Non-heme iron through the three domains of life

Metalloproteins are proteins capable of binding one or more metal ions, which are often required for their biological function or for regulation of their activities or for structural purposes. In high-throughput genome-level protein investigation efforts, such as Structural Genomics, the systematic experimental characterization of metal-binding properties (i.e. the investigation of the metalloproteome) is not always pursued, and remains far from trivial. In the present work we have applied a bioinformatic approach to investigate the occurrence of (putative) non-heme iron-binding proteins in 57 different organisms spanning the entire tree of life. It is found that the non-heme iron-proteome constitutes between 1% and 10% of the entire proteome of an organism. However, the iron-proteome constitutes a higher fraction of the proteome in archaea (on average 7.1% +/- 2.1%) than in bacteria (3.9% +/- 1.6%) and in eukaryota (1.1% +/- 0.4%). The analysis of the function of each putative iron-protein identified suggests that extant organisms have inherited the large majority of their iron-proteome from the last common ancestor.     

A model of the complex between the PfEMP1 malaria protein and the human ICAM-1 receptor

Malaria is caused by protozoan parasites of the genus Plasmodium. Four species of Plasmodium can infect humans: P. falciparum, P. malariae, P. vivax, and P. ovale. P. falciparum is the only able to cytoadhere to the surface of postcapillary endothelial cells. A key role in cytoadherence is played by the interaction between the PfEMP1 P. falciparum protein and the human intracellular adhesion molecule (ICAM-1) although very little is known about the molecular details of this complex. Here we propose a model for this interaction on the basis of a homology model of the functional domain of PfEMP1 and of the ICAM-1 three dimensional structures. Our model is consistent with the results of many experimental observations, provides a rational explanation for the different binding abilities of different strains of P. falciparum and explains the reduced binding affinity of the A4 strain of P. falciparum for the ICAM-1(Kilifi) polymorphism. On the basis of our model, we can also explain why the murine ICAM-1, although sharing 70% sequence similarity with its human homologue, does not bind PfEMP1, and why the binding of fibrinogen and PfEMP1 to ICAM-1 is mutually exclusive. The model of the complex proposed here can serve as a useful tool for the design and interpretation of biochemical and immunological experimental results.     

Evaluating the effects of gross nitrogen mineralization,immobilization, and nitrification on nitrogen fertilizer availability in soil experimentally contaminated with diesel

Sandy clay loam soil was contaminated with 5000 mg kg⁻¹ diesel, and amended with nitrogen (15.98 atom% ¹⁵N) at 0, 250, 500, and 1000 mg kg⁻¹ to determine gross rates of nitrogen transformations during diesel biodegradation at varying soil water potentials. The observed water potential values were −0.20, −0.47, −0.85, and −1.50 MPa in the 0, 250, 500, and 1000 mg kg⁻¹ nitrogen treatments respectively. Highest microbial respiration occurred in the lowest nitrogen treatment suggesting an inhibitory osmotic effect from higher rates of nitrogen application. Microbial respiration rates of 185, 169, 131, and 116 mg O₂ kg⁻¹ soil day⁻¹ were observed in the 250, 500, control and 1000 mg kg⁻¹ nitrogen treatments, respectively. Gross nitrification was inversely related to water potential with rates of 0.2, 0.04, and 0.004 mg N kg⁻¹ soil day⁻¹ in the 250, 500, and 1000 mg kg⁻¹ nitrogen treatments, respectively. Reduction in water potential did not inhibit gross nitrogen immobilization or mineralization, with respective immobilization rates of 2.2, 1.8, and 1.8 mg N kg⁻¹ soil day⁻¹, and mineralization rates of 0.5, 0.3, and 0.3 mg N kg⁻¹ soil day⁻¹ in the 1000, 500, and 250 mg kg⁻¹ nitrogen treatments, respectively. Based on nitrogen transformation rates, the duration of fertilizer contribution to the inorganic nitrogen pool was estimated at 0.9, 1.9, and 3.2 years in the 250, 500, and 1000 mg kg⁻¹ nitrogen treatments, respectively. The estimation was conservative as ammonium fixation, gross nitrogen immobilization, and nitrification were considered losses of fertilizer with only gross mineralization of organic nitrogen contributing to the most active portion of the nitrogen pool.     

