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PubMed1998

In vitro susceptibilities of 27 rickettsiae to 13 antimicrobials.

The MICs of 13 antibiotics (doxycycline, thiamphenicol, rifampin, amoxicillin, gentamicin, co-trimoxazole, ciprofloxacin, pefloxacin, ofloxacin, erythromycin, josamycin, clarithromycin, and pristinamycin) were determined for 27 available rickettsial species or strains. We used two in vitro cell culture methods described previously: the plaque assay and the microplaque colorimetric assay. Our results confirm the susceptibilities of rickettsiae to doxycycline, thiamphenicol, and fluoroquinolones. Beta-lactams, aminoglycosides, and cotrimoxazole were not active. Typhus group rickettsiae were susceptible to all macrolides tested, whereas the spotted fever group rickettsiae, R. bellii, and R. canada were more resistant, with josamycin, a safe alternative for the treatment of Mediterranean spotted fever, being the most effective compound. Strain Bar 29, R. massiliae, R. montana, R. aeschlimannii, and R. rhipicephali, which are members of the same phylogenetic subgroup, were more resistant to rifampin than the other rickettsiae tested. Heterogeneity in susceptibility to rifampin, which we report for the first time, may explain in vivo discrepancies in the effectiveness of this antibiotic for the treatment of rickettsial diseases. We hypothesize that rifampin resistance and erythromycin susceptibility may reflect a divergence during the evolution of rickettsiae.

Animals↗
PubMed1989

16S rRNA sequence indicates that plant-pathogenic mycoplasmalike organisms are evolutionarily distinct from animal mycoplasmas.

The plant-pathogenic mycoplasmalike organisms (MLOs) are so named because they lack cell walls. Many features that are essential to a definitive classification remain uncharacterized, because these organisms have resisted attempts at in vitro culturing. To establish the taxonomic position of the MLOs, the DNA region containing the 16S rRNA gene from a representative of the MLOs has been cloned and sequenced. Sequence comparisons indicate that the MLOs are related to Mycoplasma capricolum and that these two bacteria share their phylogenetic origin with Bacillus subtilis. The low G + C content of this gene and features of its deduced secondary structure further support this grouping. However, the presence of a single tRNAIle gene in the spacer between the 16S rRNA and 23S rRNA genes of the MLOs differentiates the MLOs from other representatives of the mycoplasmas, which indicates an early divergence in the evolution of the members of the class Mollicutes. The presence of certain characteristic oligonucleotides in the 16S rRNA sequence indicates that MLOs may be closely related to acholeplasmas.

Animals↗
PubMed2001

Distribution of the SsuDAT1I restriction-modification system among different serotypes of Streptococcus suis.

The SsuDAT1I restriction-modification (R-M) system, which contains two methyltransferases and two restriction endonucleases with recognition sequence 5'-GATC-3', was first found in a field isolate of Streptococcus suis serotype 2. Isoschizomers of the R-M system were found in the same locus between purH and purD in a field isolate of serotype 1/2 and the reference strains of serotypes 3, 7, 23, and 26 among 29 strains of different serotypes examined in this study. The R-M gene sequences in serotypes 1/2, 3, 7, and 23 were very similar to those of SsuDAT1I, whereas those in serotype 26 were less similar. These results indicate intraspecies recombination among them and genetic divergence through their evolution.

Amino Acid Sequence↗
PubMed2002

The superoxide dismutase gene sodM is unique to Staphylococcus aureus: absence of sodM in coagulase-negative staphylococci.

