Molecular coevolution: DNA divergence and the maintenance of function.
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Animals↗
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In vivo studies on prolactin function in the female rat: divergent effects of treatment with bromergocryptine and antisera to rat prolactin.
The effect of suppression of prolactin (PRL) serum levels on early pregnancy and lactation in the rat by means of either bromergocryptine (BEC) or rabbit antiserum to rat PRL has been examined. BEC terminated early pregnancy when given on any day from 1 to 6 and significantly impaired lactation performance when injected during the lactation period. Antibodies against rat PRI, however, showed no effect on either early pregnancy or lactation, although the sera of the treated rats contained free PRL antibodies as evidence for sufficient dosage of antiserum. This finding can be explained in two ways: either the antibodies are not able to neutralize the biological activity of the bound PRL, or the effect of BEC is not mediated by PRL-suppression alone but requires a second component not provided by the specific antiserum.
Animals↗
Preproenkephalin DNA-binding proteins in the rat: 5' flanking region.
Various extracellular signals (i.e. transmitters, hormones, growth factors, etc.), together with their respective second-messenger pathways, regulate transmitter biosynthesis and neuronal function by altering gene expression. In this study we validated a protocol for isolating rat striatum and adrenal medullary nuclei for the purpose of extracting, identifying, and characterizing, nuclear regulatory factors which may serve a functional role in signal-transduction processes. Through gel retardation studies using a 299 base pair (bp) XmnI-SacI 32P-labeled probe (derived from the 5' untranslated region of the rat preproenkephalin gene), we show that different patterns of retained bands result from nuclear extracts derived from rat adrenal medulla and striatum (as well as from other tissue). These tissue differences may have biological significance since rat adrenal medullae have low basal enkephalin levels while the striatum has high levels of this peptide and its respective mRNA. Additionally, certain retained bands were common to both cytosolic and nuclear compartments, suggesting binding factors may be located in either cell space. An initial biochemical characterization of these factors was also undertaken. Generally, salt levels of 100 mM or more reduced factor binding while 10-50 mM sodium ion levels showed preferentially enhanced bands. Binding activity appeared optimal at pH 6.8. As all retained bands were abrogated by proteinase K treatment, these factors appear to have a significant protein component. Finally, of particular interest is that this 299 bp region contains many sequences showing over 80% sequence identity with several previously characterized transcriptional control elements (i.e. cAMP and phorbol ester inducible enhancers, GCN4, AP1, Sp1, CCAAT binding factor, ATF, and AP2). If binding is confirmed (footprint analysis) and function validated (transfection studies), the evolutionary significance of the apparent presence of gene regulatory sequences and functional element divergence of the DNA region between different species can be evaluated.
Adrenal Medulla↗
Molecular evolution of epididymal lipocalin genes localized on mouse chromosome 2.
We previously identified two murine secretory proteins, mE-RABP(Lcn5) and mEP17(Lcn8), belonging to the lipocalin family and specifically expressed in the epididymis. The genes are contiguous and localized on mouse chromosome 2. We now show that five other related lipocalin genes, Lcn9, Lcn10, Lcn11, Lcn12, and Lcn13, that evolved by in situ tandem duplication are present on the same locus. Lcn9, Lcn10, Lcn12, and Lcn13 genes, like Lcn5 and Lcn8 genes, are specifically expressed in the mouse epididymis. However, each gene has a distinct spatial expression within the epididymis and different regulation. Analysis of the human genome sequence shows the presence of genes encoding lipocalins with genomic organization, chromosomal arrangement, and orientation similar to that of the corresponding murine genes, indicating that the epididymal cluster is evolutionary conserved. A phylogenetic analysis of the new epididymal proteins reveals their spread position in the lipocalin protein family tree. This suggests the preservation of the regulatory sequences, while protein sequences have greatly diverged, reflecting functional diversity and possibly multifunctionality. In terms of the cluster ancestry, epididymal expression possibly appeared in a PGDS-like lipocalin in amniotes, and the duplications generating the cluster occurred at least in the common ancestor of rodents and primates. The presence and conservation of a cluster of five genes encoding epididymal lipocalins, differently regulated and regionalized in the epididymis, strongly suggests that these proteins may play an important role for male fertility.
Acute-Phase Proteins↗
Ligand specificity and developmental expression of RXR and ecdysone receptor in the migratory locust.