Seed abortion in the sexual counterpart of <Emphasis Type="Italic">Brachiaria brizantha</Emphasis> apomicts (Poaceae)

Gametophytic organization, fertilization and reproductive success are described for the fertile diploid Brachiaria brizantha accession BRA-002747 which is being raised for use in Brachiaria breeding programs, as well as to understand and control of apomixis in this genus. The current paper reports on reproductive biology and analysis of seed set in field experiments during three consecutive years. Unsuccessful seed production in this plant is believed to correlate with early inbreeding depression, based on the reproductive features analyzed. Caryopsis development was observed using differential interference contrast microscopy with seed set determined by the number of self- and open-pollinated pistils that fully developed into viable seeds. Developing and mature female and male gametophytes were observed in the context of flower phenology, morphology and anthesis patterns. Pollen viability was determined by acetocarmine staining and by observation of germination in vivo, which was also used to observe pollen tube/pistil interaction. Although normal development was observed in floral structures, anthesis and gametophytes, seed set was low, with 2 and 6% in self- and open-pollination, respectively, producing seed. Variations observed in the female organs, such as the presence of a hermaphrodite flower in 50% of the inferior floscules and the presence of multiple embryo sacs of the Polygonum type within the same ovule in 15% of the pistils, are not related to low fertility. The majority of pollen grains are viable, in spite of the reduced number of pollen tubes within the style and ovary carpel, and a developing caryopsis was observed in 70% of self-pollinated pistils, indicating successful double fertilization from 2 days after anthesis (DAA). Nevertheless, abortion gradually increased from 2 until 7 DAA and remains elevated until 12 DAA, when caryopsis maturity is achieved. These data confirm low seed set in this accession and indicate that low fertility is not a consequence of abnormalities, either in the floral or gamete structures, or pollen tube rejection, but most likely a consequence of inbreeding depression.     

Thyroid hormone receptor α1 is a critical regulator for the expression of ion channels during final differentiation of outer hair cells

Cochlear outer hair cells (OHCs) terminally differentiate prior to the onset of hearing. During this time period, thyroid hormone (TH) dramatically influences inner ear development. It has been shown recently that TH enhances the expression of the motor protein prestin via liganded TH receptor β (TRβ) while in contrast the expression of the potassium channel KCNQ4 is repressed by unliganded TRα1. These different mechanisms of TH regulation by TRα1 or TRβ prompted us to analyse other ion channels that are required for the final differentiation of OHCs. We analysed the onset of expression of the Ca²⁺ channel Ca_V1.3, and the K⁺ channels SK2 and BK and correlated the results with the regulation via TRα1 or TRβ. The data support the hypothesis that proteins expressed in rodents prior to or briefly after birth like Ca_V1.3 and prestin are either independent of TH (e.g. Ca_V1.3) or enhanced through TRβ (e.g. prestin). In contrast, proteins expressed in rodents later than P6 like KCNQ4 (∼P6), SK2 (∼P9) and BK (∼P11) are repressed through TRα1. We hypothesise that the precise regulation of expression of the latter genes requires a critical local TH level to overcome the TRα1 repression. Harald Winter and Claudia Braig contributed equally to this work.     

Physicochemical and MRI characterization of Gd<Superscript>3+</Superscript>-loaded polyamidoamine and hyperbranched dendrimers

