Evolutionary relationships of the classes of major histocompatibility complex genes

Effect of FKBP12-Derived Intracellular Peptides on Rapamycin-Induced FKBP-FRB Interaction and Autophagy

Intracellular peptides (InPeps) generated by proteasomes were previously suggested as putative natural regulators of protein-protein interactions (PPI). Here, the main aim was to investigate the intracellular effects of intracellular peptide VFDVELL (VFD7) and related peptides on PPI. The internalization of the peptides was achieved using a C-terminus covalently bound cell-penetrating peptide (cpp; YGRKKRRQRRR). The possible inhibition of PPI was investigated using a NanoBiT^® luciferase structural complementation reporter system, with a pair of plasmids vectors each encoding, simultaneously, either FK506-binding protein (FKBP) or FKBP-binding domain (FRB) of mechanistic target of rapamycin complex 1 (mTORC1). The interaction of FKBP-FRB within cells occurs under rapamycin induction. Results shown that rapamycin-induced interaction between FKBP-FRB within human embryonic kidney 293 (HEK293) cells was inhibited by VFD7-cpp (10-500 nM) and FDVELLYGRKKRRQRRR (VFD6-cpp; 1-500 nM); additional VFD7-cpp derivatives were either less or not effective in inhibiting FKBP-FRB interaction induced by rapamycin. Molecular dynamics simulations suggested that selected peptides, such as VFD7-cpp, VFD6-cpp, VFAVELLYGRKKKRRQRRR (VFA7-cpp), and VFEVELLYGRKKKRRQRRR (VFA7-cpp), bind to FKBP and to FRB protein surfaces. However, only VFD7-cpp and VFD6-cpp induced changes on FKBP structure, which could help with understanding their mechanism of PPI inhibition. InPeps extracted from HEK293 cells were found mainly associated with macromolecular components (i.e., proteins and/or nucleic acids), contributing to understanding InPeps' intracellular proteolytic stability and mechanism of action-inhibiting PPI within cells. In a model of cell death induced by hypoxia-reoxygenation, VFD6-cpp (1 µM) increased the viability of mouse embryonic fibroblasts cells (MEF) expressing mTORC1-regulated autophagy-related gene 5 (Atg5), but not in autophagy-deficient MEF cells lacking the expression of Atg5. These data suggest that VFD6-cpp could have therapeutic applications reducing undesired side effects of rapamycin long-term treatments. In summary, the present report provides further evidence that InPeps have biological significance and could be valuable tools for the rational design of therapeutic molecules targeting intracellular PPI.

Discovery of an ancient MHC category with both class I and class II features

Two classes of major histocompatibility complex (MHC) molecules, MHC class I and MHC class II, constitute the basis of our elaborate, adaptive immune system as antigen-presenting molecules. They perform distinct, critical functions: especially, MHC class I in case of antivirus and antitumor defenses, and MHC class II, in case of effective antibody responses. This important class diversification has long been enigmatic, as vestiges of the evolutionary molecular changes have not been found. The revealed ancient MHC category represents a plausible intermediate group between the two classes, and the data suggest that class II preceded class I in molecular evolution. Fundamental understanding of the molecular evolution of MHC molecules should contribute to understanding the basis of our complex biological defense system.

Two classes of major histocompatibility complex (MHC) molecules, MHC class I and class II, play important roles in our immune system, presenting antigens to functionally distinct T lymphocyte populations. However, the origin of this essential MHC class divergence is poorly understood. Here, we discovered a category of MHC molecules (W-category) in the most primitive jawed vertebrates, cartilaginous fish, and also in bony fish and tetrapods. W-category, surprisingly, possesses class II–type α- and β-chain organization together with class I–specific sequence motifs for interdomain binding, and the W-category α2 domain shows unprecedented, phylogenetic similarity with β₂-microglobulin of class I. Based on the results, we propose a model in which the ancestral MHC class I molecule evolved from class II–type W-category. The discovery of the ancient MHC group, W-category, sheds a light on the long-standing critical question of the MHC class divergence and suggests that class II type came first.

