Analysis of phylogenetically reconstructed mutational spectra in human mitochondrial DNA control region

Analysis of mutations in mitochondrial DNA is an important issue in population and evolutionary genetics. To study spontaneous base substitutions in human mitochondrial DNA we reconstructed the mutational spectra of the hypervariable segments I and II (HVS I and II) using published data on polymorphisms from various human populations. An excess of pyrimidine transitions was found both in HVS I and II regions. By means of classification analysis numerous mutational hotspots were revealed in these spectra. Context analysis of hotspots revealed a complex influence of neighboring bases on mutagenesis in the HVS I region. Further statistical analysis suggested that a transient misalignment dislocation mutagenesis operating in monotonous runs of nucleotides play an important role for generating base substitutions in mitochondrial DNA and define context properties of mtDNA. Our results suggest that dislocation mutagenesis in HVS I and II is a fingerprint of errors produced by DNA polymerase gamma in the course of human mitochondrial DNA replication     

Domain closure,substrate specificity and catalysis of D-lactate dehydrogenase from Lactobacillus bulgaricus

NAD-dependent Lactobacillus bulgaricus D-Lactate dehydrogenase (D-LDHb) catalyses the reversible conversion of pyruvate into D-lactate. Crystals of D-LDHb complexed with NADH were grown and X-ray data collected to 2.2 A. The structure of D-LDHb was solved by molecular replacement using the dimeric Lactobacillus helveticus D-LDH as a model and was refined to an R-factor of 20.7%. The two subunits of the enzyme display strong asymmetry due to different crystal environments. The opening angles of the two catalytic domains with respect to the core coenzyme binding domains differ by 16 degrees. Subunit A is in an "open" conformation typical for a dehydrogenase apo enzyme and subunit B is "closed". The NADH-binding site in subunit A is only 30% occupied, while in subunit B it is fully occupied and there is a sulphate ion in the substrate-binding pocket. A pyruvate molecule has been modelled in the active site and its orientation is in agreement with existing kinetic and structural data. On domain closure, a cluster of hydrophobic residues packs tightly around the methyl group of the modelled pyruvate molecule. At least three residues from this cluster govern the substrate specificity. Substrate binding itself contributes to the stabilisation of domain closure and activation of the enzyme. In pyruvate reduction, D-LDH can adapt another protonated residue, a lysine residue, to accomplish the role of the acid catalyst His296. Required lowering of the lysine pK(a) value is explained on the basis of the H296K mutant structure.     

Molecular dynamics and IR spectroscopy in investigation of phase transitions in molecular crystal 4,4'-bis(11-hydroxy-1-undecyloxy)biphenyl

Molecular dynamics (MD) simulations combined with temperature-dependent IR spectroscopic measurements were used to study phase transitions in molecular crystals of the mesogenic diol 4,4'-bis(11-hydroxy-1-undecyloxy)biphenyl. DSC measurements revealed four phase transitions in this molecular crystal at approximately 327.1 K, 389.8 K, 419.1 K and 431.9 K. Analysis of the dynamic trajectories at temperatures of 300 K, 360 K, 400 K and 480 K revealed changes in conformation of the mesogenic diol molecules and consequently changes in crystal packing and crystal structure in the temperature range 300-480 K and enabled us to understand the mechanism of the phase transitions.     

Structure analysis of montmorillonite intercalated with rhodamine B: modeling and experiment

The intercalation process and the structure of montmorillonite intercalated with [rhodamine B]+ cations have been investigated using molecular modeling (molecular mechanics and molecular dynamics simulations), X-ray powder diffraction and IR spectroscopy. The structure of the intercalate depends strongly on the concentration of rhodamine B in the intercalation solution. The presence of two phases in the intercalated structure was revealed by modeling and X-ray powder diffraction: (i) phase with basal spacing 18 A and with bilayer arrangement of guests and (ii) phase with average basal spacing 23 A and with monolayer arrangement of guests. In both phases the monomeric and dimeric arrangement can coexist in the interlayer space. Three types of dimers in the interlayer structure have been found by modeling: (i) H-dimer (head-to-head arrangement) present in the 18 A phase, (ii) sandwich type of the head-to-tail arrangement (present in the 23 A phase) and (iii) J-dimer (head-to-tail arrangement) present in the 23 A phase. Figure Montmorillonite intercalated with rhodamine B cations. On the left: phase 18 A, bilayer dimeric arrangement of guests (H-dimers). On the right: phase 23 A, monolayer arrangement of guests prepared using intercalation solution with a low concentration of rhodamine B     

Differential effect of phosphatidylethanolamine depletion on raft proteins: further evidence for diversity of rafts in Saccharomyces cerevisiae

A considerable amount of evidence supports the idea that lipid rafts are involved in many cellular processes, including protein sorting and trafficking. We show that, in this process, also a non-raft lipid, phosphatidylethanolamine (PE), has an indispensable function. The depletion of this phospholipid results in an accumulation of a typical raft-resident, the arginine transporter Can1p, in the membranes of Golgi, while the trafficking of another plasma membrane transporter, Pma1p, is interrupted at the level of the ER. Both these transporters associate with a Triton (TX-100) resistant membrane fraction before their intracellular transport is arrested in the respective organelles. The Can1p undelivered to the plasma membrane is fully active when reconstituted to a PE-containing vesicle system in vitro. We further demonstrate that, in addition to the TX-100 resistance at 4 degrees C, Can1p and Pma1pa exhibit different accessibility to nonyl glucoside (NG), which points to distinct intimate lipid surroundings of these two proteins. Also, at 20 degrees C, these two proteins are extracted by TX-100 differentially. The features above suggest that Pma1p and Can1p are associated with different compartments. This is independently supported by the observations made by confocal microscopy. In addition we show that PE is involved in the stability of Can1p-raft association.     

