• Journal of Microbiology and Biotechnology
• /
• 제32권12호
• /
• pp.1527-1536
• /
• 2022

Escherichia coli can use allantoin as its sole nitrogen source under anaerobic conditions. The ureidoglycolate produced by double release of ammonia from allantoin can flow into either the glyoxylate shunt or further catabolic transcarbamoylation. Although the former pathway is well studied, the genes of the latter (catabolic) pathway are not known. In the catabolic pathway, ureidoglycolate is finally converted to carbamoyl phosphate (CP) and oxamate, and then CP is dephosphorylated to carbamate by a catabolic carbamate kinase (CK), whereby ATP is formed. We identified the ybcF gene in a gene cluster containing fdrA-ylbE-ylbF-ybcF that is located downstream of the allDCE-operon. Reverse transcription PCR of total mRNA confirmed that the genes fdrA, ylbE, ylbF, and ybcF are co-transcribed. Deletion of ybcF caused only a slight increase in metabolic flow into the glyoxylate pathway, probably because CP was used to de novo synthesize pyrimidine and arginine. The activity of the catabolic CK was analyzed using purified YbcF protein. The V_max is 1.82 U/mg YbcF for CP and 1.94 U/mg YbcF for ADP, and the K_M value is 0.47 mM for CP and 0.43 mM for ADP. With these results, it was experimentally revealed that the ybcF gene of E. coli encodes catabolic CK, which completes anaerobic allantoin degradation through substrate-level phosphorylation. Therefore, we suggest renaming the ybcF gene as allK.

• Macromolecular Research
• /
• 제16권1호
• /
• pp.1-5
• /
• 2008

The enzymatic hydrolysis of chitin has been studied for almost a century, and early work established that at least two enzymes are required, a chitinase that mainly yields the disaccharide N,N'-diacetylchitobiose, or $(GlcNAc)_2$, and a "chitobiase", or ${\beta}$-N-acetylglucosaminidase, which gives the final product G1cNAc. This pathway has not been completely identified but has remained the central concept for the chitin catabolism through the $20^{th}$ century1 including in marine bacteria. However, the chitin catabolic cascade is quite complex, as described in this review. This report describes three biologically functional genes involved in the chitin catabolic cascade of Vibrios in an attempt to better understand the metabolic pathway of chitin.

• Journal of Microbiology and Biotechnology
• /
• 제26권11호
• /
• pp.1943-1950
• /
• 2016

Polycyclic aromatic hydrocarbons (PAHs) are commonly present xenobiotics in natural and contaminated soils. We studied three (phenanthrene, naphthalene, and biphenyl) xenobiotics, catabolism, and associated proteins in Sphingobium chungbukense DJ77 by two-dimensional gel electrophoresis (2-DE) analysis. Comparative analysis of the growth-dependent 2-DE results revealed that the intensity of 10 protein spots changed identically upon exposure to the three xenobiotics. Among the upregulated proteins, five protein spots, which were putative dehydrogenase, dioxygenase, and hydrolase and involved in the catabolic pathway of xenobiotic degradation, were induced. Identification of these major multifunctional proteins allowed us to map the multiple catabolic pathway for phenanthrene, naphthalene, and biphenyl degradation. A part of the initial diverse catabolism was converged into the catechol degradation branch. Detection of intermediates from 2,3-dihydroxy-biphenyl degradation to pyruvate and acetyl-CoA production by LC/MS analysis showed that ring-cleavage products of PAHs entered the tricarboxylic acid cycle, and were mineralized in S. chungbukense DJ77. These results suggest that S. chungbukense DJ77 completely degrades a broad range of PAHs via a multiple catabolic pathway.