Structural Comparison Between MHC Classes I and II; in Evolution, a Class-II-Like Molecule Probably Came First

Structures of peptide-loaded major histocompatibility complex class I (pMHC-I) and class II (pMHC-II) complexes are similar. However, whereas pMHC-II complexes include similar-sized IIα and IIβ chains, pMHC-I complexes include a heavy chain (HC) and a single domain molecule β₂-microglobulin (β₂-m). Recently, we elucidated several pMHC-I and pMHC-II structures of primitive vertebrate species. In the present study, a comprehensive comparison of pMHC-I and pMHC-II structures helps to understand pMHC structural evolution and supports the earlier proposed—though debated—direction of MHC evolution from class II-type to class I. Extant pMHC-II structures share major functional characteristics with a deduced MHC-II-type homodimer ancestor. Evolutionary establishment of pMHC-I presumably involved important new functions such as (i) increased peptide selectivity by binding the peptides in a closed groove (ii), structural amplification of peptide ligand sequence differences by binding in a non-relaxed fashion, and (iii) increased peptide selectivity by syngeneic heterotrimer complex formation between peptide, HC, and β₂-m. These new functions were associated with structures that since their establishment in early pMHC-I have been very well conserved, including a shifted and reorganized P1 pocket (aka A pocket), and insertion of a β₂-m hydrophobic knob into the peptide binding domain β-sheet floor. A comparison between divergent species indicates better sequence conservation of peptide binding domains among MHC-I than among MHC-II, agreeing with more demanding interactions within pMHC-I complexes. In lungfishes, genes encoding fusions of all MHC-IIα and MHC-IIβ extracellular domains were identified, and although these lungfish genes presumably derived from classical MHC-II, they provide an alternative mechanistic hypothesis for how evolution from class II-type to class I may have occurred.

Thimet Oligopeptidase Biochemical and Biological Significances: Past, Present, and Future Directions

Thimet oligopeptidase (EC 3.4.24.15; EP24.15, THOP1) is a metallopeptidase ubiquitously distributed in mammalian tissues. Beyond its previously well characterized role in major histocompatibility class I (MHC-I) antigen presentation, the recent characterization of the THOP1 C57BL6/N null mice (THOP1^−/−) phenotype suggests new key functions for THOP1 in hyperlipidic diet-induced obesity, insulin resistance and non-alcoholic liver steatosis. Distinctive levels of specific intracellular peptides (InPeps), genes and microRNAs were observed when comparing wild type C57BL6/N to THOP1^−/− fed either standard or hyperlipidic diets. A possible novel mechanism of action was suggested for InPeps processed by THOP1, which could be modulating protein-protein interactions and microRNA processing, thus affecting the phenotype. Together, research into the biochemical and biomedical significance of THOP1 suggests that degradation by the proteasome is a step in the processing of various proteins, not merely for ending their existence. This allows many functional peptides to be generated by proteasomal degradation in order to, for example, control mRNA translation and the formation of protein complexes.

The Relevance of Thimet Oligopeptidase in the Regulation of Energy Metabolism and Diet-Induced Obesity

Thimet oligopeptidase (EC 3.4.24.15; EP24.15; THOP1) is a potential therapeutic target, as it plays key biological functions in processing biologically functional peptides. The structural conformation of THOP1 provides a unique restriction regarding substrate size, in that it only hydrolyzes peptides (optimally, those ranging from eight to 12 amino acids) and not proteins. The proteasome activity of hydrolyzing proteins releases a large number of intracellular peptides, providing THOP1 substrates within cells. The present study aimed to investigate the possible function of THOP1 in the development of diet-induced obesity (DIO) and insulin resistance by utilizing a murine model of hyperlipidic DIO with both C57BL6 wild-type (WT) and THOP1 null (THOP1^−/−) mice. After 24 weeks of being fed a hyperlipidic diet (HD), THOP1^−/− and WT mice ingested similar chow and calories; however, the THOP1^−/− mice gained 75% less body weight and showed neither insulin resistance nor non-alcoholic fatty liver steatosis when compared to WT mice. THOP1^−/− mice had increased adrenergic-stimulated adipose tissue lipolysis as well as a balanced level of expression of genes and microRNAs associated with energy metabolism, adipogenesis, or inflammation. Altogether, these differences converge to a healthy phenotype of THOP1^−/− fed a HD. The molecular mechanism that links THOP1 to energy metabolism is suggested herein to involve intracellular peptides, of which the relative levels were identified to change in the adipose tissue of WT and THOP1^−/− mice. Intracellular peptides were observed by molecular modeling to interact with both pre-miR-143 and pre-miR-222, suggesting a possible novel regulatory mechanism for gene expression. Therefore, we successfully demonstrated the previously anticipated relevance of THOP1 in energy metabolism regulation. It was suggested that intracellular peptides were responsible for mediating the phenotypic differences that are described herein by a yet unknown mechanism of action.

