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1.  Methylation patterns of mycoplasma transfer and ribosomal ribonucleic acid. 
Journal of Bacteriology  1980;144(3):991-998.
The methylation patterns of transfer and ribosomal ribonucleic acid (RNA) from two mycoplasmas, Mycoplasma capricolum and Acholeplasma laidlawii, have been examined. The transfer RNA from the two mycoplasmas resembled that of other procaryotes in degree of methylation and general diversity of methylated nucleotides, and bore particular resemblance to Bacillus subtilis transfer RNA. The only unusual feature was the absence of m5U from M. capricolum transfer RNA. The methylation patterns of the mycoplasma 16S RNAs were also typically procaryotic, retaining the methylated residues previously shown to be highly conserved among eubacterial 16S RNAs. The mycoplasma 23S RNA methylation patterns were, on the other hand, quite unusual. M. capricolum 23S RNA contained only four methylated residues in stoichiometric amounts, all of which were ribose methylated. A. laidlawii 23S RNA contained the same ribose-methylated residues, plus in addition approximately six m5U residues. These findings are discussed in relation to the phylogenetic status of mycoplasma, as well as the possible role of RNA methylation.
PMCID: PMC294762  PMID: 6160144
2.  Synthesis of ribonucleotides and their participation in ribonucleic acid synthesis by Coxiella burnetii. 
Journal of Bacteriology  1977;132(3):841-846.
Synthesis of ribonucleic acid (RNA) by the deoxyribonucleic acid-dependent RNA polymerase of Coxiella burnetii required adenosine, uridine, guanosine, and cytidine 5'-triphosphates. Cell-free preparations of this obligate intracellular procaryotic parasite had competence to phosphorylate ribonucleoside mono- and diphosphates in the presence of exogenous adenosine and guanosine 5'-triphosphates to the corresponding di- and triphosphates. C. burnetii contained about 2 nmol of adenosine 5'-triphosphate per mg of protein, which could serve as a approximately P donor for in vivo synthesis of nucleoside triphosphates. The latter were then used as substrates in the synthesis of RNA in a coordinated metabolic system with C. burnetii RNA polymerase. It is suggested that during infection the rickettsiae might obtain the nucleotides necessary for RNA synthesis from the vacuoles in which C. burnetii proliferates.
PMCID: PMC235586  PMID: 200603
3.  Sequence and transcription mapping of Bacillus subtilis competence genes comB and comA, one of which is related to a family of bacterial regulatory determinants. 
Journal of Bacteriology  1989;171(10):5362-5375.
The complete nucleotide sequences of the comA and comB loci of Bacillus subtilis were determined. The products of these genes are required for the development of competence in B. subtilis and for the expression of late-expressing competence genes. The major 5' termini of both the comA and comB transcripts were determined. The inferred promoters of both comA and comB contained sequences that were similar to those found at the -10 and -35 regions of promoters that are used by sigma A-RNA polymerase, the primary form of this enzyme in vegetative cells. The comB gene was located approximately 3 kilobase pairs upstream of the comA gene and encoded a 409-amino-acid protein with a predicted molecular weight of 46,693. The comA locus contained two open reading frames (ORFs) and comB contained one ORF. The predicted amino acid sequence of the comA ORF1 gene product consisted of 214 amino acids, with an aggregate molecular weight of 24,132. The ORF1 product was required for competence, while ORF2, which was cotranscribed with ORF1 and encoded a predicted protein of 126 amino acids, was not. The predicted protein sequence of the comA ORF1 gene product was found to be similar to that of several members of the effector class of procaryotic signal transducers. The C-terminal portion of the predicted comA sequence contained a possible helix-turn-helix motif, which is characteristic of DNA-binding proteins. comA ORF1 was cloned on a multicopy plasmid and was shown to complement the competence-deficient phenotype caused by the comA124 insertion of Tn917lac. Also, the presence of comA ORF1 in multiple copies interfered with sporulation. Anti-peptide antibodies raised to the predicted product of comA ORF1 reacted strongly with a single protein band of about 24,000 daltons in immunoblots. The possible roles of multiple signal transduction systems in triggering the development of competence are discussed.
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PMCID: PMC210374  PMID: 2507523
4.  The Borrelia burgdorferi flagellum-associated 41-kilodalton antigen (flagellin): molecular cloning, expression, and amplification of the gene. 
Infection and Immunity  1990;58(6):1711-1719.
