Evolution and higher-order structure of architectural proteins in silkmoth chorion.

Genomic and cDNA clones have been sequenced that encode the E2 silkmoth chorion protein. E2 assembles with E1 [Regier, J.C. and Pacholski, P. (1985) Proc. Natl. Acad. Sci. USA, 82, 6035-6039] to form the 'filler' that helps mold prominent chorion surface structures called aeropyle crowns. E2 has two distinct domains. The amino terminal domain consists of four alternating stretches of hydrophobic and hydrophilic residues, the first three of which are homologous in sequence to about half of the E1 protein. Comparison of predicted secondary structures provides further support for the localized homology of E2 and E1. The carboxy terminal domain of E2 is much longer, is hydrophilic and consists entirely of multiple tandem copies of a single, variant hexapeptide repeat sequence that is absent from E1. Numbers of hexapeptide repeat sequences differed dramatically in two animals. The types of events required for such variation are discussed. Finally, we have elaborated our earlier model for how E proteins may assemble in vivo to form filler.     

A comparative study of eggshell proteins in lepidoptera

As a first step in the study of chorion composition, biochemical development and morphogenesis, we have studied the proteins of moth chorions (eggshells). We draw attention to the extensive similarities of these proteins in a variety of species. We also report that the eggshell proteins are deposited in succession, each with its characteristic time table. This phenomenon may be related to the morphogenesis of chorion.     

Assignment of orthologous relationships among mammalian alpha-globin genes by examining flanking regions reveals a rapid rate of evolution

In order to study the relationships among mammalian alpha-globin genes, we have determined the sequence of the 3' flanking region of the human alpha 1 globin gene and have made pairwise comparisons between sequenced alpha-globin genes. The flanking regions were examined in detail because sequence matches in these regions could be interpreted with the least complication from the gene duplications and conversions that have occurred frequently in mammalian alpha-like globin gene clusters. We found good matches between the flanking regions of human alpha 1 and rabbit alpha 1, human psi alpha 1 and goat I alpha, human alpha 2 and goat II alpha, and horse alpha 1 and goat II alpha. These matches were used to align the alpha-globin genes in gene clusters from different mammals. This alignment shows that genes at equivalent positions in the gene clusters of different mammals can be functional or nonfunctional, depending on whether they corrected against a functional alpha-globin gene in recent evolutionary history. The number of alpha-globin genes (including pseudogenes) appears to differ among species, although highly divergent pseudogenes may not have been detected in all species examined. Although matching sequences could be found in interspecies comparisons of the flanking regions of alpha- globin genes, these matches are not as extensive as those found in the flanking regions of mammalian beta-like globin genes. This observation suggests that the noncoding sequences in the mammalian alpha-globin gene clusters are evolving at a faster rate than those in the beta-like globin gene clusters. The proposed faster rate of evolution fits with the poor conservation of the genetic linkage map around alpha-globin gene clusters when compared to that of the beta-like globin gene clusters. Analysis of the 3' flanking regions of alpha-globin genes has revealed a conserved sequence approximately 100-150 bp 3' to the polyadenylation site; this sequence may be involved in the expression or regulation of alpha-globin genes.      

The rabbit alpha-like globin gene cluster is polymorphic both in the sizes of BamHI fragments and in the numbers of duplicated sets of genes

The alpha-like globin gene cluster in rabbits contains embryonic zeta- globin genes, an adult alpha-globin gene, and theta-globin genes of undetermined function. The basic arrangement of genes, deduced from analysis of cloned DNA fragments, is 5'-zeta 0-zeta 1-alpha 1-theta 1- zeta 2-zeta 3-theta 2-3'. However, the pattern of restriction fragments containing zeta- and theta-globin genes varies among individual rabbits. Analysis of BamHI fragments of genomic DNA from 24 New Zealand white rabbits revealed eight different patterns of fragments containing zeta-globin genes. The large BamHI fragments containing genes zeta 0 and zeta 1 are polymorphic in length, whereas a 1.9-kb fragment containing the zeta 2 gene and the 3.5-kb fragment containing the zeta 3 gene do not vary in size. In contrast to this constancy in the size of the restriction fragments, the copy number of the zeta 2 and zeta 3 genes does vary among different rabbits. No length polymorphism was detected in the BamHI fragments containing the theta-globin genes, but again the copy number varies for restriction fragments containing the theta 2 gene. The alpha 1- and theta 1-globin genes are located in a nonpolymorphic 7.2-kb BamHI fragment. The combined data from hybridization with both zeta and theta probes shows that the BamHI cleavage pattern does not vary within the region 5'-alpha 1-theta 1- zeta 2-zeta 3-theta 2-3', but the pattern genomic blot-hybridization patterns for the progeny of parental rabbits with different zeta-globin gene patterns shows that the polymorphic patterns are inherited in a Mendelian fashion. Two different haplotypes have been mapped based on the genomic blot-hybridization data. The variation in the alpha-like globin gene cluster in the rabbit population results both from differences in the copy number of the duplication block containing the zeta-zeta-theta gene set and from the presence or absence of polymorphic BamHI sites.      

