5-thyminyl-5,6-dihydrothymine (also called spore photoproduct or SP) is the exclusive DNA photo-damage product in bacterial endospores. It is repaired by a radical SAM (S-adenosylmethionine) enzyme, the spore photoproduct lyase (SPL), at the bacterial early germination phase. Our previous studies proved that SPL utilizes the 5′-dA• generated by SAM cleavage reaction to abstract the H6proR atom to initiate the SP repair process. The resulting thymine allylic radical was suggested to take an H atom from an unknown protein source, most likely the cysteine 141. Here we show that C141 can be readily alkylated in the native SPL by iodoacetamide treatment, suggesting that it is accessible to the TpT radical. SP repair by the SPL C141A mutant yields TpTSO2− and TpT simultaneously from the very beginning of the reaction; no lag phase is observed for the TpTSO2− formation. Should any other protein residue serve as the H donor, its presence would result in TpT as the major product at least for the first enzyme turnover. These observations provide strong evidence to support C141 as the direct H atom donor. Moreover, due to the lack of this intrinsic H donor, the C141A mutant produces TpT via an unprecedented thymine cation radical reduction (proton coupled electron transfer) process, contrasting to the H atom transfer mechanism in the WT SPL reaction. The C141A mutant repairs SP at a rate which is ~3-fold slower than the WT enzyme. Formation of TpTSO2− and TpT exhibit a Vmax deuterium kinetic isotope effect (KIE) of 1.7 ± 0.2 respectively, which is smaller than the DVmax KIE of 2.8 ± 0.3 determined in the WT SPL reaction. These findings suggest that removing the intrinsic H atom donor disturbs the rate-limiting process in the enzyme catalysis. As expected, the pre-reduced C141A mutant only supports ~ 0.4 turnover, which is in sharp contrast to the > 5 turnovers exhibited by the WT SPL reaction, suggesting that the enzyme catalytic cycle (SAM regeneration) is disrupted by this single mutation.

Carbon dioxide measurements made by the Sounding of the Atmosphere using Broadband Emission Radiometry (SABER) instrument between 2002 and 2014 were analyzed to reveal the rate of increase of CO2 in the mesosphere and lower thermosphere. The CO2 data show a trend of ~5% per decade at ~80 km and below, in good agreement with the tropospheric trend observed at Mauna Loa. Above 80 km, the SABER CO2 trend is larger than in the lower atmosphere, reaching ~12% per decade at 110 km. The large relative trend in the upper atmosphere is consistent with results from the Atmospheric Chemistry Experiment Fourier Transform Spectrometer (ACE‐FTS). On the other hand, the CO2 trend deduced from the Whole Atmosphere Community Climate Model remains close to 5% everywhere. The spatial coverage of the SABER instrument allows us to analyze the CO2 trend as a function of latitude for the first time. The trend is larger in the Northern Hemisphere than in the Southern Hemisphere mesopause above 80 km. The agreement between SABER and ACE‐FTS suggests that the rate of increase of CO2 in the upper atmosphere over the past 13 years is considerably larger than can be explained by chemistry‐climate models.

The Sounding of the Atmosphere using Broadband Emission Radiometry (SABER) instrument on board the Thermosphere Ionosphere Mesosphere Energetics and Dynamics satellite has been measuring the limb radiance in 10 broadband infrared channels over the altitude range from ~ 400 km to the Earth's surface since 2002. The kinetic temperatures and CO2 volume mixing ratios (VMRs) in the mesosphere and lower thermosphere have been simultaneously retrieved using SABER limb radiances at 15 and 4.3 µm under nonlocal thermodynamic equilibrium (non‐LTE) conditions. This paper presents results of a validation study of the SABER CO2 VMRs obtained with a two‐channel, self‐consistent temperature/CO2 retrieval algorithm. Results are based on comparisons with coincident CO2 measurements made by the Atmospheric Chemistry Experiment Fourier transform spectrometer (ACE‐FTS) and simulations using the Specified Dynamics version of the Whole Atmosphere Community Climate Model (SD‐WACCM). The SABER CO2 VMRs are in agreement with ACE‐FTS observations within reported systematic uncertainties from 65 to 110 km. The annual average SABER CO2 VMR falls off from a well‐mixed value above ~80 km. Latitudinal and seasonal variations of CO2 VMRs are substantial. SABER observations and the SD‐WACCM simulations are in overall agreement for CO2 seasonal variations, as well as global distributions in the mesosphere and lower thermosphere. Not surprisingly, the CO2 seasonal variation is shown to be driven by the general circulation, converging in the summer polar mesopause region and diverging in the winter polar mesopause region.

The Global UltraViolet Imager (GUVI) onboard the Thermosphere Ionosphere Mesosphere Energetics and Dynamics (TIMED) satellite provides a data set of vertical thermospheric composition (O, N 2 , and O 2 densities) and temperature profiles from 2002-2007. Even though GUVI sampling is limited by orbital constraint, we demonstrated that the GUVI data set can be used to derive the altitude profiles of the amplitudes and phases of annual oscillation (AO) and semiannual oscillation (SAO), thereby providing important constraints on models seeking to explain these features. We performed a seasonal and interannual analysis of GUVI limb O, O 2 , and N 2 densities and volume number density ratio O/N 2 at constant pressure levels. These daytime observations of O and O/N 2 in the lower thermosphere show a strong AO at midlatitudes and a clear SAO at lower latitudes. The global mean GUVI O/N 2 number density ratio shows the AO, with slightly larger values in January than in July and a SAO with O/N 2 greater during equinoxes than at the solstices. O and N 2 densities on fixed pressure levels in the upper thermosphere are anticorrelated with solar extreme ultraviolet flux. On the other hand, O/N 2 is smaller during solar minimum and larger during solar maximum. The thermospheric AO and SAO in composition have a constant phase with altitude throughout the thermosphere.

Described here are mechanistic details of the chemical reactivities of two modified/saturated pyrimidine residues that represent naturally occurring forms of DNA damage: 5-thyminyl-5,6-dihydrothymine, commonly referred to as the “spore photoproduct” (SP), and 5,6-dihydro-2′-deoxyuridine (dHdU), formed via ionizing radiation damage to cytosine under anoxic conditions and also serving as a general model of saturated pyrimidine residues. It is shown that due to the loss of the pyrimidine C5–C6 double bond and consequent loss of ring aromaticity, the C4 position of both these saturated pyrimidines is prone to the formation of a hemiaminal intermediate via water addition. Water addition is facilitated by basic conditions; however, it also occurs at physiological pH at a slower rate. The hemiaminal species so-formed subsequently converts to a ring-opened hydrolysis product through cleavage of the pyrimidine N3–C4 bond. Further decomposition of this ring-opened product above physiological pH leads to DNA strand break formation. Taken together, these results suggest that once the aromaticity of a pyrimidine residue is lost, the C4 position becomes a “hot spot” for the formation of a tetrahedral intermediate, the decay of which triggers a cascade of elimination reactions that can under certain conditions convert a simple nucleobase modification into a DNA strand break.