[1] This paper introduced the calibration of the CE-318 sunphotometer of the China Aerosol Remote Sensing Network (CARSNET) and the validation of aerosol optical depth (AOD) by AOD module of ASTPWin software compared with the simultaneous measurements of the Aerosol Robotic Network (AERONET)/Photométrie pour le Traitement Opérationnel de Normalization Satellitaire (PHOTONS) and PREDE skyradiometer. The results show that the CARSNET AOD measurements have the same accuracy as the AERONET/PHOTONS. On the basis of a comparison between CARSNET and AERONET, the AODs from CARSNET at 1020, 870, 670, and 440 nm are about 0.03, 0.01, 0.01, and 0.01 larger than those from AERONET, respectively. The aerosol optical properties over Beijing acquired through the CE-318 sunphotometers of one AERONET/PHOTONS site and two CARSNET sites were analyzed on the basis of 4-year measurements. It was obvious that the AOD of the Shangdianzi site (rural site) was lower than that of the two urban sites (the Institute of Atmospheric Physics (IAP) site (north urban site) and the Beijing Meteorological Observatory (BJO) site (south urban site)). The AOD of BJO was about 0.05, 0.04, 0.05, and 0.06 larger than that of IAP at 1020, 870, 670, and 440 nm, respectively, indicating that there is more local pollution in the south part of Beijing. The highest AOD was found in summer because of the stagnation planetary boundary layer and transport of pollutants from large pollution centers south of Beijing. The high temperature and relative humidity in summer also favor the production of aerosol precursor and the hygroscopic growth of the existing particles locally, which results in high AOD. In contrast, the lowest AOD at the two urban sites and one rural site in Beijing occurred in winter as the frequent cold air masses help pollutants diffuse easily.

The human microbiome encodes vast numbers of uncharacterized enzymes, limiting our functional understanding of this community and its effects on host health and disease. By incorporating information about enzymatic chemistry into quantitative metagenomics, we determined the abundance and distribution of individual members of the glycyl radical enzyme superfamily among the microbiomes of healthy humans. We identified many uncharacterized family members, including a universally distributed enzyme that enables commensal gut microbes and human pathogens to dehydrate trans-4-hydroxy-L-proline, the product of the most abundant human posttranslational modification. This ‘chemically-guided functional profiling’ workflow can therefore use ecological context to facilitate the discovery of enzymes in microbial communities.

A ribonucleotide reductase (RNR) from Flavobacterium johnsoniae ( Fj) differs fundamentally from known (subclass a-c) class I RNRs, warranting its assignment to a new subclass, Id. Its β subunit shares with Ib counterparts the requirements for manganese(II) and superoxide (O) for activation, but it does not require the O-supplying flavoprotein (NrdI) needed in Ib systems, instead scavenging the oxidant from solution. Although Fj β has tyrosine at the appropriate sequence position (Tyr 104), this residue is not oxidized to a radical upon activation, as occurs in the Ia/b proteins. Rather, Fj β directly deploys an oxidized dimanganese cofactor for radical initiation. In treatment with one-electron reductants, the cofactor can undergo cooperative three-electron reduction to the II/II state, in contrast to the quantitative univalent reduction to inactive "met" (III/III) forms seen with I(a-c) βs. This tendency makes Fj β unusually robust, as the II/II form can readily be reactivated. The structure of the protein rationalizes its distinctive traits. A distortion in a core helix of the ferritin-like architecture renders the active site unusually open, introduces a cavity near the cofactor, and positions a subclass-d-specific Lys residue to shepherd O to the Mn cluster. Relative to the positions of the radical tyrosines in the Ia/b proteins, the unreactive Tyr 104 of Fj β is held away from the cofactor by a hydrogen bond with a subclass-d-specific Thr residue. Structural comparisons, considered with its uniquely simple mode of activation, suggest that the Id protein might most closely resemble the primordial RNR-β.

Escherichia coli class Ia ribonucleotide reductase is composed of two subunits (α and β), which form an α2β2 complex that catalyzes the conversion of nucleoside 5′-diphosphates to deoxynucleotides (dNDPs). β2 contains the essential tyrosyl radical (Y122•) that generates a thiyl radical (C439•) in α2 where dNDPs are made. This oxidation occurs over 35 Å through a pathway of amino acid radical intermediates (Y122 → [W48] → Y356 in β2 to Y731 → Y730 → C439 in α2). However, chemistry is preceded by a slow protein conformational change(s) that prevents observation of these intermediates. 2,3,5-Trifluorotyrosine site-specifically inserted at position 122 of β2 (F3Y•-β2) perturbs its conformation and the driving force for radical propagation, while maintaining catalytic activity (1.7 s–1). Rapid freeze–quench electron paramagnetic resonance spectroscopy and rapid chemical-quench analysis of the F3Y•-β2, α2, CDP, and ATP (effector) reaction show generation of 0.5 equiv of Y356• and 0.5 equiv of dCDP, both at 30 s–1. In the absence of an external reducing system, Y356• reduction occurs concomitant with F3Y reoxidation (0.4 s–1) and subsequent to oxidation of all α2s. In the presence of a reducing system, a burst of dCDP (0.4 equiv at 22 s–1) is observed prior to steady-state turnover (1.7 s–1). The [Y356•] does not change, consistent with rate-limiting F3Y reoxidation. The data support a mechanism where Y122• is reduced and reoxidized on each turnover and demonstrate for the first time the ability of a pathway radical in an active α2β2 complex to complete the catalytic cycle.