Rhesus macaque TRIM5 alleles have divergent antiretroviral specificities

TRIM5alpha is a potent barrier to cross-species retroviral transmission, and TRIM5alphas from different species have divergent antiretroviral specificities. Multiple TRIM5 alleles circulate within rhesus macaque populations. Here we show that they too have different antiretroviral specificities, highlighting how TRIM5 genotypes contribute to protection in an individual or a population.     

The molecular evolution of ZFY-related genes in birds and mammals

Summary We report the isolation and nucleotide sequence determination of clones derived from five ZFY-related zinc-finger genes from birds and mammals. These sequences are analyzed with reference to the previously published human genes, ZFX and ZFY, and mouse genes, Zfx, Zfa, Zfy-1, and Zfy-2. The analysis indicates that ZFY-related genes are highly conserved in birds and mammals, and that the rate of nucleotide substitution in the Y-linked genes is not as high as predicted. However, the mouse Zfy-1 and Zfy-2 genes are markedly divergent members of the ZFY gene family; we suggest this relates to X-inactivation of the mouse gene Zfx.     

Molecular evolution of the antiretroviral <Emphasis Type="Italic">TRIM5</Emphasis> gene

In 2004, the first report of TRIM5α as a cellular antiretroviral factor triggered intense interest among virologists, particularly because some primate orthologs of TRIM5α have activity against HIV. Since that time, a complex and eventful evolutionary history of the TRIM5 locus has emerged. A review of the TRIM5 literature constitutes a veritable compendium of evolutionary phenomena, including elevated rates of nonsynonymous substitution, divergence in subdomains due to short insertions and deletions, expansions and contractions in gene copy number, pseudogenization, balanced polymorphism, trans-species polymorphism, convergent evolution, and the acquisition of new domains by exon capture. Unlike most genes, whose history is dominated by long periods of purifying selection interspersed with rare instances of genetic innovation, analysis of restriction factor loci is likely to be complicated by the unpredictable and more-or-less constant influence of positive selection. In this regard, the molecular evolution and population genetics of restriction factor loci most closely resemble patterns that have been documented for immunity genes, such as class I and II MHC genes, whose products interact directly with microbial targets. While the antiretroviral activity encoded by TRIM5 provides plausible mechanistic hypotheses for these unusual evolutionary observations, evolutionary analyses have reciprocated by providing significant insights into the structure and function of the TRIM5α protein. Many of the lessons learned from TRIM5 should be applicable to the study of other restriction factor loci, and molecular evolutionary analysis could facilitate the discovery of new antiviral factors, particularly among the many TRIM genes whose functions remain as yet unidentified.     

Independent evolution of Toll and related genes in insects and mammals

 Toll and Toll-related proteins play an important role in antibacterial innate immunity in insect, plants, and mammals. We present the first comprehensive phylogenetic analyses of Toll-related genes from both insects and mammals. Drosophila melanogaster contains Toll and a highly homologous gene, Tehao. The protein, Dm Tehao, comprises 795 amino acid residues and its cytoplasmic domain shares a striking 61% identity with Dm Toll. Two Toll homologues were found in another dipteran of medical importance, Anopheles gambiae, a vector for human malaria. One Toll-like gene each was identified from Aedes aegypti and Glossina palpalis palpalis, vectors for yellow fever and trypanosomiasis, respectively. Phylogenetic analyses revealed separate clustering of Toll and related proteins from insects and mammals, suggesting independent evolution of the Toll family of proteins and of innate immunity in arthropods and vertebrates. These results also provide new avenues to understanding the function of Toll proteins in insect innate immunity against bacteria, fungi, and protozoans. Received: 25 June 1999 / Revised: 25 September 1999     