Out of Africa and back again: nested cladistic analysis of human Y chromosome variation

We surveyed nine diallelic polymorphic sites on the Y chromosomes of 1,544 individuals from Africa, Asia, Europe, Oceania, and the New World. Phylogenetic analyses of these nine sites resulted in a tree for 10 distinct Y haplotypes with a coalescence time of approximately 150,000 years. The 10 haplotypes were unevenly distributed among human populations: 5 were restricted to a particular continent, 2 were shared between Africa and Europe, 1 was present only in the Old World, and 2 were found in all geographic regions surveyed. The ancestral haplotype was limited to African populations. Random permutation procedures revealed statistically significant patterns of geographical structuring of this paternal genetic variation. The results of a nested cladistic analysis indicated that these geographical associations arose through a combination of processes, including restricted, recurrent gene flow (isolation by distance) and range expansions. We inferred that one of the oldest events in the nested cladistic analysis was a range expansion out of Africa which resulted in the complete replacement of Y chromosomes throughout the Old World, a finding consistent with many versions of the Out of Africa Replacement Model. A second and more recent range expansion brought Asian Y chromosomes back to Africa without replacing the indigenous African male gene pool. Thus, the previously observed high levels of Y chromosomal genetic diversity in Africa may be due in part to bidirectional population movements. Finally, a comparison of our results with those from nested cladistic analyses of human mtDNA and beta-globin data revealed different patterns of inferences for males and females concerning the relative roles of population history (range expansions) and population structure (recurrent gene flow), thereby adding a new sex-specific component to models of human evolution.      

Nitrogen input quality changes the biochemical composition of soil organic matter stabilized in the fine fraction: a long-term study

The chemical composition of soil organic matter (SOM) is a key determinant of its biological stability. Our objective in this study was to evaluate the effects of various sources of supplemental N on the chemical composition of SOM in the fine (<5 μm) mineral fraction. Treatments were fallow, maize/soybean in rotation, and continuous maize receiving no fertilizer (maize0N), synthetic fertilizer N (maize + N), or composted manure (maize + manure). The chemical structures in SOM associated with the fine fraction were determined using XANES spectroscopy at the C and N K-edges, which was assessed using multidimensional scaling. Analysis of amino sugar biomarkers were used to evaluate the fungal:bacterial contributions to the SOM. The addition of N to soils (i.e., maize + N, maize + manure, and maize/soybean treatments) resulted in the enrichment of proteinaceous compounds. Soils which did not receive supplemental N (i.e., fallow and maize0N treatments) were enriched in plant-derived compounds (e.g., aromatics, phenolics, carboxylic acids and aliphatic compounds), suggesting that decomposition of plant residues was constrained by N-limitation. Microbial populations assessed by amino sugar biomarker ratios showed that the highest contributions to SOM by bacteria occurred in the maize + manure treatment (high N input), and by fungi in the fallow treatment (low N input). The SOM in the maize + N and maize/soybean treatments was enriched in N-bonded aromatics; we attribute this enrichment to the abiotic reaction of inorganic N with organic C structures. The SOM in the maize + manure treatment was enriched in pyridinic-N, likely as a result of intense microbial processing and high SOM turnover. The presences of signals for ketone and pyrrole compounds in XANES spectra suggest their use as biomarkers for microbially transformed and stabilized SOM. The SOM in the maize + manure treatment was enriched in ketones which are likely microbial by-products of fatty acid catabolism. Pyrrole compounds, which may accumulate over the long term as by-products of protein transformations by an N-limited microbial community, were dominant in the fallow soil. A combination of molecular spectroscopy and biomarker analysis showed that the source of supplemental N to soil influences the stable C- and N-containing compounds of SOM in a long-term field study. Indeed, any increase in N availability allowed the microbial community to transform plant material into microbial by-products which occur as stable SOM compounds in the fine soil fraction.