ABSTRACT
Base excision is a crucial DNA repair process mediated by endonuclease IV in nucleotide excision. In Chlamydia pneumoniae, CpendoIV is the exclusive AP endonuclease IV, exhibiting DNA replication error-proofreading capabilities, making it a promising target for anti-chlamydial drug development. Predicting the structure of CpendoIV, molecular docking with DNA was performed, analyzing complex binding sites and protein surface electrostatic potential. Comparative structural studies were conducted with E. coli EndoIV and DNA complex containing AP sites.CpendoIV was cloned, expressed in E. coli, and purified via Ni-NTA chelation and size-exclusion chromatography. Low NaCl concentrations induced aggregation during purification, while high concentrations enhanced purity.CpendoIV recognizes and cleaving AP sites on dsDNA, and Zn2+ influences the activity. Crystallization was achieved under 8% (v/v) Tacsimate pH 5.2, 25% (w/v) polyethylene glycol 3350, and 1.91 Å resolution X-ray diffraction data was obtained at 100 K. This research is significant for provides a deeper understanding of CpendoIV involvement in the base excision repair process, offering insights into Chlamydia pneumoniae.
Subject(s)
Bacterial Proteins , Chlamydophila pneumoniae , Crystallization , Chlamydophila pneumoniae/enzymology , Chlamydophila pneumoniae/genetics , Chlamydophila pneumoniae/chemistry , Crystallography, X-Ray , Bacterial Proteins/chemistry , Bacterial Proteins/genetics , Bacterial Proteins/isolation & purification , Escherichia coli/genetics , Molecular Docking Simulation , Recombinant Proteins/chemistry , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Deoxyribonuclease IV (Phage T4-Induced)/chemistry , Deoxyribonuclease IV (Phage T4-Induced)/genetics , Deoxyribonuclease IV (Phage T4-Induced)/metabolism , Deoxyribonuclease IV (Phage T4-Induced)/isolation & purification , Cloning, MolecularABSTRACT
Nitrogen (N) is an important nutrient for the growth and development of rice. The application of N fertilizer has become one of the inevitable ways to increase rice yield due to insufficient soil N content. However, in order to achieve stable and high yield, farmers usually increase N fertilizer input without hesitation, resulting in a series of problems such as environmental pollution, energy waste and low production efficiency. For sustainable agriculture, improving the nitrogen use efficiency (NUE) to decrease N fertilizer input is imperative. In the present review, we firstly demonstrate the role of N in mediating root architecture, photosynthesis, metabolic balance, and yield components in rice. Furthermore, we further summarize the current agronomic practices for enhancing rice NUE, including balanced fertilization, the use of nitrification inhibitors and slow-release N fertilizers, the split application of N fertilizer, root zone fertilization, and so on. Finally, we discuss the recent advances of N efficiency-related genes with potential breeding value. These genes will contribute to improving the N uptake, maintain the N metabolism balance, and enhance the NUE, thereby breeding new varieties against low N tolerance to improve the rice yield and quality. Moreover, N-efficient varieties also need combine with precise N fertilizer management and advanced cultivation techniques to realize the maximum exploitation of their biological potential.
ABSTRACT
Tudor domain-containing (TDRD) proteins, the germline enriched protein family, play essential roles in the process of gametogenesis and genome stability through their interaction with the PIWI-interacting RNA (piRNA) pathway. Several studies have suggested the rapid evolution of the piRNA pathway in teleost lineages with striking reproductive diversity. However, there is still limited information about the function and evolution of Tdrd genes in teleost species. In this study, through genome wide screening, 13 Tdrd family genes were identified in economically important aquaculture fish, including spotted sea bass (Lateolabrax maculatus), Asian sea bass (Lates calcarifer), and tongue sole (Cynoglossus semilaevis). With copy number, structure, phylogeny, and synteny analysis, duplication of Tdrd6 and Tdrd7, as well as loss of Stk31 and Tdrd10, were characterized in teleost lineages. Codon based molecular evolution analysis indicated faster evolution of teleost Tdrd genes than that in mammals, potentially associated with the accelerated evolution of the piRNA pathway in teleost lineages. The evolutionary diversity of Tdrd genes was also detected between different teleost lineages. RNA-seq analysis showed that most teleost Tdrd genes were dominantly expressed in gonads, particularly highly expressed in testis, such as Tdrd6, Tdrd7a, Tdrd9, Ecat8, and Tdrd15. The varied expression and evolutionary pattern between the duplicated Tdrd6 and Tdrd7 in teleosts may indicate their functional diversification. All these results suggest a conserved function of teleost Tdrd family in gametogenesis and the piRNA pathway, which could lay a foundation for the evolution of Tdrd genes and be helpful for further deciphering of Tdrd functions in teleosts. Supplementary Information: The online version contains supplementary material available at 10.1007/s42995-021-00118-7.
