Journal of Microbiology

Journal Articles

Enhancement of the solubility of recombinant proteins by fusion with a short-disordered peptide: Jun Ren , Suhee Hwang , Junhao Shen , Hyeongwoo Kim , Hyunjoo Kim , Jieun Kim , Soyoung Ahn , Min-gyun Kim , Seung Ho Lee , Dokyun Na; J. Microbiol. 2022;60(9):960-967. Published online July 14, 2022; DOI: https://doi.org/10.1007/s12275-022-2122-z

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In protein biotechnology, large soluble fusion partners are widely utilized for increased yield and solubility of recombinant proteins. However, the production of additional large fusion partners poses an additional burden to the host, leading to a decreased protein yield. In this study, we identified two highly disordered short peptides that were able to increase the solubility of an artificially engineered aggregationprone protein, GFP-GFIL4, from 0.6% to 61% (D3-DP00592) and 46% (D4-DP01038) selected from DisProt database. For further confirmation, the peptides were applied to two insoluble E. coli proteins (YagA and YdiU). The peptides also enhanced solubility from 52% to 90% (YagA) and from 27% to 93% (YdiU). Their ability to solubilize recombinant proteins was comparable with strong solubilizing tags, maltosebinding protein (40 kDa) and TrxA (12 kDa), but much smaller (< 7 kDa) in size. For practical application, the two peptides were fused with a restriction enzyme, I-SceI, and they increased I-SceI solubility from 24% up to 75%. The highly disordered peptides did not affect the activity of I-SceI while I-SceI fused with MBP or TrxA displayed no restriction activity. Despite the small size, the highly disordered peptides were able to solubilize recombinant proteins as efficiently as conventional fusion tags and did not interfere with the function of recombinant proteins. Consequently, the identified two highly disordered peptides would have practical utility in protein biotechnology and industry.

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A review on computational models for predicting protein solubility
Teerapat Pimtawong, Jun Ren, Jingyu Lee, Hyang-Mi Lee, Dokyun Na
Journal of Microbiology.2025; 63(1): e:2408001. CrossRef
Synthetic intrinsically disordered protein fusion tags that enhance protein solubility
Nicholas C. Tang, Jonathan C. Su, Yulia Shmidov, Garrett Kelly, Sonal Deshpande, Parul Sirohi, Nikhil Peterson, Ashutosh Chilkoti
Nature Communications.2024;[Epub] CrossRef
Biosynthesis of Indigo Dyes and Their Application in Green Chemical and Visual Biosensing for Heavy Metals
Yan Guo, Shun-Yu Hu, Can Wu, Chao-Xian Gao, Chang-Ye Hui
ACS Omega.2024; 9(31): 33868. CrossRef
Functional small peptides for enhanced protein delivery, solubility, and secretion in microbial biotechnology
Hyang-Mi Lee, Thi Duc Thai, Wonseop Lim, Jun Ren, Dokyun Na
Journal of Biotechnology.2023; 375: 40. CrossRef
Directed Evolution of Soluble α-1,2-Fucosyltransferase Using Kanamycin Resistance Protein as a Phenotypic Reporter for Efficient Production of 2'-Fucosyllactose
Jonghyeok Shin, Seungjoo Kim, Wonbeom Park, Kyoung Chan Jin, Sun-Ki Kim, Dae-Hyuk Kweon
Journal of Microbiology and Biotechnology.2022; 32(11): 1471. CrossRef
Effects of spray drying, freeze drying, and vacuum drying on physicochemical and nutritional properties of protein peptide powder from salted duck egg white
Tianyin Du, Jicheng Xu, Shengnan Zhu, Xinjun Yao, Jun Guo, Weiqiao Lv
Frontiers in Nutrition.2022;[Epub] CrossRef

Lentibacillus cibarius sp. nov., isolated from kimchi, a Korean fermented food: Young Joon Oh , Joon Yong Kim , Hee Eun Jo , Hyo Kyeong Park , Seul Ki Lim , Min-Sung Kwon , Hak-Jong Choi; J. Microbiol. 2020;58(5):387-394. Published online April 11, 2020; DOI: https://doi.org/10.1007/s12275-020-9507-7

