Identification of methicillin-resistant staphylococci by multiplex polymerase chain reaction assay

A multiplex polymerase chain reaction (PCR) assay using oligonucleotide primers to detect mecA and 16S ribosomal RNA gene was developed to aid in identification of methicillin-resistant staphylococci. Validation included 99 isolates of staphylococcus grouped into one of five categories: methicillin-susceptible coagulase-negative staphylococcus (MSCNS), methicillin-resistant coagulase-negative staphylococcus (MRCNS), methicillin-susceptible Staphylococcus aureus (MSSA), high beta-lactamase producing S aureus (HiBSA), and methicillin-resistant S aureus (MRSA). mecA was detected in MRSA (21/21), and in MRCNS (20/20), but not in MSSA (0/20). mecA was occasionally detected in HiBSA (1/19) and MSCNS (3/19). This multiplex PCR assay was also used to test 30 clinical isolates of coagulase-negative staphylococci with discrepancies between results of in vitro tests for susceptibility to oxacillin and was found to be valuable when a more definitive determination of intrinsic methicillin-resistance was desired.

Factor V R506Q gene mutation analysis by PCR-RFLP: optimization, comparison with functional testing for resistance to activated protein C, and establishment of cell line controls

Resistance to activated protein C (APC) has been recently identified as a highly prevalent risk factor for the development of venous thrombosis. In the majority of cases, APC resistance correlates with the presence of a single point mutation in the factor V gene (FV R506Q). The mutation is present in 3% to 5% of the general population and in up to 50% of patients with a personal and family history of venous thrombosis. In the current study, the authors have optimized and implemented for clinical diagnosis a method for detection of FV R506Q using the polymerase chain reaction coupled with restriction fragment length polymorphism analysis (PCR-RFLP). Forty-one healthy adults and 139 patients referred for hypercoagulability testing were genotyped and their APC resistance ratios determined using commercially available reagents (COATEST APC Resistance Kit). Comparative analysis indicated that if functional APC resistance was defined as per manufacturer's guidelines, a significant number of individuals with a normal factor V genotype were categorized as APC resistant and conversely, a significant number of individuals heterozygous for FV R506Q were categorized as non-APC resistant. These results indicate that comparative functional and genotypic analyses in the individual clinical laboratory setting are critical for establishing normal ranges and cut-off values for functional APC resistance due to FV R506Q. To facilitate molecular evaluation of APC resistance, Epstein-Barr virus (EBV) immortalized B-lymphocyte cell lines were established from individuals heterozygous and homozygous for FV R506Q.

Two coding change mutations in the HIS2(2) allele characterize the salivary histatin 3-2 protein variant

The decoded amino acid sequence of a salivary protein variant, histatin 3-2 (formerly termed Pb c), that is found primarily and in high frequency in Black populations was determined by genomic PCR and direct sequencing of the HIS2(2) allele. Two different mutations that cause coding changes were found in exon 5. The first mutation is a single nucleotide (T-->A) substitution that causes a TAT (Tyr)-->TAA (Stop) change at residue 28. This premature stop mutation results in a 27 amino acid histatin 3-2 protein, which is 5 amino acids smaller than the common histatin 3-1 allelic protein (a product of the HIS2(1) allele). The second mutation, a single nucleotide (G-->A) substitution (located only 19 nucleotides upstream of the first mutation) causes a CGA (Arg)-->CAA (Gln) change at residue 22, which eliminates a proteolytic cleavage site. These two mutations explain the differences in electrophoretic patterns of HIS2(1) versus HIS2(2) coded histatin peptides and may have functional significance. Each mutation alters a different DNA restriction site, and this provides a DNA-based test for the mutations. This test should greatly simplify population and family studies of this protein polymorphism, since the saliva-based test is considerably more problematic. Elucidation here of the derived protein sequence of the variant histatin 3-2 protein may also facilitate functional studies.

Nucleotide sequence analysis of the human salivary protein genes HIS1 and HIS2, and evolution of the STATH/HIS gene family

Human histatins are a family of low-M(r), neutral to very basic, histidine-rich salivary polypeptides. They probably function as part of the nonimmune host defense system in the oral cavity. A 39-kb region of DNA containing the HIS1 and HIS2 genes was isolated from two human genomic phage libraries as a series of overlapping clones. The nucleotide sequences of the HIS1 gene and part of the HIS2(1) gene were determined. The transcribed region of HIS1 spans 8.5 kb and contains six exons and five introns. The HIS1 and HIS2(1) genes exhibit 89% overall sequence identity, with exon sequences exhibiting 95% identity. The two loci probably arose by a gene duplication event approximately 15-30 Mya. The HIS1 sequence data were also compared with that of STATH. Human statherin is a low-M(r) acidic phosphoprotein that acts as an inhibitor of precipitation of calcium phosphate salts in the oral cavity. The HIS1 and STATH genes show nearly identical overall gene structures. The HIS1 and STATH loci exhibit 77%-81% sequence identity in intron DNA and 80%-88% sequence identity in noncoding exons but only 38%-43% sequence identity in the protein-coding regions of exons 4 and 5. These unusual data suggest that HIS1, HIS2, and STATH belong to a single gene family exhibiting accelerated evolution between the HIS and STATH coding sequences.

