Journal of Microbiology

Editorial

Editorial] Bacterial Regulatory Mechanisms for the Control of Cellular Processes: Simple Organisms’ Complex Regulation: Jin-Won Lee; J. Microbiol. 2023;61(3):273-276. Published online April 3, 2023; DOI: https://doi.org/10.1007/s12275-023-00036-6

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Abstract: Bacteria employ a diverse array of cellular regulatory mechanisms to successfully adapt and thrive in ever-changing environments, including but not limited to temperature changes, fluctuations in nutrient availability, the presence or absence of electron acceptors such as oxygen, the availability of metal ions crucial for enzyme activity, and the existence of antibiotics. Bacteria can virtually modulate any step of gene expression from transcr!ptional initiation to posttranslational modification of a protein for the control of cellular processes. Furthermore, one gene regulator often controls another in a complex gene regulatory network. Thus, it is not easy to fully understand the intricacies of bacterial regulatory mechanisms in various environments. In this special issue, while acknowledging the challenge of covering all aspects of bacterial regulatory mechanisms across diverse environments, seven review articles are included to provide insight into the recent progress in understanding such mechanisms from different perspectives: positive regulatory mechanisms by secondary messenger (cAMP receptor protein), two-component signal transduction mechanisms (Rcs and Cpx), diverse regulatory mechanisms by a specific environmental factor in specific bacteria (oxygen availability in Mycobacterium and manganese ion availability in Salmonella), diverse regulatory mechanisms by a specific environmental factor (temperature and antibiotics), and regulatory mechanisms by antibiotics in cell wall synthesis. Bacteria, as ubiquitous organisms that can be found in almost every environment, carry out complex cellular processes that allow them to survive and thrive in a variety of different conditions despite their small size and relative simplicity. One of the key factors that allows bacteria to carry out these complex processes is their ability to regulate gene expression through various mechanisms. Gene expression is a fundamental biological process by which the genetic information encoded in a gene is transcribed into an RNA molecule and subsequently translated into a functional gene product, often a protein. Furthermore, the activity levels of proteins may further be altered by posttranslational modification. Regulation of gene expression refers to the control of the amount and timing of gene expression, and thus it can be divided into transcr!ptional, translational, and posttranslational levels.

Journal Articles

Characterization of components of a reducing system for SoxR in the cytoplasmic membrane of Escherichia coli: Kang-Lok Lee , Kyung-Chang Lee , Joon-Hee Lee , Jung-Hye Roe; J. Microbiol. 2022;60(4):387-394. Published online March 28, 2022; DOI: https://doi.org/10.1007/s12275-022-1667-1

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Abstract: A reducing system of SoxR, a regulator of redox-active molecules, was identified as rsxABCDGE gene products and RseC in Escherichia coli through genetic studies. We found that ApbE was an additional component of the reducer system. Bacterial two hybrid analysis revealed that these proteins indeed had multiple interactions among themselves. RseC and RsxB formed the core of the complex, interacting with more than five other components. RsxC, the only cytoplasmic component of the system, interacted with SoxR. It might be linked with the rest of the complex via RsxB. Membrane fractions containing the wild type complex but not the mutant complex reduced purified SoxR using NADH as an electron source. These results suggest that Rsx genes, RseC, and ApbE can form a complex using NAD(P)H to reduce SoxR.

Meiotic prophase roles of Pds5 in recombination and chromosome condensation in budding yeast: Jeong Hwan Joo , Hyun Ah Kang , Keun Pil Kim , Soogil Hong; J. Microbiol. 2022;60(2):177-186. Published online February 1, 2022; DOI: https://doi.org/10.1007/s12275-022-1635-9

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Abstract: Genetic variation in eukaryotes is mediated during meiosis by the exchange of genetic material between homologous chromosomes to produce recombinant chromosomes. Cohesin is essential to promote proper chromosome segregation, chromosome morphogenesis, and recombination in meiotic cells. Cohesin consists of three main subunits–Smc1, Smc3, and the kleisin subunit Mcd1/Scc1 (Rec8 in meiosis)–and cohesin accessory factors. In Saccharomyces cerevisiae, the cohesin regulatory subunit Pds5 plays a role in homolog pairing, meiotic axis formation, and interhomolog recombination. In this study, we examine the prophase functions of Pds5 by performing physical analysis of recombination and three-dimensional high-resolution microscopy analysis to identify its roles in meiosis-specific recombination and chromosome morphogenesis. To investigate whether Pds5 plays a role in mitoticlike recombination, we inhibited Mek1 kinase activity, which
result
ed in switching to sister template bias by Rad51-dependent recombination. Reductions in double-strand breaks and crossover products and defective interhomolog recombination occurred in the absence of Pds5. Furthermore, recombination intermediates, including single-end invasion and double-Holliday junction, were reduced in the absence of Pds5 with Mek1 kinase inactivation compared to Mek1 kinase inactivation cells. Interestingly, the absence of Pds5
result
ed in increasing numbers of chromosomes with hypercompaction of the chromosome axis. Thus, we suggest that Pds5 plays an essential role in recombination by suppressing the pairing of sister chromatids and abnormal compaction of the chromosome axis.

