Structural,genetic and functional characterization of the flagellin glycosylation process in Helicobacter pylori

Mass spectrometry analyses of the complex polar flagella from Helicobacter pylori demonstrated that both FlaA and FlaB proteins are post-translationally modified with pseudaminic acid (Pse5Ac7Ac, 5,7-diacetamido-3,5,7,9-tetradeoxy-l-glycero-l-manno -n o n-ulosonic acid). Unlike Campylobacter, flagellar glycosylation in Helicobacter displays little heterogeneity in isoform or glycoform distribution, although all glycosylation sites are located in the central core region of the protein monomer in a manner similar to that found in Campylobacter. Bioinformatic analysis revealed five genes (HP0840, HP0178, HP0326A, HP0326B, HP0114) homologous to other prokaryote genes previously reported to be involved in motility, flagellar glycosylation or polysaccharide biosynthesis. Insertional mutagenesis of four of these homologues in Helicobacter (HP0178, HP0326A, HP0326B, HP0114) resulted in a non-motile phenotype, no structural flagella filament and only minor amounts of flagellin protein detectable by Western immunoblot. However, mRNA levels for the flagellin structural genes remained unaffected by each mutation. In view of the combined bioinformatic and structural evidence indicating a role for these gene products in glycan biosynthesis, subsequent investigations focused on the functional characterization of the respective gene products. A novel approach was devised to identify biosynthetic sugar nucleotide precursors from intracellular metabolic pools of parent and isogenic mutants using capillary electrophoresis-electrospray mass spectrometry (CE-ESMS) and precursor ion scanning. HP0326A, HP0326B and the HP0178 gene products are directly involved in the biosynthesis of the nucleotide-activated form of Pse, CMP-Pse. Mass spectral analyses of the cytosolic extract from the HP0326A and HP0326B isogenic mutants revealed the accumulation of a mono- and a diacetamido trideoxyhexose UDP sugar nucleotide precursor.     

A functional study of concanavalin A-histamine binding site overlap in Tetrahymena phagocytosis test

Treatment with histamine stimulated the phagocytotic activity of the Tetrahymena to a measurable degree, which was still demonstrable after a week (about 40 generations). Concanavalin A, which binds to the same membrane binding site as histamine, inhibited the stimulatory action of subsequently added histamine, but did not in itself influence phagocytotic activity in any way. The inhibitory effect of Con A on the histamine binding site proved to be dose-dependent. These observations stress the importance of investigating the functional context--as sole realistic measure--of receptor--ligand bindings.     

Structural and functional study of Legionella pneumophila effector RavA

Legionella pneumophila is an intracellular pathogen that causes Legionnaire''s disease in humans. This bacterium can be found in freshwater environments as a free‐living organism, but it is also an intracellular parasite of protozoa. Human infection occurs when inhaled aerosolized pathogen comes into contact with the alveolar mucosa and replicates in alveolar macrophages. Legionella enters the host cell by phagocytosis and redirects the Legionella‐containing phagosomes from the phagocytic maturation pathway. These nascent phagosomes fuse with ER‐derived secretory vesicles and membranes forming the Legionella‐containing vacuole. Legionella subverts many host cellular processes by secreting over 300 effector proteins into the host cell via the Dot/Icm type IV secretion system. The cellular function for many Dot/Icm effectors is still unknown. Here, we present a structural and functional study of L. pneumophila effector RavA (Lpg0008). Structural analysis revealed that the RavA consists of four ~85 residue long α‐helical domains with similar folds, which show only a low level of structural similarity to other protein domains. The ~90 residues long C‐terminal segment is predicted to be natively unfolded. We show that during L. pneumophila infection of human cells, RavA localizes to the Golgi apparatus and to the plasma membrane. The same localization is observed when RavA is expressed in human cells. The localization signal resides within the C‐terminal sequence C⁴⁰⁹WTSFCGLF⁴¹⁷. Yeast‐two‐hybrid screen using RavA as bait identified RAB11A as a potential binding partner. RavA is present in L. pneumophila strains but only distant homologs are found in other Legionella species, where the number of repeats varies.     

