An annotated database of Arabidopsis mutants of acyl lipid metabolism

McGlew, Kathleen,Shaw, Vincent,Zhang, Meng,Kim, Ryeo Jin,Yang, Weili,Shorrosh, Basil,Suh, Mi Chung,Ohlrogge, John Springer Berlin Heidelberg 2015 Plant cell reports Vol.34 No.4

<P><B><B><I>Key message</I></B></B></P><P><B>We have constructed and annotated a web-based database of over 280 Arabidopsis genes that have characterized mutants associated with Arabidopsis acyl lipid metabolism.</B></P><P><B>Abstract</B></P><P>Mutants have played a fundamental role in gene discovery and in understanding the function of genes involved in plant acyl lipid metabolism. The first mutant in Arabidopsis lipid metabolism (<I>fad4</I>) was described in 1985. Since that time, characterization of mutants in more than 280 genes associated with acyl lipid metabolism has been reported. This review provides a brief background and history on identification of mutants in acyl lipid metabolism, an analysis of the distribution of mutants in different areas of acyl lipid metabolism and presents an annotated database (ARALIPmutantDB) of these mutants. The database provides information on the phenotypes of mutants, pathways and enzymes/proteins associated with the mutants, and allows rapid access via hyperlinks to summaries of information about each mutant and to literature that provides information on the lipid composition of the mutants. In addition, the database of mutants is integrated within the ARALIP plant acyl lipid metabolism website (http://aralip.plantbiology.msu.edu) so that information on mutants is displayed on and can be accessed from metabolic pathway maps. Mutants for at least 30 % of the genes in the database have multiple names, which have been compiled here to reduce ambiguities in searches for information. The database should also provide a tool for exploring the relationships between mutants in acyl lipid-related genes and their lipid phenotypes and point to opportunities for further research.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1007/s00299-014-1710-8) contains supplementary material, which is available to authorized users.</P>

Characterization of Nonhypersensitive Mutant and Nonpathogenic Mutant of Xanthomonas campestris pv. campestris

Kim, Mee Hyang,Bae, Dong Won,Lee, Jun Teak,Yun, Han Dae,Kim, Hee Kyu 경상대학교 유전공학연구소 1997 遺傳工學硏究所報 Vol.16 No.-

십자화과 식물에 검은썩음병을 일으키는 Xanthomonas campestris pv. campestris에 대하여 담배 18품종중 가장 과민반응을 강하게 나타내는 품종(Nicotiana tabacum cv. TC500)을 과민반응 비기주식물로 선발하였다. NTG 돌연변이를 실시하여 얻은 약 4,500개의 mutants들을 10^8 cells/ml의 농도로 주사 접종하여 비기주식물인 담배 잎에서 과민반응을 유도하지 않은 HR^- mutants(XHN 514-774, XHN620-831)를 선발하였고, 기주식물인 양배추 잎에서 병원성을 나타내지 않는 비병원성변이주(XPN 1001)를 선발하였다. HR^- mutants를 기주식물인 양배추에 접종한 결과 병원성을 나타내었고, nonpathogenic mutants를 비기주식물인 담배 잎에 접종한 결과 과민반응을 유도하였다. 담배 잎에서HR^- mutants 와wild type의 population을 조사한 결과 wild type 은 24시간 이후 급격히 감소하는 반면, HR^- mutants는 일정수준을 유지하였으나 72시간 이후에 감소하였다. 그리고 mutants들의protease, cellulase,amylase,polygalacturonate lyase분비여부를 조사한 결과 wild type과 비슷하게 분비하였다. We have screened hypersensitive responses of 18 cultivars of Nicotiana tabacum to Xanthomonas campestris pv. campestris. TC500 cultivar produced the most strong hypersensitive mutants (HR) to Xanthomonas campestris pv. campestris. By NTG mutagenesis, nonhypersensitive mutants (XHN 514-774, XHN620-831) were generated, which dose not induce hypersensitive response on tobacco leaves(Nicotiana tabacum cv. TC500). Also non-pathogenic mutant(XPN 1001), which does not incite any of the black rot symptoms on leaves was generated. We observed that HR^- mutants were still pathogenic on cabbage leaves. The in planta growth of wild type and HR^- mutants were examined for up to 120 hrs after inoculation: population of wild type strain increased to more than 10^8 in 24 hrs, but rapidly declined thereafter; HR^- mutants increased to more than 10^6 in 48 hrs after inoculation but subsequently stabilized and slowly decreased. We observed that wild type and these mutants produced similar amounts of degardative enzymes such as protease, pectate lyase, cellulase and amylase.

