Nucleosome assembly proteins NAP1L1 and NAP1L4 modulate p53 acetylation to regulate cell fate

The p53 tumor suppressor regulates expression of genes involved in various stress responses. Upon genotoxic stress, p53 induces target genes regulating cell cycle arrest for survival or apoptosis. Nevertheless, detailed mechanisms of how p53 selectively regulates these opposing outcomes remain unclear. For this study, we investigated p53 regulatory mechanisms exerted by nucleosome assembly protein 1-like 1 (NAP1L1) and NAP1L4, both of which are identified as DGKζ-interacting proteins. Here we demonstrate that, under normal conditions, NAP1L1 knockdown decreases Lys320 acetylation of p53 with attenuated proarrest p21 expression, whereas NAP1L4 knockdown increases Lys320 acetylation with enhanced p21 expression. These conditions lead respectively to facilitation and suppression of cell growth. Under genotoxic stress conditions, NAP1L1 knockdown increases Lys382 acetylation with enhanced proapoptotic Bax levels, thereby facilitating cell death. By contrast, NAP1L4 knockdown decreases Lys382 acetylation with attenuated Bax levels, thereby suppressing apoptosis. These results suggest that NAP1L1 and NAP1L4 regulate cell fate by controlling the expression of p53-responsive proarrest and proapoptotic genes through selective modulation of p53 acetylation at specific sites during normal homeostasis and in stress-induced responses.     

Analysis of B-Class Genes NAP3L3 and NAP3L4 in Narcissus tazetta var. chinensis

Very few flower organ identity genes have been characterized in Chinese narcissus (Narcissus tazetta var. chinensis), which has petaloid sepals. Here, we report the cloning of two full-length B-class genes, namely NAP3L3 and NAP3L4, that are orthologs of the DEFICIENS lineage. Both genes are highly expressed in the second whorl of the perianth and in the stamens. NAP3L4 is also expressed strongly in the ovule. The functions of these two genes were further analyzed using transgenic plants. Ectopic expression of either gene in Arabidopsis gave no obvious floral organ transformation phenotypes. In yeast two-hybrid assays, NAP3L3 and NAP3L4 failed to homodimerize and interacted weakly with each other. The data suggest that these two genes might not be involved in the formation of petaloid sepals. Isolation and functional analysis of other B-class paralogs should be conducted to fully understand petaloid tepal development in Chinese narcissus.     

Conservation of imprinting of MKRN3 and NAP1L5 in rabbits

Maternally imprinted genes of makorin ring finger protein 3 (MKRN3) and nucleosome assembly protein 1‐like 5 (NAP1L5) have been identified in many species but have not yet been investigated in rabbits. In this study, a polymorphism‐based approach and bisulfite‐sequencing PCR (BSP) were used to determine the imprinting status of MKRN3 and NAP1L5 in rabbits. The single nucleotide polymorphism (SNP)‐based sequencing results demonstrated that MKRN3 and NAP1L5 were expressed preferentially from the paternal allele. Furthermore, the BSP results showed the gamete‐specific methylation patterns and hemimethylation in brain and full methylation in liver were observed in MKRN3 and NAP1L5 respectively. Thus, we provide the first evidence that MKRN3 and NAP1L5 are paternally expressed genes and that the CpG islands located in the promoter region may be the putative differentially methylated region of these two genes in rabbits.     

Effects of ethanol and NAP on cerebellar expression of the neural cell adhesion molecule L1

The neural cell adhesion molecule L1 is critical for brain development and plays a role in learning and memory in the adult. Ethanol inhibits L1-mediated cell adhesion and neurite outgrowth in cerebellar granule neurons (CGNs), and these actions might underlie the cerebellar dysmorphology of fetal alcohol spectrum disorders. The peptide NAP potently blocks ethanol inhibition of L1 adhesion and prevents ethanol teratogenesis. We used quantitative RT-PCR and Western blotting of extracts of cerebellar slices, CGNs, and astrocytes from postnatal day 7 (PD7) rats to investigate whether ethanol and NAP act in part by regulating the expression of L1. Treatment of cerebellar slices with 20 mM ethanol, 10(-12) M NAP, or both for 4 hours, 24 hours, and 10 days did not significantly affect L1 mRNA and protein levels. Similar treatment for 4 or 24 hours did not regulate L1 expression in primary cultures of CGNs and astrocytes, the predominant cerebellar cell types. Because ethanol also damages the adult cerebellum, we studied the effects of chronic ethanol exposure in adult rats. One year of binge drinking did not alter L1 gene and protein expression in extracts from whole cerebellum. Thus, ethanol does not alter L1 expression in the developing or adult cerebellum; more likely, ethanol disrupts L1 function by modifying its conformation and signaling. Likewise, NAP antagonizes the actions of ethanol without altering L1 expression.     