Structural and functional study of FK domain of Fstl1

Fstl1 is a TGF‐β superfamily binding protein which involved in many pathological processes. The function of Fstl1 has been widely elucidated, but its structural characterization has not been explored. Here we solved the high‐resolution crystal structure of FK domain of murine Fstl1, analyzed its unique characteristics, and investigated its contribution to the function of full‐length Fstl1. We found that Fstl1‐FK forms a stable dimer in both solution and crystal, which suggest that this protein may function as a dimer during its interaction with TGF‐β, a molecule known to form dimer during activation process. We also found this FK domain is indispensable for the proper function of Fstl1 during the transduction of TGF‐β signaling. These observations provide important insights into the understanding of Fstl1 and may facilitate the exploration of this molecule in clinical study.     

Disorder of the phagocytosis process in alveolar macrophages in thermal injury

Bacteriological assay, cytochemical studies of succinate and malate dehydrogenases, acid phosphatase, glycogen and lipids, as well as electron microscopy were used in experiments on 75 rabbits to examine over time phagocytosis of alveolar macrophages and some mechanisms of its disturbance after burn trauma. It was established that the phagocytic function of alveolar macrophages gets disturbed shortly after trauma, remaining depressed up to the time of convalescence. It was demonstrated that the mechanism by which phagocytic function gets disturbed differs with time following trauma. Primary depression of phagocytosis occurs immediately after burn. At the height of burn disease the cells develop an energy deficient state, whereas the time of convalescence is marked by the emergence of poorly differentiated forms of macrophages having the reduced phagocyte capacity.     

Structural and functional analysis of Tn4430: identification of an integrase-like protein involved in the co-integrate-resolution process

The 4149-bp transposon Tn4430 from Bacillus thuringiensis is delineated by 38-bp inverted repeats and codes for a 113-kd protein that shares homology with the transposases (TnpA) of Tn3, Tn21 and Tn501. Through transpositional recombination, this protein generates the formation of co-integrates between both donor and target replicons, with duplication of Tn4430 molecules. These features are characteristic of transposons of the Tn3 family (class II elements). The second step of the transposition process, the co-integrate resolution, is mediated by a 32-kd protein. This protein (TnpI) displays regional similarities with site-specific recombinases of the integrase family, such as Int of bacteriophage lambda, Cre of bacteriophage P1 or TnpA and TnpB of the Tn554 transposon. Moreover, the 250-bp sequence upstream to the tnpI gene contains several structural features that are reminiscent of the attP attachment site of phage lambda. This unique association between the integrase-like TnpI recombinase and the TnpA transposase qualifies Tn4430 as a member of a new group within the class II mobile genetic elements.     

Effects of the ocean acidification on the functional structure of coral reef nematodes

Coral Reefs - A mesocosm experiment was designed to study the effects of acidification on the phytal nematofauna of a coral reef. We hypothesized that phytal nematodes are responsive to different...     

Ocean acidification induces biochemical and morphological changes in the calcification process of large benthic foraminifera

Large benthic foraminifera are significant contributors to sediment formation on coral reefs, yet they are vulnerable to ocean acidification. Here, we assessed the biochemical and morphological impacts of acidification on the calcification of Amphistegina lessonii and Marginopora vertebralis exposed to different pH conditions. We measured growth rates (surface area and buoyant weight) and Ca-ATPase and Mg-ATPase activities and calculated shell density using micro-computer tomography images. In A. lessonii, we detected a significant decrease in buoyant weight, a reduction in the density of inner skeletal chambers, and an increase of Ca-ATPase and Mg-ATPase activities at pH 7.6 when compared with ambient conditions of pH 8.1. By contrast, M. vertebralis showed an inhibition in Mg-ATPase activity under lowered pH, with growth rate and skeletal density remaining constant. While M. vertebralis is considered to be more sensitive than A. lessonii owing to its high-Mg-calcite skeleton, it appears to be less affected by changes in pH, based on the parameters assessed in this study. We suggest difference in biochemical pathways of calcification as the main factor influencing response to changes in pH levels, and that A. lessonii and M. vertebralis have the ability to regulate biochemical functions to cope with short-term increases in acidity.     

