Close Sequence Similarity Research Articles

The neuronal calcium sensor family of Ca2+-binding proteins

Ca(2+) plays a central role in the function of neurons as the trigger for neurotransmitter release, and many aspects of neuronal activity, from rapid modulation to changes in gene expression, are controlled by Ca(2+). These actions of Ca(2+) must be mediated by Ca(2+)-binding proteins, including calmodulin, which is involved in Ca(2+) regulation, not only in neurons, but in most other cell types. A large number of other EF-hand-containing Ca(2+)-binding proteins are known. One family of these, the neuronal calcium sensor (NCS) proteins, has a restricted expression in retinal photoreceptors or neurons and neuroendocrine cells, suggesting that they have specialized roles in these cell types. Two members of the family (recoverin and guanylate cyclase-activating protein) have established roles in the regulation of phototransduction. Despite close sequence similarities, the NCS proteins have distinct neuronal distributions, suggesting that they have different functions. Recent work has begun to demonstrate the physiological roles of members of this protein family. These include roles in the modulation of neurotransmitter release, control of cyclic nucleotide metabolism, biosynthesis of polyphosphoinositides, regulation of gene expression and in the direct regulation of ion channels. In the present review we describe the known sequences and structures of the NCS proteins, information on their interactions with target proteins and current knowledge about their cellular and physiological functions.

The Yersinia Protein Kinase A Is a Host Factor Inducible RhoA/Rac-binding Virulence Factor

The pathogenic yersiniae inject proteins directly into eukaryotic cells that interfere with a number of cellular processes including phagocytosis and inflammatory-associated host responses. One of these injected proteins, the Yersinia protein kinase A (YpkA), has previously been shown to affect the morphology of cultured eukaryotic cells as well as to localize to the plasma membrane following its injection into HeLa cells. Here it is shown that these activities are mediated by separable domains of YpkA. The amino terminus, which contains the kinase domain, is sufficient to localize YpkA to the plasma membrane while the carboxyl terminus of YpkA is required for YpkAs morphological effects. YpkAs carboxyl-terminal region was found to affect the levels of actin-containing stress fibers as well as block the activation of the GTPase RhoA in Yersinia-infected cells. We show that the carboxyl-terminal region of YpkA, which contains sequences that bear similarity to the RhoA-binding domains of several eukaryotic RhoA-binding kinases, directly interacts with RhoA as well as Rac (but not Cdc42) and displays a slight but measurable binding preference for the GDP-bound form of RhoA. Surprisingly, YpkA binding to RhoA(GDP) affected neither the intrinsic nor guanine nucleotide exchange factor-mediated GDP/GTP exchange reaction suggesting that YpkA controls activated RhoA levels by a mechanism other than by simply blocking guanine nucleotide exchange factor activity. We go on to show that YpkAs kinase activity is neither dependent on nor promoted by its interaction with RhoA and Rac but is, however, entirely dependent on heat-sensitive eukaryotic factors present in HeLa cell extracts and fetal calf serum. Collectively, our data show that YpkA possesses both similarities and differences with the eukaryotic RhoA/Rac-binding kinases and suggest that the yersiniae utilize the Rho GTPases for unique activities during their interaction with eukaryotic cells.

A xylanase produced by the rumen anaerobic protozoan Polyplastron multivesiculatum shows close sequence similarity to family 11 xylanases from gram-positive bacteria.

We report for the first time the cloning and characterisation of a protozoal enzyme involved in plant cell wall polysaccharide degradation. A cDNA library was constructed from the ruminal protozoan Polyplastron multivesiculatum and a stable clone expressing xylanase activity was isolated. The encoded enzyme belongs to the glycoside hydrolase family 11, and phylogenetic analysis indicates a closer relationship with catalytic domains from Gram-positive bacteria than the other fibrolytic eukaryotes from the rumen, the anaerobic fungi.

