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Transcription coupled-nucleotide excision repair (TC-NER) removes DNA lesions that block RNA polymerase II (Pol II) transcription. A key step in TC-NER is the recruitment of the TFIIH complex, which initiates DNA unwinding and damage verification; however, the mechanism by which TFIIH is recruited during TC-NER, particularly in yeast, remains unclear. Here, we show that the C-terminal domain (CTD) of elongation factor-1 (Elf1) plays a critical role in TC-NER in yeast by binding TFIIH. Analysis of genome-wide repair of UV-induced cyclobutane pyrimidine dimers (CPDs) using CPD-seq indicates that the Elf1 CTD in yeast is required for efficient TC-NER. We show that the Elf1 CTD binds to the pleckstrin homology (PH) domain of the p62 subunit of TFIIH in vitro, and identify a putative TFIIH-interaction region (TIR) in the Elf1 CTD that is important for PH binding and TC-NER. The Elf1 TIR shows functional, structural, and sequence similarities to a conserved TIR in the mammalian UV sensitivity syndrome A (UVSSA) protein, which recruits TFIIH during TC-NER in mammalian cells. These findings suggest that the Elf1 CTD acts as a functional counterpart to mammalian UVSSA in TC-NER by recruiting TFIIH in response to Pol II stalling at DNA lesions.

Recent studies in the rice genome-wide have established that de novo genes, evolving from noncoding sequences, enhance protein diversity through a stepwise process. However, the pattern and rate of their evolution in protein structure over time remain unclear. Here, we addressed these issues within a surprisingly short evolutionary timescale (

Transcription-coupled nucleotide excision repair (TC-NER) is a highly conserved DNA repair pathway that removes bulky lesions in the transcribed genome. Cockayne syndrome B protein (CSB), or its yeast ortholog Rad26, has been known for decades to play important roles in the lesion-recognition steps of TC-NER. Another conserved protein ELOF1, or its yeast ortholog Elf1, was recently identified as a core transcription-coupled repair factor. How Rad26 distinguishes between RNA polymerase II (Pol II) stalled at a DNA lesion or other obstacles and what role Elf1 plays in this process remains unknown. Here, we present cryo-EM structures of Pol II-Rad26 complexes stalled at different obstacles that show that Rad26 uses a common mechanism to recognize a stalled Pol II, with additional interactions when Pol II is arrested at a lesion. A cryo-EM structure of lesion-arrested Pol II-Rad26 bound to Elf1 revealed that Elf1 induces further interactions between Rad26 and a lesion-arrested Pol II. Biochemical and genetic data support the importance of the interplay between Elf1 and Rad26 in TC-NER initiation. Together, our results provide important mechanistic insights into how two conserved transcription-coupled repair factors, Rad26/CSB and Elf1/ELOF1, work together at the initial lesion recognition steps of transcription-coupled repair.

A 50‐day feeding trial was conducted to evaluate the effects of mulberry leaf powder water extract (MLE) on the growth performance, immunity, antioxidant, meat quality and intestinal microbiota of yellow feather broilers. A total of 720 birds (initial body weight 40.07 ± 0.05 g) were randomly distributed into four groups with six replicates per group and 30 birds per replicate. Four diets were formulated with 0% (CON), 200 mg/kg MLE (MLE200), 400 mg/kg MLE (MLE400) and 600 mg/kg MLE (MLE600) supplementation. Results showed that the addition of 200–600 mg/kg MLE to the diet significantly increased the body weight (BW) and average daily weight gain (ADG), but feed to gain ratio (F/G) were linearly decreased (p = 0.045) as dietary MLE increased. Birds fed MLE400 had higher (p < 0.05) total antioxidant capacity (T‐AOC), interleukin‐10 (Il‐10), secretory immunoglobulin A (SIgA) and complement 3 (C3) contents than those fed CON, whereas MLE400 had lower malondialdehyde (MDA) content than CON (p < 0.05). Analysis of 16 S rDNA indicated that supplementation with 200 mg/kg MLE increased the Shannon indices in the caecum (p < 0.05). Supplementation with MLE decreased the abundance of the phylum Proteobacteria and genus Helicobacter, and increased the abundance of the phylum Bacteroidetes in the caecum in broiler chickens (p < 0.05). The drip loss rate in the MLE600 was significantly diminished (p < 0.05), whereas the shear force was significantly elevated (p < 0.05). In summary, dietary supplementation with MLE can effectively improve growth performance, intestinal immunity, serum antioxidant capacity, meat quality and intestinal microbiota of yellow feather broilers. The most appropriate MLE supplementation level was 400 mg/kg. This study provides a practical strategy for the dietary application of MLE in yellow feather broilers. [ABSTRACT FROM AUTHOR]