The ecdysone receptor(1), which is a heterodimer of EcR and the retinoic acid receptor (RXR) homolog, Ultraspiracle (USP), has been well studied in the evolutionarily advanced and derived insects, the flies and moths. It is less well characterized in more primitive insect orders such as the Orthoptera, which include the grasshoppers and locusts. Following our previous isolation from Locusta migratoria (Lm) of a shorter RXR isoform (now called LmRXR-S), the isolation of a second, longer isoform (LmRXR-L) that appears to have characteristics of a ligand-modulated nuclear receptor is reported here. Transcripts for both isoforms, as well as LmEcR, were detected in embryos and in females during oocyte maturation. After expression in E. coli, both LmRXR-S and LmRXR-L form heterodimers with recombinant LmEcR in vitro which bind the active ecdysteroid, ponasterone A. Binding was only weakly competed for by ecdysone agonists that are known to be toxic to more advanced insects, suggesting functionally significant divergence in EcR ligand binding domains. In contrast, the DNA binding domain of LmEcR is less divergent and a protein complex, presumably LmEcR/LmRXR, that bound the ecdysone response element, IR-1, was detected in locust nuclear extracts. Because of reports of juvenile hormone (JH III) binding to Drosophila USP and the observed in silico RXR-like ligand-binding site in LmRXR-L, the recombinant proteins were also tested for binding to JH III. Neither LmRXR isoform, alone or in combination with LmEcR, bound JH III at nanomolar concentrations.
Amino Acid Sequence↗
Gene-for-gene-mediated recognition of nuclear-targeted AvrBs3-like bacterial effector proteins.
Plant disease resistance (R) genes mediate specific recognition of pathogens via perception of cognate avirulence (avr) gene products. The numerous highly similar AvrBs3-like proteins from the bacterial genus Xanthomonas provide together with their corresponding R proteins a unique biological resource to dissect the molecular basis of recognition specificity. A central question in this context is if R proteins that mediate recognition of structurally similar Avr proteins are themselves functionally similar or rather dissimilar. The recent isolation of rice xa5, rice Xa27 and tomato Bs4, R genes that collectively mediate recognition of avrBs3-like genes, provides a first clue to the molecular mechanisms that plants employ to detect AvrBs3-like proteins. Their initial characterization suggests that these R proteins are structurally and functionally surprisingly diverge. This review summarizes the current knowledge on R-protein-mediated recognition of AvrBs3-like proteins and provides working models on how recognition is achieved at the molecular level.
Amino Acid Sequence↗
Evolution of developmental traits.
The evolution of plant development can be studied in many different ways, each of which provides new insights into how plants have been modified over evolutionary time. DNA sequencing shows that most developmental genes are under purifying selection and that obvious adaptive change in proteins is rare. This may indicate that most change occurs in cis-regulatory sequences, that tests for detecting selection lack power, or both. Gene duplications are common and often correlate with divergence of function, as predicted by theory. Studies of gene expression illuminate similarities among structures in disparate plant groups and indicate that the same genes have been deployed repeatedly for similar developmental ends. Comparative functional studies remain uncommon, but promise to illuminate how changing proteins lead to changes in development. Precise characterization of phenotypes by studies of developmental morphology is beginning to occur in some taxonomic groups. The genetic variation necessary for morphological change must originate as allelic polymorphism within populations; such polymorphism has been identified in grasses and in sunflowers, although it is often cryptic.
Arabidopsis↗
Mutagenic analysis of Thr-232 in rhodanese from Azotobacter vinelandii highlighted the differences of this prokaryotic enzyme from the known sulfurtransferases.
Azotobacter vinelandii RhdA uses thiosulfate as the only sulfur donor in vitro, and this apparent selectivity seems to be a unique property among the characterized sulfurtransferases. To investigate the basis of substrate recognition in RhdA, we replaced Thr-232 with either Ala or Lys. Thr-232 was the target of this study since the corresponding Lys-249 in bovine rhodanese has been identified as necessary for catalytic sulfur transfer, and replacement of Lys-249 with Ala fully inactivates bovine rhodanese. Both T232K and T232A mutants of RhdA showed significant increase in thiosulfate-cyanide sulfurtransferase activity, and no detectable activity in the presence of 3-mercaptopyruvate as the sulfur donor substrate. Fluorescence measurements showed that wild-type and mutant RhdAs were overexpressed in the persulfurated form, thus conferring to this enzyme the potential of a persulfide sulfur donor compound. RhdA contains a unique sequence stretch around the catalytic cysteine, and the data here presented suggest a possible divergent physiological function of A. vinelandii sulfurtransferase.
