effects of dietary tannins. Due to their high binding capacity, TBSPs complex with tannins in the oral cavity, and thereby protect dietary proteins and digestive enzymes. Although the natural diet of great apes (Hominidae) is biased toward ripe fruits, analyses of food plants revealed that their natural diet contains considerable amounts of tannins, which is raising the question of possible counter-measures to cope with dietary tannins. In our study, we investigated the salivary amino acid profiles of zoo-housed Pan paniscus, Pan troglodytes, Gorilla gorilla, and Pongo abelii, and compared their results with corresponding data from Homo sapiens. Individual saliva samples of 42 apes and 17 humans were collected and quantitated by amino acid analysis, using cation-exchange chromatography with postcolumn derivatization, following acid hydrolysis. We found species-specific differences in the salivary amino acid profiles with average total salivary protein concentration ranging from 308.8 mg/dL in Po. abelii to 1165.6 mg/dL in G. gorilla. Total salivary protein was consistently higher in ape than in human saliva samples (174 mg/dL). All apes had on average also higher relative proline levels than humans did. Histidine levels had the highest concentration in the samples from Po. abelii followed by P. paniscus. In all ape species, the high salivary concentrations of proline and histidine are considered to be indicative of high concentrations of TBSPs in hominids. Given that the species differences in salivary composition obtained in this study correspond with overall patterns of secondary compound content in the diet of wild populations, we assume that salivary composition is resilient to acute and long-lasting changes in diet composition in general and tannin content in particular.

Amino Acid Fingerprinting of Authentic Nonfat Dry Milk and Skim Milk Powder and Effects of Spiking with Selected Potential Adulterants.

A collaborative study was undertaken in which five international laboratories participated to determine amino acid fingerprints in 39 authentic nonfat dry milk (NFDM)/skim milk powder (SMP) samples. A rapid method of amino acid analysis involving microwave-assisted hydrolysis followed by ultra-high performance liquid chromatography-ultraviolet detection (UHPLC-UV) was used for quantitation of amino acids and to calculate their distribution. The performance of this rapid method of analysis was evaluated and was used to determine the amino acid fingerprint of authentic milk powders. The distribution of different amino acids and their predictable upper and lower tolerance limits in authentic NFDM/SMP samples were established as a reference. Amino acid fingerprints of NFDM/SMP were compared with selected proteins and nitrogen rich compounds (proteins from pea, soy, rice, wheat, whey, and fish gelatin) which can be potential economically motivated adulterants (EMA). The amino acid fingerprints of NFDM/SMP were found to be affected by spiking with pea, soy, rice, whey, fish gelatin and arginine among the investigated adulterants but not by wheat protein and melamine. The study results establish an amino acid fingerprint of authentic NFDM/SMP and demonstrate the utility of this method as a tool in verifying the authenticity of milk powders and detecting their adulteration.

Central Metabolism and Growth Rate Impacts on Hydrogen and Carbon Isotope Fractionation During Amino Acid Synthesis in E. coli.

Compound specific stable isotope analysis (CSIA) of amino acids from bacterial biomass is a newly emerging powerful tool for exploring central carbon metabolism pathways and fluxes. By comparing isotopic values and fractionations relative to water and growth substrate, the impact of variable flow path for metabolites through different central metabolic pathways, perturbations of these paths, and their resultant consequences on intracellular pools and resultant biomass may be elucidated. Here, we explore the effects that central carbon metabolism and growth rate can have on stable hydrogen (δ2H) and carbon (δ13C) compound specific isotopic values of amino acids, and whether diagnostic isotopic fingerprints are revealed by these paired analyses. We measured δ2H and δ13C in amino acids in the wild type Escherichia coli (MG1655) across a range of growth rates in chemostat cultures to address the unknown isotopic consequences as metabolic fluxes are shuffled between catabolic and anabolic metabolisms. Additionally, two E. coli knockout mutants, one with deficiency in glycolysis –pgi (LC1888) and another inhibiting the oxidative pentose phosphate pathway (OPPP) –zwf (LC1889), were grown on glucose and used as a comparison against the wild type E. coli (MG1655) to address the isotopic changes of amino acids produced in these perturbed metabolic pathways. Amino acid δ2H values, which collectively vary in composition by more than 400‰, are altered along with δ13C values demonstrating fundamental shifts in central metabolic pathways and/or fluxes. Within our linear discriminant analysis with a simple model organism to examine potential amino acid fingerprinting, our knockout strains and variable growth rate samples plot across a wider array of organism classification than merely within the boundaries of other bacterial data.

