Accelerated pseudogenization of trace amine‐associated receptor genes in primates

Trace amines (TAs) in the mammalian brain have been investigated for four decades. Trace amine‐associated receptors (TAARs) were discovered during the search for receptors activated by TAs. TAARs are considered a second class of vertebrate olfactory receptors and successfully proliferated in conjunction with adaptation to living on the ground to detect carnivore odors. Thus, therian mammals have a high number of TAAR genes due to rapid species‐specific gene duplications. In primate lineages, however, their genomes have significantly smaller numbers of TAAR genes than do other mammals. To elucidate the evolutionary force driving these patterns, exhaustive data mining of TAAR genes was performed for 13 primate genomes (covering all four infraorders) and two nonprimate euarchontan genomes. This study identified a large number of pseudogenes in many of these primate genomes and thus investigated the pseudogenization event process for the TAAR repertoires. The degeneration of TAARs is likely associated with arboreal inhabitants reducing their exposure to carnivores, and this was accelerated by the change in the nose shape of haplorhines after their divergence from strepsirrhines. Arboreal life may have decreased the reliance on the chemosensing of predators, suggestive of leading to the depauperation of TAAR subfamilies. The evolutionary deterioration of TAARs in primates has been reestablished in recently derived primates due to high selection pressure and probably functional diversity.     

An evolutionary expressed sequence tag analysis of Drosophila spermatheca genes

This study investigates genes enriched for expression in the spermatheca, the long-term sperm storage organ (SSO) of female Drosophila. SSO genes are likely to play an important role in processes of sexual selection such as sperm competition and cryptic female choice. Although there is keen interest in the mechanisms of sexual selection at the molecular level, very little is known about the female genes that are involved. In the present study, a high proportion of genes enriched for expression in the spermatheca are evolving rapidly. Most of the rapidly evolving genes are proteases and genes of unknown function that could play a specialized role in the spermatheca. A high percentage of the rapidly evolving genes have secretion signals and thus could encode proteins that directly interact with ejaculate proteins and coevolve with them. In addition to identifying rapidly evolving genes, the present study documents categories of genes that could play a role in spermatheca function such as storing, maintaining, and utilizing sperm. In general, candidate genes discovered in this study could play a key role in sperm competition, cryptic female choice of sperm, and sexually antagonistic coevolution, and ultimately speciation.     

Drosophila Bcl-2 proteins participate in stress-induced apoptosis, but are not required for normal development

Many developing tissues require programmed cell death (PCD) for proper formation. In mice and C. elegans, developmental PCD is regulated by the Bcl-2 family of proteins. Two bcl-2 genes are encoded in the Drosophila genome (debcl/dBorg1/Drob-1/dBok and buffy/dBorg2) and previous RNAi-based studies suggested a requirement for these in embryonic development. However, we report here that, despite the fact that many tissues in fruit flies are shaped by PCD, deletion of the bcl-2 genes does not perturb normal development. We investigated whether the fly bcl-2 genes regulate non-apoptotic processes that require caspases, but found these to be bcl-2 gene-independent. However, irradiation of the mutants demonstrates that DNA damage-induced apoptosis, mediated by Reaper, is blocked by buffy and that debcl is required to inhibit buffy. Our results demonstrate that developmental PCD regulation in the fly does not rely upon the Bcl-2 proteins, but that they provide an added layer of protection in the apoptotic response to stress.     

Integrated genomics and phenotype microarray analysis of Saccharomyces cerevisiae industrial strains for rice wine fermentation and recombinant protein production

The industrial potential of Saccharomyces cerevisiae has extended beyond its traditional use in fermentation to various applications, including recombinant protein production. Herein, comparative genomics was performed with three industrial S. cerevisiae strains and revealed a heterozygous diploid genome for the 98-5 and KSD-YC strains (exploited for rice wine fermentation) and a haploid genome for strain Y2805 (used for recombinant protein production). Phylogenomic analysis indicated that Y2805 was closely associated with the reference strain S288C, whereas KSD-YC and 98-5 were grouped with Asian and European wine strains, respectively. Particularly, a single nucleotide polymorphism (SNP) in FDC1, involved in the biosynthesis of 4-vinylguaiacol (4-VG, a phenolic compound with a clove-like aroma), was found in KSD-YC, consistent with its lack of 4-VG production. Phenotype microarray (PM) analysis showed that KSD-YC and 98-5 displayed broader substrate utilization than S288C and Y2805. The SNPs detected by genome comparison were mapped to the genes responsible for the observed phenotypic differences. In addition, detailed information on the structural organization of Y2805 selection markers was validated by Sanger sequencing. Integrated genomics and PM analysis elucidated the evolutionary history and genetic diversity of industrial S. cerevisiae strains, providing a platform to improve fermentation processes and genetic manipulation.     

Muscular cell proliferative and protective effects of N-acetylcysteine by modulating activity of extracellular signal-regulated protein kinase

N-acetylcysteine (NAC), an antioxidant and a precursor of glutathione, is currently in clinical use for various pathological conditions. No data is available as to the relationship between NAC and muscular cell proliferation or muscular degenerative disease. In this study, we assessed the effect of NAC on growth of L6 myoblasts, a rat skeletal muscle cell line, under normal or bupivacaine-treated condition. Of interest, under normal growth conditions, NAC treatment concentration-dependently increased viability, cell number, and DNA incorporation of L6 cells. Remarkably, NAC treatment for 12 to 24 h led to increased phosphorylation of ERKs, a family of mitogen-activated protein kinase known to involve in cell proliferation, in L6 cells, and specific inhibition of ERKs by PD98059, a selective inhibitor of ERKs, greatly abolished the ability of NAC to increase the number of L6 cells. More importantly, pretreatment with NAC effectively blocked decrease in the number and ERKs phosphorylation in L6 cells induced by the exposure of bupivacaine, a local anesthetic with myotoxicity. These results collectively suggest that NAC has muscular cell proliferative and protective effects and the effects by NAC appear to be, in part, mediated via increase in ERKs activation.     

Cirsium japonicum var. maackii and apigenin block Hif‐2α‐induced osteoarthritic cartilage destruction

Although Hif‐2α is a master regulator of catabolic factor expression in osteoarthritis development, Hif‐2α inhibitors remain undeveloped. The aim of this study was to determine whether Cirsium japonicum var. maackii (CJM) extract and one of its constituents, apigenin, could attenuate the Hif‐2α‐induced cartilage destruction implicated in osteoarthritis progression. In vitro and in vivo studies demonstrated that CJM reduced the IL‐1β‐, IL‐6, IL‐17‐ and TNF‐α‐induced up‐regulation of MMP3, MMP13, ADAMTS4, ADAMTS5 and COX‐2 and blocked osteoarthritis development in a destabilization of the medial meniscus mouse model. Activation of Hif‐2α, which directly up‐regulates MMP3, MMP13, ADAMTS4, IL‐6 and COX‐2 expression, is inhibited by CJM extract. Although cirsimarin, cirsimaritin and apigenin are components of CJM and can reduce inflammation, only apigenin effectively reduced Hif‐2α expression and inhibited Hif‐2α‐induced MMP3, MMP13, ADAMTS4, IL‐6 and COX‐2 expression in articular chondrocytes. IL‐1β induction of JNK phosphorylation and IκB degradation, representing a critical pathway for Hif‐2α expression, was completely blocked by apigenin in a concentration‐dependent manner. Collectively, these effects indicate that CJM and one of its most potent constituents, apigenin, can lead to the development of therapeutic agents for blocking osteoarthritis development as novel Hif‐2α inhibitors.