Inferring the "Primordial Immune Complex": Origins of MHC Class I and Antigen Receptors Revealed by Comparative Genomics

Comparative analyses suggest that the MHC was derived from a prevertebrate "primordial immune complex" (PIC). PIC duplicated twice in the well-studied two rounds of genome-wide duplications (2R) early in vertebrate evolution, generating four MHC paralogous regions (predominantly on human chromosomes [chr] 1, 6, 9, 19). Examining chiefly the amphibian Xenopus laevis, but also other vertebrates, we identified their MHC paralogues and mapped MHC class I, AgR, and "framework" genes. Most class I genes mapped to MHC paralogues, but a cluster of Xenopus MHC class Ib genes (xnc), which previously was mapped outside of the MHC paralogues, was surrounded by genes syntenic to mammalian CD1 genes, a region previously proposed as an MHC paralogue on human chr 1. Thus, this gene block is instead the result of a translocation that we call the translocated part of the MHC paralogous region (MHCtrans) Analyses of Xenopus class I genes, as well as MHCtrans, suggest that class I arose at 1R on the chr 6/19 ancestor. Of great interest are nonrearranging AgR-like genes mapping to three MHC paralogues; thus, PIC clearly contained several AgR precursor loci, predating MHC class I/II. However, all rearranging AgR genes were found on paralogues derived from the chr 19 precursor, suggesting that invasion of a variable (V) exon by the RAG transposon occurred after 2R. We propose models for the evolutionary history of MHC/TCR/Ig and speculate on the dichotomy between the jawless (lamprey and hagfish) and jawed vertebrate adaptive immune systems, as we found genes related to variable lymphocyte receptors also map to MHC paralogues.

Effects of dietary Panax notoginseng extract on growth performance, fish composition, immune responses, intestinal histology and immune related genes expression of hybrid grouper (Epinephelus lanceolatus ♂ × Epinephelus fuscoguttatus ♀) fed high lipid diets

Growth, plasma biochemical parameters, fish composition, immune parameters, intestinal histology, and expressions of immune-related genes were examined in hybrid grouper (Epinephelus lanceolatus ♂ × Epinephelus fuscoguttatus ♀) that fed respectively six diets containing Panax notoginseng extract (PNE) at 0, 0.5, 1, 2, 4, and 10 g kg^-1 after 8 weeks. Results indicated that dietary PNE significantly improved growth, feed efficiency ratio, protein efficiency ratio, and protein deposit rate, and significantly increased crude protein and crude lipid levels of whole body and crude protein level of muscle. Dietary PNE significantly increased plasma total protein, alkaline phosphatase, immunoglobulin, complement 3 and complement 4 contents, but significantly decreased cholesterol, triglyceride, glucose, and low density lipoprotein cholesterol contents. Furthermore, dietary PNE increased villus length and muscle thickness in foregut, midgut, and hindgut, activities of hepatic superoxide dismutase and total antioxidant capacity, and increased the expression levels of immune related genes (IL-10, TGF-β1, TOR, MHC2 and TLR3) in the head kidney and the expression levels of antioxidant genes (CAT and GR) in fish that fed PNE at 0.5-4 g kg^-1. In conclusion, grouper fed high lipid diets supplemented with PNE at 0.5-10 g kg^-1 improved growth, feed utilization, blood immune parameters, hepatic antioxidant status, intestine morphology and expression levels of immune related genes in the head kidney.

Effects of dietary ginkgo biloba leaf extract on growth performance, plasma biochemical parameters, fish composition, immune responses, liver histology, and immune and apoptosis-related genes expression of hybrid grouper (Epinephelus lanceolatus♂ × Epinephelus fuscoguttatus♀) fed high lipid diets