An evaluation of inkjet printed amino acid fingerprint test targets for ninhydrin process monitoring − and some observations

Ninhydrin was implemented as the primary police method of developing latent fingermarks on paper, cardboard and some other porous surfaces from the late 1960s. Some researchers have used individual amino acids, or mixtures of amino acids, as a method of testing the effectiveness of reagent formulations. It was not however known whether simple mixtures of amino acids could effectively emulate latent fingermarks in reactions with reagents such as ninhydrin. The first part of this study compared the effects of ninhydrin fingermark treatments used internationally in various police laboratories on test targets created by inkjet printing graduated concentrations of a representative mixture of amino acids in a series of blocks on paper. Variations in intensity of development were observed between laboratories which used various formulations and heat and humidity post treatment protocols. In a further trial in 2015 several participants in the International Fingerprint Research Group (IFRG) meeting processed test targets in their own laboratories and submitted them for measurement. Again, variation in developed intensity was observed. The depletion of the activity of ninhydrin solutions during use was also investigated in early evaluations of the test targets. An established fingerprint laboratory then processed a number of samples from a batch of targets to examine batch consistency. This was followed by designing a new test target which enabled comparisons between the developed intensity of printed test target blocks alongside depletion series of split, natural donor fingermarks. A panel of 20 donors provided depletion fingermarks and four ninhydrin formulations and treatment protocols were used. The developed test target blocks were scanned, intensity of development measured, and the results compared with the fingermark development which was evaluated by three assessors using two types of scale. Good correlation between the intensity of the developed test targets and latent fingermark quality and intensity scores was observed with the four ninhydrin treatment protocols, including some which used deliberately downgraded ninhydrin concentrations. This type of evaluation was carried out a second time to investigate modified heat and humidity protocols. The use of such test targets for routine reagent quality control and process verification would appear to be far more accurate and reliable than the use of small numbers of donor fingermarks. It is not clear why the different ninhydrin formulations investigated in the latter part of the work have very different optimum post treatment heating regimes.

A Specific Urinary Amino Acid Profile Characterizes People with Kidney Stones.

Background Urolithiasis is the process of stone formation in the urinary tract. Its etiology is only partly known, and efficient therapeutic approaches are currently lacking. Metabolomics is increasingly used in biomarkers discovery for its ability to identify mediators of relevant (patho)physiological processes. Amino acids may be involved in kidney stone formation. The aim of the present study was to investigate the presence of an amino acid signature in stone former urine through a targeted metabolomic approach. Methods A panel of 35 amino acids and derivatives was assessed in urines from 15 stone former patients and 12 healthy subjects by UPLC-MS. Partial Least Squares Discriminant Analysis (PLS-DA) was used to define amino acid profiles of cases and controls. Results and Discussion. Our approach led to the definition of a specific amino acid fingerprint in people with kidney stones. A urinary amino acid profile of stone formers was characterized by lower levels of α-aminobutyric acid, asparagine, ethanolamine, isoleucine, methionine, phenylalanine, serine, tryptophan, and valine. Metabolomic analysis may lend insights into the pathophysiology of urolithiasis and allow tracking this prevalent condition over time.

Non-invasive Amino Acid Profiling of Embryo Culture Medium Using HPLC Correlates With Embryo Implantation Potential in Women Undergoing in vitro Fertilization.

This study aimed to determine the correlation between amino acid profiling of a 3-day-old embryo culture medium and embryo implantation potential in women undergoing in vitro fertilization (IVF). The data of 98 patients who received IVF treatment in our hospital from December 2015 to February 2017 were retrospectively analyzed. The 98 patients were grouped into a pregnant group (gemellary pregnancy), a non-pregnant group (non-pregnancy), and a blank control group. The amino acids from a 3-day-old embryo culture medium and blank control medium were collected and were analyzed using high performance liquid chromatography (HPLC). The HPLC results showed that amino acids including aspartate (ASP), serine (SER), glycine (GLY), histidine (HIS), taurine (TAU), arginine (ARG), threonine (THR), alanine (ALA), and proline (PRO) were detected in the 3-day-old embryo culture medium and blank control medium. There are significant differences between the pregnant group and non-pregnant group in peak height (H)-SER, surface area (S)-ASP, S-SER, S-HIS, and S-ALA. The discrimination analysis according to the peak height and peak area of amino acids revealed that the prediction rate of the pregnant group, non-pregnant group, and blank control group were 82.7, 95.7, and 100%. Further, by using the principal component analysis, we found that the prediction rate in these three groups were 90.4, 91.3, and 100%. Our data may suggest that using amino acid concentrations for principal component analysis and discriminant analysis has high accuracy in predicting the relationship between amino acid fingerprint and embryo implantation potential.