Superoxide dismutase (SOD) profiles of clinical isolates of Staphylococcus aureus and coagulase-negative staphylococci (CoNS) were determined by using whole-cell lysates and activity gels. All S. aureus clinical isolates exhibited three closely migrating bands of activity as previously determined for laboratory strains of S. aureus: SodM, SodA, and a hybrid composed of SodM and SodA (M. W. Valderas and M. E. Hart, J. Bacteriol. 183:3399-3407, 2001). In contrast, the CoNS produced only one SOD activity, which migrated similarly to SodA of S. aureus. Southern analysis of eight CoNS species identified only a single sod gene in each case. A full-length sod gene was cloned from Staphylococcus epidermidis and determined to be more similar to sodA than to sodM of S. aureus. Therefore, this gene was designated sodA. The deduced amino acid sequence of the S. epidermidis sodA was 92 and 76% identical to that of the SodA and SodM proteins of S. aureus, respectively. The S. epidermidis sodA gene expressed from a plasmid complemented a sodA mutation in S. aureus, and the protein formed a hybrid with SodM of S. aureus. Both hybrid SOD forms as well as the SodM and SodA proteins of S. aureus and the S. epidermidis SodA protein exist as dimers. These data indicate that sodM is found only in S. aureus and not in the CoNS, suggesting an important divergence in the evolution of this genus and a unique role for SodM in S. aureus.

Amino Acid Sequence↗
PubMed1991

Two distinct domains in the yeast transcription factor IID and evidence for a TATA box-induced conformational change.

Transcription factor IID from Saccharomyces cerevisiae (YIID) binds the TATA box element present in most RNA polymerase II promoters. In this work, partial proteolysis was used as a biochemical probe of YIID structure. YIID consists of a protease-sensitive amino terminus and a highly stable, protease-resistant carboxy-terminal core. The cleavage sites of the predominant chymotrypsin- and trypsin-derived fragments were mapped to amino acid residues 40 to 41 and 48 to 49, respectively, by amino-terminal peptide sequencing. Removal of the amino terminus resulted in a dramatic increase in the ability of YIID to form a stable complex with DNA during gel electrophoresis mobility shift assays and a two- to fourfold increase in DNA-binding affinity, as assayed by DNase I footprinting analysis. The carboxy-terminal 190-amino-acid core was competent for transcription in vitro and was similar in activity to native YIID. DNA containing a TATA element induced hypersensitive sites in the amino-terminal domain and stabilized the core domain to further proteolytic attack. Native YIID did not bind to a TATA box at 0 degrees C, whereas the carboxy-terminal DNA-binding domain did. These results suggest that YIID undergoes a conformational change upon binding to a TATA box. Southern blotting showed that the carboxy-terminal domain is highly conserved, while the amino-terminal domain diverged rapidly in evolution, even between closely related budding yeasts.

Binding Sites↗
PubMed1988

Why should surgery for early-onset strabismus be postponed?

The author presents a continued study of 82 cases of pseudoparalysis of the bilateral rectus muscles in early-onset convergent strabismus following early surgery. Up to 10 years after surgery motor results show that 72% of cases remain within +/- 10 prism dioptres after a single surgical procedure. Sensorial findings corroborate the results of other authors' studies in that binocular association is only achieved in those patients where surgery was carried out at a very young age, not older than 1 year. Surgical procedures consisting of bimedial rectus recession with retroequatorial myopexy are described and the development of alphabetical syndromes and dissociated vertical divergence discussed. The evolution of refraction in these cases is also shown.

Age Factors↗
PubMed1999

Evolutionary constraint networks in ligand-binding domains: an information-theoretic approach.

Ligand-binding sites in homologous protein domains can diverge greatly during evolution. This poses a particularly interesting problem in those cases where the ligand-binding site is situated in, or close to, the domain core, or where ligand-docking induces dramatic conformational changes. These features are present in many receptors and enzymes; the hormone-binding domain of the nuclear receptors for steroids and retinoids, for example, exhibits both characteristics. It is therefore of great interest to determine how binding sites for diverse ligands evolve in core regions of structurally dynamic domains. Are evolutionary changes locally restricted to the ligand-binding site, or are they distributed throughout the domain? We describe here an information-theoretic approach for the study of covariation between ligand-contacting residues and compensatory mutations that preserve the structural integrity and the conformational dynamics of ligand-binding domains. We apply this method to the analysis of the nuclear receptor ligand-binding domain and show that the ligand-contacting residues in the hormone-binding pocket are evolutionarily linked to an extensive network of covarying positions.

Amino Acid Sequence↗
PubMed1980

Chromosomal interrelationship of hamster species of the genus Mesocricetus.