Characterization of Nonhypersensitive Mutant and Nonpathogenic Mutant of Xanthomonas campestris pv. campestris

Mee Hyang Kim(김미향),Dong Won Bae(배동원),Jun Teak Lee(이준택),Han Dae Yun(윤한대),Hee Kyu Kim(김희규) 한국식물병리학회 1997 Plant Pathology Journal Vol.13 No.3

Saccharomyces cerevisiae deletion mutant의 세라마이드 생합성

김세경(Se Kyung Kim),노용호(Yong Ho Noh),윤현식(Hyun Shik Yun) 한국생물공학회 2009 KSBB Journal Vol.24 No.1

Saccharomyces cerevisiae의 deletion mutant를 이용하여 ydc1, ypc1, scs7, sur1, csg2, ipt1, lcb4, lcb5, dpl1의 deletion이 세라마이드의 생산에 미치는 영향을 고찰하였다. 세라마이드는 ELSD가 연결된 HPLC를 통하여 분석하였으며 △ydc1 mutant의 세라마이드 생산량이 6 mg ceramide/g cell로 최대량을 나타내었으며 △sur1 mutant, △lcb5 mutant, △dpl1 mutant의 경우 control로 사용한 BY4742와 비슷한 세라마이드 생산량을 나타내었고, 그 외 △ypc1 mutant, △scs7 mutant, △csg2 mutant, △ipt1 mutant, △lcb4 mutant는 BY4742보다 낮은 세라마이드 생산량을 나타내었다. Ceramide is important not only for the maintenance of the barrier function of the skin but also for the water-binding capacity of the stratum corneum. Though the effectiveness of ceramide is not understood fully, ceramide has become a widely used ingredient in cosmetic and pharmaceutical industries. However, ceramide production from Saccharomyces cerevisiae has not been widely studied and the quantity are very low. Gene deletion in the cell is used frequently to investigate the function of gene and verification research of drug target. Specially, deletion mutant library is useful for a large amount functional analysis of gene. In this study, deletion mutants of genes on the metabolic pathway of ceramide synthesis in S. cerevisiae were grown in a batch culture and the cellular content of ceramide was measured. The ceramide content was highest in Δydc1 mutant and 6 mg ceramide/g cell was obtained.

Characterization of Complemented Mutants in Pseudomonas fluorescens and Cloning of the DNA Region Related in Antibiotic Biosynthesis

Young Kim(김영),Yong Sup Cho(조용섭) 한국식물병리학회 1994 Plant Pathology Journal Vol.10 No.3

Vibrio fluvialis의 Oligopeptide Permease Gene 결손에 의한 생육과 Biofilm 생산의 비교

이은미,안선희,공인수,Lee, Eun Mi,Ahn, Sun Hee,Kong, In Soo 한국해양바이오학회 2006 한국해양바이오학회지 Vol.1 No.2

Vibrio fluvialis의 opp gene cluster내에 존재하는 oppABCDF 유전자를 allelic exchange 방법에 의해서 각각의 유전자가 deletion된 mutant를 제조하였다. 각각의 유전자가 deletion된 mutant의 확인은 PCR과 Southern hybridization으로 결정하였다. 각 mutant들을 BHI 배지에서 생육을 비교한 결과 배양후 4시간 이전까지는 wild strain이 모든 mutant들에 비해서 생육이 좋았으나 4시간 이후부터는 같은 수준의 생육을 보여주었다. Biofilm 생산을 비교한 결과 ${\Delta}oppA$ mutant에서 가장 높은 생산성을 보여주었다. ${\Delta}oppC,D,F$ mutant들의 biofilm 생산은 ${\Delta}oppA$ mutant 보다는 낮았으나 wild strain보다는 높은 biofilm 생산성을 보여주었다. Various ${\Delta}opp$ mutants of Vibrio fluvialis were constructed by allelic exchange method. The mutants occurred in target genes were confirmed by PCR and Southern hybridization analyses. After the exact mutants were identified, cell growth and biofilm production were examined using the respective mutants. The growth of wild strain was more rapid than mutants within 4hr incubation. Thereafter, the growth of wild strain and mutants reached to same level. When the productivities of wild strain and mutants were examined, ${\Delta}oppA$ mutant showed the highest productivity. Though ${\Delta}oppC,D$ and F mutants produced the lower production than that of ${\Delta}oppA$ mutant, the productivities of those mutants were much higher than that of wild strain.

