The helper T-cell repertoire of mice expressing class II major histocompatibility complex β chains in the absence of α chains

 Mutant mice generated by disrupting the H2-Aa ^b major histocompatibility complex (Mhc) gene are demonstrated here to express Aβ^b chains in the absence of α chains. These mice possess a CD4⁺ helper T cell (Th) repertoire that uses predominantly the Vβ7 T-cell antigen receptor (Tcr) segment for recognition of any protein antigen presented by the α-free Aβ molecule. As an alloantigen, the Aα-free Aβ molecule is recognized very poorly by T cells from a series of class II disparate mouse strains, indicating that it is grossly different from normal α/β heterodimers. Indeed, molecular modeling suggests a β/β homodimer arrangement with an altered geometry of the Tcr contact area. Interestingly, the mutant mice exhibit normal alloreactivity, without a restricted Vβ usage, toward a series of foreign α/β class II heterodimers, although their T cells developed in the absence of such heterodimers. Thus, the complementarity of Tcr to normal α/β heterodimers, and thereby also alloreactivity, appears to be an ontogeny independent (i. e., germline-encoded) feature. Received: 30 September 1996 / Revised: 18 October 1996     

Cloning and sequence analysis of cDNAs encoding the MHC class II β chain in Atlantic salmon (Salmo salar)

Atlantic salmon (Salmo salar) cDNAs encoding the major histocompatibility complex (Mhc-Sasa) class II chain were isolated from a leucocyte library by a polymerase chain reaction (PCR) approach. Three different cDNAs (c144, c22, and c157) encoding the entire mature chain have been analyzed. Clone c144 differs from clone c157 in 12.6% of the nucleotides in the 1-encoding region. The corresponding differences between clones c144 and c22, and clones c22 and c157, are 10.3% and 5.2%, respectively. This variation is, at least in part, most likely attributable to allelism. The similarity indices between the highly conserved 2 domains from Atlantic salmon and corresponding sequences from humans (DQ), chicken (BL), carp (TLAII-1), and rainbow trout (O. M. No. 55) are 45%, 40%, 66%, and 97%, respectively. Variable residues in the 1 domains from Atlantic salmon correspond with polymorphic sites of 1 domains from higher vertebrates. The frequency of substitutions in the 1-encoding region exceeds that in the 3-untranslated (UT) region with several folds, indicating extensive 1 polymorphism in Atlantic salmon.The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession numbers (C 144) X 70165, (C 157) X 70166, and (C 22) X 70167.This study was supported by grants from the Norwegian Fisheries Research Council (NFFR) and the Norwegian Agricultural Research Council (NLVF).     

Analysis of T cell receptor β chains in rat thymus,and rat Cα and C β sequences

In development, T cells first express their antigen receptors in the thymus, where they may undergo selection processes leading to major histocompatibility complex (MHC) restriction and tolerance. A high proportion of thymocytes are thought to fail this selection in some way and to be destined for intrathymic death. These cells are categorized as the cortical type since they constitute most of the cortical cells; they express both CD4 and CD8 antigens but only very low levels of MHC class I antigens. One suggested cause of thymocyte death is a failure to produce a functional T cell receptor (Tcr) due to errors in the rearrangements of germline DNA, resulting in V regions being absent or incorrectly spliced to the other segments of the transcribed gene. We have sequenced from the C region through to the V region of 14 rat Tcr chain clones isolated from thymocyte cDNA libraries. Of the 14, 13 have complete and correct rearrangements, whereas one was expressed from an unrearranged gene. Most of these clones are likely to be derived from the cortical population, for Northern blot analysis showed that these cells and total thymocytes expressed similar amounts of chain mRNA.Furthermore, the RNA from cortical-type cells contained a very similar ratio of full-length to truncated chain mRNA as did activated thymocytes and mature T lymphocytes. The data imply that defective chain gene rearrangement is not a major cause of failure in the selection of thymocytes. The sequences of the rat Tcr and chain constant regions are also reported.     