Antiviral effects of human placenta hydrolysate (Laennec) against SARS-CoV-2 in vitro and in the ferret model: Eun-Ha Kim , Young-il Kim , Seung-Gyu Jang , Minju Im , Kyeongsoo Jeong , Young Ki Choi , Hae-Jung Han; J. Microbiol. 2021;59(11):1056-1062. Published online October 6, 2021; DOI: https://doi.org/10.1007/s12275-021-1367-2

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Abstract: The COVID-19 pandemic has caused unprecedented health, social, and economic crises worldwide. However, to date, there is an only a limited effective treatment for this disease. Human placenta hydrolysate (hPH) has previously been shown to be safe and to improve the health condition in patients with hyperferritinemia and COVID-19. In this study, we aimed to determine the antiviral effects of hPH against SARS-CoV-2 in vitro and in vivo models and compared with Remdesivir, an FDA-approved drug for COVID-19 treatment. To assess whether hPH inhibited SARS-CoV-2 replication, we determined the CC50, EC50, and selective index (SI) in Vero cells by infection with a SARS-CoV-2 at an MOI of 0.01. Further, groups of ferrets infected with 105.8 TCID50/ml of SARS-CoV-2 and treated with hPH at 2, 4, 6 dpi, and compared their clinical manifestation and virus titers in respiratory tracts with PBS control-treated group. The mRNA expression of immunerelated cytokines was determined by qRT-PCR. hPH treatment attenuated virus replication in a dose-dependent manner in vitro. In a ferret infection study, treatment with hPH resulted in minimal bodyweight loss and attenuated virus replication in the nasal wash, turbinates, and lungs of infected ferrets. In addition, qRT-PCR results revealed that the hPH treatment remarkably upregulated the gene expression of type I (IFN-α and IFN-β) and II (IFN-γ) IFNs in SARS-CoV-2 infected ferrets. Our data collectively suggest that hPH has antiviral efficacy against SARS-CoV-2 and might be a promising therapeutic agent for the treatment of SARS-CoV-2 infection.

Effects of mycosubtilin homolog algicides from a marine bacterium, Bacillus sp. SY-1, against the harmful algal bloom species Cochlodinium polykrikoides: Seong-Yun Jeong , Hong-Joo Son; J. Microbiol. 2021;59(4):389-400. Published online March 29, 2021; DOI: https://doi.org/10.1007/s12275-021-1086-8

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Abstract: The marine bacterium, Bacillus sp. SY-1, produced algicidal compounds that are notably active against the bloom-forming alga Cochlodinium polykrikoides. We isolated three algicidal compounds and identified these as mycosubtilins with molecular weights of 1056, 1070, and 1084 (designated MS 1056, 1070, and 1084, respectively), based on amino acid analyses and 1H, 13C, and two-dimensional nuclear magnetic resonance spectroscopy, including 1H-15N heteronuclear multiple bond correlation analysis. MS 1056 contains a β- amino acid residue with an alkyl side chain of C15, which has not previously been seen in known mycosubtilin families. MS 1056, 1070, and 1084 showed algicidal activities against C. polykrikoides with 6-h LC50 values of 2.3 ± 0.4, 0.8 ± 0.2, and 0.6 ± 0.1 μg/ml, respectively. These compounds also showed significant algicidal activities against other harmful algal bloom species. In contrast, MS 1084 showed no significant growth inhibitory effects against other organisms, including bacteria and microalgae, although does inhibit the growth of some fungi and yeasts. These observations imply that the algicidal bacterium Bacillus sp. SY-1 and its algicidal compounds could play an important role in regulating the onset and development of harmful algal blooms in natural environments.