The similarity of chromosomes and the mode by which differences occurred in the chromosomes of the species comprising the genus Mesocricetus, M. auratus (2n = 44), two "cryptic" species of M. brandti (2n = 44 and 2n = 42) and M. newtoni (2n = 38) were determined. Most of the autosomes and the sex chromosomes have either complete or partial G-band correspondence and thus provide definitive evidence for the taxonomic relationship of these species. The karyotypic differences occurred primarily as a result of deletion of sex chromosome heterochromatin and of autosomal translocations that frequently involved chromosomes with heterochromatic short arms or chromosomes bearing NOR's. Only one Robertsonian centric fusion occurred. Despite the conservatism of arrangement of the genetic material, the chromosomal distribution of heterochromatin diverged during the evolution of these species. M. brandti and newtoni each have a metacentric chromosome with a common long arm matching a submetacentric M. auratus autosome, but a short arm corresponding to two different M. auratus chromosomes. These translocations are crucial for explaining the direction of chromosomal evolution of these species and indicate that M. auratus was the commmon ancestral species and that M. brandti and newtoni subsequently evolved independently.

Animals↗
PubMed1994

Serine proteinases of mast cell and leukocyte granules. A league of their own.

Serine proteinases are hydrolases that use serine's side chain hydroxyl group to attack and cleave internal peptide bonds in peptides and proteins. They reside in all mammalian tissues, including the lung and airway. As a group, they vary tremendously in form and target specificity and have a vast repertoire of functions, many of which are critical for life. A subset of these proteinases is expressed primarily in the cytosolic granules of leukocytes from bone marrow, including mast cells. Examples are elastase-related proteinases and cathepsin G of monocytes and neutrophils, the many "granzymes" of cytotoxic T lymphocytes and natural killer (NK) cells, and the tryptases and chymases of mast cells. The pace of discovery and characterization of these granule-associated serine proteinases, fueled by technical advances in molecular biology, has accelerated rapidly in the past few years. Progress has been made in assigning possible functions to individual proteinases. However, the burgeoning numbers of these enzymes; their cell, tissue and species-dependent differences in expression; and their variety of action in vitro (despite, in many cases, shared modes of activation and recent divergence in protein evolution) have vexed and challenged those of us who are anxious to establish their roles in mammalian biology. Certainly, much remains to be discovered and clarified. The purpose of this overview is to capture the state of the art in this field, stressing the similarities as well as the differences among individual granule-associated proteinases and focusing particularly on those enzymes likely to be important in the human lung and airways.

Animals↗
PubMed2006

Phylogenetic and structural analysis of centromeric DNA and kinetochore proteins.

BACKGROUND: Kinetochores are large multi-protein structures that assemble on centromeric DNA (CEN DNA) and mediate the binding of chromosomes to microtubules. Comprising 125 base-pairs of CEN DNA and 70 or more protein components, Saccharomyces cerevisiae kinetochores are among the best understood. In contrast, most fungal, plant and animal cells assemble kinetochores on CENs that are longer and more complex, raising the question of whether kinetochore architecture has been conserved through evolution, despite considerable divergence in CEN sequence. RESULTS: Using computational approaches, ranging from sequence similarity searches to hidden Markov model-based modeling, we show that organisms with CENs resembling those in S. cerevisiae (point CENs) are very closely related and that all contain a set of 11 kinetochore proteins not found in organisms with complex CENs. Conversely, organisms with complex CENs (regional CENs) contain proteins seemingly absent from point-CEN organisms. However, at least three quarters of known kinetochore proteins are present in all fungi regardless of CEN organization. At least six of these proteins have previously unidentified human orthologs. When fungi and metazoa are compared, almost all have kinetochores constructed around Spc105 and three conserved multi-protein linker complexes (MIND, COMA, and the NDC80 complex). CONCLUSION: Our data suggest that critical structural features of kinetochores have been well conserved from yeast to man. Surprisingly, phylogenetic analysis reveals that human kinetochore proteins are as similar in sequence to their yeast counterparts as to presumptive Drosophila melanogaster or Caenorhabditis elegans orthologs. This finding is consistent with evidence that kinetochore proteins have evolved very rapidly relative to components of other complex cellular structures.

