Journal of Microbiology

Meta-Analysis

Exploring COVID-19 Pandemic Disparities with Transcriptomic Meta-analysis from the Perspective of Personalized Medicine: Medi Kori, Ceyda Kasavi, Kazim Yalcin Arga; J. Microbiol. 2024;62(9):785-798. Published online July 9, 2024; DOI: https://doi.org/10.1007/s12275-024-00154-9

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Abstract: Infection with SARS-CoV2, which is responsible for COVID-19, can lead to differences in disease development, severity and mortality rates depending on gender, age or the presence of certain diseases. Considering that existing studies ignore these differences, this study aims to uncover potential differences attributable to gender, age and source of sampling as well as viral load using bioinformatics and multi-omics approaches. Differential gene expression analyses were used to analyse the phenotypic differences between SARS-CoV-2 patients and controls at the mRNA level. Pathway enrichment analyses were performed at the gene set level to identify the activated pathways corresponding to the differences in the samples. Drug repurposing analysis was performed at the protein level, focusing on host-mediated drug candidates to uncover potential therapeutic differences. Significant differences (i.e. the number of differentially expressed genes and their characteristics) were observed for COVID-19 at the mRNA level depending on the sample source, gender and age of the samples. The results of the pathway enrichment show that SARS-CoV-2 can be combated more effectively in the respiratory tract than in the blood samples. Taking into account the different sample sources and their characteristics, different drug candidates were identified. Evaluating disease prediction, prevention and/or treatment strategies from a personalised perspective is crucial. In this study, we not only evaluated the differences in COVID-19 from a personalised perspective, but also provided valuable data for further experimental and clinical efforts. Our findings could shed light on potential pandemics.

Journal Articles

Effects of Light and Dark Conditions on the Transcriptome of Aging Cultures of Candidatus Puniceispirillum marinum IMCC1322: Ji Hyen Lee, Hyun-Myung Oh; J. Microbiol. 2024;62(4):297-314. Published online April 25, 2024; DOI: https://doi.org/10.1007/s12275-024-00125-0

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Abstract: To elucidate the function of proteorhodopsin in Candidatus Puniceispirillum marinum strain IMCC1322, a cultivated representative of SAR116, we produced RNA-seq data under laboratory conditions. We examined the transcriptomes of six different cultures, including sets of expression changes under constant dark (DD), constant light (LL), and diel-cycled (LD; 14 h light: 10 h dark) conditions at the exponential and stationary/death phases. Prepared mRNA extracted from the six samples was analyzed on the Solexa Genome Analyzer with 36 cycles. Differentially expressed genes on the IMCC1322 genome were distinguished as four clusters by K-mean clustering and each CDS (n = 2546) was annotated based on the KEGG BRITE hierarchy. Cluster 0 (n = 1573) covered most constitutive genes including proteorhodopsin, retinoids, and glycolysis/TCA cycle. Cluster 1 genes (n = 754) were upregulated in stationary/death phase under constant dark conditions and included genes associated with bacterial defense, membrane transporters, nitrogen metabolism, and senescence signaling. Cluster 2 genes (n = 197) demonstrated upregulation in exponential phase cultures and included genes involved in genes for oxidative phosphorylation, translation factors, and transcription machinery. Cluster 3 (n = 22) contained light-stimulated upregulated genes expressed under stationary/phases. Stringent response genes belonged to cluster 2, but affected genes spanned various cellular processes such as amino acids, nucleotides, translation, transcription, glycolysis, fatty acids, and cell wall components. The coordinated expression of antagonistic stringent genes, including mazG, ppx/gppA, and spoT/relA may provide insight into the controlled cultural response observed between constant light and constant dark conditions in IMCC1322 cultures, regardless of cell numbers and biomass.

