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- Volume 58(1); January 2020
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Review
- [Minireview]Recent advances in genetic engineering tools based on synthetic biology
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Jun Ren , Jingyu Lee , Dokyun Na
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J. Microbiol. 2020;58(1):1-10. Published online January 2, 2020
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DOI: https://doi.org/10.1007/s12275-020-9334-x
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Abstract
- Genome-scale engineering is a crucial methodology to rationally
regulate microbiological system operations, leading
to expected biological behaviors or enhanced bioproduct yields.
Over the past decade, innovative genome modification
technologies have been developed for effectively regulating
and manipulating genes at the genome level. Here, we discuss
the current genome-scale engineering technologies used for
microbial engineering. Recently developed strategies, such
as clustered regularly interspaced short palindromic repeats
(CRISPR)-Cas9, multiplex automated genome engineering
(MAGE), promoter engineering, CRISPR-based regulations,
and synthetic small regulatory RNA (sRNA)-based knockdown,
are considered as powerful tools for genome-scale engineering
in microbiological systems. MAGE, which modifies
specific nucleotides of the genome sequence, is utilized as a
genome-editing tool. Contrastingly, synthetic sRNA, CRISPRi,
and CRISPRa are mainly used to regulate gene expression
without modifying the genome sequence. This review introduces
the recent genome-scale editing and regulating technologies
and their applications in metabolic engineering.
Journal Articles
- [Protocol]Rapid method for chromatin immunoprecipitation (ChIP) assay in a dimorphic fungus, Candida albicans
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Jueun Kim , Jung-Shin Lee
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J. Microbiol. 2020;58(1):11-16. Published online June 11, 2019
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DOI: https://doi.org/10.1007/s12275-020-9143-2
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Abstract
- A chromatin immunoprecipitation (ChIP) assay is a method
to identify how much a protein of interest binds to the DNA
region. This method is indispensable to study the mechanisms
of how the transcription factors or chromatin modifications
regulate the gene expression. Candida albicans is a dimorphic
pathogenic fungus, which can change its morphology very rapidly
from yeast to hypha in response to the environmental
signal. The morphological change of C. albicans is one of the
critical factors for its virulence. Therefore, it is necessary to
understand how to regulate the expression of genes for C.
albicans to change its morphology. One of the essential methods
for us to understand this regulation is a ChIP assay.
There have been many efforts to optimize the protocol to lower
the background signal and to analyze the results accurately
because a ChIP assay can provide very different results even
with slight differences in the experimental procedure. We
have optimized the rapid and efficient ChIP protocol so that
it could be applied equally for both yeast and hyphal forms of
C. albicans. Our method in this protocol is also comparatively
rapid to the method widely used. In this protocol, we described
our rapid method for the ChIP assay in C. albicans in
detail.
- Paraflavitalea soli gen. nov., sp. nov., isolated from greenhouse soil
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Jun Heo , Hang-Yeon Weon , Hayoung Cho , Seung-Beom Hong , Jeong-Seon Kim , Soo-Jin Kim , Soon-Wo Kwon
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J. Microbiol. 2020;58(1):17-23. Published online November 23, 2019
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DOI: https://doi.org/10.1007/s12275-020-9236-y
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7
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Abstract
- A bacterial strain designated 5GH32-13T was isolated from
greenhouse soil in Yongin-city, Republic of Korea. Cells were
Gram-stain-negative, strictly aerobic, motile rods of two different
shapes. The strain was catalase-positive and oxidasenegative.
