Structure prediction and fold recognition for the ferrochelatase family of proteins

An α/β barrel is predicted for the three-dimensional (3D) structure of Bacillus subtilis ferrochelatase. To arrive at this structure, the THREADER program was used to find possible homologous 3D structures and to predict the secondary structure for the ferrochelatase sequence. The secondary structure was fit by hand to the selected homologous 3D structure then the MODELLER program was used to predict the fold of ferrochelatase. Molecular biological information about the conserved residues of ferrochelatase was used as the criteria to help select the homologous 3D structure used to predict the fold of ferrochelatase. Based on the predicted structure possible, ligands binding to the iron and protoporphyrin IX are discussed. The structure has been deposited in the Brookhaven database as ID 1FJI. © 1997 Wiley-Liss Inc.     

Reactivity of cytochromes c and f with mutant forms of spinach plastocyanin.

The reduction of plastocyanin by cytochromes c and f has been investigated with mutants of spinach plastocyanin in which individual, highly conserved surface residues have been modified. These include Leu-12 and Phe-35 in the 'northern' hydrophobic patch and Tyr-83 and Asp-42 in the 'eastern' acidic patch. The differences observed all involved binding rather than the intrinsic rates of electron transfer. The Glu-12 and Ala-12 mutants showed small but significant decreases in binding constant with cytochrome c, even though the cytochrome is not expected to make contact with the northern face of plastocyanin. These results, and small changes in the EPR parameters, suggested that these mutations cause small conformational changes in surface residues on the eastern face of plastocyanin, transmitted through the copper centre. In the case of cytochrome f, the Glu-12 and Ala-12 mutants also bound less strongly, but Leu12Asn showed a marked increase in binding constant, suggesting that cytochrome f can hydrogen bond directly to Asn-12 in the reaction complex. A surprising result was that the kinetics of reduction of Asp42Asn were not significantly different from wild type, despite the loss of a negative charge.     

Critical role of the major histocompatibility complex and IL-10 in matrilin-1-induced relapsing polychondritis in mice

Relapsing polychondritis (RP) is an autoimmune disease that affects extra-articular cartilage. Matrilin-1-induced relapsing polychondritis (MIRP) is a model for RP and is useful for studies of the pathogenic mechanisms in this disease. There are indications that the major histocompatibility complex (MHC) class II plays a major role in RP, since DR4⁺ patients are more commonly affected than controls. We have now addressed the role of the MHC region, as well as the non-MHC contribution, using congenic mouse strains. Of the MHC congenic strains, B10.Q (H2 ^q ) was the most susceptible, the B10.P (H2 ^p ) and B10.R (H2 ^r ) strains developed mild disease, while B10 strains carrying the v, b, f, or u H2 haplotypes were resistant. A slight variation of susceptibility of H2 ^q strains (B10.Q> C3H.Q> DBA/1) was observed and the (B10.Q × DBA/1)F₁ was the most susceptible of all strains. Furthermore, macrophages and CD4⁺ T cells were the most prominent cell types in inflammatory infiltrates of the tracheal cartilage. Macrophages are the major source of many cytokines, such as interleukin-10 (IL-10), which is currently being tested as a therapeutic agent in several autoimmune diseases. We therefore investigated B10.Q mice devoid of IL-10 through gene deletion and found that they developed a significantly more severe disease, with an earlier onset, than their heterozygous littermates. In conclusion, MHC genes, as well as non-MHC genes, are important for MIRP induction, and IL-10 plays a major suppressive role in cartilage inflammation of the respiratory tract.     

Biphasic response to 3',5'-cyclic adenosine monophosphate (cAMP) at the messenger ribonucleic acid level for a regulatory subunit of cAMP-dependent protein kinase