Regulatory role of cysteines in (2R, 3R)-butanediol dehydrogenase BdhA of Bacillus velezensis strain GH1-13: Yunhee Choi , Yong-Hak Kim; J. Microbiol. 2022;60(4):411-418. Published online March 14, 2022; DOI: https://doi.org/10.1007/s12275-022-2018-y

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Abstract

Bacillus velezensis strain GH1-13 contains a (2R,3R)-butanediol dehydrogenase (R-BDH) BdhA which converts acetoin to R-BD reversibly, however, little is known about its regulatory cysteine and biological significance. We performed sitedirected mutation of three cysteines in BdhA. The C37S mutant had no enzyme activity and the C34S and C177S mutants differed from each other and wild type (WT). After zinc affinity chromatography, 1 mM ZnCl2 treatment resulted in a 3-fold enhancement of the WT activity, but reduced activity of the C34S mutant by more than 2 folds compared to the untreated ones. However, ZnCl2 treatment did not affect the activity of the C177S mutant. Most of the double and triple mutant proteins (C34S/C37S, C34S/C177S, C37S/C177S, and C34S/C37S/C177S) were aggregated in zinc resins, likely due to the decreased protein stability. All of the purified WT and single mutant proteins increased multiple intermolecular disulfide bonds in the presence of H2O2 as the buffer pH decreased from 7.5 to 5.5, whereas an intramolecular disulfide bond of cysteine 177 and another cysteine in the CGIC motif region was likely formed at pH higher than pKa of 7.5. When pH varied, WT and its C34S or C177S mutants reduced acetoin to R-BD at the optimum pH 5.5 and oxidized R-BD to acetoin at the optimum pH 10. This study demonstrated that cysteine residues in BdhA play a regulatory role for the production of acetoin and R-BD depending on pH as well as metal binding and oxidative stress.

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Significantly enhanced specific activity of Bacillus subtilis (2,3)-butanediol dehydrogenase through computer-aided refinement of its substrate-binding pocket
Bochun Hu, Xiaoqi Xi, Fugang Xiao, Xiaomeng Bai, Yuanyuan Gong, Yifan Li, Xueqin Qiao, Cunduo Tang, Jihong Huang
International Journal of Biological Macromolecules.2024; 281: 136443. CrossRef
Structural and enzymatic characterization of Bacillus subtilis R,R-2,3-butanediol dehydrogenase
Xiaofei Wang, Lingyun Jia, Fangling Ji
Biochimica et Biophysica Acta (BBA) - General Subjects.2023; 1867(4): 130326. CrossRef
Engineering a BsBDHA substrate-binding pocket entrance for the improvement in catalytic performance toward (R)-phenyl-1,2-ethanediol based on the computer-aided design
Bo-Chun Hu, Meng-Ran Li, Ying-Ying Li, Xin-Shuang Yuan, Yu-Ye Hu, Fu-Gang Xiao
Biochemical Engineering Journal.2023; 194: 108907. CrossRef

Antibacterial pathway of cefquinome against Staphylococcus aureus based on label-free quantitative proteomics analysis: Linglin Gao , Hao Zhu , Yun Chen , Yuhui Yang; J. Microbiol. 2021;59(12):1112-1124. Published online November 9, 2021; DOI: https://doi.org/10.1007/s12275-021-1201-x

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Abstract

Cefquinome (CEQ) is a novel β-lactam antibiotic that exhibits excellent antibacterial activity against Staphylococcus aureus. However, the bacterial protein targets of CEQ are unclear. To evaluate the relationship between the pharmacokinetic/ pharmacodynamic (PK/PD) parameters of CEQ and strains with varying degrees of resistance and to elucidate bacterial protein responses to CEQ treatment, label-free quantitative proteomics analysis was conducted. The sensitive S. aureus ATCC6538 and the resistant 2MIC and 8MIC were tested for differentially expressed proteins. An in vitro model was treated with different concentrations of CEQ (3, 5, or 10 μg/ml) with different terminal half-lives (2.5 or 5 h) at different intervals (12 or 24 h). Differentially expressed proteins were evaluated using Gene Ontology analysis followed by KEGG pathway enrichment analysis and STRING network analysis. RT-qPCR was performed to validate the differentially expressed proteins at the molecular level. The results showed that the degree of resistance increased in a cumulative manner and increased gradually with the extension of administration time. The resistant strain would not have appeared in the model only if %T > mutant prevention concentration ≥ 50%. The expression of 45 proteins significantly changed following CEQ treatment, among which 42 proteins were obviously upregulated and 3 were downregulated. GO analysis revealed that the differentially expressed proteins were mainly present on cells and the cell membrane, participated in metabolic and intracellular processes, and had catalytic and binding activities. The RPSO, SDHB, CITZ, ADK, and SAOUHSC 00113 genes in S. aureus may play important roles in the development of resistance to CEQ. These results provided important reference candidate proteins as targets for overcoming S. aureus resistance to CEQ.