부가 탄소원이 Bacillus sp. 79-23의 변이주에서 셀룰라제의 생산성에 미치는 영향

윤기홍,신인경 우송대학교 부설 산업연구원 1999 산업연구 Vol.1 No.2

Bacillus sp. 79-23의 포자를 감마선으로 조사하여 얻은 7개 변이주의 CMCase 생산성에 미치는 탄소원의 영향을 모균주와 비교 분석하였다. LB 배지에 부가탄소원으로 glucose, xylose, maltose, lactose, CMC, starch, 볏짚, 밀기울을 첨가하여 배양한 후 배양상등액에 존재하는 CMCase의 활성을 측정한 결과 변이주의 효소생산성은 탄소원에 의해 모균주와 유사한 영향을 받는 것으로 나타났으나 변이주에 따라 약간의 차이는 존재하였다. 특히 xylose와 볏짚에 의한 변이주들의 효소생산량간에 차이가 나타났다. 대부분 변이주의 성장정도도 모 균주와 유사한 것으로 확인되었으며 효서는 성장과 연계되어 생산되었다. 그러나 변이주 48에 잇어서 탄소원에 의한 효소 생산성의 영향은 유사하지만 모균주나 다른 변이주에 비해 성장정도가 매우 낮으며 효소 생산량도 다른 균주에 비해 낮은 것으로 밝혀졌다. 이로보아 변이주에서의 유전자 변이는 서로 다른 지역에서 일어난 것으로 생각된다. 한편 CMCase를 코드하는 유전자를 포함한 부위가 모든 변이주와 모균주의 총 유전체 DNA로부터 동일한 primers로 증폭되었으며 그 크기가 전기영동상에서 동일한 것으로 확인되었다. 그러므로 감마선 조사에 의해 얻어진 변이주는 CMCase 유전자 부위에 삽입이나 결손등의 변이가 일어나지 않은 것으로 판단된다. In seven mutant strains which were derived from Bacillus sp. 79-23 by gamma-irradiation of the parental spores, effects of carbon sources were investigated on carboxymethylcellulase (CMCase) production. By measuring the CMCase activity in the supernatants of bacterial cultures which were grown in LB medium containing glucose, xylose, maltose, lactose, carboxymethylcellulose, strach, rice straw, and wheat bran as additional carbon sources, it was identified that seven mutants were comparable to the parent strain. Among the additional carbon sources, xylose and reice straw affected differently the CMCase production according to the mutant stains. It was found that the enzyme production was in association with the growth of parent and mutant strains. Growth of mutant strains reached the level of parent strains. Growth of mutant strains reached the level of parent strain except mutant 47. Mutant strain 48 was poorly grown and produced CMCase less than other mutant strains. As the results of them, it was suggested that mutagenesis of the mutant strains occurred in different positions of their chromosomal DNAs, respectively. DNA fragments with an identical molecular size of 1.6 kb corresponding to the gene encording a Bacillus sp. 79-23 CMCase were amplified from genomic DNAs of all mutants and parent strain using same primers by polymerase chain reaction, proposing that mutations did not be cuased by the insertion and deletion in the structural CMcase genes of the seven mutants.