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Abstract

Two bacterial strains designated NKC220-2T and NKC851-2 were isolated from commercial kimchi from different areas in Korea. The strains were Gram-positive, aerobic, oxidaseand catalase-positive, rod-shaped, spore-forming, non-motile, and halophilic bacteria. Both strains grew without NaCl, unlike type species in the genus Lentibacillus. The optimal pH for growth was 8.0, higher than that of the type species in the genus Lentibacillus, although growth was observed at pH 5.5–9.0. 16S rRNA gene sequence-based phylogenetic analysis indicated that the two strains (99.3–99.9% similarity) are grouped within the genus Lentibacillus and most closely related to Lentibacillus juripiscarius IS40-3T (97.4–97.6% similarity) isolated from fish sauce in Thailand. OrthoANI value between two novel strains and Lentibacillus lipolyticus SSKP1- 9T (79.5–79.6% similarity) was far lower than the species demarcation threshold. Comparative genomic analysis displayed differences between the two strains as well as among other strains belonging to Lentibacillus. Furthermore, each isolate had strain-specific groups of orthologous genes based on pangenome analysis. Genomic G + C contents of strains NKC- 220-2T and NKC851-2 were 41.9 and 42.2 mol%, respectively. The strains contained meso-diaminopimelic acid in their cell walls, and the major menaquinone was menaquinone-7. Phosphatidylglycerol, diphosphatidylglycerol, and an unidentified glycolipid, aminophospholipid, and phospholipid were the major polar lipid components of both strains. The major cellular fatty acids of the strains were anteiso-C15:0 and anteiso- C17:0. Based on phenotypic, genomic, phylogenetic, and chemotaxonomic features, strains NKC220-2T and NKC851-2 represent novel species of the genus Lentibacillus, for which the name Lentibacillus cibarius sp. nov. is proposed. The type strain is NKC220-2T (= KACC 21232T = JCM 33390T).

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Detection of the Microbial Composition of Some Commercial Fermented Liquid Products via Metagenomic Analysis
Cansu Çelik Doğan, Hafize Tuğba Yüksel Dolgun, Serkan İkiz, Şükrü Kırkan, Uğur Parın
Foods.2023; 12(19): 3538. CrossRef
Lentibacillus daqui sp. nov., isolated from high-temperature Daqu, a starter for production of Chinese Jiang-flavour Baijiu
Yuan Liang, Zhen-Ming Lu, Wei Shi, Lin-Huan Wu, Li-Juan Chai, Xiao-Juan Zhang, Su-Yi Zhang, Song-Tao Wang, Cai-Hong Shen, Zheng-Hong Xu
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Occurrence of biogenic amines and their correlation with bacterial communities in the Ivorian traditional fermented fish adjuevan during the storage
Marina Ghislaine Abré, Clémentine Amenan Kouakou-Kouamé, Florent Kouadio N’guessan, Corinne Teyssier, Didier Montet
Folia Microbiologica.2023; 68(2): 257. CrossRef
Description of Corynebacterium poyangense sp. nov., isolated from the feces of the greater white-fronted geese (Anser albifrons)
Qian Liu, Guoying Fan, Kui Wu, Xiangning Bai, Xi Yang, Wentao Song, Shengen Chen, Yanwen Xiong, Haiying Chen
Journal of Microbiology.2022; 60(7): 668. CrossRef
Parasphingorhabdus cellanae sp. nov., isolated from the gut of a Korean limpet, Cellana toreuma
Ji-Ho Yoo, Jeong Eun Han, June-Young Lee, Su-Won Jeong, Yun-Seok Jeong, Jae-Yun Lee, So-Yeon Lee, Hojun Sung, Euon Jung Tak, Hyun Sik Kim, Pil Soo Kim, Jee-Won Choi, Do-Yeon Kim, In Chul Jeong, Do-Hun Gim, Seo Min Kang, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Isolation and characterization of tick-borne Roseomonas haemaphysalidis sp. nov. and rodent-borne Roseomonas marmotae sp. nov.
Wentao Zhu, Juan Zhou, Shan Lu, Jing Yang, Xin-He Lai, Dong Jin, Ji Pu, Yuyuan Huang, Liyun Liu, Zhenjun Li, Jianguo Xu
Journal of Microbiology.2022; 60(2): 137. CrossRef
The Methods of Digging for “Gold” within the Salt: Characterization of Halophilic Prokaryotes and Identification of Their Valuable Biological Products Using Sequencing and Genome Mining Tools
Jakub Lach, Paulina Jęcz, Dominik Strapagiel, Agnieszka Matera-Witkiewicz, Paweł Stączek
Genes.2021; 12(11): 1756. CrossRef
Lentibacillus saliphilus. sp. nov., a moderately halophilic bacterium isolated from a saltern in Korea
Yun Wang, Gang-Qiang Jiang, Hong-Ping Lin, Peng Sun, Hong-Yan Zhang, Dong-Mei Lu, Li-Yun Wang, Chang-Jin Kim, Shu-Kun Tang
Archives of Microbiology.2021; 203(2): 621. CrossRef
Salicibibacter cibarius sp. nov. and Salicibibacter cibi sp. nov., two novel species of the family Bacillaceae isolated from kimchi
Young Joon Oh, Joon Yong Kim, Seul Ki Lim, Min-Sung Kwon, Hak-Jong Choi
Journal of Microbiology.2021; 59(5): 460. CrossRef
Flaviflexus ciconiae sp. nov., isolated from the faeces of the oriental stork, Ciconia boyciana
Jae-Yun Lee, Woorim Kang, Pil Soo Kim, So-Yeon Lee, Na-Ri Shin, Hojun Sung, June-Young Lee, Ji-Hyun Yun, Yun-Seok Jeong, Jeong Eun Han, Mi-Ja Jung, Dong-Wook Hyun, Hyun Sik Kim, Euon Jung Tak, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology.2020; 70(10): 5439. CrossRef
List of new names and new combinations that have appeared in effective publications outside of the IJSEM and are submitted for valid publication
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2019;[Epub] CrossRef