Monoclonal antibodies directed against the major Borrelia burgdorferi flagellar protein, the 41-kilodalton (kDa) protein flagellin, were used to monitor cloning and expression of the flagellin gene from a Borrelia burgdorferi genomic library. The structure of the gene was analyzed, and recombinant nonfusion flagellin was produced in Escherichia coli. A DNA sequence analysis of the 41-kDa flagellin gene revealed the presence of an open reading frame that encoded a protein having 336 amino acid residues and a calculated molecular mass of 35.8 kDa, indicating that there was posttranslational modification of the natural 41-kDa flagellin protein. Upstream from the AUG start codon sequence we identified motifs corresponding to consensus procaryotic promoter elements which could be utilized by the cloned flagellin gene when it was expressed in E. coli MC1061. The deduced flagellin protein sequence exhibited high levels of homology to sequences of flagellin proteins from Bacillus subtilis and Salmonella typhimurium. The levels of sequence similarity for the amino- and carboxy-terminal portions were about 65 and 56%, respectively. DNA sequence information on the flagellin gene was used to design oligonucleotides for gene amplification by the polymerase chain reaction method, and by using this method 0.01 pg of Borrelia burgdorferi DNA could be detected. Our results provide a basis for further biochemical analysis of the 41-kDa flagellin protein, investigation of the role of this protein in host-pathogen interactions, and development of a standardized reagent for diagnostic systems for Borrelia burgdorferi infections.
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PMCID: PMC258713  PMID: 2341173
5.  Significance of ribosomal ribonucleic acid synthesis for control of the G1 period in the cell cycle of the heterobasidiomycetous yeast Rhodosporidium toruloides. 
Journal of Bacteriology  1980;144(2):772-780.
A cell cycle mutant strain which is defective in the G1 period, B2-39, was selected from 1,200 temperature-sensitive mutants of the heterobasidiomycetous yeast Rhodosporidium toruloides M-1057. In the mutant cells, ribosomal ribonucleic acid synthesis was initially inhibited upon temperature shift-up from a permissive (25 degrees C) to a restrictive (36 degrees C) temperature. Moreover, the mutant was found to be temperature sensitive in deoxyribonucleic acid-dependent ribonucleic acid polymerase I activity in vitro. In a revertant-mutant strain, B2-39-R-2, both ribosomal ribonucleic acid synthesis in vivo and enzyme activity in vitro were simultaneously recovered. These results indicate that the mutant has a temperature-sensitive, deoxyribonucleic acid-dependent ribonucleic acid polymerase I and suggest that ribosomal ribonucleic acid synthesis acts as one of the control factors for initiation of both deoxyribonucleic acid synthesis and bud emergence.
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PMCID: PMC294728  PMID: 7430071
6.  NhaD type sodium/proton-antiporter of Halomonas elongata: a salt stress response mechanism in marine habitats? 
Saline Systems  2006;2:10.
Background
Sodium/proton-antiporters (Nha) are known to play an important role in pH- and Na+-homeostasis. In microorganisms several types with different capacity, affinity and selectivity for Na+ and Li+ exist. The homeostasis system of E. coli, NhaA and NhaB, is well researched, but the function of other types of Na+/H+-antiporters like NhaD is yet to be fully understood. Since several antiporters play an important role at various points in the physiology of higher organisms, one can speculate that the main functions of some of those procaryotic antiporters differ from pH- and Na+-homeostasis.
Results
This study investigates the function and regulation of a gene encoding for a NhaD type antiporter which was discovered in the halophilic eubacterium Halomonas elongata.
The deduced primary amino acid sequence of the abovementioned gene showed more than 60% identity to known antiporters of the NhaD type from Alkalimonas amylolytica, Shewanella oneidensis and several other marine organisms of the γ-Proteobacteria. Evidence was found for a dual regulation of H. elongata NhaD expression. The gene was cloned and expressed in E. coli. Antiporter deficient NaCl and LiCl sensitive E. coli mutants EP432 and KNabc were partially complemented by a plasmid carrying the H. elongata nhaD gene. Surprisingly the LiCl sensitivity of E. coli strain DH5α having a complete homeostasis system was increased when NhaD was co-expressed.
Conclusion
Since NhaD is an antiporter known so far only from halophilic or haloalcaliphilic Proteobacteria one can speculate that this type of antiporter provides a special mechanism for adaptation to marine habitats. As was already speculated – though without supporting data – and substantiated in this study this might be active Na+-import for osmoregulatory purposes.
doi:10.1186/1746-1448-2-10
PMCID: PMC1552076  PMID: 16872527
7.  Rifampin resistance mutations that alter the efficiency of transcription termination at the tryptophan operon attenuator. 
