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The mucosal surface of the human gastrointestinal (GI) tract is about 200-300 m2 and is colonized by 1013-14 bacteria of 400 different species and subspecies. Savage has defined and categorized the gastrointestinal microflora into two types, autochthonous flora (indigenous flora) and allochthonous flora (transient flora). Autochthonous microorganisms colonize particular habitats, i.e., physical spaces in the GI tract, whereas allochthonous microorganisms cannot colonize particular habitats except under abnormal conditions. Most pathogens are allochthonous microorganisms; nevertheless, some pathogens can be autochthonous to the ecosystem and normally live in harmony with the host, except when the system is disturbed. The prevalence of bacteria in different parts of the GI tract appears to be dependent on several factors, such as pH, peristalsis, redox potential, bacterial adhesion, bacterial cooperation, mucin secretion, nutrient availability, diet, and bacterial antagonism. Because of the low pH of the stomach and the relatively swift peristalsis through the stomach and the small bowel, the stomach and the upper two-thirds of the small intestine (duodenum and jejunum) contain only low numbers of microorganisms, which range from 103 to 104 bacteria/mL of the gastric or intestinal contents, mainly acid-tolerant lactobacilli and streptococci. In the distal small intestine (ileum), the microflora begin to resemble those of the colon, with around 107-108 bacteria/mL of the intestinal contents. With decreased peristalsis, acidity, and lower oxidation-reduction potentials, the ileum maintains a more diverse microflora and a higher bacterial population. Probably because of slow intestinal motility and very low oxidation-reduction potentials, the colon is the primary site of microbial colonization in humans. The colon harbors tremendous numbers and species of bacteria. However, 99.9% of colonic microflora are obligate anaerobes.
Methods Mol Biol 2004
PMID:Microflora of the gastrointestinal tract: a review. 1515 63

The KorB protein of the broad-host-range plasmid RP4 acts as a multifunctional regulator of plasmid housekeeping genes, including those responsible for replication, maintenance and conjugation. Additionally, KorB functions as the ParB analog of the plasmid's partitioning system. The protein structure consists of eight helices, two of which belong to a predicted helix-turn-helix motif. Each half-site of the palindromic operator DNA binds one copy of the protein in the major groove. As confirmed by mutagenesis, recognition specificity is based mainly on two side chain interactions outside the helix-turn-helix motif with two bases next to the central base pair of the 13-base pair operator sequence. The surface of the KorB DNA-binding domain mirrors the overall acidity of KorB, whereas DNA binding occurs via a basic interaction surface. We present a model of KorB, including the structure of its dimerization domain, and discuss its interactions with the highly basic ParA homolog IncC.
Nat Struct Mol Biol 2004 Jul
PMID:Sequence-specific DNA binding determined by contacts outside the helix-turn-helix motif of the ParB homolog KorB. 1517 Jan 77

The sulfonamide moiety was introduced as a potential transition state isostere of the hydrolysis of the amide bond. Subsequently, the increased acidity of a sulfonamide N-H as compared to a regular amide N-H was explored in the development of peptidosulfonamide synthetic receptor molecules for binding and catalysis. The required building blocks for these compounds were accessible via an efficient synthesis, which also enabled the synthesis of oligopeptidosulfonamides as well as peptidosulfonamide-betapeptide hybrids. The structural consequences of the introduction of the peptidosulfonamide residues were studied and were further explored by the synthesis of cyclic peptidosulfonamides e.g. by ring-closing metathesis.
Mol Divers 2004
PMID:Peptide transformation leading to peptide-peptidosulfonamide hybrids and oligo peptidosulfonamides. 1520 57

