Representing Amino Acids Research Articles

The N‐Hydroxymethyl Group as a Traceless Activating Group for the CAL‐B‐Catalysed Ring Cleavage of β‐Lactams: A Type of Two‐Step Cascade Reaction

AbstractAn efficient enzymatic two‐step cascade procedure has been devised for rapid access to diverse amino acids from N‐hydroxymethyl‐β‐lactams; representative amino acids include the antifungal agent cispentacin, intermediates for the taxol side‐chain, and assorted cathepsin inhibitors. When CAL‐B‐catalysed hydrolyses of racemic N‐hydroxymethyl‐β‐lactams were performed with H2O (0.5 equiv.) in iPr2O at 60 °C, relatively quick (vs. non‐activated counterparts) and enantioselective (E > 200) ring cleavage reactions took place. As the ring‐opened amino acids formed, the hydroxymethyl group, as a traceless activating group, underwent spontaneous in situ degradation. Consequently, the desired β‐amino acid and unreacted N‐hydroxymethyl‐β‐lactam enantiomers (ee > 95 %) were formed. The formation of polymers, induced by liberation of formaldehyde, was successfully restricted by the addition of benzylamine as a capture agent, to the enzymatic reactions.

Nutritional ingredients from spent brewer's yeast obtained by hydrolysis and selective membrane filtration integrated in a pilot process

Spent brewer's yeast is a natural surplus from brewing industry. In order to up-grade this by-product, isolation of compounds has been tentatively assessed. The main objective of this work focuses on the use of ultrafiltration and nanofiltration pilot system for recovering cell compounds. Initially, yeast was autolyzed and ultrafiltered with a 10 kDa cut-off, and the two fractions obtained were hydrolyzed with Cynara cardunculus extract and nanofiltered with 3 kDa cut-off. Four fractions with different molecular weights were obtained, with protein and sugar contents ranging between 30–69% and 20–48%, respectively. Sodium and potassium were the major minerals present, whereas glutamine, glutamic acid and alanine, the most representative free amino acids. Peptide profile showed peptides with hydrophilic and hydrophobic characteristics, usually associated with biological activities, including antihypertensive and antioxidant. Thus, based on their compositions, all fractions show technological and biological potential, and can be used as nutritional ingredients in food and feed.

Biomimetic synthesis of highly biocompatible gold nanoparticles with amino acid-dithiocarbamate as a precursor for SERS imaging

Amino acid-dithiocarbamate (amino acid-DTC) was developed as both the reductant and ligand stabilizer for biomimetic synthesis of gold nanoparticles (AuNPs), which served as an excellent surface-enhanced Raman scattering (SERS) contrast nanoprobe for cell imaging. Glycine (Gly), glutamic acid (Glu), and histidine (His) with different isoelectric points were chosen as representative amino acid candidates to synthesize corresponding amino acid-DTC compounds through mixing with carbon disulfide (CS2), respectively. The pyrogenic decomposition of amino acid-DTC initiated the reduction synthesis of AuNPs, and the strong coordinating dithiocarbamate group of amino acid-DTC served as a stabilizer that grafted onto the surface of the AuNPs, which rendered the as-prepared nanoparticles a negative surface charge and high colloidal stability. MTT cell viability assay demonstrated that the biomimetic AuNPs possessed neglectful toxicity to the human hepatoma cell, which guaranteed them good biocompatibility for biomedical application. Meanwhile, the biomimetic AuNPs showed a strong SERS effect with an enhancement factor of 9.8 × 105 for the sensing of Rhodamine 6G, and two distinct Raman peaks located at 1363 and 1509 cm−1 could be clearly observed in the cell-imaging experiments. Therefore, biomimetic AuNPs can be explored as an excellent SERS contrast nanoprobe for biomedical imaging, and the amino acid-DTC mediated synthesis of the AuNPs has a great potential in bio-engineering and biomedical imaging applications.

Mechanisms of CO2 capture in ionic liquids: a computational perspective.