The evolution of milk casein genes from tooth genes before the origin of mammals

Caseins are among cardinal proteins that evolved in the lineage leading to mammals. In milk, caseins and calcium phosphate (CaP) form a huge complex called casein micelle. By forming the micelle, milk maintains high CaP concentrations, which help altricial mammalian neonates to grow bone and teeth. Two types of caseins are known. Ca-sensitive caseins (α(s)- and β-caseins) bind Ca but precipitate at high Ca concentrations, whereas Ca-insensitive casein (κ-casein) does not usually interact with Ca but instead stabilizes the micelle. Thus, it is thought that these two types of caseins are both necessary for stable micelle formation. Both types of caseins show high substitution rates, which make it difficult to elucidate the evolution of caseins. Yet, recent studies have revealed that all casein genes belong to the secretory calcium-binding phosphoprotein (SCPP) gene family that arose by gene duplication. In the present study, we investigated exon-intron structures and phylogenetic distributions of casein and other SCPP genes, particularly the odontogenic ameloblast-associated (ODAM) gene, the SCPP-Pro-Gln-rich 1 (SCPPPQ1) gene, and the follicular dendritic cell secreted peptide (FDCSP) gene. The results suggest that contemporary Ca-sensitive casein genes arose from a putative common ancestor, which we refer to as CSN1/2. The six putative exons comprising CSN1/2 are all found in SCPPPQ1, although ODAM also shares four of these exons. By contrast, the five exons of the Ca-insensitive casein gene are all reminiscent of FDCSP. The phylogenetic distribution of these genes suggests that both SCPPPQ1 and FDCSP arose from ODAM. We thus argue that all casein genes evolved from ODAM via two different pathways; Ca-sensitive casein genes likely originated directly from SCPPPQ1, whereas the Ca-insensitive casein genes directly differentiated from FDCSP. Further, expression of ODAM, SCPPPQ1, and FDCSP was detected in dental tissues, supporting the idea that both types of caseins evolved as Ca-binding proteins. Based on these findings, we propose two alternative hypotheses for micelle formation in primitive milk. The conserved biochemical characteristics in caseins and their immediate ancestors also suggest that many slight genetic modifications have created modern caseins, proteins vital to the sustained success of mammals.     

Adaptive evolution of Toll-like receptor 5 in domesticated mammals

ABSTRACT: BACKGROUND: Previous studies have proposed that mammalian toll like receptors (TLRs) have evolved under diversifying selection due to their role in pathogen detection. To determine if this is the case, we examined the extent of adaptive evolution in the TLR5 gene in both individual species and defined clades of the mammalia. RESULTS: In support of previous studies, we find evidence of adaptive evolution of mammalian TLR5. However, we also show that TLR5 genes of domestic livestock have a concentration of single nucleotide polymorphisms suggesting a specific signature of adaptation. Using codon models of evolution we have identified a concentration of rapidly evolving codons within the TLR5 extracellular domain a site of interaction between host and the bacterial surface protein flagellin. CONCLUSIONS: The results suggest that interactions between pathogen and host may be driving adaptive change in TLR5 by competition between species. In support of this, we have identified single nucleotide polymorphisms (SNP) in sheep and cattle TLR5 genes that are co-localised and co-incident with the predicted adaptive codons suggesting that adaptation in this region of the TLR5 gene is on-going in domestic species.     

DNA sequence adjacent to flagellar genes and evolution of flagellar-phase variation

A variety of factors, including phase variation, are involved in the regulation of flagellin gene expression in Salmonella sp. Flagellar-phase variation refers to the alternate expression of two different flagellin genes, H1 and H2. Site-specific inversion of a DNA segment adjacent to the H2 gene is responsible for switching expression. The segment includes the H2 promoter as well as the hin gene, which is required to mediate the inversion. Sequences in this region have homology with the corresponding sequences adjacent to the H1 flagellin gene in Salmonella sp. and the hag flagellin gene in Escherichia coli. The hin gene has also been shown to be homologous to the gin gene, which is found on bacteriophage Mu. To understand gene expression and the origin of these relationships, we have compared the DNA sequence adjacent to all three flagellin genes. The sequence data suggest a mechanism for the evolution of the hin-H2 locus.     

Diversity and evolution of T-cell receptor variable region genes in mammals and birds

