Probing the active site of the sugar isomerase domain from E. coli arabinose-5-phosphate isomerase via X-ray crystallography

Lipopolysaccharide (LPS) biosynthesis represents an underexploited target pathway for novel antimicrobial development to combat the emergence of multidrug‐resistant bacteria. A key player in LPS synthesis is the enzyme D ‐arabinose‐5‐phosphate isomerase (API), which catalyzes the reversible isomerization of D ‐ribulose‐5‐phosphate to D ‐arabinose‐5‐phosphate, a precursor of 3‐deoxy‐D ‐manno‐octulosonate that is an essential residue of the LPS inner core. API is composed of two main domains: an N‐terminal sugar isomerase domain (SIS) and a pair of cystathionine‐β‐synthase domains of unknown function. As the three‐dimensional structure of an enzyme is a prerequisite for the rational development of novel inhibitors, we present here the crystal structure of the SIS domain of a catalytic mutant (K59A) of E. coli D ‐arabinose‐5‐phosphate isomerase at 2.6‐Å resolution. Our structural analyses and comparisons made with other SIS domains highlight several potentially important active site residues. In particular, the crystal structure allowed us to identify a previously unpredicted His residue (H88) located at the mouth of the active site cavity as a possible catalytic residue. On the basis of such structural data, subsequently supported by biochemical and mutational experiments, we confirm the catalytic role of H88, which appears to be a generally conserved residue among two‐domain isomerases.     

The body size of the New Zealand orb-weaving spider Waitkera waitakerensis (Uloboridae) is directly related to temperature and affects fecundity

Abstract. Waitkera waitakerensis occupies lowland forests of New Zealand's North Island, where temperatures decrease in a southwestward direction. The mean annual temperatures of 18 collecting sites, as extracted from GIS data, are directly related to the first femur length of adult females. Neither site elevation nor phylogeny affected spider size or other variables examined. The direct relationship between spider body size and environmental temperature followed a pattern observed in other terrestrial arthropods with a univoltine life cycle and can probably be explained by the longer growing season of warmer regions. Egg diameter was uniform across the species. Site temperature and female first femur length were each directly related to the number of eggs deposited in egg sacs. The date of egg sac collection was inversely related to egg number, suggesting that clutch size declines during the reproductive season. Females deposit eggs beneath a triangular platform and then cover them with a lower silk sheet. The area of this upper platform and the volume of the egg sac were each directly related to egg number, but not to female first femur length. The depth of the lower covering was not related to egg number or to spider first femur length. This suggests that spiders use information about the volume of eggs in their abdomens to construct an egg sac whose volume will accommodate the volume of eggs to be laid and that females do so principally by adjusting the size of the sac's upper triangular platform.     

Synthesis of sulfonamide-containing N-hydroxyindole-2-carboxylates as inhibitors of human lactate dehydrogenase-isoform 5

N-Hydroxyindole-2-carboxylates possessing sulfonamide-substituents at either position 5 or 6 were designed and synthesized. The inhibitory activities of these compounds against isoforms 1 and 5 of human lactate dehydrogenase were analysed, and K_i values of the most efficient inhibitors were determined by standard enzyme kinetic studies. Some of these compounds displayed state-of-the-art inhibitory potencies against isoform 5 (K_i values as low as 5.6 μM) and behaved as competitive inhibitors versus both the substrate and the cofactor.     

Phosphatidylcholine and phosphatidylethanolamine content of partially synchronized rice cell suspension cultures

Knowledge of phospholipids in relation to cell cycle phases would facilitate the manipulation of tissue culture cells for crop improvement. Rice cells, Oryza sativa L. introduction PI 353–705, were initiated from anther cultures and grown as liquid suspensions. Replicate cultures were harvested for analysis at various time periods up to 21 days. Phosphatidylcholine (PC) and phosphatidylethanolamine (PEA) content rapidly increased 2.5 fold by 3 days, follwed by a progressive decrease in both compounds to 15 days to below initial transfer levels. There was an increase in PC and PEA back to transfer levels from 16 to 21 days. Cells in the linear phase were transferrred 11 days after inoculation to media minus sucrose. Carbohydrate starvation of the cells and subsequent release from inhibition with 3% sucrose resulted in partially synchronized cultures as seen by rapid [³H]-thymidine incorporation up to 24 h followed by a decrease to a minimum at 72 h. Phosphatidylcholine and phosphatidylethanolamine increased linearly throughout the DNA synthesis period in synchronized cells, reaching a maximum at 48 h and 60 h, respectively. The levels of both compounds 72 h after release from sucrose starvation are only 30% of non-starved controls 72 h after transfer to fresh media.     

Structural bases for heme binding and diatomic ligand recognition in truncated hemoglobins

Truncated hemoglobins (trHbs) are low-molecular-weight oxygen-binding heme-proteins distributed in eubacteria, cyanobacteria, unicellular eukaryotes, and in higher plants, constituting a distinct group within the hemoglobin (Hb) superfamily. TrHbs display amino acid sequences 20-40 residues shorter than classical (non)vertebrate Hbs and myoglobins, to which they are scarcely related by sequence similarity. The trHb tertiary structure is based on a 2-on-2 alpha-helical sandwich, which represents a striking editing of the highly conserved 3-on-3 alpha-helical globin fold, achieved through deletion/truncation of alpha-helices and specific residue substitutions. Despite their 'minimal' polypeptide chain span, trHbs display an inner tunnel/cavity system held to support ligand diffusion to/from the heme distal pocket, accumulation of heme ligands within the protein matrix, and/or multiligand reactions. Moreover, trHbs bind and effectively stabilize the heme and recognize diatomic ligands (i.e., O2, CO, NO, and cyanide), albeit with varying thermodynamic and kinetic parameters. Here, structural bases for heme binding and diatomic ligand recognition by trHbs are reviewed.     