Flexirubin-like pigments were not detected. β-Carotene
was produced. The strain grew in the range of 10–37°C
(optimum of 28–30°C) and pH 6–8 (optimum of pH 7) and
tolerated up to 1% (w/v) NaCl (optimum of 0%). According
to the 16S rRNA gene sequence comparison, strain 5GH32-
13T shared a sequence similarity of less than 96.0% with all
validly named taxa, having the highest sequence similarity
with Pseudoflavitalea soli KIS20-3T (95.8%), Pseudoflavitalea
rhizosphaerae T16R-265T (95.4%), Flavitalea gansuensis
JCN-23T (95.3%), Pseudobacter ginsenosidimutans Gsoil 221T
(95.3%), and Flavitalea populi HY-50RT (95.2%). A phylogenetic
tree showed that strain 5GH32-13T was not grouped
consistently into any specific genus. Its only polyamine was
homospermidine, and its major fatty acids (> 10% of total
fatty acids) were iso-C15:0, iso-C17:0 3-OH, and iso-C15:1 G. The
strain’s only respiratory quinone was MK-7, and its polar
lipids were phosphatidylethanolamine, one unidentified phospholipid,
six unidentified aminolipids and four unidentified
lipids. Its DNA G + C content was 47.5 mol%. The results
from chemotaxonomic, phenotypic and phylogenetic analyses
indicated that strain 5GH32-13T represents a novel species
of a novel genus of the family Chitinophagaceae, and the
name Paraflavitalea soli gen. nov., sp. nov. is proposed. The
type strain is 5GH32-13T (= KACC 17331T = JCM 33061T).
- Saccharibacillus brassicae sp. nov., an endophytic bacterium isolated from kimchi cabbage (Brassica rapa subsp. pekinensis) seeds
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Lingmin Jiang , Chan Ju Lim , Song-Gun Kim , Jae Cheol Jeong , Cha Young Kim , Dae-Hyuk Kim , Suk Weon Kim , Jiyoung Lee
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J. Microbiol. 2020;58(1):24-29. Published online November 25, 2019
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DOI: https://doi.org/10.1007/s12275-020-9346-6
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10
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Abstract
- Strain ATSA2T was isolated from surface-sterilized kimchi
cabbage (Brassica rapa subsp. pekinensis) seeds and represents
a novel bacterium based on the polyphasic taxonomic
approach. A phylogenetic analysis based on 16S rRNA gene
sequences showed that strain ATSA2T formed a lineage within
genus Saccharibacillus and was most closely to Saccharibacillus
deserti WLG055T (98.1%) and Saccharibacillus qingshengii
H6T (97.9%). The whole-genome of ATSA2T comprised
a 5,619,468 bp of circular chromosome with 58.4% G + C
content. The DNA-DNA relatedness values between strain
ATSA2T and its closely related type strains S. deserti WLJ055T
and S. qingshengii H6T were 26.0% and 24.0%, respectively.
Multiple gene clusters associated with plant growth promotion
activities (stress response, nitrogen and phosphorus metabolism,
and auxin biosynthesis) were annotated in the
genome. Strain ATSA2T was Gram-positive, endospore-forming,
facultatively anaerobic, and rod-shaped. It grew at
15–37°C (optimum 25°C), pH 6.0–10.0 (optimum pH 8.0),
and in the presence of 0–5% (w/v) NaCl (optimum 1%). The
major cellular fatty acids (> 10%) of strain ATSA2T were anteiso-
C15:0 and C16:0. MK-7 was the major isoprenoid quinone.
The major polar lipids present were diphosphatidylglycerol,
phosphatidylglycerol, and three unknown glycolipids. Based
on its phylogenetic, genomic, phenotypic, and chemotaxonomic
features, strain ATSA2T is proposed to represent a
novel species of genus Saccharibacillus, for which the name is
Saccharibacillus brassicae sp. nov. The type strain is ATSA2T
(KCTC 43072T = CCTCC AB 2019223T).
- Sterilization efficiency of pathogen-contaminated cottons in a laundry machine
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Yoonjae Shin , Jungha Park , Woojun Park
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J. Microbiol. 2020;58(1):30-38. Published online November 25, 2019
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DOI: https://doi.org/10.1007/s12275-020-9391-1
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8
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Abstract
- Pathogenic bacteria on abiotic surfaces such as fabrics, bedding,
patient wears, and surgical tools are known to increase
the risk of bacterial diseases in infants and the elderly. The
desiccation tolerance of bacteria affects their viability in cotton.