Regulation of Ethylene Biosynthesis in Phytochrome Mutants of the Arabidopsis Root

Ji Hye Park(박지혜),Soon Young Kim(김순영) 한국생명과학회 2012 생명과학회지 Vol.22 No.4

식물생장과 발달에 중요한 역할을 하는 phytochrome이 ethylene 생합성에 미치는 영향을 조사하기 위하여 여러 빛 조건에서 키운 phyA, phyB, phyAB에서 ethylene 생합성과 생합성에 관여하는 enzyme activity를 측정하였다. White light에서 키웠을 때 모든 mutant에서 ethylene 생합성이 감소되었다. 특히 double mutant에서는 wild type과 비교하여 37%가 감소하였다. Dark에서 키웠을 때에는 wild type만 감소하였고, mutant에서는 감소효과가 나타나지 않았다. Red light에서 키웠을 때 double mutant에서 급격한 감소가 일어났다. Far-red light 에서 키웠을 때는 phyB만 감소가 일어나지 않았다. Ethylene 생합성에 관여하는 enzyme인 ACO 활성 패턴과는 달리ACS 활성 패턴은 ethylene 생성 패턴과 유사하게 나타났다. 이 결과를 바탕으로 ethylene 생합성에는 phytochromeA와 B 모두 중요한 작용을 하며 특히 Pr 형태의 phytochrome이 ethylene 생성량을 조절한다는 것을 제시한다. 또한 phytochrome은 ethylene 생합성 단계에서 AdoMet가 ACC로 전환되는 단계에서 조절하는 것을 제시한다. In order to investigate the effect of phytochromes on the regulation of ethylene biosynthesis, we measured the ethylene production and the activities of enzymes involved in ethylene biosynthesis using phytochrome mutants such as phyA, phyB, and phyAB of Arabidopsis. The ethylene production was decreased in mutants grown in white light. In particular, double mutants showed a 37% decrease compared to the wild type in ethylene production. When Arabidopsis roots were grown in the dark, mutants did not show a decrease in ethylene production; however, production was significantly decreased in the double mutant grown in red light. Only phyB did not show the decrease in the ethylene production in far-red light. Unlike the ACO activities, the ACS activities of mutants showed the same pattern as the ethylene production under several light conditions. The results of ACS activities confirmed the expression of the ACS gene by RT-PCR analysis. The decrease of ethylene production in mutants was due to the lower activity of ACC synthase, which converts the S-adenosyl-L-methionine (AdoMet) to 1-aminocyclopropane-1-carboxylic acid (ACC), the precursor of ethylene. These results suggested that both phytochrome A and B play an important role in the regulation of ethylene biosynthesis in Arabidopsis roots in the conversion step of AdoMet to ACC, which is regulated by ACS.

Introduction, Development, and Characterization of Supernodulating Soybean Mutant -Nitrate Inhibition of Nodulation and Nitrogen Fixation in Supernodulating Soybean Mutant-

Lee, Hong-Suk,Lee, Suk-Ha The Korean Society of Crop Science 1998 Korean journal of crop science Vol.43 No.1

Inhibition of nodule formation and nitrogen fixation by soil nitrogen, primarily nitrate, is well known in legume plants. The present study was undertaken to evaluate the effect of ${NO_3}^-$ on the nodulation, nitrogenase activity, and growth of supernodulating soybean mutant and its wild type. A greenhouse study was conducted to compare two of supernodulating mutants, 'SS2-2' and 'nts 382', with the normal nodulating cultivar 'Sinpaldalkong 2' when grown in a 1-l styroform cup filled with sand, and fertilized with five levels of ${NO_3}^-$ (0, 2, 4, 8, and 12 mM). During the growth period, each plant was supplied two or three times a week with 50 mL of nutrient solution. Supernodulating soybean mutants, SS2-2 and nts 382, showed more nodules and nodule mass, and greater $C_2\;H_2$ activity than the wild type, Sinpaldalkong 2, regardless of the level of exogeneous nitrogen supply. On the other hand, total dry weight of SS2-2 mutant, which was smaller than Sinpaldalkong 2, did not respond to the various ${NO_3}^-$-N levels. This suggested that supernodulating SS2-2 mutant could maintain fairly high total dry weight at the low ${NO_3}^-$-N level, even in the absence of exogeneous ${NO_3}^-$-N in the nutrient solution. From the reduced top growth and high nitrogen fixing ability of supernodulating mutants, it was surmised that supernodulating mutant could potentially protect agricultural environments from pollution through the reduction in nitrogen fertilization as well as maintain fairly high yield with increasing planting density.