Structural and functional sex differences in the human hypothalamus

Sex differences in the brain may be the basis not only for sex differences in reproduction, gender identity (the feeling of being male or female), and sexual orientation (heterosexuality vs homosexuality), but also for the sex difference in prevalence of psychiatric and neurological diseases ( Swaab and Hofman, 1995 ). In this brief article we discuss a few examples of structural and functional sex differences in the human brain.     

Structural and functional organization of the respiratory center

The main experimental data on the organization of the respiratory center accumulated during the past 200 years are summarized. It is emphasized that the existence of separate, reciprocally interrelated, inspiratory and expiratory centers has never been proved. The notion of multiple respiratory centers in the CNS, including pneumotaxic, apneustic, gasping, and deep-exhalation centers, which allegedly underlie the multiple forms of respiratory movements, is demonstrated to be unjustified. Upon systemic consideration, the evidence in favor of the decisive role of neurons of the pre-Bötzinger complex and preinspiratory neurons in initiating the respiratory rhythm and maintaining rhythm generation in the respiratory center is contradictory and unconvincing. It is assumed that the respiratory center located in the medullary region of the brain of intact animals and humans fulfills the main functions of endogenous self-sustained generation of the respiratory rhythm, chemoregulation, and mechanoregulation in the respiratory system in an integrated manner, according to the general requirements of the body at a given moment.     

Structural and functional properties of the non-muscle tropomyosins

Summary The non-muscle tropomyosins (TMs), isolated from such tissues as platelets, brain and thyroid, are structurally very similar to the muscle TMs, being composed of two highly -helical subunits wound around each other to form a rod-like molecule. The non-muscle TMs are shorter than the muscle TMs; sequence analysis demonstrates that each subunit of equine platelet TM consists of 247 amino acids, 37 fewer than for skeletal muscle TM. The major differences in sequence between platelet and skeletal muscle TM are found near the amino and carboxyl terminal ends of the proteins. Probably as the result of such alterations, the non-muscle TMs aggregate in a linear end-to-end manner much more weakly than do the muscle TMs. Since end-to-end interactions are responsible for the highly cooperative manner in which TM binds to actin, the non-muscle TMs have a lower affinity for actin filaments than do the muscle TMs. However, the attachment of other proteins to actin (e.g. the Tn-I subunit of skeletal muscle troponin or the S-1 subfragment of skeletal muscle myosin) can increase the affinity of actin filaments for non-muscle TM. The non-muscle TMs interact functionally with the Tn-I component of skeletal muscle troponin to inhibit the ATPase activity of muscle actomyosin and with whole troponin to regulate the muscle actomyosin ATPase in a Ca⁺⁺-dependent manner, even though one of the binding sites for troponin on skeletal TM is missing in non-muscle TM. A novel actomyosin regulatory system can be produced using Tn-I, calmodulin and non-muscle TM; in this case inhibition is released when the non-muscle TM detaches from the actin filament in the presence of Ca⁺⁺. Although it has not yet been demonstrated that the non-muscle TMs participate in a Ca⁺⁺-dependent contractile regulatory system in vivo it does appear that they are associated with actin filaments in vivo.     

Structural and functional topography of the human ribosome

This review covers data on the structural organization of functional sites in the human ribosome, namely, the messenger RNA binding center, the binding site of the hepatitis C virus RNA internal ribosome entry site, and the peptidyl transferase center. The data summarized here have been obtained primarily by means of a site-directed cross-linking approach with application of the analogs of the respective ribosomal ligands bearing cross-linkers at the designed positions. These data are discussed taking into consideration available structural data on ribosomes from various kingdoms obtained with the use of cryo-electron microscopy, X-ray crystallography, and other approaches.     