Centromere↗
PubMed1984

The renin-angiotensin system in nonmammalian vertebrates.

The most primitive components of the RAS appeared early in the phylogenetic history of vertebrate animals. It is probable that renin granules were present in the kidneys of ancestral chordates before divergence in the evolution of actinopterygian fish and tetrapods occurred. Granulated juxtaglomerular cells similar to the renin-containing cells of the mammalian nephron are found in most extant vertebrate species although not in agnathan and elasmobranch fish. A macula densa occurs in amphibians, birds and mammals; and an extraglomerular mesangium, only in birds and mammals. Renin-like activity and angiotensin-like pressor material have been demonstrated in all classes of vertebrates. The amino acid sequences of native ANG I have been determined for representative species of teleost fish, amphibian, reptile and bird. These peptides differ from mammalian angiotensins at positions 1, 5 and 9. The RAS appears to be involved in osmoregulation, ionoregulation and the control of blood circulation. Prolonged hypovolemic hypotension or sodium depletion increases renin levels. Angiotensins elicit drinking and stimulate transepithelial ion transport. However, direct steroidogenic and antidiuretic hormone-releasing activities, which would promote mineral and fluid conservation, have not been demonstrated unambiguously in nonmammalian vertebrates. ANG II raises blood pressure by direct vasoconstrictor action on arteriolar muscles in some animals, but perhaps more generally by acting on the nervous system and adrenal paraneurons. In birds the hormone also has a hypotensive effect. ANG II stimulates the SNS in agnathans, elasmobranchs, teleosts, amphibians, reptiles, birds and mammals. Thus, modulation of sympathetic activity may be one of the most primitive and conservative functions of the RAS. For this reason, nonmammalian vertebrates are valuable models for studying the neurogenic actions of angiotensin II relevant to hypertensive disease.

Amphibians↗
PubMed1993

Characterization of mannose 6-phosphate receptors (MPRs) from opossum liver: opossum cation-independent MPR binds insulin-like growth factor-II.

Bovine, human, and rat cation-independent mannose 6-phosphate receptors (CI-MPRs) are capable of binding both mannose 6-phosphate and insulin-like growth factor-II (IGF-II). However, the receptor isolated from either chicken or frog lacks the high affinity IGF-II-binding site. To determine whether CI-MPRs isolated from a species that is closely related to placental mammals can bind IGF-II, the MPRs were purified from a marsupial, the American opossum (Didelphis virginiana), by phosphomannan-Sepharose affinity chromatography and then tested for their ability to bind IGF-II. Opossum liver expressed both the CI-MPR and the cation-dependent MPR (CD-MPR). Both receptors contained Asn-linked oligosaccharides. In contrast to CD-MPRs isolated from other species, the opossum CD-MPR displayed heterogeneity with respect to the number of Asn-linked oligosaccharide chains it contains. The CI-MPR isolated from opossum liver, like the CI-MPR from bovine liver, bound iodinated human recombinant IGF-II. However, Scatchard analysis revealed that the opossum CI-MPR bound IGF-II with a lower affinity (Kd = 14.5 nM) than the bovine receptor (Kd = 0.2 nM). The addition of excess IGF-II, but not IGF-I or insulin, inhibited binding to [125I]IGF-II, indicating that the opossum CI-MPR exhibits specificity for IGF-II. These results suggest that the emergence of a high affinity IGF-II-binding site in the CI-MPR occurred in evolution before the divergence of marsupials and placental mammals from their last common ancestor.

Animals↗
PubMed1997

Exon skipping in the gene encoding pituitary adenylate cyclase-activating polypeptide in salmon alters the expression of two hormones that stimulate growth hormone release.

