The microaerophilic nitrogen-fixing bacterium Azospirillum brasilense formed a sharply defined band in a spatial gradient of oxygen. As a result of aerotaxis, the bacteria were attracted to a specific low concentration of oxygen (3 to 5 M). Bacteria swimming away from the aerotactic band were repelled by the higher or lower concentration of oxygen that they encountered and returned to the band. This behavior was confirmed by using temporal gradients of oxygen. The cellular energy level in A. brasilense, monitored by measuring the proton motive force, was maximal at 3 to 5 M oxygen. The proton motive force was lower at oxygen concentrations that were higher or lower than the preferred oxygen concentration. Bacteria swimming toward the aerotactic band would experience an increase in the proton motive force, and bacteria swimming away from the band would experience a decrease in the proton motive force. It is proposed that the change in the proton motive force is the signal that regulates positive and negative aerotaxis. The preferred oxygen concentration for aerotaxis was similar to the preferred oxygen concentration for nitrogen fixation. Aerotaxis is an important adaptive behavioral response that can guide these free-living diazotrophs to the optimal niche for nitrogen fixation in the rhizosphere.Aerotaxis (chemotaxis to oxygen) enables bacteria to find concentrations of dissolved oxygen that are favorable for their metabolic lifestyle (reviewed in references 39 and 40). Aerotaxis was the first behavioral response reported for microorganisms: in 1881, Engelmann described accumulation of Bacterium termo around plant cells that were producing oxygen (10). Among the bacteria described by Engelmann, the most sensitive to oxygen was Spirillum tenue, which accumulated at a low oxygen concentration (11). In 1893, Beijerinck described the formation of bacterial "Atmungsfiguren" around the source of oxygen. The bacteria, most likely spirilla, formed a band at some distance from the oxygen source; the band descended if air was replaced by oxygen or ascended if air was replaced by hydrogen (4). In 1901, Jennings and Crosby investigated the aggregation of Spirillum species in the region of illuminated algae that were evolving oxygen. The bacteria that were distant from the algae swam randomly. However, the cells became trapped if they entered a zone around the algae that had an optimal concentration of oxygen. Whenever the bacteria reached the edge of the zone, the direction of their movement was reversed (20). This aerotactic response, originally termed phobo-chemotaxis (33), resulted in the accumulation of bacteria in the zone of optimal oxygen concentration.Formation of aerotactic bands is a characteristic of motile bacterial species. Aerotaxis in the aerobe Bacillus subtilis (41), in the facultative anaerobes Escherichia coli, Salmonella typhimurium (1, 34, 36), and Halobacterium salinarium (7,29), and in the anaerobe Desulfovibrio vulgaris (22) has been extensively investigated. At least one motile bacterial species, R...

Escherichia coli bacteria sensed the redox state in their surroundings and they swam to a niche that had a preferred reduction potential. In a spatial redox gradient of benzoquinone/benzoquinol, E. coli cells migrated to form a sharply defined band. Bacteria swimming out of either face of the band tumbled and returned to the preferred conditions at the site of the band. This behavioral response was named redox taxis. Redox molecules, such as substituted quinones, that elicited redox taxis, interact with the bacterial electron transport system, thereby altering electron transport and the proton motive force. The magnitude of the behavioral response was dependent on the reduction potential ofthe chemoeffector. The Tsr, Tar, Trg, Tap, and CheR proteins, which have a role in chemotaxis, were not essential for redox taxis. A cheB mutant had inverted responses in redox taxis, as previously demonstrated in aerotaxis. A model is proposed in which a redox effector molecule perturbs the electron transport system, and an unknown sensor in the membrane detects changes in the proton motive force or the redox status of the electron transport system, and transduces this information into a signal that regulates phosphorylation of the CheA protein. A similar mechanism has been proposed for aerotaxis. Redox taxis may play an important role in the distribution of bacterial species in natural environments.