Mycoplasma pneumoniae Community-Acquired Respiratory Distress Syndrome Toxin Uses a Novel KELED Sequence for Retrograde Transport and Subsequent Cytotoxicity.

ABSTRACTMycoplasma pneumoniae is an atypical bacterium that causes respiratory illnesses in humans, including pharyngitis, tracheobronchitis, and community-acquired pneumonia (CAP). It has also been directly linked to reactive airway disease, asthma, and extrapulmonary pathologies. During its colonization, M. pneumoniae expresses a unique ADP-ribosylating and vacuolating cytotoxin designated community-acquired respiratory distress syndrome (CARDS) toxin. CARDS toxin persists and localizes in the airway in CAP patients, asthmatics, and trauma patients with ventilator-associated pneumonia. Although CARDS toxin binds to specific cellular receptors, is internalized, and induces hyperinflammation, histopathology, mucus hyperplasia, and other airway injury, the intracellular trafficking of CARDS toxin remains unclear. Here, we show that CARDS toxin translocates through early and late endosomes and the Golgi complex and concentrates at the perinuclear region to reach the endoplasmic reticulum (ER). Using ER-targeted SNAP-tag, we confirmed the association of CARDS toxin with the ER and determined that CARDS toxin follows the retrograde pathway. In addition, we identified a novel CARDS toxin amino acid fingerprint, KELED, that is required for toxin transport to the ER and subsequent toxin-mediated cytotoxicity.

Single amino acid fingerprinting of the human antibody repertoire with high density peptide arrays

The antibody species that patrol in a patient's blood are an invaluable part of the immune system. While most of them shield us from life-threatening infections, some of them do harm in autoimmune diseases. If we knew exactly all the antigens that elicited all the antibody species within a group of patients, we could learn which ones correlate with immune protection, are irrelevant, or do harm. Here, we demonstrate an approach to this question: First, we use a plethora of phage-displayed peptides to identify many different serum antibody binding peptides. Next, we synthesize identified peptides in the array format and rescreen the serum used for phage panning to validate antibody binding peptides. Finally, we systematically vary the sequence of validated antibody binding peptides to identify those amino acids within the peptides that are crucial for binding “their” antibody species. The resulting immune fingerprints can then be used to trace them back to potential antigens. We investigated the serum of an individual in this pipeline, which led to the identification of 73 antibody fingerprints. Some fingerprints could be traced back to their most likely antigen, for example the immunodominant capsid protein VP1 of enteroviruses, most likely elicited by the ubiquitous poliovirus vaccination. Thus, with our approach, it is possible, to pinpoint those antibody species that correlate with a certain antigen, without any pre-information. This can help to unravel hitherto enigmatic diseases.

人血清中游离氨基酸指纹图谱的初步研究

目的：建立人血清中游离氨基酸的指纹图谱。方法：采用L-8900全自动氨基酸分析仪测定健康人群血清中的游离氨基酸，选择15个主要特征峰为指纹图谱共有峰。结果：建立了12批人血清样品的游离氨基酸指纹图谱。结论：建立的指纹图谱有较好的精密度、重复性和稳定性，可作为人血清游离氨基酸指纹图谱库的理论基础。 Object: To establish free amino acid fingerprint of human serum. Method: The free amino acid of serum from the healthy persons was determined by the L-8900 automatic amino acid analyzer, and 15 major characteristic peaks of fingerprint were chosen as the common peak. Result: Free amino acid fingerprint of 12 batches of human serum was established. Conclusion: The fingerprint has preferably precision, repeatability and stability; it can be used as the theoretical basis of free amino acid fingerprint database of human serum.