The impact of the C-terminal domain on the interaction of human DNA topoisomerase II α and β with DNA

Background

Type II DNA topoisomerases are essential, ubiquitous enzymes that act to relieve topological problems arising in DNA from normal cellular activity. Their mechanism of action involves the ATP-dependent transport of one DNA duplex through a transient break in a second DNA duplex; metal ions are essential for strand passage. Humans have two isoforms, topoisomerase IIα and topoisomerase IIβ, that have distinct roles in the cell. The C-terminal domain has been linked to isoform specific differences in activity and DNA interaction.

Methodology/Principal Findings

We have investigated the role of the C-terminal domain in the binding of human topoisomerase IIα and topoisomerase IIβ to DNA in fluorescence anisotropy assays using full length and C-terminally truncated enzymes. We find that the C-terminal domain of topoisomerase IIβ but not topoisomerase IIα affects the binding of the enzyme to the DNA. The presence of metal ions has no effect on DNA binding. Additionally, we have examined strand passage of the full length and truncated enzymes in the presence of a number of supporting metal ions and find that there is no difference in relative decatenation between isoforms. We find that calcium and manganese, in addition to magnesium, can support strand passage by the human topoisomerase II enzymes.

Conclusions/Significance

The C-terminal domain of topoisomerase IIβ, but not that of topoisomerase IIα, alters the enzyme''s K_D for DNA binding. This is consistent with previous data and may be related to the differential modes of action of the two isoforms in vivo. We also show strand passage with different supporting metal ions for human topoisomerase IIα or topoisomerase IIβ, either full length or C-terminally truncated. They all show the same preferences, whereby Mg > Ca > Mn.     

Comparison of Alexa Fluor<Superscript>®</Superscript> and CyDye<Superscript>™</Superscript> for practical DNA microarray use

Microarrays are a powerful tool for comparison and understanding of gene expression levels in healthy and diseased states. The method relies upon the assumption that signals from microarray features are a reflection of relative gene expression levels of the cell types under investigation. It has previously been reported that the classical fluorescent dyes used for microarray technology, Cy3 and Cy5, are not ideal due to the decreased stability and fluorescence intensity of the Cy5 dye relative to the Cy3, such that dye bias is an accepted phenomena necessitating dye swap experimental protocols and analysis of differential dye affects. The incentive to find new fluorophores is based on alleviating the problem of dye bias through synonymous performance between counterpart dyes. Alexa Fluor 555 and Alexa Fluor 647 are increasingly promoted as replacements for CyDye in microarray experiments. Performance relates to the molecular and steric similarities, which will vary for each new pair of dyes as well as the spectral integrity for the specific application required. Comparative analysis of the performance of these two competitive dye pairs in practical microarray applications is warranted towards this end. The findings of our study showed that both dye pairs were comparable but that conventional CyDye resulted in significantly higher signal intensities (P < 0.05) and signal minus background levels (P < 0.05) with no significant difference in background values (P > 0.05). This translated to greater levels of differential gene expression with CyDye than with the Alexa Fluor counterparts. However, CyDye fluorophores and in particular Cy5, were found to be less photostable over time and following repeated scans in microarray experiments. These results suggest that precautions against potential dye affects will continue to be necessary and that no one dye pair negates this need.     

Molecular evidence for five distinct MHC class II α genes in the rabbit

Human HLA class 11 gene probes were used to identify five distinct genes encoding the class 11 heavy chain (a chain) in the rabbit. The rabbit genes were defined by both mapping data and hybridization studies of genomic clones derived from the inbred B/J rabbit strain. Analysis of the clones by hybridization at graded stringencies indicated that one group of clones corresponded to HLA-DR, one group to HLA-DQ, and two groups to HLA-DP. Clones within a fifth group, designated DN, hybridized weakly to HLA-DR and may carry a fourth species of class II genes in the rabbit. Clones within the group showing high homology to HLA-DR were found to also contain sequences hybridizing with a probe for HLA-DR . No HLA-DP, -DQ, or -DR sequences were detected in any of the other class II clones. Distinct banding patterns observed in Southern blot analyses using either human or rabbit class II probes revealed restriction fragment length polymorphism for the different rabbit haplotypes studied. TheDN, DQ, andDR genes appear to be present as single copies whereas there are two distinctDP-like genes in the rabbit.Abbreviations used in this paper RLA major histocompatibility complex of the rabbit - RFLP restriction fragment length polymorphism - RL-5 rabbit T-cell line - SSC 0.15 M sodium chloride, 0.015 M sodium citrate     