We present computational studies of CO2 sorption in two different classes of ionic liquid. The addition of carbon dioxide to four superbase ionic liquids, [P3333][Benzim], [P3333][124Triz], [P3333][123Triz] and [P3333][Bentriz], was studied using the DFT approach and considering anions alone and individual ion pairs. The addition of CO2 to the anion alone clearly resulted in the formation of a covalently-bound carbamate function with the strength of binding correlated to experimental capacity. In the ion pair however the cation significantly alters the nature of the bonding such that the overall cohesive energy is reduced. Formation of a strong carbamate function occurs at the expense of weakening the interaction between anion and cation. In [N1111][l-ALA], a representative amino acid ionic liquid, evidence was found for a low-energy monomolecular mechanism for carbamate formation, explaining the 1 : 1 molar uptake ratio observed in some amino acid ionic liquids. The mechanism involves proton transfer to the carboxylate group of the aminate anion.

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED.

Profiling microbial community function from metagenomic sequencing data remains a computationally challenging problem. Mapping millions of DNA reads from such samples to reference protein databases requires long run-times, and short read lengths can result in spurious hits to unrelated proteins (loss of specificity). We developed ShortBRED (Short, Better Representative Extract Dataset) to address these challenges, facilitating fast, accurate functional profiling of metagenomic samples. ShortBRED consists of two components: (i) a method that reduces reference proteins of interest to short, highly representative amino acid sequences (“markers”) and (ii) a search step that maps reads to these markers to quantify the relative abundance of their associated proteins. After evaluating ShortBRED on synthetic data, we applied it to profile antibiotic resistance protein families in the gut microbiomes of individuals from the United States, China, Malawi, and Venezuela. Our results support antibiotic resistance as a core function in the human gut microbiome, with tetracycline-resistant ribosomal protection proteins and Class A beta-lactamases being the most widely distributed resistance mechanisms worldwide. ShortBRED markers are applicable to other homology-based search tasks, which we demonstrate here by identifying phylogenetic signatures of antibiotic resistance across more than 3,000 microbial isolate genomes. ShortBRED can be applied to profile a wide variety of protein families of interest; the software, source code, and documentation are available for download at http://huttenhower.sph.harvard.edu/shortbred

Contribution of the Antibiotic Chloramphenicol and Its Analogues as Precursors of Dichloroacetamide and Other Disinfection Byproducts in Drinking Water.

Dichloroacetamide (DCAcAm), a disinfection byproduct, has been detected in drinking water. Previous research showed that amino acids may be DCAcAm precursors. However, other precursors may be present. This study explored the contribution of the antibiotic chloramphenicol (CAP) and two of its analogues (thiamphenicol, TAP; florfenicol, FF) (referred to collectively as CAPs), which occur in wastewater-impacted source waters, to the formation of DCAcAm. Their formation yields were compared to free and combined amino acids, and they were investigated in filtered waters from drinking-water-treatment plants, heavily wastewater-impacted natural waters, and secondary effluents from wastewater treatment plants. CAPs had greater DCAcAm formation potential than two representative amino acid precursors. However, in drinking waters with ng/L levels of CAPs, they will not contribute as much to DCAcAm formation as the μg/L levels of amino acids. Also, the effect of advanced oxidation processes (AOPs) on DCAcAm formation from CAPs in real water samples during subsequent chlorination was evaluated. Preoxidation of CAPs with AOPs reduced the formation of DCAcAm during postchlorination. The results of this study suggest that CAPs should be considered as possible precursors of DCAcAm, especially in heavily wastewater-impacted waters.

Non-enzymatic PLP-dependent oxidative deamination of amino acids induces higher alcohol synthesis

Pyridoxal phosphate (PLP) is an organic cofactor found in all transaminase enzymes. In this study PLP was used to replace the enzymatic deamination step in the Ehrlich pathway, for the oxidative conversion of amino acids into 2-keto acids. PLP functions in an enzymeindependent manner. It was further used in the synthesis of higher alcohols through a sequential enzymatic reduction in vitro and in vivo. PLP-dependent oxidation was investigated against five representative amino acids: valine, leucine, isoleucine, norvaline, and phenylalanine. In vitro amino acid oxidation resulted in approximately 45 ~ 75% [mole/mole] of each 2-keto acid conversion and in vitro ammonia formation was less than 2-keto acid formation, with 20% of conversion yields. Whole cell E. coli expressing reduction enzymes KivD/ADH with both single amino acid and amino acid mixture (4% yeast extract) gave the highest yield (30 ~ 55%) in the presence of the PLP-Cu complex and following enzymatic reactions.

The folate-coupled enzyme MTHFD2 is a nuclear protein and promotes cell proliferation.