Infectious Pancreatic Necrosis Virus Causing Clinical and Subclinical Infections in Atlantic Salmon Have Different Genetic Fingerprints.

Infectious pancreatic necrosis virus (IPNV) is the causative agent of IPN, an important disease of salmonids. IPNV infections result in either sub-clinical or overt disease and the basis of this difference is not well-understood. The objective of the present study was to determine the VP2 gene of the virus associated with the different forms of clinical manifestation. Groups of Atlantic salmon (Salmo salar L.) reared in farms located in different IPN disease pressures were monitored from brood stock until grow-out over a 3 year period. Hatcheries A1 and B1 as well as cooperating seawater farms were located in a low disease risk area while hatcheries A2 and B2 as well as their cooperating seawater farms were in high IPN risk areas. Samples including eggs, milt, whole fry, kidney depending on the stage of production were collected during outbreaks or in apparently healthy populations where no outbreaks occurred. The virus was re-isolated in CHSE cells and the VP2 gene amplified by RT-PCR followed by sequencing. During the freshwater stage, there were no disease outbreaks at hatcheries A1, A2, and B1 (except in one fish group that originated from hatchery B2), although IPNV was isolated from some of the fish groups at all 3 hatcheries. By contrast, all fish groups at hatchery B2 suffered IPN outbreaks. In seawater, only groups of fish originating from hatchery A1 had no IPN outbreaks albeit virus being isolated from the fish. On the other hand, fish originating from hatcheries A2, B1, and B2 experienced outbreaks in seawater. The VP2 amino acid fingerprint of the virus associated with subclinical infections from A1 and co-operating seawater sites was V64A137P217T221A247N252S281D282E319. By contrast, all virus isolates associated with clinical infections had the motif I64T137T217A221T247V252T281N282A319, where underlined amino acids represent the avirulent and highly virulent motif, respectively. Phylogenetic analysis of amino acid sequences showed 2 clades, one of isolates associated with subclinical infections (from A1 and cooperating seawater farms) and the other of isolates from fish with overt disease (all other sites). Furthermore, the clustering pattern of isolates suggests more circulation of virus within fish groups rather than between them.

Evolution of the amino acid fingerprint in the unsterilized rhizosphere of a legume in relation to plant maturity

The exudation of low-molecular-weight compounds, such as amino acids, contributes to the structure of rhizospheric microbial communities and plays a crucial role in nutrient mobility throughout the vegetative cycle of the plant. Due to their low concentration and their constant removal by microorganisms, the study of amino acids is difficult in unsterilized rhizospheric soil. Our aim was to investigate the dynamics of amino acids in unsterilized soil.Since there was currently no available method to estimate accurately amino acid exudation in soil, a methodology was developed to assess amino-acid fingerprints in the rhizosphere. This proved a viable approach for understanding the dynamics of amino-acid release into the rhizosphere. The method was tested on Medicago truncatula, with the hypothesis that the fingerprint of amino acids in the rhizosphere should reflects amino acid exudation from leguminous plants, subject to the influence of microbiological components of the soil, and should be correlated with the stage of plant growth. M. truncatula plants were grown in either unsterilized or sterilized substrate. Amino acids in the substrate samples were identified and quantified by gas chromatography-mass spectrometry (GC-MS) and microbial biomass in the soil samples was also assessed.The total content of amino acids in the sterilized rhizospheric substrate increased substantially during plant growth with the highest content observed at the end of the vegetative stage. Despite the probable continual removal of amino acids by microorganisms, we also observed a significant quantitative and qualitative plant-dependent effect on the amino acid fingerprint in unsterilized soil. A clear chronological differentiation of this fingerprint in the rhizosphere of unsterilized and sterilized substrate was revealed by principal component analysis. We observed predominantly serine and glycine in the sterilized rhizosphere, whereas asparagine became prominent before flowering in the unsterilized rhizosphere soil. Root amino acid metabolic pathways and exudation appear to differ in unsterilized soil compared to in sterilized substrate, indicating an adaption to the rhizospheric environment.The established method could be used in other applications, for example, for future ecophysiological studies aiming at following root exudation of amino acids in response to changing environmental conditions.

Amyloid-β peptides act as allosteric modulators of cholinergic signalling through formation of soluble BAβACs.