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Detection of Antibiotic Resistance in Feline-Origin ESBL Escherichia coli from Different Areas of China and the Resistance Elimination of Garlic Oil to Cefquinome on ESBL E. coli
Yin-Chao Tong, Peng-Cheng Li, Yang Yang, Qing-Yi Lin, Jin-Tong Liu, Yi-Nuo Gao, Yi-Ning Zhang, Shuo Jin, Su-Zhu Qing, Fu-Shan Xing, Yun-Peng Fan, Ying-Qiu Liu, Wei-Ling Wang, Wei-Min Zhang, Wu-Ren Ma
International Journal of Molecular Sciences.2023; 24(11): 9627. CrossRef

Role of melatonin in murine “restraint stress”-induced dysfunction of colonic microbiota: Rutao Lin , Zixu Wang , Jing Cao , Ting Gao , Yulan Dong , Yaoxing Chen; J. Microbiol. 2021;59(5):500-512. Published online February 25, 2021; DOI: https://doi.org/10.1007/s12275-021-0305-7

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Abstract

Intestinal diseases caused by physiological stress have become a severe public health threat worldwide. Disturbances in the gut microbiota-host relationship have been associated with irritable bowel disease (IBD), while melatonin (MT) has antiinflammatory and antioxidant effects. The objective of this study was to investigate the mechanisms by which MT-mediated protection mitigated stress-induced intestinal microbiota dysbiosis and inflammation. We successfully established a murine restraint stress model with and without MT supplementation. Mice subjected to restraint stress had significantly elevated corticosterone (CORT) levels, decreased MT levels in their plasma, elevated colonic ROS levels and increased bacterial abundance, including Bacteroides and Tyzzerella, in their colon tract, which led to elevated expression of Toll-like receptor (TLR) 2/4, p-P65 and p-IκB. In contrast, supplementation with 20 mg/kg MT reversed the elevation of the plasma CORT levels, downregulated the colon ROS levels and inhibited the changes in the intestinal microbiota induced by restraint stress. These effects, in turn, inhibited the activities of TLR2 and TLR4, p-P65 and p-IκB, and decreased the inflammatory reaction induced by restraint stress. Our results suggested that MT may mitigate “restraint stress”-induced colonic microbiota dysbiosis and intestinal inflammation by inhibiting the activation of the NF-κB pathway.