The dependence of leaf hydraulic conductance on irradiance during HPFM measurements: any role for stomatal response?

This paper examines the dependence of whole leaf hydraulic conductance to liquid water (K(L)) on irradiance when measured with a high pressure flowmeter (HPFM). During HPFM measurements, water is perfused into leaves faster than it evaporates hence water infiltrates leaf air spaces and must pass through stomates in the liquid state. Since stomates open and close under high versus low irradiance, respectively, the possibility exists that K(L) might change with irradiance if stomates close tightly enough to restrict water movement. However, the dependence of K(L) on irradiance could be due to a direct effect of irradiance on the hydraulic properties of other tissues in the leaf. In the present study, K(L) increased with irradiance for 6 of the 11 species tested. Whole leaf conductance to water vapour, g(L), was used as a proxy for stomatal aperture and the time-course of changes in K(L) and g(L) was studied during the transition from low to high irradiance and from high to low irradiance. Experiments showed that in some species K(L) changes were not paralleled by g(L) changes. Measurements were also done after perfusion of leaves with ABA which inhibited the g(L) response to irradiance. These leaves showed the same K(L) response to irradiance as control leaves. These experimental results and theoretical calculations suggest that the irradiance dependence of K(L) is more consistent with an effect on extravascular (and/or vascular) tissues rather than stomatal aperture. Irradiance-mediated stimulation of aquaporins or hydrogel effects in leaf tracheids may be involved.     

Systemic dysregulation of CEACAM1 in melanoma patients

It was previously shown that CEACAM1 on melanoma cells strongly predicts poor outcome. Here, we show a statistically significant increase of serum CEACAM1 in 64 active melanoma patients, as compared to 48 patients with no evidence of disease and 37 healthy donors. Among active patients, higher serum CEACAM1 correlated with LDH values and with decreased survival. Multivariate analysis with neutralization of LDH showed that increased serum CEACAM1 carries a hazard ratio of 2.40. In vitro, soluble CEACAM1 was derived from CEACAM1(+), but neither from CEACAM1(?) melanoma cells nor from CEACAM1(+) lymphocytes, and directly correlated with the number of CEACAM1(+) melanoma cells. Production of soluble CEACAM1 depended on intact de novo protein synthesis and secretion machineries, but not on metalloproteinase function. An unusually high percentage of CEACAM1(+) circulating NK and T lymphocytes was demonstrated in melanoma patients. CEACAM1 inhibited killing activity in functional assays. CEACAM1 expression could not be induced on lymphocytes by serum from patients with high CEACAM1 expression. Further, expression of other NK receptors was impaired, which collectively indicate on a general abnormality. In conclusion, the systemic dysregulation of CEACAM1 in melanoma patients further denotes the role of CEACAM1 in melanoma and may provide a basis for new tumor monitoring and prognostic platforms.     

Two distinct heme distal site states define Cerebratulus lacteus mini-hemoglobin oxygen affinity

The nerve tissue hemoglobin of Cerebratulus lacteus (CerHb) is the smallest naturally occurring known hemoglobin. Stabilization of the diatomic bound species (e.g., O(2)) is achieved through a network of hydrogen bonds based on three key residues TyrB10, GlnE7, and ThrE11. The first two residues are typically associated in hemoglobins with enhanced O(2) affinity, related to hydrogen bond stabilization of the heme-bound O(2) resulting in a decrease of the ligand dissociation rates. In contrast to the above observations, the affinity of CerHb for O(2) is only moderate, and the rate of O(2) dissociation is unexpectedly high. To gain insight on the diverse molecular mechanisms controlling ligand affinities, we have analyzed w.t. CerHb and its ThrE11-->Val mutant by means of joint molecular dynamics and quantum mechanics simulation techniques, complementing recent site-directed mutagenesis experiments. Our results suggest that the observed O(2) dissociation rates can only be explained through a dynamic equilibrium between high and low affinity states of the w.t. CerHb heme distal site.     

XHas2 activity is required during somitogenesis and precursor cell migration in Xenopus development

In vertebrates, hyaluronan biosynthesis is regulated by three transmembrane catalytic enzymes denoted Has1, Has2 and Has3. We have previously cloned the Xenopus orthologues of the corresponding genes and defined their spatiotemporal distribution during development. During mammalian embryogenesis, Has2 activity is known to be crucial, as its abrogation in mice leads to early embryonic lethality. Here, we show that, in Xenopus, morpholino-mediated loss-of-function of XHas2 alters somitogenesis by causing a disruption of the metameric somitic pattern and leads to a defective myogenesis. In the absence of XHas2, early myoblasts underwent apoptosis, failing to complete their muscle differentiation programme. XHas2 activity is also required for migration of hypaxial muscle cells and trunk neural crest cells (NCC). To approach the mechanism whereby loss of HA, following XHas2 knockdown, could influence somitogenesis and precursor cell migration, we cloned the orthologue of the primary HA signalling receptor CD44 and addressed its function through an analogous knockdown approach. Loss of XCD44 did not disturb somitogenesis, but strongly impaired hypaxial muscle precursor cell migration and the subsequent formation of the ventral body wall musculature. In contrast to XHas2, loss of function of XCD44 did not seem to be essential for trunk NCC migration, suggesting that the HA dependence of NCC movement was rather associated with an altered macromolecular composition of the ECM structuring the cells' migratory pathways. The presented results, extend our knowledge on Has2 function and, for the first time, demonstrate a developmental role for CD44 in vertebrates. On the whole, these data underlie and confirm the emerging importance of cell-ECM interactions and modulation during embryonic development.