Amyloid-β peptides, through highly sophisticated enzymatic machinery, are universally produced and released in an action potential synchronized manner into the interstitial fluids in the brain. Yet no native functions are attributed to amyloid-β. The amyloid-β hypothesis ascribes just neurotoxicity properties through build-up of soluble homomeric amyloid-β oligomers or fibrillar deposits. Apolipoprotein-ε4 (APOE4) allele is the only confirmed genetic risk factor of sporadic Alzheimer's disease; once more it is unclear how it increases the risk of Alzheimer's disease. Similarly, central cholinergic signalling is affected selectively and early in the Alzheimer's disease brain, again why cholinergic neurons show this sensitivity is still unclear. However, the three main known Alzheimer's disease risk factors, advancing age, female gender and APOE4, have been linked to a high apolipoprotein-E and accumulation of the acetylcholine degrading enzyme, butyrylcholinesterase in cerebrospinal fluids of patients. Furthermore, numerous reports indicate that amyloid-β interacts with butyrylcholinesterase and apolipoprotein-E. We have proposed that this interaction leads to formation of soluble ultrareactive acetylcholine-hydrolyzing complexes termed BAβACs, to adjust at demand both synaptic and extracellular acetylcholine signalling. This hypothesis predicted presence of acetylcholine-synthesizing enzyme, choline acetyltransferase in extracellular fluids to allow maintenance of equilibrium between breakdown and synthesis of acetylcholine through continuous in situ syntheses. A recent proof-of-concept study led to the discovery of this enzyme in the human extracellular fluids. We report here that apolipoprotein-E, in particular ε4 isoprotein acts as one of the strongest endogenous anti-amyloid-β fibrillization agents reported in the literature. At biological concentrations, apolipoprotein-E prevented amyloid-β fibrillization for at least 65 h. We show that amyloid-β interacts readily in an apolipoprotein-facilitated manner with butyrylcholinesterase, forming highly stable and soluble complexes, BAβACs, which can be separated in their native states by sucrose density gradient technique. Enzymological analyses further evinced that amyloid-β concentration dependently increased the acetylcholine-hydrolyzing capacity of cholinesterases. In silico biomolecular analysis further deciphered the allosteric amino acid fingerprint of the amyloid-β-cholinesterase molecular interaction in formation of BAβACs. In the case of butyrylcholinesterase, the results indicated that amyloid-β interacts with a putative activation site at the mouth of its catalytic tunnel, most likely leading to increased acetylcholine influx into the catalytic site, and thereby increasing the intrinsic catalytic rate of butyrylcholinesterase. In conclusion, at least one of the native physiological functions of amyloid-β is allosteric modulation of the intrinsic catalytic efficiency of cholinesterases, and thereby regulation of synaptic and extrasynaptic cholinergic signalling. High apolipoprotein-E may pathologically alter the biodynamics of this amyloid-β function.

UPLC-QTOF (ESI +) MS Analysis Applied for Targeted Profiling of Human Urine Amino Acids

Amino acids, the building blocks of proteins are providing fundamental information about metabolic status and early disease diagnosis. For an accurate interpretation of metabolic status, amino acid reference values for healthy humans are required. Most studies have pointed out that, the most accurate, reliable and sensitive tool to evaluate amino acids in biofluids ( blood or urine) is liquid chromatography coupled with mass spetrometry (LC/MS). The aim of this study was to determine and optimize the urine amino acids profile by LC-QTOF (ESI+) MS, comparatively, using two generic samples from a healthy male and female. Urine aminoacids were purified using solid phase extraction, a pre-column derivatization and liquid/liquid extraction according to Ez-Faast kit (Phenomenex). The derivatized samples were analyzed by LC-QTOF-(ESI+)-MS and data were processed by Data Analysis-Extracted Ion Chromatogram software. A number of 16 amino acids were found in both samples, the male urine showed higher values for 10 amino acids (hydroxyproline, alanine, sarcosine, lysine, histidine, tryptophan, leucine, phenylalanine, cysteine and tyrosine), while glutamine and valine were higher in female urine. Most of the amino acids identified were essential amino acids found in both cases like: glutamine, proline, lysine, histidine, valine, tryptophan, leucine and phenylalanine. The main differences between the male vs female aminoacid fingerprints of urine were mainly quantitative and not qualitative. The amino acid concentrations ranged from 1.48 nmol/mg creatinine (proline) to 203.13 nmol/mg (histidine). The concentration of amino acids in man were 2 times higher than for female, while the percentages of essential amino acids were similar in both gender.