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Microbial melatonin metabolism in the human intestine as a therapeutic target for dysbiosis and rhythm disorders
Petra Zimmermann, Salome Kurth, Benoit Pugin, Nicholas A. Bokulich
npj Biofilms and Microbiomes.2024;[Epub] CrossRef
Toll-like receptor 4 plays a vital role in irritable bowel syndrome: a scoping review
Xuemeng Wan, Liyuan Wang, Zhiling Wang, Chaomin Wan
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Christensenella minuta mitigates behavioral and cardiometabolic hallmarks of social defeat stress
A. Agusti, GV. Molina-Mendoza, M. Tamayo, V. Rossini, MC. Cenit, C. Frances-Cuesta, V. Tolosa-Enguis, EM. Gómez Del Pulgar, A. Flor-Duro, Y. Sanz
Biomedicine & Pharmacotherapy.2024; 180: 117377. CrossRef
The impact of acute and chronic stress on gastrointestinal physiology and function: a microbiota–gut–brain axis perspective
Sarah‐Jane Leigh, Friederike Uhlig, Lars Wilmes, Paula Sanchez‐Diaz, Cassandra E. Gheorghe, Michael S. Goodson, Nancy Kelley‐Loughnane, Niall P. Hyland, John F. Cryan, Gerard Clarke
The Journal of Physiology.2023; 601(20): 4491. CrossRef
Melatonin as a Mediator of the Gut Microbiota–Host Interaction: Implications for Health and Disease
María-Ángeles Bonmatí-Carrión, Maria-Angeles Rol
Antioxidants.2023; 13(1): 34. CrossRef
INVESTIGATION OF THE ROLE OF STRESS IN MALE INFERTILITY AND THE EFFECT OF CURRENT MELATONIN HORMONE TREATMENTS
İshak GÖKÇEK, Leyla AYDIN
Veteriner Farmakoloji ve Toksikoloji Derneği Bülteni.2023; 14(1): 36. CrossRef
The double burden of malnutrition and environmental enteric dysfunction as potential factors affecting gut-derived melatonin in children under adverse environments
Alane N. Bezerra, Caroline L. Peixoto, Synara C. Lopes, Veralice M. S. Bruin, Pedro Felipe C. Bruin, Reinaldo B. Oriá
Frontiers in Nutrition.2023;[Epub] CrossRef
Melatonin: Both a Messenger of Darkness and a Participant in the Cellular Actions of Non-Visible Solar Radiation of Near Infrared Light
Dun-Xian Tan, Russel J. Reiter, Scott Zimmerman, Ruediger Hardeland
Biology.2023; 12(1): 89. CrossRef
Glucocorticoids coordinate the bladder peripheral clock and diurnal micturition pattern in mice
Ichiro Chihara, Hiromitsu Negoro, Jin Kono, Yoshiyuki Nagumo, Haruki Tsuchiya, Kosuke Kojo, Masanobu Shiga, Ken Tanaka, Shuya Kandori, Bryan J. Mathis, Hiroyuki Nishiyama
Communications Biology.2023;[Epub] CrossRef
The Microbiota-Dependent Worsening Effects of Melatonin on Gut Inflammation
Jefferson Luiz da Silva, Lia Vezenfard Barbosa, Camila Figueiredo Pinzan, Viviani Nardini, Irislene Simões Brigo, Cássia Aparecida Sebastião, Jefferson Elias-Oliveira, Vânia Brazão, José Clóvis do Prado Júnior, Daniela Carlos, Cristina Ribeiro de Barros C
Microorganisms.2023; 11(2): 460. CrossRef
The Effects of Stress and Diet on the “Brain–Gut” and “Gut–Brain” Pathways in Animal Models of Stress and Depression
Mauritz F. Herselman, Sheree Bailey, Larisa Bobrovskaya
International Journal of Molecular Sciences.2022; 23(4): 2013. CrossRef
Intestinal microbiota and melatonin in the treatment of secondary injury and complications after spinal cord injury
Yiwen Zhang, Rui Lang, Shunyu Guo, Xiaoqin Luo, Huiting Li, Cencen Liu, Wei Dong, Changshun Bao, Yang Yu
Frontiers in Neuroscience.2022;[Epub] CrossRef
Protective Effects and Mechanisms of Melatonin on Stress Myocardial Injury in Rats
Jia-yao Chen, Ting Li, Jiao-ling Wang, Zhan-le Wang, Yun Zhang, Lin-quan Zang
Journal of Cardiovascular Pharmacology.2022; 80(3): 417. CrossRef
Rescue of social deficits by early-life melatonin supplementation through modulation of gut microbiota in a murine model of autism
Xia Liu, Yi Cui, Yuhan Zhang, Guo Xiang, Meng Yu, Xianshu Wang, Bin Qiu, Xin-gang Li, Wei Liu, Di Zhang
Biomedicine & Pharmacotherapy.2022; 156: 113949. CrossRef
Roles of PRR-Mediated Signaling Pathways in the Regulation of Oxidative Stress and Inflammatory Diseases
Pengwei Li, Mingxian Chang
International Journal of Molecular Sciences.2021; 22(14): 7688. CrossRef