Folate metabolism is central to cell proliferation and a target of commonly used cancer chemotherapeutics. In particular, the mitochondrial folate-coupled metabolism is thought to be important for proliferating cancer cells. The enzyme MTHFD2 in this pathway is highly expressed in human tumors and broadly required for survival of cancer cells. Although the enzymatic activity of the MTHFD2 protein is well understood, little is known about its larger role in cancer cell biology. We here report that MTHFD2 is co-expressed with two distinct gene sets, representing amino acid metabolism and cell proliferation, respectively. Consistent with a role for MTHFD2 in cell proliferation, MTHFD2 expression was repressed in cells rendered quiescent by deprivation of growth signals (serum) and rapidly re-induced by serum stimulation. Overexpression of MTHFD2 alone was sufficient to promote cell proliferation independent of its dehydrogenase activity, even during growth restriction. In addition to its known mitochondrial localization, we found MTHFD2 to have a nuclear localization and co-localize with DNA replication sites. These findings suggest a previously unknown role for MTHFD2 in cancer cell proliferation, adding to its known function in mitochondrial folate metabolism.

A Modular Synthesis of Multidentate S-, N- and O-Containing Meta- and Paracyclophanes

© 2015 Wiley-VCH Verlag GmbH andCo. KGaA, Weinheim. The development of a modular approach to macrocycle assembly has enabled the synthesis of a library of pyridine-based macrocycles possessing multiple donor sites where chirality was readily introduced from (R)- or (S)-alanine, a representative amino acid. The facile, regioselective, nucleophilic ring opening of aziridines by dithiols enabled the synthesis of thioether-based linkers which on subsequent alkylation provided access to optically pure macrocycles. A modular approach to macrocyclic assembly has enabled the synthesis of a library of macrocycles possessing multiple donor sites where chirality was readily introduced from (S)-alanine. Key to this approach was the facile, regioselective, nucleophilic ring opening of aziridines by dithiols followed by macrocylisation under conditions of high dilution.

Biomimetic repeat protein derived from Xenopus tropicalis for fibrous scaffold fabrication.

Collagen, silk, and elastin are the fibrous proteins consist of representative amino acid repeats. Because these proteins exhibited distinguishing mechanical properties, they have been utilized in diverse applications, such as fiber-based sensors, filtration membranes, supporting materials, and tissue engineering scaffolds. Despite their infinite prevalence and potential, most studies have only focused on a few repeat proteins. In this work, the hypothetical protein with a repeat motif derived from the frog Xenopus tropicalis was obtained and characterized for its potential as a novel protein-based material. The codon-optimized recombinant frog repeat protein, referred to as 'xetro', was produced at a high rate in a bacterial system, and an acid extraction-based purified xetro protein was successfully fabricated into microfibers and nanofibers using wet spinning and electrospinning, respectively. Specifically, the wet-spun xetro microfibers demonstrated about 2- and 1.5-fold higher tensile strength compared with synthetic polymer polylactic acid and cross-linked collagen, respectively. In addition, the wet-spun xetro microfibers showed about sevenfold greater stiffness than collagen. Therefore, the mass production potential and greater mechanical properties of the xetro fiber may result in these fibers becoming a new promising fiber-based material for biomedical engineering.

Extraction of Peptidoglycan from L. paracasei subp. Paracasei X12 and Its Preliminary Mechanisms of Inducing Immunogenic Cell Death in HT-29 Cells.

L. paracasei subp. paracasei X12 was previously isolated from a Chinese traditional fermented cheese with anticancer activities and probiotic potential. Herein, the integral peptidoglycan (X12-PG) was extracted by a modified trichloroacetic acid (TCA) method. X12-PG contained the four representative amino acids Asp, Glu, Ala and Lys, and displayed the similar lysozyme sensitivity, UV-visible scanning spectrum and molecular weight as the peptidoglycan standard. X12-PG could induce the production of apoptotic bodies observed by transmission electron microscopy (TEM). X12-PG could significantly induced the translocation of calreticulin (CRT) and the release of high mobility group box 1 protein (HMGB1), the two notable hallmarks of immunogenic cell death (ICD), with the endoplastic reticulum (ER) damaged and subsequently intracellular [Ca2+] elevated. Our findings implied that X12-PG could induce the ICD of HT-29 cells through targeting at the ER. The present results may enlighten the prospect of probiotics in the prevention of colon cancer.

