Journal of Microbiology

Review

Signification and Application of Mutator and Antimutator Phenotype‑Induced Genetic Variations in Evolutionary Adaptation and Cancer Therapeutics: Woo-Hyun Chung; J. Microbiol. 2023;61(12):1013-1024. Published online December 15, 2023; DOI: https://doi.org/10.1007/s12275-023-00091-z

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Abstract: Mutations present a dichotomy in their implications for cellular processes. They primarily arise from DNA replication errors or damage repair processes induced by environmental challenges. Cumulative mutations underlie genetic variations and drive evolution, yet also contribute to degenerative diseases such as cancer and aging. The mutator phenotype elucidates the heightened mutation rates observed in malignant tumors. Evolutionary adaptation, analogous to bacterial and eukaryotic systems, manifests through mutator phenotypes during changing environmental conditions, highlighting the delicate balance between advantageous mutations and their potentially detrimental consequences. Leveraging the genetic tractability of Saccharomyces cerevisiae offers unique insights into mutator phenotypes and genome instability akin to human cancers. Innovative reporter assays in yeast model organisms enable the detection of diverse genome alterations, aiding a comprehensive analysis of mutator phenotypes. Despite significant advancements, our understanding of the intricate mechanisms governing spontaneous mutation rates and preserving genetic integrity remains incomplete. This review outlines various cellular pathways affecting mutation rates and explores the role of mutator genes and mutation-derived phenotypes, particularly prevalent in malignant tumor cells. An in-depth comprehension of mutator and antimutator activities in yeast and higher eukaryotes holds promise for effective cancer control strategies.

Journal Articles

Characterization of Marinilongibacter aquaticus gen. nov., sp. nov., a unique marine bacterium harboring four CRISPR-Cas systems in the phylum Bacteroidota: Dao-Feng Zhang , Yu-Fang Yao , Hua-Peng Xue , Zi-Yue Fu , Xiao-Mei Zhang , Zongze Shao; J. Microbiol. 2022;60(9):905-915. Published online August 1, 2022; DOI: https://doi.org/10.1007/s12275-022-2102-3

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5 Citations

Abstract: A novel bacterium, designated YYF0007T, was isolated from an agar-degrading co-culture. The strain was found harboring four CRISPR-Cas systems of two classes in the chromosome and subsequently subjected to a study on polyphasic taxonomy. Pairwise analyses of the 16S rRNA gene sequences indicated that strain YYF0007T had highest 16S rRNA gene sequence similarity (92.2%) to Jiulongibacter sediminis JN- 14-9T. The phylogenomic trees based on the 16S rRNA gene and 269 single-copy orthologous gene clusters (OCs) indicated that strain YYF0007T should be recognized as a novel genus of the family Spirosomaceae. The cells were Gramstain- negative, nonmotile, strictly aerobic, and straight long rods with no flagellum. Optimum growth occurred at 28°C and pH 7.0 with the presence of NaCl concentration 1.0–3.0% (w/v). The strain showed oxidase and catalase activities. The major fatty acids were C16:1ω5c, iso-C15:0 and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The predominant isoprenoid quinone was MK-7. The complete genome size was 4.64 Mb with a DNA G + C content of 44.4%. Further typing of CRISPR-Cas systems in the family Spirosomaceae and the phylum Bacteroidota indicated that it was remarkable for strain YYF0007T featured by such a set of CRISPR-Cas systems. This trait highlights the applications of strain YYF- 0007T in studies on the evolutionary dynamics and bacterial autoimmunity of CRISPR-Cas system as a potential model. The name Marinilongibacter aquaticus gen. nov., sp. nov. is proposed, and the type strain is YYF0007T (= MCCC 1K06017T = GDMCC 1.2428T = JCM 34683T).