For thousands of years, leaves from the Ginkgo biloba tree have been a common treatment in Chinese medicine. The present study was conducted to investigate the effects of dietary ginkgo biloba leaf extract (GBE) supplementation on growth performance, plasma biochemical parameters, fish composition, immune responses, liver histology, and immune and apoptosis-related genes expression of hybrid grouper (Epinephelus lanceolatus♂ × Epinephelus fuscoguttatus♀) fed high lipid diets. A basal diet supplemented with GBE at 0, 0.50, 1.00, 2.00, 4.00 and 10.00 g kg^-1 was fed to hybrid grouper for 8 weeks. The study indicated that dietary GBE did not improve growth performance and feed utilization but it reduced intraperitoneal fat rate. There were no significant differences in condition factor, viscerosomatic index, hepatosomatic index, spleen index, relative gut length, food intake, protein deposit rate and survival among all groups (P > 0.05). Dietary supplementation with 0.50-4.00 g GBE kg^-1 diets effectively increased plasma HDL content and decreased plasma GLU, LDL and TG content in fish. Furthermore, dietary GBE had a significant effect on moisture, crude protein and lipid in the liver, and protein in the whole body of fish (P < 0.05). Dietary supplementation with 0.50-1.00 g GBE kg^-1 diets effectively decreased occurrence rates of the hepatocyte swelling, hepatocyte vacuolization, and nuclei shifting to the cellular periphery cytoplasmic vacuolization, meanwhile hepatic antioxidant enzymes (SOD, CAT and T-AOC) activities significantly increased whereas MDA content significantly decreased in fish fed diets supplemented with GBE (P < 0.05). Moreover, dietary GBE up-regulated the expression of antioxidant genes (CAT, GPx and GR), immune-related genes (MHC2 and TLR3) and anti-inflammatory cytokines (IL-10 and TGF-β1), while dietary supplementation with 0.50-4.00 g GBE kg^-1 diets down-regulated apoptosis-related genes (p53, caspase-9, caspase-8 and caspase-3) expression in the head kidney of hybrid grouper. These results indicated that hybrid grouper fed diets supplemented with GBE did not improve growth performance and feed utilization but it had hypolipidemic effects, improved hepatic antioxidant status, maintained normal liver histology and preserved liver function, increased immune-related genes expression and decreased apoptosis-related genes expression in the head kidney of hybrid grouper.

The importance of evolution in the development and course of rheumatoid arthritis

Rheumatoid arthritis (RA) is a complex autoimmune disease of recent evolutionary origin. Genetic drift determines diverse polymorphisms implicated in the susceptibility to RA including the major histocompatibility complex (MHC) class II genes in the so-called shared epitope. These genes originated after the divergence between Homo and Pan from their common ancestry Ardipithecus ramidus about 5 million years ago. Natural selection determined the particular changes in the legs (bipedal position), hands, neck, brain and eusociality in humans which influence the clinical presentation of RA. In this article, we hypothesized that the origin and course of RA may be explainable in the light of evolution.

The biological significance of evolution in autoimmune phenomena

It is an inherent part of living to be in constant modification, which are due to answers resulting from environmental changes. The different systems make adaptations based on natural selection. With respect to the immune system of mammals, these changes have a lot to do with the interactions that occur continuously with other living species, especially microorganisms. The immune system is primarily designed to defend from germs and this response triggers inflammatory reactions which must be regulated in order not to generate damage to healthy tissue. The regulatory processes were added over time to prevent such damage. Through evolution the species have stored “an immunological experience,” which provides information that is important for developing effective responses in the future. The human species, which is at a high level of evolutionary immunological accumulation, have multiple immune defense strategies which, in turn, are highly regulated. Imbalances in these can result in autoimmunity.

“There is nothing permanent except change.”

(Heraclitus)

Primordial linkage of β2-microglobulin to the MHC

β2-Microglobulin (β2M) is believed to have arisen in a basal jawed vertebrate (gnathostome) and is the essential L chain that associates with most MHC class I molecules. It contains a distinctive molecular structure called a constant-1 Ig superfamily domain, which is shared with other adaptive immune molecules including MHC class I and class II. Despite its structural similarity to class I and class II and its conserved function, β2M is encoded outside the MHC in all examined species from bony fish to mammals, but it is assumed to have translocated from its original location within the MHC early in gnathostome evolution. We screened a nurse shark bacterial artificial chromosome library and isolated clones containing β2M genes. A gene present in the MHC of all other vertebrates (ring3) was found in the bacterial artificial chromosome clone, and the close linkage of ring3 and β2M to MHC class I and class II genes was determined by single-strand conformational polymorphism and allele-specific PCR. This study satisfies the long-held conjecture that β2M was linked to the primordial MHC (Ur MHC); furthermore, the apparent stability of the shark genome may yield other genes predicted to have had a primordial association with the MHC specifically and with immunity in general.