Thus, washing and drying machines are required to use
conditions that ensure the sterilization of bacteria in cotton.
The objective of this study is to determine the effects of various
sterilization conditions of washing and drying machines
on the survival of three pathogenic bacteria (Acinetobacter
baumannii, Pseudomonas aeruginosa, and Staphylococcus
aureus) commonly presented in contaminated cotton and two
non-pathogenic bacteria (Bacillus subtilis and Escherichia coli)
in cotton. High survival rates of A. baumannii and S. aureus
in desiccated cotton were observed based on scanning electron
microscope and replicate organism direct agar contact
assay. The survival rates of A. baumannii and S. aureus exposed
in desiccated cotton for 8 h were higher (14.4 and 5.0%,
respectively) than those of other bacteria (< 0.5%). All tested
bacteria were eradicated at low-temperature (< 40°C) washing
with activated oxygen bleach (AOB). However, bacterial
viability was shown in low temperature washing without AOB.
High-temperature (> 60°C) washing was required to achieve
99.9% of the sterilization rate in washing without AOB. The
sterilization rate was 93.2% using a drying machine at 60°C
for 4 h. This level of sterilization was insufficient in terms
of time and energy efficiency. High sterilization efficiency
(> 99.9%) at 75°C for 3 h using a drying machine was confirmed.
This study suggests standard conditions of drying
machines to remove bacterial contamination in cotton by
providing practical data.
- Identification and characterization of a novel light-induced promoter for recombinant protein production in Pleurotus ostreatus
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Chaomin Yin , Xiuzhi Fan , Kun Ma , Zheya Chen , Defang Shi , Fen Yao , Hong Gao , Aimin Ma
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J. Microbiol. 2020;58(1):39-45. Published online November 4, 2019
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DOI: https://doi.org/10.1007/s12275-020-9230-4
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Abstract
- A lectin gene (plectin) with a high level of expression was previously
identified by comparative transcriptome analysis of
Pleurotus ostreatus. In this study, we cloned a 733-bp DNA
fragment from the start codon of the plectin gene. Sequence
analysis showed that the plectin promoter (Plp) region contained
several eukaryotic transcription factor binding motifs,
such as the TATA-box, four possible CAAT-box, light responsiveness
motifs and MeJA-responsiveness motifs. To determine
whether the Plp promoter was a light-regulated promoter,
we constructed an expression vector with the fused
egfp-hph fragment under the control of the Plp promoter and
transformed P. ostreatus mycelia via Agrobacterium tumefaciens.
PCR and Southern blot analyses confirmed the Plpegfp-
hph fragment was integrated into the chromosomal DNA
of transformants. qRT-PCR, egfp visualization, and intracellular
egfp determination experiments showed the Plp promoter
could be a light-induced promoter that may be suitable
for P. ostreatus genetic engineering. This study lays the foundation
for gene homologous expression in P. ostreatus.