Influences of genetically perturbing synthesis of the typical yellow pigment on conidiation, cell wall integrity, stress tolerance, and cellulase production in Trichoderma reesei: Weixin Zhang , Ning An , Junqi Guo , Zhixing Wang , Xiangfeng Meng , Weifeng Liu; J. Microbiol. 2021;59(4):426-434. Published online January 26, 2021; DOI: https://doi.org/10.1007/s12275-021-0433-0

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14 Citations

Abstract: The prominent protein producing workhorse Trichoderma reesei secretes a typical yellow pigment that is synthesized by a gene cluster including two polyketide synthase encoding genes sor1 and sor2. Two transcription factors (YPR1 and YPR2) that are encoded in the same cluster have been shown to regulate the expression of the sor genes. However, the physiological relevance of the yellow pigment synthesis in T. reesei is not completely clear. In this study, a yellow pigment hyper-producer OEypr1 and three yellow pigment non-producers, OEypr1-sor1, Δypr1, and OEypr2, were constructed. Their phenotypic features in mycelial growth, conidiation, cell wall integrity, stress tolerance, and cellulase production were determined. Whereas hyperproduction of the yellow pigment caused significant defects in all the physiological aspects tested, the non-producers showed similar colony growth, but improved conidiation, maintenance of cell wall integrity, and stress tolerance compared to the control strain. Moreover, in contrast to the severely compromised extracellular cellobiohydrolase production in the yellow pigment hyperproducer, loss of the yellow pigment hardly affected induced cellulase gene expression. Our results demonstrate that interfering with the yellow pigment synthesis constitutes an engineering strategy to endow T. reesei with preferred features for industrial application.

Georgenia faecalis sp. nov. isolated from the faeces of Tibetan antelope: Xiaoxia Wang , Jing Yang , Yuyuan Huang , Xiaomin Wu , Licheng Wang , Limei Han , Sha Li , Huan Li , Xiaoying Fu , Hai Chen , Xiong Zhu; J. Microbiol. 2020;58(9):734-740. Published online July 24, 2020; DOI: https://doi.org/10.1007/s12275-020-0060-1

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2 Citations

Abstract: Two aerobic, Gram-stain-positive, non-motile, non-sporulating coccoid strains, designated ZLJ0423T and ZLJ0321, were isolated from the faeces of Tibetan antelope (Pantholops hodgsonii). Their optimal temperature, NaCl concentration and pH for growth were 28°C, 0.5% (w/v) NaCl and pH 7.5, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strains ZLJ0423T and ZLJ0321 were very similar to each other (99.8%) and had a sequence similarity of 97.0% with Georgenia satyanarayanai NBRC 107612T and Georgenia subflava CGMCC 1.12782T. Phylogenomic analysis based on 688 core genes indicated that these strains formed a clade with G. satyanarayanai NBRC 107612T and Georgenia wutianyii Z294T. The predominant cellular fatty acids were anteiso-C15:0, anteiso-C15:1 A and C16:0. The major menaquinone was MK-8(H4). The cell-wall amino acids consisted of alanine, lysine, glycine and aspartic acid, with lysine as the diagnostic diamino acid. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides and two unidentified lipids formed the polar lipid profile. The DNA G + C content of both isolates was 73.9 mol%. The digital DNA–DNA hybridization value between strains ZLJ0423T and ZLJ0321 was 91.2%, but their values with closely related species and other available type strains of the genus Georgenia were lower than the 70% threshold. On the basis of polyphasic taxonomic data, strains ZLJ0423T and ZLJ0321 represent a novel species within the genus Georgenia, for which the name Georgenia faecalis sp. nov. is proposed. The type strain is ZLJ0423T (= CGMCC 1.13681T = JCM 33470T).

Burkholderia thailandensis outer membrane vesicles exert antimicrobial activity against drug-resistant and competitor microbial species: Yihui Wang , Joseph P. Hoffmann , Chau-Wen Chou , Kerstin Höner zu Bentrup , Joseph A. Fuselier , Jacob P. Bitoun , William C. Wimley , Lisa A. Morici; J. Microbiol. 2020;58(7):550-562. Published online April 11, 2020; DOI: https://doi.org/10.1007/s12275-020-0028-1