B형 만성 간질환 환자들의 간조직내 HBV precore 돌연변이종에 관한 관찰

정정명,이상욱,김석주,하희근,김민기,박영홍 인제대학교 1998 仁濟醫學 Vol.19 No.1

HBV의 C 유전자 영역에는 두 개의 개시 codon이 있는데 앞쪽 개시 codon에서 HBeAg이 합성되고 뒤쪽 개시 codon으로부터 HBcAg가 합성된다. 그리고 이 두 개의 개시 codon 사이를 precore 유전자 영역이라 명명하는데 이 부위에서 HBeAg의 합성과 분비를 나타낸다. 따라서 이 precore 유전자 영역에 변이종이 발생되면 이 영역이 비활성화되고 결과적으로 HBV의 증식은 지속되나 HBeAg의 생산이나 표현은 되지 않을 가능성이 있다. 그리고 이러한 사실은 실제 anti-HBe가 양성인데도, 혈중에 HBV DNA가 고농도로 존재하며, 비전형적인 간염을 나타낸 환자들에서 precore 영역의 염기서열을 분석한 결과 이 유전자 부위에 변이가 있음이 증명되고 있다. HBV precore 변이증에 대한 연구는 현재 세계적으로 진행되고 있으나 아직도 질병과의 관계는 확실히 알려져 있지 않다. 따라서. 저자들은 우리나라의 HBV precore 변이종의 양상과 질병과의 관계를 파악하기 위하여 본 연구를 시행하였다. 그 결과 우리나라의 경우 HBV precore 변이종의 양상은 첫째, 염기서열 1896의 G가 A로 치환된 변이종이 주종을 나타내고 있으며. 둘째, 이 1896변이종은 precore의 다른 유전자 부위에 변이를 동반하는 경향이 높으며, 셋째, HBV precore 변이종은 모든 B형 만성 간질환에서 발생될 수 있을 것으로 사료되나. 간세포암이나 간경변증과 같은 중한 간질환과의 관계에 대해서는 향후 계속적인 연구가 필요할 것으로 사료된다. Aims : In order to determine the relationship between the HBV precore mutant and the severity of liver disease in Korea, we performed liver biopsies in patients with HBV associat ed chronic liver disease and compared the types of HBV precore mutation and histologic findings in the same limier tissue. Method : HBV DNA in liver tissues was amplified by polymerase chain reaction(PCR). The precore mutants were detected by the direct sequencing for them. Results : 1.Total of 59 cases (43 males, 16 females) were studied and the age ranged from 19 to 72 years with a mean age of 36.3 years. The subjects were composed of 26 cases with chronic active hepatitis, 8 with chronic persistent hepatitis, 3 wish chronic lobular hepatitis, 9 with minimal changes, 5 with cirrhosis and 8 with hepatocellular carcinoma. 2.The HBV precore mutants were found in 27 cases(45.8%) and all mutations were G to A changes at nucleotide 1896, creating a stop codon at codon 28. However, 15 cases among 27 mutants of 1896 also had mutation at different precore regions ; one case at 1937, 3 cases at 1840, 6 cases at 1846, 2 cases at 1856 and 3 cases at 1899. respectively. Also, all HBV precore mutants were combined with wild type HBV sequence. 3.The relationship between HBV precore mutants and HBeAg status revealed that 9 cases from 31 HBeAg positive (29.0%), and 18 from 28 HBeAg negative or anti-HBe positive (64.3%) were mutants. More frequent mutations were observed in HBeAg negative cases. 4.In analysis of the types of mutants and histopathological findings of liver disease, 16 among 26 chronic active hepatitis (46.2%), 1 among 8 chronic persistent hepatitis (12.5%), 1 among 3 chronic lobular hepatitis (33.3%), 5 among 9 minimal changes (55.6%), 2 among 5 liver cirrhosis (40.0%) and 6 among 8 hepatocellular carcinoma (75.0%) showed precore mutations. Conclusion : The patterns of HBV precore mutants in Korea could be summarized as follows. Firstly, mast of the mutations were composed of G to A change at nucleotide 1896. Secondly. most of the mutants at nucleotide 1896 are associated with simultaneous mutations at another precore regions. Thirdly, although precore mutations can happen in any histologic status of chronic liver diseases, its possible relationships with serious conditions, such as cirrhosis and hepatocellular carcinoma, need further investigation.