Review

[MINIREVIEW] Alanine dehydrogenases in mycobacteria: Ji-A Jeong , Jeong-Il Oh; J. Microbiol. 2019;57(2):81-92. Published online January 31, 2019; DOI: https://doi.org/10.1007/s12275-019-8543-7

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Abstract

Since NAD(H)-dependent L-alanine dehydrogenase (EC 1.1.4.1; Ald) was identified as one of the major antigens present in culture filtrates of Mycobacterium tuberculosis, many studies on the enzyme have been conducted. Ald catalyzes the reversible conversion of pyruvate to alanine with concomitant oxidation of NADH to NAD+ and has a homohexameric quaternary structure. Expression of the ald genes was observed to be strongly upregulated in M. tuberculosis and Mycobacterium smegmatis grown in the presence of alanine. Furthermore, expression of the ald genes in some mycobacteria was observed to increase under respiration-inhibitory conditions such as oxygen-limiting and nutrient-starvation conditions. Upregulation of ald expression by alanine or under respiration-inhibitory conditions is mediated by AldR, a member of the Lrp/AsnC family of transcriptional regulators. Mycobacterial Alds were demonstrated to be the enzymes required for utilization of alanine as a nitrogen source and to help mycobacteria survive under respiration-inhibitory conditions by maintaining cellular NADH/NAD+ homeostasis. Several inhibitors of Ald have been developed, and their application in combination with respiration-inhibitory antitubercular drugs such as Q203 and bedaquiline was recently suggested.