Deciphering Hidden DNA Meta-Codes -The Great Unification & Master Code of Biology

This article presents multi-layered basic research culminating in what we call the Master Code of Biology. First, we review the “Formula for Life” discovery. This simple formula unifies all the components of life, structuring them in a kind of “Periodic table of Biology”. These components include bio-atoms, CONHSP, nucleotides, UTCAG, amino acids, DNA and RNA strands, proteins, genes, chromosomes and genomes. This discovery opens the door to powerful insights in exobiology, proposing a specific life-emerging constraint on the tuning and balancing of isotope proportions. Second, we introduce the “Master Code of Biology”, digital language supplying a common alphabet to the three fundamental languages of Genetics, Biology and Genomics. This synthesis goes above and beyond their three representative DNA, RNA and amino acids codes. There is a universal common code which unifies, connects and contains all these three languages. This “Master Code of Biology” provides a great Unification between the Master Code patterned images of Genomics (DNA) and Proteomics (amino acids), which appear highly correlated while RNA images curiously appear flat like a neutral or zero-like code. Third, the functionality of this discovery is evidenced by two examples. Analyzing textures of the Genomic and Proteomic patterned curves reveals the emergence of binary codes and discrete waveforms. These predict the well-known karyotypes- white/grey/black bands overlapping and characterizing the human chromosomes. Mapping “the Master Code of Biology” to SNP genomic areas, we show that SNPs are determined to be more functional by their location within the genome than by their local values– TCAG nucleotide changes. Finally, we demonstrate that a chromosomal DNA sequences systematic reshaping combined with periodic waves highlighted above brings out, at whole chromosome scale, interferometry-like interference fields manifested by resonances, tunings, and even resonances that exhibit Fibonacci number proportions differentiating human and great primates at whole chromosome4 scale.

Dissecting Ligand Binding Sites : A Layer at a Time

Biological phenomena at a molecular level are a consequence of complex interplay of interactions between ligands and their associated protein targets. Such interactions are localized to defined protein regions termed as binding sites (residues within ∼4.5A from ligand). Numerous cases exist wherein proteins of diverse folds bind to similar ligands. We undertake a study with an objective to quantify similarities in binding sites, that utilize the structural information of a binding site at atomistic detail, in order to examine extension of such similarities to additional regions surrounding the binding site. We find that 68% and 22% of high scoring comparisons among single-domain and multi-domain proteins respectively, exhibit similarity at the binding site that extrapolates to regions beyond it (an additional 4.5A from binding site). Such similarities in binding sites as well as their extension to adjoining regions are analysed along with residue-wise correspondences and pairwise structural alignment of binding sites. Sequence identity and ligand topology are found to be independent of the extent of binding site similarity. Statistical validation of these findings re-iterates their relevance by means of p-value calculation as well as decoy site generation.Occurrences of similarity beyond the binding site are also further investigated using Protein Side-chain Networks (PScN). Such networks are created wherein each node represents amino acid residues, and an edge is constructed based on interaction strength between side chain of non-covalently bonded residues. PScNs lead to the identification of densely connected modules i.e cliques and communities in regions of binding site and surrounding areas. Thus, a combinatorial approach capturing atomistic details of binding site architecture and global perspectives of ligand-binding by PScNs could aid in providing valuable insights to current understanding of molecular recognition events.

Effect of Moringa oleifera Leaf Powder Supplementation on the Micronutrient and Toxicant Contents of Maize – Soybean – Peanut Complementary Food Formulations

