Protein methylation plays important roles in most, if not all, cellular processes. Lysine and arginine methyltransferases are known to regulate the function of histones and non-histone proteins through the methylation of specific sites. However, the role of the carboxyl-methyltransferase protein L-isoaspartyl methyltransferase (PIMT) in the regulation of protein functions is relatively less understood. Here we show that PIMT negatively regulates the tumour suppressor protein p53 by reducing p53 protein levels, thereby suppressing the p53-mediated transcription of target genes. In addition, PIMT depletion upregulates the proapoptotic and checkpoint activation functions of p53. Moreover, PIMT destabilizes p53 by enhancing the p53–HDM2 interaction. These PIMT effects on p53 stability and activity are attributed to the PIMT-mediated methylation of p53 at isoaspartate residues 29 and 30. Our study provides new insight into the molecular mechanisms by which PIMT suppresses the p53 activity through carboxyl methylation, and suggests a therapeutic target for cancers.

A Gram-negative-staining, non-spore-forming bacterium devoid of flagella, designated strain B9 T , was isolated from rice paddy soil associated with the roots of Oryza sativa collected from Jinju, South Korea. Cells were straight rods, were catalase-and oxidase-positive and were able to hydrolyse pectin, xylan and laminarin. Growth of strain B9 T was observed between 15 and 35 6C(optimum 25-30 6C) and between pH 5.0 and 8.0 (optimum pH 6.5-7.5). Strain B9 T contained menaquinone-7 (MK-7) as a major isoprenoid quinone and summed feature 3 (C 16 : 1 v7c and/or iso-C 15 : 0 2-OH), iso-C 15 : 0 and C 16 : 0 as major fatty acids. The G+C content of the genomic DNA was 44.4 mol%. Comparative 16S rRNA gene sequence analysis showed that strain B9 T belonged to the genus Mucilaginibacter, a member of the family Sphingobacteriaceae, and was most closely related to Mucilaginibacter kameinonensis SCK T (95.9 % sequence similarity). On

Prior research revealed that Polaromonas naphthalenivorans CJ2 carries and expresses genes encoding the gentisate metabolic pathway for naphthalene. These metabolic genes are split into two clusters, comprising nagRAaGHAbAcAdBFCQEDJI-orf1-tnpA and nagR2-orf2I؆KL (C. O. Jeon, M. Park, H. Ro, W. Park, and E. L. Madsen, Appl. Environ. Microbiol. 72:1086-1095, 2006). BLAST homology searches of sequences in GenBank indicated that the orf2 gene from the small cluster likely encoded a salicylate 5-hydroxylase, presumed to catalyze the conversion of salicylate into gentisate. Here, we report physiological and genetic evidence that orf2 does not encode salicylate 5-hydroxylase. Instead, we have found that orf2 encodes 3-hydroxybenzoate 6-hydroxylase, the enzyme which catalyzes the NADH-dependent conversion of 3-hydroxybenzoate into gentisate. Accordingly, we have renamed orf2 nagX. After expression in Escherichia coli, the NagX enzyme had an approximate molecular mass of 43 kDa, as estimated by gel filtration, and was probably a monomeric protein. The enzyme was able to convert 3-hydroxybenzoate into gentisate without salicylate 5-hydroxylase activity. Like other 3-hydroxybenzoate 6-hydroxylases, NagX utilized both NADH and NADPH as electron donors and exhibited a yellowish color, indicative of a bound flavin adenine dinucleotide. An engineered mutant of P. naphthalenivorans CJ2 defective in nagX failed to grow on 3-hydroxybenzoate but grew normally on naphthalene. These results indicate that the previously described small catabolic cluster in strain CJ2 may be multifunctional and is essential for the degradation of 3-hydroxybenzoate. Because nagX and an adjacent MarR-type regulatory gene are both closely related to homologues in Azoarcus species, this study raises questions about horizontal gene transfer events that contribute to operon evolution.Polaromonas naphthalenivorans CJ2, previously found to be responsible for the degradation of naphthalene in situ at a coal tar waste-contaminated site (10), is able to utilize naphthalene as the sole carbon source. Recent sequencing and analysis of the entire naphthalene degradation pathway of P. naphthalenivorans CJ2 (12) revealed that the naphthalene-catabolic (nag) genes in P. naphthalenivorans CJ2 are homologous to those in Ralstonia sp. strain U2, which metabolizes naphthalene via the gentisate pathway, converting naphthalene into fumarate and pyruvate via salicylate (2-hydroxybenzoate) and gentisate (2,5-dihydroxybenzoate) (5). This finding has recently been confirmed biochemically (G. M. Pumphrey and E. L. Madsen, submitted for publication). In contrast to the nag genes of strain U2, which are organized in a single operon, the naphthalenecatabolic genes of strain CJ2 are organized into two gene clusters (Fig. 1A), comprising nagRAaGHAbAcAdBFCQEDJIЈ-orf1-tnpA (large cluster) and nagR2-orf2IЉKL (small cluster). LysR-type (nagR) and MarR-type (nagR2) transcriptional regulators act, respectively, to up-regulate and down-regulate the growth of strain CJ2 on naphthalene in min...