The cytoplasmic loops of AgrC contribute to the quorum-sensing activity of Staphylococcus aureus: Qian Huang , Yihui Xie , Ziyu Yang , Danhong Cheng , Lei He , Hua Wang , Qian Liu , Min Li; J. Microbiol. 2021;59(1):92-100. Published online November 17, 2020; DOI: https://doi.org/10.1007/s12275-021-0274-x

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Abstract

In Staphylococcus aureus, the accessory gene regulator (agr) quorum-sensing system is thought to play an important role in biofilm formation. The histidine kinase AgrC is one of the agr system components and activated by the self-generated auto-inducing peptide (AIP), which is released continuously into the extracellular environment during bacterial growth. The extracellular loops (Extra-loops) of AgrC are crucial for AIP binding. Here, we reported that the cytoplasmic loops (Cyto-loops) of AgrC are also involved in Agr activity. We identified S. aureus ST398 clinical isolates containing a naturally occurring single amino acid substitution (lysine to isoleucine) at position 73 of an AgrC Cyto-loop that exhibited significantly stronger biofilm formation and decreased Agr activity compared to the wild-type strain. A constructed strain containing the K73I point mutation in AgrC Cyto-loop continued to show a growth dependent induction of the agr system, although the growth dependent induction was delayed by about 6 h compared to the wild-type. In addition, a series of strains containing deletion mutants of the AgrC Cyto- and Extra-loops were constructed and revealed that the removal of the two Cyto-loops and Extra-loops 2 and 3 totally abolished the Agr activity and the growth-dependence on the agr system induction. Remarkably, the Extra-loop 1 deletion did not affect the Agr activity. In conclusion, the AgrC Cyto-loops play a crucial role in the S. aureus quorum-sensing activity.

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Emerging trends in the inhibition of bacterial molecular communication: An overview
B.R. Maha Swetha, M. Saravanan, Prakash Piruthivraj
Microbial Pathogenesis.2024; 186: 106495. CrossRef
In vitro and in silico evaluation of anti-quorum sensing activity of marine red seaweeds-Portieria hornemannii and Halymenia dilatata
Prakash Piruthivraj, B.R. Maha Swetha, A. Anita Margret, A. Sherlin Rosita, Parthasarathi Rengasamy, Rajapandiyan Krishnamoorthy, Mansour K. Gatasheh, Khalid Elfaki Ibrahim, Sekhu Ansari, Natesan Vijayakumar
Journal of King Saud University - Science.2024; 36(6): 103188. CrossRef
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Nadira Nurxat, Lili Wang, Qichen Wang, Shujing Li, Chen Jin, Yaran Shi, Ayjiamali Wulamu, Na Zhao, Yanan Wang, Hua Wang, Min Li, Qian Liu
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Review

[MINIREVIEW]Bacterial bug-out bags: outer membrane vesicles and their proteins and functions: Kesavan Dineshkumar , Vasudevan Aparna , Liang Wu , Jie Wan , Mohamod Hamed Abdelaziz , Zhaoliang Su , Shengjun Wang , Huaxi Xu; J. Microbiol. 2020;58(7):531-542. Published online June 10, 2020; DOI: https://doi.org/10.1007/s12275-020-0026-3

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Abstract

Among the major bacterial secretions, outer membrane vesicles (OMVs) are significant and highly functional. The proteins and other biomolecules identified within OMVs provide new insights into the possible functions of OMVs in bacteria. OMVs are rich in proteins, nucleic acids, toxins and virulence factors that play a critical role in bacteria-host interactions. In this review, we discuss some proteins with multifunctional features from bacterial OMVs and their role involving the mechanisms of bacterial survival and defence. Proteins with moonlighting activities in OMVs are discussed based on their functions in bacteria. OMVs harbour many other proteins that are important, such as proteins involved in virulence, defence, and competition. Overall, OMVs are a power-packed aid for bacteria, harbouring many defensive and moonlighting proteins and acting as a survival kit in
case
of an emergency or as a defence weapon. In summary, OMVs can be defined as bug-out bags for bacterial defence and, therefore, survival.

