Journal of Microbiology

Review

Dissection of plant microbiota and plant-microbiome interactions: Kihyuck Choi , Raees Khan , Seon-Woo Lee; J. Microbiol. 2021;59(3):281-291. Published online February 23, 2021; DOI: https://doi.org/10.1007/s12275-021-0619-5

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Plants rooted in soil have intimate associations with a diverse array of soil microorganisms. While the microbial diversity of soil is enormous, the predominant bacterial phyla associated with plants include Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia. Plants supply nutrient niches for microbes, and microbes support plant functions such as plant growth, development, and stress tolerance. The interdependent interaction between the host plant and its microbes sculpts the plant microbiota. Plant and microbiome interactions are a good model system for understanding the traits in eukaryotic organisms from a holobiont perspective. The holobiont concept of plants, as a consequence of co-evolution of plant host and microbiota, treats plants as a discrete ecological unit assembled with their microbiota. Dissection of plant-microbiome interactions is highly complicated; however, some reductionist approaches are useful, such as the synthetic community method in a gnotobiotic system. Deciphering the interactions between plant and microbiome by this reductionist approach could lead to better elucidation of the functions of microbiota in plants. In addition, analysis of microbial communities’ interactions would further enhance our understanding of coordinated plant microbiota functions. Ultimately, better understanding of plantmicrobiome interactions could be translated to improvements in plant productivity.

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Journal Articles

GABA-producing Lactobacillus plantarum inhibits metastatic properties and induces apoptosis of 5-FU-resistant colorectal cancer cells via GABAB receptor signaling: JaeJin An , Heon Seok , Eun-Mi Ha; J. Microbiol. 2021;59(2):202-216. Published online February 1, 2021; DOI: https://doi.org/10.1007/s12275-021-0562-5

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Abstract

5-Fluorouracil (5-FU) is an essential drug in systemic chemotherapy treatments for colorectal cancer (CRC). Despite the development of several treatment strategies over the past decades, the patient benefits of 5-FU-based therapies have been compromised by the development of chemoresistance. Differences in treatment responses among CRC patients may be due to genetic and epigenetic factors unique to individuals. Therefore, important factors for realizing personalized medicine are to accurately understand the causes and mechanisms of drug resistance to 5-FU-based therapies and to identify and validate prognostic biomarkers. Gut microbes that interact directly with the host contribute to human health and cancer control. Lactobacillus plantarum, in particular, has the potential to be a therapeutic agent by producing bioactive compounds that may benefit the host. Here, we investigated the gamma-aminobutyric acid (GABA) and GABAB receptor (GABABR)-dependent signaling pathway as a treatment option for 5-FU-resistant HT-29 cells. GABA-producing L. plantarum activates anti-proliferative, anti-migration, and anti-invasion effects against 5-FU-resistant HT-29 cells. The inhibitory effects of GABA-producing L. plantarum are mediated via GABABR. Activated GABABR induces apoptosis through the inhibition of cAMP-dependent signaling pathways and cellular inhibitor of apoptosis protein 2 (cIAP2) expression. Thus, the GABAergic system has potential in 5- FU-resistant HT-29 cells as a predictive biomarker. In addition, GABA-producing L. plantarum is promising as an adjuvant treatment for 5-FU-resistant CRC, and its intervention in neurobiological signaling imply new possibilities for chemoprevention and the treatment of colon cancer-related diseases.

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Mutation of the cyclic di-GMP phosphodiesterase gene in Burkholderia lata SK875 attenuates virulence and enhances biofilm formation: Hae-In Jung , Yun-Jung Kim , Yun-Jung Lee , Hee-Soo Lee , Jung-Kee Lee , Soo-Ki Kim; J. Microbiol. 2017;55(10):800-808. Published online September 28, 2017; DOI: https://doi.org/10.1007/s12275-017-7374-7

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Abstract

Burkholderia sp. is a gram-negative bacterium that commonly exists in the environment, and can cause diseases in plants, animals, and humans. Here, a transposon mutant library of a Burkholderia lata isolate from a pig with swine respiratory disease in Korea was screened for strains showing attenuated virulence in Caenorhabditis elegans. One such mutant was obtained, and the Tn5 insertion junction was mapped to rpfR, a gene encoding a cyclic di-GMP phosphodiesterase that functions as a receptor. Mutation of rpfR caused a reduction in growth on CPG agar and swimming motility as well as a rough colony morphology on Congo red agar. TLC analysis showed reduced AHL secretion, which was in agreement with the results from plate-based and bioluminescence assays. The mutant strain produced significantly more biofilm detected by crystal violet staining than the parent strain. SEM of the mutant strain clearly showed that the overproduced biofilm contained a filamentous structure. These results suggest that the cyclic di-GMP phosphodiesterase RpfR plays an important role in quorum sensing modulation of the bacterial virulence and biofilm formation.