Journal of Bacteriology  1981;145(3):1334-1341.
Rifampin-resistant mutants of Escherichia coli were isolated which had altered patterns of resistance or sensitivity to the inhibitory compounds 5-methyltryptophan and 5-methylanthranilate. The levels of tryptophan (trp) operon polypeptides in different rifampin-resistant mutants were elevated or reduced, in a manner consistent with their sensitivity to the two analogs. Complementation tests established that the mutations were in rpoB, the structural gene for the beta subunit of ribonucleic acid polymerase. Introduction of these rpoB mutations into mutant strains which terminate transcription abnormally at the trp operon attenuator established that the rpoB mutations alter trp operon expression by increasing or decreasing transcription termination at the attenuator. The rpoB mutations affected transcription termination at the attenuator only in strains which were able to form what is thought to be a ribonucleic acid termination structure. These findings suggest that alteration of the beta subunit of ribonucleic acid polymerase directly or indirectly affects ribonucleic acid polymerase's recognition of the transcription termination signal at the trp operon attenuator.
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PMCID: PMC217137  PMID: 7009579
8.  Altered nutritional requirements associated with mutations affecting the structures of ribonucleic acid polymerase in Lactobacillus casei. 
Journal of Bacteriology  1976;125(2):416-422.
Rifampin-resistant mutants were isolated from Lactobacillus casei S1 and examined for possible simultaneous alteration in nutritional properties. Among the 36 mutants obtained either spontaneously or after mutagenesis with 2-aminopurine, 22 were found to be altered with respect to the specific growth requirements. The majority (20 of 22) of the latter mutants were shown to require L-glutamine in addition to the nutrients required by the parental strain for maximal growth, whereas the remaining mutants had apparently lost the requirement for L-aspartate. Further studies with one of the glutamine-requiring mutants revealed that the rifampin resistance of this strain is due to the resistance of ribonucleic acid polymerase itself and that a single mutation is responsible for both rifampin resistance and the glutamine requirement. These results strongly indicate that a structural alteration of the ribonucleic acid polymerase caused by the rifampin resistance mutation somehow affected glutamine metabolism, possibly through change in selective transcription of the genes involved.
PMCID: PMC236098  PMID: 1379
9.  Isolation and Characterization of φ80 Transducing Bacteriophage for a Ribonucleic Acid Polymerase Gene 
Journal of Bacteriology  1973;116(2):511-516.
A new method for isolating specialized transducing phages is described. It was used to isolate a group of φ80 transducing phages which carry various bacterial markers from the metB region of the Escherichia coli chromosome. Some of the phages selected for transduction of the supA36 marker were also shown to carry rif, a locus known to specify the β subunit of ribonucleic acid polymerase. Expression of the prophage rifr gene in lysogens was demonstrated by its ability to confer rifampin resistance on part of the cellular ribonucleic acid polymerase pool.
PMCID: PMC285411  PMID: 4583236
10.  Ribonucleic acid polymerase of germinating Bacillus cereus T. 
Journal of Bacteriology  1975;124(1):542-549.
It appears that a de novo synthesis of the deoxyribonucleic acid-dependent ribonucleic acid-polymerase in Bacillus cereus T takes place fairly late in outgrowth, at the onset of the vegetative cycle. Therefore, the ribonucleic acid-polymerase used by germinating spores is the one carried on from sporulating cells. However, the sporal enzyme is less soluble that the vegetative one, and its "core" is bound to two extra peptides. This complexing to other molecules could play a role in the regulation of gene expression during germination.
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PMCID: PMC235924  PMID: 809425
11.  Purification to homogeneity and partial amino acid sequence of a fragment which includes the methyl acceptor site of the human DNA repair protein for O6-methylguanine. 
Nucleic Acids Research  1990;18(6):1351-1359.