 The receptor of a T lymphocyte (TCR) recognizes nonself antigens in the company of major histocompatibility complex (MHC) molecules presented to it by the antigen-presenting cell. The variable region of TCR is encoded by either a concatenation of variable region (TCR-V), diversity region (TCR-D), and joining region (TCR-J) genes, or a concatenation of TCR-V and TCR-J genes. The TCR-V genes exist as a multigene family in vertebrate species. Here we study the evolutionary relationships of TCR-V genes from humans, sheep, cattle, rabbits, mice, and chicken. These six species can be classified into two groups according to the frequency of γδ T-cells in their peripheral T-cell populations. The "γδ low" group of species includes humans and mice, in which γδ T-cells constitute very limited portion of the T-cell population. The "γδ high" group includes sheep, cattle, rabbits, and chicken, in which γδ T-cells comprise up to 60% of the T-cell population. Here, we compiled TCR-V sequences from the six species and conducted a phylogenetic analysis. We identified various TCR-V gene subgroups based on the analysis. We found that humans and mice have representatives from nearly all of the subgroups identified, while other species have lost subgroups to different extent. Therefore, the γδ low species have a high degree of diversity of TCR-V genes, while γδ high species all have limited diversity of TCR-V genes. This pattern is similar to that found for immunoglobulin variable region (IGV) genes. Received: 20 May 1999 / Revised: 13 July 1999     

Encephalization and the evolution of longevity in mammals

Allometric principles account for most of the observed variation in maximum life span among mammals. When body-size effects are controlled for, most of the residual variance in mammalian life span can be explained by variations in brain size, metabolic rate and body temperature. It is shown that species with large brains for a given body size and metabolic rate, such as anthropoid primates, also have long maximum life spans. Conversely, mammals with relatively high metabolic rates and low levels of encephalization, as in most insectivores and rodents, tend to have short life spans. The hypothesis is put forward that encephalization and metabolic rate, which may govern other life history traits, such as growth and reproduction, are the primary determinants directing the evolution of mammalian longevity.     

Origin and evolution of TRIM proteins: new insights from the complete TRIM repertoire of zebrafish and pufferfish

Tripartite motif proteins (TRIM) constitute a large family of proteins containing a RING-Bbox-Coiled Coil motif followed by different C-terminal domains. Involved in ubiquitination, TRIM proteins participate in many cellular processes including antiviral immunity. The TRIM family is ancient and has been greatly diversified in vertebrates and especially in fish. We analyzed the complete sets of trim genes of the large zebrafish genome and of the compact pufferfish genome. Both contain three large multigene subsets--adding the hsl5/trim35-like genes (hltr) to the ftr and the btr that we previously described--all containing a B30.2 domain that evolved under positive selection. These subsets are conserved among teleosts. By contrast, most human trim genes of the other classes have only one or two orthologues in fish. Loss or gain of C-terminal exons generated proteins with different domain organizations; either by the deletion of the ancestral domain or, remarkably, by the acquisition of a new C-terminal domain. Our survey of fish trim genes in fish identifies subsets with different evolutionary dynamics. trims encoding RBCC-B30.2 proteins show the same evolutionary trends in fish and tetrapods: they evolve fast, often under positive selection, and they duplicate to create multigenic families. We could identify new combinations of domains, which epitomize how new trim classes appear by domain insertion or exon shuffling. Notably, we found that a cyclophilin-A domain replaces the B30.2 domain of a zebrafish fintrim gene, as reported in the macaque and owl monkey antiretroviral TRIM5α. Finally, trim genes encoding RBCC-B30.2 proteins are preferentially located in the vicinity of MHC or MHC gene paralogues, which suggests that such trim genes may have been part of the ancestral MHC.     

Different subcellular localisations of TRIM22 suggest species-specific function

The B30.2/SPRY domain is present in many proteins, including various members of the tripartite motif (TRIM) protein family such as TRIM5α, which mediates innate intracellular resistance to retroviruses in several primate species. This resistance is dependent on the integrity of the B30.2 domain that evolves rapidly in primates and exhibits species-specific anti-viral activity. TRIM22 is another positively selected TRIM gene. Particularly, the B30.2 domain shows rapid evolution in the primate lineage and recently published data indicate an anti-viral function of TRIM22. We show here that human and rhesus TRIM22 localise to different subcellular compartments and that this difference can be assigned to the positively selected B30.2 domain. Moreover, we could demonstrate that amino acid changes in two variable loops (VL1 and VL3) are responsible for the different subcellular localisations.     

Structure and evolution of 5S rRNA genes and pseudogenes in the genusAspergillus

Summary We have cloned and determined the nucleotide sequence of 18 DNA fragments hybridizing to 5S rRNA from twoAspergillus species-A. wentii andA. awamori. Four of the analyzed sequences were pseudogenes. The gene sequences of these two species were very similar and differed fromAspergillus nidulans at both constant and microheterogeneous sites.     