A Gram-negative bacterium, designated strain EMB71T , was isolated from activated sludge used for enhanced biological phosphorus removal in a sequencing batch reactor. The cells of the isolate were facultatively aerobic, motile rods with single polar flagella. Growth was observed to occur at 15-35 6C (optimally at 30 6C) and at pH 6.0-9.0 (optimally at pH 7.0-8.0). The predominant fatty acids of strain EMB71 T were C 16 : 0 and summed feature 3 (C 16 : 1 v7c and/or iso-C 15 : 0 2-OH), and the polar lipids comprised a large amount of phosphatidylethanolamine and a small amount of diphosphatidylglycerol. The G+C content of the genomic DNA was 61.6 mol % and the major quinone was Q-8. Comparative 16S rRNA gene sequence analyses showed that strain EMB71 T formed a phyletic lineage with the genus Hydrogenophaga within the family Comamonadaceae. The levels of 16S rRNA gene sequence similarity with respect to the type strains of Hydrogenophaga species ranged from 95.1 to 96.9 %. On the basis of the phenotypic, chemotaxonomic and molecular data, strain EMB71 T represents a novel species of the genus Hydrogenophaga, for which the name Hydrogenophaga caeni sp. nov. is proposed.

A Gram-stain-negative, strictly aerobic bacterium, designated strain N7 T , was isolated from a rice paddy in South Korea. Cells of strain N7 T were non-motile, non-spore-forming rods. Growth was observed at 15-35 6C (optimum of 25-30 6C) and between pH 6.0 and 8.0 (optimum of pH 6.5-7.5). The predominant isoprenoid quinone was menaquinone-7. The major cellular fatty acids of strain N7 T were summed feature 3 (comprising C 16 : 1 v7c and/or iso-C 15 : 0 2-OH), iso-C 15 : 0 , anteiso-C 15 : 0 , C 15 : 0 and iso-C 16 : 0 . The G+C content of the genomic DNA was 37.7 mol%. Comparative 16S rRNA gene sequence analyses showed that strain N7 T formed a distinct phyletic line within the genus Pedobacter. Phylogenetic distances from strains of other Pedobacter species with validly published names were greater than 5.0 % (i.e. ,95.0 % 16S rRNA gene sequence similarities). On the basis of phenotypic and molecular data, it is clear that strain N7 T represents a novel species within the genus Pedobacter, for which the name Pedobacter oryzae sp. nov. is proposed. The type strain is N7 T (5KACC 12821 T 5DSM 19973 T ).Since the genus Pedobacter, which belongs to the family Sphingobacteriaceae of the phylum Bacteroidetes, was first proposed by Steyn et al. (1998) to reclassify two Sphingobacterium species and to accommodate two novel species, a large number of Pedobacter species have been isolated from various habitats such as soil (Ten et al., 2006;Yoon et al., 2007a, b, c, d), water (Gallego et al., 2006Muurholm et al., 2007), a glacier (Shivaji et al., 2005), sludge (Vanparys et al., 2005) and the rhizosphere (Kwon et al., 2007). In this study, taxonomic characterization is reported of strain N7 T , which was isolated from a rice paddy and is related phylogenetically to members of the genus Pedobacter.Strain N7 T was isolated from rice paddy soil associated with the roots of Oryzae sativa in Jinju (35 u 199 N 128 u 099 E), South Korea. Rice roots were sampled in September 2006, soil debris was removed from the roots by washing with sterile saline (0.9 %, w/v) and the suspension was serially diluted using 0.9 % (w/v) saline. The different dilutions were spread on R2A agar (Difco) and incubated at 25 u C for 5 days. Subcultivation was done routinely on R2A agar aerobically at 30 u C for 3 days, except where indicated otherwise, and the bacterial isolate was maintained as a glycerol stock at 280 uC.Amplification and sequencing of the 16S rRNA gene of strain N7 T was carried out as described by Kim et al. (2008). Briefly, a single colony of strain N7 T grown on R2A agar was resuspended in 100 ml of 5 % (w/v) Chelex-100 solution (Bio-Rad) and boiled for 10 min to prepare crude genomic DNA lysates. PCR amplification of 16S rRNA genes from the crude lysates was performed using the universal primers F1 (59-AGAGTTTGATCMTGGCTCAG-39) and R13 (59-TACGGYTACCTTGTTACGACTT-39) as described previously (Lu et al., 2006). The resulting 16S rRNA gene sequence (1486 nt) was compared with available 16S rRNA gene sequences from GenBank using the ...