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Amino Acid Biosynthesis Inhibitors in Tuberculosis Drug Discovery
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Alanine dehydrogenases from four different microorganisms: characterization and their application in L-alanine production
Pengfei Gu, Qianqian Ma, Shuo Zhao, Qiang Li, Juan Gao
Biotechnology for Biofuels and Bioproducts.2023;[Epub] CrossRef
Application of reductive amination by heterologously expressed Thermomicrobium roseum L-alanine dehydrogenase to synthesize L-alanine derivatives
Huri Dedeakayoğulları, Jarkko Valjakka, Ossi Turunen, Berin Yilmazer, Ğarip Demir, Janne Jänis, Barış Binay
Enzyme and Microbial Technology.2023; 169: 110265. CrossRef
A review on enzyme complexes of electron transport chain from Mycobacterium tuberculosis as promising drug targets
Pragya Anand, Yusuf Akhter
International Journal of Biological Macromolecules.2022; 212: 474. CrossRef
Alanine synthesized by alanine dehydrogenase enables ammonium-tolerant nitrogen fixation in Paenibacillus sabinae T27
Qin Li, Haowei Zhang, Yi Song, Minyang Wang, Chongchong Hua, Yashi Li, Sanfeng Chen, Ray Dixon, Jilun Li
Proceedings of the National Academy of Sciences.2022;[Epub] CrossRef
Antibacterial Activity of Squaric Amide Derivative SA2 against Methicillin-Resistant Staphylococcus aureus
Moxi Yu, Yachen Hou, Meiling Cheng, Yongshen Liu, Caise Ling, Dongshen Zhai, Hui Zhao, Yaoyao Li, Yamiao Chen, Xiaoyan Xue, Xue Ma, Min Jia, Bin Wang, Pingan Wang, Mingkai Li
Antibiotics.2022; 11(11): 1497. CrossRef
Mining for Perchlorate Resistance Genes in Microorganisms From Sediments of a Hypersaline Pond in Atacama Desert, Chile
Jorge Díaz-Rullo, Gustavo Rodríguez-Valdecantos, Felipe Torres-Rojas, Luis Cid, Ignacio T. Vargas, Bernardo González, José Eduardo González-Pastor
Frontiers in Microbiology.2021;[Epub] CrossRef
Targeting amino acid metabolism of Mycobacterium tuberculosis for developing inhibitors to curtail its survival
Soujanya D. Yelamanchi, Avadhesha Surolia
IUBMB Life.2021; 73(4): 643. CrossRef
Targeting Non-Replicating Mycobacterium tuberculosis and Latent Infection: Alternatives and Perspectives (Mini-Review)
Anna Egorova, Elena G. Salina, Vadim Makarov
International Journal of Molecular Sciences.2021; 22(24): 13317. CrossRef
Distinctive gene and protein characteristics of extremely piezophilic Colwellia
Logan M. Peoples, Than S. Kyaw, Juan A. Ugalde, Kelli K. Mullane, Roger A. Chastain, A. Aristides Yayanos, Masataka Kusube, Barbara A. Methé, Douglas H. Bartlett
BMC Genomics.2020;[Epub] CrossRef
Comparison of Extracellular Proteins from Virulent and Avirulent Vibrio parahaemolyticus Strains to Identify Potential Virulence Factors
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Journal of Food Protection.2020; 83(1): 155. CrossRef

Research Support, Non-U.S. Gov't

Note] Identification of High-Specificity H-NS Binding Site in LEE5 Promoter of Enteropathogenic Esherichia coli (EPEC): Abhay Prasad Bhat , Minsang Shin , Hyon E. Choy; J. Microbiol. 2014;52(7):626-629. Published online March 7, 2014; DOI: https://doi.org/10.1007/s12275-014-3562-x

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Abstract

Histone-like nucleoid structuring protein (H-NS) is a small but abundant protein present in enteric bacteria and is involved in compaction of the DNA and regulation of the transcription. Recent reports have suggested that H-NS binds to a specific AT rich DNA sequence than to intrinsically curved DNA in sequence independent manner. We detected two high-specificity H-NS binding sites in LEE5 promoter of EPEC centered at -110 and -138, which were close to the proposed consensus H-NS binding motif. To identify H-NS binding sequence in LEE5 promoter, we took a random mutagenesis approach and found the mutations at around -138 were specifically defective in the regulation byH-NS. It was concluded that H-NS exertsmaximumrepression via the specific sequence at around -138 and ubsequently contacts α subunit of RNAP through oligomerization.