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Biocontrol of bacterial wilt disease in tomato using Bacillus subtilis strain R31
Yunhao Sun, Yutong Su, Zhen Meng, Jie Zhang, Li Zheng, Shuang Miao, Di Qin, Yulan Ruan, Yanhui Wu, Lina Xiong, Xun Yan, Zhangyong Dong, Ping Cheng, Mingwei Shao, Guohui Yu
Frontiers in Microbiology.2023;[Epub] CrossRef
Comprehensive genome analysis of Burkholderia contaminans SK875, a quorum-sensing strain isolated from the swine
Eiseul Kim, Hae-In Jung, Si Hong Park, Hae-Yeong Kim, Soo-Ki Kim
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The cis -2-Dodecenoic Acid (BDSF) Quorum Sensing System in Burkholderia cenocepacia
Mingfang Wang, Xia Li, Shihao Song, Chaoyu Cui, Lian-Hui Zhang, Yinyue Deng, Gladys Alexandre
Applied and Environmental Microbiology.2022;[Epub] CrossRef
A c-di-GMP Signaling Cascade Controls Motility, Biofilm Formation, and Virulence in Burkholderia thailandensis
Zhuo Wang, Xiaorong Xie, Daohan Shang, Laigong Xie, Yueyue Hua, Li Song, Yantao Yang, Yao Wang, Xihui Shen, Lei Zhang, Gladys Alexandre
Applied and Environmental Microbiology.2022;[Epub] CrossRef
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Viola Camilla Scoffone, Gabriele Trespidi, Giulia Barbieri, Samuele Irudal, Aygun Israyilova, Silvia Buroni
Applied Microbiology and Biotechnology.2021; 105(24): 9019. CrossRef
Complete Genome Sequence of Burkholderia contaminans SK875, Isolated from the Respiratory Tract of a Pig in the Republic of Korea
Hae-In Jung, Sang-Won Lee, Soo-Ki Kim, Irene L. G. Newton
Microbiology Resource Announcements.2020;[Epub] CrossRef
Key Players and Individualists of Cyclic-di-GMP Signaling in Burkholderia cenocepacia
Anja M. Richter, Mustafa Fazli, Nadine Schmid, Rebecca Shilling, Angela Suppiger, Michael Givskov, Leo Eberl, Tim Tolker-Nielsen
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Research Support, Non-U.S. Gov'ts

Reductive Divergence of Enterobacterial Repetitive Intergenic Consensus Sequences among Gammaproteobacteria Genomes: Young-Gun Zo; J. Microbiol. 2011;49(1):35-45. Published online March 3, 2011; DOI: https://doi.org/10.1007/s12275-011-1024-2

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Abstract

Enterobacterial repetitive intergenic consensus (ERIC) sequence is a transcription-modulating, nonautonomous, miniature inverted-repeat transposable element. Its origin and the mechanism of highly varying incidences, limited to Enterobacteriaceae and Vibrionaceae, have not been identified. In this study, distribution and divergence of ERICs along bacterial taxonomic units were analyzed. ERICs were found among five families of gammaproteobacteria, with the copy numbers varying with exponential increments. The variability was explained by genus (45%) and species (36%) affiliations, indicating that copy numbers are specific to subfamily taxa. ERICs were interspersed in genomes with considerable divergences. Locations of ERICs in a genome appeared to be strongly conserved in a strain, moderately in a species or a genus, and weakly in a family. ERICs in different species of a genus were from the identical population of sequences while ERICs in different genera of a family were nearly identical. However, ERICs in different families formed distinct monophylectic groups, implying vertical transmission of diverging population of sequences. In spite of large difference in copy numbers, overall intra-genome evolutionary distances among ERICs were similar among different species, except for a few genomes. The exceptions substantiated hypotheses of genetic drifts and horizontal gene transfers of mobility capacity. Therefore, the confined, variable distribution of ERIC could be explained as a two-step evolution: introduction and proliferation of ERIC in one of the progenitors of gammaproteobacteria, followed by vertical transmission under negative selection. Deterioration of sequences and reduction in copy number were concluded to be the predominant patterns in the evolution of ERIC loci.

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Functional Roles and Genomic Impact of Miniature Inverted-Repeat Transposable Elements (MITEs) in Prokaryotes
Michael F. Minnick
Genes.2024; 15(3): 328. CrossRef

NOTE] Identification of Genes That Are Dispensable for Animal Infection by Salmonella typhimurium: Hyun-Ju Kim , Hyon E. Choy; J. Microbiol. 2010;48(3):399-403. Published online June 23, 2010; DOI: https://doi.org/10.1007/s12275-010-9332-5

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Abstract: In the current study, we generated a pool of Salmonella typhimurium mutants using the Tn10d-cam minitransposon. This pool of mutants was administered to BALB/c mice through the oral route, and bacteria were recovered from the spleen 3 days post-infection. After three rounds of serial passage, we observed enrichment of two insertion mutants, a yddG insertion and an amyA insertion. These two genes have been implicated in growth on plant products (amyA) and survival in the presence of paraquat (yddG), both of which are natural environments for Salmonella. Thus, while in vivo expression technology has identified S. typhimurium genes that are absolutely necessary for animal infection, other genes involved in vegetative growth also appear to play role in the establishment of pathogenesis.