The effect of Moringa oleifera leaf powder supplementation on the micronutrient and toxicant composition of maize - soybean - peanut food formulations was determined. Maize, soybeans and peanut (MSP) flours were blended in a ratio of 60:30:10 (through material balancing to give 16g protein/100g) food as recommended by the protein advisory group (PAG) for infant diets. While one part was used unfortified as control food sample (MSPA), the remaining three parts were fortified with 5% (125g), 10% (250g) and 15% (375g) Moringa oleifera powder, giving samples MSPB, MSPC and MSPD respectively. Standard methods of analysis were then used to determine the content of some representative vitamins, amino acids, minerals and antinutritional factors in the food formulations. There was significantly increase (p < 0.05) in Vitamins A (� -Carotene) and C as well as amino acids lysine and tryptophan with increase in Moringa oleifera powder, with values ranging from 2.40 to 5.43mg/100g, 2.00 to 3.80mg/100g, 34 to 145mg/100g and 13 to 45mg/100g for � -Carotene, Vitamin C, Lysine and Tryptophan respectively. Supplementation also significantly (p <0.05) increased the contents of all the mineral elements with values ranging from 498.90 to 631.72mg/100g, 81.10 to 110.94mg/100g 1.40 to 5.48mg/100g, 39.20 to 356.67mg/100g and 38.70 to 77.60mg/100g and 1.59 to 2.38mg/100g for potassium, magnesium, iron, calcium, phosphorus and zinc respectively; while oxalates, phytates and phenols contents increased significantly (p <0.05) with increase in Moringa oleifera leaf powder addition, with values ranging from 70.42 to 84.80mg/100g, 68.00 to 90.04mg/100g and 80.00 to 83.40mg/100g respectively.

Computer Modeling of Obesity Links Theoretical Energetic Measures with Experimental Measures of Fuel Use for Lean and Obese Men

The goal of this research was to use a computational model of human metabolism to predict energy metabolism for lean and obese men. The model is composed of 6 state variables representing amino acids, muscle protein, visceral protein, glucose, triglycerides, and fatty acids (FAs). Differential equations represent carbohydrate, amino acid, and FA uptake and output by tissues based on ATP creation and use for both lean and obese men. Model parameterization is based on data from previous studies. Results from sensitivity analyses indicate that model predictions of resting energy expenditure (REE) and respiratory quotient (RQ) are dependent on FA and glucose oxidation rates with the highest sensitivity coefficients (0.6, 0.8 and 0.43, 0.15, respectively, for lean and obese models). Metabolizable energy (ME) is influenced by ingested energy intake with a sensitivity coefficient of 0.98, and a phosphate-to-oxygen ratio by FA oxidation rate and amino acid oxidation rate (0.32, 0.24 and 0.55, 0.65 for lean and obese models, respectively). Simulations of previously published studies showed that the model is able to predict ME ranging from 6.6 to 9.3 with 0% differences between published and model values, and RQ ranging from 0.79 to 0.86 with 1% differences between published and model values. REEs >7 MJ/d are predicted with 6% differences between published and model values. Glucose oxidation increases by ∼0.59 mol/d, RQ increases by 0.03, REE increases by 2 MJ/d, and heat production increases by 1.8 MJ/d in the obese model compared with lean model simulations. Increased FA oxidation results in higher changes in RQ and lower relative changes in REE. These results suggest that because fat mass is directly related to REE and rate of FA oxidation, body fat content could be used as a predictor of RQ.

PHI-DAC: protein homology database through dihedral angle conservation.

Finding related conformations in the Protein Data Bank is essential in many areas of bioscience. To assist this task, we designed a dihedral angle database for searching protein segment homologs. The search engine relies on encoding of the protein coordinates into text characters representing amino acid sequence, φ and ψ dihedral angles. The search engine is advantageous owing to its high speed and interactive nature and is expected to assist scientists in discovering conformation homologs and evolutionary kinship. The search engine is fast, with query times lasting a few seconds, and freely available at http://tarshish.md.biu.ac.il/∼samsona. Supplementary data are available at Bioinformatics online.

Seeing the results of a mutation with a vertex weighted hierarchical graph.

BackgroundWe represent the protein structure of scTIM with a graph-theoretic model. We construct a hierarchical graph with three layers - a top level, a midlevel and a bottom level. The top level graph is a representation of the protein in which its vertices each represent a substructure of the protein. In turn, each substructure of the protein is represented by a graph whose vertices are amino acids. Finally, each amino acid is represented as a graph where the vertices are atoms. We use this representation to model the effects of a mutation on the protein.MethodsThere are 19 vertices (substructures) in the top level graph and thus there are 19 distinct graphs at the midlevel. The vertices of each of the 19 graphs at the midlevel represent amino acids. Each amino acid is represented by a graph where the vertices are atoms in the residue structure. All edges are determined by proximity in the protein's 3D structure. The vertices in the bottom level are labelled by the corresponding molecular mass of the atom that it represents. We use graph-theoretic measures that incorporate vertex weights to assign graph based attributes to the amino acid graphs. The attributes of the corresponding amino acids are used as vertex weights for the substructure graphs at the midlevel. Graph-theoretic measures based on vertex weighted graphs are subsequently calculated for each of the midlevel graphs. Finally, the vertices of the top level graph are weighted with attributes of the corresponding substructure graph in the midlevel.ResultsWe can visualize which mutations are more influential than others by using properties such as vertex size to correspond with an increase or decrease in a graph-theoretic measure. Global graph-theoretic measures such as the number of triangles or the number of spanning trees can change as the result. Hence this method provides a way to visualize these global changes resulting from a small, seemingly inconsequential local change.ConclusionsThis modelling method provides a novel approach to the visualization of protein structures and the consequences of amino acid deletions, insertions or substitutions and provides a new way to gain insight on the consequences of diseases caused by genetic mutations.