Transcriptomic and proteomic profiling revealed global changes in Streptococcus thermophilus during pH-controlled batch fermentations: Yali Qiao , Cong Leng , Gefei Liu , Yanjiao Zhang , Xuepeng Lv , Hongyu Chen , Jiahui Sun , Zhen Feng; J. Microbiol. 2019;57(9):769-780. Published online June 14, 2019; DOI: https://doi.org/10.1007/s12275-019-8604-y

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Abstract: Understanding global changes of physiological processes at the molecular level during the growth of Streptococcus thermophilus is essential for the rational design of cultivation media and the optimization of bioprocesses. Transcriptomics and proteomics were combined to investigate the global changes at the transcript and protein level during the growth of S. thermophilus. The expression of 1396 genes (FDR ≤ 0.001) and 876 proteins (P < 0.05) changed significantly over time. The most remarkable growth phase dependent changes occurred in the late-lag phase and were related to heterofermentation, glycolysis, peptidoglycan biosynthesis, conversion between amino acids and stress response. The present
results
could provide theoretical guidance for high-cell-density culture, help design cultivation media, and help attain a high biomass of S. thermophilus.

De novo transcriptome assembly and characterization of the 10-hydroxycamptothecin-producing Xylaria sp. M71 following salicylic acid treatment: Xiaowei Ding , Kaihui Liu , Yonggui Zhang , Feihu Liu; J. Microbiol. 2017;55(11):871-876. Published online October 27, 2017; DOI: https://doi.org/10.1007/s12275-017-7173-1

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Abstract: In the present study, we identified genes that are putatively involved in the production of fungal 10-hydroxycamptothecin via transcriptome sequencing and characterization of the Xylaria sp. M71 treated with salicylic acid (SA). A total of 60,664,200 raw reads were assembled into 26,044 unigenes. BLAST assigned 8,767 (33.7%) and 10,840 (41.6%) unigenes to 40 Gene Ontology (GO) annotations and 108 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. A total of 3,713 unigenes comprising 1,504 upregulated and 2,209 downregulated unigenes were found to be differentially expressed between SA-induced and control fungi. Based on the camptothecin biosynthesis pathway in plants, 13 functional genes of Xylaria sp. M71 were mapped to the mevalonate (MVA) pathway, suggesting that the fungal 10-hydroxycamptothecin is produced via the MVA pathway. In summary, analysis of the Xylaria sp. M71 transcriptome allowed the identification of unigenes that are putatively involved in 10-hydroxycamptothecin biosynthesis in fungi.

Review

REVIEW] Mechanisms of Synergy in Polymicrobial Infections: Justine L. Murray , Jodi L. Connell , Apollo Stacy , Keith H. Turner , Marvin Whiteley; J. Microbiol. 2014;52(3):188-199. Published online March 1, 2014; DOI: https://doi.org/10.1007/s12275-014-4067-3

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133 Citations

Abstract: Communities of microbes can live almost anywhere and contain many different species. Interactions between members of these communities often determine the state of the habitat in which they live. When these habitats include sites on the human body, these interactions can affect health and disease. Polymicrobial synergy can occur during infection, in which the combined effect of two or more microbes on disease is worse than seen with any of the individuals alone. Powerful genomic methods are increasingly used to study microbial communities, including metagenomics to reveal the members and genetic content of a community and metatranscriptomics to describe the activities of community members. Recent efforts focused toward a mechanistic understanding of these interactions have led to a better appreciation of the precise bases of polymicrobial synergy in communities containing bacteria, eukaryotic microbes, and/or viruses. These studies have benefited from advances in the development of in vivo models of polymicrobial infection and modern techniques to profile the spatial and chemical bases of intermicrobial communication. This review describes the breadth of mechanisms microbes use to interact in ways that impact pathogenesis and techniques to study polymicrobial communities.

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

NOTE] rRNASelector: A Computer Program for Selecting Ribosomal RNA Encoding Sequences from Metagenomic and Metatranscriptomic Shotgun Libraries: Jae-Hak Lee , Hana Yi , Jongsik Chun; J. Microbiol. 2011;49(4):689-691. Published online September 2, 2011; DOI: https://doi.org/10.1007/s12275-011-1213-z

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Abstract: Metagenomic and metatranscriptomic shotgun sequencing techniques are gaining popularity as more cost-effective next-generation sequencing technologies become commercially available. The initial stage of bioinformatic analysis generally involves the identification of phylogenetic markers such as ribosomal RNA genes. The sequencing reads that do not code for rRNA can then be used for protein-based analysis. Hidden Markov model is a well-known method for pattern recognition. Hidden Markov models that are trained on well-curated rRNA sequence databases have been successfully used to identify DNA sequence coding for rRNAs in prokaryotes. Here, we introduce rRNASelector, which is a computer program for selecting rRNA genes from massive metagenomic and metatranscriptomic sequences using hidden Markov models. The program successfully identified prokaryotic 5S, 26S, and 23S rRNA genes from Roche 454 FLX Titanium-based metagenomic and metatranscriptomic libraries. The rRNASelector program is available at http://sw.ezbiocloud.net/rrnaselector.

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