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PubMed1997

Circadian rhythms in rapidly dividing cyanobacteria.

The long-standing supposition that the biological clock cannot function in cells that divide more rapidly than the circadian cycle was investigated. During exponential growth in which the generation time was 10 hours, the profile of bioluminescence from a reporter strain of the cyanobacterium Synechococcus (species PCC 7942) matched a model based on the assumption that cells proliferate exponentially and the bioluminescence of each cell oscillates in a cosine fashion. Some messenger RNAs showed a circadian rhythm in abundance during continuous exponential growth with a doubling time of 5 to 6 hours. Thus, the cyanobacterial circadian clock functions in cells that divide three or more times during one circadian cycle.

Cell Division↗
PubMed1974

Absence of 3'-terminal residues from transfer ribonucleic acid of dormant spores of Bacillus megaterium.

Essentially all (>97%) of the transfer ribonucleic acid (tRNA) in log-phase and sporulating cells of Bacillus megaterium contains a complete 3'-cytidyl-cytidyl-adenosine terminus. However, about one-third of the tRNA in the dormant spore lacks the 3'-terminal adenosine 5'-monophosphate (AMP) residue, and some of the adjacent cytosine monophosphate residues are also missing. Examination of specific tRNAs indicated that those specific for isoleucine, leucine, and methionine are missing 30 to 40% of their terminal residue, whereas tRNAs specific for tyrosine lack 88% of the 3'-terminal AMP. Defective spore tRNA is not degraded during germination, but the missing residues are added back in the first minutes of the process. The enzyme catalyzing the addition reaction, tRNA nucleotidyltransferase, is present in the dormant spore at a level similar to that found in the vegetative cell.

Adenosine Monophosphate↗
PubMed1974

Percent charging of transfer ribonucleic acid and levels of ppGpp and pppGpp in dormant and germinated spores of Bacillus megaterium.

The levels of transfer ribonucleic acids (tRNAs) specific for 14 amino acids were almost identical in dormant spores and in spores germinated from 6 to 75 min. Germinated spore tRNAs specific for all amino acids tested were between 63 and 93% charged, and there was no significant change in this value from 6 to 75 min of germination. In contrast, tRNAs isolated from dormant spores specific for nine different amino acids were almost completely(>93%) uncharged. However, some dormant spore tRNAs, i.e., those for arginine, histidine, isoleucine, and valine, showed significant (21 to 72%) levels of aminoacylation. Dormant spores contained no detectable guanosine penta- (pppGpp), tetra- (ppGpp), or triphosphate (GTP). However, these nucleotides appeared in the first minutes of germination, and thereafter all increased in parallel with a ratio of pppGpp plus ppGpp to GTP of 0.07 to 0.11, which is characteristic of unstarved vegetative cells.

Amino Acids↗
PubMed1975

Alteration of tyrosine isoaccepting transfer ribonucleic acid species in wild-type and asporogenous strains of Bacillus subtilis.

The relative amounts of two isoacceping species of tyrosine transfer ribonucleic acid, tRNATyrI and tRNATyrII, determined from reversed phase 5 profiles of tyrosyl-tRNA, prepared from Bacillus subtilis strain W168, were growth phase and medium dependent. The growth phase-dependent alterations in the relative amounts of tRNATyr species were also demonstrated in 11 asporogenous strains of B. subtilis. The proportion of tRNA-Tyr species and the extent of the alteration in their relative amounts during the transition from the exponential to the stationary phase of growth of these strains was not directly correlated with the formation of spores by strain W168 grown in various media or the stage at which the asporogenous strains are blocked in the process of sporulation.

Acylation↗
PubMed1978

Post-transcriptional modifications of the anticodon loop region: alterations in isoaccepting species of tRNA's during development in Bacillus subtilis.