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37 Citations

Abstract: Gram-negative bacteria secrete outer membrane vesicles (OMVs) that play critical roles in intraspecies, interspecies, and bacteria-environment interactions. Some OMVs, such as those produced by Pseudomonas aeruginosa, have previously been shown to possess antimicrobial activity against competitor species. In the current study, we demonstrate that OMVs from Burkholderia thailandensis inhibit the growth of drug-sensitive and drug-resistant bacteria and fungi. We show that a number of antimicrobial compounds, including peptidoglycan hydrolases, 4-hydroxy-3-methyl-2-(2-nonenyl)- quinoline (HMNQ) and long-chain rhamnolipid are present in or tightly associate with B. thailandensis OMVs. Furthermore, we demonstrate that HMNQ and rhamnolipid possess antimicrobial and antibiofilm properties against methicillin- resistant Staphylococcus aureus (MRSA). These findings indicate that B. thailandensis secretes antimicrobial OMVs that may impart a survival advantage by eliminating competition. In addition, bacterial OMVs may represent an untapped resource of novel therapeutics effective against biofilm- forming and multidrug-resistant organisms.

Differential expression of the major catalase, KatA in the two wild type Pseudomonas aeruginosa strains, PAO1 and PA14: Bi-o Kim , In-Young Chung , You-Hee Cho; J. Microbiol. 2019;57(8):704-710. Published online June 11, 2019; DOI: https://doi.org/10.1007/s12275-019-9225-1

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9 Citations

Abstract: KatA is the major catalase required for hydrogen peroxide (H2O2) resistance and acute virulence in Pseudomonas aeruginosa PA14, whose transcription is governed by its dual promoters (katAp1 and katAp2). Here, we observed that KatA was not required for acute virulence in another wild type P. aeruginosa strain, PAO1, but that PAO1 exhibited higher KatA expression than PA14 did. This was in a good agreement with the observation that PAO1 was more resistant than PA14 to H2O2 as well as to the antibiotic peptide, polymyxin B (PMB), supposed to involve reactive oxygen species (ROS) for its antibacterial activity. The higher KatA expression in PAO1 than in PA14 was attributed to both katAp1 and katAp2 transcripts, as assessed by S1 nuclease mapping. In addition, it was confirmed that the PMB resistance is attributed to both katAp1 and katAp2 in a complementary manner in PA14 and PAO1, by exploiting the promoter mutants for each -10 box (p1m, p2m, and p1p2m). These results provide an evidence that the two widely used P. aeruginosa strains display different virulence mechanisms associated with OxyR and Anr, which need to be further characterized for better understanding of the critical virulence pathways that may differ in various P. aeruginosa strains.

A computationally simplistic poly-phasic approach to explore microbial communities from the Yucatan aquifer as a potential sources of novel natural products: Marfil-Santana Miguel David , O’Connor-Sánchez Aileen , Ramírez-Prado Jorge Humberto , De los Santos-Briones Cesar , López- Aguiar , Lluvia Korynthia , Rojas-Herrera Rafael , Lago-Lestón Asunción , Prieto-Davó Alejandra; J. Microbiol. 2016;54(11):774-781. Published online October 29, 2016; DOI: https://doi.org/10.1007/s12275-016-6092-x

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3 Citations

Abstract: The need for new antibiotics has sparked a search for the microbes that might potentially produce them. Current sequencing technologies allow us to explore the biotechnological potential of microbial communities in diverse environments without the need for cultivation, benefitting natural product discovery in diverse ways. A relatively recent method to search for the possible production of novel compounds includes studying the diverse genes belonging to polyketide synthase pathways (PKS), as these complex enzymes are an important source of novel therapeutics. In order to explore the biotechnological potential of the microbial community from the largest underground aquifer in the world located in the Yucatan, we used a polyphasic approach in which a simple, non-computationally intensive method was coupled with direct amplification of environmental DNA to assess the diversity and novelty of PKS type I ketosynthase (KS) domains. Our results suggest that the bioinformatic method proposed can indeed be used to assess the novelty of KS enzymes; nevertheless, this in silico study did not identify some of the KS diversity due to primer bias and stringency criteria outlined by the metagenomics pipeline. Therefore, additionally implementing a method involving the direct cloning of KS domains enhanced our results. Compared to other freshwater environments, the aquifer was characterized by considerably less diversity in relation to known ketosynthase domains; however, the metagenome included a family of KS type I domains phylogenetically related, but not identical, to those found in the curamycin pathway, as well as an outstanding number of thiolases. Over all, this first look into the microbial community found in this large Yucatan aquifer and other fresh water free living microbial communities highlights the potential of these previously overlooked environments as a source of novel natural products.