<Superscript>1</Superscript>H, <Superscript>13</Superscript>C,and <Superscript>15</Superscript>N resonance assignments for the pro-inflammatory cytokine interleukin-36α

Interleukin-36α (IL-36α) is a recently characterised member of the interleukin-1 superfamily. It is involved in the pathogenesis of inflammatory arthritis in one third of psoriasis patients. By binding of IL-36α to its receptor IL-36R via the NF-κB pathway other cytokines involved in inflammatory and apoptotic cascade are activated. The efficacy of complex formation is controlled by N-terminal processing. To obtain a more detailed view on the structure function relationship we performed a heteronuclear multidimensional NMR investigation and here report the ¹H, ¹³C, and ¹⁵N resonance assignments for the backbone and side chain nuclei of the pro-inflammatory cytokine interleukin-36α.     

Synthesis of the β-amyloid fragment <Superscript>5</Superscript>RHDSGY<Superscript>10</Superscript> and its isomers

The peptide RHDSGY, a fragment of the human β-amyloid Zn-binding site, and its isomers RH(D-Asp)SGY and RH(β-Asp)SGY have been obtained as amides by means of solid-phase synthesis and analyzed by HPLC and various mass spectrometric methods. The problem of low yield of the RHDSGY peptide and its isomers attributed to 9-fluorenylmethoxycarbonyl (Fmoc)-amino acids and/or formation of such side-products as RH(β-Asp)SGY (or RHDSGY during synthesis of RH(β-Asp)SGY) and RH(Asp-imide) SGY was solved via selection of individual reagents for removal of Fmoc groups from α-amino groups of the growing peptide chain.     

Molecular characterization of MHC class II antigens (β 1 domain) in the BB diabetes-prone and -resistant rat

The BB or BB/Worcester (BB/W) rat is widely recognized as a model for human insulin-dependent diabetes mellitus (IDDM). Of at least three genes implicated in genetic susceptibility to IDDM in this strain, one is clearly linked to the major histocompatibility complex (MHC). In an attempt to define the diabetogenic gene(s) linked to the MHC of the BB rat, cDNA clones encoding the class II MHC gene products of the BB diabetes-prone and diabetes-resistant sublines have been isolated and sequenced. For comparison, the ₁ domain of class II genes of the Lewis rat (RTl^L) were sequenced. Analysis of the sequence data reveals that the first domain of RT1.D and RT1.B chain of the BB rat are different from other rat or mouse class 11 sequences. However, these sequences were identical in both the BB diabetes-prone and BB diabetes-resistant sublines. The significance of these findings is discussed in relation to MHC class II sequence data in IDDM patients and in the nonobese diabetic (NOD) mouse strain.     

Sequence of a cDNA coding for a rat class II Aα chain: Extensive DNA and protein sequence identity to H-2 Aα and HLA-DC1 α chains

The rat major histocompatibility complex (RT1-B region) codes for two sets of class II molecules (la antigens) referred to as A and E. Each class II molecule is composed of two glycoprotein chains called the A and A or E and E . Two cDNA clones encoding rat A chains were identified from cDNA derived from rat spleen mRNA using a combination of mRNA selection and colony hybridization techniques. The complete nucleotide sequence of the cDNA insert of one of these cDNA clones, pRIa.2, was determined. This sequence codes for the carboxy-terminal 129 amino acids of the rat A chain and 293 nucleotides of 3 untranslated sequence. The rat A chain was shown to be highly homologous in terms of both protein and DNA sequence identities to HLA-DC and H-2 A chains. Comparison between the coding regions of the cDNA insert of pRla.2 and the corresponding region of a cDNA insert encoding an HLA-DC1 chain showed sequence identities of 85% and 81% at the protein and DNA levels, respectively. Comparison between pRIa.2 and cDNA encoding an H-2 A chain sequence showed identities of 91% for both protein and DNA. Results are discussed which strongly suggest that the class II A and E primordial genes arose by gene duplication prior to the evolutionary divergence of the mammals.     