In mammals, GRF and pituitary adenylate cyclase-activating polypeptide (PACAP) are encoded in separate genes. We report here that in the salmon a 4.5-kilobase gene contains five exons that encode the biologically active part of the GRF-like peptide (amino acids 1-32) on exon 4 and PACAP on exon 5. Analysis of two fish messenger RNAs reveals that a long precursor containing GRF and PACAP and a short precursor containing only PACAP are both expressed in the brain of at least five species of salmon, whereas mice express only the long precursor encoded by the PACAP gene. Synthetic salmon PACAP-38 and salmon GRF-like peptide-45 both stimulated GH release from cultured salmon pituitary cells; PACAP stimulated a concentration-dependent release of GH at both 4 and 24 h of incubation, whereas GRF-like peptide did not. Alternative splicing, resulting in the short precursor in which GRF-32 is excised, may provide a means for differential control of GH secretion with higher production of the more potent PACAP. A duplication of the GRF-like/PACAP gene in evolution after the divergence of fish and tetrapods would explain separate genes and regulation for GRF and PACAP in mammals.

Alternative Splicing↗
PubMed1999

Conserved and distinct roles of kreisler in regulation of the paralogous Hoxa3 and Hoxb3 genes.

During anteroposterior patterning of the developing hindbrain, the anterior expression of 3' Hox genes maps to distinct rhombomeric boundaries and, in many cases, is upregulated in specific segments. Paralogous genes frequently have similar anterior boundaries of expression but it is not known if these are controlled by common mechanisms. The expression of the paralogous Hoxa3 and Hoxb3 genes extends from the posterior spinal cord up to the rhombomere (r) 4/5 boundary and both genes are upregulated specifically in r5. However, in this study, we have found that Hoxa3 expression is also upregulated in r6, showing that there are differences in segmental expression between paralogues. We have used transgenic analysis to investigate the mechanisms underlying the pattern of segmental expression of Hoxa3. We found that the intergenic region between Hoxa3 and Hoxa4 contains several enhancers, which summed together mediate a pattern of expression closely resembling that of the endogenous Hoxa3 gene. One enhancer specifically directs expression in r5 and r6, in a manner that reflects the upregulation of the endogenous gene in these segments. Deletion analysis localized this activity to a 600 bp fragment that was found to contain a single high-affinity binding site for the Maf bZIP protein Krml1, encoded by the kreisler gene. This site is necessary for enhancer activity and when multimerized it is sufficient to direct a kreisler-like pattern in transgenic embryos. Furthermore the r5/r6 enhancer activity is dependent upon endogenous kreisler and is activated by ectopic kreisler expression. This demonstrates that Hoxa3, along with its paralog Hoxb3, is a direct target of kreisler in the mouse hindbrain. Comparisons between the Krml1-binding sites in the Hoxa3 and Hoxb3 enhancers reveal that there are differences in both the number of binding sites and way that kreisler activity is integrated and restricted by these two control regions. Analysis of the individual sites revealed that they have different requirements for mediating r5/r6 and dorsal roof plate expression. Therefore, the restriction of Hoxb3 to r5 and Hoxa3 to r5 and r6, together with expression patterns of Hoxb3 in other vertebrate species suggests that these regulatory elements have a common origin but have later diverged during vertebrate evolution.

Amino Acid Sequence↗
PubMed1996

Presence and expression of G2 cyclins in the coelenterate hydra.

In hydra all cell-cycle control occurs in the G2/M transition. Cyclins acting at this restriction point in the cell cycle belong to the cyclin A and B families. In agreement with this we isolated cDNAs coding for a cyclin A and a cyclin B from the multiheaded mutant of Chlorohydra viridissima and a cyclin B from Hydra vulgaris. The two B-type cyclins from hydra show 85.6% identity at the amino acid level, and 84.8% at the nucleotide level. The relatedness is less extensive than that found for mammals, e.g. human and mouse, and is evidence that the two hydra species diverged early in evolution. From each hydra species only one B-type cyclin was found, showing equal relatedness to the B1 and B2 subtypes of cyclins, hinting at a role as common ancestor before the split into B1 and B2 cyclins occurred. All three hydra cyclins contain regulation signals typical for G2/M cyclins, such as a ubiquitin destruction box at the amino terminus, needed for rapid degradation of the protein, and translation and polyadenylation elements in the 3' untranslated region to regulate RNA storage and RNA degradation. In hydra cell-cycle times vary depending on feeding regime and growth conditions. Cyclin B RNA expression was found to precede the daily mitotic rhythm induced by feeding. During head regeneration cyclin B expression showed the expected drop early during regeneration and an increase later. At the cellular level strongest expression of cyclin B RNA and protein was detected in interstitial cells which possess with one day the shortest cell-cycle time in hydra. Epithelial cells with a three-day cell-cycle rhythm showed variable, and differentiated cells no cyclin B expression. Regions of hydra containing high numbers of proliferating cells, such as developing buds exhibited elevated levels of cyclin B expression.