Nucleotide excision repair (NER) of UV-induced cyclobutane pyrimidine dimers (CPDs) was measured in the individual strands of transcriptionally active and inactive ribosomal genes of yeast. Ribosomal genes (rDNA) are present in multiple copies, but only a fraction of them is actively transcribed. Restriction enzyme digestion was used to specifically release the transcriptionally active fraction from yeast nuclei, and selective psoralen crosslinking was used to distinguish between active and inactive rDNA chromatin. Removal of CPDs was followed in both rDNA populations, and the data clearly show that strand-specific repair occurs in transcriptionally active rDNA while being absent in the inactive rDNA fraction. Thus, transcription-coupled repair occurs in RNA polymerase I-transcribed genes in yeast. Moreover, the nontranscribed strand of active rDNA is repaired faster than either strand of inactive rDNA, implying that NER has preferred access to the active, non-nucleosomal rDNA chromatin. Finally, restriction enzyme accessibility to active rDNA varies during NER, suggesting that there is a change in ribosomal gene chromatin structure during or soon after CPD removal. N ucleotide excision repair (NER) removes different types of lesions from DNA, including bulky adducts caused by chemicals, interstrand or intrastrand crosslinks, and the UV photoproducts cis-syn cyclobutane pyrimidine dimer (CPD) and pyrimidine (6-4) pyrimidone (1). If DNA lesions are not removed, mutations can occur after translesion replication (2). It is now well established that many transcriptionally active genes are repaired faster than inactive DNA (3, 4). Furthermore, preferential removal of CPDs from active genes is caused mainly by an increased rate of repair of the transcribed strand (TS). This transcription-coupled repair (TCR) was first discovered in mammalian cells (5), then in Escherichia coli (6) and yeast (7). Elongation by RNA polymerase II (pol II) is required for TCR (8, 9), and it is thought that only pol II-transcribed genes are subject to TCR (10).RNA polymerase I (pol I) transcribes ribosomal genes (rDNA) at a very high rate. The rDNA is localized in the nucleolus, which is a dense chromatin region composed of rDNA, pol I, rRNA, assembling ribosomes, and proteins involved in cell-cycle regulation (11,12). It is known that mammalian cells repair rDNA damaged by UV radiation (13) and chemicals (14-16). However, in rodent and human cells, CPDs are less efficiently repaired in rDNA than in either total genomic DNA or pol II-transcribed genes (16)(17)(18)(19)(20). Moreover, DNA repair does not exhibit strand bias in the rDNA of these cells (17,19). To the contrary, CPDs are rapidly removed from both strands of total rDNA in yeast (21,22). In addition, a strand bias during repair of total rDNA was observed in rad7 and rad16 mutants, even though strand-specific repair was not observed in total rDNA of wild-type cells (21).Ribosomal genes are present in multiple copies organized in long tandem repeats (11), and in most cells only a f...

The cis-syn cyclobutane pyrimidine dimer (CPD) is the major photoproduct induced in DNA by low wavelength ultraviolet radiation. An improved method was developed to detect CPD formation and removal in genomic DNA that avoids the problems encountered with the standard method of endonuclease detection of these photoproducts. Since CPD-specific endonucleases make single-strand cuts at CPD sites, quantification of the frequency of CPDs in DNA is usually done by denaturing gel electrophoresis. The standard method of ethidium bromide staining and gel photography requires more than 10 microg of DNA per gel lane, and correction of the photographic signal for the nonlinear film response. To simplify this procedure, a standard Southern blot protocol, coupled with phosphorimage analysis, was developed. This method uses random hybridization probes to detect genomic sequences with minimal sequence bias. Because of the vast linearity range of phosphorimage detection, scans of the signal profiles for the heterogeneous population of DNA fragments can be integrated directly to determine the number-average size of the population.

Chromatin rearrangements occur during repair of cyclobutane pyrimidine dimers (CPDs) by nucleotide excision repair (NER). Thereafter, the original structure must be restored to retain normal genomic functions. How NER proceeds through nonnucleosomal chromatin and how open chromatin is reestablished after repair are unknown. We analyzed NER in ribosomal genes (rDNA), which are present in multiple copies but only a fraction are actively transcribed and nonnucleosomal. We show that removal of CPDs is fast in the active rDNA and that chromatin reorganization occurs during NER. Furthermore, chromatin assembles on nonnucleosomal rDNA during the early events of NER but in the absence of DNA repair. The resumption of transcription after removal of CPDs correlates with the reappearance of nonnucleosomal chromatin. To date, only the passage of replication machinery was thought to package ribosomal genes in nucleosomes. In this report, we show that early events after formation of UV photoproducts in DNA also promote chromatin assembly.Nucleotide excision repair (NER) removes several types of lesions from DNA, including bulky adducts caused by chemicals, inter-or intrastrand cross-links, and the UV photoproducts cis-syn cyclobutane pyrimidine dimer (CPD) and pyrimidine (6-4) pyrimidone (15). In general, transcriptionally active genes are repaired faster than inactive DNA due to preferential removal of DNA lesions from the transcribed strands (TS) (37,58,62). This transcription-coupled repair process (or TCR) has been thought to require elongating RNA polymerase II (5, 27). However, recently TCR was found in the active fraction of ribosomal genes (rDNA) in yeast wild-type (wt) cells (7,35), which are transcribed at a very high rate by RNA polymerase I. Furthermore, strand-specific repair was observed in total rDNA of rad7⌬, rad16⌬, and rad4⌬ Saccharomyces cerevisiae strains (61).The yeast RAD26 gene is the counterpart to the human Cockayne syndrome B (CSB) gene, and its inactivation creates a defect in the TCR of UV lesions (60). Since UV photoproducts present on the TS of active genes block RNA polymerases and arrest transcription (21), it was proposed that the Rad26/ CSB proteins may act in the displacement of RNA polymerase II arrested at damaged sites and, subsequently, help in the recruitment of NER proteins to the lesion sites (62). Also, there are indications that Rad26 plays a role in RNA polymerase II-dependent transcription elongation in the absence of DNA damage (28). Thus, the Rad26/CSB proteins may promote RNA polymerase II transcription through damaged DNA bases (29).Ribosomal genes are localized in the nucleolus, a dense chromatin region composed of rDNA, RNA polymerase I, rRNA, and assembling ribosomes, among other proteins (reviewed in reference 39). The ribosomal genes are present in multiple copies (ϳ150 in yeast) that are organized in long tandem repeats (55). In most organisms only a portion of rDNA is transcriptionally active (reviewed in references 20 and 32), and the fraction of active rDNA varies mar...