Asymmetric mutations in the tetrameric R67 dihydrofolate reductase reveal high tolerance to active-site substitutions

Type II R67 dihydrofolate reductase (DHFR) is a bacterial plasmid-encoded enzyme that is intrinsically resistant to the widely-administered antibiotic trimethoprim. R67 DHFR is genetically and structurally unrelated to E. coli chromosomal DHFR and has an unusual architecture, in that four identical protomers form a single symmetrical active site tunnel that allows only one substrate binding/catalytic event at any given time. As a result, substitution of an active-site residue has as many as four distinct consequences on catalysis, constituting an atypical model of enzyme evolution. Although we previously demonstrated that no single residue of the native active site is indispensable for function, library selection here revealed a strong bias toward maintenance of two native protomers per mutated tetramer. A variety of such “half-native” tetramers were shown to procure native-like catalytic activity, with similar K_M values but k_cat values 5- to 33-fold lower, illustrating a high tolerance for active-site substitutions. The selected variants showed a reduced thermal stability (T_m ∼12°C lower), which appears to result from looser association of the protomers, but generally showed a marked increase in resilience to heat denaturation, recovering activity to a significantly greater extent than the variant with no active-site substitutions. Our results suggest that the presence of two native protomers in the R67 DHFR tetramer is sufficient to provide native-like catalytic rate and thus ensure cellular proliferation.     

Decreased influenza-specific B cell responses in rheumatoid arthritis patients treated with anti-tumor necrosis factor

Introduction

As a group, rheumatoid arthritis (RA) patients exhibit increased risk of infection, and those treated with anti-tumor necrosis factor (TNF) therapy are at further risk. This increased susceptibility may result from a compromised humoral immune response. Therefore, we asked if short-term effector (d5-d10) and memory (1 month or later) B cell responses to antigen were compromised in RA patients treated with anti-TNF therapy.

Methods

Peripheral blood samples were obtained from RA patients, including a subset treated with anti-TNF, and from healthy controls to examine influenza-specific responses following seasonal influenza vaccination. Serum antibody was measured by hemagglutination inhibition assay. The frequency of influenza vaccine-specific antibody secreting cells and memory B cells was measured by EliSpot. Plasmablast (CD19+IgD-CD27hiCD38hi) induction was measured by flow cytometry.

Results

Compared with healthy controls, RA patients treated with anti-TNF exhibited significantly decreased influenza-specific serum antibody and memory B cell responses throughout multiple years of the study. The short-term influenza-specific effector B cell response was also significantly decreased in RA patients treated with anti-TNF as compared with healthy controls, and correlated with decreased influenza-specific memory B cells and serum antibody present at one month following vaccination.

Conclusions

RA patients treated with anti-TNF exhibit a compromised immune response to influenza vaccine, consisting of impaired effector and consequently memory B cell and antibody responses. The results suggest that the increased incidence and severity of infection observed in this patient population could be a consequence of diminished antigen-responsiveness. Therefore, this patient population would likely benefit from repeat vaccination and from vaccines with enhanced immunogenicity.     

The C-terminal cytoplasmic domain of human proEGF is a negative modulator of body and organ weights in transgenic mice

We generated transgenic mice to study the in vivo role of the cytoplasmic domain of human proEGF (proEGFcyt). Post-pubertal proEGFcyt transgenic (tg) mice displayed an up to 15% reduction in body weight, including smaller kidney and brain weights as compared to control littermates. Renal histology, gene expression profiles, and functional parameters were normal. In both sexes, serum levels of IGFBP-3 were reduced. Circulating IGF-I/IGF-II levels were unchanged. Histomorphological analysis revealed isolated foci of liver necrosis specific to proEGFcyt tg mice. In conclusion, we identified proEGF cytoplasmic domain as a novel modulator of whole body and organ-specific growth in mice.     

Discovery of glycosyltransferases using carbohydrate arrays and mass spectrometry

Glycosyltransferases catalyze the reaction between an activated sugar donor and an acceptor to form a new glycosidic linkage. Glycosyltransferases are responsible for the assembly of oligosaccharides in vivo and are also important for the in vitro synthesis of these biomolecules. However, the functional identification and characterization of new glycosyltransferases is difficult and tedious. This paper describes an approach that combines arrays of reactions on an immobilized array of acceptors with an analysis by mass spectrometry to screen putative glycosyltransferases. A total of 14,280 combinations of a glycosyltransferase, an acceptor and a donor in four buffer conditions were screened, leading to the identification and characterization of four new glycosyltransferases. This work is notable because it provides a label-free method for the rapid functional annotation of putative enzymes.     