NUCLEAR MAGNETIC RESONANCE METABOLIC PROFILING OF LEAVES FROM VITIS VINIFERA INFESTED WITH ROOT-FEEDING GRAPE PHYLLOXERA (DAKTULOSPHAIRA VITIFOLIAE FITCH) UNDER FIELD CONDITIONS

Partial least squares discriminant analysis (PLS-DA) models developed from 1 H NMR spectra acquired from aqueous extracts Vitis vinifera leaf material successfully discriminated between grape phylloxera-infested and uninfested grapevines under field conditions. Loadings plots demonstrated differences in the metabolic profile between treatments in the aromatic, carbohydrate and amino acid fingerprint regions of the 1 H NMR spectrum. Resonances consistent with sucrose and the phenolic moeities caffeic acid and quercetin were up-regulated in infested grapevines, while α- and β- anomers of glucose and leucine were down regulated in infested grapevines. The detection of putative quercetin resonances corroborated with the results from a previous LC/MS study. This may lead to its inclusion as a potential candidate biomarker of grape phylloxera infestation once further validation trials have been undertaken.

Amino acid fingerprint of a grassland soil reflects changes in plant species richness

A positive plant diversity to plant aboveground productivity relation has been shown to alter carbon and nitrogen fluxes in soils. Thus, most investigations focussed on the C- and N-input via litter fall, widely neglecting the importance of root exudation. As microbes, which are known to be important drivers of matter fluxes in soil, feed on these root exudates, increased knowledge on the availability of these compounds in soil might help to understand biodiversity effects on soil. We therefore investigated the effect of plant diversity on size and composition of the free soil amino acid pool in a grassland experiment, as amino acids are an important C- as well as N-source for microbes. Despite a positive diversity effect on plant productivity, we only found an insignificant increase of the size of the free amino acid pool in soil. This was most likely caused by an increase of the microbial population and thus an increased amino acid mineralization. At the same time the composition of the amino acid pool changed significantly between plant diversity levels. This most likely reflects differences in plant input as well as differences in microbial mineralization and enabled us to separate diversity levels by means of discriminant analysis.

Characterization of a Neutral and Thermostable Glucoamylase from the Thermophilic Mold Thermomucor indicae-seudaticae: Activity, Stability, and Structural Correlation

Glucoamylase from the thermophilic mold Thermomucor indicae-seudaticae was purified by anion exchange and gel filtration chromatographic techniques using a fast protein liquid chromatographic system. The structure and thermal stability of this unique 'thermostable and neutral glucoamylase' were analyzed by circular dichroism (CD). T. indicae-seudaticae glucoamylase (TGA) contained typical aromatic amino acid (tryptophan/tyrosine) fingerprints in its tertiary structure. Analysis of the far-UV CD spectrum at pH 7.0 and 25 degrees Celsius revealed the presence of 45% alpha-helix, 43% beta-sheet, and 12% remaining structures. The alpha-helix content was highest at pH 7.0, where glucoamylase is optimally active. This observation points towards the possible (alpha/alpha)(6) barrel catalytic domain in TGA, as reported in microbial glucoamylases. Thermal denaturation curves of the pure protein at different pH values revealed maximum stability at pH 7.0, where no change in the secondary structure was observed upon heating in the temperature range between 20 degrees Celsius and 60 degrees Celsius. The observed midpoint of thermal denaturation (T (m)) of glucoamylase at pH 7.0 was 67.1 degrees Celsius, which decreased on either sides of this pH. Thermostability of TGA enhanced in the presence of starch (0.1%) as no transition curve was obtained in the temperature range between 20 degrees Celsius and 85 degrees Celsius. The only product of TGA action on starch was glucose, and it did not exhibit transglycosylation activity even at 40% glucose that can also be considered as an advantage during starch saccharification.