Animals↗
The yeast and plant plasma membrane H+ pump ATPase: divergent regulation for the same function.
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Cell Membrane↗
Establishment of a new human cell line (EN) with TP53 mutation derived from endometrial carcinoma.
We present a new cell line, EN, established from an invasive endometrioid adenocarcinoma of the uterine corpus in 50-year-old patient. The cells show rapid growth in culture with a doubling time of 24.4 hours and high migration activity. Monolayer-cultured cells were polygonal in shape and showed a tendency to pile up without contact inhibition. Subcutaneous transplantation of the EN cells into nude mice formed solid tumors that were histologically diagnosed as adenocarcinoma, whereas no metastasis was observed. Cultured EN cells produced tissue polypeptide antigen. Genetic and molecular analyses revealed high telomerase activity and estrogen receptor beta but not alpha expression. Using the polymerase chain reaction-single strand conformation polymorphism technique, we have screened EN cells for TP53 mutation in exons 5-8. A mobility shift was observed in this cell line in exon 8. A nucleotide insertion (CGT-->CAGT) was detected at codon 273, which resulted in a creation of a stop codon at codon 308. This cell line thus appears to represent the development of a more malignant clone with divergent receptor function and growth behavior, and provides us with an interesting new tool for the study of tumorigenesis in the human endometrium.
Animals↗
Trypanosoma brucei RNase HI requires its divergent spacer subdomain for enzymatic function and its conserved RNA binding motif for nuclear localization.
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Amino Acid Motifs↗
Mitochondrial genomics flies high.
A new pair of papers reports the complete coding sequences for 28 mitochondrial DNAs in Drosophila. By examining the patterns of polymorphism and divergence among functionally distinct classes of synonymous and nonsynonymous nucleotide sites, Bill Ballard provides a comprehensive whole-genome picture of how mtDNA sequence evolution can depart from the strictly neutral and nearly neutral models of molecular evolution.
Journal Article↗
RMPs: recombination/replication mediator proteins.
Enzymes for DNA replication and recombination need to gain access to single-stranded DNA (ssDNA) but ssDNA-binding proteins (SSBs) present an obstacle to the formation of enzyme-ssDNA replication and recombination complexes. A specialized class of SSBs, which we designate as recombination/replication mediator proteins (RMPs), promotes enzyme- ssDNA assembly by overcoming SSB inhibition. RMPs exhibit strong conservation of function across divergent species, and display species-specific interactions with SSB and enzymes to neutralize the SSB barrier to enzyme-ssDNA assembly.
Bacteriophage T4↗
SMRTER, a Drosophila nuclear receptor coregulator, reveals that EcR-mediated repression is critical for development.
The Drosophila ecdysone receptor (EcR)/ultraspiracle (USP) heterodimer is a key regulator in molting and metamorphoric processes, activating and repressing transcription in a sequence-specific manner. Here, we report the isolation of an EcR-interacting protein, SMRTER, which is structurally divergent but functionally similar to the vertebrate nuclear corepressors SMRT and N-CoR. SMRTER mediates repression by interacting with Sin3A, a repressor known to form a complex with the histone deacetylase Rpd3/HDAC. Importantly, we identify an EcR mutant allele that fails to bind SMRTER and is characterized by developmental defects and lethality. Together, these results reveal a novel nuclear receptor cofactor that exhibits evolutionary conservation in the mechanism to achieve repression and demonstrate the essential role of repression in hormone signaling.
Amino Acid Sequence↗
alpha-Conotoxin EI, a new nicotinic acetylcholine receptor antagonist with novel selectivity.