Structural similarities of tRNA's were compared using three sets of isoaccepting species that had previously been shown to undergo significant changes in chromatographic elution properties as a function of developmental stage in Bacillus subtilis. Comparisons of the structures of the tRNA's were based on the composition of their modified nucleosides, comparisons of oligonucleotide elution profiles from RPC-5 columns, and two-dimensional electrophoretic fingerprint analysis of oligonucleotides. The tRNA's studied were tRNA(Lys) (1) and tRNA(Lys) (3); tRNA(Tyr) (1) and tRNA(Tyr) (2); and tRNA(Trp) (1) and tRNA(Trp) (2). The results suggest that the difference among these pairs of isoaccepting species is a difference in the degree of post-transcriptional modifications of the anticodon loop region. The nucleosides involved were N(6)-(Delta(2)-isopentenyl)adenosine (i(6)A), 2-methylthio-N(6)-(Delta(2)-isopentenyl)adenosine (ms(2)i(6)A), and an unknown nucleoside K, which occurred in a position analogous to N-[9-(beta-d-ribofuranosyl)purin-6-ylcarbamoyl]threonine. The amounts of i(6)A and ms(2)i(6)A, determined using total tRNA from exponential-or stationary-phase cells, suggest that the thiomethylation of i(6)A is a pleiotropic phenomenon affecting several tRNA species. As opposed to the situation in Escherichia coli tRNA, where ms(2)i(6)A constitutes about 90% of the total hydrophobic nucleosides at all growth stages, B. subtilis tRNA's have i(6)A as the predominant hydrophobic nucleoside in exponential growth and ms(2)i(6)A as the predominant nucleoside in stationary phase. Thus, the enzyme system which forms i(6)A and the enzyme system which thiomethylates i(6)A are not coordinated during growth in B. subtilis as they are in E. coli. It is suggested that these changes in anticodon loop modifications in B. subtilis may be related to changes in the translational apparatus which occur during sporulation.

Bacillus subtilis↗
PubMed1979

Transfer ribonucleic acid synthesis during sporulation and spore outgrowth in Bacillus subtilis studied by two-dimensional polyacrylamide gel electrophoresis.

The synthesis of transfer ribonucleic acid (tRNA) was examined during spore formation and spore outgrowth in Bacillus subtilis by two-dimensional polyacrylamide gel electrophoresis of in vivo 32P-labeled RNA. The two-dimensional gel system separated the B. subtilis tRNA's into 32 well-resolved spots, with the relative abundances ranging from 0.9 to 17% of the total. There were several spots (five to six) resolved which were not quantitated due to their low abundance. All of the tRNA species resolved by this gel system were synthesized at every stage examined, including vegetative growth, different stages of sporulation, and different stages of outgrowth. Quantitation of the separated tRNA's showed that in general the tRNA species were present in approximately the same relative abundances at the different developmental periods. tRNA turnover and compartmentation occurring during sporulation were examined by labeling during vegetative growth followed by the addition of excess phosphate to block further 32P incorporation. The two-dimensional gels of these samples showed the same tRNA's seen during vegetative growth, and they were in approximately the same relative abundances, indicating minimal differences in the rates of turnover of individual tRNA's. Vegetatively labeled samples, chased with excess phosphate into mature spores, also showed all of the tRNA species seen during vegetative growth, but an additional five to six minor spots were also observed. These are hypothesized to arise from the loss of 3'-terminal residues from preexisting tRNA's.

Bacillus subtilis↗
PubMed1998

Growth rate-dependent accumulation of RNA from plasmid-borne rRNA operons in Escherichia coli.

Inadequate regulation of the expression of additional plasmid-borne rRNA operons in Escherichia coli was exaggerated at slow growth rates, resulting in increases of approximately 100% for RNA concentration and 33% for doubling time. These observations are consistent with the hypothesis that multiple rRNA operons constitute a metabolic burden at slow growth rates.

Escherichia coli↗
PubMed1978

Suppression of temperature-sensitive sporulation of a Bacillus subtilis elongation factor G mutant by RNA polymerase mutations.

A class of rifampin-resistant (rfm) mutations of Bacillus subtilis suppresses the temperature-sensitive sporulation of a fusidic acid-resistant mutant. FUS426, which has an altered elongation factor G. The rfm mutation suppressed only the sporulation defect caused by the elongation factor G mutation, but could not suppress other types of induced sporulation defects. Genetic and biochemical analyses showed that the sporulation suppression by the rfm mutation was caused by a single mutation in RNA polymerase. After the early sporulation phase, the apparent rate of RNA synthesis of FUS426, measured by [3H]uracil or [3H]uridine incorporation into RNA, became lower than that of the wild-type strain, and this decrease was reversed by the rfm mutation. However, when the total rate of RNA synthesis of FUS426 was calculated by measuring the specific activity of [3H]UTP and [3H]CTP, it was higher than that of the rfm mutant, RIF122FUS426. The possible mechanism of the functional interaction between elongation factor G and RNA polymerase during sporulation is discussed.

Bacillus subtilis↗
PubMed1978

High molecular weight ribosomal ribonucleic acid from vegetative hyphae and spores of Streptomyces griseus.