Characterization of major histocompatibility complex (MHC) DRB exon 2 and DRA exon 3 fragments in a primary terrestrial rabies vector (Procyon lotor)

The major histocompatibility complex (MHC) presents a unique system to explore links between genetic diversity and pathogens, as diversity within MHC is maintained in part by pathogen driven selection. While the majority of wildlife MHC studies have investigated species that are of conservation concern, here we characterize MHC variation in a common and broadly distributed species, the North American raccoon (Procyon lotor). Raccoons host an array of broadly distributed wildlife diseases (e.g., canine distemper, parvovirus and raccoon rabies virus) and present important human health risks as they persist in high densities and in close proximity to humans and livestock. To further explore how genetic variation influences the spread and maintenance of disease in raccoons we characterized a fragment of MHC class II DRA exon 3 (250bp) and DRB exon 2 (228 bp). MHC DRA was found to be functionally monomorphic in the 32 individuals screened; whereas DRB exon 2 revealed 66 unique alleles among the 246 individuals screened. Between two and four alleles were observed in each individual suggesting we were amplifying a duplicated DRB locus. Nucleotide differences between DRB alleles ranged from 1 to 36 bp (0.4–15.8% divergence) and translated into 1 to 21 (1.3–27.6% divergence) amino acid differences. We detected a significant excess of nonsynonymous substitutions at the peptide binding region (P = 0.005), indicating that DRB exon 2 in raccoons has been influenced by positive selection. These data will form the basis of continued analyses into the spatial and temporal relationship of the raccoon rabies virus and the immunogenetic response in its primary host.

Gonadotropin hormone and receptor sequences from model teleost species

Fish offer some advantages for the study of vertebrate reproductive physiology. Only a few of the genes encoding the components of the hypothalamic-pituitary-gonadal axis have been identified from model teleosts. This study describes a combination of database searching and molecular approaches to identify the FSH and LH gonadotropin beta-subunits (fshb and lhb, respectively), and the LH receptor (lhr) from two model teleost species: zebrafish (Danio rerio) and Fugu (Takifugu rubripes). Sequence and phylogenetic analyses were used to examine the relationships that exist between gonadotropins and their receptors from species representing several piscine orders. The gonadotropin alpha-subunit (Cga) is highly conserved among teleosts and tetrapods. The presence of a genomic pseudogene (cgap) was also noted in zebrafish. Generally, teleostean FSHbeta protein sequences share less identity with each other than do LHbeta protein sequences, supporting the hypothesis that FSHbeta diverged more rapidly during teleost evolution. Interestingly, and uniquely, zebrafish Fshb lacked two highly conserved cysteine residues in the "determinant loop" which is thought to contribute towards receptor binding and specificity. Teleost gonadotropin receptor sequences clearly diverged into two distinct groups, FSHR and LHR. As has been seen with mammalian gonadotropin receptor transcripts, splice variants of zebrafish lhr were also observed.

Evolutionary biology of CD1

The recognition more than a decade ago that lipids presented by CD1 could function as T cell antigens revealed a startling and previously unappreciated complexity to the adaptive immune system. The initial novelty of lipid antigen presentation by CD1 has since given way to a broader perspective of the immune system's capacity to sense and respond to a diverse array of macromolecules. Some immune recognition systems such as Toll-like receptors can trace their origins back into the deep history of sea urchins and arthropods. Others such as the major histocompatibility complex (MHC) appear relatively recently and interestingly, only in animals that also possess a jaw. The natural history of CD1 is thus part of the wider story of immune system evolution and should be considered in this context. Most evidence indicates that CD1 probably evolved from a classical MHC class I (MHC I) gene at some point during vertebrate evolution. This chapter reviews the evidence for this phylogenetic relationship and attempts to connect CD1 to existing models of MHC evolution. This endeavor is facilitated today by the recent availability of whole genome sequence data from a variety of species. Investigators have used these data to trace the ultimate origin of the MHC to a series of whole genome duplications that occurred roughly 500 million years ago. Sequence data have also revealed homologs of the mammalian MHC I and MHC II gene families in virtually all jawed vertebrates including sharks, bony fishes, reptiles, and birds. In contrast, CD1 genes have thus far been found only in a subset of these animal groups. This pattern of CD1 occurrence in the genomes of living species suggests the emergence of CD 1 in an early terrestrial vertebrate.