DNA repair by O6-methylguanine-DNA methyltransferase (O6-MT) is accomplished by removal by the enzyme of the methyl group from premutagenic O6-methylguanine-DNA, thereby restoring native guanine in DNA. The methyl group is transferred to an acceptor site cysteine thiol group in the enzyme, which causes the irreversible inactivation of O6-MT. We detected a variety of different forms of the methylated, inactivated enzyme in crude extracts of human spleen of molecular weights higher and lower than the usually observed 21-24kDa for the human O6-MT. Several apparent fragments of the methylated form of the protein were purified to homogeneity following reaction of partially-purified extract enzyme with O6-[3H-CH3]methylguanine-DNA substrate. One of these fragments yielded amino acid sequence information spanning fifteen residues, which was identified as probably belonging to human methyltransferase by virtue of both its significant sequence homology to three procaryote forms of O6-MT encoded by the ada, ogt (both from E. coli) and dat (B. subtilis) genes, and sequence position of the radiolabelled methyl group which matched the position of the conserved procaryote methyl acceptor site cysteine residue. Statistical prediction of secondary structure indicated good homologies between the human fragment and corresponding regions of the constitutive form of O6-MT in procaryotes (ogt and dat gene products), but not with the inducible ada protein, indicating the possibility that we had obtained partial amino acid sequence for a non-inducible form of the human enzyme. The identity of the fragment sequence as belonging to human methyltransferase was more recently confirmed by comparison with cDNA-derived amino acid sequence from the cloned human O6-MT gene from HeLa cells (1). The two sequences compared well, with only three out of fifteen amino acids being different (and two of them by only one nucleotide in each codon).
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PMCID: PMC330497  PMID: 2109306
12.  Characterization of promoter-cloning plasmids: analysis of operon structure in the rif region of Escherichia coli and isolation of an enhanced internal promoter mutant. 
Journal of Bacteriology  1980;144(3):904-916.
Using the promotor-cloning vehicle described by An and Friesen (J. Bacteriol. 140:400-410, 1979), Escherichia coli chromosomal deoxyribonucleic acid fragments derived from the lambda drifd18 transducing phage were cloned in one of several unique restriction endonuclease sites adjacent to tetracycline(tet) genes that lack their own promotor. One of these plasmids has been used to isolate nine variants having mutations that lie in a putative internal promoter which is located between rplL and rpoB. Deoxyribonucleic acid sequence analysis revealed that, in all nine mutants, a single base change, C to T, in the ribonucleic acid polymerase recognition site led to a large increase in promoter activity. Analysis of a variety of plasmids in which tet is fused to various promoters yielded the following results: (i) rplK and rplA, genes for ribosomal protein L11 and L1, respectively, were cotranscribed from a common promoter located upstream from rplK; (ii) there was a strong promoter in the region between the rplKA operon and rplJ, the gene for ribosomal protein L10; (iii) an attenuator region was located between rplL, the gene for ribosomal protein L12, and rpoB, the gene for ribonucleic acid polymerase subunit beta; (iv) transcription terminated immediately after rpoC, the gene for ribonucleic acid polymerase subunit beta'; (v) a gene coding for unknown protein U, which is located between tufB and the rplKA operon, had its own promoter; (vi) the tufB gene was separated from all of the genes described above and had its own promoter.
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PMCID: PMC294752  PMID: 7002914
13.  Taxonomic Comparison of the Amino Termini of Microbial Cell Proteins 
Journal of Bacteriology  1969;98(2):368-374.
A comparison was made of the distribution of amino terminal end groups in the cellular proteins of a number of microbes. Among the procaryotes, methionine is a highly variable but virtually ubiquitous major protein end group. This is consistent with its possible role as a general amino acid initiator of protein biosynthesis in the procaryotes. Generally, however, alanine is the most abundant of the major end groups, followed in decreasing order by serine, threonine, the acidic amino acids, and occasionally lysine. No other new major end-groups were found. Among 15 representatives of the Enterobacteriaceae, retention of the initiating methionine terminus of the cellular protein varies considerably at a tribal level and is randomized at a familial level. The profiles of the five remaining end groups, however, are strikingly uniform, and are, for example, close to but significantly different from those of the Erwineae. Among the taxonomically more heterogeneous Bacillaceae, end-group profiles vary more and are sometimes unrelated. End-group analysis is thus particularly useful as a molecular criterion of taxonomy in assessing familial homogeneity. Free NH2 termini in eucaryote cell proteins are fewer, and they have increased acidic amino acid components and no methionine; they are otherwise similar to those of the procaryotes.
PMCID: PMC284823  PMID: 5784197
14.  Cloning and expression in Escherichia coli of isopenicillin N synthetase genes from Streptomyces lipmanii and Aspergillus nidulans. 