The virulence of pathogenic bacteria is dependent on their adaptation to and survival in the stressful conditions encountered in their hosts. Helicobacter pylori exclusively colonizes the acid stomach of primates, making it an ideal study model. Little is known about how H. pylori responds to the moderately acidic conditions encountered at its colonization site, the gastric mucus layer. Thus, we compared gene expression profiles of H. pylori 26695 grown at neutral and acidic pH, and validated the data for a selection of genes by real-time polymerase chain reaction, dot-blots or enzymatic assays. During growth in acidic conditions, 56 genes were upregulated and 45 genes downregulated. We found that acidity is a signal modulating the expression of several virulence factors. Regulation of genes related to metal ion homeostasis suggests protective mechanisms involving diminished transport and enhanced storage. Genes encoding subunits of the F0F1 ATPase and of a newly identified Na+/H+ antiporter (NhaC-HP0946) were downregulated, revealing that this bacterium uses original mechanisms to control proton entry. Five of the upregulated genes encoded proteins controlling intracellular ammonia synthesis, including urease, amidase and formamidase, underlining the major role of this buffering compound in the protection against acidity in H. pylori. Regulatory networks and transcriptome analysis as well as enzymatic assays implicated two metal-responsive transcriptional regulators (NikR and Fur) and an essential two-component response regulator (HP0166, OmpR-like) as effectors of the H. pylori acid response. Finally, a nikR-fur mutant is attenuated in the mouse model, emphasizing the link between response to acidity, metal metabolism and virulence in this gastric pathogen.
Mol Microbiol 2004 Jul
PMID:Responsiveness to acidity via metal ion regulators mediates virulence in the gastric pathogen Helicobacter pylori. 1522 39

Infrared and electronic spectra were used to investigate the tautomerism of some azo compounds, in both the solid and solution states. It was found that the compounds exist in azo<==>hydrazone tautomeric equilibrium in solid and in solutions. The different bands displayed in the electronic spectra of the compounds in various organic solvents are assigned to the suitable electronic transitions. The solvatochromic behavior of the compounds was investigated by studying their visible spectra in pure and mixed organic solvents. DeltaG and formation constant, Kf, values of the molecular complexes formed in solution have been determined. Effect of concentration of the compounds in DMF and EtOH solutions has been investigated. The basicity and acidity constants of the different compounds were determined from the spectra of these compounds in aqueous-ethanolic solutions of varying pH values. Some complexes of copper(II) with these compounds in solution were tested as for their antibacterial and antifungal activity.
Spectrochim Acta A Mol Biomol Spectrosc 2004 Jul
PMID:Tautomeric structures, electronic spectra, acid-base properties of some 7-aryl-2,5-diamino-3(4-hydroxyphenyazo)pyrazolo[1,5-a]pyrimidine-6-carbonitriles, and effect of their copper(II) complex solutions on some bacteria and fungi. 1524 68

To elucidate the mechanisms of pH response in an acid-tolerant Sinorhizobium medicae strain we have identified acid-activated gene transcription and now complement this approach by using a proteomic analysis to identify the changes that occur following exposure to acidity. Protein profiles of persistently or transiently acid-stressed S. medicae cells were compared to those grown in pH neutral, buffered media. Fifty pH-regulated proteins were identified; N-terminal sequences for 15 of these were obtained using the Edman degradation. Transient acid exposure downregulated GlnA and GlnK and upregulated a hypothetical protein. Continuing acid exposure downregulated ClpP, an ABC transporter, a hypothetical protein, a lipoprotein, the Trp-like repressor WrbA1 and upregulated DegP, fructose bisphosphate aldolase, GroES, malate dehydrogenase and two hypothetical proteins. These findings implicate proteolytic, chaperone and transport processes as key components of pH response in S. medicae.
J Mol Microbiol Biotechnol 2004
PMID:Probing for pH-regulated proteins in Sinorhizobium medicae using proteomic analysis. 1526 18

The trivalent lanthanide ions are chemically similar to Ca(II) ions, making them useful Ca analogs for a multitude of applications. In addition, Ln(III) ions are efficient catalysts of hydrolysis due to their much stronger Lewis acidity relative to Ca(II) ions. Ln-binding peptides thus offer both the opportunity to study known Ca sites as well as to explore new biological functions with an entire family of spectroscopically rich and reactive ions. This review discusses Ln-binding peptides in three roles: (i) as models of Ca-protein structure and function, (ii) as spectroscopic tags for protein expression and characterization and (iii) as designed artificial endonucleases. The creation of hydrolytically active Ln peptides that can fold, bind, cleave and discriminate among substrates shows that the design of Ln enzymes can be accomplished, and they will serve as versatile biochemical tools to investigate protein folding, structure and nuclease function.
Cell Mol Life Sci 2004 Sep
PMID:Lanthanide-binding peptides and the enzymes that Might Have Been. 1533 50