Serial cultivation of epithelial cells from human and macaque salivary glands

To study the regulation of human salivary-type gene expression we developed cell culture systems to support the growth and serial cultivation of salivary gland epithelial and fibroblastic cell types. We have established 22 independent salivary gland epithelial cell strains from parotid or submandibular glands of human or macaque origin. Nineteen strains were derived from normal tissues and three from human parotid gland tumors. Both the normal and the tumor-derived salivary gland epithelial cells could be serially cultivated with the aid of a 3T3 fibroblast feeder layer in a mixture of Ham's F12 and Dulbecco's modified Eagle's media supplemented with fetal bovine serum, calcium, cholera toxin, hydrocortisone, insulin, and epidermal growth factor. Salivary gland epithelial cells cultured under these conditions conditioned to express the genes for at least two acinar-cell-specific markers at early passages. Amylase enzyme activity was detected in conditioned media from cultured rhesus parotid epithelial cells as late as Passage 5. Proline-rich-protein-specific RNAs were detected in primary cultures of both rhesus and human parotid epithelial cells. Neither amylase enzyme activity nor PRP-specific RNAs were detected in fibroblasts isolated from the same tissues. In addition, salivary gland epithelial cells cultured under our conditions retain the capacity to undergo dramatic morphologic changes in response to different substrata. The cultured salivary gland epithelial cells we have established will be important tools for the study of salivary gland differentiation and the tissue-specific regulation of salivary-type gene expression.

mRNAs for PRPs, statherin, and histatins in von Ebner's gland tissues

A search was made for expression of genes for proline-rich proteins (PRPs) and other salivary-type proteins, including statherin and histatins, in taste-bud tissues of mice and primates because of previous genetic findings in mice (Azen et al., 1986) that Prp and taste genes for certain bitter substances are either the same or closely linked. Taste-bud tissues and other tissues were tested for specific mRNAs with labeled DNA probes by Northern blotting and in situ hybridization. It was found that PRP mRNAs were present in von Ebner's glands of mice and macaques, and that there was a much greater degree of PRP mRNA induction in mouse parotid (16-fold) than in von Ebner's gland (two-fold) after in vivo isoproterenol stimulation. This difference may be due, in part, to differences in autonomic nerve innervation. Statherin and histatin mRNAs were found in macaque taste-bud tissues containing von Ebner's gland, and statherin protein was found in human von Ebner's gland by immunohistochemistry. The finding of PRP gene expression in von Ebner's gland, whose secretions have been suggested to play a role in taste stimulation, adds further support to a possible function of PRPs in bitter tasting. The possible functions of statherin and histatins in von Ebner's gland secretions may be related to statherin's regulation of salivary calcium and histatins' antibacterial and antifungal properties.

Structure and sequence determination of the gene encoding human salivary statherin

Human statherin (STT) is a low-Mr (43 amino acids) acidic phosphoprotein secreted mainly by salivary glands. It acts as an inhibitor of precipitation of Ca.phosphate salts in the oral cavity. DNA (12.2 kb) was isolated from human genomic phage lambda libraries as a series of overlapping clones, and the nucleotide sequence of the STT-encoding gene (STT) was determined. The transcribed region spans 6.5 kb and contains six exons and five introns. Upstream DNA (1.6 kb) was also sequenced and a number of possible regulatory elements were identified. The exon-intron boundaries of the STT gene roughly coincide with the protein-coding regions of the mRNA and with the functional domains of STT. This pattern of organization has been seen in a variety of eukaryotic genes and is consistent with the domain theory of gene evolution.

The human cystatin C gene (CST3) is a member of the cystatin gene family which is localized on chromosome 20

The fourth gene from the human cystatin gene family of salivary-type cysteine-proteinase inhibitors has been isolated and partially characterized by DNA analysis. The gene, which we name CST3, codes for human cystatin C, and has the same organization as the CST1 gene for cystatin SN and the CST2 gene for cystatin SA. Southern analysis of EcoR I digested DNAs from 32 independent somatic cell hybrid clones hybridized to a probe from CST1 demonstrated that all members of the cystatin gene family segregate with human chromosome 20. These results indicate that the genes for salivary-type cystatins and cystatin C are members of a multigene family--the cystatin gene family.