Journal of Bacteriology  1988;170(9):3817-3826.
beta-Lactam antibiotics such as penicillins and cephalosporins are synthesized by a wide variety of microbes, including procaryotes and eucaryotes. Isopenicillin N synthetase catalyzes a key reaction in the biosynthetic pathway of penicillins and cephalosporins. The genes encoding this protein have previously been cloned from the filamentous fungi Cephalosporium acremonium and Penicillium chrysogenum and characterized. We have extended our analysis to the isopenicillin N synthetase genes from the fungus Aspergillus nidulans and the gram-positive procaryote Streptomyces lipmanii. The isopenicillin N synthetase genes from these organisms have been cloned and sequenced, and the proteins encoded by the open reading frames were expressed in Escherichia coli. Active isopenicillin N synthetase enzyme was recovered from extracts of E. coli cells prepared from cells containing each of the genes in expression vectors. The four isopenicillin N synthetase genes studied are closely related. Pairwise comparison of the DNA sequences showed between 62.5 and 75.7% identity; comparison of the predicted amino acid sequences showed between 53.9 and 80.6% identity. The close homology of the procaryotic and eucaryotic isopenicillin N synthetase genes suggests horizontal transfer of the genes during evolution.
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PMCID: PMC211376  PMID: 3045077
15.  Nuclear Fraction of Bacillus subtilis as a Template for Ribonucleic Acid Synthesis 
Journal of Bacteriology  1968;95(4):1221-1237.
A “nuclear fraction” prepared from Bacillus subtilis was a more efficient template than purified deoxyribonucleic acid for the synthesis of ribonucleic acid by exogenously added ribonucleic acid polymerase isolated from B. subtilis. The initial rate of synthesis with the nuclear fraction was higher and synthesis continued for several hours, yielding an amount of ribonucleic acid greater than the amount of deoxyribonucleic acid used as the template. The product was heterogenous in size, with a large portion exceeding 23S. When purified deoxyribonucleic acid was the template, a more limited synthesis was observed with a predominantly 7S product. However, the ribonucleic acids produced in vitro from these templates were very similar to each other and to in vivo synthesized ribonucleic acid as determined by the competition of ribonucleic acid from whole cells in the annealing of in vitro synthesized ribonucleic acids to deoxyribonucleic acid. Treatment of the nuclear fraction with heat (60 C for 15 min) or trypsin reduced the capacity of the nuclear fraction to synthesize ribonucleic acid to the level observed with purified deoxyribonucleic acid.
PMCID: PMC315075  PMID: 4296512
16.  Sequence heterogeneity, multiplicity, and genomic organization of alpha- and beta-tubulin genes in sea urchins. 
Molecular and Cellular Biology  1981;1(12):1125-1137.
We analyzed the multiplicity, heterogeneity, and organization of the genes encoding the alpha and beta tubulins in the sea urchin Lytechinus pictus by using cloned complementary deoxyribonucleic acid (cDNA) and genomic tubulin sequences. cDNA clones were constructed by using immature spermatogenic testis polyadenylic acid-containing ribonucleic acid as a template. alpha- and beta-tubulin clones were identified by hybrid selection and in vitro translation of the corresponding messenger ribonucleic acids, followed by immunoprecipitation and two-dimensional gel electrophoresis of the translation products. The alpha cDNA clone contains a sequence that encodes the 48 C-terminal amino acids of alpha tubulin and 104 base pairs of the 3' nontranslated portion of the messenger ribonucleic acid. The beta cDNA insertion contains the coding sequence for the 100-C terminal amino acids of beta tubulin and 83 pairs of the 3' noncoding sequence. Hybrid selections performed at different criteria demonstrated the presence of several heterogeneous, closely related tubulin messenger ribonucleic acids, suggesting the existence of heterogeneous alpha- and beta-tubulin genes. Hybridization analyses indicated that there are at least 9 to 13 sequences for each of the two tubulin gene families per haploid genome. Hybridization of the cDNA probes to both total genomic DNA and cloned germline DNA fragments gave no evidence for close physical linkage of alpha-tubulin genes with beta-tubulin genes at the DNA level. In contrast, these experiments indicated that some genes within the same family are clustered.
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PMCID: PMC369739  PMID: 6287219
17.  Principal sigma subunit of the Caulobacter crescentus RNA polymerase. 
Journal of Bacteriology  1995;177(23):6854-6860.
