• Journal of Microbiology
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• v.39 no.4
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• pp.334-337
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• 2001

The degradative pathway of homoprotocatechuate (HPC) is the bacterial routhe wherby 3,4-dihydrox-yphenylactic acid is catabolized to pyruvate and succinate by a series of sequential reactions . The HPC is catalzed by homoprotocatechuate 2, 3-dioxygenase(HPC-2,3O) to from 5-carboxymethy1-2-hydroxy-muco semialdehyde. In this study, the hha D gene encoding. HPC, 2, 3O was Cloned from the chromo-somal DNA of Pseudomonas sp. DJ-12 and its nucleotide sequence was analyzed. The open reding frame of hpaD gene was found to be composed of 864 nucleotide pairs and to encode a poypetide with 287 amino acide residues. The deduced amino acid sequence of the HPC-2,3O from Pseudomonas. sp. DJ-12 exhibited 60~64% homology with those of the corresponding enzymes from E. coli. Salmonella enterica, and Klebsiella pneumoniae.

• Molecules and Cells
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• v.40 no.7
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• pp.441-449
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• 2017

Proteolysis in eukaryotic cells is mainly mediated by the ubiquitin (Ub)-proteasome system (UPS) and the autophagy-lysosome system (hereafter autophagy). The UPS is a selective proteolytic system in which substrates are recognized and tagged with ubiquitin for processive degradation by the proteasome. Autophagy is a bulk degradative system that uses lysosomal hydrolases to degrade proteins as well as various other cellular constituents. Since the inception of their discoveries, the UPS and autophagy were thought to be independent of each other in components, action mechanisms, and substrate selectivity. Recent studies suggest that cells operate a single proteolytic network comprising of the UPS and autophagy that share notable similarity in many aspects and functionally cooperate with each other to maintain proteostasis. In this review, we discuss the mechanisms underlying the crosstalk and interplay between the UPS and autophagy, with an emphasis on substrate selectivity and compensatory regulation under cellular stresses.

• Biomolecules & Therapeutics
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• v.29 no.6
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• pp.605-614
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• 2021

Autophagy is an important degradative pathway that eliminates misfolded proteins and damaged organelles from cells. Autophagy is crucial for neuronal homeostasis and function. A lack of or deficiency in autophagy leads to the accumulation of protein aggregates, which are associated with several neurodegenerative diseases. Compared with non-neuronal cells, neurons exhibit rapid autophagic flux because damaged organelles or protein aggregates cannot be diluted in post-mitotic cells; because of this, these cells exhibit characteristic features of autophagy, such as compartment-specific autophagy, which depends on polarized structures and rapid autophagy flux. In addition, neurons exhibit compartment-specific autophagy, which depends on polarized structures. Neuronal autophagy may have additional physiological roles other than amino acid recycling. In this review, we focus on the characteristics and regulatory factors of neuronal autophagy. We also describe intracellular selective autophagy in neurons and its association with neurodegenerative diseases.

• Biomedical Science Letters
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• v.27 no.3
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• pp.182-186
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• 2021

Parkinson disease (PD) is becoming one of the most neurodegenerative disorder worldwide. The deposited aggregates have been connected in the pathophysiology of PD, which are degraded either by ubiquitin-proteasomal system (UPS) or autophagy-lysosomal pathway (ALP). Leucin-rich repeat kinase 2 (LRRK2), one of the neurodegenerative proteins of PD is also stringently controlled by both UPS and ALP degradation as well. However, the polyubiquitination pattern of LRRK2 aggregates is largely unknown. Here, we found that K63-linked polyubiquitinations of G2019S mutant, most familial variant for PD, is highly enhanced compared to those of wild type LRRK2 (WT). In addition, in the presence of overexpressed p62/SQSTM-1, ubiquitination of LRRK2 WT or D1994A was reduced, whereas G2019S mutant was not diminished significantly. Therefore, we propose that degradation of G2019S via UPS is more involved with K63-linked ubiquitination than K48-linked ubiquitination, and overexpressed p62/SQSTM-1 does not enhance degradative effect on G2019S variant.