PprM is necessary for up-regulation of katE1, encoding the major catalase of Deinococcus radiodurans, under unstressed culture conditions: Sun-Wook Jeong , Ho Seong Seo , Min-Kyu Kim , Jong-Il Choi , Heon-Man Lim , Sangyong Lim; J. Microbiol. 2016;54(6):426-431. Published online May 27, 2016; DOI: https://doi.org/10.1007/s12275-016-6175-8

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15 Citations

Abstract: Deinococcus radiodurans is a poly-extremophilic organism, capable of tolerating a wide variety of different stresses, such as gamma/ultraviolet radiation, desiccation, and oxidative stress. PprM, a cold shock protein homolog, is involved in the radiation resistance of D. radiodurans, but its role in the oxidative stress response has not been investigated. In this study, we investigated the effect of pprM mutation on catalase gene expression. pprM disruption decreased the mRNA and protein levels of KatE1, which is the major catalase in D. radiodurans, under normal culture conditions. A pprM mutant strain (pprMMT) exhibited decreased catalase activity, and its resistance to hydrogen peroxide (H2O2) decreased accordingly compared with that of the wild-type strain. We confirmed that RecG helicase negatively regulates katE1 under normal culture conditions. Among katE1 transcriptional regulators, the positive regulator drRRA was not altered in pprM-, while the negative regulators perR, dtxR, and recG were activated more than 2.5-fold in pprMMT. These findings suggest that PprM is necessary for KatE1 production under normal culture conditions by down-regulation of katE1 negative regulators.

Review

MINIREVIEW] Regulation of Escherichia coli RNase III activity: Boram Lim , Minji Sim , Howoon Lee , Seogang Hyun , Younghoon Lee , Yoonsoo Hahn , Eunkyoung Shin , Kangseok Lee; J. Microbiol. 2015;53(8):487-494. Published online July 31, 2015; DOI: https://doi.org/10.1007/s12275-015-5323-x

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12 Citations

Abstract: Bacterial cells respond to changes in the environment by adjusting their physiological reactions. In cascades of cellular responses to stresses of various origins, rapid modulation of RNA function is known to be an effective biochemical adaptation. Among many factors affecting RNA function, RNase III, a member of the phylogenetically highly conserved endoribonuclease III family, plays a key role in posttranscriptional regulatory pathways in Escherichia coli. In this review, we provide an overview of the factors affecting RNase III activity in E. coli.

Research Support, Non-U.S. Gov'ts

Molecular Characterization of the Alpha Subunit of Multicomponent Phenol Hydroxylase from 4-Chlorophenol-Degrading Pseudomonas sp. Strain PT3: Wael S. El-Sayed , Mohamed K. Ibrahim , Salama A. Ouf; J. Microbiol. 2014;52(1):13-19. Published online January 4, 2014; DOI: https://doi.org/10.1007/s12275-014-3250-x

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8 Citations

Abstract: Multicomponent phenol hydroxylases (mPHs) are diiron enzymes that use molecular oxygen to hydroxylate a variety of phenolic compounds. The DNA sequence of the alpha subunit (large subunit) of mPH from 4-chlorophenol (4-CP)- degrading bacterial strain PT3 was determined. Strain PT3 was isolated from oil-contaminated soil samples adjacent to automobile workshops and oil stations after enrichment and establishment of a chlorophenol-degrading consortium. Strain PT3 was identified as a member of Pseudomonas sp. based on sequence analysis of the 16S rRNA gene fragment. The 4-CP catabolic pathway by strain PT3 was tentatively proposed to proceed via a meta-cleavage pathway after hydroxylation to the corresponding chlorocatechol. This hypothesis was supported by polymerase chain reaction (PCR) detection of the LmPH encoding sequence and UV/VIS spectrophotometric analysis of the culture filtrate showing accumulation of 5-chloro-2-hydroxymuconic semialdehyde (5-CHMS) with λmax 380. The detection of catabolic genes involved in 4-CP degradation by PCR showed the presence of both mPH and catechol 2,3-dioxygenase (C23DO). Nucleotide sequence analysis of the alpha subunit of mPH from strain PT3 revealed specific phylogenetic grouping to known mPH. The metal coordination encoding regions from strain PT3 were found to be conserved with those from the homologous dinuclear oxo-iron bacterial monooxygenases. Two DE(D)XRH motifs was detected in LmPH of strain PT3 within an approximate 100 amino acid interval, a typical arrangement characteristic of most known PHs.