• 한국체육학회지인문사회과학편
• /
• 제55권6호
• /
• pp.691-700
• /
• 2016

본 연구의 목적은 장기간의 지구성 운동 또는 저항성 운동이 중년 흰쥐의 골격근 내 단백질 합성과 분해에 미치는 영향을 규명하는 것이다. 50 주령의 male Wistar rat 30 마리를 이용하여 3집단(좌업, 지구성 운동집단, 저항성 운동집단)으로 무선배정한 후 12 주간 처치를 실시하였다. 연구결과 12주간의 저항성운동은 중년 쥐의 족저근 내 Akt/mTOR 신호전달체계를 활성화시켰고, FoxO1/MuRF1 단백질 발현을 저해하였다. 지구성 운동은 mTOR 신호전달체계에는 영향을 미치지 않았으나 FoxO1/MuRF1 단백질 발현을 저해하였고, AMPK/PGC-1α 발현을 증가시켰다. 요약하면 12주간의 운동트레이닝은 중년 흰쥐의 골격근 내 단백질 동화/이화반응에 긍정적인 영향을 미쳤으며, 지구성 운동은 근단백질 이화반응의 저해를 통해서 노화근육의 단백질 균형에 영향을 미치는 것으로 나타났다. 이러한 결과를 통해서 근 손실에 따른 근 기능의 저하가 가시화되기 시작하는 중년을 대상으로 실시되는 운동처방 시 근 감소증 예방 및 치료를 위해 저항성 운동만이 아니라 중강도 이상의 지구성 운동도 유효할 것으로 생각된다.

• Journal of Microbiology and Biotechnology
• /
• 제28권7호
• /
• pp.1037-1051
• /
• 2018

The genus Rhodococcus is a phylogenetically and catabolically diverse group that has been isolated from diverse environments, including polar and alpine regions, for its versatile ability to degrade a wide variety of natural and synthetic organic compounds. Their metabolic capacity and diversity result from their diverse catabolic genes, which are believed to be obtained through frequent recombination events mediated by large catabolic plasmids. Many rhodococci have been used commercially for the biodegradation of environmental pollutants and for the biocatalytic production of high-value chemicals from low-value materials. Recent studies of their physiology, metabolism, and genome have broadened our knowledge regarding the diverse biotechnological applications that exploit their catabolic enzymes and pathways.

• Biotechnology and Bioprocess Engineering:BBE
• /
• 제5권6호
• /
• pp.449-455
• /
• 2000

Pseudomonas sp. strain DJ-12 is a bacterial isolate capable of degrading 4-chlorobiphenyl (4CBP) as a carbon and energy source. The catabolic degradation of 4CBP by the strain DJ-12 was studied along with the genetic organization of the genes responsible for the crucial steps of the catabolic degradation. The catabolic pathway was characterized as being conducted by consecutive reactions of the meta-cleavage of 4CBP, hydrolytic dechlorination of 4-chlorobenzoate (4CBA), hydroxylation of 4-hydroxybenzoate, and meta-cleavage of protocatechuate. The pcbC gene responsible for the meta-cleavage of 4CBP only showed a 30 to 40% homology in its deduced amino acid sequence compared to those of the corresponding genes from other strains. The amino acid sequence of 4CBA-CoA dechlorinase showed an 86% homology with that of Pseudomonas sp. CBS3, yet only a 50% homology with that of Arthrobacter spp. However, the fcb genes for the hydrolytic dechlorination of 4CBA in Pseudomonas sp. DJ-12 showed an uniquely different organization from those of CBS3 and other reported strains. Accordingly, these results indicate that strain DJ-12 can degrade 4CBA completely via meta-cleavage and hydrolytic dechlorination using enzymes that are uniquely different in their amino acid sequences from those of other bacterial strains with the same degradation activities.

• Asian-Australasian Journal of Animal Sciences
• /
• 제29권10호
• /
• pp.1515-1521
• /
• 2016

Anethole and garlic have an immune modulatory effects on avian coccidiosis, and these effects are correlated with gene expression changes in intestinal epithelial lymphocytes (IELs). In this study, we integrated gene expression datasets from two independent experiments and investigated gene expression profile changes by anethole and garlic respectively, and identified gene expression signatures, which are common targets of these herbs as they might be used for the evaluation of the effect of plant herbs on immunity toward avian coccidiosis. We identified 4,382 and 371 genes, which were differentially expressed in IELs of chickens supplemented with garlic and anethole respectively. The gene ontology (GO) term of differentially expressed genes (DEGs) from garlic treatment resulted in the biological processes (BPs) related to proteolysis, e.g., "modification-dependent protein catabolic process", "proteolysis involved in cellular protein catabolic process", "cellular protein catabolic process", "protein catabolic process", and "ubiquitin-dependent protein catabolic process". In GO analysis, one BP term, "Proteolysis", was obtained. Among DEGs, 300 genes were differentially regulated in response to both garlic and anethole, and 234 and 59 genes were either up- or down-regulated in supplementation with both herbs. Pathway analysis resulted in enrichment of the pathways related to digestion such as "Starch and sucrose metabolism" and "Insulin signaling pathway". Taken together, the results obtained in the present study could contribute to the effective development of evaluation system of plant herbs based on molecular signatures related with their immunological functions in chicken IELs.