• Proceedings of the Microbiological Society of Korea Conference
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• 2001.11a
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• pp.157-163
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• 2001

Mycolic acid-containing gram-positive bacteria, so called nocardioform actinomycetes, have become a great interest to environmental microbiologists due to their metabolic versatility, multidegradative capacity and potential for bioremediation of priority pollutants. For example, Rhodococcus rhodochrous N75 was able to metabolize 4-methy1catechol via a modified $\beta$-ketoadipate pathway whereby 4-methylmuconolactone methyl isomerase catalyzes the conversion of 4-methylmuconolactone to 3-methylmuconolactone in order to circumvent the accumulation of the 'dead-end' metabolite, 4-methylmuconolactone. R. rhodochrous N75 has also shown the ability to transform a range of alkyl-substituted catechols to the corresponding muconolactones. A novel 3-methylmuconolactone-CoAsynthetase was found to be involved in the degradation of 3-methylmuconolactone, which is not mediated in a manner analogous to the classical $\beta$-ketoadipate pathway but activated by the addition of CoA prior to hydrolysis of lactone ring, suggesting that the degradative pathway for methylaromatic compounds by gram-positive bacteria diverges from that of proteobacteria. Mycobacterium sp. Strain PYR-l isolated from oil-contaminated soil was capable of mineralizing various polyaromatic hydrocarbons (PAHs), such as naphthalene, phenanthrene, pyrene, fluoranthrene, 1-nitropyrene, and 6-nitrochrysene. The pathways for degradation of PAHs by this organism have been elucidated through the isolation and characterization of chemical intermediates. 2-D gel electrophoresis of PAH-induced proteins enabled the cloning of the dioxygenase system containing a dehydrogenase, the dioxygenase small ($\beta$)-subunit, and the dioxygenase large ($\alpha$)-subunit. Phylogenetic analysis showed that the large a subunit did not cluster with most of the known sequences except for three newly described a subunits of dioxygenases from Rhodococcus spp. and Nocardioides spp. 2-D gel analysis also showed that catalase-peroxidase, which was induced with pyrene, plays a role in the PAH metabolism. The survival and performance of these bacteria raised the possibility that they can be excellent candidates for bioremediation purposes.

• Journal of Microbiology
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• v.35 no.2
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• pp.117-122
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• 1997

Several dominant 4-CPA-degrading bacteria were isoalted from agricultural soils. Most of the isolates were identified as Burkholderia species by fatty acid methyl ester (FAME) analysis, but they were idstinct in chromosomal patterns obtained by PCR amplification of repetitive extragenic palindromic (REP) sequences. These strains were generally restricted in their substrate utilization capabilities. The 4-CPA degradative enzymes were idnducible by 4-CPA and some isolates appeared to mineralize 4-CPA via formation of 4-chlorophenol and 4-chlorocatechol as intermediates during its biodegradation pathway. Plasmid DNAs were not detected from most of the isoaltes and their 4-CPA genes wer on the chromosomal DAN. The 4-CPA degradation patterns in axenic cultures and natural soils varied depending on the strains and soils. The inoculation of 4-CPA degraders much improved the removal of 4-CPA from the 4-CPA treated soils.

• Applied Biological Chemistry
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• v.39 no.6
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• pp.472-476
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• 1996

The major portions of two DNA fragments, one from degradative plasmid, pRA4000 from Pseudomonas putida NCIMB 9866, and the other from degradative plasmid, pRA500 from P. putida NCIMB 9869, which harbor the structural genes for the flavoprotein (pchF) and cytochrome (pchC) subunits of p-cresol methylhydroxylase (PCMH), have been sequenced. The DNA and deduced amino acid sequences for pchC and pchF have been published. In these fragments, a coding region (dhal) for an aldehyde dehydrogenase has been identified. It is proposed that this gene encodes for the aldehyde dehydrogenase which converts p-hydroxybenzyaldehyde to p-hydroxybenzoate. p-Hydroxybezealdehyde is the product of oxidation of p-cresol by PCMH. The fragment from P. putida 9869 also harbors the genes for the ${\alpha}$ (pcaG) and ${\beta}$ (pcaH) subunits of protocatechuate 3,4-dioxigenase. The fragment from 9866 does not have any portion of these genes in the corresponding region A possible open reading frame (ORF) between pchC and pchF is seen for both clones, and a second putative open reading frame (ORF') also exists in the 9866 clone. The gene organizations are dhal-pchC-ORF-pchF-pcaGH for the DNA fragment from 9869, and ORF-dhal-pchC-ORF-pchF for the DNA fragment from 9866.