A xylanase produced by the rumen anaerobic protozoan Polyplastron multivesiculatum shows close sequence similarity to family 11 xylanases from Gram-positive bacteria

We report for the first time the cloning and characterisation of a protozoal enzyme involved in plant cell wall polysaccharide degradation. A cDNA library was constructed from the ruminal protozoan Polyplastron multivesiculatum and a stable clone expressing xylanase activity was isolated. The encoded enzyme belongs to the glycoside hydrolase family 11, and phylogenetic analysis indicates a closer relationship with catalytic domains from Gram-positive bacteria than the other fibrolytic eukaryotes from the rumen, the anaerobic fungi.

The 42-Amino Acid Insert in the FMN Domain of Neuronal Nitric-oxide Synthase Exerts Control over Ca2+/Calmodulin-dependent Electron Transfer

The neuronal and endothelial nitric-oxide synthases (nNOS and eNOS) differ from inducible NOS in their dependence on the intracellular Ca(2+) concentration. Both nNOS and eNOS are activated by the reversible binding of calmodulin (CaM) in the presence of Ca(2+), whereas inducible NOS binds CaM irreversibly. One major divergence in the close sequence similarity between the NOS isoforms is a 40-50-amino acid insert in the middle of the FMN-binding domains of nNOS and eNOS. It has previously been proposed that this insert forms an autoinhibitory domain designed to destabilize CaM binding and increase its Ca(2+) dependence. To examine the importance of the insert we constructed two deletion mutants designed to remove the bulk of it from nNOS. Both mutants (Delta40 and Delta42) retained maximal NO synthesis activity at lower concentrations of free Ca(2+) than the wild type enzyme. They were also found to retain 30% of their activity in the absence of Ca(2+)/CaM, indicating that the insert plays an important role in disabling the enzyme when the physiological Ca(2+) concentration is low. Reduction of nNOS heme by NADPH under rigorous anaerobic conditions was found to occur in the wild type enzyme only in the presence of Ca(2+)/CaM. However, reduction of heme in the Delta40 mutant occurred spontaneously on addition of NADPH in the absence of Ca(2+)/CaM. This suggests that the insert regulates activity by inhibiting electron transfer from FMN to heme in the absence of Ca(2+)/CaM and by destabilizing CaM binding at low Ca(2+) concentrations, consistent with its role as an autoinhibitory domain.

The Chicken Leptin Gene: Has It Been Cloned?

The DNA sequence of a chicken leptin gene that shares 95% nucleotide similarity with the mouse leptin sequence has been recently reported (Taouis et al., 1998, Gene 208, 239–242). Experiments have been performed independently in two laboratories to try to confirm this finding. Fourteen PCR primers based on the mouse leptin sequence were designed to amplify the avian leptin gene. Four of the primers were identical to the mouse and published chicken leptin sequences. PCR amplification was carried out on genomic DNA and reverse-transcribed mRNA from the fat, liver, and pancreas of several chicken strains and from the domestic turkey, goose, and Japanese quail. No PCR products sharing close similarity to the mouse leptin sequence were generated from any avian templates. Amplification of mouse leptin sequence was consistently obtained when control mouse templates were used. Northern hybridization using a mouse leptin probe failed to produce a signal with poly(A)+ RNA from chicken fat and liver and from the fat and liver of force-fed geese but a strong signal was obtained from control mouse fat total RNA. Southern hybridization under low stringency washing conditions revealed hybridization of a mouse leptin probe to chicken genomic DNA. Under higher stringency washing conditions, the chicken signal disappeared, while those from control mouse and sheep genomic DNA remained. This suggests that the putative chicken leptin sequence shares less than the 83% nucleotide sequence identity between the mouse and sheep genes. It is concluded that a chicken leptin gene sequence with close sequence similarity to mouse leptin is not present in the chicken genome. Furthermore, mRNA sharing high sequence identity with mouse leptin is not present in the fat or liver of the domestic chicken, turkey, goose, or Japanese quail.