In the present study we have examined the effect of long-term stimulation with (Bu)2cAMP on mRNA levels for the hormone responsive regulatory subunit (RII beta) of cAMP-dependent protein kinase in cultured rat Sertoli cells. The effects of the same treatment on two other mRNAs [androgen binding protein (ABP) and cellular retinol binding protein (cRBP)], shown to be regulated by cAMP, were examined simultaneously. The addition of (Bu)2cAMP (0.1 mM) to primary Sertoli cell cultures, for 14 and 24 h, caused a 50- to 60-fold stimulation in the steady state levels of mRNA for RII beta. During the same period of stimulation, we also observed a significant increase (2- to 3-fold) in the mRNA levels for ABP, and a 80% decrease in the mRNA levels for cRBP. Continued stimulation for 36 and 48 h was associated with a significant time-dependent decrease in the mRNA level for RII beta, in spite of the continuous presence of (Bu)2cAMP (0.1 mM) in the medium. This reduced response by long term stimulation with (Bu)2cAMP appears to be specific for RII beta, since mRNA for ABP remained elevated and mRNA for cRBP remained depressed during the entire period of cAMP stimulation. Our data demonstrate the presence of a biphasic type of regulation at the mRNA level, specific for the regulatory subunit RII beta of cAMP-dependent protein kinase. This response may be analogous to the desensitization mechanisms observed at other levels of the cAMP signalling pathway. For proteins constituting part of the signal transduction pathway this type of biphasic regulation, may be particularly important in maintaining homeostasis in the cell.     

Contrasting results from GWAS and QTL mapping on wing length in great reed warblers

A major goal in evolutionary biology is to understand the genetic basis of adaptive traits. In migratory birds, wing morphology is such a trait. Our previous work on the great reed warbler (Acrocephalus arundinaceus) shows that wing length is highly heritable and under sexually antagonistic selection. Moreover, a quantitative trait locus (QTL) mapping analysis detected a pronounced QTL for wing length on chromosome 2, suggesting that wing morphology is partly controlled by genes with large effects. Here, we re‐evaluate the genetic basis of wing length in great reed warblers using a genomewide association study (GWAS) approach based on restriction site‐associated DNA sequencing (RADseq) data. We use GWAS models that account for relatedness between individuals and include covariates (sex, age and tarsus length). The resulting association landscape was flat with no peaks on chromosome 2 or elsewhere, which is in line with expectations for polygenic traits. Analysis of the distribution of p‐values did not reveal biases, and the inflation factor was low. Effect sizes were however not uniformly distributed on some chromosomes, and the Z chromosome had weaker associations than autosomes. The level of linkage disequilibrium (LD) in the population decayed to background levels within c. 1 kbp. There could be several reasons to why our QTL study and GWAS gave contrasting results including differences in how associations are modelled (cosegregation in pedigree vs. LD associations), how covariates are accounted for in the models, type of marker used (multi‐ vs. biallelic), difference in power or a combination of these. Our study highlights that the genetic architecture even of highly heritable traits is difficult to characterize in wild populations.     

Cell-CAM 105-an adhesive cell surface glycoprotein

Summary Cell recognition and adhesion are important events in embryonic development as well as in adult physiology. In recent years several cell adhesion molecules (CAMs), that mediate adhesive interactions between vertebrate cells, have been identified and characterized. These CAMs are in general cell surface-associated high molecular weight glycoproteins. Two groups of CAMs have been classified: primary CAMs, that appear early in development; secondary CAMs, that become expressed later and with a more restricted tissue distribution. One example of a secondary CAM is cellCAM 105. This glycoprotein was originally identified in rat hepatocytes, and was shown to be involved in the reaggregation of freshly isolated hepatocytesin vitro. Physico-chemical studies on pure cellCAM 105 have demonstrated that it has adhesive properties and can bind to itself in a homophilic, calcium-independent reaction. Immunochemical and immunohistochemical investigations have shown that cellCAM 105 occurs in liver, several epithelia, vessel endothelia, platelets and polymorphonuclear leukocytes, and that it is expressed primarily in terminally differentiated cells or cells that are undergoing terminal differentiation. Available information suggests that cellCAM 105 has different functions in different cell types, and that the common functional denominator might be membrane-membrane binding. Recent data indicate that cellCAM 105 is a calmodulin-binding protein, suggesting that cellCAM-mediated cell binding could be involved in transmembrane signalling.Abbreviation CAM cell adhesion molecule     

The Bacillus subtilis hemAXCDBL gene cluster, which encodes enzymes of the biosynthetic pathway from glutamate to uroporphyrinogen III.