Citations

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Horizontally Acquired Homologs of Xenogeneic Silencers: Modulators of Gene Expression Encoded by Plasmids, Phages and Genomic Islands
Alejandro Piña-Iturbe, Isidora D. Suazo, Guillermo Hoppe-Elsholz, Diego Ulloa-Allendes, Pablo A. González, Alexis M. Kalergis, Susan M. Bueno
Genes.2020; 11(2): 142. CrossRef
Recent advances in genetic engineering tools based on synthetic biology
Jun Ren, Jingyu Lee, Dokyun Na
Journal of Microbiology.2020; 58(1): 1. CrossRef
Regulation of the Locus of Enterocyte Effacement in Attaching and Effacing Pathogens
R. Christopher D. Furniss, Abigail Clements, William Margolin
Journal of Bacteriology.2018;[Epub] CrossRef
Bacterial-Chromatin Structural Proteins Regulate the Bimodal Expression of the Locus of Enterocyte Effacement (LEE) Pathogenicity Island in Enteropathogenic Escherichia coli
Hervé Leh, Ahmad Khodr, Marie-Christine Bouger, Bianca Sclavi, Sylvie Rimsky, Stéphanie Bury-Moné, Susan Gottesman
mBio.2017;[Epub] CrossRef
Alternative Synthesis Route of Biocompatible Polyvinylpyrrolidone Nanoparticles and Their Effect on Pathogenic Microorganisms
Vedran Milosavljevic, Pavlina Jelinkova, Ana Maria Jimenez Jimenez, Amitava Moulick, Yazan Haddad, Hana Buchtelova, Sona Krizkova, Zbynek Heger, Lukas Kalina, Lukas Richtera, Pavel Kopel, Vojtech Adam
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H-NS and RNA polymerase: a love–hate relationship?
Robert Landick, Joseph T Wade, David C Grainger
Current Opinion in Microbiology.2015; 24: 53. CrossRef
Effect of promoter-upstream sequence on σ38-dependent stationary phase gene transcription
Hyung-Ju Lim, Kwangsoo Kim, Minsang Shin, Jae-Ho Jeong, Phil Youl Ryu, Hyon E. Choy
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Journal Article

DNA Adenine Methylation of sams1 Gene in Symbiont-Bearing Amoeba proteus: Taeck J. Jeon; J. Microbiol. 2008;46(5):564-570. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0129-8

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Abstract: The expression of amoeba sams genes is switched from sams1 to sams2 when amoebae are infected with Legionella jeonii. To elucidate the mechanism for the inactivation of host sams1 gene by endosymbiotic bacteria, methylation states of the sams1 gene of D and xD amoebae was compared in this study. The sams1 gene of amoebae was methylated at an internal adenine residue of GATC site in symbiont-bearing xD amoebae but not in symbiont-free D amoebae, suggesting that the modification might have caused the inactivation of sams1 in xD amoebae. The sams1 gene of xD amoebae was inactivated at the transcriptional level. Analysis of DNA showed that adenine residues in L. jeonii sams were also methylated, implying that L. jeonii bacteria belong to a Dam methylase-positive strain. In addition, both SAM and Met appeared to act as negative regulators for the expression of sams1 whereas the expression of sams2 was not affected in amoebae.

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

Modulation of Secreted Virulence Factor Genes by Subinhibitory Concentrations of Antibiotics in Pseudomonas aeruginosa: Lixin Shen , Ying Shi , Dan Zhang , Jinhua Wei , Michael G. Surette , Kangmin Duan; J. Microbiol. 2008;46(4):441-447. Published online August 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0054-x

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Abstract: Recent studies have shown that subinhibitory antibiotics play important roles in regulating bacterial genes including virulence factor genes. In this study, the expression of 13 secreted virulence related gene clusters of Pseudomonas aeruginosa, an important opportunistic pathogen, was examined in the presence of subinhibitory concentrations of 4 antibiotics: vancomycin, tetracycline, ampicilin and azithromycin. Activation of gene expression was observed with phzA1, rhlAB, phzA2, lasB, exoY, and exoS. Subinhibitory concentrations of vancomycin resulted in more than 10-fold increase of rhlAB and phzA2 transcription. Both rhamnolipid production and pyocyanin production were significantly elevated, correlating phenotypes with the increased transcription. P. aeruginosa swarming and swimming motility also increased. Similar results were observed with subinhibitory tetracycline, azithromycin and ampicillin. These results indicate that the antibiotics at low concentrations can up-regulate virulence factors and therefore influence bacterial pathogenesis.

