Tempo and mode of evolution of the Rh blood group genes before and after gene duplication

The Rh blood group genes became duplicated in a common ancestor of human–chimpanzee–gorilla. We compared the evolutionary rates of the Rh blood group genes for each exon for branches connecting to humans, having duplicated Rh loci, and to orangutan, gibbon, and Old World monkeys, species having a single Rh locus. Our results show that evolutionary rates of nonsynonymous substitutions at exon 7 became accelerated in the human lineage. Furthermore, we surveyed the sequence variation in the region surrounding exon 7 of gibbons to clarify whether the diversity of the human exon 7 was introduced after the duplication or had been maintained before it. Two amino acid polymorphisms in white-handed gibbons were observed in the immediate vicinity of the D-specific motif in the human exon 7. Although the evolutionary rate of exon 7 was accelerated after the gene duplication, our results suggest that exon 7 had the potential for change even before the gene duplication. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Structural basis for type II membrane protein binding by ERM proteins revealed by the radixin-neutral endopeptidase 24.11 (NEP) complex

ERM (Ezrin/Radixin/Moesin) proteins mediate formation of membrane-associated cytoskeletons by simultaneously binding actin filaments and the C-terminal cytoplasmic tails of adhesion molecules (type I membrane proteins). ERM proteins also bind neutral endopeptidase 24.11 (NEP), a type II membrane protein, even though the N-terminal cytoplasmic tail of NEP possesses the opposite peptide polarity to that of type I membrane proteins. Here, we determined the crystal structure of the radixin FERM (Four point one and ERM) domain complexed with the N-terminal NEP cytoplasmic peptide. In the FERM-NEP complex, the amphipathic region of the peptide forms a beta strand followed by a hairpin that bind to a shallow groove of FERM subdomain C. NEP binding is stabilized by beta-beta interactions and docking of the NEP hairpin into the hydrophobic pocket of subdomain C. Whereas the binding site of NEP on the FERM domain overlaps with the binding site of intercellular adhesion molecule (ICAM)-2, NEP lacks the Motif-1 sequence conserved in ICAM-2 and related adhesion molecules. The NEP hairpin, although lacking the typical inter-chain hydrogen bond but is stabilized by hydrogen bonds with the main chain and side chains of subdomain C, directs the C-terminal basic region of the NEP peptide away from the groove and toward the membrane. The overlap of the binding sites on subdomain C for NEP and Motif-1 adhesion molecules such as CD44 provides the structural basis for the suppression of cell adhesion through interaction between NEP and ERM proteins.     

Effect of aging on EGF-stimulated replication of specific genes in rat hepatocytes

EGF-stimulated replication of specific genes was examined in primary hepatocyte cultures from mature (6 months) and senescent (24 months) rats. Basal and EGF-stimulated [³H]thymidine incorporation and DNA polymerase α activities, as well as total cellular DNA, were also assessed. The genes examined were dihydrofolate reductase (DHFR) and c-myc, as well as total mitochondrial DNA (mt DNA). Although [³H]thymidine incorporation, DNA polymerase α activity, total cellular DNA, DHFR, and c-myc gene specific DNA replication stimulated by EGF are reduced with age, mt DNA replication is not affected by either EGF or age. Chromosomal DNA replication is mediated mainly by DNA polymerase α while mt DNA replication is mediated by its own DNA polymerase γ. Thus, the age-related decline in stimulated DNA replication appears to be associated mainly with the DNA polymerase α activation pathway. J. Cell. Physiol. 176:32–39, 1998. Published 1998 Wiley-Liss, Inc.

1 This article is a US Government work and, as such, is in the public domain in the United States of America.

     

Regional expression of the rice KN1-type homeobox gene family during embryo, shoot, and flower development.