Assessment of genomic imprinting of PPP1R9A, NAP1L5 and PEG3 in pigs

Imprinted genes play significant roles in the regulation of fetal growth and development, function of the placenta, and maternal nurturing behaviour in mammals. At present, few imprinted genes have been reported in pigs compared to human and mouse. In order to increase understanding of imprinted genes in swine, a polymorphism-based approach was used to assess the imprinting status of three porcine genes in 12 tissue types, obtained from F1 pigs of reciprocal crosses between Rongchang and Landrace pure breeds. In contrast to human and mouse homologues, porcine PPP1R9A was not imprinted, and was found to be expressed in all tissues examined. The expression of porcine NAP1L5 was detected in pituitary, liver, spleen, lung, kidney, stomach, small intestine, skeletal muscle, fat, ovary, and uterus, but undetectable in heart. Furthermore, porcine NAP1L5 was paternally expressed in the tissues where it's expression was observed. For PEG3, pigs expressed the paternal allele in skeletal muscle, liver, spleen, kidney, and uterus, but biallele in heart, lung, fat, stomach, small intestine, and ovary. Our data indicate that tissue distribution of the three gene differs among mammals, and the imprinting of NAP1L5 and PEG3 is well conserved.     

人源核小体组装蛋白1类似蛋白5（NAP1L5）促进293T细胞增殖

人源NAP1L5为核小体组装蛋白（NAP-1）家族成员,目前功能未知。肝癌研究暗示Nap1l5可能为抑癌基因,抑制细胞增殖;但NAP-1家族其他功能已知的一些成员,可促进细胞增殖和加快周期进程。人源NAP1L5是促进还是抑制细胞增殖,目前未知。本研究里,我们发现过表达Nap1l5促进293T细胞增殖,抑制表达则降低293T细胞增殖速度。细胞周期分析表明：Nap1l5过表达增加G2期、减少G1期细胞比例;抑制Nap1l5表达,则增加G1期、减少G2期细胞比例。我们的研究表明：人源NAP1L5会加快293T细胞周期进程,促进增殖,并且提示原来关于Nap1l5是抑癌基因的推测是不对的。     

Rat NAP1: cDNA cloning and upregulation by Mpl ligand

The Mpl ligand is a hematopoietic cytokine which exerts its effects through association with the c-Mpl receptor. It regulates the proliferation, polyploidization and maturation of platelet precursors, the megakaryocytes. Using a differential display polymerase chain reaction (PCR) approach, we have identified an mRNA, belonging to a family of nucleosome assembly proteins, whose expression is upregulated in response to Mpl ligand. Multiple size classes of this mRNA (1.7, 2.5 and 4.3 kb) are readily detected in rat primary bone marrow cells and hematopoietic tissues. The size classes are also expressed to different extents in cell lines of all hematopoietic lineages. We isolated the full-length cDNA encoding the rat megakaryocyte 1.7 kb mRNA, referred to as rNAP1. Bacterially expressed recombinant protein encoded by the 1.7 kb cDNA facilitates the formation of nucleosomes on relaxed circular DNA in vitro. Our data indicate that rNAPs, which may facilitate chromatin reorganization, are upregulated by Mpl ligand. It is possible that NAPs contribute to Mpl ligand's induced effects on hematopoietic cells.     