Characterization of GFR, a novel guanine nucleotide exchange factor for Rap1

Three groups of Rap1-specific guanine nucleotide exchange factors including C3G, CalDAG-GEFI, and Epac/cAMP-GEFI/II have been identified to date. In the present study, we report a new Rap1 guanine nucleotide exchange factor which we have named GFR ( g uanine nucleotide exchange f actor for R ap1). GFR shows close sequence similarity to EPAC/cAMP-GEFI/II although GFR lacks a cAMP binding domain and contains a nuclear localization signal. We demonstrated that GFR can activate Rap1 but not H-Ras in 293T cells and that the cdc25 domain of GFR is required for the activation of Rap1. Northern blot analysis suggested that GFR mRNA is strongly expressed in the brain. In transfected HeLa cells, GFR has been found to be localized in the nuclei.

A Neurally Enriched Coronin-like Protein, ClipinC, Is a Novel Candidate for an Actin Cytoskeleton-Cortical Membrane-linking Protein

Brain-enriched human FC96 protein shows a close sequence similarity to the Dictyostelium actin-binding protein coronin, which has been implicated in cell motility, cytokinesis, and phagocytosis. A phylogenetic tree analysis revealed that FC96 and two other mammalian molecules (p57 and IR10) form a new protein family, the coronin-like protein (Clipin) family; thus hereafter we refer to FC96 as ClipinC. A WD domain and a succeeding alpha-helical region are conserved among coronin and Clipin family members. ClipinC is predominantly expressed in the brain, and discrete areas in the mouse brain were intensely labeled with anti-ClipinC antibodies. ClipinC was also shown to bind directly to F-actin in vitro. Immunocytochemical analysis revealed that ClipinC accumulated at focal adhesions as well as at neurite tips and stress fibers. Furthermore, ClipinC was associated with vinculin, which is a major component of focal contacts. These results indicate that ClipinC is also a component part of the cross-bridge between the actin cytoskeleton and the plasma membrane. These findings and the previously reported function of coronin suggest that ClipinC may play specific roles in the reorganization of neuronal actin structure, a change that has been implicated in both cell motility and growth cone advance.

Analysis, expression and prevalence of the Mycobacterium tuberculosis homolog of bacterial virulence regulating proteins

We have previously reported the identification of a gene from Mycobacterium tuberculosis, H 37Rv, which on the basis of its nucleotide sequence encoded a protein product of 38 kDa. This 38-Kda mycobacterial protein designated as VirS exhibits homology with the VirF protein of Shigella, the VirFy protein of Yersinia and the Cfad, Rns and FapR proteins from various enterotoxigenic Escherichia coli strains. In this communication, we show the close sequence and structural similarities of the VirS protein with VirF, VirFy, Cfad, Rns and FapR and describe the results of our studies on the characterization of the virS gene promoter and its expression in E. coli and mycobacteria. virS was present exclusively in the species belonging to the M. tuberculosis complex as revealed by Southern blot and PCR analysis. Our findings suggest the involvement of virS in the regulation of pathogenesis of M. tuberculosis.

Analysis, expression and prevalence of the Mycobacterium tuberculosis homolog of bacterial virulence regulating proteins.

We have previously reported the identification of a gene from Mycobacterium tuberculosis, H37Rv, which on the basis of its nucleotide sequence encoded a protein product of 38 kDa. This 38-Kda mycobacterial protein designated as VirS exhibits homology with the VirF protein of Shigella, the VirFy protein of Yersinia and the Cfad, Rns and FapR proteins from various enterotoxigenic Escherichia coli strains. In this communication, we show the close sequence and structural similarities of the VirS protein with VirF, VirFy, Cfad, Rns and FapR and describe the results of our studies on the characterization of the virS gene promoter and its expression in E. coli and mycobacteria. virS was present exclusively in the species belonging to the M. tuberculosis complex as revealed by Southern blot and PCR analysis. Our findings suggest the involvement of virS in the regulation of pathogenesis of M. tuberculosis.