A Gram-negative bacterium, designated strain EMB34 T , was isolated from a wastewater treatment plant in Korea. Growth was observed between 10 and 40 6C (optimum, 25-35 6C) and between pH 6.0 and 9.5 (optimum, pH 7.5-8.0). The cells were non-motile rods, linked with extracellular fibrils. The predominant fatty acids of strain EMB34 T were iso-C 15 : 0 , C 15 : 0 , iso-C 15 : 1 G, iso-C 16 : 0 3-OH and iso-C 15 : 0 3-OH and the strain contained phosphatidylethanolamine and phosphatidylinositol as the polar lipids. The G+C content of the genomic DNA was 34.2 mol% and the major quinone was menaquinone-6. Comparative 16S rRNA gene sequence analyses showed that strain EMB34 T formed a distinct phyletic line within the genus Flavobacterium. The levels of 16S rRNA gene sequence similarity with other Flavobacterium species were less than 94.5 %. On the basis of phenotypic, chemotaxonomic and molecular data, it is clear that strain EMB34 T represents a novel species within the genus Flavobacterium, for which the name Flavobacterium filum sp. nov. is proposed. The type strain is EMB34 T (5KCTC 12610 T 5DSM 17961 T ).Since the genus Flavobacterium, which belongs to the phylum Bacteroidetes, was established (Bergey et al., 1923), its description has been emended repeatedly and many novel Flavobacterium species have been described from diverse habitats such as micromats, fresh water and seawater, Antarctic lakes, soil, gut of an earthworm and sediments (Bernardet et al., 1996;McCammon & Bowman, 2000;Van Trappen et al., 2004; Kämpfer et al., 2006;Cousin et al., 2007). Physiological characteristics of Flavobacterium strains are also very diverse: they can be psychrophilic, psychrotolerant or mesophilic, they can be halotolerant, halophilic or sensitive to salts and they produce a variety of enzymes (Humphry et al., 2001;Tamaki et al., 2003;Aslam et al., 2005;Zhang et al., 2006), suggesting that they may have important roles in environmental habitats. Activated sludge processes have been used to remove organic compounds as well as nutrients from wastewater and insights regarding their bacterial communities are a prerequisite for understanding the mechanisms involved. Therefore, efforts have been made in our laboratory to isolate and characterize members of the bacterial community in activated sludge (Park et al., 2006(Park et al., , 2007. Here we describe the taxonomic characterization of a novel species belonging to the genus Flavobacterium.Strain EMB34 T was isolated from a wastewater treatment plant in Korea that performed enhanced biological phosphorus removal. The sludge sample was serially diluted with 1 % (w/v) saline solution, spread on R2A agar (Difco) and incubated at 20 u C for 5 days. The strain was grown routinely aerobically on R2A agar at 30 u C for 3 days.Sequencing of the 16S rRNA gene of strain EMB34 T was carried out as described previously by Lane (1991). The resulting 16S rRNA gene sequence (1436 nucleotides) was compared with available 16S rRNA gene sequences from GenBank using the BLAST program (http://...

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This study aims to identify the types of intergenerational solidarity between parents and adult children and examine the significant factors of solidarity types. To this end, this study employs data from the 7th (2018) of Korean Longitudinal Study of Aging with 2,028 parents living apart from their children. The provision and reception of functional solidarity between parents and adult children are set as the first-order latent variables, associational solidarity and functional solidarity as the second-order latent variables, and intergenerational solidarity as the third-order latent variable. Four types are derived using a Generalized Structural Equations Model (GSEM): ‘Disconnected Type’ with low associational and functional solidarity, ‘Associational Solidarity Type’ with only minimal high-level associational solidarity, ‘Loose Solidarity Type’ with a medium level of associational and functional solidarity, and ‘Strong Solidarity Type’ with both high level of associational and functional solidarity. As a result of analyzing the influence factors focusing on the ‘Strong Solidarity Type’ - the highest intergenerational solidarity – the geographical proximity between parents and children, the income of parent households, and the residential areas are found to be important determinants. From these results, policy implications are presented, and suggestions are put forth for follow-up research.