Molecular cloning, mRNA expression and imprinting status of PEG3, NAP1L5 and PPP1R9A genes in pig

Imprinted genes are expressed monoallelically depending on their parental origin, and play important roles in the regulation of fetal growth, development, and postnatal behavior. Most genes known to be imprinted have been identified and studied in the human and the mouse. However, there are only a small number of reported imprinted genes in pigs. Therefore, identification and characterization of more imprinted genes in pigs is useful for comparative analysis of genomic imprinting across species. In this study, we cloned the porcine PEG3, NAP1L5 and PPP1R9A genes. The imprinting status of these genes was determined using sequencing directly and single nucleotide polymorphisms (SNPs) identified in individuals from reciprocal cross of Meishan and Large White pigs. Imprinting analysis was carried out in 13 different tissues (skeletal muscle, fat, pituitary gland, heart, lung, liver, kidney, spleen, stomach, small intestine, uterus, ovary and testis) from twelve 2-month-old piglets. Imprinting analysis showed that PEG3 and NAP1L5 were exclusively expressed from the paternal allele whereas PPP1R9A was biallelically expressed in all tissues tested where the genes were expressed. The study is of interest to understand the conservation of genomic imprinting among mammals at the 3 loci.     

Assessment of genomic imprinting of SLC38A4, NNAT, NAP1L5, and H19 in cattle

Background

Sesame is an important oil crop in tropical and subtropical areas. Despite its nutritional value and historic and cultural importance, the research on sesame has been scarce, particularly as far as its genetic diversity is concerned. The aims of the present study were to clarify genetic relationships among 32 sesame accessions from the Venezuelan Germplasm Collection, which represents genotypes from five diversity centres (India, Africa, China-Korea-Japan, Central Asia and Western Asia), and to determine the association between geographical origin and genetic diversity using amplified fragment length polymorphism (AFLP).

Results

Large genetic variability was found within the germplasm collection. A total of 457 AFLP markers were recorded, 93 % of them being polymorphic. The Jaccard similarity coefficient ranged from 0.38 to 0.85 between pairs of accessions. The UPGMA dendrogram grouped 25 of 32 accessions in two robust clusters, but it has not revealed any association between genotype and geographical origin. Indian, African and Chinese-Korean-Japanese accessions were distributed throughout the dendrogram. A similar pattern was obtained using principal coordinates analysis. Genetic diversity studies considering five groups of accessions according to the geographic origin detected that only 20 % of the total diversity was due to diversity among groups using Nei's coefficient of population differentiation. Similarly, only 5% of the total diversity was attributed to differences among groups by the analysis of molecular variance (AMOVA). This small but significant difference was explained by the fact that the Central Asia group had a lower genetic variation than the other diversity centres studied.

Conclusion

We found that our sesame collection was genetically very variable and did not show an association between geographical origin and AFLP patterns. This result suggests that there was considerable gene flow among diversity centres. Future germplasm collection strategies should focus on sampling a large number of plants. Covering many diversity centres is less important because each centre represents a major part of the total diversity in sesame, Central Asia centre being the only exception. The same recommendation holds for the choice of parents for segregant populations used in breeding projects. The traditional assumption that selecting genotypes of different geographical origin will maximize the diversity available to a breeding project does not hold in sesame.     

Proteomic Analysis of a NAP1 Clostridium difficile Clinical Isolate Resistant to Metronidazole

Background

Clostridium difficile is an anaerobic, Gram-positive bacterium that has been implicated as the leading cause of antibiotic-associated diarrhea. Metronidazole is currently the first-line treatment for mild to moderate C. difficile infections. Our laboratory isolated a strain of C. difficile with a stable resistance phenotype to metronidazole. A shotgun proteomics approach was used to compare differences in the proteomes of metronidazole-resistant and -susceptible isolates.

Methodology/Principal Findings

NAP1 C. difficile strains CD26A54_R (Met-resistant), CD26A54_S (reduced- susceptibility), and VLOO13 (Met-susceptible) were grown to mid-log phase, and spiked with metronidazole at concentrations 2 doubling dilutions below the MIC. Peptides from each sample were labeled with iTRAQ and subjected to 2D-LC-MS/MS analysis. In the absence of metronidazole, higher expression was observed of some proteins in C. difficile strains CD26A54_S and CD26A54_R that may be involved with reduced susceptibility or resistance to metronidazole, including DNA repair proteins, putative nitroreductases, and the ferric uptake regulator (Fur). After treatment with metronidazole, moderate increases were seen in the expression of stress-related proteins in all strains. A moderate increase was also observed in the expression of the DNA repair protein RecA in CD26A54_R.

Conclusions/Significance

This study provided an in-depth proteomic analysis of a stable, metronidazole-resistant C. difficile isolate. The results suggested that a multi-factorial response may be associated with high level metronidazole-resistance in C. difficile, including the possible roles of altered iron metabolism and/or DNA repair.