The origins of AIDS

“Chimpanzee meat blamed for AIDS epidemic” was the headline of a front page article in the Times on 1 February, which began: “Chimpanzees slaughtered for food in west central Africa were the original source of AIDS.” The Daily Telegraph flagged the story in a similar way: “AIDS started by humans eating chimps.”Strengthened by the UK's recent climate of concern over food safety issues such as Salmonella, Escherichia coli 0157 and bovine spongiform encephalopathy (BSE), the implication was clear. Humans had first contracted AIDS by eating chimpanzee meat containing the virus. The television programme Newsnight on BBC2 continued the theme by comparing AIDS with BSE, and asking “What's next?”A paper given the previous day at a conference in Chicago by Beatrice Hahn from the University of Alabama at Birmingham, USA, was the trigger for these and many similar media stories. Previewing a paper in that week's Nature showing the close sequence similarity between strains of human immunodeficiency virus-1 (HIV-1) and a simian immunodeficiency virus strain (SIVcpz) isolated from a captive chimp belonging to a subspecies of Pan troglodytes troglodytes, Hahn had argued that close contact between people and chimps had probably allowed an ancestor of HIV-1 to cross the species barrier into humans. The bushmeat trade, associated with logging and deforestation, was under keen suspicion.But the suggested route of infection was, of course, exposure to blood during hunting and butchering, not ingestion through the gut. This crucial point did not come out strongly in any of the newspaper stories and was absent from some altogether. It appeared more than halfway through a lengthy account in the Daily Telegraph, near the very end of an equally prominent report in the Guardian, and nowhere at all in the Daily Mail's story.Most radio and television news bulletins, despite severe limits on time, provided more balanced coverage. Variously using interviews with the authors of the paper and with Andrew McMichael and Sarah Rowland-Jones of the Institute of Molecular Medicine in Oxford — who are working on boosting immune responses to the virus — they were effective in explaining the implications of the discovery for our understanding of AIDS and the development of vaccines.A live interview on Newsnight with Hilton Whittle, Deputy Director of the Medical Research Council Laboratories in The Gambia, was less successful. There is no reason why Whittle should be a charismatic TV personality: he is not, and that is not what the MRC pays him to be. The real problem was the interviewer's bizarre steering of the story line. At one point, immediately after Whittle had explained that viruses probably moved frequently from animals to humans without causing illness, he was asked why the consequences were “always catastrophic.”Even on the following day, when the Times published a second substantial piece, it failed to mention blood as the vehicle of infection. “The pace of destruction of African rainforests by logging companies and their employees, who poach hundreds of tonnes of primate meat, means that mass infections would be difficult to control,” the article said.Yet it was also on the second day that the most illuminating article of all appeared. Writing in the Guardian, Paul Brown and Hilary Bower linked the new finding with the puzzle of Nairobi prostitutes who are repeatedly infected with HIV-1 yet do not develop AIDS, and explored the implications of this resistance for the inherently difficult task of immunisation against the disease. The work of McMichael and Rowland-Jones was again used to illuminate the issues.This is by no means the first time that a national newspaper has produced a more thoughtful, more fully researched feature with the benefit of a further day's work. The fierceness of the current circulation war makes the argument seem unrealistic at present, yet many readers would surely prefer a definitive piece later to an imperfect piece sooner.To make this point is not to overlook the considerable skill that goes into the composition of newspaper articles which journalists are obliged to complete within a few hours of receiving the ‘breaking news’. Nevertheless, it is significant that on this occasion arguably the best of the first crop of reports, headlined “AIDS virus is thousands of years old,” was co-authored by Steve Connor in the Independent.Connor has previously written not only a highly regarded book on AIDS but also many articles on the origin of HIV-1. He was thus ideally placed to put the development in context and highlight its key implications.Describing the newspaper magnate Lord Northcliffe in My Northcliffe Diary (Victor Gollancz, 1931), Tom Clark recalled that he insisted on “experts” for everything — “an electrical engineer to criticise the telephones, an American to describe baseball, a sailor to report yachting…” Sounds quaint — but not a bad principle?