We have identified the gene encoding the Caulobacter crescentus principal sigma subunit, RpoD. The rpoD gene codes for a polypeptide of 653 amino acids with a predicted molecular mass of 72,623 Da (sigma 73). The C. crescentus sigma subunit has extensive amino acid sequence homology with the principal sigma factors of a number of divergent procaryotes. In particular, the segments designated region 2 that are involved in core polymerase binding and promoter recognition were identical among these bacteria despite the fact that the -10 region recognized by the C. crescentus sigma 73 differs significantly from that of the other bacteria. Thus, it appears that additional sigma factor regions must be involved in -10 region recognition. This conclusion was strengthened by a heterologous complementation assay in which C. crescentus sigma 73 was capable of complementing the Escherichia coli rpoD285 temperature-sensitive mutant. Furthermore, C. crescentus sigma 73 conferred new specificity on the E. coli RNA polymerase, allowing the expression of C. crescentus promoters in E. coli. Thus, the C. crescentus sigma 73 appears to have a broader specificity than does the sigma 70 of the enteric bacteria.
PMCID: PMC177553  PMID: 7592478
18.  Topical Rapamycin Suppresses the Angiogenesis Pathways Induced by Pulsed Dye Laser: Molecular Mechanisms of Inhibition of Regeneration and Revascularization of Photocoagulated Cutaneous Blood Vessels 
Lasers in surgery and medicine  2012;44(10):796-804.
Background and Objectives
Pulsed dye laser (PDL) is the most effective treatment for port wine stain (PWS) birthmarks. However, regeneration and revascularization of photocoagulated blood vessels may result in poor therapeutic outcome. We have recently shown that rapamycin (RPM), an angiogenesis inhibitor, can reduce the regeneration and revascularization of photocoagulated blood vessels. Herein, we attempt to further elucidate the molecular pathophysiology on the inhibition of the regeneration and revascularization of photocoagulated blood vessels by topical RPM in an animal model.
Materials and Methods
Two separate skin areas on each hamster were irradiated by PDL. After PDL exposure, topical RPM was applied daily to one of the randomly selected test sites. PDL, PDL + RPM and normal skin test sites were biopsied on day 3 after PDL exposure. The total ribonucleic acid (RNA) and protein were extracted from biopsied skin samples and quantified. Real-time reverse transcription-polymerase chain reaction (RT-PCR) and immunoblot were subsequently performed to quantify the mRNA and protein levels of hypoxia-inducible factor-1alpha (HIF-1α), vascular endothelial growth factor (VEGF) and ribosomal protein S6 kinase (S6). The phosphorylation levels of S6 and AKT were also evaluated by immunoblot.
Results
The mRNA and protein levels of HIF-1α, VEGF, and S6 significantly increased after PDL exposure as compared to the normal hamster skin. Topical application of 1% RPM suppressed the PDL-induced increase in mRNA and protein levels of those genes on day 3 post-PDL exposure. The phosphorylation levels of S6 and AKT increased after PDL exposure but the increases were suppressed by the topical application of RPM.
Conclusion
The increase in expression of HIF-1α, VEGF, and S6 after PDL-exposure suggests that angiogenesis pathways play very active roles in the process of skin blood vessel regeneration and revascularization. Topical application of 1% RPM can suppress the angiogenesis pathways and, therefore, reduce the regeneration and revascularization of photocoagulated blood vessels.
doi:10.1002/lsm.22101
PMCID: PMC3982879  PMID: 23213008
pulsed dye laser; port wine stain; rapamycin; angiogenesis; HIF-1α; VEGF
19.  Participation of deoxyribonucleic acid polymerase alpha in amplification of ribosomal deoxyribonucleic acid in Xenopus laevis. 
Molecular and Cellular Biology  1981;1(8):680-686.
Aphidicolin, a known inhibitor of eucaryotic deoxyribonucleic acid (DNA) polymerase alpha, efficiently inhibited amplification of ribosomal DNA during oogenesis in Xenopus laevis. DNA polymerase alpha, but not DNA polymerase gamma, as isolated from ovaries, was sensitive to aphidicolin. DNA polymerase beta was not detectable in Xenopus ovary extracts. Therefore, DNA polymerase alpha plays a major role in ribosomal ribonucleic acid gene amplification.
PMCID: PMC369348  PMID: 9279381
20.  In vivo translation of a region within the rrnB 16S rRNA gene of Escherichia coli. 
Journal of Bacteriology  1987;169(4):1691-1701.