Tissue distribution of RNAs for cystatins, histatins, statherin, and proline-rich salivary proteins in humans and macaques

The tissue distribution of the mRNAs for a number of salivary proteins [proline-rich proteins (PRPs), statherin, cystatins, and the histatins] has been examined in humans and macaques in order to investigate their possible functions and tissue-specific regulation. We have shown that PRP RNAs (0.8-1.5 kb) are expressed in human and rhesus parotid and submandibular glands, and in the human bronchus. The genes for the acidic and basic PRPs are differentially regulated in these tissues. RNAs for acidic PRPs are predominantly expressed in the submandibular gland, for basic PRPs in the respiratory tract, and for both acidic and basic PRPs in the parotid gland. Protein studies of secretions from these tissues confirm the RNA results. Statherin RNA (0.65 kb) was detected in human and rhesus parotid and submandibular glands and the human bronchus, as well as in rhesus lacrimal glands. Statherin was found by tissue immunoperoxidase staining in the serous cells of respiratory tract submucosal glands, which is the same location for the synthesis of PRPs. Several cystatin RNAs (0.8-1.3 kb) were differentially expressed in human parotid glands, submandibular glands, and the bronchus, and in lacrimal glands from both rhesus and cynomolgus macaques. RNAs (0.6 kb) for the histatins were found only in parotid and submandibular glands. Thus, it appears that PRPs, statherin, and cystatins may play a broader role in the physiology of biological fluids and secretions than previously suspected, since they are found in secretions other than saliva. However, the functions of the histatins are restricted to saliva. These studies also pose some interesting questions regarding the differential expression of these genes in a variety of secretory tissues.

Histatins, a family of salivary histidine-rich proteins, are encoded by at least two loci (HIS1 and HIS2)

We screened a human parotid gland cDNA library with mixed synthetic oligonucleotide probes representing a central coding region common to histatins 1 and 3. Sequence analysis of 12 histatin cDNA clones strongly suggests that the histatin protein family is encoded by at least two closely related loci (HIS1 and HIS2) such that histatins 1 and 3 are primary products of HIS1(1) and HIS2(1) alleles, respectively, and that histatins 4-6 are derived from histatin 3 by proteolysis. We present additional data indicating that histatin 2 may represent the non-phosphorylated form of histatin 1.

cDNA cloning and chromosomal localization (4q11-13) of a gene for statherin, a regulator of calcium in saliva

On the basis of the known amino acid sequence of statherin, a human salivary protein, mixed synthetic oligonucleotides were synthesized and used to screen a cDNA library constructed from human parotid-gland mRNA. A cDNA clone coding for statherin was isolated from this library and has been completely sequenced. The cDNA represents a full-length (or nearly full-length) copy of an approximately 640-bp statherin mRNA. Statherin appears to be coded by a single-copy gene that maps to chromosome 4q11-4q13 when somatic-cell hybrids are used.

Drosophila histone H2A.2 is associated with the interbands of polytene chromosomes

Drosophila chromatin contains two antigenically distinct H2A histones, H2A.1 and H2A.2. Indirect immunofluorescence analyses revealed that anti-H2A.1 binding was distributed throughout polytene chromosomes, whereas anti-H2A.2 binding was interband-specific. Thus, H2A.2 probably contributes to the less compacted structure of interbands. Since each band-interband region is thought to contain a single gene, our results suggest that the distribution of H2A.2 echoes the functional organization of the Drosophila genome. Similar H2A histones occur in eukaryotes ranging from protozoa to mammals. Their placement might be an important determinant of chromatin structure.

Drosophila virilis histone gene clusters lacking H1 coding segments

Approximately 30-40% of Drosophila virilis DNA complementary to cloned Drosophila histone genes is reduced to 3.4-kilobase-pair (kbp) segments by Bgl I or Bgl II digestion. The core histone genes of a 3.4-kbp Bgl II segment cloned in the plasmid pDv3/3.4 have the same order as the D. melanogaster core histone genes in the plasmid cDm500: H2B H3 H4 H2A. Nonetheless, pDv3/3.4 and cDm500 have different histone gene configurations: In pDv3/3.4, the region between the H2B and H3 genes contains 0.35 kbp and cannot encode histone H1; in cDm500, the region contains 2.0 kbp and encodes histone H1. The lack of an H1 gene between the H2B and H3 genes in 30-40% of D. virilis histone gene clusters suggests that changes in histone gene arrays have occurred during the evolution of Drosophila. The ancestors of modern Drosophila may have possessed multiple varieties of histone gene clusters, which were subsequently lost differentially in the virilis and melanogaster lineages. Alternatively, they may have possessed a single variety, which was rearranged during evolution. The H1 genes of D. virilis and D. melanogaster did not cross-hybridize in vitro under conditions that maintain stable duplexes between DNAs that are 75% homologous. Consequently, D. virilis H1 genes could not be visualized by hybridization to an H1-specific probe and thus remain unidentified. Our observations suggest that the coding segments in the H1 genes of D. virilis and D. melanogaster are greater than 25% divergent.(ABSTRACT TRUNCATED AT 250 WORDS)

