Comparison of protein and mRNA expression evolution in humans and chimpanzees

Even though mRNA expression levels are commonly used as a proxy for estimating functional differences that occur at the protein level, the relation between mRNA and protein expression is not well established. Further, no study to date has tested whether the evolutionary differences in mRNA expression observed between species reflect those observed in protein expression. Since a large proportion of mRNA expression differences observed between mammalian species appears to have no functional consequences for the phenotype, it is conceivable that many or most mRNA expression differences are not reflected at the protein level. If this is true, then differences in protein expression may largely reflect functional adaptations observed in species phenotypes. In this paper, we present the first direct comparison of mRNA and protein expression differences seen between humans and chimpanzees. We reproducibly find a significant positive correlation between mRNA expression and protein expression differences. This correlation is comparable in magnitude to that found between mRNA and protein expression changes at different developmental stages or in different physiological conditions within one species. Noticeably, this correlation is mainly due to genes with large expression differences between species. Our study opens the door to a new level of understanding of regulatory evolution and poses many new questions that remain to be answered.     

Estrogen inhibits the early development of mouse follicles through regulating the expression of Kit ligand

Estrogen inhibits cyst breakdown and primordial follicle assembling of germ cells, but little is known about the underlying mechanisms. We aimed to analyze the effects of estrogen on the early development of mouse follicles using an in vitro ovary culture system and in vivo injection. Newborn mouse ovarian tissues were cultured in vitro for 2 or 4 days with estrogen of 0 M, 10⁻⁸ M and 10⁻⁴ M, respectively, and neonatal mice were injected with 5 mg/kg/day estrogen. We found that the percentages of different-stage follicles significantly varied between the control and estrogen-treated groups. In vitro experiments showed that the unassembled follicles accounted for 70.5 ± 2.7% and the primordial follicles accounted for 29.5 ± 2.7% in the treatment group, but in the control group, ovaries had 61.7 ± 8.4% unassembled follicles. In vivo experiments showed that the percentages of unassembled follicles and primordial follicles were 37.1 ± 5.2% and 51.6 ± 2.4% in the control group, while they were 72.6 ± 5.2% and 25.1 ± 5.5% in the treatment group. Moreover, we analyzed the expression of Kit ligand in mouse ovaries treated by estrogen with real-time PCR and western blot technology, and found that compared with the control group, both mRNA and protein expression levels were decreased in the treatment group (P < 0.05). These results indicate that estrogen inhibits the development of mouse ovarian follicles by regulating the expression of Kit ligand.     

Kit ligand 2 promotes murine oocyte growth in vitro

Oocyte-granulosa cell communication, mediated by paracrine factors, is essential for oocyte development. Kit ligand (KITL) is expressed in granulosa cells as soluble (KITL1) or membrane-associated (KITL2) proteins. However, the relative biopotency of each isoform during oocyte development is unknown. Our initial results showed that Kitl2 was down-regulated in cultured granulosa cells. To determine the effect of the two isoforms of KITL on oocyte growth, Kitl-deficient fibroblasts were transfected with constructs expressing either KITL1 or KITL2, and growing oocytes were isolated from 12-day-old mice and cultured on the transfected fibroblasts for 2 days. At the end of culture, oocyte diameters were measured, the incidence of spontaneous germinal vesicle breakdown (GVBD) was noted, and oocytes were analyzed for KIT receptor expression. Oocyte growth occurred only in the presence of the KITL2-producing fibroblasts, and suppression of KITL2 expression impaired oocyte growth. Up-regulation of KIT expression occurred in the presence of KITL2 but not KITL1. The presence of KITL2 inhibited spontaneous GVBD. Meiosis inhibitors did not attenuate the GVBD that occurred in the absence of KITL2, suggesting that this process reflects oocyte degeneration rather than meiotic progression. These results indicate that KITL2 is the principal KITL isoform required for oocyte growth and survival in vitro.     

Genetics, development and evolution of adaptive pigmentation in vertebrates

The study of pigmentation has played an important role in the intersection of evolution, genetics, and developmental biology. Pigmentation's utility as a visible phenotypic marker has resulted in over 100 years of intense study of coat color mutations in laboratory mice, thereby creating an impressive list of candidate genes and an understanding of the developmental mechanisms responsible for the phenotypic effects. Variation in color and pigment patterning has also served as the focus of many classic studies of naturally occurring phenotypic variation in a wide variety of vertebrates, providing some of the most compelling cases for parallel and convergent evolution. Thus, the pigmentation model system holds much promise for understanding the nature of adaptation by linking genetic changes to variation in fitness-related traits. Here, I first discuss the historical role of pigmentation in genetics, development and evolutionary biology. I then discuss recent empirically based studies in vertebrates, which rely on these historical foundations to make connections between genotype and phenotype for ecologically important pigmentation traits. These studies provide insight into the evolutionary process by uncovering the genetic basis of adaptive traits and addressing such long-standing questions in evolutionary biology as (1) are adaptive changes predominantly caused by mutations in regulatory regions or coding regions? (2) is adaptation driven by the fixation of dominant mutations? and (3) to what extent are parallel phenotypic changes caused by similar genetic changes? It is clear that coloration has much to teach us about the molecular basis of organismal diversity, adaptation and the evolutionary process.     