We have recently reported (M. Petricek, L. Rutberg, I. Schr?der, and L. Hederstedt, J. Bacteriol. 172: 2250-2258, 1990) the cloning and sequence of a Bacillus subtilis chromosomal DNA fragment containing hemA proposed to encode the NAD(P)H-dependent glutamyl-tRNA reductase of the C5 pathway for 5-aminolevulinic acid (ALA) synthesis, hemX encoding a hydrophobic protein of unknown function, and hemC encoding hydroxymethylbilane synthase. In the present communication, we report the sequences and identities of three additional hem genes located immediately downstreatm of hemC, namely, hemD encoding uroporphyrinogen III synthase, hemB encoding porphobilinogen synthase, and hemL encoding glutamate-1-semialdehyde 2,1-aminotransferase. The six genes are proposed to constitute a hem operon encoding enzymes required for the synthesis of uroporphyrinogen III from glutamyl-tRNA. hemA, hemB, hemC, and hemD have all been shown to be essential for heme synthesis. However, deletion of an internal 427-bp fragment of hemL did not create a growth requirement for ALA or heme, indicating that formation of ALA from glutamate-1-semialdehyde can occur spontaneously in vivo or that this reaction may also be catalyzed by other enzymes. An analysis of B. subtilis carrying integrated plasmids or deletions-substitutions in or downstream of hemL indicates that no further genes in heme synthesis are part of the proposed hem operon.     

Cellular localization and age dependent changes in mRNA for glutathione S-transferase-P in rat testicular cells

Using Northern blotting techniques we report that mRNA for Glutathione S-transferase-P (GST-P or GST 7-7) is present in rat testis. GST-P mRNA was detected in cultured Sertoli cells, cultured peritubular cells, as well as in transplantable Leydig cell tumor. However, no GST-P mRNA was detected in rat germ cell fractions. There was a marked increase in mRNA for GST-P from day 5 to day 20 in rats, after which a decrease was seen. The decreased level of mRNA for GST-P in the testis after 20 days of age, coincided in time with the exponential increase in germ cells, and accompanying relative decrease in somatic cells. The results show that mRNA for GST-P is primarily present in somatic cells of the rat testis.     

Effects of barbiturates on ultrastructure and polymerization of microtubules in vitro

Summary Barbiturates were examined for in vitro effects on ultrastructure of the frog sciatic system and polymerization of microtubules (MT) in a brain supernatant. Exposure for 5–17 h to 2.0 mM barbiturates caused a considerable loss of MT in ganglionic cell bodies and sciatic axons. This was mostly followed by a proliferation of 10 nm filaments. Under similar conditions treatment with 1 mM NaCN or 0.1 mM 2,4-DNP did not change the number or ultrastructure of MT and filaments.Eight barbiturates, varying in binding ratios to serum albumin and partition coefficients, were tested for effects on polymerization of MT using viscometry. Inhibitory effects were found which correlated with their reported ability to bind to albumin and brain fractions. Dimethylsulphoxide and ethanol were used as solvents for some of the barbiturates. These solvents at 1% had stabilizing effects on MT.The present results are discussed in relation to previous findings of inhibition of rapid axonal transport in vitro in the frog sciatic system by barbiturates.The present work was supported by grants from Statens Naturvetenskapliga Forskningsråd (No. 2535-0011), Statens Medicinska Forskningsråd (B 75-12x-2543-07), Wilhelm och Martina Lundgrens Vetenskapsfond, Magnus Bergwalls Stifteise och Göteborgs Kungl. Vetenskapsoch Vitterhetssamhälle. Thanks are due to Miss Monica Lindhé for her expert technical assistance.     

Acetaldehyde stimulation of the growth of Saccharomyces cerevisiae in the presence of inhibitors found inlignocellulose-to-ethanol fermentations

The addition of small quantities of acetaldehyde to fermentations containing inhibitory concentrations of furfural, acetate and other compounds typically present in lignocellulosic hydrolyzates significantly reduced the lag phase of yeast growth and stimulated ethanol production. Similar effects were observed when acetaldehyde (0.06 g l⁻¹) was added to fermentations of a birch wood hydrolyzate produced by steam/acid pretreatment. Acetaldehyde addition appears to have potential as a low-cost alternative (or adjunct) to current procedures for medium detoxification in lignocellulose-to-ethanol fermentations, particularly those in which high inhibitor concentrations are generated through recycling of the culture broth. Journal of Industrial Microbiology & Biotechnology (2000) 25, 104–108. Received 18 March 2000/ Accepted in revised form 02 June 2000