Expression of the succinate dehydrogenase genes ( sdhCAB ) from the facultatively anaerobic Paenibacillus macerans during aerobic growth

Paenibacillus (formerly Bacillus) macerans is capable of succinate oxidation under oxic conditions and fumarate reduction under anoxic conditions. The reactions are catalyzed by different enzymes, succinate dehydrogenase (Sdh) and fumarate reductase (Frd). The genes encoding Sdh (sdhCAB) were analyzed. The gene products of sdhA and sdhB were similar to the subunits of known Sdh and Frd enzymes. The hydrophobic subunit SdhC showed close sequence similarity to the class of Sdh/Frd enzymes containing diheme cytochrome b. From the sdhCAB gene cluster two transcripts were produced, one comprising sdhCAB, the other sdhAB. The transcripts were found only during aerobic growth, and the amount was directly proportional to Sdh activity, but inversely proportional to Frd activity.

Lim6, a novel LIM homeobox gene in the zebrafish: Comparison of its expression pattern with lim1

A novel LIM class homeobox gene, lim6, was isolated from a zebrafish embryonic cDNA library. The encoded protein shares a high degree of sequence similarity with the previously described Lim1 and Lim5 proteins. This study compares the spatial and temporal expression pattern of the closely related lim6 and lim1 genes during early embryogenesis. Generally, lim6 mRNA was found at rather low amounts compared to lim1 mRNA. At the shield stage, lim6 mRNA, similar to lim1 mRNA, was predominantly expressed in the shield. Lim6 was transiently expressed in a restricted region of the anterior neural plate at the bud stage, distinct from the expression of lim1 in the notochord and the pronephros and pronephric ducts. During the segmentation period, the lim6 gene started to be expressed in single cells in the spinal cord, followed by a gradually increasing wide-spread expression throughout the CNS. During this stage, lim1 mRNA disappeared in the notochord and pronephric ducts and was found in the pronephroi and single cells in the CNS. In 24 hr embryos, lim6 and lim1 were expressed in the fore-, mid-, and hindbrain and the spinal cord, except that lim1 mRNA was limited to two small domains in the telencephalon, whereas lim6 mRNA was widely expressed in this region. A comparison of expression of lim1and lim6 and of the previously characterized lim5 show that, in spite of close sequence similarity, distinct expression patterns imply nonredundant functions for each member of this group of genes. Dev. Dyn. 209:406–417, 1997. © 1997 Wiley-Liss, Inc. This article is a US Government work and, as such, is in the public domain in the United States of America.

Characterization of the mouse Tcra-V22 gene subfamily.

T-cell receptors (Tcrs) of higher organisms play a key role in the specific recognition of self and non-self molecules in the immune system. The large number of Tcr variable (V) genes have been organized into V gene subfamilies according to their sequence similarity at the nucleotide and amino acid level. We cloned and characterized four new members of the Tcra-V22 gene subfamily at the genomic level using a simple and sensitive technique that can rapidly clone members of any multi-member gene family. Sequence analysis reveals that the four Tcra-V22 gene subfamily members have more than 98% sequence similarity in their coding regions, at the nucleotide and amino acid levels. However, the intron between the leader and the coding region varies up to 7% between members of the Tcra-V22 gene subfamily. Comparison of the multi-member Tcra-V22 gene subfamily with other multi-member Tcra-V gene subfamilies (V2, V8, and V11), shows that Tcra-V22 is unique in that it has multiple members with nearly identical amino acid sequence and which are not inherently pseudogenes. Sequence similarity analysis of the Tcra-V22 subfamily with the prototypes of all other Tcra-V subfamilies revealed that the Tcra-V22 subfamily has the closest sequence similarity to that of Tcra-V18 (77% at the nucleotide level and 71% at the amino acid level).

Structures Important in NAD(P)(H) Specificity for Mammalian Retinol and 11-Cis-Retinol Dehydrogenases

Mammalian retinol and 11-cisretinol dehydrogenases catalyze the formation of retinaldehyde from retinol and 11-cisretinaldehyde from 11-cisretinol, respectively. Although their amino acid sequences are 54% identical, these enzymes have different cofactor specificities: rat retinol dehydrogenase uses NADP+, while cow 11-cisretinol dehydrogenase uses NAD+. We used their close sequence similarity and the availability of 3D structures of their homologs to construct a 3D model of the two retinol dehydrogenases to investigate the determinants for cofactor specificity. The structure of rat retinol dehydrogenase shows that lysine-64 is important in stabilizing binding of 2′-phosphate on NADP+in two ways: lysine's positively charged side chain has a coulombic attraction to the 2′-phosphate and partially compensates for the negative charge of aspartic acid-38. Cow 11-cisretinol dehydrogenase has threonine-61 at the position homologous to lysine-64. Threonine-61 does not have a stabilizing coulombic interaction with NADP+, nor can threonine-61 counteract the repulsive interaction between NADP+and aspartic acid-37 in 11-cisretinol dehydrogenase. This suggests that aspartic acid-37 and threonine-61 are important in the specificity of 11-cisretinol dehydrogenase for NAD+.