Phylogenetic Relationships of Korean Sparassis latifolia Based on Morphological and ITS rDNA Characteristics: Rhim Ryoo , Hong-Duck Sou , Kang-Hyeon Ka , Hyun Park; J. Microbiol. 2013;51(1):43-48. Published online March 2, 2013; DOI: https://doi.org/10.1007/s12275-013-2503-4

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22 Citations

Abstract: Recent studies based on morphological characteristics and molecular analyses have revealed that the characteristics of Sparassis crispa from Asia are not concordant with those of collections from Europe and North America. Consequently, the Asian isolate was redefined as Sparassis latifolia. This study is the first report of Sparassis latifolia collected in Korea. The taxonomic relationships and replacement of Sparassis species were inferred from a comparison of the morphological characteristics and by molecular sequence analysis of the internal transcribed spacer (ITS) rDNA regions. In particular, this study focused on the phylogenetic relationships inferred from the biogeographical distribution of isolates within the genus Sparassis.

Clades of γ-Glutamyltransferases (GGTs) in the Ascomycota and Heterologous Expression of Colletotrichum graminicola CgGGT1, a Member of the Pezizomycotina-only GGT Clade: Marco H. Bello , Lynn Epstein; J. Microbiol. 2013;51(1):88-99. Published online March 2, 2013; DOI: https://doi.org/10.1007/s12275-013-2434-0

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8 Citations

Abstract: Gamma-glutamyltransferase (GGT, EC 2.3.2.2) cleaves the γ-glutamyl linkage in glutathione (GSH). Ascomycetes in either the Saccharomycotina or the Taphrinomycotina have one to three GGTs, whereas members of the Pezizomycotina have two to four GGTs. A Bayesian analysis indicates there are three well-supported main clades of GGTs in the Ascomycota. 1) A Saccharomycotina and a Taphrinomycotinaspecific GGT sub-clade form a yeast main clade. This clade has the three relatively well-characterized fungal GGTs: (Saccharomyces cerevisiae CIS2 and Schizosaccharomyces pombe Ggt1 and Ggt2) and most of its members have all 14 of the highly conserved and critical amino acids that are found in GGTs in the other kingdoms. 2) In contrast, a main clade (GGT3) differs in 11 of the 14 highly conserved amino acids that are found in GGTs in the other kingdoms. All of the 44 Pezizomycotina analyzed have either one or two GGT3s. 3) There is a Pezizomycotina-only GGT clade that has two wellsupported sub-clades (GGT1 and GGT2); this clade differs in only two of the 14 highly conserved amino acids found in GGTs in the other kingdoms. Because the Pezizomycotina GGTs differ in apparently critical amino acids from the crosskingdom consensus, a putative GGT from Colletotrichum graminicola, a member of the Pezizomycotina, was cloned and the protein product was expressed as a secreted protein in Pichia pastoris. A GGT enzyme assay of the P. pastoris supernatant showed that the recombinant protein was active, thereby demonstrating that CgGGT1 is a bona fide GGT.

Catabolite Control Protein A of Streptococcus suis Type 2 Contributes to Sugar Metabolism and Virulence: Yulong Tang , Wei Wu , Xiaoyan Zhang , Zhongyan Lu , Jianshun Chen , Weihuan Fang; J. Microbiol. 2012;50(6):994-1002. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2035-3