• Journal of the Korean Wood Science and Technology
• /
• 제45권2호
• /
• pp.168-181
• /
• 2017

Whole cell of Phanerochaete chrysosporium with reducing agent was applied to verify the degradation mechanism of aromatic compounds derived from lignin precisely. Unlike the free-reducing agent experiment, various degraded products of aromatic compounds were detected under the fungal treatment. Our results suggested that demethoxylation, $C_{\alpha}$ oxidation and ring cleavage of aromatic compounds occurred under the catabolic system of P. chrysosporium. After that, degraded products stimulated the primary metabolism of fungus, so succinic acid was ultimately main degradation product of lignin derived-aromatic compounds. Especially, hydroquinone was detected as final intermediate in the degradation of aromatics and production of succinic acid. In conclusions, P. chrysosporium has an unique catabolic metabolism related to the production of succinic acid from lignin derived-aromatic compounds, which was meaningful in terms of lignin valorization.

• 미생물학회지
• /
• 제25권1호
• /
• pp.28-33
• /
• 1987

Celluloytic bacteria, -Gram positive, Gram negative and actionmycetes-were used to study their catabolic pathways of carbohydrate. It was found that Embden-Meyerhof-Parnas(EMP) pathway and hexose monophosphate(MHP) shunt were operated in Cellulomonase sp. CS1-1, C. flavigena, and Pseudomonas fluorescens subsp. cellulosa when they were cultured in a glucose containing medium, whilst gluconate was catabolised mainly via Entner-Doudoroff(ED) pathway, and to some extend through HMP shunt. Enzymes of ED pathway in the orgamisms were induced by gluconate. On the other hand Nocardia cellulans catabolised glucose and gluconate via EMP pathway and HMP shunt. The growth rate of N. Cellulans on gluconate were much slower than that on glucose.

• BMB Reports
• /
• 제52권6호
• /
• pp.373-378
• /
• 2019

The nucleotide-binding and oligomerization domain (NOD) is an innate pattern recognition receptor that recognizes pathogen- and damage-associated molecular patterns. The 29-kDa amino-terminal fibronectin fragment (29-kDa FN-f) is a matrix degradation product found in the synovial fluids of patients with osteoarthritis (OA). We investigated whether NOD2 was involved in 29-kDa FN-f-induced pro-catabolic gene expression in human chondrocytes. The expression of mRNA and protein was measured using quantitative real-time polymerase chain reaction (qrt-PCR) and Western blot analysis. Small interfering RNAs were used for knockdown of NOD2 and toll-like receptor 2 (TLR-2). An immunoprecipitation assay was performed to examine protein interactions. The NOD2 levels in human OA cartilage were much higher than in normal cartilage. NOD1 and NOD2 expression, as well as pro-inflammatory cytokines, including interleukin-1beta (IL-$1{\beta}$) and tumor necrosis factor-alpha (TNF-${\alpha}$), were upregulated by 29-kDa FN-f in human chondrocytes. NOD2 silencing showed that NOD2 was involved in the 29-kDa FN-f-induced expression of TLR-2. Expressions of IL-6, IL-8, matrix metalloproteinase (MMP)-1, -3, and -13 were also suppressed by TLR-2 knockdown. Furthermore, NOD2 and TLR-2 knockdown data demonstrated that both NOD2 and TLR-2 modulated the expressions of their adaptors, receptorinteracting protein 2 (RIP2) and myeloid differentiation 88, in 29-kDa FN-f-treated chondrocytes. 29-kDa FN-f enhanced the interaction of NOD2, RIP2 and transforming growth factor beta-activated kinase 1 (TAK1), an indispensable signaling intermediate in the TLR-2 signaling pathway, and activated nuclear factor-${\kappa}B$ (NF-${\kappa}B$), subsequently leading to increased expressions of pro-inflammatory cytokines and cartilage-degrading enzymes. These results demonstrate that 29-kDa FN-f modulated pro-catabolic responses via cross-regulation of NOD2 and TLR-2 signaling pathways.