Generation 4 polyamidoamine (PAMAM) and, for the first time, hyperbranched poly(ethylene imine) or polyglycerol dendrimers have been loaded with Gd³⁺ chelates, and the macromolecular adducts have been studied in vitro and in vivo with regard to MRI contrast agent applications. The Gd³⁺ chelator was either a tetraazatetracarboxylate DOTA-pBn⁴⁻ or a tetraazatricarboxylate monoamide DO3A-MA³⁻ unit. The water exchange rate was determined from a ¹⁷O NMR and ¹H Nuclear Magnetic Relaxation Dispersion study for the corresponding monomer analogues [Gd(DO3A-AEM)(H₂O)] and [Gd(DOTA-pBn-NH₂)(H₂O)]⁻ (k _ex²⁹⁸ = 3.4 and 6.6 × 10⁶ s⁻¹, respectively), where H₃DO3A-AEM is {4-[(2-acetylaminoethylcarbamoyl)methyl]-7,10-bis(carboxymethyl-1,4,7,10-tetraazacyclododec-1-yl)}-acetic acid and H₄DOTA-pBn-NH₂ is 2-(4-aminobenzyl)-1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid. For the macromolecular complexes, variable-field proton relaxivities have been measured and analyzed in terms of local and global motional dynamics by using the Lipari–Szabo approach. At frequencies below 100 MHz, the proton relaxivities are twice as high for the dendrimers loaded with the negatively charged Gd(DOTA-pBn)⁻ in comparison with the analogous molecule bearing the neutral Gd(DO3A-MA). We explained this difference by the different rotational dynamics: the much slower motion of Gd(DOTA-pBn)⁻-loaded dendrimers is likely related to the negative charge of the chelate which creates more rigidity and increases the overall size of the macromolecule compared with dendrimers loaded with the neutral Gd(DO3A-MA). Attachment of poly(ethylene glycol) chains to the dendrimers does not influence relaxivity. Both hyperbranched structures were found to be as good scaffolds as regular PAMAM dendrimers in terms of the proton relaxivity of the Gd³⁺ complexes. The in vivo MRI studies on tumor-bearing mice at 4.7 T proved that all dendrimeric complexes are suitable for angiography and for the study of vasculature parameters like blood volume and permeability of tumor vessels. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Enteropathogenic Escherichia coli Tir is an SH2/3 ligand that recruits and activates tyrosine kinases required for pedestal formation

Enteropathogenic Escherichia coli (EPEC) cause intestinal inflammation, severe diarrhoea and mortality, particularly among children in developing nations. Upon attachment to intestinal epithelial cells, EPEC induces actin-filled membrane protrusions called 'pedestals' and disrupts microvilli to form attaching and effacing (A/E) lesions. EPEC also disrupts epithelial barrier function and causes colitis. Here we have investigated how virulence factors which orchestrate formation of actin pedestals interface with host tyrosine kinases. We show that Tec-family tyrosine kinases localize beneath EPEC and, with Abl-family kinases, comprise a set of redundant host kinases utilized by EPEC to form actin pedestals. We also show that Tir, a virulence factor required for pathogenesis, contains a polyproline region (PPR) that interacts with SH3 domains of redundant kinases, and a phosphorylation site (Y474) that interacts with kinase SH2 domains. These interactions are essential for pedestal formation, and mimic activation of kinases by cellular ligands. Our results suggest that a positive feedback loop exists in which initial phosphorylation of Tir on Y474 by tyrosine kinases causes recruitment of additional redundant kinases via PPR-SH3 interactions and PO(3)-Y474-SH2 interactions, which in turn phosphorylate other Tir molecules as well as proteins that catalyse formation of actin pedestals.     

The growth-hormone inducible transmembrane protein (Ghitm) belongs to the Bax inhibitory protein-like family

The conserved protein domain UPF0005 is a protein family signature distributed among many species including fungi and bacteria. Although of unknown functionality this motif has been found in newly identified antiapoptotic proteins comprising the BI-1 family, namely Bax-inhibitory Protein-1 (BI-1), Lifeguard (LFG), and h-GAAP. In a search for vertebrate proteins presumably belonging to the BI-1 family, we found that Growth-hormone inducible transmembrane protein (Ghitm) is another prospective member of the BI-1 family. Here we characterise Ghitm in a first analysis regarding its phylogeny, expression in cancer cell lines, and proteomical properties.     

Immunology of pregnancy: cellular mechanisms allowing fetal survival within the maternal uterus

Pregnancy success remains a fascinating phenomenon to immunologists as it defies the immunological rules of rejection. Although it was previously thought that the maternal immune system does not see the fetus, it is now well documented that fetal cells reach the maternal body and encounter host immune cells. Natural tolerance mechanisms following this interaction remain to be fully elucidated. This article reviews the current literature on mechanisms of adaptive immunity, with emphasis on regulatory T cells and heme oxygenase 1 (HO-1). We propose a scenario in which regulatory T cells create a tolerant microenvironment at the fetal-maternal interface characterised by the presence of tolerance-associated molecules such as HO-1, which has been shown to be of vital importance for fetal survival.