Ni(II) and Co(II) Sensing by Escherichia coli RcnR

Escherichia coli RcnR and Mycobacterium tuberculosis CsoR are the founding members of a recently identified, large family of bacterial metal-responsive DNA-binding proteins. RcnR controls the expression of the metal efflux protein RcnA only in response to Ni(II) and Co(II) ions. Here, the interaction of Ni(II) and Co(II) with wild-type and mutant RcnR proteins is examined to understand how these metals function as allosteric effectors. Both metals bind to RcnR with nanomolar affinity and stabilize the protein to denaturation. X-ray absorption and electron paramagnetic resonance spectroscopies reveal six-coordinate high-spin sites for each metal that contains a thiolate ligand. Experimental data support a tripartite N-terminal coordination motif (NH2-Xaa-NH-His) that is common for both metals. However, the Ni(II)- and Co(II)-RcnR complexes are shown to differ in the remaining coordination environment. Each metal coordinates a conserved Cys ligand but with distinct M-S distances. Co(II)-thiolate coordination has not been observed previously in Ni(II)-/Co(II)-responsive metalloregulators. The ability of RcnR to recruit ligands from the N-terminal region of the protein distinguishes it from CsoR, which uses a lower coordination geometry to bind Cu(I). These studies facilitate comparisons between Ni(II)-RcnR and NikR, the other Ni(II)-responsive transcriptional regulator in E. coli, to provide a better understanding how different nickel levels are sensed in E. coli. The characterization of the Ni(II)- and Co(II)-binding sites in RcnR, in combination with bioinformatics analysis of all RcnR/CsoR family members, identified a four amino acid fingerprint that likely defines ligand-binding specificity, leading to an emerging picture of the similarities and differences between different classes of RcnR/CsoR proteins.

DNA and Metal Binding of the E. coli Transcription Factor RcnR

Escherichia coli RcnR is a founding member of a new family of bacterial ligand‐responsive transcription factors. RcnR controls the expression of the nickel and cobalt efflux protein RcnA. To better understand the functions of this family, we have investigated the DNA and metal binding properties of RcnR. We find that RcnR binds a pair of inverted repeats in the rcnA promoter. DNA binding is negatively regulated by the direct interaction of RcnR with Ni(II) and Co(II) in vitro and in vivo. X‐ray absorption spectroscopy and mutagenesis experiments reveal a 6‐coordinate metal site with a His3(N/O)2S ligand set for Ni(II) and Co(II), where the strength of the thiolate interaction allows for discrimination of the two metals. Structural and functional comparisons with the regulatory sites of NikR, another nickel responsive regulator in E. coli, allow for a better understanding of how different nickel levels can be sensed within the same cell. Residues at the N‐terminus of this protein fold are important for recognition of metals that require higher coordination numbers, while the conserved cysteine aids in recognition of metals with the same preferred coordination number. Sequence analysis of other related proteins reveals a four amino acid fingerprint that enables predictions for ligand specificities, leading to an emerging picture of the diversity of this protein family. This work is supported by NSF Grant MCB‐0520877.

Rubredoxin reductase of Pseudomonas oleovorans: Structural relationship to other flavoprotein oxidoreductases based on one NAD and two FAD fingerprints

The oxidation of alkanes to alkanols by Pseudomonas oleovorans involves a three-component enzyme system: alkane hydroxylase, rubredoxin and rubredoxin reductase. Alkane hydroxylase and rubredoxin are encoded by the alkBFGHJKL operon, while previous studies indicated that rubredoxin reductase is most likely encoded on the second alk cluster: the alkST operon. In this study we show that alkT encodes the 41 × 10 3 M r, rubredoxin reductase, on the basis of a comparison of the expected amino acid composition of AlkT and the previously established amino acid composition of the purified rubredoxin reductase. The alkT sequence revealed significant similarities between AlkT and several NAD(P)H and FAD-containing reductases and dehydrogenases. All of these enzymes contain two ADP binding sites, which can be recognized by a common βαβ-fold or fingerprint, derived from known structures of cofactor binding enzymes. By means of this amino acid fingerprint we were able to determine that one ADP binding site in rubredoxin reductase (AlkT) is located at the N terminus and is involved in FAD binding, while the second site is located in the middle of the sequence and is involved in the binding of NAD or NADP. In addition, we derived from the sequences of FAD binding reductases a second amino acid fingerprint for FAD binding, and we used this fingerprint to identify a third amino acid sequence in AlkT near the carboxy terminus for binding of the flavin moiety of FAD. On the basis of the known architecture and relative spatial orientations of the NAD and FAD binding sites in related dehydrogenases, a model for part of the tertiary structure of AlkT was developed.