Amino Acid Sequence↗
PubMed1983

Homologies in the structures of bull seminal plasma acrosin inhibitors and comparison with other homologous proteinase inhibitors of the Kazal type.

After determination of the amino-acid sequence of a further acrosin inhibitor isolated from bull seminal plasma, the primary structures of the three seminal inhibitors known so far were compared with other homologous structures of protein-protein inhibitors. From the matrix of minimal base changes, a high divergence in the evolution of the seminal inhibitors can be seen. Inhibitors from bull seminal plasma show even a higher degree of relationship to dog submandibular gland inhibitor domain II and the 3rd domain of quail ovomucoid than to acrosin inhibitor from boar seminal plasma.

Acrosin↗
PubMed1990

Two human lysosomal membrane glycoproteins, h-lamp-1 and h-lamp-2, are encoded by genes localized to chromosome 13q34 and chromosome Xq24-25, respectively.

We have isolated previously cDNAs encoding two related human lysosomal membrane glycoproteins, h-lamp-1 and h-lamp-2 (Fukuda, M., Viitala, J., Matteson, J., and Carlsson, S.R. (1988) J. Biol. Chem. 263, 18920-18928). In the present study, we have determined the chromosomal localization of genes for h-lamp-1 and h-lamp-2. By using the method of in situ hybridization, we have localized the gene for h-lamp-1 to chromosome 13q34 and its related gene to chromosome 12p133. The hybridization of h-lamp-1 cDNA to chromosome 12p133 was observed even when probes representing different portions of h-lamp-1 cDNA were used. On ther other hand, the gene for h-lamp-2 were localized to Xq24-25 but no cross-hybridization to chromosome 12p133 was observed even though h-lamp-1 and h-lamp-2 are highly related. These results clearly indicate that human lamp-1 and lamp-2 are coded by separate genes on different chromosomes. The present results support our hypothesis that lamp-1 and lamp-2 diverged early in evolution and they have distinct functions which emerged as soon as eukaryotic cells acquired lysosomes as subcellular compartments.

Antigens, CD↗
PubMed1989

Chicken and Xenopus mannose 6-phosphate receptors fail to bind insulin-like growth factor II.

The recent demonstration that a single mammalian receptor protein binds both mannose 6-phosphate (Man-6-P) and insulin-like growth factor II (IGF-II) with high affinity has suggested a multifunctional physiological role for this receptor, possibly including signal transduction. In order to better understand the functions of this receptor, we have investigated the properties of Man-6-P receptors from non-mammalian species. Receptors were affinity-purified from Triton X-100 extracts of total membranes from Xenopus and chicken liver as well as rat placenta using pentamannosyl 6-phosphate-Sepharose. The Man-6-P receptor was adsorbed to the pentamannosyl 6-phosphate-Sepharose and specifically eluted by Man-6-P in all three species, as evaluated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis followed by silver staining. When the purified receptors from these three species were cross-linked to 125I-IGF-II with disuccinimidyl suberate, only receptors isolated from rat membranes were affinity-labeled. To further evaluate the properties of these Man-6-P receptors, binding of 125I-rat-IGF-II and 125I-chicken Tyr-Gly-Thr-Ala-IGF-II to purified receptors from Xenopus, chicken, and rat was evaluated by polyethylene glycol precipitation. Only the rat Man-6-P receptor exhibited detectable binding of 125I-IGF-II. These data suggest that the emergence of a high affinity IGF-II binding site on the Man-6-P receptor occurred in evolution after the divergence of mammals from other vertebrates. Thus, the biological actions of IGF-II in chickens and frogs appear to be initiated by the type I IGF receptor.

Animals↗