An active TRIM5 protein in rabbits indicates a common antiviral ancestor for mammalian TRIM5 proteins

The recent identification of antiretroviral tripartite motif-bearing restriction factors that protect against retroviral infection has revealed a novel branch of innate immunity. The factors target the retroviral capsid and inhibit infectivity soon after the capsid has entered the cytoplasm by an incompletely characterized mechanism. Restriction is species specific. For example, TRIM5alpha from Old World monkeys, but not humans, restricts human immunodeficiency virus type 1 infection. Here, we identify an antiviral TRIM5 molecule in rabbits that is closely related to antiviral TRIM5 of both primates and cattle. We demonstrate that the rabbit TRIM5 protein is active against divergent retroviruses and leads to a strong block to viral DNA synthesis and infectivity. Furthermore, we show that antiviral activity is directed against the viral capsid and that human TRIM5 proteins are dominant negative to restriction in rabbit cells. We propose that the sequence and restriction characteristics conserved between restriction factors from primates, cattle, and rabbits indicate that these factors have evolved from a common ancestor with antiretroviral properties.     

The evolution of concepts on the evolution of endothermy in birds and mammals

Warm-blooded animals, mammals and birds, are unique not because they are endothermic in the strict sense of the term but because they use an extravagant economy: they have high energy budgets and spend a large part of their energy resources on basic maintenance. Although several advantages of endothermy are easy to indicate, mechanisms behind evolution of such a wasteful life strategy remain unclear and have been subject to intensive debate. For two decades, the aerobic capacity model has been widely recognized as a promising hypothesis and has catalyzed a new direction in ecological and evolutionary physiology--the study of correlated evolution of behavioral and morphophysiological traits. Recently, two alternative models have been proposed, both of which see evolution of high metabolic rates in birds and mammals as an element in evolution of intensive parental care. Unlike previous models, which treated individuals as static objects of fixed properties, the parental care models explicitly incorporate life histories into a evolutionary-physiology research program. The aim of this article was to outline the process of evolution of major concepts in the field, which reflects development of the paradigm of modern evolutionary physiology.     

Disruption of quinoprotein ethanol dehydrogenase gene and adjacent genes in Pseudomonas putida HK5

Pseudomonas putida HK5 produces three different quinoprotein alcohol dehydrogenases: ADH-I, ADH-IIB and ADH-IIG. Gene organization of qedA , the gene for ADH-I, and other 10 genes in the cluster was related to the genome sequences of five other Pseudomonas strains. Insertion mutations in either qedA , exaE or agmR eliminated ADH-I activity, although the mutants were still able to grow on ethanol but more slowly than the wild-type strain. Mutant analysis demonstrated the requirement of agmR and exaE in ADH-I expression, and the tentative involvement of agmR , but not exaE , in the induction of ADH-IIB and ADH-IIG activities.     

Expansion of symmetric exon-bordering domains does not explain evolution of lineage specific genes in mammals

In order to examine the evolution of lineage specific genes, we analyzed intron phase distributions and exon-bordering domains in primate and rodent specific genes. We found that the expansion of symmetric exon-bordering domains could not explain the evolution of lineage specific genes. Rather internal intron loss of a domain can partially explain the excess of class 1–1 intron phases in the lineage specific genes. We suggest the event that led to excess of symmetric exons in lineage specific genes had little bearing on shaping the phenotypes specific to the individual lineage. Instead, Kruppel-associated box (KRAB) proteins associated with zinc finger C2H2 (zf-C2H2) type are likely to be responsible for the lineage specific function.     

Functional aspects of hemoglobin evolution in the mammals

Summary Comparative studies of red cell 2,3 Diphosphoglycerate (DPG) and its effect on hemoglobin oxygen affinity from a taxonomically diverse set of mammals indicate two anomalous groups: members of the superfamilies Bovoidea (Actiodactyla) and Feloidea (Carnivora). In both taxa all of the individuals assayed had very low or unmeasurable quantities of DPG and red cell lysates with little, if any, DPG effect as measured by the change in oxygen affinity in the absence and presence of the phosphate. However, in both groups compensatory changes have occurred in hemoglobin structure and function so as to reduce the native oxygen affinity and thus cause them to resemble the hemoglobins of DPG-utilizing mammals as they occur in the setting of the red cell. We conclude that this parallelism of function is the result of convergent evolution.