SUMMARY PAS domains are newly recognized signaling domains that are widely distributed in proteins from members of the Archaea and Bacteria and from fungi, plants, insects, and vertebrates. They function as input modules in proteins that sense oxygen, redox potential, light, and some other stimuli. Specificity in sensing arises, in part, from different cofactors that may be associated with the PAS fold. Transduction of redox signals may be a common mechanistic theme in many different PAS domains. PAS proteins are always located intracellularly but may monitor the external as well as the internal environment. One way in which prokaryotic PAS proteins sense the environment is by detecting changes in the electron transport system. This serves as an early warning system for any reduction in cellular energy levels. Human PAS proteins include hypoxia-inducible factors and voltage-sensitive ion channels; other PAS proteins are integral components of circadian clocks. Although PAS domains were only recently identified, the signaling functions with which they are associated have long been recognized as fundamental properties of living cells.

Magnetotactic cocci swim persistently along local magnetic field lines in a preferred direction that corresponds to downward migration along geomagnetic field lines. Recently, high cell concentrations of magnetotactic cocci have been found in the water columns of chemically stratified, marine and brackish habitats, and not always in the sediments, as would be expected for persistent, downward-migrating bacteria. Here we report that cells of a pure culture of a marine magnetotactic coccus, designated strain MC-1, formed microaerophilic bands in capillary tubes and used aerotaxis to migrate to a preferred oxygen concentration in an oxygen gradient. Cells were able to swim in either direction along the local magnetic field and used magnetotaxis in conjunction with aerotaxis, i.e., magnetically assisted aerotaxis, or magneto-aerotaxis, to more efficiently migrate to and maintain position at their preferred oxygen concentration. Cells of strain MC-1 had a novel, aerotactic sensory mechanism that appeared to function as a two-way switch, rather than the temporal sensory mechanism used by other bacteria, including Magnetospirillum megnetotacticum, in aerotaxis. The cells also exhibited a response to short-wavelength light (< or = 500 nm), which caused them to swim persistently parallel to the magnetic field during illumination.

We identified a protein, Aer, as a signal transducer that senses intracellular energy levels rather than the external environment and that transduces signals for aerotaxis (taxis to oxygen) and other energy-dependent behavioral responses in Escherichia coli. Domains in Aer are similar to the signaling domain in chemotaxis receptors and the putative oxygen-sensing domain of some transcriptional activators. A putative FAD-binding site in the N-terminal domain of Aer shares a consensus sequence with the NifL, Bat, and Wc-1 signal-transducing proteins that regulate gene expression in response to redox changes, oxygen, and blue light, respectively. A double mutant deficient in aer and tsr, which codes for the serine chemoreceptor, was negative for aerotaxis, redox taxis, and glycerol taxis, each of which requires the proton motive force and͞or electron transport system for signaling. We propose that Aer and Tsr sense the proton motive force or cellular redox state and thereby integrate diverse signals that guide E. coli to environments where maximal energy is available for growth.

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▪ Abstract  Energy taxis is widespread in motile bacteria and in some species is the only known behavioral response. The bacteria monitor their cellular energy levels and respond to a decrease in energy by swimming to a microenvironment that reenergizes the cells. This is in contrast to classical Escherichia coli chemotaxis in which sensing of stimuli is independent of cellular metabolism. Energy taxis encompasses aerotaxis (taxis to oxygen), phototaxis, redox taxis, taxis to alternative electron acceptors, and chemotaxis to a carbon source. All of these responses share a common signal transduction pathway. An environmental stimulus, such as oxygen concentration or light intensity, modulates the flow of reducing equivalents through the electron transport system. A transducer senses the change in electron transport, or possibly a related parameter such as proton motive force, and initiates a signal that alters the direction of swimming. The Aer and Tsr proteins in E. coli are newly recognized transducers for energy taxis. Aer is homologous to E. coli chemoreceptors but unique in having a PAS domain and a flavin-adenine dinucleotide cofactor that is postulated to interact with a component of the electron transport system. PAS domains are energy-sensing modules that are found in proteins from archaea to humans. Tsr, the serine chemoreceptor, is an independent transducer for energy taxis, but its sensory mechanism is unknown. Energy taxis has a significant ecological role in vertical stratification of microorganisms in microbial mats and water columns. It plays a central role in the behavior of magnetotactic bacteria and also appears to be important in plant-microbe interactions.