Immunogenicity of<Emphasis Type="Italic"> Torpedo</Emphasis> acetylcholine receptor in the context of different rat MHC class II haplotypes and non-MHC genomes

The nicotinic acetylcholine receptor (nAChR) is the autoantigen in seropositive myasthenia gravis (MG), a T-cell-dependent B-cell-mediated autoimmune disease. The nAChR is a pentameric transmembrane receptor comprising chains. During early postnatal development the nAChR chain is replaced by the nAChR chain. We tested the myasthenogenicity in experimental autoimmune myasthenia gravis (EAMG) of the native nAChR derived from the electric ray Torpedo californica (T-nAChR) in various inbred and MHC -congenic rat strains. Differences in the disease course emerged dependent on the MHC haplotype and non-MHC genes. Interestingly, no tested rat strain was completely resistant to EAMG, but there were strong differences in disease severity mainly depending on the MHC haplotype. In the LEW non-MHC genome, the B-cell response and the severity of EAMG were dependent on the expressed MHC haplotype. This study underscores the influence of genetic factors on disease severity, disease course and on the degree of the emerging antibody responses in EAMG.     

<Superscript>15</Superscript>N, <Superscript>13</Superscript>C and <Superscript>1</Superscript>H backbone resonance assignments of an artificially engineered TEM-1/PSE-4 class A β-lactamase chimera and its deconvoluted mutant

The widespread use of β-lactam antibiotics has given rise to a dramatic increase in clinically-relevant β-lactamases. Understanding the structure/function relation in these variants is essential to better address the ever-growing incidence of antibiotic resistance. We previously reported the backbone resonance assignments of a chimeric protein constituted of segments of the class A β-lactamases TEM-1 and PSE-4 (Morin et al. in Biomol NMR Assign 4:127–130, 2010. doi: 10.1007/s12104-010-9227-8). That chimera, cTEM17m, held 17 amino acid substitutions relative to TEM-1 β-lactamase, resulting in a well-folded and fully functional protein with increased dynamics. Here we report the ¹H, ¹³C and ¹⁵N backbone resonance assignments of chimera cTEM-19m, which includes 19 substitutions and exhibits increased active-site perturbation, as well as one of its deconvoluted variants, as the first step in the analysis of their dynamic behaviours.     

PA1b,a plant peptide,induces intracellular [Ca<Superscript>2+</Superscript>] increase via Ca<Superscript>2+</Superscript> influx through the L-type Ca<Superscript>2+</Superscript> channel and triggers secretion in pancreatic β cells

Using alginic acid to adsorb polypeptides at pH 2.7, we isolated a peptide pea albumin 1b (PA1b) from pea seeds. The PA1b is a single chain peptide consisting of 37 amino acid residues with 6 cysteines which constitutes the cystine-knot structure. Using microfluorometry and patch clamp techniques, we found that PA1b significantly elevated the intracellular calcium level ([Ca²⁺]_i) and elicited membrane capacitance increase in the primary rat pancreatic β cells. The PA1b effect on [Ca²⁺]_i elevation was abolished in the absence of extracellular Ca²⁺ or in the presence of L-type Ca²⁺ channel blocker, nimodipine. Interestingly, we found that PA1b significantly depolarized membrane potential, which could lead to the opening of voltage-dependent L-type Ca²⁺ channels and influx of extracellular Ca²⁺, and then evoke robust secretion. In this study we identified the plant peptide PA1b which is capable of affecting the excitability and function of mammalian pancreatic β cell.