High molecular weight ribosomal ribonucleic acids (rRNAs) were isolated from young vegetative cells and spores of a streptomycin non-producing Streptomyces griseus, and their electrophoretic mobility was compared to each other and to that of rRNAs of Escherichia coli K-12. The electrophoretic mobility of 23 and 16S rRNAs from vegetative cells and spores of S. griseus was identical, but the 23S rRNAs of streptomyces ribosomes migrated more slowly on polyacrylamide gel than those of E. coli ribosomes. Intact, electrophoretically homogenous rRNAs could be isolated from S. griseus (No. 45-H) only in the presence of diethyl 1 pyrocarbonate (DEP), and intact rRNAs could be obtained from spores only if DEP had been added before breaking the spores. Otherwise instead of two distinct bands, three were obtained on polyacrylamide gel.

Electrophoresis, Polyacrylamide Gel↗
PubMed2006

Composition of the bacterial flora in tonsilloliths.

Tonsilloliths are a potential cause of oral malodor. In this study, microbial profiles and composition of tonsilloliths were determined using culture-independent molecular methods and scanning electron microscopy. 16S ribosomal RNA bacterial genes (16S rDNAs) isolated from tonsilloliths of 6 individuals were amplified by PCR and cloned into Escherichia coli. Partial 16S rDNA sequences of approximately 600 bases of cloned inserts were used to determine species identity by comparison with sequences of known species. Characteristics of bacteria on the surface and inside the tonsillolith were analyzed using scanning electron microscopy. Anaerobic bacteria detected in tonsilloliths belonged to the genera Eubacterium, Fusobacterium, Megasphaera, Porphyromonas, Prevotella, Selenomonas and Tannerella, all of which appear to be associated with production of volatile sulfur compounds. Electron microscopy revealed cocci and rods on the surface and rods predominating inside the tonsilloliths. These results support the tonsillolith as an origin of oral malodor.

Adult↗
PubMed2002

Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein.

In prokaryotes, Hfq regulates translation by modulating the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences. To elucidate the mechanisms of target recognition and translation regulation by Hfq, we determined the crystal structures of the Staphylococcus aureus Hfq and an Hfq-RNA complex to 1.55 and 2.71 A resolution, respectively. The structures reveal that Hfq possesses the Sm-fold previously observed only in eukaryotes and archaea. However, unlike these heptameric Sm proteins, Hfq forms a homo-hexameric ring. The Hfq-RNA structure reveals that the single-stranded hepta-oligoribonucleotide binds in a circular conformation around a central basic cleft, whereby Tyr42 residues from adjacent subunits stack with six of the bases, and Gln8, outside the Sm motif, provides key protein-base contacts. Such binding suggests a mechanism for Hfq function.

Amino Acid Motifs↗
PubMedDate not supplied

Rifampin: mechanisms of action and resistance.

Rifampin specifically inhibits bacterial RNA polymerase, the enzyme responsible for DNA transcription, by forming a stable drug-enzyme complex with a binding constant of 10(-9) M at 37 C. The corresponding mammalian enzymes are not affected by rifampin. Bacterial resistance to rifampin is caused by mutations leading to a change in the structure of the beta subunit of RNA polymerase. Such resistance is not an all-or-nothing phenomenon; rather, a large number of RNA polymerases with various degrees of sensitivity to rifampin have been found. No strict correlation exists between enzyme sensitivity and MIC values, since inhibition of RNA synthesis does not always show up to the same extent in the two different test systems used for the determination of these values.

DNA-Directed RNA Polymerases↗
PubMed1994

Expression of human liver fatty acid-binding protein in Escherichia coli and comparative analysis of its binding characteristics with muscle fatty acid-binding protein.