In this study we show that a segment of the Escherichia coli rrnB 16S gene can be translated in vivo. Other laboratories have previously reported that there are internal transcription and translation signals and open reading frames within the E. coli rrnB rRNA operon. Their studies revealed a translation start signal followed by a 252-base-pair open reading frame (ORF16) within the 16S gene and detected a promoter (p16) in the same general region by using in vitro RNA polymerase binding and transcription initiation assays. By using plasmid gene fusions of ORF16 to lacZ we showed that an ORF16'-'beta-galactosidase fusion protein was made in vivo. Transcripts encoding the fusion protein were expressed either from the rrnB p1p2 control region or from a hybrid trp-lac promoter (tacP), but the amount of expression was considerably less than for a lacZ control plasmid. We used fusions to the cat gene to show that p16 is one-half as active as lacP. Deletions were used to show that p16 is located within ORF16 and thus cannot promote a transcript encoding the ORF16 peptide. A comparison of sequences from different organisms shows that ORF16 and p16 lie in a highly conserved region of the procaryotic 16S RNA structure. The first 20 amino acids of ORF16 are conserved in most eubacterial and plant organellar sequences, and promoter activity has been detected in this region of the Caulobacter crescentus sequence by other workers.
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PMCID: PMC212001  PMID: 2435709
21.  Molecular analysis of the Azotobacter vinelandii glnA gene encoding glutamine synthetase. 
Journal of Bacteriology  1990;172(11):6529-6539.
The gene encoding glutamine synthetase (GS), glnA, was cloned from Azotobacter vinelandii on a 6-kb EcoRI fragment that also carries the ntrBC genes. The DNA sequence of 1,952 bp including the GS-coding region was determined. An open reading frame of 467 amino acids indicated a gene product of Mr 51,747. Transcription of glnA occurred from a C residue located 32 bases upstream of an ATG considered to be the initiator codon because (i) it had a nearby potential ribosome-binding site and (ii) an open reading frame translated from this site indicated good N-terminal homology to 10 other procaryotic GSs. Sequences similar to the consensus RNA polymerase recognition sites at -10 and -35 were present at the appropriate distance upstream of the transcription initiation site. As expected from earlier genetic studies indicating that expression of A. vinelandii glnA did not depend on the rpoN (ntrA; sigma 54) gene product, no sigma 54 recognition sequences were present, nor was there significant regulation of glnA expression by fixed nitrogen. Repeated attempts to construct glutamine auxotrophs by recombination of glnA insertion mutations were unsuccessful, Although the mutated DNA could be found by hybridization experiments in drug-resistant A. vinelandii transformants, the wild-type glnA region was always present. These results suggest that glnA mutations are lethal in A. vinelandii. In [14C]glutamine uptake experiments, very little glutamine was incorporated into cells, suggesting that glutamine auxotrophs are nonviable because they cannot be supplied with sufficient glutamine to support growth.
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PMCID: PMC526842  PMID: 1977737
22.  Bacillus sporulation gene spo0H codes for sigma 30 (sigma H). 
Journal of Bacteriology  1988;170(3):1054-1062.
The DNA sequences of the spo0H genes from Bacillus licheniformis and B. subtilis are described, and the predicted open reading frames code for proteins of 26,097 and 25,447 daltons, respectively. The two spo0H gene products are 91% identical to one another and about 25% identical to most of the procaryotic sigma factors. The predicted proteins have a conserved 14-amino-acid sequence at their amino terminal end, typical of sigma factors. Antibodies raised against the spo0H gene product of B. licheniformis specifically react with RNA polymerase sigma factor protein, sigma 30, purified from B. subtilis. We conclude that the spo0H genes of B. licheniformis and B. subtilis code for sigma 30, now known as sigma H.
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PMCID: PMC210873  PMID: 3277943
23.  A procaryotic regulatory factor with a histone H1-like carboxy-terminal domain: clonal variation of repeats within algP, a gene involved in regulation of mucoidy in Pseudomonas aeruginosa. 
Journal of Bacteriology  1990;172(10):5544-5554.
