• Journal of Microbiology and Biotechnology
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• v.20 no.1
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• pp.45-53
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• 2010

We have developed an efficient and precise method for genome manipulations in Bacillus subtilis that allows rapid alteration of a gene sequence or multiple gene sequences without altering the chromosome in any other way. In our approach, the Escherichia coli toxin gene mazF, which was used as a counter-selectable marker, was placed under the control of a xylose-inducible expression system and associated with an antibiotic resistance gene to create a "mazF-cassette". A polymerase chain reaction (PCR)-generated fragment, consisting of two homology regions joined to the mazF-cassette, was integrated into the chromosome at the target locus by homologous recombination, using positive selection for antibiotic resistance. Then, the excision of the mazF-cassette from the chromosome by a single-crossover event between two short directly repeated (DR) sequences, included in the design of the PCR products, was achieved by counter-selection of mazF. We used this method efficiently and precisely to deliver a point mutation, to inactivate a specific gene, to delete a large genomic region, and to generate the in-frame deletion with minimal polar effects in the same background.

• Journal of Microbiology and Biotechnology
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• v.25 no.10
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• pp.1648-1652
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• 2015

Azaphilone polyketides are synthesized by iterative non-reducing fungal polyketide synthases (NR-fPKSs) with a C-terminus reductive domain (-R). Several azaphilone biosynthetic gene clusters contain a putative serine hydrolase gene; the Monascus azaphilone pigment (MAzP) gene cluster harbors mppD. The MAzP productivity was significantly reduced by a knockout of mppD, and the MAzP NR-fPKS-R gene (MpPKS5) generated its product in yeast only when co-expressed with mppD. Site-directed mutations of mppD for conserved Ser/Asp/His residues abolished the product formation from the MpPKS5/mppD co-expression. MppD and its homologs are thus proposed as a new protein factor involved in the product formation of NR-fPKS-R.

• Genomics & Informatics
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• v.21 no.1
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• pp.7.1-7.11
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• 2023

The gram-positive bacterium Listeria monocytogenes is an important foodborne intracellular pathogen that is widespread in the environment. The functions of hypothetical proteins (HP) from various pathogenic bacteria have been successfully annotated using a variety of bioinformatics strategies. In this study, a HP Imo0888 (NP_464414.1) from the Listeria monocytogenes EGD-e strain was annotated using several bioinformatics tools. Various techniques, including CELLO, PSORTb, and SOSUIGramN, identified the candidate protein as cytoplasmic. Domain and motif analysis revealed that the target protein is a PemK/MazF-like toxin protein of the type II toxin-antitoxin system (TAS) which was consistent with BLASTp analysis. Through secondary structure analysis, we found the random coil to be the most frequent. The Alpha Fold 2 Protein Structure Prediction Database was used to determine the three-dimensional (3D) structure of the HP using the template structure of a type II TAS PemK/MazF family toxin protein (DB ID_AFDB: A0A4B9HQB9) with 99.1% sequence identity. Various quality evaluation tools, such as PROCHECK, ERRAT, Verify 3D, and QMEAN were used to validate the 3D structure. Following the YASARA energy minimization method, the target protein's 3D structure became more stable. The active site of the developed 3D structure was determined by the CASTp server. Most pathogens that harbor TAS create a crucial risk to human health. Our aim to annotate the HP Imo088 found in Listeria could offer a chance to understand bacterial pathogenicity and identify a number of potential targets for drug development.

• Korean Journal of Pharmacognosy
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• v.7 no.3
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• pp.199-208
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• 1976

저자(著者)등은 1976년(年) 7월(月) 17일(日)부터 동년(同年) 11월(月) 14일(日)까지의 기간(期間)동안 서울과 경기도내(內) 5개지역(서울 : 관악산, 경기도 : 수원, 광릉, 갈매리, 오산리)으로부터 100여 종(種)의 한국산(韓國産) 고등균류(高等菌類)를 채집하였으며, 이중 31종(種)을 분류(分類) 확인(確認)하였다. 분류(分類)된 31종중(種中) 9종(種) 즉 (1) Scutellinia scutellata $(St.\;A_{MANS})$ $L_{AM}$ (2) Peziza vesiculsa $F_{R}.$ (3) Helvella atra $F_{R}.$ (4) Neobulgaria pura $(P_{ERS}.)$ $P_{ETRAK}$ (5) Trametes coccinea $F_{R}.$ (6) Amanita melleiceps $H_{ONGO}$ (7) Cotylidia burtina $(P_{T}.)$ $I_{MAZ}.$ (8) Sarcodontia copelandii $(P_{AT}.)$ $I_{MAZ}.$ comb nov. (9) Sphaerobolus stellatus $P_{ERS}.$은 한국 미기록종(種)이며, 이외에 2종(種) (1) Lycoperdon D.M.C-2 및 (2) Tuber melanosporum도 잠정적으로 미기록종(種)이라 사료된다. 한편 Neobulgaria pira $P_{ERS}.$가 속해있는 과(科)인 Helotiaceae와 Sphaerobolus stellatus $P_{ERS}.$가 속해있는 과(科)인 Sphaerobolaceae는 각각(各各) 한국 미기록과(科)이다. 이에 저자등은 이들에게 신칭을 붙여 각각(各各)의 외부(外部)형태와 현미경적 특징에 대하여 기술하고, 이들의 사진과 함께 보고 하는 바이다.