Effect of Ammonium in Medium on Ansamitocin P-3 Production by Actinosynnema pretiosum

Jinxia Lin,Linquan Bai,Zixin Deng,Jian-Jiang Zhong 한국생물공학회 2010 Biotechnology and Bioprocess Engineering Vol.15 No.1

Ansamitocin P-3 (AP-3) is an antitumor agent produced by Actinosynnema pretiosum with a market demand for large and cheap supply, but its productivity is yet low. This work investigated the effects of ammonium in medium on the productivity, enzyme activities, and gene transcription for AP-3 biosynthesis. As observed, AP-3 production was depressed by medium ammonium, although the dry cell weight and the consumption of total sugar and isobutanol were not influenced obviously. From the onset of AP-3 accumulation, isobutyrate accumulation showed a different behavior in medium with or without ammonium. Isobutanol dehydrogenase activity was enhanced during production phase in medium with ammonium, but valine dehydrogenase activity was not substantially changed. qRT-PCR analysis revealed that transcriptional levels of structure genes asm14, asm24, asm43, and asm19 were down-regulated by medium ammonium. The transcription of regulatory gene asm2, asm29, and asm31 were slightly up-regulated while that of asm39 was down-regulated by ammonium. The results indicated that inhibition of AP-3 production by ammonium might be related to the AP-3 ester side chain supply and the repression of gene transcription responsible for 3-amino-5-hydroxybenzoic acid and methoxymalonyl-ACP biosynthesis. The information is useful for future AP-3 productivity enhancement.

Recent Advances in Cardiac Magnetic Resonance Imaging

Sang-Eun Lee,Christopher Nguyen,Yibin Xie,Zixin Deng,Zhengwei Zhou,Debiao Li,장혁재 대한심장학회 2019 Korean Circulation Journal Vol.49 No.2

Cardiac magnetic resonance (CMR) imaging provides accurate anatomic information and advanced soft contrast, making it the reference standard for assessing cardiac volumes and systolic function. In this review, we summarize the recent advances in CMR sequences. New technical development has widened the use of CMR imaging beyond the simple characterization of myocardial scars and assessment of contractility. These novel CMR sequences offer comprehensive assessments of coronary plaque characterization, myocardial fiber orientation, and even metabolic activity, and they can be readily applied in clinical settings. CMR imaging is able to provide new insights into understanding the pathophysiologic process of underlying cardiac disease, and it can help physicians choose the best treatment strategies. Although several limitations, including the high cost and time-consuming process, have limited the widespread clinical use of CMR imaging so far, recent advances in software and hardware technologies have made the future more promising.

New currents: 관상동맥 경화반(coronary plaque) 측정 시 사용되는 PC-VENC 기법을 이용한 MR-FFR(Fractional Flow Reserve) 측정 방법의 유용성

도지훈,이길백,박시섭,박순규,김윤국,임재식,Zixin Deng 대한자기공명기술학회 2016 대한자기공명기술학회지 Vol.26 No.-

목 적 : Fractional Flow Reserve(분획혈류예비력:FFR)은 관상동맥 질환이 있는 환자에서 중간 동맥 협착의 기능적 중요성을 평가하는 방법이다. 이는 관상동맥 협착 부위의 원위부와 근위부 정상혈관의 최대 혈류량의 비율(ΔP)을 말하며 카데터(catheter)가 혈관에 삽입되어 FFR 측정 위치까지 이동되는 방법이 사용된다. 그러나 이 방법은 침습적(invasive)이어서 환자가 불편하고, 신체에 손상을 줄 위험이 있어 비침습적(non-invasive) 방법으로 혈관의 병변(lesions)을 진단 및 평가하는 방법이 주목 받고 있다. 이중 MRI PC-VENC 기법을 이용한 MR-FFR이 그 대안으로 평가되고 있어 MR-FFR 사용에 대한 임상적 유용성을 알아보고자 한다. 대상 및 방법 : 2015년 8월부터 2015년 12월까지 관상동맥의 근위부에 의미 있는 동맥경화반이 관찰되어 FFR측정이 예정된 환자 5명과 건강한 성인 11명에 대해 MR-FFR 검사를 진행하였다. 3.0T MRI 장비를 사용하였고 코일은 phased-array body coil을 사용하였다. CT에서 재구성된 관상동맥 경화반의 범위를 참조하여 coronary LAD MPR(multi planner reconstruction) 영상을 만든 후 혈관의 정상 부위와 동맥 경화반 부위를 포함하여 scan 부위를 결정하여 PC-VENC 영상을 얻는다. 사용된 parameter는 VENC=35-65cm/s in all 3 directions, FA=15˚, cardiac phase=2(70ms/phase), in-plane resolution =0.5-0.6×0.5-0.6mm², slice thickness=3.2mm, scan time은 2-6 min/slice으로 설정하였다. 얻어진 VENC 영상에서 ΔPMR를 구하기위해 MATLAB을 사용하여 각 슬라이스에서 산출된 최대 속도를 적분하여 Navier-Stokes(NS) 공식을 이용하여 data를 산출하였다. 결 과 : Proximal left anterior descending coronary artery(pLAD)에서 stenosis의 area percentage가 증가 할수록 ΔPMR 값을 산출할 수 있는 mmHg 값도 높게 나타났다. 이는 stenosis 정도가 심할수록 분획혈유예비력(FFR) 값이 증가함을 의미하며 기존 FFR을 구하는 방식과 비교했을 때 환자 군(6.40±4.43mmHg), 정상군(0.62±0.49mmHg)에서 유의한 값(p<0.001)으로 나타났다. 기존 FFR 과 MR-FFR 간 결정계수 값은 R2=0.938으로 나타나 MR-FFR 기법과 기존 FFR 측정차가 크게 없음을 알 수 있었다. 결 론 : 현재까지 진행된 연구에서 관상동맥 경화반이 있는 혈관과 정상 혈관 모두에서 기존 FFR 값과 비교했을 때 ΔPMR 분석은 매우 유의한 값을 나타내고 있었다. 이에 따라 다른 종류의 침습적인 방법인 intravascular ultrasound(IVUS), optical coherence tomography (OCT) 등를 이용한 FFR 과 MR-FFR의 비교 연구가 진행되고 있으며 또한 공간적, 시간적 해상도 및 노이즈 감소의 관점에서 기술의 개선과 정확성을 향상시키기 위한 시퀀스 개발도 진행되고 있다. 따라서 비침습적이고 피폭이 없으며 환자에게 유용한 정보가 많은 MR-FFR 측정 방법은 앞으로 임상에서 유용하게 쓰여질 것으로 판단된다.