Escherichia coli survives pH 2 acid stress at a level rivalling Helicobacter pylori. Of the three E. coli acid resistance systems involved, the one most efficient and most studied uses isozymes of glutamate decarboxylase (GadA/GadB) to consume intracellular protons, and a glutamate:gamma-amino butyric acid (GABA) anti-porter (GadC) to expel GABA in exchange for extracellular glutamate. Because acid resistance is a critical factor in resisting stomach acidity, mechanisms that control this system are extremely important. Here we show that an Era-like, molecular switch GTPase called TrmE regulates glutamate-dependent acid resistance. Western blot analysis revealed a TrmE-dependent, glucose-induced system and a TrmE-independent, glucose-repressed pathway. Gene fusion studies indicated that the TrmE requirement for GadA/B production takes place at both the transcriptional and translational levels. TrmE controls GAD transcription by affecting the expression of GadE, the essential activator of the gadA and gadBC genes. TrmE most probably controls gadE expression indirectly by influencing the synthesis or activity of an unknown regulator that binds the gadE control region. Translational control of GAD production by TrmE appears to be more direct, affecting synthesis of the decarboxylase and the anti-porter proteins. TrmE GTPase activity was critical for both the transcriptional and translational effects. Thus, TrmE is part of an increasingly complex control network designed to integrate diverse physiological signals and forecast future exposures to extreme acid. The significance of this network extends beyond acid resistance as the target of this control, GadE, regulates numerous genes in addition to gadA/BC.
Mol Microbiol 2004 Nov
PMID:The Era-like GTPase TrmE conditionally activates gadE and glutamate-dependent acid resistance in Escherichia coli. 1552 79

In this paper we determine the overlapping pK(a) values of resorcinol in water, applying a UV-Vis spectroscopic method that uses absorbance diagrams. On the other hand, in order to explain the pK(a) values obtained, we also investigate the molecular conformations and solute-solvent interactions of the resorcinate anions, using ab initio and density functional theory methods. Several ionization reactions and equilibria in protic solvents, which possess a high hydrogen-bond-donor capability, are proposed. The mentioned reactions and equilibria constituted the indispensable theoretical basis to calculate the acidity constants of resorcinol. Basis sets at the HF/6-31 + G(d) and B3LYP/6-31 + G(d) levels of theory were used for calculations. Tomasi's method was used to analyze the formation of intermolecular hydrogen bonds between the resorcinate anions and water molecules. In this way, it was determined that in alkaline aqueous solutions the monoanion and dianion of resorcinol are solvated with two and four molecules of water, respectively. The agreement between the experimentally determined pK(a) values and those reported in the literature demonstrates the applicability and accurateness of the spectroscopic method here used. On the other hand, the agreement between the experimental and theoretically calculated pK(a) values provides solid support for the acid-base reactions proposed in this work.
Spectrochim Acta A Mol Biomol Spectrosc 2005 Jan 01
PMID:Determination of the overlapping pKa values of resorcinol using UV-visible spectroscopy and DFT methods. 1555 26

In this work, the results are presented concerning the influence of time on the spectral behaviour of adrenaline (C(9)H(13)NO(3)) (AD) and of the determination of its acidity constants by means of spectrophotometry titrations and point-by-point analysis, using for the latter freshly prepared samples for each analysis at every single pH. As the catecholamines are sensitive to light, all samples were protected against it during the course of the experiments. Each method rendered four acidity constants corresponding each to the four acid protons belonging to the functional groups present in the molecule; for the point-by-point analysis the values found were: log beta(1) = 38.25 +/- 0.21, log beta(2) = 29.65 +/- 0.17, log beta (3) = 21.01 +/- 0.14, log beta(4) = 11.34 +/- 0.071.
Spectrochim Acta A Mol Biomol Spectrosc 2005 Jan 01
PMID:Study on the stability of adrenaline and on the determination of its acidity constants. 1555 54


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