- Development of a neutralization assay based on the pseudotyped chikungunya virus of a Korean isolate
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Woo-Chang Chung , Kwang Yeon Hwang , Suk-Jo Kang , Jae-Ouk Kim , Moon Jung Song
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J. Microbiol. 2020;58(1):46-53. Published online November 25, 2019
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DOI: https://doi.org/10.1007/s12275-020-9384-0
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4
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Abstract
- The Chikungunya virus (CHIKV) belongs to the Alphavirus
genus of Togaviridae family and contains a positive-sense
single stranded RNA genome. Infection by this virus mainly
causes sudden high fever, rashes, headache, and severe joint
pain that can last for several months or years. CHIKV, a mosquito-
borne arbovirus, is considered a re-emerging pathogen
that has become one of the most pressing global health
concerns due to a rapid increase in epidemics. Because handling
of CHIKV is restricted to Biosafety Level 3 (BSL-3) facilities,
the evaluation of prophylactic vaccines or antivirals
has been substantially hampered. In this study, we first identified
the whole structural polyprotein sequence of a CHIKV
strain isolated in South Korea (KNIH/2009/77). Phylogenetic
analysis showed that this sequence clustered within the East/
Central/South African CHIKV genotype. Using this sequence
information, we constructed a CHIKV-pseudotyped lentivirus
expressing the structural polyprotein of the Korean
CHIKV isolate (CHIKVpseudo) and dual reporter genes of
green fluorescence protein and luciferase. We then developed
a pseudovirus-based neutralization assay (PBNA) using
CHIKVpseudo. Results from this assay compared to those
from the conventional plaque reduction neutralization test
showed that our PBNA was a reliable and rapid method to
evaluate the efficacy of neutralizing antibodies. More importantly,
the neutralizing activities of human sera from CHIKVinfected
individuals were quantitated by PBNA using CHIKVpseudo.
Taken together, these results suggest that our PBNA
for CHIKV may serve as a useful and safe method for testing
the neutralizing activity of antibodies against CHIKV
in BSL-2 facilities.
- Human cytomegalovirus IE86 protein aa 136–289 mediates STING degradation and blocks the cGAS-STING pathway
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Jun-Kyu Lee , Jung-Eun Kim , Bang Ju Park , Yoon-Jae Song
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J. Microbiol. 2020;58(1):54-60. Published online January 2, 2020
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DOI: https://doi.org/10.1007/s12275-020-9577-6
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9
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Abstract
- We previously reported that human cytomegalovirus (HCMV)
86 kDa immediate-early 2 gene product (IE86) promotes
proteasome-dependent degradation of STING. In the present
study, we determined the specific residues of IE86 responsible
for STING degradation using a STING-firefly luciferase
fusion protein expression system for quantitative measurement
of STING protein levels. IE86 amino acids (aa)
136–289 were sufficient to promote STING degradation and
further induced down-regulation of 23-cyclic GMP-AMP
(cGAMP)-mediated IFN-β promoter activation. Interestingly,
transactivation domains (TAD) of the IE86 protein located
at the N- and C-termini were required for down-regulation
of Toll/interleukin-1 receptor (TIR) domain-containing adaptor-
inducing interferon β (IFN-β) (TRIF)-mediated IFN-β-
and p65/RelA-induced NF-κB-dependent promoter activation
while amino acids (aa) 136–289 had no significant effects.
Our collective data suggest that the IE86 protein utilizes the
aa 136–289 region to promote STING degradation and inhibit
the cGAS-STING pathway.
- Repositioning of a mucolytic drug to a selective antibacterial against Vibrio cholerae
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In-Young Chung† , Bi-o Kim† , Hye-Jeong Jang† , You-Hee Cho
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J. Microbiol. 2020;58(1):61-66. Published online January 2, 2020
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DOI: https://doi.org/10.1007/s12275-020-9590-9
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Abstract
- Drug repositioning, the approach to explore existing drugs
for use in new therapeutic indications, has emerged as an alternative
drug development strategy. In this study, we found
that a mucolytic drug, N-acetylcysteine (NAC) showed antibacterial
activity against Vibrio cholerae. NAC can provide
acid stress that selectively inhibited the growth of V. cholerae
among other bacterial pathogens. To address the antibacterial
mechanism of NAC against V. cholerae, six acr (acetylcysteine-
resistant) mutants were isolated from 3,118 random
transposon insertion clones. The transposon insertion sites
of the six mutants were mapped at the five genes. All these
mutants did not display NAC resistance under acidic conditions,
despite their resistance to NAC under alkaline conditions,
indicating that the NAC resistance directed by the
acr mutations was independent of the unusual pH-sensitivity
of V. cholerae. Furthermore, all these mutants displayed
attenuated virulence and reduced biofilm formation, suggesting
that the acr genes are required for pathogenesis of
V. cholerae. This study validates the relevance of drug repositioning
for antibacterials with new modes of action and will
provide an insight into a novel antibacterial therapy for V.
cholerae infections to minimize side effects and resistance
emergence.