Microarrays reveal distinct gene signatures in the thymus of seropositive and seronegative myasthenia gravis patients and the role of CC chemokine ligand 21 in thymic hyperplasia

Myasthenia gravis (MG) is an autoimmune disease mainly caused by antiacetylcholine receptor autoantibodies (seropositive (SP) disease) or by Abs against unknown autoantigenic target(s) (seronegative (SN) disease). Thymectomy is usually beneficial although thymic hyperplasia with ectopic germinal centers is mainly observed in SP MG. To understand the role of thymus in the disease process, we compared the thymic transcriptome of non-MG adults to those of SP patients with a low or high degree of hyperplasia or SN patients. Surprisingly, an overexpression of MHC class II, Ig, and B cell marker genes is observed in SP but also SN MG patients. Moreover, we demonstrate an overexpression of CXCL13 in all MG thymuses leading probably to the generalized B cell infiltration. However, we find different chemotactic properties for MG subgroups and, especially, a specific overexpression of CCL21 in hyperplastic thymuses triggering most likely ectopic germinal center development. Besides, SN patients present a peculiar signature with an abnormal expression of genes involved in muscle development and synaptic transmission, but also genes implicated in host response, suggesting that viral infection might be related to SN MG. Altogether, these results underline differential pathogenic mechanisms in the thymus of SP and SN MG and propose new research areas.

Genetic dissection of thymus development in mouse and zebrafish

Lymphoid organs represent a specialized microenvironment for interaction of stromal and lymphoid cells. In primary lymphoid organs, these interactions are required to establish a self-tolerant repertoire of lymphocytes. While detailed information is available about the genes that control lymphocyte differentiation, little is known about the genes that direct the establishment and differentiation of principal components of such microenvironments. Here, we discuss genetic studies addressing the role of thymic epithelial cells (TECs) during thymopoiesis. We have identified an evolutionarily conserved key regulator of TEC differentiation, Foxn1, that is required for the immigration of prothymocytes into the thymic primordium. Because Foxn1 specifies the prospective endodermal domain that gives rise to thymic epithelial cells, it can be used to identify the evolutionary origins of this specialized cell type. In the course of these studies, we have found that early steps of thymus development in zebrafish are very similar to those in mice. Subsequently, we have used chemical mutagenesis to derive zebrafish lines with aberrant thymus development. Strengths and weaknesses of mouse and zebrafish models are largely complementary such that genetic analysis of mouse and zebrafish mutants may lead to a better understanding of thymus development.

Comparative genomic analysis of the MHC: the evolution of class I duplication blocks, diversity and complexity from shark to man

The major histocompatibility complex (MHC) genomic region is composed of a group of linked genes involved functionally with the adaptive and innate immune systems. The class I and class II genes are intrinsic features of the MHC and have been found in all the jawed vertebrates studied so far. The MHC genomic regions of the human and the chicken (B locus) have been fully sequenced and mapped, and the mouse MHC sequence is almost finished. Information on the MHC genomic structures (size, complexity, genic and intergenic composition and organization, gene order and number) of other vertebrates is largely limited or nonexistent. Therefore, we are mapping, sequencing and analyzing the MHC genomic regions of different human haplotypes and at least eight nonhuman species. Here, we review our progress with these sequences and compare the human MHC structure with that of the nonhuman primates (chimpanzee and rhesus macaque), other mammals (pigs, mice and rats) and nonmammalian vertebrates such as birds (chicken and quail), bony fish (medaka, pufferfish and zebrafish) and cartilaginous fish (nurse shark). This comparison reveals a complex MHC structure for mammals and a relatively simpler design for nonmammalian animals with a hypothetical prototypic structure for the shark. In the mammalian MHC, there are two to five different class I duplication blocks embedded within a framework of conserved nonclass I and/or nonclass II genes. With a few exceptions, the class I framework genes are absent from the MHC of birds, bony fish and sharks. Comparative genomics of the MHC reveal a highly plastic region with major structural differences between the mammalian and nonmammalian vertebrates. Additional genomic data are needed on animals of the reptilia, crocodilia and marsupial classes to find the origins of the class I framework genes and examples of structures that may be intermediate between the simple and complex MHC organizations of birds and mammals, respectively.