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Bacterial membrane vesicles in the pathogenesis and treatment of inflammatory bowel disease
Chinasa Valerie Olovo, Dickson Kofi Wiredu Ocansey, Ying Ji, Xinxiang Huang, Min Xu
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Microbe-host interactions: structure and functions of Gram-negative bacterial membrane vesicles
Min Xiao, Guiding Li, Hefeng Yang
Frontiers in Microbiology.2023;[Epub] CrossRef
Wild Wheat Rhizosphere-Associated Plant Growth-Promoting Bacteria Exudates: Effect on Root Development in Modern Wheat and Composition
Houssein Zhour, Fabrice Bray, Israa Dandache, Guillaume Marti, Stéphanie Flament, Amélie Perez, Maëlle Lis, Llorenç Cabrera-Bosquet, Thibaut Perez, Cécile Fizames, Ezekiel Baudoin, Ikram Madani, Loubna El Zein, Anne-Aliénor Véry, Christian Rolando, Hervé
International Journal of Molecular Sciences.2022; 23(23): 15248. CrossRef
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Yanhong Pang, Ludwig Ermann Lundberg, Manuel Mata Forsberg, David Ahl, Helena Bysell, Anton Pallin, Eva Sverremark-Ekström, Roger Karlsson, Hans Jonsson, Stefan Roos
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Teresa Faddetta, Giovanni Renzone, Alberto Vassallo, Emilio Rimini, Giorgio Nasillo, Gianpiero Buscarino, Simonpietro Agnello, Mariano Licciardi, Luigi Botta, Andrea Scaloni, Antonio Palumbo Piccionello, Anna Maria Puglia, Giuseppe Gallo, Gladys Alexandre
Applied and Environmental Microbiology.2022;[Epub] CrossRef
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Shiana Malhotra, Zarinah M. Amin, Garima Dobhal, Sophie Cottam, Thomas Nann, Renee V. Goreham
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Journal Articles

Ciceribacter ferrooxidans sp. nov., a nitrate-reducing Fe(II)-oxidizing bacterium isolated from ferrous ion-rich sediment: Tongchu Deng , Youfen Qian , Xingjuan Chen , Xunan Yang , Jun Guo , Guoping Sun , Meiying Xu; J. Microbiol. 2020;58(5):350-356. Published online April 27, 2020; DOI: https://doi.org/10.1007/s12275-020-9471-2

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Abstract

A nitrate-reducing Fe(II)-oxidizing bacterial strain, F8825T, was isolated from the Fe(II)-rich sediment of an urban creek in Pearl River Delta, China. The strain was Gram-negative, facultative chemolithotrophic, facultative anaerobic, nonspore- forming, and rod-shaped with a single flagellum. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that it belongs to the genus Ciceribacter and is most closely related to C. lividus MSSRFBL1T (99.4%), followed by C. thiooxidans F43bT (98.8%) and C. azotifigens A.slu09T (98.0%). Fatty acid, polar lipid, respiratory quinone, and DNA G + C content analyses supported its classification in the genus Ciceribacter. Multilocus sequence analysis of concatenated 16S rRNA, atpD, glnII, gyrB, recA, and thrC suggested that the isolate was a novel species. DNA–DNA hybridization and genome sequence comparisons (90.88 and 89.86%, for values of ANIm and ANIb between strains F8825T with MSSRFBL1T, respectively) confirmed that strain F8825T was a novel species, different from C. lividus MSSRFBL1T, C. thiooxidans F43bT, and C. azotifigens A.slu09T. The physiological and biochemical properties of the strain, such as carbon source utilization, nitrate reduction, and ferrous ion oxidation, further supported that this is a novel species. Based on the polyphasic taxonomic results, strain F8825T was identified as a novel species in the genus Ciceribacter, for which the name Ciceribacter ferrooxidans sp. nov. is proposed. The type strain is F8825T (= CCTCC AB 2018196T = KCTC 62948T).