Abstract.We review the history of the South American summer monsoon (SASM) over the past ∼ 2000 yr based on high-resolution stable isotope proxies from speleothems, ice cores and lake sediments. Our review is complemented by an analysis of an isotope-enabled atmospheric general circulation model (GCM) for the past 130 yr. Proxy records from the monsoon belt in the tropical Andes and SE Brazil show a very coherent behavior over the past 2 millennia with significant decadal to multidecadal variability superimposed on large excursions during three key periods: the Medieval Climate Anomaly (MCA), the Little Ice Age (LIA) and the current warm period (CWP). We interpret these three periods as times when the SASM's mean state was significantly weakened (MCA and CWP) and strengthened (LIA), respectively. During the LIA each of the proxy archives considered contains the most negative δ 18 O values recorded during the entire record length. On the other hand, the monsoon strength is currently rather weak in a 2000-yr historical perspective, rivaled only by the low intensity during the MCA. Our climatic interpretation of these archives is consistent with our isotope-based GCM analysis, which suggests that these sites are sensitive recorders of large-scale monsoon variations.We hypothesize that these centennial-scale climate anomalies were at least partially driven by temperature changes in the Northern Hemisphere and in particular over the North Atlantic, leading to a latitudinal displacement of the ITCZ and a change in monsoon intensity (amount of rainfall upstream over the Amazon Basin). This interpretation is supported by several independent records from different proxy archives and modeling studies. Although ENSO is the main forcing for δ 18 O variability over tropical South America on interannual time scales, our results suggest that its influence may be significantly modulated by North Atlantic climate variability on longer time scales.Finally, our analyses indicate that isotopic proxies, because of their ability to integrate climatic information on large spatial scales, could complement more traditional proxies such as tree rings or documentary evidence. Future climate reconstruction efforts could potentially benefit from including isotopic proxies as large-scale predictors in order to better constrain past changes in the atmospheric circulation.

We review the history of the South American summer monsoon (SASM) over the past ~2000 yr based on high-resolution stable isotope proxies from speleothems, ice cores and lake sediments. Our review is complemented by an analysis of an isotope-enabled atmospheric General Circulation Model (GCM) for the past 130 yr. Proxy records from the monsoon belt in the tropical Andes and SE Brazil show a very coherent behavior over the past 2 millennia with significant decadal to multidecadal variability superimposed on large excursions during three key periods, the Medieval Climate Anomaly (MCA), the Little Ice Age (LIA) and the Current Warm Period (CWP). We interpret these three periods as times when the SASM's mean state was significantly weakened (MCA and CWP) and strengthened (LIA), respectively. During the LIA each of the proxy archives considered contains the most negative &delta;¹⁸O values recorded during the entire record length. On the other hand the monsoon strength is currently rather weak in a 2000-yr historical perspective, rivaled only by the low intensity during the MCA. Our climatic interpretation of these archives is consistent with our isotope-based GCM analysis, which suggests that these sites are sensitive recorders of large-scale monsoon variations. <br><br> We hypothesize that these centennial-scale climate anomalies were at least partially driven by temperature changes in the Northern Hemisphere and in particular over the North Atlantic, leading to a latitudinal displacement of the ITCZ and a change in monsoon intensity over the tropical continent. This interpretation is supported by several independent proxy archives and modeling studies. Although ENSO is the main forcing for &delta;¹⁸O variability over tropical South America on interannual time scales, our results suggest that its influence may be significantly modulated by North Atlantic climate variability on longer time scales. <br><br> Finally our analyses indicate that isotopic proxies, because of their ability to integrate climatic information on large spatial scales, could complement more traditional proxies such as tree rings or historical archives. Future climate reconstruction efforts could potentially benefit from including isotopic proxies as large-scale predictors in order to better constrain past changes in the atmospheric circulation

PAS domains sense oxygen, redox potential and light, and are implicated in behaviour, circadian rhythmicity, development and metabolic regulation. Although PAS domains are widespread in archaea, bacteria and eukaryota, the mechanism of signal transduction has been elucidated only for the bacterial photo sensor PYP and oxygen sensor FixL. We investigated the signalling mechanism in the PAS domain of Aer, the redox potential sensor and aerotaxis transducer in Escherichia coli. Forty‐two residues in Aer were substituted using cysteine‐replacement mutagenesis. Eight mutations resulted in a null phenotype for aerotaxis, the behavioural response to oxygen. Four of them also led to the loss of the non‐covalently bound FAD cofactor. Three mutant Aer proteins, N34C, F66C and N85C, transmitted a constant signal‐on bias. One mutation, Y111C, inverted signalling by the transducer so that positive stimuli produced negative signals and vice versa. Residues critical for signalling were mapped onto a three‐dimensional model of the Aer PAS domain, and an FAD‐binding site and ‘active site’ for signal transduction are proposed.