Physicochemical studies and biological activity of mixed ligand complexes involving bivalent transition metals with a novel Schiff base and glycine as a representative amino acid

The mixed-ligand complexes of Co(II), Ni(II), Mn(II) and Zn(II) with 2-aminomethyl thiophenyl-4-bromosalicylaldehyde Schiff base (ATS) and glycine as a representative example of amino acids have been achieved. These complexes namely [Ni(ATS)(Gly)] (1), [Co(ATS)(Gly)].H 2 O (2) [Mn(ATS)(Gly)].2H 2 O (3), and [Zn(ATS)(Gly)] (4) were characterized by elemental, molar conductance, infrared, magnetic moment, and electronic spectra. ATS behaves as mononegatively charged bidentate ligand with coordination through azomethine nitrogen and phenolate oxygen groups while glycine acts as monobasic bidentate ligand is coordinated via amino and ionized carboxylate group after deprotonation. The low molar conductance values suggest the non-electrolytic nature of these complexes. The magnetic and spectral data indicates a square planar geometry for Ni(II) complex, tetrahedral geometry for Zn(II) and octahedral geometry for both Mn(II) and Co(II) complexes. The isolated chelates have been screened for their antimicrobial activity.

A distance‐ and orientation‐dependent energy function of amino acid key blocks

Blocks are the selected portions of amino acids. They have been used effectively to represent amino acids in distinguishing the native conformation from the decoys. Although many statistical energy functions exist, most of them rely on the distances between two or more amino acids. In this study, the authors have developed a pairwise energy function "DOKB" that is both distance and orientation dependent, and it is based on the key blocks that bias the distal ends of side chains. The results suggest that both the distance and the orientation are needed to distinguish the fine details of the packing geometry. DOKB appears to perform well in recognizing native conformations when compared with six other energy functions. Highly packed clusters play important roles in stabilizing the structure. The investigation about the highly packed clusters at the residue level suggests that certain residue pairs in a low-energy region have lower probability to appear in the highly packed clusters than in the entire protein. The cluster energy term appears to significantly improve the recognition of the native conformations in ig_structal decoy set, in which more highly packed clusters are contained than in other decoy sets.

Regulatory Networks Controlling Nitrogen Sensing and Uptake in Candida albicans

Nitrogen is one of the key nutrients for microbial growth. During infection, pathogenic fungi like C. albicans need to acquire nitrogen from a broad range of different and changing sources inside the host. Detecting the available nitrogen sources and adjusting the expression of genes for their uptake and degradation is therefore crucial for survival and growth as well as for establishing an infection. Here, we analyzed the transcriptional response of C. albicans to nitrogen starvation and feeding with the infection-relevant nitrogen sources arginine and bovine serum albumin (BSA), representing amino acids and proteins, respectively. The response to nitrogen starvation was marked by an immediate repression of protein synthesis and an up-regulation of general amino acid permeases, as well as an up-regulation of autophagal processes in its later stages. Feeding with arginine led to a fast reduction in expression of general permeases for amino acids and to resumption of protein synthesis. The response to BSA feeding was generally slower, and was additionally characterized by an up-regulation of oligopeptide transporter genes. From time-series data, we inferred network interaction models for genes relevant in nitrogen detection and uptake. Each individual network was found to be largely specific for the experimental condition (starvation or feeding with arginine or BSA). In addition, we detected several novel connections between regulator and effector genes, with putative roles in nitrogen uptake. We conclude that C. albicans adopts a particular nitrogen response network, defined by sets of specific gene-gene connections for each environmental condition. All together, they form a grid of possible gene regulatory networks, increasing the transcriptional flexibility of C. albicans.