Shedding Genomic Ballast: Extensive Parallel Loss of Ancestral Gene Families in Animals

Loss of ancestral gene families has played an important role in genomic specialization in animals. An examination of the pattern of gene family loss in completely sequenced animal genomes revealed that the same gene families have been lost independently in different lineages to a far greater extent than expected if gene loss occurred at random. This result implies that certain ancestral gene families—and thus the biological functions they encode—have been more expendable than others over the radiation of the animal phyla.Reviewing Editor: Dr. Manyuan Long     

Between-host evolution of cytotoxic T-lymphocyte epitopes in human immunodeficiency virus type 1: an approach based on phylogenetically independent comparisons

In human immunodeficiency virus type 1 (HIV-1), mutations that escape from cytotoxic T-lymphocyte (CTL) recognition have been documented, and sequence analyses have provided indirect support for the hypothesis that natural selection has favored CTL escape mutants within an infected host. In spite of such evidence for within-host selection by CTL, it has been more difficult to determine how natural selection by host CTL has influenced long-term evolution of HIV-1. We used statistical analysis of published HIV-1 genomic sequences to examine the role of natural selection in between-host evolution of CTL epitopes. Based on a phylogenetic analysis, we identified 21 pairs of closely related genomes isolated from different hosts and examined the pattern of nucleotide substitution in genomic regions encoding well-characterized CTL epitopes. The results revealed that certain CTL epitopes have been subject to repeated positive selection across the population, while others are generally conserved. Furthermore, evidence of positive selection was associated with divergence from the canonical epitope sequence and with an enhanced frequency of convergent amino acid sequence changes in CTL epitopes. The results support the hypothesis that CTL-driven selection has been a major factor in the long-term evolution of HIV-1.     

NTB-A, a new activating receptor in T cells that regulates autoimmune disease

The CD28 co-stimulatory pathway is well established for T cell activation; however, results from CD28 -/- mice suggest the existence of additional co-stimulatory pathways. Here we report the further characterization of a new member of the CD2 superfamily, NTB-A, important in T cell co-stimulation. NTB-A is expressed on T cells, and its expression is up-regulated on activated cells. Triggering of NTB-A with monoclonal antibodies in the absence of CD28 signals leads to T cell proliferation and interferon-gamma secretion but not interleukin-4. Cross-linking of NTB-A also induces phosphorylation of NTB-A and the association of SAP (SLAM-associated protein), the protein absent in X-linked lymphoproliferative disease. T helper cells differentiated by cross-linking NTB-A and CD3 developed predominantly into Th1 cells not Th2 cells. In vivo blocking of NTB-A interactions with its ligands by using soluble NTB-A-Fc fusion protein inhibits B cell isotype switching to IgG2a and IgG3, commonly induced by Th1-type cytokines. Most important, treatment of mice with NTB-A-Fc delays the onset of antigen-induced experimental allergic encephalomyelitis in myelin basic protein-T cell receptor transgenic mice, suggesting a role in T cell-mediated autoimmune disease. Regulation of interferon-gamma secretion, and not interleukin-4 in vitro, as well as inhibition of Th1 cell-induced isotype switching and attenuation of experimental allergic encephalomyelitis indicate that NTB-A is important for Th1 responses. The observation that cross-linking of NTB-A induces T cell activation, expansion, and Th1-type cytokine production suggests NTB-A is a novel co-stimulatory receptor. The identification of NTB-A as a regulator of T cell response paves the way to provide novel therapeutic approaches for modulation of the immune response.     