Effect of Mutations of Five Conserved Histidine Residues in the Catalytic Subunit of the cbb3 Cytochrome c Oxidase on its Function: Jeong-Il Oh; J. Microbiol. 2006;44(3):284-292.; DOI: https://doi.org/2384 [pii]

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Abstract: The cbb3 cytochrome c oxidase has the dual function as a terminal oxidase and oxygen sensor in the photosynthetic bacterium, Rhodobacter sphaeroides. The cbb3 oxidase forms a signal transduction pathway together with the PrrBA two-component system that controls photosynthesis gene expression in response to changes in oxygen tension in the environment. Under aerobic conditions the cbb3 oxidase generates an inhibitory signal, which shifts the equilibrium of PrrB kinase/phosphatase activities towards the phosphatase mode. Photosynthesis genes are thereby turned off under aerobic conditions. The catalytic subunit (CcoN) of the R. sphaeroides cbb3 oxidase contains five histidine residues (H214, H233, H303, H320, and H444) that are conserved in all CcoN subunits of the cbb3 oxidase, but not in the catalytic subunits of other members of copper-heme superfamily oxidases. H214A mutation of CcoN affected neither catalytic activity nor sensory (signaling) function of the cbb3 oxidase, whereas H320A mutation led to almost complete loss of both catalytic activity and sensory function of the cbb3 oxidase. H233V and H444A mutations brought about the partial loss of catalytic activity and sensory function of the cbb3 oxidase. Interestingly, the H303A mutant form of the cbb3 oxidase retains the catalytic function as a cytochrome c oxidase as compared to the wild-type oxidase, while it is defective in signaling function as an oxygen sensor. H303 appears to be implicated in either signal sensing or generation of the inhibitory signal to the PrrBA two-component system.

Regulation of Class II Bacteriocin Production by Cell-Cell Signaling: Luis E. N. Quadri; J. Microbiol. 2003;41(3):175-182.

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Abstract: Production of ribosomally synthesized antimicrobial peptides usually referred to as bacteriocins is an inducible trait in several gram positive bacteria, particularly in those belonging to the group of lactic acid bacteria. In many of these organisms, production of bacteriocins is inducible and induction requires secretion and extracellular accumulation of peptides that act as chemical messengers and trigger bacteriocin production. These inducer peptides are often referred to as autoinducers and are believed to permit a quorum sensing-based regulation of bacteriocin production. Notably, the peptides acting as autoinducers are dedicated peptides with or without antimicrobial activity or the bacteriocins themselves. The autoinducer-dependent induction of bacteriocin production requires histidine protein kinases and response regulator proteins of two-component signal transduction systems. The current working model for the regulation of class II bacteriocin production in lactic acid bacteria and the most relevant direct and indirect pieces of evidence supporting the model are discussed in this minireview.

Salmonella Invasion Gene Regulation: A Story of Environmental Awareness: Bradley D. Jones; J. Microbiol. 2005;43(1):110-117.

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Abstract: Salmonella enterica serovar Typhimurium causes human gastroenteritis and a systemic typhoid-like infection in mice. A critical virulence determinant of Salmonella is the ability to invade mammalian cells. The expression of genes required for invasion is tightly regulated by environmental conditions and a variety of regulatory genes. The hilA regulator encodes an OmpR/ToxR family transcriptional regulator that activates the expression of invasion genes in response to both environmental and genetic regulatory factors. Work from several laboratories has highlighted that regulation of hilA expression is a key point for controlling expression of the invasive phenotype. A number of positive regulators of hilA expression have been identified including csrAB, sirA/barA, pstS, hilC/sirC/sprA, fis, and hilD. HilD, an AraC/XylS type transcriptional regulator, is of particular importance as a mutation in hilD results in a 14-fold decrease in chromosomal hilA::Tn5lacZY-080 expression and a 53-fold decrease in invasion of HEp-2 cells. It is believed that HilD directly regulates hilA expression as it has been shown to bind to hilA promoter sequences. In addition, our research group, and others, have identified genes (hilE, hha, pag, and lon) that negatively affect hilA transcription. HilE appears to be an important Salmonella-specific regulator that plays a critical role in inactivating hilA expression. Recent work in our lab has been directed at understanding how environmental signals that affect hilA expression may be processed through a hilE pathway to modulate expression of hilA and the invasive phenotype. The current understanding of this complex regulatory system is reviewed.

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