<Superscript>1</Superscript>H, <Superscript>15</Superscript>N and <Superscript>13</Superscript>C backbone resonance assignments of pentaerythritol tetranitrate reductase from <Emphasis Type="Italic">Enterobacter cloacae</Emphasis> PB2

Pentaerythritol tetranitrate reductase (PETNR) is a flavoenzyme possessing a broad substrate specificity and is a member of the Old Yellow Enzyme family of oxidoreductases. As well as having high potential as an industrial biocatalyst, PETNR is an excellent model system for studying hydrogen transfer reactions. Mechanistic studies performed with PETNR using stopped-flow methods have shown that tunneling contributes towards hydride transfer from the NAD(P)H coenzyme to the flavin mononucleotide (FMN) cofactor and fast protein dynamics have been inferred to facilitate this catalytic step. Herein, we report the near-complete ¹H, ¹⁵N and ¹³C backbone resonance assignments of PETNR in a stoichiometric complex with the FMN cofactor in its native oxidized form, which were obtained using heteronuclear multidimensional NMR spectroscopy. A total of 97% of all backbone resonances were assigned, with 333 out of a possible 344 residues assigned in the ¹H–¹⁵N TROSY spectrum. This is the first report of an NMR structural study of a flavoenzyme from the Old Yellow Enzyme family and it lays the foundation for future investigations of functional dynamics in hydride transfer catalytic mechanism.     

Novel approach to microbiological air monitoring in show caves

Air microbial pollution in touristic areas poses a risk for both the integrity of an ecosystem and human health. Microbiological monitoring together with environmental parameters monitoring allows for the assessment of the impacts and formulation of sound management decisions to protect humans and ecosystems. Four show caves from the Carpathian Mountains were selected for our study. The caves were sampled monthly to obtain an overview of the changes that occur over a yearly cycle. For the microbial monitoring, we used RIDA^®COUNT test plates, while the environmental parameters were monitored with a variety of devices. Second and third generations of microbes extracted from the plates were grown on specific media for the purpose of 16S rRNA and 18S rRNA extraction and taxa identification. The bacterial communities identified in the air samples in the four investigated show caves were dominated by Staphylococcus, while regarding the fungi communities, Penicillium was more likely to occur in the touristic part of the caves and Cladosporium in the non-visited passages. Together with data on number of visitors, number of bats and radon levels we were able understand the impact of tourists on the cave environment and to generate microbiological risk maps for human health. This type of comprehensive study can be used not only to protect the integrity of a touristic area from the impacts caused by the introduction of allochthonous organic matter, but also for the protection of the tourists and guides from potential pathogenic taxa.     

Environmental assessment of municipal wastewater discharges: a comparative study of evaluation methods

Purpose

Wastewater treatment plants produce high environmental impacts on receiving water bodies and pose economic burdens on municipalities or industrial facilities. Their overall operational costs and achieved effluent quality depend very much on the influent type, presence of priority pollutants, treatment technology and required effluent quality (for discharge or for recycle/reuse). Life cycle assessment (LCA), environmental impact quantification (EIQ) and water footprint (WF) are important instruments for sustainability assessments applied for products, production and consumption evaluations in connection with natural resources depletion and pollution threats. This study focuses on the environmental assessment of a municipal wastewater treatment plant (MWWTP) discharges by means of these three evaluation methods with the purpose to understand their (methodological) weak and strong points in capturing the impacts. Such a comparative analysis is necessary to understand how the (individual) advantages provided by each of these instruments can be complimentarily used to improve an assessment framework for various stakeholders concerned with water use cycle management (regional water operators, water management authority, public authorities, research entities, societal organizations, etc.).

Methods

The three assessment methodologies (LCA, EIQ, WF) are presented, implemented and critically analysed based on a unitary set of data concerning the MWWTP of Iasi city (a municipality of approx. 300,000 inhabitants situated in the North Eastern region of Romania), the wastewater and river water quality indicators as well as all the other relevant data being collected for the year 2012.

Results and discussion

Although the three methodologies have different principles for environmental impact quantification, the results have shown that most impacts induced to surface waters due to Iasi MWWTP effluents are given by the nutrients (nitrogen and phosphorous compounds), which could induce an eutrophication impact, and to a lesser extent by pollutants responsible for toxicity impacts (such as heavy metals).

Conclusions

Based on the results of this comparative study, a critical analysis of these three methods was realized by considering the data requirements, their development and integration status. Furthermore, the strong and weak points that are relevant for each method implementation and their subsequent use by decision-makers and Water Authorities are discussed, in the context of legislative requirements (including the Water Framework Directive), actual development of regional water operators and stakeholders' interests.