Water pulses and biogeochemical cycles in arid and semiarid ecosystems

The episodic nature of water availability in arid and semiarid ecosystems has significant consequences on belowground carbon and nutrient cycling. Pulsed water events directly control belowground processes through soil wet-dry cycles. Rapid soil microbial response to incident moisture availability often results in almost instantaneous C and N mineralization, followed by shifts in C/N of microbially available substrate, and an offset in the balance between nutrient immobilization and mineralization. Nitrogen inputs from biological soil crusts are also highly sensitive to pulsed rain events, and nitrogen losses, particularly gaseous losses due to denitrification and nitrate leaching, are tightly linked to pulses of water availability. The magnitude of the effect of water pulses on carbon and nutrient pools, however, depends on the distribution of resource availability and soil organisms, both of which are strongly affected by the spatial and temporal heterogeneity of vegetation cover, topographic position and soil texture. The inverse texture hypothesis for net primary production in water-limited ecosystems suggests that coarse-textured soils have higher NPP than fine-textured soils in very arid zones due to reduced evaporative losses, while NPP is greater in fine-textured soils in higher rainfall ecosystems due to increased water-holding capacity. With respect to belowground processes, fine-textured soils tend to have higher water-holding capacity and labile C and N pools than coarse-textured soils, and often show a much greater flush of N mineralization. The result of the interaction of texture and pulsed rainfall events suggests a corollary hypothesis for nutrient turnover in arid and semiarid ecosystems with a linear increase of N mineralization in coarse-textured soils, but a saturating response for fine-textured soils due to the importance of soil C and N pools. Seasonal distribution of water pulses can lead to the accumulation of mineral N in the dry season, decoupling resource supply and microbial and plant demand, and resulting in increased losses via other pathways and reduction in overall soil nutrient pools. The asynchrony of resource availability, particularly nitrogen versus water due to pulsed water events, may be central to understanding the consequences for ecosystem nutrient retention and long-term effects on carbon and nutrient pools. Finally, global change effects due to changes in the nature and size of pulsed water events and increased asynchrony of water availability and growing season will likely have impacts on biogeochemical cycling in water-limited ecosystems.     

Multiple fatty acid sensing mechanisms operate in enteroendocrine cells: novel evidence for direct mobilization of stored calcium by cytosolic fatty acid

Fatty acids (FA) with at least 12 carbon atoms increase intracellular Ca(2+) ([Ca(2+)](i)) to stimulate cholecystokinin release from enteroendocrine cells. Using the murine enteroendocrine cell line STC-1, we investigated whether candidate intracellular pathways transduce the FA signal, or whether FA themselves act within the cell to release Ca(2+) directly from the intracellular store. STC-1 cells loaded with fura-2 were briefly (3 min) exposed to saturated FA above and below the threshold length (C(8), C(10), and C(12)). C(12), but not C(8) or C(10), induced a dose-dependent increase in [Ca(2+)](i), in the presence or absence of extracellular Ca(2+). Various signaling inhibitors, including d-myo-inositol 1,4,5-triphosphate receptor antagonists, all failed to block FA-induced Ca(2+) responses. To identify direct effects of cytosolic FA on the intracellular Ca(2+) store, [Ca(2+)](i) was measured in STC-1 cells loaded with the lower affinity Ca(2+) dye magfura-2, permeabilized by streptolysin O. In permeabilized cells, again C(12) but not C(8) or C(10), induced release of stored Ca(2+). Although C(12) released Ca(2+) in other permeabilized cell lines, only intact STC-1 cells responded to C(12) in the presence of extracellular Ca(2+). In addition, 30 min exposure to C(12) induced a sustained elevation of [Ca(2+)](i) in the presence of extracellular Ca(2+), but only a transient response in the absence of extracellular Ca(2+). These results suggest that at least two FA sensing mechanisms operate in enteroendocrine cells: intracellularly, FA (>/=C(12)) transiently induce Ca(2+) release from intracellular Ca(2+) stores. However, they also induce sustained Ca(2+) entry from the extracellular medium to maintain an elevated [Ca(2+)](i).     