- Zur-regulated lipoprotein A contributes to the fitness of Acinetobacter baumannii
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Eun Kyung Lee , Chul Hee Choi , Man Hwan Oh
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J. Microbiol. 2020;58(1):67-77. Published online January 2, 2020
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DOI: https://doi.org/10.1007/s12275-020-9531-7
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Abstract
- Acinetobacter baumannii is a notorious nosocomial pathogen
that commonly infects severely ill patients. Zinc (Zn) is
essential to survive and adapt to different environment and
host niches in A. baumannii. Of the Zinc uptake regulator
(Zur)-regulated genes in A. baumannii, the A1S_3412 gene
encoding a Zur-regulated lipoprotein A (ZrlA) is critical for
cell envelope integrity and overcoming antibiotic exposure.
This study investigated whether ZrlA contributes to the fitness
of A. baumannii in vitro and in vivo using the wildtype
A. baumannii ATCC 17978, ΔzrlA mutant, and zrlAcomplemented
strains. The ΔzrlA mutant showed reduced
biofilm formation, surface motility, and adherence to and
invasion of epithelial cells compared to the wild-type strain.
In a mouse pneumonia model, the ΔzrlA mutant showed significantly
lower bacterial numbers in the blood than the wildtype
strain. These virulence traits were restored in the zrlAcomplemented
strain. Under static conditions, the expression
of csuCDE, which are involved in the chaperone-usher
pili assembly system, was significantly lower in the ΔzrlA
mutant than in the wild-type strain. Moreover, the expression
of the bfmR/S genes, which regulate the CsuA/BABCDE system,
was significantly lower in the ΔzrlA mutant under static
conditions than in the wild-type strain. Our results indicate
that the zrlA gene plays a role in the fitness of A. baumannii
by regulating the BfmR/S two-component system and subsequently
the CsuA/BABCDE chaperone-usher pili assembly
system, suggesting it as a potential target for anti-virulence
strategies against A. baumannii.
Published Erratums
- Erratum]Vibrio parahaemolyticus cqsA controls production of quorum sensing signal molecule 3-hydroxyundecan-4-one and regulates colony morphology
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Kui Wu , Yangyun Zheng , Qingping Wu , Haiying Chen , Songzhe Fu , Biao Kan , Yongyan Long , Xiansheng Ni , Junling Tu
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J. Microbiol. 2020;58(1):78-78.
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DOI: https://doi.org/10.1007/s12275-020-9721-3
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Abstract
- In the article by Wu et al. published in Journal of Microbiology 2019; 57, 1105–1114, the figure 8 is unfortunately incorrect.
The figure 8 should be corrected as below.
We apologize for any inconvenience that this may have caused.
- Erratum]Methylobacterium terrae sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil
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Jiyoun Kim , Geeta Chhetri , Inhyup Kim , Hyungdong Kim , Myung Kyum Kim , Taegun Seo
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J. Microbiol. 2020;58(1):79-79.
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DOI: https://doi.org/10.1007/s12275-020-9722-2
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Abstract
- In the article by Kim et al. published in Journal of Microbiology 2019; 57, 959–966, The NBRC accession number NBRC 112879T
on 33th line of 2nd paragraph in the section of ‘Description of Methylobacterium terrae sp. nov.’ on page 964 should be corrected
in NBRC 112873T.
The sentence in abstract should have read: The GenBank/EMBL/DDBJ accession numbers for the 16S rRNA gene and genome
sequences of the type strain 17Sr1-28T (= KCTC 52904T = NBRC 112873T) are KY939566 and CP029553, respectively.
We apologize for any inconvenience that this may have caused.
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