CDNA cloning and tissue-specific expression of a novel basic helix-loop-helix/PAS factor (Arnt2) with close sequence similarity to the aryl hydrocarbon receptor nuclear translocator (Arnt).

We isolated mouse cDNA clones (Arnt2) that are highly similar to but distinct from the aryl hydrocarbon receptor (AhR) nuclear translocator (Arnt). The composite cDNA covered a 2,443-bp sequence consisting of a putative 2,136-bp open reading frame encoding a polypeptide of 712 amino acids. The predicted Arnt2 polypeptide carries a characteristic basic helix-loop-helix (bHLH)/PAS motif in its N-terminal region with close similarity (81% identity) to that of mouse Arnt and has an overall sequence identity of 57% with Arnt. Biochemical properties and interaction of Arnt2 with other bHLH/PAS proteins were investigated by coimmunoprecipitation assays, gel mobility shift assays, and the yeast two-hybrid system. Arnt2 interacted with AhR and mouse Sim as efficiently as Arnt, and the Arnt2-AhR complex recognized and bound specifically the xenobiotic responsive element (XRE) sequence. Expression of Arnt2 successfully rescued XRE-driven reporter gene activity in the Arnt-defective c4 mutant of Hepa-1 cells. RNA blot analysis revealed that expression of Arnt2 mRNA was restricted to the brains and kidneys of adult mice, while Arnt mRNA was expressed ubiquitously. In addition, whole-mount in situ hybridization of 9.5-day mouse embryos showed that Arnt2 mRNA was expressed in the dorsal neural tube and branchial arch 1, while Arnt transcripts were detected broadly in various tissues of mesodermal and endodermal origins. These results suggest that Arnt2 may play different roles from Arnt both in adult mice and in developing embryos. Finally, sequence comparison of the currently known bHLH/PAS proteins indicates a division into two phylogenetic groups: the Arnt group, containing Arnt, Arnt2, and Per, and the AhR group, consisting of AhR, Sim, and Hif-1alpha.

Chimeric Vesicular Monoamine Transporters Identify Structural Domains That Influence Substrate Affinity and Sensitivity to Tetrabenazine

The vesicular monoamine transporters (VMATs) 1 and 2 show close sequence similarity but substantial differences in apparent substrate affinity and drug sensitivity. To identify structural domains that determine these functional characteristics, chimeric transporters were constructed and their properties were analyzed in a heterologous expression system. The results implicate multiple regions in the recognition of serotonin and histamine and the sensitivity to tetrabenazine. Two domains of VMAT2, one extending from transmembrane domain (TMD) 5 to the beginning of TMD8 and the other from the end of TMD9 through TMD12, increase the affinity for serotonin and histamine as well as the sensitivity to tetrabenazine but only in the context of more C-terminal and more N-terminal VMAT2 sequences, respectively. In addition, the extreme N terminus of VMAT2 alone suffices to confer a partial increase in substrate affinity and tetrabenazine sensitivity. Despite these similarities among the interactions with serotonin, histamine, and tetrabenazine, the region of VMAT2 from TMD3 through TMD4 increases serotonin affinity but not histamine affinity or tetrabenazine sensitivity, and whereas the region from TMD5 to TMD8 of VMAT2 increases serotonin affinity in the context of more C-terminal VMAT2 sequences, the region encompassing TMD5 through TMD7 reduces serotonin but not histamine affinity or tetrabenazine sensitivity in the context of more N-terminal VMAT2 sequences. Thus, the chimeric analysis also reveals differences between serotonin recognition and the recognition of both histamine and tetrabenazine that may account for the observed differences in their interaction with the transport protein.