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Biological denitrification performance of a novel sulfur-slow-release carbon source mixed filler
Zhen Peng, Hang Shi, Shengkai Wu, Yao Fan, Xu Ye, Qisong Liu, Bo Liu
Journal of Water Process Engineering.2024; 62: 105257. CrossRef
Pathways and contributions of sulfate reducing-bacteria to arsenic cycling in landfills
Lifang Hu, Feng Huang, Yating Qian, Tao Ding, Yuzhou Yang, Dongsheng Shen, Yuyang Long
Journal of Hazardous Materials.2024; 473: 134582. CrossRef
Ciceribacter sichuanensis sp. nov., a plant growth promoting rhizobacterium isolated from root nodules of soybean in Sichuan, China
Yanqin Zhang, Yuanxue Chen, Petri Penttinen, Xing Wang, Ying Quan, Licheng Wen, Miao Yang, Xiaoping Zhang, Qiang Chen, Lingzi Zhang, Junjie Zhang, Xiaoxia Zhang, Kaiwei Xu
Antonie van Leeuwenhoek.2024;[Epub] CrossRef
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Bhagyashri J. Poddar, Anshuman A. Khardenavis
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Rong Peng, Junhao Shen, Shuang Li, Hui Liu
Letters in Applied Microbiology.2023;[Epub] CrossRef
New Anaerobic Iron-Cycling Bacteria Isolated from the Yessentukskoye Mineral Water Deposit
D. G. Zavarzina, V. A. Pikhtereva, A. A. Klyukina, A. Yu. Merkel, S. N. Gavrilov
Microbiology.2023; 92(S1): S12. CrossRef
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International Committee on Systematics of Prokaryotes, Subcommittee on the taxonomy of Rhizobia and Agrobacteria, minutes of the annual meeting by videoconference, 5 July 2021, followed by online discussion until 31 December 2021
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Transcriptome analysis to understand the effects of the toxoflavin and tropolone produced by phytopathogenic Burkholderia on Escherichia coli: Jungwook Park , Hyun-Hee Lee , Hyejung Jung , Young-Su Seo; J. Microbiol. 2019;57(9):781-794. Published online August 27, 2019; DOI: https://doi.org/10.1007/s12275-019-9330-1

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Abstract

The phytopathogenic Burkholderia species B. glumae and B. plantarii are the causal agents of bacterial wilt, grain rot, and seedling blight, which threaten the rice industry globally. Toxoflavin and tropolone are produced by these phytopathogens and are considered the most hostile biohazards with a broad spectrum of target organisms. However, despite their nonspecific toxicity, the effects of toxoflavin and tropolone on bacteria remain unknown. RNA-seq based transcriptome analysis was employed to determine the genome-wide expression patterns under phytotoxin treatment. Expression of 2327 and 830 genes was differentially changed by toxoflavin and tropolone, respectively. Enriched biological pathways reflected the down-regulation of oxidative phosphorylation and ribosome function, beginning with the inhibition of membrane biosynthesis and nitrogen metabolism under oxidative stress or iron starvation. Conversely, several systems such as bacterial chemotaxis, flagellar assembly, biofilm formation, and sulfur/taurine transporters were highly expressed as countermeasures against the phytotoxins. In addition, our findings revealed that three hub genes commonly induced by both phytotoxins function as the siderophore enterobactin, an ironchelator. Our study provides new insights into the effects of phytotoxins on bacteria for better understanding of the interactions between phytopathogens and other microorganisms. These data will also be applied as a valuable source in subsequent applications against phytotoxins, the major virulence factor.