Structural and functional implications of the hexokinase-nickel interaction

The interaction between nickel and yeast hexokinase was studied. The binding of nickel showed a positive cooperativity, and saturation was not reached. The nickel binding induced modifications in the secondary structure of the protein; thus, a lost of alpha helix and beta turns, as well as an increase of the random structure and beta sheet was observed. The monomer/dimmer equilibrium of the protein was modified in the presence of nickel, and the monomer state was mainly obtained at the highest nickel concentrations studied. These changes on the protein structure caused a decrease in the enzyme activity. According to kinetic studies, nickel caused a non-competitive inhibition when glucose was the variable substrate and a linear competitive inhibition when ATP was the variable substrate.     

Structural and functional units in the pial microvascular system

A study was made of the pial arterial microcircles formed upon successive branching and anastomosing of the terminal pial vessels on the brain cortex surface at different levels of the phylogenetic development of the vertebrata. It was discovered that the pial arterial microcircles progressively become more complicated in the following order: chicken, rabbit, cat, dog, monkey. The morphological signs of the microcircles undergo progressive development: 1) they are formed primarily from small pial arterial branches possessing high vasomotor activity; 2) the area of each circle becomes less and less and their amount per unit of the brain surface increases respectively; 3) the quantity of the feeding arterial branches rises despite the reduction of the circle size; 4) the number of outgoing precortical and radial arteries entering the brain cortex increases; 5) the areas of the brain cortex supplied by individual radial arteries become less and less. This ensures increasingly delicate regulation of adequate blood supply of the smallest areas of the brain cortex.     

Structural and functional diversity of the microbial kinome

The eukaryotic protein kinase (ePK) domain mediates the majority of signaling and coordination of complex events in eukaryotes. By contrast, most bacterial signaling is thought to occur through structurally unrelated histidine kinases, though some ePK-like kinases (ELKs) and small molecule kinases are known in bacteria. Our analysis of the Global Ocean Sampling (GOS) dataset reveals that ELKs are as prevalent as histidine kinases and may play an equally important role in prokaryotic behavior. By combining GOS and public databases, we show that the ePK is just one subset of a diverse superfamily of enzymes built on a common protein kinase-like (PKL) fold. We explored this huge phylogenetic and functional space to cast light on the ancient evolution of this superfamily, its mechanistic core, and the structural basis for its observed diversity. We cataloged 27,677 ePKs and 18,699 ELKs, and classified them into 20 highly distinct families whose known members suggest regulatory functions. GOS data more than tripled the count of ELK sequences and enabled the discovery of novel families and classification and analysis of all ELKs. Comparison between and within families revealed ten key residues that are highly conserved across families. However, all but one of the ten residues has been eliminated in one family or another, indicating great functional plasticity. We show that loss of a catalytic lysine in two families is compensated by distinct mechanisms both involving other key motifs. This diverse superfamily serves as a model for further structural and functional analysis of enzyme evolution.     

Structural and functional analysis of the sarcoglycan-sarcospan subcomplex

Sarcospan is a component of the dystrophin-glycoprotein complex that forms a tight subcomplex with the sarcoglycans. The sarcoglycan-sarcospan subcomplex functions to stabilize α-dystroglycan at the plasma membrane and perturbations of this subcomplex are associated with autosomal recessive limb-girdle muscular dystrophy. In order to characterize protein interactions within this subcomplex, we first demonstrate that sarcospan forms homo-oligomers within the membrane. Experiments with a panel of site-directed mutants reveal that proper structure of the large extracellular loop is an important determinant of oligo formation. Furthermore, the intracellular N- and C-termini contribute to stability of sarcospan-mediated webs. Point mutation of each cysteine residue reveals that Cys 162 and Cys 164 within the large extracellular loop form disulfide bridges, which are critical for proper sarcospan structure. The extracellular domain of sarcospan also forms the main binding site for the sarcoglycans. We propose a model whereby sarcospan forms homo-oligomers that cluster the components of the dystrophin-glycoprotein complex within the membrane.