Human Alanyl-tRNA Synthetase: Conservation in Evolution of Catalytic Core and Microhelix Recognition

The class II Escherichia coli and human alanyl-tRNA synthetases cross-acylate their respective tRNAs and require, for aminoacylation, an acceptor helix G3:U70 base pair that is conserved in evolution. We report here the primary structure and expression in the yeast Pichia of an active human alanyl-tRNA synthetase. The N-terminal 498 amino acids of the 968-residue polypeptide have substantial (41%) identity with the E. coli protein. A closely related region encompasses the class-defining domain of the E. coli enzyme and includes the part needed for recognition of the acceptor helix. As a result, previously reported mutagenesis, modeling, domain organization, and biochemical characterization on the E. coli protein appear valid as a template for the human protein. In particular, we show that both the E. coli enzyme and the human enzyme purified from Pichia aminoacylate 9-base pair RNA duplexes whose sequences are based on the acceptor stems of either E. coli or human alanine tRNAs. In contrast, the sequences of the two enzymes completely diverge in an internal portion of the C-terminal half that is essential for tetramer formation by the E. coli enzyme, but that is dispensable for microhelix aminoacylation. This divergence correlates with the expressed human enzyme behaving as a monomer. Thus, the region of close sequence similarity may be a consequence of strong selective pressure to conserve the acceptor helix G3:U70 base pair as an RNA signal for alanine.

Gypsy/Ty3-class retrotransposons integrated in the DNA of herring, tunicate, and echinoderms

Eight new examples of retrotransposons of the Gypsy/Ty3 class have been identified in marine species. A 525-nt pol gene-coding region was amplified using degenerate primers from highly conserved regions and has extended the range of recognition of Gypsy/Ty3 far beyond those previously known. The following matrix shows the percentage AA divergence of the translations of this segment of the pol gene coding region. [table: see text] The underlines separate three groups of retrotransposons that can be recognized on the basis of this amino acid sequence. The new upper group shows surprising amino acid sequence similarity among members from the DNA of herring, sea urchin, starfish, and a tunicate. For example, the herring element differs by only 41% from the Ciona element and 46% from the sea urchin element. The group between the lines includes members close to previously known elements (marked by asterisks) and has so far been found only in sea urchins. The two upper groups differ from each other by 55-60% and yet members of both groups (e.g., Spr1 and Spr2) are integrated into the DNA of one species--S. purpuratus. Below the lower underline is listed the only known representative of a very distant group, which occurs in starfish DNA. In spite of large divergence, amino acid sequence comparisons indicate that all of the elements shown in the array are members of the LTR-containing class of retrotransposons that includes Gypsy of Drosophila and Ty3 of yeast. Of all known mobile elements this class shows the closest sequence similarity to retroviruses and has the same arrangement of genes as simpler retroviruses.

The 5' flanking region of the rat beta 3-adrenergic receptor gene: divergence with the human gene and implications for species-specific gene expression.

beta 3-adrenergic receptor mRNAs exhibit species-specific expression (human vs. rodent) in distinct anatomical regions and appear to be expressed abundantly within rodent adipose tissue, but only at low levels within corresponding human tissues. In order to determine the genetic basis of the differential expression of the rat and human beta 3-adrenergic receptor genes, we cloned and sequence the rat gene and compared the 5' flanking regions of the two genes to identify potential discriminators in transcriptional regulation. We have found that the rat and human beta 3-adrenergic receptor 5' flanking regions are only 67% similar, unlike the close sequence similarity observed between the coding blocks (> 90%) and also observed between species for the 5' flanking regions of other beta-adrenergic receptor subtype genes (> 90%). In addition, the rat beta 3-adrenergic receptor gene lacks the four potential cAMP responsive elements identified within the 5' flanking region of the human receptor gene. The striking divergence in regulatory sequences between the rat and human beta 3-adrenergic receptor genes may potentially explain the differences in species-specific expression and tissue localization of the rat and human receptor mRNAs.