• Molecules and Cells
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• 제40권7호
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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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• 제29권6호
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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.

• 대한의생명과학회지
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• 제27권3호
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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.

• 한국미생물학회:학술대회논문집
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• 한국미생물학회 2001년도 추계학술대회
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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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• 제35권2호
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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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• 제39권6호
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• pp.472-476
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• 1996

P.putida NCIMB 9869와 P. putida NCIMB 9866의 분해 plasmid pRA 4000과 pRA500으로부터 p-cresol mothylhydroxylase(PCMH)의 flavoprotein(pchF) 및 cytochrome(pCHC) subunit의 구조유전자를 sequencing하였다. 이 두개의 유전자의 DNA 및 아미노산의 염기 서열은 이미 발표를 하였다. 이 두 개의 유전자 이외에도 aldehyde dehydrogenase 유전자가 확인되었다. 이 aldehyde dehydrogenase는 p-hydroxybezaldehyde를 p-hydroxybenzonate로 전환시키는데 p-hydroxybezaldehyde는 P-cresol의 PCMH에 의한 분해 산물이다. 그 외에도 P. putida 9869의 protocatechuate 3,4-dioxigenase의 alpha(pcaG) 및 beta(pcaH) subunit 가 확인되었다. 반면에 P. putida 9866는 상응하는 영역에 이 유전자들을 가지고 있지 않았다(protocatechuate는 p-hydroxyben-zonate hydroxylase에 의해 p-hydroxybenzonate로부터 생성된다). pchC와 pchF사이에 open reading frame이 존재하며 9866로 부터는 추가로 다른 하나의 open reading frame (ORF')가 존재한다. 9869과 9866의 유전자 구조는 각각 dhal-pchC-ORF-pchF-pcaGH과 ORF'-dhal-pchC-ORF-pchF다.

• KSBB Journal
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• 제18권3호
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• pp.174-179
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• 2003

폐광지역으로부터 quinoline (2,3-benzopyridine)을 유일한 탄소원, 질소원, 그리고 에너지원으로 이용하는 세균 NFQ-1을 농화 배양기법을 통하여 분리하였다. 분리된 세균은 그람음성의 간균으로서 BIOLOG 시험을 통하여 Pseudomonas nitroreducens로 동정되었으며, 본 연구에서는 Pseudomonas sp. NFQ-1으로 명명하였다. Quinoline의 분해는 호기적 조건하의 B-배지에서 Pseudomonas sp. NFQ-1를 이용하여 실시되었다. 균주 NFQ-1 세균은 2.5 mM quinoline을 9시간 이내 완전히 분해하였다. 배양기간 동안 quinoline 분해의 중간대사산물인 2-hydroxyquinoline이 일시적으로 생성되었다가 배양기간 후반부에 사라졌다. 배양의 초기 pH 8.0은 6.8로 감소하다가 배양이 진행됨에 따라 7.0이 되었다. 대상 기질로서 quinoline의 농도가 증가함에 따라 생장곡선에서 유도기가 길어졌으며, 고농도의 quinoline (＞15 mM)은 주어진 조건에서 균주의 생장과 quinoline의 분해를 억제하였다. 부가 질소원으로 7.6 mM $(\textrm{NH}_{4})_{2}\textrm{SO}_{4}$의 첨가조건하에서 Pseudomonas sp. NFQ-1은 2-hydroxyquinoline, p-coumaric acid, benzoic acid, p-cresol, p-hydroxybenzoate, protocatechuic acid, catechol 등의 다양한 화합물을 이용할 수 있었으나 일부 화합물들 (예, 6-hydroxyquinoline, 8-hydroxyquinoline, coumarin, indoline, pyridine, lepidine, quinaldine, 4-bydroxycournarin, benzene, salicylic acid, phenol, phthalate)은 탄소원으로 이용되지 못하였다. euinoline의 분해경로를 규명하기 위하여 catechol dioxygenases의 specific activity를 결정하였다. 그 값은 catechol 1,2-dioxygenase에서 약 184.7 U/mg, 그리고 catechol 1,2-dioxygenase에서 약 33.19 U/mg이었다. 그 결과 균주 NFQ-1은 quinoline를 분해하기 위하여 주로 ortho-분해경로를, 그리고 부분적으로 meta-분해경로를 이용하는 것을 보여주었다.

• 한국지하수토양환경학회지:지하수토양환경
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• 제11권1호
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• pp.1-6
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• 2006

환경 내에서 생물학적 복원을 이해하기 위해서는 미생물 기능성 군집 및 활성을 분석하는 것은 필수적이다. 본 연구에서는 유류오염 토양의 미생물 군집을 모니터링하기 위하여 난분해성 물질의 생물학적 분해에 관여하는 100개의 알려진 대사경로 및 유전자를 기반으로 한 oligonucleotide microarray를 개발하였다. 본 연구에 사용된 microarray는 유류오염 분해 대사에 관련된 유전자를 진단하기 위한 15개의 고유한 probe를 포함하고 있다. 디자인된 probe의 hybridization specificity는 표준 균주, Pseudomonas aeruginosa KCTC1636을 이용하여 확인 하였으며, 유류오염토양 시료의 분석결과 alkane, naphthalene, biphenyl, pyrene(PAH ring-hydroxylating) 분해에 관련된 8개의 유전자 발현을 확인 하였다. 이러한 결과는 DNA microarray가 유류오염토양환경에서 생물학적 분해유전자 진단에 효과적으로 이용될 수 있을 뿐만 아니라 생물학적 복원의 가능성을 진단하기에도 적합한 기법이라는 것을 나타내고 있다.

• 한국생물공학회:학술대회논문집
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• 한국생물공학회 2000년도 추계학술발표대회 및 bio-venture fair
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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.

• 한국지하수토양환경학회:학술대회논문집
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• 한국지하수토양환경학회 2000년도 추계학술대회
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• pp.153-162
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• 2000

A field study was performed to test effectiveness of a bloluminescent genetically engineered microorganism (GEM) for bioremediation process monitoring and control. The study employed Pseudomonas fluorescens HK44 that was the first strain approved for field application in the U.S. for bioremediation purposes. HK44 contains lux gene fused within a naphthalene degradative pathway, allowing this GEM to bioluminesce as it degrades naphthalene as well as substituted naphthalenes and other polycyclic aromatic hydrocarbons (PAHs) , Results showed that HK44 was maintained in both PAH-contarninated and uncontaminated soils even 660 days after inoculation. HK44 was able to produce bioluminescence in response to PAHs in soil. Although effectiveness of chemical remediation was not assessed due to heterogeneous distribution of contaminants, decreased concentration of naphthalene was shown in the soils, Taken together, HK44 was useful for in situ bioremediation process monitoring and control. This work is so far the only field release of a GEM for bioremediation purposes.