• KSBB Journal
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• v.18 no.3
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• pp.174-179
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• 2003

The bacterium NFQ-1 capable of utilizing quinoline (2,3-benzopyridine) as the sole source of carbon, nitrogen and energy was enriched and isolated from soil samples of dead coal pit areas. Strain NFQ-1 was identified as Pseudomonas nitroreducens NFQ-1 by BIOLOG system, and assigned to Pseudomonas sp. NFO-1. Pseudomonas sp. NFQ-1 was used with the concentration range of 1 to 10 mM quinoline. Strain NFQ-1 could degrade 2.5 mM quinoline within 9 hours of incubation. Initial pH 8.0 in the culture was reduced to 6.8, and eventually 7.0 as the incubation was proceeding. 2-Hydroxyquinoline, the first intermediate of the degradative pathway, accumulated transiently in the growth medium. The highest concentration of quinoline (15 mM) in this work inhibited cell growth and quinoline degradation. Pseudomonas sp. NFQ-1 was able to utilize various quinoline derivatives and aromatic compounds including 2-hydroxyquinoline, p-comaric acid, benzoic acid, p-cresol, p-hydroxybenzoate, protocatechuic acid, and catechol. The specific activity of catechol oxygenases was determined to approximately 184.7 unit/㎎ for catechol 1.2-dioxygenase and 33.19 unit/㎎ for catechol 2,3-dioxygenase, respectively. As the result, it showed that strain NFQ-1 degraded quinoline via mainly orthp-cleavage pathway, and in partial meta-cleavage pathway.

• Journal of Soil and Groundwater Environment
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• v.11 no.1
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• pp.1-6
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• 2006

The analysis of functional population and its dynamics on the environment is essential for understanding bioremediation in environment. Here, we report a method for oligonucleotide microarray for the monitoring of aliphatic and aromatic degradative genes. This microarray contained 15 unique and group-specific probes which were based on 100 known genes involved pathways in biodegradation. Hybridization specificity tests with pure cultures, strain Pseudomonas aeruginosa KCTC 1636 indicated that the designed probes on the arrays appeared to be specific to their corresponding target genes. It was found that the presence of 8 genes encoding alkane, naphthalene, biphenyl, pyrene (PAH ring-hydroxylating) degradation pathway could be detected in oil contaminated soil sample. Therefore, the findings of this study strongly suggest that oligonucleotide microarray is an effective diagnostic tool for evaluating biodegradation capability in oil contaminated subsurface environment.

• 한국생물공학회:학술대회논문집
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• 2000.11a
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• pp.489-492
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• 2000

The eventual goal of this study is to elucidate roles of plant terpenoids (e.g., cymene, limonene and others) as natural substrates in the cometabolic biodegradation of PCBs and to develop an effective PCB bioremediation technology. The aim of this study was to examine how plant terpenoids, as natural substrates or inducers would affect the biodegradation of PCB congeners. Various PCB degraders that could grow on biphenyl and several terpenoids were tested for their PCB degradation capabilities. The PCB congener degradation activities were first monitored through resting cell assay technique that could detect degradation products of the substrate. The congener removal was also confirmed by concommitant GC analysis. The PCB degraders, Pseudononas sp. P166 and Caynebacterium sp. T104 were found to grow on both biphenyl and terpenoids ((S)-(-) limonene, p-cymene and ${\alpha}-terpinene$) whereas Arthrobacter B1B could not grow on the terpenoids as a sole carbon source. The strain B1B grown on biphenyl showed a good degradation activity for 4,4'-dichlorobiphenyl (DCBp) while strains P166 and T104 gave about 25% of B1B activity. Induction of degradation by cymene, limonene and terpine was hardly detected by the resting cell assay technique. This appeared to be due to relatively lower induction effect of these terpenoids compared with biphenyl. However, a subsequent GC analysis showed that the congener could be removed up to 30% by the resting cells of T104 grown on the terpenoids. This indicates that terpenoids, widely distributed in nature, could be utilized as both growth and/or inducer substrate for PCB biodegradation.