We report the isolation, sequence, and pattern of gene expression of members of the KNOTTED1 (KN1)-type class 1 homeobox gene family from rice. Phylogenetic analysis and mapping of the rice genome revealed that all of the rice homeobox genes that we have isolated have one or two direct homologs in maize. Of the homeobox genes that we tested, all exhibited expression in a restricted region of the embryo that defines the position at which the shoot apical meristem (SAM) would eventually develop, prior to visible organ formation. Several distinct spatial and temporal expression patterns were observed for the different genes in this region. After shoot formation, the expression patterns of these homeobox genes were variable in the region of the SAM. These results suggest that the rice KN1-type class 1 homeobox genes function cooperatively to establish the SAM before shoot formation and that after shoot formation, their functions differ.     

Evolution of Rh Blood Group Genes Have Experienced Gene Conversions and Positive Selection

There are two tightly linked loci (D and CE) for the human Rh blood group. Their gene products are membrane proteins having 12 transmembrane domains and form a complex with Rh50 glycoprotein on erythrocytes. We constructed phylogenetic networks of human and nonhuman primate Rh genes, and the network patterns suggested the occurrences of gene conversions. We therefore used a modified site-by-site reconstruction method by using two assumed gene trees and detected 9 or 11 converted regions. After eliminating the effect of gene conversions, we estimated numbers of nonsynonymous and synonymous substitutions for each branch of both trees. Whichever gene tree we selected the branch connecting hominoids and Old World monkeys showed significantly higher nonsynonymous than synonymous substitutions, an indication of positive selection. Many other branches also showed higher nonsynonymous than synonymous substitutions; this suggests that the Rh genes have experienced some kind of positive selection. Received: 16 March 1999 / Accepted: 17 June 1999     

Transglycosylase and endopeptidase participate in the degradation of murein during autolysis of Escherichia coli.

The cell wall degradation products released from Escherichia coli during autolysis triggered by cephaloridine or trichloroacetic acid were isolated and characterized. Murein was selectively lost from the disaccharide tetrapeptides and the bisdisaccharide tetrapeptide components. Two major autolytic products accounted for more than 85% of the released material. Compound 1 (60 to 80% of released material) was a disaccharide tetrapeptide monomer containing a 1,6-anhydromuramic acid residue. Compound 2 (15 to 30% of released material) was a mixture of a tritripeptide and a tritetrapeptide without hexosamines. Taken together the findings suggest that autolytic cell wall degradation in E. coli is selective and involves the activity of both the hydrolytic transglycosylase and an endopeptidase. Upon release, at least some of the wall components were also exposed to the activity of the N-acetylmuramic acid-L-alanine amidase.     

Spontaneous production of interleukin-1-like cytokine from a mouse osteoblastic cell line (MC3T3-E1)

We have investigated the role of interleukin-1 in the regulatory mechanisms of a bone remodeling system. Osteoblastic cell line (MC3T3-E1) established from newborn mouse calvaria spontaneously produced interleukin-1-like cytokine. Although the interleukin-1-like activity was not observed in culture supernatants of the cells during their exponential phase of growth, a most remarkable interleukin-1-like activity was detected in the supernatants of cells cultured in serum-free alpha-MEM on day 5 after the cells had formed a confluent monolayer. Gel filtration analysis indicated that the interleukin-1-like cytokine exhibits some heterogeneity in size.     

Restricted diffusion effect on the binding of proteins to porous polymer resins as studied by repetitive injection method

A solution of bovine serum albumin (BSA) is repeatedly injected into a column packed with highly porous and hydrophobic polymer resins at appropriate intervals. The injected BSA is thoroughly retained in the column for 10 injections and, afterwards, starts to be eluted from the column gradually. Taking into consideration the restricting effect of already bound BSA upon the diffusion of newly injected BSA into the pores of the polymer resins, we can interpret the BSA elution profile from columns packed with polymer resin of various pore sizes and porosities. The effects of the binding rate constant and BSA concentration upon the elution profiles of BSA are also analyzed. Formyl groups are introduced into the polymers as a binding site with proteins, and the elution profiles of BSA from the column packed with the formylated resin are also analyzed.