Advances in CRISPR-Cas systems for RNA targeting, tracking and editing

Wang, Fei,Wang, Lianrong,Zou, Xuan,Duan, Suling,Li, Zhiqiang,Deng, Zixin,Luo, Jie,Lee, Sang Yup,Chen, Shi Elsevier 2019 BIOTECHNOLOGY ADVANCES Vol.37 No.5

<P><B>Abstract</B></P> <P>Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) systems, especially type II (Cas9) systems, have been widely used in gene/genome targeting. Modifications of Cas9 enable these systems to become platforms for precise DNA manipulations. However, the utilization of CRISPR-Cas systems in RNA targeting remains preliminary. The discovery of type VI CRISPR-Cas systems (Cas13) shed light on RNA-guided RNA targeting. Cas13d, the smallest Cas13 protein, with a length of only ~930 amino acids, is a promising platform for RNA targeting compatible with viral delivery systems. Much effort has also been made to develop Cas9, Cas13a and Cas13b applications for RNA-guided RNA targeting. The discovery of new RNA-targeting CRISPR-Cas systems as well as the development of RNA-targeting platforms with Cas9 and Cas13 will promote RNA-targeting technology substantially. Here, we review new advances in RNA-targeting CRISPR-Cas systems as well as advances in applications of these systems in RNA targeting, tracking and editing. We also compare these Cas protein-based technologies with traditional technologies for RNA targeting, tracking and editing. Finally, we discuss remaining questions and prospects for the future.</P> <P><B>Highlights</B></P> <P> <UL> <LI> RNA targeting and editing are becoming increasingly important </LI> <LI> CRISPR-Cas systems are advancing for RNA targeting, tracking and editing </LI> <LI> The type VI CRISPR-Cas systems are useful for RNA-guided RNA targeting </LI> <LI> Use of Cas9 and Cas13 will advance RNA-targeting technologies </LI> </UL> </P>

Spot 42 RNA regulates putrescine catabolism in Escherichia coli by controlling the expression of puuE at the post-transcription level

Xin Sun,Ruyan Li,Guochen Wan,Wanli Peng,Shuangjun Lin,Zixin Deng,Rubing Liang 한국미생물학회 2021 The journal of microbiology Vol.59 No.2

Putrescine, a typical polyamine compound important for cell growth and stress resistance, can be utilized as an energy source. However, the regulation of its catabolism is unclear. Here the small RNA (sRNA) Spot 42, an essential regulator of carbon catabolite repression (CCR), was confirmed to participate in the post-transcriptional regulation of putrescine catabolism in Escherichia coli. Its encoding gene spf exclusively exists in the γ-proteobacteria and contains specific binding sites to the 5 -untranslated regions of the puuE gene, which encodes transaminase in the glutamylated putrescine pathway of putrescine catabolism converting γ-aminobutyrate (GABA) into succinate semialdehyde (SSA). The transcription of the spf gene was induced by glucose, inhibited by putrescine, and unaffected by PuuR, the repressor of puu genes. Excess Spot 42 repressed the expression of PuuE significantly in an antisense mechanism through the direct and specific base-pairing between the 51–57 nt of Spot 42 and the 5 - UTR of puuE. Interestingly, Spot 42 mainly influenced the stability of the puuCBE transcript. This work revealed the regulatory role of Spot 42 in putrescine catabolism, in the switch between favorable and non-favorable carbon source utilization, and in the balance of metabolism of carbon and nitrogen sources.