We report the isolation and characterization of a novel nicotinic acetylcholine receptor (nAChR) ligand. The toxin is an 18 amino acid peptide and is the first reported alpha-conotoxin from an Atlantic fish-hunting Conus. The peptide was purified from the venom of Conus ermineus and is called alpha-conotoxin EI. The sequence diverges from that of previously isolated alpha-conotoxins. We demonstrate that this structural divergence has functional consequences. In Torpedo nAChRs, alpha-conotoxin EI selectively binds the agonist site near the alpha/delta subunit interface in contrast to alpha-conotoxin MI which selectively targets the alpha/gamma agonist binding site. In mammalian nAChRs alpha-conotoxin EI shows high affinity for both the alpha/delta and alpha/gamma subunit interfaces (with some preference for the alpha/delta site), whereas alpha-conotoxin MI is highly selective for the alpha/delta ligand binding site. The sequence of the peptide is: Arg-Asp-Hyp-Cys-Cys-Tyr-His-Pro-Thr-Cys-Asn-Met-Ser-Asn-Pro-Gln-Ile-Cys- NH2, with disulfide bridging between Cys4-Cys10 and Cys5-Cys18, analogous to those of previously described alpha-conotoxins. This sequence has been verified by total chemical synthesis. Thus, alpha-conotoxin EI is a newly-available tool with unique structure and function for characterization of nAChRs.
Amino Acid Sequence↗
Evidence for detection of one duration sample and default responding to other duration samples by pigeons may result from an artifact of retention-test ambiguity.
S. C. Gaitan and J. T. Wixted (2000) proposed that when pigeons are trained on a conditional discrimination to associate 1 duration sample with 1 comparison and 2 other duration samples with a 2nd comparison, they detect only the single duration, and on trials involving either of the 2 other duration samples, they respond to the other comparison by default. In 2 experiments, the authors show instead that pigeons lend to treat the retention intervals (such as those used by Gaitan and Wixted) as intertrial intervals, and thus, they tend to treat all trials with a delay as 0-s sample trials. The authors tested this hypothesis by showing that divergent retention functions do not appear when the retention interval is discriminably different from the intertrial interval.
Animals↗
Insulin-like growth factor II precursor gene organization in relation to insulin gene family.
The insulin gene family, comprised of insulin, relaxin, insulin-like growth factors I and II (IGF-I and IGF-II) and possibly the beta-subunit of 7S nerve growth factor, represents a group of structurally related polypeptides whose biological functions have diverged. The IGFs, or somatomedins, constitute a class of polypeptides that have a key role in pre-adolescent mammalian growth (see ref. 4 for review). IGF-I expression is regulated by growth hormone and mediates postnatal growth, while IGF-II appears to be induced by placental lactogen during prenatal development. The primary structures of both human IGFs have been determined and are closely related. A polypeptide highly homologous to human IGF-II is secreted by the rat liver cell line, BRL-3A. As this polypeptide, termed multiplication stimulating activity (MSA), differs from human IGF-II by only five amino acid residues, MSA probably represents the rat IGF-II protein. Using molecular cloning techniques, we have isolated cDNA and chromosomal genes coding for the MSA and human IGF-II precursors, respectively. Our data, presented here, indicate that both MSA and human IGF-II are synthesized initially as larger precursor molecules. The deduced preprohormones both have molecular weights (MWs) of 20,100 and contain C-terminal propeptides of 89 amino acid residues, which we have named E-peptides. The organization of the IGF-II precursor gene is discussed in relation to that of other insulin gene family members.
Amino Acid Sequence↗
Possible involvement of the membrane-bound form of peroxiredoxin 4 in acrosome formation during spermiogenesis of rats.
Peroxiredoxins are novel peroxidases that exhibit divergent biological functions. The fourth member, Prx4, is synthesized with a signal sequence and, after processing, secreted as a 27-kDa form in most tissues. A 31-kDa Prx4 which corresponds to the unprocessed, membrane-bound form is found only in testis. This study was undertaken in order to investigate the role of the membrane-bound Prx4 during spermiogenesis in rats. The Prx4 transcript was observed in testes at 14 days of age, the age before puberty, and its level increased only slightly during aging. Only the secretable form of Prx4 was present before 30 days of age, but the membrane-bound Prx4 became detectable in adult testes, although sum of the two forms appeared to be the same after 21 days old. While weak immunoreactivity to the Prx4 antibody was detected in spermatogenic cells for all ages, a strong immunoreactivity was observed in the elongating spermatid and residual body of adult testis. Prx4 was present in the lumen of the endoplasmic reticulum, Golgi bodies, and the perinuclear space in young rat testes. However, the localization of Prx4 was restricted to membranes of the acrosomal vesicle of the elongated spermatid and was not detected in spermatozoon. Once spermiogenesis is accomplished, vesicles containing the membrane-bound Prx4 were released into the residual body, along with residual membranous components. Thus the conversion of the soluble form to the membrane-bound form may have a role in the acrosome formation during vesicular reorganization during spermiogenesis.
Acrosome Reaction↗