Stress renders T cell blasts sensitive to killing by activated syngeneic NK cells

Exposure of primary T cell blasts to stress in the forms of heat, hydrogen peroxide, or high-density growth conditions resulted in a state of enhanced susceptibility to killing by syngeneic IL-2-activated NK cells or lymphokine-activated killer cells, but not to killing by CTL. Cytotoxicity was perforin mediated and was not due to decreased target expression of total MHC class I. The levels of stress used had little effect on cell viability. For thermal stress, sensitization increased with temperature, required a minimum exposure time, and disappeared when cells were given a long enough recovery time. Our data support a model that predicts that activated NK cells play a role in the immunosurveillance of nontransformed stressed cells in normal animals.

Peptide binding by class I and class II MHC molecules

Major histocompatibility complex (MHC) antigens bind peptides of diverse sequences with high affinity. They do this in order to generate maximal immunological protection by covering the spectrum of peptides that may be seen by a host over the course of its lifetime. However, in many circumstances the immune system does not recognize a particular peptide that it should for maximum advantage over the pathogen. In other situations, the immune system goes awry and incorrectly recognizes a self-peptide that it should not. This results in disease characterized by recognition and attack of self. Rheumatoid arthritis is an example of just such a disease. In either of these situations, peptide-based modalities for immune therapy would be an advantage. However, peptide-based therapies require a thorough understanding of the forces involved in peptide binding. Great strides have been made in elucidating the mechanisms by which these MHC proteins may bind peptides with diverse sequences and high affinity. This review summarizes the current data obtained from crystallographic analyses of peptide binding for both class I and class II MHC molecules. Unfortunately, as yet these data have not allowed us to predict which peptides will bind with high affinity to a specific MHC molecule.

Molecular evolution of the vertebrate immune system

Adaptive immunity is unique to the vertebrates, and the molecules involved (including immunoglobulins, T cell receptors and the major histocompatibility complex molecules) seem to have diversified very rapidly early in vertebrate history. Reconstruction of gene phylogenies has yielded insights into the evolutionary origin of a number of molecular systems, including the complement system and the major histocompatibility complex (MHC). These analyses have indicated that the C5 component of complement arose by gene duplication prior to the divergence of C3 and C4, which suggests that the alternative complement pathway was the first to evolve. In the case of the MHC, phylogenetic analysis supports the hypothesis that MHC class II molecules evolved before class I molecules. The fact that the MHC-linked proteasome components that specifically produce peptides for presentation by class I MHC appear to have originated before the separation of jawed and jawless vertebrates suggests that the MHC itself may have been present at this time. Immune system gene families have evolved by gene duplication, interlocus recombination and (in some cases) positive Darwinian selection favoring diversity at the amino acid level.

Major histocompatibility complex gene mapping in the amphibian Xenopus implies a primordial organization

One of the most provocative recent discoveries in immunology was the description of a genetic linkage in the major histocompatibility complex (MHC) between structurally unrelated genes whose products are involved in processing and presentation of antigens for recognition by T lymphocytes. Genes encoding MHC class I molecules, which bind and present at the cell surface proteolytic fragments of cytosolic proteins, are linked to nonhomologous genes whose products are involved in the production and subsequent transfer of such fragments into the endoplasmic reticulum. In mammals, the class I presentation and processing genes are found in different regions of the MHC. To examine the evolutionary origins of this genetic association, linkage studies were carried out with Xenopus, an amphibian last sharing an ancestor with mammals over 350 million years ago. In contrast to mammals, the single copy Xenopus class I gene is located between the class II and III regions, speculated to be in close linkage with the processing and transport genes. In addition to suggesting a primordial organization of genes involved in class I antigen presentation, these linkage studies further provide insight into the origins of the MHC class III region and the phenomenon of class I gene instability in the mammalian MHC.

Population biology of antigen presentation by MHC class I molecules

In principle, the function of major histocompatibility complex (MHC) molecules is simple: to bind a peptide and engage a T cell. In practice, placing this function within the context of the immune response begs questions of population biology; How does the immune response emerge from the interactions among populations of peptides, T cells and MHC molecules? Within a population of vertebrates, how does MHC polymorphism stamp individuality on the response? Does polymorphism confer differential advantages in responding to parasites? How are the pressures on the MHC reflected in turnover of alleles? The role of mutation, recombination, selection, and drift in the generation and maintenance of MHC class 1 polymorphism are considered.