Structural analysis and biosynthetic engineering of a solubility-improved and less-hemolytic nystatin-like polyene in Pseudonocardia autotrophica.

Lee, Mi-Jin,Kong, Dekun,Han, Kyuboem,Sherman, David H,Bai, Linquan,Deng, Zixin,Lin, Shuangjun,Kim, Eung-Soo Springer International 2012 Applied microbiology and biotechnology Vol.95 No.1

<P>Polyene antibiotics such as nystatin are a large family of very valuable antifungal polyketide compounds typically produced by soil actinomycetes. Previously, using a polyene cytochrome P450 hydroxylase-specific genome screening strategy, Pseudonocardia autotrophica KCTC9441 was determined to contain an approximately 125.7-kb region of contiguous DNA with a total of 23 open reading frames, which are involved in the biosynthesis and regulation of a structurally unique polyene natural product named NPP. Here, we report the complete structure of NPP, which contains an aglycone identical to nystatin and harbors a unique di-sugar moiety, mycosaminyl-(α1-4)-N-acetyl-glucosamine. A mutant generated by inactivation of a sole glycosyltransferase gene (nppDI) within the npp gene cluster can be complemented in trans either by nppDI-encoded protein or by its nystatin counterpart, NysDI, suggesting that the two sugars might be attached by two different glycosyltransferases. Compared with nystatin (which bears a single sugar moiety), the di-sugar containing NPP exhibits approximately 300-fold higher water solubility and 10-fold reduced hemolytic activity, while retaining about 50% antifungal activity against Candida albicans. These characteristics reveal NPP as a promising candidate for further development into a pharmacokinetically improved, less-cytotoxic polyene antifungal antibiotic.</P>

Occurrence, evolution, and functions of DNA phosphorothioate epigenetics in bacteria

Tong, Tong,Chen, Si,Wang, Lianrong,Tang, You,Ryu, Jae Yong,Jiang, Susu,Wu, Xiaolin,Chen, Chao,Luo, Jie,Deng, Zixin,Li, Zhiqiang,Lee, Sang Yup,Chen, Shi National Academy of Sciences 2018 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.115 No.13

<P><B>Significance</B></P><P>Phosphorothioate (PT) modification of the DNA sugar-phosphate backbone is an important microbial epigenetic modification governed by DndABCDE, which together with DndFGH, constitutes a restriction-modification system. We show that up to 45% of 1,349 identified bacterial <I>dnd</I> systems exhibit the form of solitary <I>dndABCDE</I> without the restriction counterparts of <I>dndFGH</I>. The combination of epigenomics, transcriptome analysis, and metabolomics suggests that in addition to providing a genetic barrier against invasive DNA, PT modification is a versatile player involved in the epigenetic control of gene expression and the maintenance of cellular redox homeostasis. This finding provides evolutionary and functional insights into this unusual epigenetic modification. Our results imply that PT systems might evolve similar to other epigenetic modification systems with multiple cellular functions.</P><P>The chemical diversity of physiological DNA modifications has expanded with the identification of phosphorothioate (PT) modification in which the nonbridging oxygen in the sugar-phosphate backbone of DNA is replaced by sulfur. Together with DndFGH as cognate restriction enzymes, DNA PT modification, which is catalyzed by the DndABCDE proteins, functions as a bacterial restriction-modification (R-M) system that protects cells against invading foreign DNA. However, the occurrence of <I>dnd</I> systems across a large number of bacterial genomes and their functions other than R-M are poorly understood. Here, a genomic survey revealed the prevalence of bacterial <I>dnd</I> systems: 1,349 bacterial <I>dnd</I> systems were observed to occur sporadically across diverse phylogenetic groups, and nearly half of these occur in the form of a solitary <I>dndBCDE</I> gene cluster that lacks the <I>dndFGH</I> restriction counterparts. A phylogenetic analysis of 734 complete PT R-M pairs revealed the coevolution of M and R components, despite the observation that several PT R-M pairs appeared to be assembled from M and R parts acquired from distantly related organisms. Concurrent epigenomic analysis, transcriptome analysis, and metabolome characterization showed that a solitary PT modification contributed to the overall cellular redox state, the loss of which perturbed the cellular redox balance and induced <I>Pseudomonas fluorescens</I> to reconfigure its metabolism to fend off oxidative stress. An in vitro transcriptional assay revealed altered transcriptional efficiency in the presence of PT DNA modification, implicating its function in epigenetic regulation. These data suggest the versatility of PT in addition to its involvement in R-M protection.</P>