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Mélanie Gonzales, Pauline Jacquet, Floriane Gaucher, Éric Chabrière, Laure Plener, David Daudé
Journal of Natural Products.2024; 87(4): 1268. CrossRef
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Hui Wang, Lili Hu, Xiaotu Chang, Yuge Hu, Yan Zhang, Peng Zhou, Xiaojiao Cui
Food Chemistry.2023; 399: 134010. CrossRef
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Abstract

Thermococcus onnurineus NA1, an obligate anaerobic hyperthermophilic archaeon, showed variable oxygen (O2) sensitivity depending on the types of substrate employed as an energy source. Unexpectedly, the culture with yeast extract as a sole energy source showed enhanced growth by 2-fold in the presence of O2. Genome-wide transcriptome analysis revealed the upregulation of several antioxidant-related genes encoding thioredoxin peroxidase (TON_0862), rubrerythrin (TON_0864), rubrerythrin-related protein (TON_0873), NAD(P)H rubredoxin oxidoreductase (TON_0865), or thioredoxin reductase (TON_1603), which can couple the detoxification of reactive oxygen species with the regeneration of NAD(P)+ from NAD(P)H. We present a plausible mechanism by which O2 serves to maintain the intracellular redox balance. This study demonstrates an unusual strategy of an obligate anaerobe underlying O2-mediated growth enhancement despite not having heme-based or cytochrome-type proteins.

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Abstract

Interspecific mycelial interactions between white rot fungi are always accompanied by an increased production of laccase. In this study, the potential of the white rot fungus Dichomitus squalens to enhance laccase production during interactions with two other white rot fungi, Trametes versicolor or Pleurotus ostreatus, was assessed. To probe the mechanism of laccase induction and the role that laccase plays during combative interaction, we analyzed the differential gene expression profile of the laccase induction response to stressful conditions during fungal interaction. We further confirmed the expression patterns of 16 selected genes by qRT-PCR analysis. We noted that many differentially expressed genes (DEGs) encoded proteins that were involved in xenobiotic detoxification and reactive oxygen species (ROS) generation or reduction, including aldo/keto reductase, glutathione S-transferases, cytochrome P450 enzymes, alcohol oxidases and dehydrogenase, manganese peroxidase and laccase. Furthermore, many DEG-encoded proteins were involved in antagonistic mechanisms of nutrient acquisition and antifungal properties, including glycoside hydrolase, glucanase, chitinase and terpenoid synthases. DEG analyses effectively revealed that laccase induction was likely caused by protective responses to oxidative stress and nutrient competition during interspecific fungal interactions.

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

NOTE] Next-Generation Sequencing-Based Transcriptome Analysis of L-Lysine-Producing Corynebacterium glutamicum ATCC 21300 Strain: Hong-Il Kim , Jae-Young Nam , Jae-Yong Cho , Chang-Soo Lee , Young-Jin Park; J. Microbiol. 2013;51(6):877-880. Published online December 19, 2013; DOI: https://doi.org/10.1007/s12275-013-3236-0

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Abstract

In the present study, 151 genes showed a significant change in their expression levels in Corynebacterium glutamicum ATCC 21300 compared with those of C. glutamicum ATCC 13032. Of these 151 genes, 56 genes (2%) were up-regulated and 95 genes (3%) were down-regulated. RNA sequencing analysis also revealed that 11 genes, involved in the L-lysine biosynthetic pathway of C. glutamicum, were up- or downregulated compared with those of C. glutamicum ATCC 13032. Of the 151 genes, 10 genes were identified to have mutations including SNP (9 genes) and InDel (1 gene). This information will be useful for genome breeding of C. glutamicum to develop an industrial amino acid-producing strain with minimal mutation.

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RETRACTED ARTICLE: Comparative analysis of the Corynebacterium glutamicum transcriptome in response to changes in dissolved oxygen levels
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