The inheritance and evolution of leaf pigmentation and pubescence in teosinte

To investigate the genetic mechanisms that underlie morphological evolution in natural populations, we employed QTL mapping to dissect the inheritance of leaf sheath characters that distinguish Chalco from Balsas teosinte. Abundant macrohairs (trichomes) and intense anthocyanin accumulation are found in Chalco teosinte sheaths whereas Balsas teosinte leaf sheaths are green and glabrous. These character states may represent adaptations to the cooler highland (Chalco) vs. warmer middle-elevation (Balsas) climates. QTL mapping in multiple populations revealed a mix of major- and minor-effect QTL affecting both sheath color (anthocyanin) and macrohair abundance. The major QTL for macrohairs accounts for 52% of the parental difference. Epistatic interactions were detected between the major-effect QTL and multiple other QTL for both traits, accounting for substantial portions of phenotypic variance. Developmental analyses suggest that regulatory program changes underlie the phenotypic differences. Sheath anthocyanin QTL are clearly associated with b1 and a3, both of which are regulators of anthocyanin biosynthesis. Our findings suggest that changes in a small number of QTL can lead to morphological evolution by modulating existing developmental programs.     

Light-mediated changes in pigmentation of Pseudomonas aeruginosa cultures.

Cultures of Pseudomonas aeruginosa PAO grown under uninterrupted broad-spectrum light showed different pigmentation from dark-grown cultures. Whereas dark-grown bacteria produced pigments which resulted in blue-purple coloured agar, light-grown organisms produced red coloured plates. Extraction and quantification of pigments showed that both dark- and light-grown cultures produced similar concentrations of pyorubrin (red) and pyoverdin (yellow). In contrast, the concentration of pyocyanin (blue) was substantially reduced under certain lighting conditions. This decrease was dependent on both the light intensity and wavelength and occurred with light in the ultraviolet and violet region of the spectrum. After its release from bacteria, pyocyanin was rapidly and nonreversibly photoinactivated with first-order kinetics to produce colourless photoproduct(s).     

Kit ligand mediates survival of type a spermatogonia and dividing spermatocytes in postnatal mouse testes

In the mouse testis, spontaneous death of spermatogonia has a large impact on the output of differentiating spermatids. The tyrosine kinase receptor c-kit is expressed in type A, intermediate, and B spermatogonia, and kit-ligand (KL) is expressed in Sertoli cells. Previous work indicated a depletion of type A spermatogonia after in vivo exposure to an antibody that blocks c-kit function. The present work was undertaken to determine whether blocking c-kit function results in apoptosis of spermatogonia or in an inability of spermatogonia to proliferate. Testes sections were stained by a method that detects apoptotic cells in situ. In testes of 8-day postnatal (P8) males, type A spermatogonia are the predominant germ cell type present. Stained sections from P8 males injected with the c-kit antagonistic antibody ACK2 showed a fivefold higher rate of cell death than uninjected controls. At least a twofold increase was observed in P12 and P30 injected males and in P30 SI^d + males as compared to uninjected controls. Determination of the stage of germ cell development that was affected in P30 males indicated that the frequency of gonial cell death was increased fourfold, but the frequency of death in spermatocytes around the time of the meiotic division was increased 15-fold. It is concluded that KL acts to prevent apoptosis in the testis in vivo, that the membrane bound form of KL may be more effective, and that survival of late meiotic and dividing spermatocytes is regulated by KL through an indirect mechanism probably mediated by Sertoli cells. Thus, KL is an important regulator of spermatid output. © 1995 wiley-Liss, Inc.     

Conservation versus parallel gains in intron evolution

Orthologous genes from distant eukaryotic species, e.g. animals and plants, share up to 25–30% intron positions. However, the relative contributions of evolutionary conservation and parallel gain of new introns into this pattern remain unknown. Here, the extent of independent insertion of introns in the same sites (parallel gain) in orthologous genes from phylogenetically distant eukaryotes is assessed within the framework of the protosplice site model. It is shown that protosplice sites are no more conserved during evolution of eukaryotic gene sequences than random sites. Simulation of intron insertion into protosplice sites with the observed protosplice site frequencies and intron densities shows that parallel gain can account but for a small fraction (5–10%) of shared intron positions in distantly related species. Thus, the presence of numerous introns in the same positions in orthologous genes from distant eukaryotes, such as animals, fungi and plants, appears to reflect mostly bona fide evolutionary conservation.