Multiple cathepsin B isoforms in schistosomula of Trichobilharzia regenti: identification, characterisation and putative role in migration and nutrition

Among schistosomatids, Trichobilharzia regenti, displays an unusual migration through the peripheral and central nervous system prior to residence in the nasal cavity of the definitive avian host. Migration causes tissue degradation and neuromotor dysfunction both in birds and experimentally infected mice. Although schistosomula have a well-developed gut, the peptidases elaborated that might facilitate nutrition and migration are unknown. This is, in large part, due to the difficulty in isolating large numbers of migrating larvae. We have identified and characterised the major 33 kDa cathepsin B-like cysteine endopeptidase in extracts of migrating schistosomula using fluorogenic peptidyl substrates with high extinction coefficients and irreversible affinity-labels. From first strand schistosomula cDNA, degenerate PCR and Rapid Amplification of cDNA End protocols were used to identify peptidase isoforms termed TrCB1.1-TrCB1.6. Highest sequence homology is to the described Schistosoma mansoni and Schistosoma japonicum cathepsins B1. Two isoforms (TrCB1.5 and 1.6) encode putatively inactive enzymes as the catalytic cysteine is substituted by glycine. Two other isoforms, TrCB1.1 and 1.4, were functionally expressed as zymogens in Pichia pastoris. Specific polyclonal antibodies localised the peptidases exclusively in the gut of schistosomula and reacted with a 33kDa protein in worm extracts. TrCB1.1 zymogen was unable to catalyse its own activation, but was trans-processed and activated by S. mansoni asparaginyl endopeptidase (SmAE aka. S. mansoni legumain). In contrast, TrCB1.4 zymogen auto-activated, but was resistant to the action of SmAE. Both activated isoforms displayed different pH-dependent specificity profiles with peptidyl substrates. Also, both isoforms degraded myelin basic protein, the major protein component of nervous tissue, but were inefficient against hemoglobin, thus supporting the adaptation of T. regenti gut peptidases to parasitism of host nervous tissue.     

Microflora of the honeybee gastrointestinal tract

Microorganisms in the midgut and rectum of the honeybee were enumerated and characterized. Counts of aerobic microorganisms were distinctly lower than counts of anaerobes (10(5)-10(6) viable cells per g of intestinal content vs. 10(8)-10(9) per g). Total numbers of anaerobic microorganisms were almost identical with the count of anaerobic Gram-positive acid resistant rods. A higher number of coliform bacteria and Bacillus spp. was detected in the rectum (10(5) per g). Anaerobic and aerobic microorganisms, coliforms, enterococci, Bacillus spp., Pseudomonas spp. and yeasts were found in all bees; lactobacilli, staphylococci and moulds were not found.     

Structural basis of the 14-3-3 protein-dependent activation of yeast neutral trehalase Nth1

Background

Trehalases are highly conserved enzymes catalyzing the hydrolysis of trehalose in a wide range of organisms. The activity of yeast neutral trehalase Nth1 is regulated in a 14-3-3- and a calcium-dependent manner. The Bmh proteins (the yeast 14-3-3 isoforms) recognize phosphorylated Nth1 and enhance its enzymatic activity through an unknown mechanism.

Methods

To investigate the structural basis of interaction between Nth1 and Bmh1, we used hydrogen/deuterium exchange coupled to mass spectrometry, circular dichroism spectroscopy and homology modeling to identify structural changes occurring upon the complex formation.

Results

Our results show that the Bmh1 protein binding affects structural properties of several regions of phosphorylated Nth1: the N-terminal segment containing phosphorylation sites responsible for Nth1 binding to Bmh, the region containing the calcium binding domain, and segments surrounding the active site of the catalytic trehalase domain. The complex formation between Bmh1 and phosphorylated Nth1, however, is not accompanied by the change in the secondary structure composition but rather the change in the tertiary structure.

Conclusions

The 14-3-3 protein-dependent activation of Nth1 is based on the structural change of both the calcium binding domain and the catalytic trehalase domain. These changes likely increase the accessibility of the active site, thus resulting in Nth1 activation.

General significance

The results presented here provide a structural view of the 14-3-3 protein-dependent activation of yeast neutral trehalase Nth1, which might be relevant to understand the process of Nth1 activity regulation as well as the role of the 14-3-3 proteins in the regulation of other enzymes.