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Abstract: Catabolite control protein A (CcpA) is the major transcriptional regulator in carbon catabolite repression in several Gram-positive bacteria. We attempted to characterize the role of a CcpA homologue of Streptococcus suis type 2 in sugar metabolism and virulence. Addition of glucose or sucrose to the defined medium significantly reduced the activity of raffinose-inducible α-galactosidase, cellobiose-inducible β-glucosidase, and maltose-inducible α-glucosidase of the wildtype strain by about 9, 4, and 2-3 fold, respectively. Deletion of ccpA substantially derepressed the effects of repressing sugars on α-galactosidase or β-glucosidase activity. The ccpA deletion mutant showed reduced expression of virulence genes sly and eno (P<0.05), decreased adhesion to and invasion into endothelial cells (P<0.05), and attenuated virulence to mice with significant reduction of death rate and bacterial burden in organs, as compared to the wild-type strain. Both the in vitro and in vivo defect phenotypes were reversible by ccpA complementation. Thus, this study shows that CcpA of S. suis type 2 plays an important role in carbon catabolite repression and virulence.

Expression of the Lactobacillus plantarum malE Gene Is Regulated by CcpA and a MalR-Like Protein: Lidia Muscariello , Valeria Vastano , Rosa A. Siciliano , Margherita Sacco , Rosangela Marasco; J. Microbiol. 2011;49(6):950-955. Published online December 28, 2011; DOI: https://doi.org/10.1007/s12275-011-0495-5

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Abstract: Lactobacillus plantarum is commonly used in the food industry as a starter in various fermentations, especially in vegetable fermentations, in which starch is a common substrate. This polysaccharide, which is obtained from potatoes or corn and is hydrolysed mainly to maltose and glucose by acids or enzymes, is commercially used for the production of lactate by lactic acid fermentation. In this study, we describe the regulation of malE gene expression in L. plantarum. This gene, located in a 7-gene cluster, probably organized in an operon, encodes a putative maltose/maltodextrin-binding protein. We studied the expression of malE in L. plantarum LM3 (wild type) and in LM3-2 (ccpA1), which carries a null mutation in the ccpA gene, encoding the catabolite control protein A (CcpA). In the presence of glucose, expression of the MalE protein was higher in the mutant strain as compared to that in the wild-type strain. Transcription of the malE gene was induced by maltose and regulated by a CcpA-mediated carbon catabolite repression. Further, we isolated strains carrying mutations in 2 genes, lp_0172 and lp_0173, whose deduced amino acid sequences share significant identity with MalR, a regulator of the maltose operon in several gram-positive bacteria. A double mutant exhibited glucose-insensitive malE transcription, while absence of the functional Lp_0172 open reading frame had no effect on malE expression.

Differential Expression of citA Gene Encoding the Mitochondrial Citrate Synthase of Aspergillus nidulans in Response to Developmental Status and Carbon Sources: In Sook Min , Ji Young Bang , Soon Won Seo , Cheong Ho Lee , Pil Jae Maeng; J. Microbiol. 2010;48(2):188-198. Published online May 1, 2010; DOI: https://doi.org/10.1007/s12275-010-0096-8

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6 Citations

Abstract: As an extension of our previous studies on the mitochondrial citrate synthase of Aspergillus nidulans and cloning of its coding gene (citA), we analyzed differential expression of citA in response to the progress of development and change of carbon source. The cDNA consisted of 1,700 nucleotides and was predicted to encode a 474-amino acid protein. By comparing the cDNA sequence with the corresponding genomic sequence, we confirmed that citA gene contains 7 introns and that its transcription starts at position -26 (26-nucleotide upstream from the initiation codon). Four putative CreA binding motifs and three putative stress-response elements (STREs) were found within the 1.45-kb citA promoter region. The mode of citA expression was examined by both Northern blot and confocal microscopy using green fluorescent protein (sGFP) as a vital reporter. During vegetative growth and asexual development, the expression of citA was ubiqiutous throughout the whole fungal body including mycelia and conidiophores. During sexual development, the expression of citA was quite strong in cleistothecial shells, but significantly weak in the content of cleistothecia including ascospores. Acetate showed a strong inductive effect on citA expression, which is subjected to carbon catabolite repression (CCR) caused by glucose. The recombinant fusion protein CitA40::sGFP (sGFP containing the 40-amino acid N-terminal segment of CitA) was localized into mitochondria, which supports that a mitochondrial targeting signal is included within the 40-amino acid N-terminal segment of CitA.

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