Two patterns of genome organization in mammals: the chromosomal distribution of duplicate genes in human and mouse

Gene duplication occurs repeatedly in the evolution of genomes, and the rearrangement of genomic segments has also occurred repeatedly over the evolution of eukaryotes. We studied the interaction of these two factors in mammalian evolution by comparing the chromosomal distribution of multigene families in human and mouse. In both species, gene families tended to be confined to a single chromosome to a greater extent than expected by chance. The average number of families shared between chromosomes was nearly 60% higher in mouse than in human, and human chromosomes rarely shared large numbers of gene families with more than one or two other chromosomes, whereas mouse chromosomes frequently did so. A higher proportion of duplicate gene pairs on the same chromosome originated from recent duplications in human than in mouse, whereas a higher proportion of duplicate gene pairs on separate chromosomes arose from ancient duplications in human than in mouse. These observations are most easily explained by the hypotheses that (1) most gene duplications arise in tandem and are subsequently separated by segmental rearrangement events, and (2) that the process of segmental rearrangement has occurred at a higher rate in the lineage of mouse than in that of human.     

A novel mechanism for adenylyl cyclase inhibition from the crystal structure of its complex with catechol estrogen

Catechol estrogens are steroid metabolites that elicit physiological responses through binding to a variety of cellular targets. We show here that catechol estrogens directly inhibit soluble adenylyl cyclases and the abundant trans-membrane adenylyl cyclases. Catechol estrogen inhibition is non-competitive with respect to the substrate ATP, and we solved the crystal structure of a catechol estrogen bound to a soluble adenylyl cyclase from Spirulina platensis in complex with a substrate analog. The catechol estrogen is bound to a newly identified, conserved hydrophobic patch near the active center but distinct from the ATP-binding cleft. Inhibitor binding leads to a chelating interaction between the catechol estrogen hydroxyl groups and the catalytic magnesium ion, distorting the active site and trapping the enzyme substrate complex in a non-productive conformation. This novel inhibition mechanism likely applies to other adenylyl cyclase inhibitors, and the identified ligand-binding site has important implications for the development of specific adenylyl cyclase inhibitors.     

Cellular FLIP long form augments caspase activity and death of T cells through heterodimerization with and activation of caspase-8

Caspase activity is required not only for the death of T cells, but also for their activation. A delicate balance of caspase activity is thus required during T cell activation at a level that will not drive cell death. How caspase activity is initiated and regulated during T cell activation is not known. One logical candidate for this process is cellular FLIP long form (c-FLIP(L)), because it can block caspase-8 recruitment after Fas (CD95) ligation as well as directly heterodimerize with and activate caspase-8. The current findings demonstrate that after T cell activation, caspase-8 and c-FLIP(L) associate in a complex enriched for active caspases. This occurs coincidently with the cleavage of two known caspase-8 substrates, c-FLIP(L) and receptor interacting protein 1. Caspase activity is higher in wild-type CD8(+) than CD4(+) effector T cells. Increased expression of c-FLIP(L) results in augmented caspase activity in resting and effector T cells to levels that provoke cell death, especially of the CD8 subset. c-FLIP(L) is thus not only an inhibitor of cell death by Fas, it can also act as a principal activator of caspases independently of Fas.     

Unusually high frequency MHC class I alleles in Mauritian origin cynomolgus macaques

Acute shortages of Indian origin Rhesus macaques significantly hinder HIV/AIDS research. Cellular immune responses are particularly difficult to study because only a subset of animals possess MHC class I (MHC I) alleles with defined peptide-binding specificities. To expand the pool of nonhuman primates suitable for studies of cellular immunity, we defined 66 MHC I alleles in Cynomolgus macaques (Macaca fascicularis) of Chinese, Vietnamese, and Mauritian origin. Most MHC I alleles were found only in animals from a single geographic origin, suggesting that Cynomolgus macaques from different origins are not interchangeable in studies of cellular immunity. Animals from Mauritius may be particularly valuable because >50% of these Cynomolgus macaques share the MHC class I allele combination Mafa-B*430101, Mafa-B*440101, and Mafa-B*460101. The increased MHC I allele sharing of Mauritian origin Cynomolgus macaques may dramatically reduce the overall number of animals needed to study cellular immune responses in nonhuman primates while simultaneously reducing the confounding effects of genetic heterogeneity in HIV/AIDS research.