Functional Analysis of pilQ Gene in Xanthomanas oryzae pv. oryzae, Bacterial Blight Pathogen of Rice: Seon-Hwa Lim , Byoung-Ho So , Ji-Chun Wang , Eun-Seong Song , Young-Jin Park , Byoung-Moo Lee , Hee-Wan Kang; J. Microbiol. 2008;46(2):214-220. Published online June 11, 2008; DOI: https://doi.org/10.1007/s12275-007-0173-9

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Abstract: Bacterial blight (BB) of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), is the most devastating bacterial disease in rice. A virulence-attenuated mutant strain HNU89K9 of X. oryzae pv. oryzae (KACC10331), with a transposon insertion in the pilQ gene was used for this study. The pilQ was involved in the gene cluster pilMNOPQ of the Xoo genome. Growth rate of the pilQ mutant was similar to that of wild-type. At level of amino acids, PilQ of Xoo showed that a high sequence identities more than 94% and 70% to Xanthomonas species and to Xyllela fastidiosa, respectively but a low sequence homology less than 30% to other bacterial species. The twitching motility forming a marginal fringe on PSA media was observed on colony of the wild-type strain KACC10331, but not in mutant HNU89K9. Wild-type Xoo cells formed a biofilm on the surface of the PVC plastic test tube, while the mutant strain HNU89K9 did not form a biofilm. The results suggest that the pilQ gene of X. oryzae pv. oryzae plays a critical role in pathogenicity, twitching motility, and biofilm formation.

Isolation of Citrobacter sp. Mutants Defective in Decolorization of Brilliant Green by Transposon Mutagenesis: Moon-Sun Jang , Young-Mi Lee , Yong-Lark Choi , Young-Su Cho , Young-Choon Lee; J. Microbiol. 2004;42(2):139-142.; DOI: https://doi.org/2032 [pii]

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Abstract: To identify genes involved in the decolorization of brilliant green, we isolated random mutants generated by transposon insertion in brilliant green-decolorizing bacterium, Citrobacter sp. The resulting mutant bank yielded 19 mutants with a complete defect in terms of the brilliant green color removing ability. Southern hybridization with a Tn5 fragment as a probe showed a single hybridized band in 7 mutants and these mutants appeared to have insertions at different sites of the chromosome. Tn5- inserted genes were isolated and the DNA sequence flanking Tn5 was determined. By comparing these with a sequence database, putative protein products encoded by bg genes were identified as follows: bg 3 as a LysR-type regulatory protein; bg 11 as a MalG protein in the maltose transport system; bg 14 as an oxidoreductase; and bg 17 as an ABC transporter. The sequences deduced from the three bg genes, bg 2, bg 7 and bg 16, showed no significant similarity to any protein with a known function, suggesting that these three bg genes may encode unidentified proteins responsible for the decolorization of brilliant green.

Identification and characterization of pH-regulated genes in saccharomyces cerevisiae: Hong, Sung Ki , Choi, Eui Yul; J. Microbiol. 1996;34(4):327-333.

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Abstract: Yeast, like many other microbes, encounters large variations in ambient pH in their natural environments. Microorganisms capable of growing over a wide pH range require a versatile, efficient pH homeostatic mechanism protecting intracellular processes against extremes of pH. In several organisms, fusions to the bacterial lacZ gene have been extremely useful for the identification of genes expressed at different time during the life cycle or under different growth conditions. In this study, using the lacZ gene screening system, we surveyed a large number of yeast strains with lacZ insertion to identify genes regulated by pH. A yeast genomic library was constructed and inserted with lacZ by a shuttle mutagenesis procedure. The yeast transformants were individually picked up with a toothpick, replica-plated, and grown in alkaline pH medium. Among the 35,000 colonies screened, 10 candidate strains were identified initially by the β-gal assay. We finally confirmed two yeast strains carrying the genes whose expression are strictly dependent on pH of growth medium. One of the fusions showing a 10-fodl induction in expression level in response to alkali pH was selected and further characterized. The pH-regulated gene was cloned by inverse PCR and a partial sequence of the gene was determined. Identification and characterization of the gene is currently under investigation.

Characterization of a new staphylococcal site-specific recombinase sin and genetic organization of its flanking region: Yong, Jun Hyong , Kim, Young Sun , Byeon, Woo Hyeon; J. Microbiol. 1997;35(2):92-96.

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Abstract: A new site-specific recombinase sin, as a component of a putative transposon has been cloned and its base sequence has been determined. The proposed sin shows a high degree of homology with pI9789-sin and pSK1-sin. There is a large (16 bp) inverted repeat downstream of proposed sin and the postulate dhelix-turn-helix motif is located at the extreme C-terminus of the proposed Sin. The transposase gene (tnpA) and β-lactamase gene (blaZ) are located upstream of sin and arsenate reductase gene (arsC) and arsenic efflux pump protein gene (ars B) are downstream. This genetic arrangement seems to be a part of a new putative transposon because there is no known transposon with a gene arrangement of tnpA-blaZ-sin-arsC.

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