Spore photoproduct lyase: the known, the controversial, and the unknown

Spore photoproduct lyase (SPL) repairs 5-thyminyl-5,6-dihydrothymine, a thymine dimer that is also called the spore photoproduct (SP), in germinating endospores. SPL is a radical S-adenosylmethionine (SAM) enzyme, utilizing the 5′-deoxyadenosyl radical generated by SAM reductive cleavage reaction to revert SP to two thymine residues. Here we review the current progress in SPL mechanistic studies. Protein radicals are known to be involved in SPL catalysis; however, how these radicals are quenched to close the catalytic cycle is under debate

Insights into the Activity Change of Spore Photoproduct Lyase Induced by Mutations at a Peripheral Glycine Residue

UV radiation triggers the formation of 5-thyminyl-5,6-dihydrothymine, i.e., the spore photoproduct (SP), in the genomic DNA of bacterial endospores. These SPs, if not repaired in time, may lead to genome instability and cell death. SP is mainly repaired by spore photoproduct lyase (SPL) during spore outgrowth via an unprecedented protein-harbored radical transfer pathway that is composed of at least a cysteine and two tyrosine residues. This mechanism is consistent with the recently solved SPL structure that shows all three residues are located in proximity and thus able to participate in the radical transfer process during the enzyme catalysis. In contrast, an earlier in vivo mutational study identified a glycine to arginine mutation at the position 168 on the B. subtilis SPL that is >15 Å away from the enzyme active site. This mutation appears to abolish the enzyme activity because endospores carrying this mutant were sensitive to UV light. To understand the molecular basis for this rendered enzyme activity, we constructed two SPL mutations G168A and G168R, examined their repair of dinucleotide SP TpT, and found that both mutants exhibit reduced enzyme activity. Comparing with the wildtype (WT) SPL enzyme, the G168A mutant slows down the SP TpT repair by 3~4-fold while the G168R mutant by ~ 80-fold. Both mutants exhibit a smaller apparent (DV) kinetic isotope effect (KIE) but a bigger competitive (DV/K) KIE than that by the WT SPL. Moreover, the G168R mutant also produces a large portion of the abortive repair product TpT-[Formula: see text]; the formation of which indicates that cysteine 141 is no longer well positioned as the H-donor to the thymine allylic radical intermediate. All these data imply that the mutation at the remote glycine 168 residue alters the enzyme 3D structure, subsequently reducing the SPL activity by changing the positions of the essential amino acids involved in the radical transfer process

Optimal ALOHA-like random access with heterogeneous QoS guarantees for multi-packet reception aided visible light communications

There is a paucity of random access protocols designed for alleviating collisions in visible light communication (VLC) systems where carrier sensing is hard to be achieved due to the directionality of light. To resolve the problem of collisions, we adopt the successive interference cancellation (SIC) algorithm to enable the coordinator to simultaneously communicate with multiple devices, which is referred to as the multi-packet reception (MPR) capability. However, the MPR capability could be fully utilized only when random access algorithms are accordingly designed. Considering the characteristics of the random access VLC system with SIC, we propose a novel effective capacity (EC)-based ALOHA-like random access algorithm for MPR-aided uplink VLC systems having heterogeneous quality-of-service (QoS) guarantees. Firstly, we model the VLC network as a conflict graph and derive the EC for each device. Then, we formulate the VLC QoS-driven random access problem as a saturation throughput maximization problem subject to multiple statistical QoS constraints. Finally, the resultant non-concave optimization problem (OP) is solved by a memetic search algorithm relying on invasive weed optimization and differential evolution (IWO-DE). We demonstrate that our derived EC expression matches the Monte Carlo simulation results accurately, and the performance of our proposed algorithm is competitive

Three-dimensional structure of the milky way dust: modeling of LAMOST data

We present a three-dimensional modeling of the Milky Way dust distribution by fitting the value-added star catalog of LAMOST spectral survey. The global dust distribution can be described by an exponential disk with scale-length of 3,192 pc and scale height of 103 pc. In this modeling, the Sun is located above the dust disk with a vertical distance of 23 pc. Besides the global smooth structure, two substructures around the solar position are also identified. The one located at $150^{\circ}<l<200^{\circ}$ and $-5^{\circ}<b<-30^{\circ}$ is consistent with the Gould Belt model of \citet{Gontcharov2009}, and the other one located at $140^{\circ}<l<165^{\circ}$ and $0^{\circ}<b<15^{\circ}$ is associated with the Camelopardalis molecular clouds.Comment: 15 pages, 6 figure, accepted by Ap

CrossFusion: Interleaving Cross-modal Complementation for Noise-resistant 3D Object Detection

The combination of LiDAR and camera modalities is proven to be necessary and typical for 3D object detection according to recent studies. Existing fusion strategies tend to overly rely on the LiDAR modal in essence, which exploits the abundant semantics from the camera sensor insufficiently. However, existing methods cannot rely on information from other modalities because the corruption of LiDAR features results in a large domain gap. Following this, we propose CrossFusion, a more robust and noise-resistant scheme that makes full use of the camera and LiDAR features with the designed cross-modal complementation strategy. Extensive experiments we conducted show that our method not only outperforms the state-of-the-art methods under the setting without introducing an extra depth estimation network but also demonstrates our model's noise resistance without re-training for the specific malfunction scenarios by increasing 5.2\% mAP and 2.4\% NDS

Spore photoproduct within DNA is a surprisingly poor substrate for its designated repair enzyme—The spore photoproduct lyase

DNA repair enzymes typically recognize their substrate lesions with high affinity to ensure efficient lesion repair. In UV irradiated endospores, a special thymine dimer, 5-thyminyl-5,6-dihydrothymine, termed the spore photoproduct (SP), is the dominant DNA photolesion, which is rapidly repaired during spore outgrowth mainly by spore photoproduct lyase (SPL) using an unprecedented protein-harbored radical transfer process. Surprisingly, our in vitro studies using SP-containing short oligonucleotides, pUC 18 plasmid DNA, and E. coli genomic DNA found that they are all poor substrates for SPL in general, exhibiting turnover numbers of 0.01–0.2 min−1. The faster turnover numbers are reached under single turnover conditions, and SPL activity is low with oligonucleotide substrates at higher concentrations. Moreover, SP-containing oligonucleotides do not go past one turnover. In contrast, the dinucleotide SP TpT exhibits a turnover number of 0.3–0.4 min−1, and the reaction may reach up to 10 turnovers. These observations distinguish SPL from other specialized DNA repair enzymes. To the best of our knowledge, SPL represents an unprecedented example of a major DNA repair enzyme that cannot effectively repair its substrate lesion within the normal DNA conformation adopted in growing cells. Factors such as other DNA binding proteins, helicases or an altered DNA conformation may cooperate with SPL to enable efficient SP repair in germinating spores. Therefore, both SP formation and SP repair are likely to be tightly controlled by the unique cellular environment in dormant and outgrowing spore-forming bacteria, and thus SP repair may be extremely slow in non-spore-forming organisms