Structural homology between Drosophila melanogaster and Escherichia coli acidic ribosomal proteins

Antibodies raised against Drosophila melanogaster ribosomal proteins (r-proteins) were used to examine possible structural relationships between eukaryotic and prokaryotic r-proteins. The antisera were raised against either groups of r-proteins or individually purified r-proteins. Two antisera showed a cross-reaction with total Escherichia coli r-proteins in Ouchterlony double immunodiffusion assays: an antiserum against the D. melanogaster small subunit protein S14 (anti-S14) and an antiserum against a group of D. melanogaster r-proteins (anti-TP80). The specificity of the antisera and the identity of the homologous E. coli r-proteins were characterized by using immunooverlay and immunoblot assays. These assays indicated that anti-S14 was highly specific for protein S14 and anti-TP80 was a multispecific serum that recognized several of the D. melanogaster ribosomal proteins. The E. coli protein homologous to D. melanogaster protein S14 was identified as E. coli protein S6. By adsorption of the anti-TP80 serum, we determined that D. melanogaster protein 7/8 is homologous to the acidic E. coli protein L7/L12. D. melanogaster acidic protein 13 was also shown to be immunologically related to D. melanogaster protein 7/8.

Homology between Drosophila melanogaster and Escherichia coli ribosomal proteins

Antibodies raised against D. melanogaster ribosomal proteins were used to examine possible structural relationships between eukaryotic and prokaryotic ribosomal proteins. The antisera were raised against either groups of ribosomal proteins or purified individual ribosomal proteins from D. melanogaster. The specificity of each antiserum was confirmed and the identity of the homologous E. coli ribosomal protein was determined by immunochemical methods. Immuno-overlay assays indicated that the antiserum against the D. melanogaster small subunit protein S14 (anti-S14) was highly specific for protein S14. In addition, anti-S14 showed a cross-reaction with total E. coli ribosomal proteins in Ouchterlony double immunodiffusion assays and with only E. coli protein S6 in immuno-overlay assays. From these and other experiments with adsorption of anti-S14 with individual purified proteins, the E. coli protein homologous to the D. melanogaster protein S14 was established as protein S6.

Purification of Drosophila acidic ribosomal proteins

The relatively acidic proteins (group A80) of Drosophila melanogaster ribosomes were separated by ion-exchange chromatography. Fractions containing one or more acidic proteins were combined into thirteen pools. The criterion for the combination was the migration pattern in one-dimensional polyacrylamide gels containing sodium dodecyl sulphate. Five proteins (7/8, S25/S27, S14, L1/L2 and L5/L6) required no further purification. The others were further purified as follows: proteins S7, and S9 by preparative gel electrophoresis: and protein 13 (to newly identified protein) by adsorption with conconavalin-A--agarose. Four proteins had no detectable contamination, and in each of the others the impurities were no greater than 3%. The amount of purified protein recovered from a starting amount of 2.63 g total 80-S ribosomal protein and a starting amount of 105 mg group A80 varied from 0.4 mg to 8.8 mg. The molecular weight of the proteins was estimated by polyacrylamide gel electrophoresis in sodium dodecyl sulphate. The amino acid composition of the individual purified proteins was determined. Several phosphorylated proteins were identified. Proteins 13b and 13c are phosphorylated derivatives of 13a; 7b/8b and 7c/8c are phosphorylated derivatives of 7a and/or 8a. Proteins 7/8 and 13 are distinct proteins but are very similar in amino acid composition.

Group fractionation and determination of the number of ribosomal subunit proteins from Drosophila melanogaster embryos

Proteins were extracted from ribosomes and (for the first time) from ribosomal subunits of Drosophila melanogaster embryos. The ribosomal proteins were analyzed by two-dimensional polyacrylamide gel electrophoresis. The electrophoretograms displayed 78 spots for the 80S monomers, 35 spots for the 60S subunits, and 31 spots for the 40S subunits. On the basis of present information, we propose what we believe to be a reliable and convenient nomenclature for the proteins of the ribosomes and each of the subunits. A pair of acidic proteins from D. melanogaster appears to be very similar in electrophoretic mobility to the acidic proteins L7/L12 from Escherichia coli and L40/L41 from rat liver. The electrophoretogram of proteins from embryonic ribosomes shows both qualitative and quantitative differences from those of larvae, pupae, and adults previously reported by others. The proteins of the 40S subunit range in molecular weight from approximately 10,000 to 50,000, and those from the 60S subunit range from approximately 11,000 to 50,000.