A novel procaryotic transcriptional regulatory element, AlgP, with a histone H1-like carboxy-terminal domain was identified in Pseudomonas aeruginosa. AlgP is required for transcription of the key biosynthetic gene algD, which is necessary for production of the exopolysaccharide alginate causing mucoidy in P. aeruginosa. Mucoidy is a critical virulence determinant of P. aeruginosa invariably associated with the respiratory infections causing high mortality in cystic fibrosis. Here we show that AlgP and histones H1 both have repeated units of the Lys-Pro-Ala-Ala motif (KPAA) and its variations within their long (over 100 amino acids) carboxy-terminal domains. This region of histone H1 tails has been shown to bind to the linker DNA in eucaryotic chromatin fibers. A synthetic 50-mer peptide consisting of repeats from the AlgP carboxy-terminal domain was found to bind DNA in a mobility shift DNA-binding assay. AlgP is encoded by a gene that contains multiple direct repeats organized as tandem, head-to-tail, 12-base-pair (bp) units overlapping with six highly conserved 75-bp units. The repetitive structure of the algP gene appears to participate in the processes underlying the metastable character of mucoidy in P. aeruginosa. Relatively large DNA rearrangements spanning the region with tandem direct repeats encoding the carboxy-terminal histone H1-like structure of AlgP were detected in several strains upon conversion from the mucoid to the nonmucoid phenotype. The frequency of the detectable algP rearrangements associated with the transition into the nonmucoid state varied from strain to strain and ranged from 0 to 50%. The nonmucoid derivatives with the clearly rearranged chromosomal copy of algP were complemented to mucoidy with plasmids containing algP from P. aeruginosa PAO. When a random collection of mucoid strains, isolated from different cystic fibrosis patients, was analyzed by using polymerase chain reaction, an additional level of strain-dependent sequence variation in algP was observed. Variations in the number of the 12-bp repeats were found; however, they did not appear to influence the mucoid status of the strains examined. Thus, the repeated region of algP appears to be a hot spot for DNA rearrangements and strain-dependent variability.
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PMCID: PMC526865  PMID: 1698761
24.  Transcription of minute virus of mice, an autonomous parvovirus, may be regulated by attenuation. 
Journal of Virology  1984;52(1):266-276.
To characterize the transcriptional organization and regulation of minute virus of mice, an autonomous parvovirus, viral transcriptional complexes were isolated and cleaved with restriction enzymes. The in vivo preinitiated nascent RNA was elongated in vitro in the presence of [alpha-32P]UTP to generate runoff transcripts. The lengths of the runoff transcripts were analyzed by gel electrophoresis under denaturing conditions. On the basis of the map locations of the restriction sites and the lengths of the runoff transcripts, the in vivo initiation sites were determined. Two major initiation sites having similar activities were thus identified at residues 201 +/- 5 and 2005 +/- 5; both of them were preceded by a TATAA sequence. When uncleaved viral transcriptional complexes or isolated nuclei were incubated in vitro in the presence of [alpha-32P]UTP or [alpha-32P]CTP, they synthesized labeled RNA that, as determined by polyacrylamide gel electrophoresis, contained a major band of 142 nucleotides. The RNA of the major band was mapped between the initiation site at residue 201 +/- 5 and residue 342. We noticed the potential of forming two mutually exclusive stem-and-loop structures in the 142-nucleotide RNA; one of them is followed by a string of uridylic acid residues typical of a procaryotic transcription termination signal. We propose that, as in the transcription of simian virus 40, RNA transcription in minute virus of mice may be regulated by attenuation and may involve eucaryotic polymerase B, which can respond to a transcription termination signal similar to that of the procaryotic polymerase.
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PMCID: PMC254514  PMID: 6090703
25.  Cloning and nucleotide sequence of braC, the structural gene for the leucine-, isoleucine-, and valine-binding protein of Pseudomonas aeruginosa PAO. 
Journal of Bacteriology  1989;171(11):6300-6306.
The gene for the leucine-, isoleucine-, and valine-binding protein (LIVAT-BP) in Pseudomonas aeruginosa PAO was isolated, and its nucleotide sequence was determined. The gene consisted of 1,119 nucleotides specifying a protein of 373 amino acid residues. Determination of the N-terminal amino acid sequence of the LIVAT-BP purified from P. aeruginosa shock fluid suggested that the N-terminal 26 residues of the gene product are cleaved off posttranslationally, showing the characteristic features of procaryotic signal peptides. The amino acid composition of the mature product predicted from the nucleotide sequence was in good agreement with that of the purified LIVAT-BP. The plasmid carrying the LIVAT-BP gene restored the activity of the high-affinity branched-chain amino acid transport system (the leucine, isoleucine, valine [LIV-I] transport system) in the braC310 mutant of P. aeruginosa, confirming that braC is the structural gene for LIVAT-BP. The mutant LIVAT-BP lacking a 16-amino-acid peptide in the middle was found to be functional in the LIV-I transport system. LIVAT-BP showed extensive homology (51% identical) to the LIV- and leucine-specific-binding proteins of Escherichia coli K-12, which are coded for by the livJ and livK genes, respectively, suggesting that the role of the proteins in the LIV-I transport systems is analogous in both organisms.
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PMCID: PMC210503  PMID: 2509433

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