Human liver fatty acid-binding protein (L-FABP) has been efficiently expressed in Escherichia coli. The cDNA encoding human liver FABP was under the control of T7 RNA polymerase promoter in the expression vector pET-3b. Expression required overnight induction with isopropyl beta-D-thiogalactopyranoside in the presence of the bacterial RNA polymerase inhibitor, rifampicin. The protein could be purified by (NH4)2SO4 fractionation, anion-exchange and gel filtration chromatography, and was recognized by anti-(human L-FABP) antiserum. The binding characteristics of delipidated recombinant human L-FABP and muscle FABP (M-FABP) for fatty acids of different chain length and saturation grade, and for various hydrophobic ligands, were determined by radiochemical analysis and also by fluorescence for L-FABP. The apparent binding affinity of the ligands was calculated by using displacement curves of oleic acid and dansylamino-undecanoic acid (DAUDA). L-FABP showed a preference for the binding of long-chain saturated and unsaturated fatty acids up to C24:1, whereas the M-FABP has a preference for unsaturated fatty acids, especially those with 18 C atoms. L-FABP also binds palmitoyl derivatives and many other hydrophobic ligands--however, generally with a lower affinity than fatty acids. M-FABP binds--besides with fatty acids--only with oestradiol and testosterone with high affinity. Fatty acids with fluorescent reporter groups are also more tightly bound by L-FABP. A direct assay and displacement study of oleic acid gave the same Kd value of DAUDA for L-FABP. Fluorescence enhancement and displacement studies indicate that the binding of fluorescent fatty acids is determined by both the fluorescent reporter group and the acyl carbon chain.

Base Sequence↗
PubMed2003

Self-organization: making complex infectious viral particles from purified precursors.

Viruses have served as excellent model systems in which to study biological self-organization. Purified virion structural constituents have been shown to self-assemble into particles that can initiate a productive infection in the host cell resulting in the release of progeny virions. Accumulating information on virus structures and assembly principles has revealed unexpected similarities between viruses that infect hosts as diverse as bacteria and humans, suggesting that these viruses had an early common ancestor. I will describe, in more detail, the assembly pathway of a complex double-stranded RNA bacterial virus. In this system, infectious viral particles are produced starting from purified protein and nucleic acid constituents through an elaborate self-assembly, RNA-packaging and synthesis pathway.

Biological Evolution↗
PubMed2000

Presence of bacterial 16S ribosomal RNA gene segments in human intestinal lymph follicles.

BACKGROUND: There is currently no information regarding microbial agents inside the intestinal lymph follicles. METHODS: Biopsy or resected specimens, mostly from macroscopically normal areas, were sectioned with a cryostat. DNA was extracted from microdissected samples, exclusively from the lymph follicle. Amplification of DNA was performed using universal primers designed from conserved regions of bacterial 16S ribosomal RNA (rRNA). Several clones with inserts of around 400 base pairs were subjected to DNA sequence analysis followed by a database homology search. RESULTS: Bacterial 16S rRNA gene segments were detected in the lymph follicle in 2 of 14 (14%) non-inflammatory bowel disease (IBD) cases, 4 of 14 (28%) Crohn disease cases, and in 2 of 5 (40%) ulcerative colitis cases. Nineteen 16S rRNA gene segments were recognized in the eight positive cases. Five segments showed 100% identity to known bacterial 16S rRNAs, namely staphylococcus species, Streptococcus sanguis, and Paracoccus marcusii. However, the other 14 segments showed below 100% identity, indicating either the presence of unknown bacteria or of bacteria without known DNA data. No single identified or unidentified bacterium, characteristic of IBD, including Mycobacterium paratuberculosis and Listeria monocytogenes, was detected. CONCLUSIONS: The present study confirms the presence of bacterial 16S rRNA gene segments in human intestinal lymph follicles and paves the way for new investigations into the microbiology of the lymph follicle. Whether or not bacteria inside the lymph follicle is a primary stimulus in IBD has yet to be clarified.

Adolescent↗
PubMed2004

Bacterial DNA and RNA induce rat cardiac myocyte contraction depression in vitro.

Sepsis and septic shock, the systemic immunologic and pathophysiologic response to overwhelming infection, are associated with perturbation of a variety of metabolic cell pathways and with multiple organ failure (MOF) including cardiac depression. This depression has been attributed to the effect of several circulating and locally produced proinflammatory mediators. Recent data suggest that bacterial nucleic acids can produce profound systemic inflammatory responses characterized by circulatory shock in intact animals. In this study, bacterial DNA and RNA derived from pathogenic clinical S. aureus and E. coli isolates are shown to induce early concentration-dependent depression of maximum extent and peak velocity of contraction of electrically paced neonatal rat ventricular myocytes in culture. Significant but more modest depression was generated by a nonpathogenic E. coli isolate. Pretreatment with a DNase or RNase abrogated this effect. Further, synthetic, double-stranded RNA (dsRNA) also induced concentration-dependent depression of myocyte contraction, with the effect also being prevented by pretreatment with RNase. These data suggest that bacterial DNA and RNA may contribute to myocardial depression during bacterial sepsis and septic shock.

Animals↗