Genomic organization of a mouse MHC class II region including the H2-M and Lmp2 loci

The region encompassing the Ma, Mb1, Mb2, and Lmp2 genes of the mouse class II major histocompatibility complex (MHC) was sequenced. Since this region contains clusters of genes required for efficient class I and class II antigen presentation, it was interesting to search for putative additional genes in the 21 kilobase gap between the Mb1 and Lmp2 genes. Computer predictions of coding regions and CpG islands, exon trapping experiments, and cross-species comparison with the corresponding human sequence indicate that no additional functional gene is present in that stretch. However, computer analysis revealed the possible existence of an alternative 3' exon for Mb1. Except for the fact that the mouse MHC contains two Mb genes, the genomic organization of the H2-M loci was found to be almost identical to the organization of the human HLA-DM genes. The promoter regions of the Ma and Mb genes also resemble classical class II promoters, containing typical S, X, and Y boxes. Like the human genes, the three H2-M genes displayed very limited polymorphism when we compared the cDNA sequences from six haplotypes. Finally, comparison of DMB with Mb1 and Mb2, both at the genomic level and in their coding regions, suggests that the Mb gene was recently duplicated, probably only in certain rodents.

Fish major histocompatibility complex genes: an expansion

The advent of polymerase chain reaction technology has provoked a large amount of progress in the field of fish major histocompatibility complex (MHC) research. Many new teleost sequences have been reported in the last four years, including representatives of all classes of MHC genes. While the intron-exon structure of teleost MHC genes is now becoming clear, the organisation of the genes within the teleost MHC is still unclear. The sequences reported to date have been used for phylogenetic analysis and, due to their evolutionary position, are discussed in relation to hypotheses regarding the origin of the MHC. Teleost MHC gene sequences are also examined to see if conserved features of the both the nucleotide and amino acid sequences of higher vertebrate MHC genes are present. Differences in these features will reflect functional differences between teleost and mammalian MHC genes and may also have evolutionary implications.

Novel molecules related to MHC antigens

Several types of molecules related to classical class I and II antigens of the MHC have been recently discovered. At the same time we have learnt more about the functions of non-classical (class Ib) antigens. This has shed light on the possible evolutionary origins and the likely roles that these molecules may play in the immune response.

Comparative analysis of the three major histocompatibility complex-linked heat shock protein 70 (Hsp70) genes of the rat

The organization of the three major histocompatibility complex (Mhc)-linked heat shock protein 70 (Hsp70) genes Hsp70-1, Hsp70-2, and Hsp70-3, and the nucleotide sequences of these genes, are presented for the rat. Hsp70-1 and Hsp70-2 gene products are identical at the amino acid level. From the pattern of sequence similarity of the orthologous Mhc-linked Hsp70 genes of rat, human, and mouse, it is concluded that the gene duplications leading to the three-gene cluster occurred before the separation of the primate and rodent lines and that the Hsp70-1 and Hsp70-2 genes of rat and human might have undergone homogenization of their sequences.

The evolution of functionally novel proteins after gene duplication

A widely cited model of the evolution of functionally novel proteins (here called the model of mutation during non-functionality (MDN model)) holds that, after gene duplication, one gene copy is redundant and free to accumulate substitutions at random. By chance, some of these substitutions may suit the protein encoded by such a non-functional gene to a new function, which it can subsequently assume. Several lines of evidence contradict this hypothesis: (i) comparison of expressed duplicate genes from the tetraploid frog Xenopus laevis suggests that such genes are subject to purifying selection and are thus not free to accumulate substitutions at random; (ii) in a number of multi-gene families, there is now evidence that functionally distinct proteins have arisen not as a result of chance fixation of neutral variants but rather as a result of positive Darwinian selection; and (iii) the phenomenon of gene sharing, in which a single gene encodes a protein having two distinct functions, shows that gene duplication is not a necessary prerequisite to the evolution of a new protein function. A model for the evolution of new protein is proposed under which a period of gene sharing ordinarily precedes the evolution of functionally distinct proteins. Gene duplication then allows each daughter gene to specialize for one of the functions of the ancestral gene.(ABSTRACT TRUNCATED AT 250 WORDS)

Composite origin of major histocompatibility complex genes

Major histocompatibility complex (MHC) genes have now been cloned from representatives of all vertebrate classes except Agnatha. The recent accumulation of sequence data has given great insight into the course of evolution of these genes. Although the primary structure of the MHC genes varies greatly from class to class and also within the individual classes, the general features of the tertiary and quaternary structure have been conserved remarkably well during more than 400 million years of evolution. The ancestral MHC genes may have been assembled from at least three structural elements derived from different gene families. Class II MHC genes appear to have been assembled first, and then to have given rise to class I genes.