Plant lipid transfer proteins (LTPs) are small basic proteins that play important roles in the regulation of various plant biological processes as well as the response to biotic and abiotic stresses. However, knowledge is limited on how this family of proteins is regulated in response to nematode infection in cucumber. In the present study, a total of 39 CsLTP_2 genes were identified by querying databases for cucumber-specific LTP_2 using a Hidden Markov Model approach and manual curation. The family has a five-cysteine motif (5CM) with the basic form CC-Xn-CXC-Xn-C, which differentiates it from typical nsLTPs. The members of CsLTP_2 were grouped into six families according to their structure and their phylogenetic relationships. Expression data of CsLTP_2 genes in 10 cucumber tissues indicated that they were tissue-specific genes. Two genes showed significant expression change in roots of resistant and susceptible lines during nematode infection, indicating their involvement in response to Meloidogyne incognita. This systematic analysis provides a foundation of knowledge for future studies of the biological roles of CsLTP_2 genes in cucumber in response to nematode infection and may help in the efforts to improve M. incognita-resistance breeding in cucumber. Key words: cucumber, CsLTP_2, expression data, M. incognita resistance. Resume: Chez les plantes, les proteines de transfert des lipides (LTP) sont de petites proteines basiques qui jouent des roles importants dans la regulation de divers processus biologiques ainsi que la reponse aux stress biotiques et abiotiques. Cependant, les connaissances sont limitees sur la facon dont cette famille de proteines est regulee en reponse a l'infection par des nematodes chez le concombre. Dans le present travail, 39 genes CsLTP_2 ont ete identifies en interrogeant les bases de donnees pour des LTP_2 specifiques du concombre au moyen d'une approche << Hidden Markov Model >> et d'une curation manuelle. La famille possede un motif a cinq cysteines (5CM) de forme CC-Xn-CXC-Xn-C, ce qui la differencie des nsLTP typiques. Les membres de la famille CsLTP_2 ont ete groupes en six familles en fonction de leur structure et de leurs relations phylogenetiques. Les donnees sur l'expression des genes CsLTP_2 au sein de dix tissus du concombre ont indique qu'il y avait des genes a expression tissu-specifique. Deux genes ont montre une difference significative dans leur expression au cours de l'infection par le nematode selon la variete, resistante ou sensible, ce qui suggere qu'ils sont impliques dans leur reponse au Meloidogyne incognita. Cette analyse systematique apporte une assise de connaissances pour de futures etudes des roles biologiques des genes CsLTP_2 chez le concombre en reponse a l'infection par le nematode et pourrait contribuer aux efforts visant a selectionner une resistance accrue face au M. incognita chez le concombre. [Traduit par la Redaction] Mots-cles : concombre, CsLTP_2, donnees d'expression, resistance au M incognita., Introduction Plant lipid transfer proteins (LTPs) are small basic proteins widely distributed in various plant species such as rice, peach, cumin, and coffee (Liu et al. 2002; Pasquato et al. [...]

Objective To establish a Nomogram model for assessing the risk of intestinal colonization by Carbapenem-Resistant Klebsiella pneumoniae (CRKP) to determine the specific probability of colonization and adopt individualized prevention strategies for the purpose of reducing the occurrence of colonization and secondary infection of neonatal CRKP. Methods A total of 187 neonates hospitalized between January 2021 and October 2022 and diagnosed with CRKP colonization by rectal swab/fecal culture as well drug sensitivity identification 48 h after admission were assigned to the CRKP group. Another 187 neonates without non-CRKP colonization during the same period were set as the non-CRKP group. All the data of the two groups were used for a retrospective analysis. The caret package in R 4.2.1 was used to randomly divide the 374 cases into the model group and validation group at a ratio of 3:1. Then the glmnet package in R 4.2.1 was used to conduct a LASSO regression analysis over the data from the model group to determine the predictive factors for modeling and the rms software package was used to build a Nomogram model. The pROC and rms packages in R 4.2.1 were used to examine the data, analyzing the consistency indexes (Cindex), receiver operating characteristic curves (ROC), and area under the curves (AUC) and performing the internal and external validation of the efficacy of the Nomogram model via the calibration curves. Results LASSO regression analysis determined eight predictors from the 35 factors probably affecting neonatal CRKP colonization: gender, cesarean section, breastfeeding, nasogastric tube, enema, carbapenems, probiotics, and hospital stay. The Nomogram model constructed using these eight predictors as variables could predict CRKP colonization to a moderate extent, with the area under the ROC curve of 0.835 and 0.800 in the model and validation group, respectively. The Hosmer-Lemeshow test showed that the predicted probability was highly consistent with the actual probability (the modeling group: P = 0.678 > 0.05; the validation group: P = 0.208 > 0.05), presenting a higher degree of fitting. Conclusion The Nomogram model containing such variables as gender, cesarean section, breastfeeding, nasogastric tube, enema, carbapenems, probiotics, and hospital stay is more effective in predicting the risk of neonatal CRKP colonization. Therefore, preventive measures should be individualized based on the colonization probability predicted by the Nomogram model in order to keep neonates from CRKP colonization and reduce the incidence of secondary CRKP infections among them. [ABSTRACT FROM AUTHOR]

Peptidoglycan recognition proteins (PGRPs) are one of the receptors in insects' immune pathways, essential for insects to recognize the exogenous pathogens in order to activate the Toll and immune deficiency (IMD) pathway. In the silkworm Bombyx mori, previous studies focused on the short PGRPs and less is known about the long PGRPs. In this study, a long PGRP in silkworm BmPGRP‐L4 was cloned and its expression and function were analysed. The results showed that BmPGRP‐L4 contains a transmembrane region, a conserved PGRP domain, and an amidase‐2 domain. The expression profile demonstrated that BmPGRP‐L4 existed in diverse tissues including epidermis, fat body, midgut, and silk glands, with remarkably high expression in the midgut in the 5th instar. Oral infection with Escherichia coli and Staphylococcus aureus significantly induced BmPGRP‐L4 in the midgut and epidermis, as well as in the fat body and silk glands. Peptidoglycan also induced the expression of BmPGRP‐L4 in midgut tissue ex vivo and BmN4 cells in vitro. RNAi of BmPGRP‐L4 was effective in the midgut and epidermis, while the efficiency in the fat body was transient. RNAi‐mediated knock‐down of BmPGRP‐L4 reduced the weight and growth of the silkworm, possibly due to its participation in the immune response and the regulation of the microbiota in the midgut lumen of the silkworm larvae. [ABSTRACT FROM AUTHOR]