     

Acute phase inflammation is characterized by rapid changes in plasma/peritoneal fluid <Emphasis Type="Italic">N</Emphasis>-glycosylation in mice

Murine zymosan-induced peritonitis is a widely used model for studying the molecular and cellular events responsible for the initiation, persistence and/or resolution of inflammation. Among these events, it is becoming increasingly evident that changes in glycosylation of proteins, especially in the plasma and at the site of inflammation, play an important role in the inflammatory response. Using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS)-based glycosylation profiling, we investigated the qualitative and quantitative effect of zymosan-induced peritonitis on N-glycosylation in mouse plasma and peritoneal fluid. Our results show that both N-glycomes exhibit highly similar glycosylation patterns, consisting mainly of diantennary and triantennary complex type N-glycans with high levels (>95 %) of galactosylation and sialylation (mostly NeuGc) and a medium degree of core fucosylation (30 %). Moreover, MS/MS structural analysis, assisted by linkage-specific derivatization of sialic acids, revealed the presence of O-acetylated sialic acids as well as disialylated antennae (“branching sialylation”) characterized by the presence of α2-6-linked NeuGc on the GlcNAc of the NeuGcα2-3-Galβ1-3-GlcNAc terminal motif. A significant decrease of (core) fucosylation together with an increase of both α2-3-linked NeuGc and “branching sialylation” were observed in N-glycomes of mice challenged with zymosan, but not in control mice injected with PBS. Importantly, substantial changes in glycosylation were already observed 12 h after induction of peritonitis, thereby demonstrating an unexpected velocity of the biological mechanisms involved.     

Oligomeric structure of the neutral amino acid transporters KAAT1 and CAATCH1

The highly homologous neutral amino acid transporters KAAT1 and CAATCH1, cloned from the midgut epithelium of the Manduca sexta larva, are members of the Na⁺/Cl^–-dependent transporter family. Recent evidence indicates that transporters of this family form constitutive oligomers. CAATCH1 and KAAT1 give rise to specific kinds of current depending on the transported amino acid, cotransported ion, pH, and membrane voltage. Different substrates induce notably distinct transport-associated currents in the two proteins that represent useful tools in structural-functional studies. To determine whether KAAT1 and CAATCH1 form functional oligomers, we have constructed four concatameric proteins for electrophysiological analysis, consisting of one KAAT1 protein covalently linked to another KAAT1 (K-K concatamer) or to CAATCH1 (K-C concatamer) and vice versa (C-C concatamer and C-K concatamer), and eight constructs where the two transporters were linked to yellow or cyan fluorescent protein in the NH₂ or COOH terminus, to determine the oligomer formation and the relative distance between the different subunits by fluorescence resonance energy transfer (FRET) analysis. Heterologous expression of the concatenated constructs and coinjection of the original proteins in different proportions allowed us to compare the characteristics of the currents to those of the oocytes expressing only the wild-type proteins. All the constructs were fully active, and their electrophysiological behavior was consistent with the activity as monomeric proteins. However, the FRET studies indicate that these transporters form oligomers in agreement with the LeuT_Aa atomic structure and confirm that the COOH termini of the adjacent subunits are closer than NH₂ termini. transport; oligomerization; Slc6; fret     

Structure and function relations with a T-cell-activating polysaccharide antigen using circular dichroism

Studies centered on understanding how molecular structure affects biological function have historically focused on proteins. Circular dichroism (CD) is commonly used to analyze protein secondary structure, yet its application to other molecules is far less explored. In fact, little is known about how glycan conformation might affect function, likely because of a lack of tools for measuring dynamic structural changes of carbohydrates. In the present study, we developed a method based on CD to monitor conformational changes in the zwitterionic T-cell-activating glycoantigen polysaccharide A1 (PSA). We found that PSA helical structure produces a CD spectrum that is strikingly similar to proteins rich in alpha-helical content and is equally sensitive to nonpolar solvents. Like conventional T-cell-dependent proteins, PSA requires processing before major histocompatibility complex class II (MHCII) binding. CD spectra of PSA fragments of varying sizes indicated that fragments smaller than three repeating units lack helical content and are incapable of MHCII binding. Likewise, neutralization of charged groups in the repeating unit resulted in major conformational changes as measured by CD, which correlated with a lack of MHCII presentation. These data represent two significant findings: CD can be used to measure conformational changes in carbohydrates and the functional epitope from PSA is dependent on a specific conformation that is stabilized by adjacent repeating units and a zwitterionic charge motif. As a result, this work demonstrates that CD is a valuable tool for use in functional glycomics efforts that seek to align chemical and conformational structure with biological activity.